text:
7, 3430 2008 , expanding the cases studied by adding the pentacene dimer. The SAPT decomposition of the acene interactions provides a more realistic picture of the interactions than that from the energy decomposition analysis previously reported. The data suggest that parallel-displaced and T-shaped acene dimers both feature a special stabilizing - interaction arising from electron correlation terms which are signiﬁcantly more stabilizing than expected on the basis of pairwise −C6R−6 estimates. These terms are qualitatively the same in T-shaped as in parallel-displaced geometries, although they are roughly a factor of 2 smaller in T-shaped geometries because of the larger distances between the intermolecular pairs of electrons.",
	collection = "molecular interactions",
	doi = "10.1063/1.3426316",
	localfile = "molecular interactions/2010 - Density fitting and Cholesky decomposition approximations in symmetry-adapted perturbation theory: implementation and application to probe the nature of pi-pi interactions in linear acenes.pdf",
	year = 2010
}

@Article{2010-Hong-LWKXJZNW,
	Author = "Augustin J. Hong and Chi-Chun Liu and Yong Wang and Jiyoung Kim and Faxian Xiu and Shengxiang Ji and Jin Zou and Paul F. Nealey and Kang L. Wang",
	Title = "{Metal nanodot memory by self-assembled block copolymer lift-off}",
	Journal = "Nano Lett.",
	Volume = "10",
	Pages = "224–229",
	abstract = "As information technology demands for larger capability in data storage continue, ultrahigh bit density memory devices have been extensively investigated. To produce an ultrahigh bit density memory device, multilevel cell operations that require several states in one cell have been proposed as one solution, which can also alleviate the scaling issues in the current state-of-the-art complementary metal oxide semiconductor technology. Here, we report the ﬁrst demonstration of metal nanodot memory using a self-assembled block copolymer lift-off. This metal nanodot memory with simple low temperature processes produced an ultrawide memory window of 15 V at the (18 V voltage sweep. Such a large window can be adopted for multilevel cell operations. Scanning electron microscopy and transmission electron microscopy studies showed a periodic metal nanodot array with uniform distribution deﬁned by the block copolymer pattern. Consequently, this metal nanodot memory has high potential to reduce the variability issues that metal nanocrystal memories previously had and multilevel cells with ultrawide memory windows can be fabricated with high reliability and manufacturability.",
	collection = "block copolymers",
	doi = "10.1021/nl903340a",
	keywords = "block copolymers; memory materials",
	localfile = "block copolymer nanocomposites/2010 - Metal nanodot memory by self-assembled block copolymer lift-off.pdf",
	year = 2010
}

@Article{2010-Horowitz-ECQSLH,
	Author = "Eric D. Horowitz and Aaron E. Engelhart and Michael C. Chen and Kaycee A. Quarles and Michael W. Smith and David G. Lynn and Nicholas V. Hud",
	Title = "{Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world}",
	Journal = "Proc. Natl. Acad. Sci.",
	Volume = "107",
	Number = "12",
	Pages = "5288–5293",
	abstract = "The RNA world hypothesis proposes that nucleic acids were once responsible for both information storage and chemical catalysis, before the advent of coded protein synthesis. However, it is difficult to imagine how nucleic acid polymers first appeared, as the abiotic chemical formation of long nucleic acid polymers from mononucleotides or short oligonucleotides remains elusive, and barriers to achieving this goal are substantial. One specific obstacle to abiotic nucleic acid polymerization is strand cyclization. Chemically activated short oligonucleotides cyclize efficiently, which severely impairs polymer growth. We show that intercalation, which stabilizes and rigidifies nucleic acid duplexes, almost totally eliminates strand cyclization, allowing for chemical ligation of tetranucleotides into duplex polymers of up to 100 base pairs in length. In contrast, when these reactions are performed in the absence of intercalators, almost exclusively cyclic tetra- and octa-nucleotides are produced. Intercalator-free polymerization is not observed, even at tetranucleotide concentrations >10; 000-fold greater than those at which intercalators enable polymerization. We also demonstrate that intercalation-mediated polymerization is most favored if the size of the intercalator matches that of the base pair; intercalators that bind to Watson–Crick base pairs promote the polymerization of oligonucleotides that form these base pairs. Additionally, we demonstrate that intercalation-mediated polymerization is possible with an alternative, non-Watson–Crick-paired duplex that selectively binds a complementary intercalator. These results support the hypothesis that intercalators (acting as ‘molecular midwives’) could have facilitated the polymerization of the first nucleic acids and possibly helped select the first base pairs, even if only trace amounts of suitable oligomers were available.",
	collection = "nucleic acid intercalation",
	localfile = "nucleic acid intercalation/2010 - Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonicleotides in a prebiotic world.pdf",
	year = 2010
}

@Article{2010-Ishikawa-Kuwata,
	Author = "Takeshi Ishikawa and Kazuo Kuwata",
	Title = "{Interaction analysis of the native structure of prion protein with quantum chemical calculations}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "6",
	Pages = "538–547",
	abstract = "Abstract: We examined the solvent interaction and intramolecular interaction of the native structure of prion protein (PrP) using quantum chemical calculations based on the fragment molecular orbital (FMO) method. The inﬂuence due to the geometrical ﬂuctuation was taken into account by performing calculations on forty different conformations. Each FMO calculation was carried out at the MP2 level of theory with the cc-pVDZ in which the resolution of the identity approximation was employed to reduce the computational cost. The solvent interaction energies obtained from the calculations provided information about the hydrophilicity of the three R-helices. We examined the roles of the charged residues in retaining the native structure of PrP with the calculated intramolecular interaction energies. The analysis, focused on van der Waals interaction, showed that the hydrophobic residues were important for the stability of the native structure. Our results were also discussed in relation to the identiﬁed pathogenetic mutations of prion diseases. Additionally, we examined the distribution of the calculated values with 40 structures, in which we demonstrated the inﬂuence of geometrical ﬂuctuations on quantum chemical calculations.",
	collection = "proteins",
	doi = "10.1021/ct900456v",
	localfile = "proteins/2010 - Interaction analysis of the native structure of prion protein with quantum chemical calculations.pdf",
	year = 2010
}

@Article{2010-Jancar-DSKCLS,
	Author = "J. Jancar and J. F. Douglas and F. W. Starr and S. K. Kumar and P. Cassagnau and A. J. Lesser and S. S. Sternstein and M. J. Buehler",
	Title = "{Current issues in research on structure-property relationships in polymer nanocomposites}",
	Journal = "Polymer",
	Volume = "51",
	Pages = "3321–3343",
	collection = "polymer nanocomposites",
	doi = "10.1016/j.polymer.2010.04.074",
	keywords = "polymer nanocomposites; structure-property relationships; nanoparticle dispersion",
	localfile = "polymer nanocomposites/2010 - Current issues in research on structure-property relationships in polymer nancomposites.pdf",
	rating = "2",
	read = "2012-04-09",
	type = "Review",
	year = 2010
}

@Article{2010-Janowski-FP,
	Author = "Tomasz Janowski and Alan R. Ford and Peter Pulay",
	Title = "{Accurate correlated calculation of the intermolecular potential surface in the coronene dimer}",
	Journal = "Mol. Phys.",
	Volume = "108",
	Number = "3-4",
	Pages = "249–257",
	abstract = "The binding energy of the coronene dimer was determined by high level ab initio calculations. In the first step a potential energy surface was determined for the stacked dimer at the SCS-MP2/aTZ level. The energy of the stacked parallel dimer was scanned with respect to the lateral displacement of the two molecules at various interplane distances, and the minima and saddle points were determined. These results were refined by high level quadratic CI (QCISD(T)/aDZ) calculations. The aTZ and aDZ basis sets employed are derived from the aug-cc-pVDZ and aug-cc-pVTZ basis sets but diffuse functions are placed only at every second carbon atom, alleviating the severe numerical difficulties of the full augmented basis sets while retaining all important contributions. To estimate the QCISD(T) energies for larger basis set, we employed commonly used procedure of adding basis set correction values obtained at the MP2 level. This hybrid scheme was used to obtain the final optimised geometries and binding energies; these are believed to be close approximations to the basis set limit QCISD(T) values. A few calculations were also performed to the T-shaped conformer, although this is less important in the coronene dimer than in the benzene dimer. The high-level results were used as a benchmark to assess the performance of simpler and less expensive ab initio methods for these large rings with small HOMO–LUMO gaps, for instance the SCS-MP2 method, and modern DFT versions that are optimised for dispersion dominated systems.",
	collection = "stacking",
	doi = "10.1080/00268970903397249",
	localfile = "molecular stacking/2010 - Accurate correlated calculation of the intermolecular potential surface in the coronene dimer.pdf",
	methods = "SCS-MP2/aTZ, QCISD(T)/aDZ",
	systems = "coronene dimer",
	year = 2010
}

@Article{2010-Jouault-DSCSJB,
	Author = "Nicolas Jouault and Florent Dalmas and Emanuela Di Cola and Ralf Schweins and Jacques Jestin and Francois Boue",
	Title = "{Direct measurement of polymer chain conformation in well-controlled model nanocomposites by combining SANS and SAXS}",
	Journal = "Macromolecules",
	Volume = "43",
	Pages = "9881–9891",
	abstract = "We studied by small-angle neutron scattering (SANS) the polymer chain conformation in model silica/polystyrene (PS) nanocomposites. Using the zero average contrast method, we can properly match silica signal to directly measure the form factor of a single PS chain. An important effort has been put to eliminate the silica scattering using two distinct approaches (called respectively “three” and “four” components methods) leading to analogue results. By combining SANS data with small-angle X-ray scattering (SAXS) measurements and transmission electronic microscopy (TEM) images on the same samples, we obtain a very clear result about the effect on polymer chain conformation of the filler dispersion, either at low filler volume fraction, where silica arrange in small aggregates or at higher concentration where it forms a connected network. From SANS the chain conformation in nanocomposites is identical to the one without silica in a large q range illustrating that the chain conformation remains independent of the filler dispersion whatever the silica connectivity or the polymer molecular weight. This result opens the way to a better overview of the polymer chain conformation contribution, especially adsorption or chain mobility modification effects, in the complex mechanical reinforcement mechanisms of nanocomposites. However, at low q, an unexpected shoulder appears in the SANS curves: this effect does not vary in a systematic way neither with chain molecular weight nor with silica concentration. The non reproducibility of these observations could be related to unusual phase separation between normal and deuterated chains.",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma101682t",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2010 - Direct measurement of polymer chain conformation in well-controlled model nanocomposites by combining SANS and SAXS.pdf.pdf",
	year = 2010
}

@Article{2010-Jouault-DSCSJH,
	Author = "Nicolas Jouault and Florent Dalmas and Sylvere Said and Emanuela Di Cola and Ralf Schweins and Jacques Jestin and Francois Boue",
	Title = "{Direct small-angle-neutron-scattering observation of stretched chain conformation in nanocomposites: more insight on polymer contributions in mechanical reinforcement}",
	Journal = "Phys. Rev. E",
	Volume = "82",
	Pages = "031801",
	abstract = "In this paper we present a direct measurement of stretched chain conformation in polymer nanocomposites in a large range of deformation using a speciﬁc contrast-matched small angle neutron scatttering SANS method. Whatever are the ﬁller structure and the chain length the results show a clear identity of chain deformation in pure and reinforced polymer and offer more insight on the polymer chain contribution in the mechanical reinforcement. It suggests that glassy layer or glassy paths, recently proposed, should involve only a small fraction of chains. As a result, the remaining ﬁller contribution appears strikingly constant with deformation as explained by continuous locking-unlocking rearrangement process of the particles.",
	collection = "polymer nanocomposites",
	doi = "10.1103/PhysRevE.82.031801",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2010 - Direct small-angle-neutron-scattering observation of stretched chain conformation in nanocomposites: more insight on polymer contributions in mechanical reinforcement.pdf",
	year = 2010
}

@Article{2010-Kamerlin-Warshel,
	Author = "Shina C. L. Kamerlin and Arieh Warshel",
	Title = "{At the dawn of the 21st century: is dynamics the missing link for understanding enzyme catalysis?}",
	Journal = "Proteins",
	Volume = "78",
	Pages = "1339–1375",
	abstract = "Enzymes play a key role in almost all biological processes, accelerating a variety of metabolic reactions as well as controlling energy transduction, the transcription, and translation of genetic information, and signaling. They possess the remarkable capacity to accelerate reactions by many orders of magnitude compared to their uncatalyzed counterparts, making feasible crucial processes that would otherwise not occur on biologically relevant timescales. Thus, there is broad interest in understanding the catalytic power of enzymes on a molecular level. Several proposals have been put forward to try to explain this phenomenon, and one that has rapidly gained momentum in recent years is the idea that enzyme dynamics somehow contributes to catalysis. This review examines the dynamical proposal in a critical way, considering basically all reasonable definitions, including (but not limited to) such proposed effects as ‘‘coupling between conformational and chemical motions,’’ ‘‘landscape searches’’ and ‘‘entropy funnels.’’ It is shown that none of these proposed effects have been experimentally demonstrated to contribute to catalysis, nor are they supported by consistent theoretical studies. On the other hand, it is clarified that careful simulation studies have excluded most (if not all) dynamical proposals. This review places significant emphasis on clarifying the role of logical definitions of different catalytic proposals, and on the need for a clear formulation in terms of the assumed potential surface and reaction coordinate. Finally, it is pointed out that electrostatic preorganization actually accounts for the observed catalytic effects of enzymes, through the corresponding changes in the activation free energies.",
	collection = "enzymes",
	doi = "10.1002/prot.22654",
	localfile = "enzymes/2010 - At the dawn of the 21st century: is dynamics the missing link for understanding enzyme catalysis.pdf",
	year = 2010
}

@Article{2010-Khashman,
	Author = "Adnan Khashman",
	Title = "{Modeling congitive and emotional processes: a novel neural network architecture}",
	Journal = "Neural Networks",
	Volume = "23",
	Pages = "1155–1163",
	Note = "Page 1156: Our hypothesis is that the emotional and cognitive processes which are activated by visual stimuli, such as an image, can be modeled in machines, and the way to model these two kinds of processes, is to clearly define separate 'routes' for emotional and congitive information within the model, while processing the information collectively. (...) We associate the ventral/emotional information with global representation of input visual stimuli and the dorsal/cognitive information with the local representation.",
	collection = "neuroscience",
	doi = "10.1016/j.neunet.2010.07.004",
	keywords = "neural network; emotion; cognition",
	localfile = "neuroscience/2010 - Modeling cognitive and emotional processes: a novel neural network architecture.pdf",
	rating = "2",
	read = "2013-08-20",
	year = 2010
}

@Article{2010-Kim-LY,
	Author = "Shin-Hyun Kim and Su Yeon Lee and Seung-Man Yang",
	Title = "{Janus microspheres for a highly flexible and impregnable water-repelling interface}",
	Journal = "Angew. Chem. Int. Ed.",
	Volume = "122",
	Pages = "2589–2592",
	collection = "nanoparticles",
	doi = "10.1002/ange.201000108",
	keywords = "Janus particles; nanospheres",
	localfile = "nanoparticles/2010 - Janus microspheres for a highly flexible and impregnable water-repelling interface.pdf",
	year = 2010
}

@Article{2010-Kim-PH,
	Author = "Ho-Cheol Kim and Sang-Min Park and William D. Hinsberg",
	Title = "{Block copolymer based nanostructures: materials, processes, and applications to electronics}",
	Journal = "Chem. Rev.",
	Volume = "110",
	Pages = "146–177",
	collection = "block copolymers",
	doi = "10.1021/cr900159v",
	keywords = "block copolymers; memory materials",
	localfile = "block copolymer nanocomposites/2010 - Block copolymer based nanostructures: materials, processes, and applications to electornics.pdf",
	type = "Review",
	year = 2010
}

@Article{2010-Kirmizialtin-Elber,
	Author = "Serdal Kirmizialtin and Ron Elber",
	Title = "{Computational exploration of mobile ion distributions around RNA duplex}",
	Journal = "J. Phys. Chem. B",
	Volume = "114",
	Pages = "8207–8220",
	abstract = "Atomically detailed distributions of ions around an A-form RNA are computed. Different mixtures of monovalent and divalent ions are considered explicitly. Studies of tightly bound and of diffusive (but bound) ions around 25 base pairs RNA are conducted in explicit solvent. Replica exchange simulations provide detailed equilibrium distributions with moderate computing resources (20 ns of simulation using 64 replicas). The simulations show distinct behavior of single and double charged cations. Binding of Mg2+ ion includes tight binding to speciﬁc sites while Na+ binds only diffusively. The tight binding of Mg2+ is with a solvation shell while Na+ can bind directly to RNA. Negative mobile ions can be found near the RNA but must be assisted by proximate and mobile cations. At distances larger than 16 Å from the RNA center, a model of RNA as charged rod in a continuum of ionic solution provides quantitative description of the ion density (the same as in atomically detailed simulation). At shorter distances, the structure of RNA (and ions) has a signiﬁcant impact on the pair correlation functions. Predicted binding sites of Mg2+ at the RNA surface are in accord with structures from crystallography. Electric ﬁeld relaxation is investigated. The relaxation due to solution rearrangements is completed in tens of picoseconds, while the contribution of RNA tumbling continues to a few nanoseconds.",
	collection = "nucleic acids",
	doi = "10.1021/jp911992t",
	localfile = "nucleic acids/2010 - Computational exploration of mobile ion distirbutions around RNA duplex.pdf",
	year = 2010
}

@Article{2010-Kolar-KH,
	Author = "Michal Kolář and Tomáš Kubař and Pavel Hobza",
	Title = "{Sequence-dependent configurational entropy change of DNA upon intercalation}",
	Journal = "J. Phys. Chem. B",
	Volume = "114",
	Number = "42",
	Pages = "13446–13454",
	abstract = "We investigated the intercalation of an antitumor drug ellipticine into four adenine-thymine (AT) rich DNA duplexes with the focus on the conﬁgurational entropy, by means of molecular dynamics (MD) simulations. Two possible binding orientations of ellipticine in a DNA double helix were studied, and the orientation with the pyrrole nitrogen exposed into a major groove was identiﬁed as the more probable. The conﬁgurational entropy change of DNA is shown to contribute signiﬁcantly to the binding free energy. The magnitude of this contribution depends on the exact DNA sequence. A detailed analysis revealed that the largest ﬂexibility changes occurred in the sugar-phosphate backbone, resulting in an entropy gain in the most cases. The nucleobases were not involved in the changes of ﬂexibility and entropy. BI/BII-like conformational transitions were observed after the intercalation of ellipticine, and the consequences of these transitions for the evaluation of entropy are discussed.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/jp1019153",
	localfile = "nucleic acid intercalation/2010 - Sequence-dependent configurational entropy change of DNA upon intercalation.pdf",
	year = 2010
}

@Article{2010-Kuilla-BYKBL,
	Author = "Tapas Kuilla and Sambhu Bhadra and Dahu Yao and Nam Hoom Kim and Saswata Bose and Joong Hee Lee",
	Title = "{Recent advances in graphene based polymer composites}",
	Journal = "Prog. Polym. Sci.",
	Volume = "35",
	Pages = "1350–1375",
	collection = "polymer nanocomposites",
	doi = "10.1016/j.progpolymsci.2010.07.005",
	keywords = "graphene; polymer nanocomposites",
	localfile = "polymer nanocomposites/2010 - Recent advances in graphene based polymer composites.pdf",
	type = "Review",
	year = 2010
}

@Article{2010-Kumar-Krishnamoorti,
	Author = "Sanat K. Kumar and Ramanan Krishnamoorti",
	Title = "{Nanocomposites: structure, phase behavior, and properties}",
	Journal = "Annu. Rev. Chem. Biomol. Eng.",
	Volume = "1",
	Pages = "37–58",
	Note = "Although quite brief and selective, contains excellent references.",
	abstract = "It is well recognized that nanocomposites formed by adding nanoparticles to polymers can have signiﬁcantly enhanced properties relative to the native polymer. This review focuses on three aspects that are central to the outstanding problem of realizing these promised property improvements. First, we ask if there exist general strategies to control nanoparticle spatial distribution. This is an important question because it is commonly accepted that the nanoparticle dispersion state crucially affects property improvements. Because ideas on macroscale composites suggest that optimizing different properties requires different dispersion states, we next ask if we can predict a priori the particle dispersion and organization state that can optimize one (or more) properties of the resulting nanocomposite. Finally, we examine the role that particle shape plays in affecting dispersion and hence property control. This review focuses on recent advances concerning these underpinning points and how they affect measurable properties relevant to engineering applications.",
	collection = "polymer nanocomposites",
	doi = "10.1146/annurev-chembioeng-073009-100856",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2010 - Nanocomposites: structure, phase behavior, and properties.pdf",
	rating = "2",
	read = "2011-10-11",
	type = "Review",
	year = 2010
}

@Article{2010-Li-Gu,
	Author = "Yang Li and Ning Gu",
	Title = "{Thermodynamics of charged nanoparticle adsorption on charge-neutral membranes: a simulation study}",
	Journal = "J. Phys. Chem. B",
	Volume = "114",
	Pages = "2749–2754",
	abstract = "The interactions between charged nanoparticles (NPs) and charge-neutral phospholipid membranes are investigated by coarse-grained molecular dynamics simulations. Three kinds of nanoparticles are modeled with different surface charge densities: the uncharged one, the positively charged one, and the negatively charged one. We ﬁnd that the electrostatic attraction improves the adhesion of a charged nanoparticle to the membrane. With the increase of electrostatic energy, a charged NP can be almost fully wrapped by the membrane. In addition, analyses of structural variations suggest that the adhesion of a charged NP induces a local transition in ﬂuid bilayers. Some thermodynamic quantities such as free energy, entropy, and enthalpy are also obtained to explain the process of NPs binding. Furthermore, the bending energy of wrapping of NPs against the electrostatic potential energy is also discussed based on the Helfrich theory, indicating that the driving force of the wrap originates from the gain in electrostatic energy at the cost of the elastic energy of biomembranes. Our observations shed light on the origin of experiments of the wrap as well as the mechanism of structural transitions of membranes due to the electrostatic binding.",
	collection = "nanoparticles",
	doi = "10.1021/jp904550b",
	keywords = "biological nanocomposites; lipid bilayers; nanospheres",
	localfile = "nanoparticles/2010 - Thermodynamics of charged nanoparticle adsorption on charge-netrual membranes: a simulation study.pdf",
	methods = "CG MD",
	year = 2010
}

@Article{2010-Liang-CM,
	Author = "Qing Liang and Qing-Hu Chen and Yu-quang Ma",
	Title = "{Membrane-mediated interactions between nanoparticles on a substrate}",
	Journal = "J. Phys. Chem. B",
	Volume = "114",
	Pages = "5359–5364",
	abstract = "Investigations of the interactions between nanoparticles and lipid bilayer may yield insight into the understanding of the protein-biomembrane interactions and the cytotoxicity of drugs. Here, we theoretically investigate the membrane-mediated interactions between two nanoparticles supported on a substrate. We examine the effects of the packing density of lipids, the direct nanoparticle-lipid interaction, and the direct substrate-lipid interaction on the effective interactions between the nanoparticles and ﬁnd the effective interactions between the two nanoparticles are mainly dominated by the competition of the deformations of the different parts of the lipid bilayers as well as the stretching of the lipid chains sandwiched between the nanoparticles. By varying the above-mentioned effects, the effective interactions between the two nanoparticles can be efﬁciently modulated. The results may provide some theoretical insight into experiments on the membrane-mediated nanoparticle organization on a substrate and organization of the membrane proteins or drug nanoparticles on the surfaces of the cellular membranes.",
	collection = "nanoparticles",
	doi = "10.1021/jp910852d",
	keywords = "biological nanocomposites; lipid bilayers; nanospheres; thin films",
	localfile = "nanoparticles/2010 - Membrane-mediated interactions between nanoparticles on a substrate.pdf",
	year = 2010
}

@Article{2010-Lodola-SFRMM,
	Author = "Alessio Lodola and Jitnapa Sirirak and Natalie Fey and Silvia Rivara and Marco Mor and Adrian J. Mulholland",
	Title = "{Structural fluctuations in enzyme-catalyzed reactions: determinants of reactivity in fatty acid amide hydrolase from multiviriate statistical analysis of quantum mehcanics/molecular mechanics paths}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "6",
	Pages = "2948–2960",
	abstract = "The effects of structural ﬂuctuations, due to protein dynamics, on enzyme activity are at the heart of current debates on enzyme catalysis. There is evidence that fatty acid amide hydrolase (FAAH) is an enzyme for which reaction proceeds via a high-energy, reactive conformation, distinct from the predominant enzyme-substrate complex (Lodola et al. Biophys. J. 2007, 92, L20-22). Identifying the structural causes of differences in reactivity between conformations in such complex systems is not trivial. Here, we show that multivariate analysis of key structural parameters can identify structural determinants of barrier height by analysis of multiple reaction paths. We apply a well-tested quantum mechanics/molecular mechanics (QM/MM) method to the ﬁrst step of the acylation reaction between FAAH and oleamide substrate for 36 different starting structures. Geometrical parameters (consisting of the key bond distances that change during the reaction) were collected and used for principal component analysis (PCA), partial least-squares (PLS) regression analysis, and multiple linear regression (MLR) analysis. PCA indicates that different “families” of enzyme-substrate conformations arise from QM/MM molecular dynamics simulation and that rarely sampled, catalytically signiﬁcant conformational states can be identiﬁed. PLS and MLR analyses allowed the construction of linear regression models, correlating the calculated activation barriers with simple geometrical descriptors. These analyses reveal the presence of two fully independent geometrical effects, explaining 78\% of the variation in the activation barrier, which are directly correlated with transition-state stabilization (playing a major role in catalysis) and substrate binding. These results highlight the power of statistical approaches of this type in identifying crucial structural features that contribute to enzyme reactivity.",
	collection = "enzymes",
	doi = "10.1021/ct100264j",
	localfile = "enzymes/2010 - Structural fluctuations in enzyme-catalyzed reactions: determinants of reactivity in fatty acid amide hydrolase from multivariate statistical analysis of quantum mechanics-molecular mechanics paths.pdf",
	year = 2010
}

@Article{2010-Meth-Lustig,
	Author = "Jeffrey S. Meth and Steven Raymond Lustig",
	Title = "{Polymer interphase structure near nanoscale inclusions: comparison between random walk theory and experiment}",
	Journal = "Polymer",
	Volume = "51",
	Pages = "4259–4266",
	abstract = "We propose a theory for the structure of the interphase in polymeric nanocomposites based on the freely-jointed chain near an impermeable spherical inclusion. The theory considers only the entropic exclusion between a polymer and the inclusion. The radius of gyration of the polymer chain and its distortion from spherical symmetry are perturbed strongly when the chain end is closer than 3Rg0 from the surface of the sphere, where Rg0 is the unperturbed radius of gyration. Also, the maximum expansion of the chain is bounded by (4/3)½, equal to a 15\% increase. The shape of the polymer chain is elongated tangentially to the surface when the chain end originates in the interphase, but elongates radially due to entropic repulsion when the chain end is very close to the surface of the sphere. All the distortions of the polymer conformation from ideality, and hence the spatial extent of the interphase, occur within the depletion region associated with colloids. The model is used to explain recent experimental results showing that polymer chain dimensions increase in the presence of nanoparticles. The model quantitatively reproduces the observations at low ﬁller loadings using no adjustable parameters, suggesting that entropic arguments can describe the majority of the effect there.",
	collection = "nanoparticles",
	doi = "10.1016/j.polymer.2010.06.043",
	keywords = "nanospheres; polymer nanocomposites",
	localfile = "nanoparticles/2010 - Polymer interphase structure near nanoscale inclusions: comparison between random walk theory and experiment.pdf",
	year = 2010
}

@Article{2010-Neuman-Nave,
	Author = "Yair Neuman and Ophir Nave",
	Title = "{Why the brain needs language in order ot be self-conscious}",
	Journal = "New Ideas Psychol.",
	Volume = "38",
	Pages = "37–48",
	Note = "Gathers some stimulating ideas from previous literature and suggests a general mechanism by which the capacity of language to refer to itself is central to the ability of the human mind to reflect on itself. The discussion is grounded in dynamical systems, the reconstruction of their phase space trajectories and recurrent points, although the technical details of how this applies to the brain this are not substantial.",
	collection = "neuroscience",
	doi = "10.1016/j.newideapsych.2009.05.001",
	keywords = "self-consciousness; inner speech; dynamical systems",
	localfile = "neuroscience/2010 - Why the brain needs language in order to be self-conscious.pdf",
	rating = "2",
	read = "2013-08-17",
	year = 2010
}

@Article{2010-Pitonak-NH,
	Author = "Michal Pitoňák and P. Neogrády and Pavel Hobza",
	Title = "{Three- and four-body nonadditivities in nucleic acid tetramers: a CCSD(T) study}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "12",
	Pages = "1369–1378",
	abstract = "Three- and four-body nonadditivities in the uracil tetramer (in DNA-like geometry) and the GC step (in crystal geometry) were investigated at various levels of the wave-function theory: HF, MP2, MP3, L-CCD, CCSD and CCSD(T). All of the calculations were performed using the 6-31G**(0.25,0.15) basis set, whereas the HF, MP2 and the MP3 nonadditivities were, for the sake of comparison, also determined with the much larger aug-cc-pVDZ basis set. The HF and MP2 levels do not provide reliable values for many-body terms, making it necessary to go beyond the MP2 level. The benchmark CCSD(T) three- and four-body nonadditivities are reasonably well reproduced at the MP3 level, and almost quantitative agreement is obtained (fortuitously) either on the L-CCD level or as an average of the MP3 and the CCSD results. Reliable values of many-body terms (especially their higher-order correlation contributions) are obtained already when the rather small 6-31G**(0.25,0.15) basis set is used. The four-body term is much smaller when compared to the three-body terms, but it is deﬁnitely not negligible, e.g. in the case of the GC step it represents about 16\% of all of the three- and four-body terms. While investigating the geometry dependence of many-body terms for the GG step at the MP3/6-31G**(0.25,0.15) level, we found that it is necessary to include at least three-body terms in the determination of optimal geometry parameters.",
	collection = "nucleic acid bases",
	localfile = "nucleic acid bases/2010 - Three- and four-body nonadditivities in nucleic acid tetramers: a CCSD(T) study.pdf",
	year = 2010
}

@Article{2010-Platts-Hill,
	Author = "James A. Platts and J. Grant Hill",
	Title = "{Non-covalent interactions using local correlation methods: energy partitioning, geometry optimisation and harmonic frequency calculations}",
	Journal = "Mol. Phys.",
	Volume = "108",
	Number = "11",
	Pages = "1497–1504",
	abstract = "The performance of density fitting, local correlation methods (DF-LMP2 and DF-LCCSD) in studies of non-covalent interactions is tested against literature data for a standard set of 22 inter-molecular complexes. Partitioning of interaction energy in the local correlation approach, based on the classes of occupied and virtual orbital involved in the interaction, clearly distinguishes the three types of interaction present in the set of complexes, in agreement with previous classifications. Geometry optimisation is found to be straightforward with DF-LMP2 without the need for counterpoise correction, resulting in geometries very close to previous, counterpoise-corrected structures. Spin-component scaling of gradients to correct for the known shortcomings of conventional MP2 has only a small effect on geometries in most cases, but significantly alters the distance between aromatic rings in stacked complexes. Harmonic frequency calculation is made possible by efficient use of parallel computing resources, and confirms all structures to be true minima, unlike previous estimates using density functional theory. Corrections for the change in zero-point vibrational energy are determined from this data, and typically constitute between 10 and 50\% of the overall binding energy of the complex.",
	collection = "molecular interactions",
	doi = "10.1080/00268971003757977",
	keywords = "noncovalent interactions",
	localfile = "molecular interactions/2010 - Non-covalent interactions using local correlation methods: energy partitioning, geometry optimisation and harmonic frequency calcualtions.pdf",
	year = 2010
}

@Article{2010-Ploshnik-SBS,
	Author = "Elina Ploshnik and Asaf Salant and Uri Banin and Roy Shenhar",
	Title = "{Hierarchical surface patterns of nanorods obtained by co-assembly with block copolymers in ultrathin films}",
	Journal = "Adv. Mater.",
	Volume = "22",
	Pages = "2774–2779",
	Note = "Coated CdSe nanorods assembling in rows inside the PS domains of a PS-b-PMMA thin film.",
	collection = "block copolymer nanocomposites",
	doi = "10.1002/adma.201000573",
	keywords = "block copolymers; self-assembly; nanorods; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2010 - Hierarchical surface patterns of nanorods obtained by co-assembly with block copolymers in ultrathin films.pdf",
	methods = "AFM, SEM",
	rating = "2",
	systems = "CdSe(rods)-S@PS-PMMA",
	year = 2010
}

@Article{2010-Ploshnik-SBS-1,
	Author = "Elina Ploshnik and Asaf Salant and Uri Banin and Roy Shenhar",
	Title = "{Co-assembly of block copolymers and nanorods in ultrathin films: effects of copolymer size and nanorod filling fraction}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "12",
	Pages = "11885–11893",
	collection = "block copolymer nanocomposites",
	keywords = "block copolymers; self-assembly; nanorods; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2010 - Co-assembly of block copolymers and nanorods in ultrathin films: effects of copolymer size and nanorod filling fraction.pdf",
	methods = "AFM, SEM",
	rating = "2",
	year = 2010
}

@Article{2010-Posocco-PFLP,
	Author = "Paola Posocco and Zbyšek Posel and Maurizio Fermeglia and Martin Lísal and Sabrina Pricl",
	Title = "{A molecular simulation approach to the prediction of the morphology of self-assembled nanoparticles in diblock copolymers}",
	Journal = "J. Mater. Chem.",
	Volume = "20",
	Pages = "10511–10520",
	collection = "block copolymer nanocomposites",
	doi = "10.1039/c0jm01561j",
	keywords = "block copolymers; nanoparticle aggregation; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2010 - A molecular simulation approach to the prediction of the morphology of self-assembled nanoparticles in diblock copolymers.pdf",
	methods = "DPD",
	rating = "2",
	year = 2010
}

@Article{2010-Riley-PCH,
	Author = "Kevin E. Riley and Michal Pitoňák and Jiří Černý and Pavel Hobza",
	Title = "{On the structure and geometry of biomolecular binding motifs (hydrogen-bonding, stacking, X-H···π): WFT and DFT calculations}",
	Journal = "J. Chem. Theory Comp.",
	Number = "6",
	collection = "molecular interactions",
	doi = "10.1021/ct900376r",
	localfile = "molecular interactions/2010 - On the structure and geometry of biomolecular binding motifs.pdf",
	year = 2010
}

@Article{2010-Riley-PJH,
	Author = "Kevin E. Riley and Michal Pitoňák and Petr Jurečka and Pavel Hobza",
	Title = "{Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories}",
	Journal = "Chem. Rev.",
	Volume = "110",
	Pages = "5023–5063",
	abstract = "More than 20 years ago, we published in Chemical Reviews a paper entitled “Intermolecular Interactions between Medium-Sized Systems. Nonempirical and Empirical Calculations of Interaction Energy: Successes and Failures”. The situation in interactions at that time can be best characterized by the question we posed at the very beginning of the review: “Can quantum chemistry describe vdW (van der Waals; today we call it noncovalent) interactions as successfully as covalent interactions?” Our answer then was “unambiguously yes”. We had good reason for an optimistic “yes” since we presented the ﬁrst coupled-cluster calculations including triple excitations for a (at that time) large complex – the water dimer.",
	collection = "molecular interactions",
	doi = "10.1021/cr1000173",
	keywords = "noncovalent interactions",
	localfile = "molecular interactions/2010 - Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories.pdf",
	type = "Review",
	year = 2010
}

@Article{2010-Santiago-CRALKDE,
	Author = "A. A. Hernandez Santiago and Salvador Rosas Castilla and Albino Morales Rodriguez and Elena Aeskerova and Anastasia Lantushenko and Viktor V. Kostjukov and David Davies and Maxim Evstigneev",
	Title = "{Relation between structure and enthalpy for stacking interactions of aromatic molecules}",
	Journal = "Mol. Phys.",
	Volume = "108",
	Number = "15",
	Pages = "1941–1947",
	abstract = "An approximately linear correlation has been found between the enthalpy of complexation and the area of overlap of the chromophores using published structural and thermodynamical data on the self- and hetero-association of aromatic molecules measured under similar solution conditions. This finding is consistent with the assumption that short-range van-der-Waals forces dominate over other contributions to the enthalpy of stacking of aromatic molecules. It provides a ‘model-independent’ approach for a priori estimation of theenthalpy of aromatic–aromatic stacking interactions from knowledge of the structural properties or vice versa.",
	collection = "stacking",
	doi = "10.1080/00268976.2010.498389",
	keywords = "aromatic stacking",
	localfile = "molecular stacking/2010 - Relation between structure and enthalpy for stacking interactions of aromatic molecules.pdf",
	year = 2010
}

@Article{2010-Schwabe-HG,
	Author = "Tobias Schwabe and Robert Huenerbein and Stefan Grimme",
	Title = "{Large molecules – small energies: challanges for contemporary quantum chemistry}",
	Journal = "SYNLETT",
	Number = "10",
	Pages = "1431–1441",
	abstract = "New developments in computational chemistry which allow an accurate treatment of large molecules are presented. Along with a short introduction to the theoretical methods, highlights of current applications in organic chemistry are given. The so-called ‘chemical accuracy’ is now often achievable when modern methods and sophisticated techniques are applied.",
	collection = "quantum chemistry",
	doi = "10.1055/s-0029-1219930",
	localfile = "/home/kml/data/library/quantum chemistry/2010 - Large molecules - small energies: challanges for contemporary quantum chemistry.pdf",
	year = 2010
}

@Article{2010-Seifpour-SNJ,
	Author = "Arezou Seifpour and Philip Spicer and Nitish Nair and Arthi Jayaraman",
	Title = "{Effect of monomer sequences on conformation of copolymers grafted on spherical nanoparticles: a Monte Carlo simulation study}",
	Journal = "J. Chem. Phys.",
	Volume = "132",
	Pages = "164901",
	Note = "Radius of gyration and monomer aggregation at small grafting densities.",
	abstract = "Functionalizing nanoparticles with organic ligands, such as oligomers, polymers, DNA, and proteins, is an attractive way to manipulate the interfacial interactions between the nanoparticles and the medium the particles are placed in, and thus control the nanoparticle assembly. In this paper we have conducted a Monte Carlo simulation study on copolymer grafted spherical nanoparticles to show the tremendous potential of using monomer sequence on the copolymers to tune the grafted chain conformation, and thus the effective interactions between copolymer grafted nanoparticles. We have studied AB copolymers with alternating, multiblock, or diblock sequences, where either A monomers or B monomers have monomer-monomer attractive interactions. Our focus has been to show the nontrivial effect of monomer sequence on the conformations of the grafted copolymers at various particle diameters, grafting densities, copolymer chain lengths, and monomer-monomer interactions in an implicit small molecule solvent. We observe that the monomer sequence, particle diameter, and grafting density dictate whether a the grafted chains aggregate to bring attractive monomers from multiple grafted chains together interchain and intrachain monomer aggregation if the enthalpy gained by doing so offsets the entropic loss caused by stretching of chains, or b each grafted chain folds onto itself to bring its attractive monomers together only intrachain monomer aggregation if the entropic loss from interchain aggregation cannot be overcome by the enthalpic gain. For six copolymers of chain length N = 24 grafted on a spherical particle of diameter D = 4, interchain and intrachain monomer aggregation occurs, and the radius of gyration varies nonmonotonically with increasing blockiness of the monomer sequence. At larger particle diameters the grafted chains transition to purely intrachain monomer aggregation. The radius of gyration varies monotonically with monomer sequence for intrachain monomer aggregation because as the sequence becomes blockier like monomers are grouped together , the copolymer chain has to fold less compactly to maximize the enthalpically favorable contacts while maintaining high conformational entropy. The radius of gyration of alternating and diblock copolymers scales with chain length N through a power law Rg2 1/2 = N with the prefactor and scaling exponent, varying with monomer sequence and monomer-monomer attraction strength.",
	collection = "nanoparticles",
	doi = "10.1063/1.3385469",
	keywords = "nanoparticle grafts; nanoconfinement",
	localfile = "nanoparticles/2010 - Effect of monomer sequences on conformations of copolymers grafted on spherical nanoparticles: a Monte Carlo simulation study.pdf",
	methods = "Monte Carlo",
	year = 2010
}

@Article{2010-Stojkovic-MOP,
	Author = "Marijana Radić Stojković and Saska Marczi and Ljubica Glavaš-Obrovac and Ivo Piantanida",
	Title = "{Permanent positive charge strongly influences DNA/RNA binding and antiproliferative activity of urea-phenanthridinium conjugates}",
	Journal = "Eur. J. Med. Chem.",
	Volume = "45",
	Pages = "3281–3292",
	abstract = "An introduction of the permanent positive charge by methylation of heterocyclic nitrogen on a series of previously studied bis-urea phenanthridine derivatives substantially changed their interactions with DNA and RNA as well as biological activity. At variance to non-methylated analogues, novel methylated derivatives interacted with DNA/RNA not only at pH 5 but also at pH 7, and some compounds switched the DNA binding mode from the minor groove binding (non-methylated derivatives) to the intercalation (novel, methylated derivatives). Moreover, selective ds-RNA over ds-DNA thermal stabilization of previously observed non-methylated derivatives was reversed for novel, methylated derivatives. The variation of a linker length connecting two ureaephenanthridinium conjugates regulated their binding modes toward double stranded polynucleotides. All novel compounds were able to distinguish between polynucleotides of AeT(U) and GeC basepair composition by a speciﬁc ﬂuorescence change. Moreover, the introduction of the permanent positive charge on the phenanthridinium moiety resulted in significantly higher biological potency in respect to non-methylated analogues.",
	collection = "nucleic acid intercalation",
	doi = "10.1016/j.ejmech.2010.04.006",
	localfile = "nucleic acid intercalation/2010 - Permanent positive charge strongly influences DNA and RNA binding and antiproliferative activity of urea-phenanthridinium conjugates.pdf",
	year = 2010
}

@Article{2010-Stone-Korley,
	Author = "David A. Stone and LaShanda T. J. Korley",
	Title = "{Bioinspired polymeric nanocomposites}",
	Journal = "Macromolecules",
	Volume = "43",
	Pages = "9217–9226",
	abstract = "Nature employs several strategies in fabricating high-performance materials from which scientists can garner important lessons for producing synthetic materials with enhanced properties. When the mechanical properties of a single-phase system are insufficient for an application, composite materials offer an important strategy to impart increased strength and toughness. By introducing nanoscale filler components, greater enhancement in mechanical function compared to traditional macro- and microscale fillers is possible due to the greater surface area and lower percolation thresholds stemming from the higher aspect ratios of the nanoscale fillers. In this Perspective, we will discuss polymer nanocomposites drawing from the lessons of wood (network of preformed, high-modulus cellulose nanorods), spider silk (self-assembly of ordered domains), and tendon (hierarchical ordering).",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma101661p",
	keywords = "biological nanocomposites",
	localfile = "polymer nanocomposites/2010 - Bioinspired polymeric nanocomposites.pdf",
	type = "Perspective",
	year = 2010
}

@Article{2010-Svozil-HS,
	Author = "Daniel Svozil and Pavel Hobza and Jiří Šponer",
	Title = "{Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?}",
	Journal = "J. Phys. Chem. B",
	Volume = "114",
	Pages = "1191–1203",
	abstract = "High level ab initio methods have been used to study stacking interactions in ten unique base pair steps both in A-RNA and in B-DNA duplexes. The protocol for selection of geometries based on molecular dynamics (MD) simulations is proposed, and its suitability is demonstrated by comparison with stacking in steps at fiber diffraction geometries. It is shown that fiber diffraction geometries are not sufficiently accurate for interaction energy calculations. In addition, the protocol for selection of geometries based on MD simulations allows for the evaluation of the variability of the intrinsic stacking energies along the MD trajectories. The uncertainty in stacking energies (difference between the most and least stable geometry) due to the dynamical nature of systems can be, in some cases, as large as 3.0 kcal center dot mol(-1), which is almost 50\% of the actual sequence dependence of base stacking energies (the energy difference between the most and least stable sequences). Thus, assessing the relative magnitude of the gas phase stacking energy using a single geometry for each sequence is insufficient to obtain an unambiguous order of gas phase stacking energies in canonical double helices. Though the ordering of ten unique dinucleotide steps cannot be definitive, some general conclusions were drawn. The stacking energies of base pair steps in A-RNA are more evenly separated compared to B-DNA, and their ordering is less sensitive to the dynamics of the system compared to be B-DNA. The most stable step both in B-DNA W A-RNA is the CG/CG step that is well separated from the second most stable step GC/GC. Also the leas/stable step (the CC/GG step) is well separated from the rest of the structures. The calculations further show that B-DNA stacking is favorable only marginally (on average by 1.14 kcal center dot mol(-1) per base pair step) over A-RNA stacking, and this difference vanishes after subtracting the stabilizing van der Waals effect of the thymine 5-methyl group that is absent in RNA. Basically, no correlation between the sequence dependence of gas phase stacking energies and the sequence dependence of Delta G degrees(37) free energies used in nearest-neighbor models was found either for B-DNA or for A-RNA. This reflects the complexity of the balance of forces that are responsible for the sequence dependence of thermodynamics stability of nucleic acids, which masks the effect of the intrinsic interactions between the stacked base pairs.",
	collection = "stacking",
	doi = "10.1021/jp910788e",
	localfile = "molecular stacking/2010 - Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum chemical calcualtions.pdf",
	year = 2010
}

@Article{2010-Takatani-HMMS,
	Author = "Tait Takatani and Edward G. Hohenstein and Massimo Malagoli and Michael S. Marshall and C. David Sherrill",
	Title = "{Basis set consistent revision of the S22 test set of noncovalent interaction energies}",
	Journal = "J. Chem. Phys.",
	Volume = "132",
	Pages = "144104",
	abstract = "The S22 test set of interaction energies for small model complexes [Phys. Chem. Chem. Phys. 8, 1985 2006] has been very valuable for benchmarking new and existing methods for noncovalent interactions. However, the basis sets utilized to compute the CCSD(T) interaction energies for some of the dimers are insufﬁcient to obtain converged results. Here we consistently extrapolate all CCSD(T)/complete basis set (CBS) interaction energies using larger basis sets for the CCSD(T) component of the computation. The revised values, which we designate S22A, represent the most accurate results to date for this set of dimers. The new values appear to be within a few hundredths of 1 kcal mol−1 of the true CCSD(T)/CBS limit at the given geometries, but the former S22 values are off by as much as 0.6 kcal mol−1 compared to the revised values. Because some of the most promising methods for noncovalent interactions are already achieving this level of agreement or better compared to the S22 data, more accurate benchmark values would clearly be helpful. The MP2, SCS-MP2, SCS-CCSD, SCS MI -MP2, and B2PLYP-D methods have been tested against the more accurate benchmark set. The B2PLYP-D method outperforms all other methods tested here, with a mean average deviation of only 0.12 kcal mol−1. However, the consistent, slight underestimation of the interaction energies computed by the SCS-CCSD method an overall mean absolute deviation and mean deviation of 0.24 and −0.23 kcal mol−1, respectively suggests that the SCS-CCSD method has the potential to become even more accurate with a reoptimization of its parameters for noncovalent interactions.",
	collection = "molecular interactions",
	doi = "10.1063/1.3378024",
	localfile = "molecular interactions/2010 - Basis set consistent revision of the S22 test set of noncovalent interaction energies.pdf",
	year = 2010
}

@Article{2010-Thompson,
	Author = "Russell B. Thompson",
	Title = "{Tilt grain boundaries in a diblock copolymer ordered nanocomposite lamellar phase}",
	Journal = "J. Chem. Phys.",
	Volume = "133",
	Pages = "144902",
	abstract = "A hybrid self-consistent field theory/density functional theory method is applied to predict tilt (kink) grain boundary structures between lamellar domains of a symmetric diblock copolymer with added spherical nanoparticles. Structures consistent with experimental observations are found and theoretical evidence is provided in support of a hypothesis regarding the positioning of nanoparticles. Some particle distributions are predicted for situations not yet examined by experiment.",
	collection = "block copolymer nanocomposites",
	doi = "10.1063/1.3498784",
	keywords = "block copolymers; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2010 - Tilt grain boundaries in a diblock copolymer ordered nanocomposite lamellar phase.pdf",
	year = 2010
}

@Article{2010-Valiev-BGKSDWNAWJ,
	Author = "M. Valiev and E. J. Bylaska and N. Govind and K. Kowalski and T. P. Straatsma and H. J. J. {van Dam} and D. Wang and J. Nieplocha and E. Apra and Theresa L. Windus and W. A. {de Jong}",
	Title = "{NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations}",
	Journal = "Comput. Phys. Commun.",
	Volume = "181",
	Number = "9",
	Pages = "1477–1489",
	abstract = "The latest release of NWChem delivers an open-source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance.",
	collection = "cheminformatics",
	doi = "10.1016/j.cpc.2010.04.018",
	localfile = "cheminformatics/2010 - NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations.pdf",
	year = 2010
}

@Article{2010-Villet-Fredrickson,
	Author = "Michael C. Villet and Glenn H. Fredrickson",
	Title = "{Numerical coarse-graining of fluid field theories}",
	Journal = "J. Chem. Phys.",
	Volume = "132",
	Pages = "034109",
	abstract = "We present a formalism for the systematic numerical coarse-graining of ﬁeld-theoretic models of ﬂuids that draws upon techniques from both the Monte Carlo renormalization group and particle-based coarse-graining literature. A force-matching technique initially developed for coarse-graining particle-based interaction potentials is adapted to calculate renormalized ﬁeld-theoretic coupling coefﬁcients in a complex-valued ﬁeld theory, and a related method is introduced for coarse-graining ﬁeld-theoretic operators. The viability of this methodology is demonstrated by coarse-graining a ﬁeld-theoretic model of a Gaussian-core ﬂuid and thereby reducing lattice discretization errors.",
	collection = "coarse graining",
	doi = "10.1063/1.3289723",
	keywords = "coarse graining",
	localfile = "coarse graining/2010 - Numerical coarse-graining of fluid field theories.pdf",
	year = 2010
}

@Article{2010-Wang-Dormidontova,
	Author = "Shihu Wang and Elena E. Dormidontova",
	Title = "{Nanoparticle design optimization for enhanced targeting: Monte Carlo simulations}",
	Journal = "Biomacromolecules",
	Volume = "11",
	Number = "7",
	Pages = "1785–1795",
	abstract = "Using computer simulations, we systematically studied the inﬂuence of different design parameters of a spherical nanoparticle tethered with monovalent ligands on its efﬁciency of targeting planar cell surfaces containing mobile receptors. We investigate how the nanoparticle afﬁnity can be affected by changing the binding energy, the percent of functionalization by ligands, tether length, grafting density, and nanoparticle core size. In general, using a longer tether length or increasing the number of tethered chains without increasing the number of ligands increases the conformational penalty for tether stretching/compression near the cell surface and leads to a decrease in targeting efﬁciency. At the same time, using longer tethers or a larger core size allows ligands to interact with receptors over a larger cell surface area, which can enhance the nanoparticle afﬁnity toward the cell surface. We also discuss the selectivity of nanoparticle targeting of cells with a high receptor density. Based on the obtained results, we provide recommendations for improving the nanoparticle binding afﬁnity and selectivity, which can guide future nanoparticle development for diagnostic and therapeutic purposes.",
	collection = "nanoparticles",
	doi = "10.1021/bm100248e",
	keywords = "nanoparticle grafts; nanospheres; receptors",
	localfile = "nanoparticles/2010 - Nanoparticle design optimization for enhanced targeting: Monte Carlo simulations.pdf",
	year = 2010
}

@Article{2010-Wong-Pollack,
	Author = "Gerard C. L. Wong and Lois Pollack",
	Title = "{Electrostatics of strongly charged biological polymers: ion-mediated interactions and self-organization in nulceic acids and proteins}",
	Journal = "Annu. Rev. Phys. Chem.",
	Volume = "61",
	Pages = "171–189",
	collection = "nucleic acids",
	doi = "10.1146/annurev.physchem.58.032806.104436",
	localfile = "nucleic acids/2010 - Electrostatics of strongly charged biological polymers: ion-mediated interactions and self-organization in nulceic acids and proteins.pdf",
	rating = "2",
	read = "2012-08-13",
	year = 2010
}

@Article{2010-Xu-CW,
	Author = "Xiafei Xu and Dapeng Cao and Jianzhong Wu",
	Title = "{Density functional theory for predicting polymeric forces against surface fouling}",
	Journal = "Soft Matter",
	Volume = "6",
	Pages = "4631–4646",
	abstract = "Polymer-based ‘‘non-stick’’ surfaces have been proposed as the next generation of effective and environmentally-friendly coating materials for protecting implanted biomedical devices and for marine antifouling. However, identiﬁcation of polymeric systems for universal fouling control is often impeded by the poor knowledge of interactions between biological substances and polymeric substrates in diverse aqueous environments. In this article, we review predictions of the polymer density functional theory (DFT) on the structural and surface properties of polymer brushes and polymer nanocomposites that are potentially useful for antifouling applications. In comparison to alternative theoretical methods, DFT exhibits versatile features that are ideal for investigating various polymer-mediated interactions, self-organization of nanoparticles, and surface-induced phase transitions. It is capable of explicit description of important microscopic details of polymeric systems including the molecular excluded-volume effects, associating interactions, van der Waals attraction, Coulomb forces, and inter- and intra- molecular correlations. The theoretical descriptions of surface forces may provide helpful guidelines in the design and development of polymeric materials for preventing non-speciﬁc adsorption of biological substances.",
	collection = "polymer nanocomposites",
	doi = "10.1039/c0sm00034e",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2010 - Density functional theory for predicting polymeric forces against surface fouling.pdf",
	methods = "DFT",
	type = "Review",
	year = 2010
}

@Article{2010-Xu-FY,
	Author = "Guang-Kui Xu and Xi-Qiao Feng and Shou-Wen Yu",
	Title = "{Controllable nanostructural transitions in grafted nanoparticle-block copolymer composites}",
	Journal = "Nano Res.",
	Volume = "3",
	Pages = "356–362",
	abstract = "We report a theoretical investigation of self-assembled nanostructures of polymer-grafted nanoparticles in a block copolymer and explore underlying physical mechanisms by employing the self-consistent field method. By varying the particle concentration or the chain length and density of the grafted polymer, one can not only create various ordered morphologies (e.g., lamellar or hexagonally packed patterns) but also control the positions of nanoparticles either at the copolymer interfaces or in the center of one-block domains. The nanostructural transitions we here report are mainly attributed to the competition between entropy and enthalpy.",
	collection = "block copolymer nanocomposites",
	doi = "10.1007/s12274-010-1039-8",
	keywords = "block copolymers; mesophase transitions; nanoparticle distribution; nanoparticle grafts; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2010 - Controllable nanostructural transitions in grafted nanoparticle-block copolymer composites.pdf",
	methods = "SCFT",
	year = 2010
}

@Article{2010-Yager-FZBKJ,
	Author = "Kevin G. Yager and Nathaniel J. Fredin and Xiaohua Zhang and Brian C. Berry and Alamgir Karim",
	Title = "{Evolution of block-copolymer order through a moving thermal zone}",
	Journal = "Soft Matter",
	Volume = "6",
	Pages = "92–99",
	Note = "So the idea is nice, but I've heard it has already been tried before and is hard to perfect and scale. Might be a good process to optimize through simulation.",
	collection = "block copolymers",
	doi = "10.1039/b916200c",
	keywords = "thin films; alignment",
	localfile = "block copolymers/2010 - Evolution of block-copolymer order through a moving thermal zone.pdf",
	methods = "AFM, CZA, SAXS",
	rating = "2",
	read = "2011-04-05",
	systems = "PS-b-PMMA",
	year = 2010
}

@Article{2010-Yan-PGB,
	Author = "Li-Tang Yan and Nicole Popp and Sujit-Kumar Ghosh and Alexander Böker",
	Title = "{Self-assembly of Janus nanoparticles in diblock copolymers}",
	Journal = "ACS Nano",
	Volume = "4",
	Number = "2",
	Pages = "913–920",
	abstract = "Janus nanoparticles with two chemically different compartments have been shown to be a unique class of building blocks in solution. Here we perform mesoscale simulations to explore the self-assembly of Janus nanoparticles with widely varying architectures in diblock copolymers. We demonstrate that the coassembly of these amphiphilic building blocks forms novel and tunable structures at the interfaces of block copolymers, and consequently inﬂuences the interface stabilization and structural evolution kinetics. Our simulations suggest that Janus nanoparticle self-assembly at block copolymer interfaces yields considerable control over the creation of polymer nanocomposites with improved shear behavior. In this context, the approach is a viable strategy for creating functional materials with enhanced processing properties.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/nn901739v",
	keywords = "block copolymers; Janus particles; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2010 - Self-assembly of Janus nanoparticles in diblock copolymers.pdf",
	methods = "DPD",
	year = 2010
}

@Article{2010-Yan-SB,
	Author = "Li-Tang Yan and Heiko G. Schoberth and Alexander Böker",
	Title = "{Lamellar microstructure and dynamic behavior of diblock copolymer/nanoparticle composites under electric fields}",
	Journal = "Soft Matter",
	Volume = "6",
	Pages = "5956–5964",
	abstract = "We investigate the microstructure and dynamic behavior of diblock copolymer/nanoparticle composites under electric ﬁelds by a series of cell dynamical system simulations. The study focuses on the effects of two factors, i.e., the electric ﬁeld strength and the polymer/nanoparticle coupling interaction strength. Our simulations demonstrate that the presence of nanoparticles can evidently inﬂuence the morphology and orientation dynamics of the lamellar microstructure in diblock copolymer nanocomposites under electric ﬁelds. The nanoparticles can be still conﬁned within their preferential phase during the electric ﬁeld-induced orientation process and exhibit a spatial distribution with both short and long range order. The diblock/nanoparticle coupling strength and the electric ﬁeld strength permit effective accesses to control the distribution of nanoparticles in the systems with hierarchical nanostructures. Our simulations shed light on the possible use of nanoparticles in designing and processing of various functional nanostructured systems.",
	collection = "block copolymer nanocomposites",
	doi = "10.1039/c0sm00184h",
	keywords = "block copolymers; electric fields; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2010 - Lamellar microstructure and dynamic behavior of diblock copolymer-nanoparticle composites under electric fields.pdf",
	methods = "CDS/BD",
	rating = "1",
	read = "2011-04-10",
	year = 2010
}

@Article{2010-Ye-Carroll,
	Author = "Shengrong Ye and R. Lloyd Carroll",
	Title = "{Design and fabrication of bimetallic colloidal Janus particles}",
	Journal = "Appl. Mater. Inter.",
	Volume = "2",
	Number = "3",
	Pages = "616–620",
	abstract = "In this work, we demonstrate the results of a novel approach developed in our lab to prepare bimetallic Janus particles, which are composed of silica particles with differing metals on opposite hemispheres. SEM imaging, EDS mapping, and XPS analysis clearly indicate that beads are capped with two different metals, typically leaving an equatorial belt around the particle composed of uncoated silica. Oxidation of some metal components can be induced by oxygen plasma exposure, producing compositional and morphological changes. The facile conversion of metal to metal oxide heralds a wide variety of Janus particles with different electronic, optical, and magnetic properties.",
	collection = "nanoparticles",
	doi = "10.1021/am900839w",
	keywords = "Janus particles; nanospheres",
	localfile = "nanoparticles/2010 - Design and fabrication of bimetallic colloidal Janus particles.pdf",
	year = 2010
}

@Article{2011-Alexandridis-Tsianou,
	Author = "Paschalis Alexandridis and Marina Tsianou",
	Title = "{Block copolymer-directed metal nanoparticle morphogenesis and organization}",
	Journal = "Eur. Polym. J.",
	Volume = "47",
	Pages = "569–583",
	collection = "block copolymer nanocomposites",
	doi = "10.1016/j.eurpolymj.2010.10.021",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2011 - Block copolymer-directed metal nanoparticle morphogenesis and organization.pdf",
	type = "Review",
	year = 2011
}

@Article{2011-Bencher-SMCCCSTTHH,
	Author = "Chris Bencher and Jeffrey Smith and Liyan Miao and Cathy Cai and Yongmei Chen and Joy Y. Cheng and Daniel P. Sanders and Melia Tjio and Hoa D. Truong and Steven Holmes and William D. Hinsberg",
	Title = "{Self-assembly patterning for sub-15nm half-pitch: a transition from lab to fab}",
	Journal = "Proc. SPIE",
	Volume = "7970",
	Pages = "79700F",
	abstract = "Directed self-assembly is an emerging technology that to-date has been primarily driven by research efforts in university and corporate laboratory environments. Through these environments, we have seen many promising demonstrations of forming self-assembled structures with small half pitch (<15 nm), registration control, and various device-oriented shapes. Now, the attention turns to integrating these capabilities into a 300mm pilot fab, which can study directed selfassembly in the context of a semiconductor fabrication environment and equipment set. The primary aim of this study is to create a 300mm baseline process of record using a 12nm half-pitch PS-b-PMMA lamellae block copolymer in order to establish an initial measurement of the defect density due to inherent polymer phase separation defects such as dislocations and disclinations.",
	collection = "block copolymers",
	doi = "10.1117/12.881293",
	keywords = "block copolymers; thin films",
	localfile = "block copolymers/2011 - Self-assembly patterning for sub-15nm half-pitch.pdf",
	rating = "2",
	year = 2011
}

@Article{2011-Benkova-SC,
	Author = "Zuzana Benkova and Borys Szefczyk and Natalia D. S. Cordeiro",
	Title = "{Molecular dymamics study of hydrated poly(ethylene oxide) chains grafted on siloxane surface}",
	Journal = "Macromolecules",
	Volume = "44",
	Pages = "3639–3648",
	collection = "polymer brushes",
	doi = "10.1021/ma200233g",
	keywords = "polymer brushes",
	localfile = "polymer brushes/2011 - Molecular dynamics study of hydrated poly(ethylene oxide) chains grafted on siloxane surface.pdf",
	methods = "MD",
	rating = "2",
	year = 2011
}

@Article{2011-Chen-Ruckenstein,
	Author = "Houyang Chen and Eli Ruckenstein",
	Title = "{Aggregation of nanoparticles in a block copolymer bilayer}",
	Journal = "J. Coll. Int. Sci.",
	Volume = "363",
	Pages = "573–578",
	collection = "block copolymer nanocomposites",
	keywords = "block copolymers; nanoparticle aggregation; nanospheres; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2011 - Aggregation of nanoaprticles in a block copolymer bilayer.pdf",
	methods = "DPD",
	year = 2011
}

@Article{2011-Dror-AMMPXBS,
	Author = "Ron O. Dror and Daniel H. Arlow and Paul Maragakis and Thomas J. Mildorf and Albert C. Pan and Huafeng Xu and David W. Borhani and David E. Shaw",
	Title = "{Activation mechanism of the β2-adrenergic receptor}",
	Journal = "Proc. Natl. Acad. Sci.",
	Volume = "108",
	Number = "46",
	Pages = "18684–18689",
	abstract = "A third of marketed drugs act by binding to a G-protein-coupled receptor (GPCR) and either triggering or preventing receptor activation. Although recent crystal structures have provided snapshots of bot hactive and inactive functional states of GPCRs, these structures do not reveal the mechanism by which GPCRs transition between these states. Here we propose an activation mechanis mfor the β2-adrenergic receptor, a prototypical GPCR, based on atomic-level simulations in which an agonist-bound receptor transitions spontaneously fro mthe active to the inactive crystallgoraphically observed conformation. A loosely coupled allosteric network, comprising three regions that cna each switch individually between multiple distinct conformations, links small perturbations at the intracellular G-protein-binding site. Out simulation also exhibit an intermediate that may represent a receptor confomation to which a G protein binds during activation, and suggest that the first structural changes during receptor actvation often take place on the intracellular side of the receptor, far from the drug-binding site. By capturing this fundamental signaling process in atomic detail, our results may provide a foundation for hte design of drugs that control receptor signaling more preceisley by stabilizing specific receptor confromations.",
	collection = "molecular signaling",
	doi = "10.1073/pnas.1110499108",
	localfile = "molecular signaling/2011 - Activation mechanism of the B2-adrenergic receptor.pdf",
	methods = "MD",
	rating = "2",
	year = 2011
}

@Article{2011-Dror-PABMSXS,
	Author = "Ron O. Dror and Albert C. Pan and Daniel H. Arlow and David W. Borhani and Paul Maragakis and Yibing Shan and Huafeng Xu and David E. Shaw",
	Title = "{Pathway and mechanism of drug binding to G-protein-coupled receptors}",
	Journal = "Proc. Natl. Acad. Sci.",
	Volume = "108",
	Number = "32",
	Pages = "13118–13123",
	abstract = {How drugs bind to their receptors–from initial association through drug entry into the binding pocket, to adsorption of the final bound conformation, or "pose"–has remained unknown, even for G-rotein-coupled receptor modulators, which constitute one-third of all marketed drugs. We captures this pharmaceutically critical process in atomic detail using the first unbiased molecular dynamics simulations in which drug molecules spontaneously associate with G-protein-coupled receptors to achieve final poses metching those determined crystallographically. We found that several beta blockers and a beta agonist all traverse the same well-defined, dominant pathway as they bind to the β1- and β2-adrenergic receptors, intially making contact with a vestibule on each receptor's extracellular surface. Surprisingly, association with this vestibule, at a distnace of 15 Å from the binding pokcet, often present the largets energetic barrier to binding, despite the fact that subsequent entry into the binding pocket requires the receptor to deform and the drug to squeeze through a narrow passage. The early barrier appears to reflect the substantial dehydration that takes place as the drug associates with the vestibule. Our atomic-level description of the binding process suggests opportunities for allosteric modulation and provides a structural foundation for future optimization of drug–receptor binding and unbinding rates.},
	collection = "molecular signaling",
	doi = "10.1073/pnas.1104614108",
	localfile = "molecular signaling/2011 - Pathway and mechanism of drug binding to G-protein-coupled receptors.pdf",
	year = 2011
}

@Article{2011-Faver-BHRWMSM,
	Author = "John C. Faver and Mark L. Benson and Xiao He and Benjamin P. Roberts and Bing Wang and Michael S. Marshall and C. David Sherrill and Kenneth M. Merz Jr.",
	Title = "{The energy computationa paradox and ab initio protein folding}",
	Journal = "PLoS ONE",
	Volume = "6",
	Pages = "e18868",
	collection = "protein structure",
	doi = "10.1371/journal.pone.0018868",
	localfile = "protein structure/2011 - The energy computation paradox and ab initio protein folding.pdf",
	methods = "MD; MP2; CCSD",
	rating = "2",
	year = 2011
}

@Article{2011-Fischer-SKWF,
	Author = "Steffen Fischer and Andrea Salcher and Andread Knorowski and Horst Weller and Stephan Forster",
	Title = "{Completely miscible nanocomposites}",
	Journal = "Angew. Chem. Int. Ed.",
	Volume = "50",
	Pages = "7811–7814",
	collection = "polymer nanocomposites",
	doi = "10.1002/anie.201006746",
	keywords = "nanoparticle distribution; polymer nanocomposites",
	localfile = "polymer nanocomposites/2011 - Completely miscible nanocomposites.pdf",
	year = 2011
}

@Article{2011-Fraaije-NRG,
	Author = "Johannes G. E. M. Fraaije and Shyamal K. Nath and Klaas Remerie and Jan Groenewold",
	Title = "{Phase evolution theory for polymer blends with extreme chemical dispersity: parametrization of DDFT simulations and application to poly(propylene) impact copolymers}",
	Journal = "Macromol. Theory Simul.",
	Volume = "20",
	Pages = "133–145",
	abstract = "DDFT is applied to phase formation in homopolymer/copolymer blends in which the copolymer is extremely disperse with a uniform chemical composition distribution. Such systems develop a core/shell structure with a thick interface. This study is motivated by peculiarities in the phase evolution of industrial PP high-impact copolymers. It is demonstrated that it is possible to reach time and length scales of relevance for realistic industrial blend systems. A rational method for improving the numerical efﬁciency of the calculations is presented. The model can be applied to a variety of industrially relevant systems with similar ‘‘random chemistry’’ or extreme copolymer dispersity in coatings, crude oil recovery systems, food emulsions, and so forth.",
	collection = "block copolymers",
	doi = "10.1002/mats.201000056",
	localfile = "block copolymers/2011 - Phase evolution theory for polymer blends with extreme chemical dispersity: parametrization of DDFT simulations and application to poly(propylene) impact copolymers.pdf",
	year = 2011
}

@Article{2011-Fritz-KHVK,
	Author = "Domini Fritz and Konstantin Koschke and Vagelis A. Harmandaris and Nico F. A. van der Vegt and Kurt Kremer",
	Title = "{Mutliscale modeling of soft matter: scaling of dynamics}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "13",
	Pages = "10412–10420",
	abstract = "Many physical phenomena and properties of soft matter systems are characterized by an interplay of interactions and processes that span a wide range of length- and time scales. Computer simulation approaches require models, which cover these scales. These are typically multiscale models that combine and link different levels of resolution. In order to reach mesoscopic time- and length scales, necessary to access material properties, coarse-grained models are developed. They are based on microscopic, atomistic descriptions of systems and represent these systems on a coarser, mesoscopic level. While the connection between length scales can be established immediately, the link between the different time scales that takes into account the faster dynamics of the coarser system cannot be obtained directly. In this perspective paper we discuss methods that link the time scales in structure based multiscale models. Concepts which try to rigorously map dynamics of related models are limited to simple model systems, while the challenge in soft matter systems is the multitude of fluctuating energy barriers of comparable height. More pragmatic methods to match time scales are applied successfully to quantitatively understand and predict dynamics of one-component soft matter systems. However, there are still open questions. We point out that the link between the dynamics on different resolution levels can be affected by slight changes of the system, as for different tacticities. Furthermore, in two-component systems the dynamics of the host polymer and of additives are accelerated very differently.",
	collection = "coarse graining",
	doi = "10.1039/c1cp20247b",
	keywords = "coarse graining",
	localfile = "coarse graining/2011 - Multiscale modeling of soft matter: scaling of dynamics.pdf",
	type = "Perspective",
	year = 2011
}

@Article{2011-Frohlich-Zifferer,
	Author = "Markus G. Fröhlich and Gerhard Zifferer",
	Title = "{Atomistic molecular dynamics simulation of surface grafted PMMA}",
	Journal = "Macromol. Theory Simul.",
	Volume = "20",
	Pages = "399–410",
	collection = "polymer brushes",
	doi = "10.1002/mats.201100019",
	keywords = "polymer brushes",
	localfile = "polymer brushes/2011 - Atomistic molecular dynamics simulation of surface grafted PMMA.pdf",
	methods = "MD",
	year = 2011
}

@Article{2011-Gam-CCOHC,
	Author = "Sangah Gam and Aysenur Corlu and Hyun-Joong Chung and Kohji Ohno and Michael J.A. Hore and Russell J. Composto",
	Title = "{A jamming morphology map of polymer blend nanocomposite films}",
	Journal = "Soft Matter",
	Volume = "7",
	Pages = "7262–7268",
	collection = "jamming",
	doi = "10.1039/c1sm05619k",
	keywords = "jamming; nanospheres; polymer blends; polymer nanocomposites; thin films",
	localfile = "jamming/2011 - A jamming morphology map of polymer blend nanocomposite films.pdf",
	year = 2011
}

@Article{2011-Gerlt-AAABCDIJMPRSSS,
	Author = "John A. Gerlt and Karen N. Allen and Steven C. Almo and Richard N. Armstrong and Patricia C. Babbitt and John E. Cronan and Debra Dunaway-Mariano and Heidi J. Imker and MAtthew P. Jacobsen and Wladek Minor and C. Dale Poulter and Frank M. Raushel and Andrej Sali and Brian K. Shoichet and Jonathan V. Sweedler",
	Title = "{The enzyme function initiative}",
	Journal = "Biochemistry",
	Volume = "50",
	Pages = "9950–9962",
	collection = "enzymes",
	doi = "10.1021/bi201312u",
	localfile = "enzymes/2011 - The enzyme function initiative.pdf",
	rating = "3",
	read = "2012-10-10",
	year = 2011
}

@Article{2011-Goel-PDSMK,
	Author = "Vivek Goel and Joanna Pietrasik and Hongchen Dong and Jitendra Sharma and Krzysztof Matyjaszewski and Ramanan Krishnamoorti",
	Title = "{Structure of polymer tethered highly grafted nanoparticles}",
	Journal = "Macromolecules",
	Volume = "44",
	Pages = "8129–8135",
	abstract = "Spherical nanoparticles of silica grafted with a dense brush of low-polydispersity polymers prepared by living radical polymerization are shown to form ordered crystalline structures. The minimum distance between nanoparticle surfaces, a good measure of the end-to-end distance of the tethered polymers, scales as the square root of the molecular weight of the polymer chains. The blending of the grafted nanoparticles with homopolymers of matched and mismatched molecular weights indicates that the crystalline order persists even with high amounts of homopolymer added and for such diluted systems with as little as 0.7 vol \% silica.",
	collection = "nanoparticles",
	doi = "10.1021/ma200621r",
	keywords = "nanoparticle grafts; nanospheres; polymer mixtures; suspensions",
	localfile = "nanoparticles/2011 - Structure of polymer tethered highly grafted nanoparticles.pdf",
	systems = "silica(15nm)@PBA, silica(15nm)@PS-PA",
	year = 2011
}

@Article{2011-Griffiths-VM,
	Author = "G. H. Griffiths and Bart Vorselaars and Mark W. Matsen",
	Title = "{Unit-cell approximation for diblock-copolymer brushes grafted to spherical particles}",
	Journal = "Macromolecules",
	Volume = "44",
	Pages = "3649–3655",
	collection = "nanoparticles",
	doi = "10.1021/ma2003745",
	keywords = "nanoparticle grafts",
	localfile = "nanoparticles/2011 - Unit-cell approximation for diblock-copolymer brushes grafted to spherical particles.pdf",
	methods = "SCFT",
	year = 2011
}

@Article{2011-Hall-Schweizer,
	Author = "Lisa M. Hall and Kenneth S. Schweizer",
	Title = "{Impact of monomer sequence, composition and chemical heterogeneity on copolymer-mediated effective interactions between nanoparticles in melts}",
	Journal = "Macromolecules",
	Volume = "44",
	Pages = "3149–3160",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma200079z",
	keywords = "nanospheres; alternating copolymers; polymer blends; polymer nanocomposites; random copolymers",
	localfile = "polymer nanocomposites/2011 - Impact of monomer sequence, composition and chemical heterogeneity on copolymer-mediated effective interactions between nanoparticles in melts.pdf",
	methods = "PRISM",
	year = 2011
}

@Article{2011-Henz-CACLB,
	Author = "Brian J. Henz and Peter W. Chung and Jan W. Andzelm and Tanya L. Chantawansri and Joseph L. Lenhart and Frederick L. Beyer",
	Title = "{Determination of binding energy and solubility parameters for functionalized gold nanoparticles by molecular dynamics simulation}",
	Journal = "Langmuir",
	Volume = "27",
	Pages = "7836–7842",
	abstract = "The binding energy, density, and solubility of functionalized gold nanoparticles in a vacuum are computed using molecular dynamics simulations. Numerous parameters including surface coverage fraction, functional group (-CH3, -OH, -NH2), and nanoparticle orientation are considered. The analysis includes computation of minimum interparticle binding distances and energies and an analysis of mechanisms that may contribute to changes in system potential energy. A number of interesting trends and results are observed, such as increasing binding distance with higher terminal group electronegativity and a minimum particleÀparticle binding energy (solubility parameter) based upon surface coverage. These results provide a fundamental understanding of ligand-coated nanoparticle interactions required for the design and processing of high-density polymer composites. The computational model and results are presented as support for these conclusions.",
	collection = "nanoparticles",
	doi = "10.1021/la2005024",
	keywords = "nanoparticle grafts",
	localfile = "nanoparticles/2011 - Determination of binding energy and solubility parameters for functionalized gold nanoparticles by molecular dynamics simulation.pdf",
	year = 2011
}

@Article{2011-Hulkko-LKLKPH,
	Author = "Eero Hulkko and Olga Lopez-Acevedo and Jaakko Koivisto and Yael Levi-Kalisman and Roger D. Kornberg and Mika Pettersson and Hannu Hakkinen",
	Title = "{Electronic and vibrational signatures of the AU102(p-MBA)44 cluster}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "133",
	Pages = "3752–3755",
	collection = "nanoparticles",
	doi = "10.1021/ja111077e",
	keywords = "nanoparticle structure",
	localfile = "nanoparticles/2011 - Electronic and vibrational signatures of the Au102(p-MBA)44 cluster.pdf",
	rating = "2",
	year = 2011
}

@Article{2011-Irwin-BS,
	Author = "David M. Irwin and Jason M. Biegel and Caro-Beth Stewart",
	Title = "{Evolution of the mammalian lysozyme gene family}",
	Journal = "BMC Evol. Biol.",
	Volume = "11",
	Pages = "166",
	Note = "Identifies new members in the lysozyme gene family and suggest some of their biological functions (also pseudogenes).",
	collection = "molecular genetics",
	doi = "10.1186/1471-2148-11-166",
	keywrods = "lysozyme",
	localfile = "molecular genetics/2011 - Evolution of the mammalian lysozyme gene family.pdf",
	methods = "BLAST",
	rating = "2",
	read = "2013-06-10",
	year = 2011
}

@Article{2011-Isa-ASDIKR,
	Author = "Lucio Isa and Esther Amstad and Konrad Schwenke and Emanuela Del Gado and Patrick Ilg and Martin Kröger and Erik Reimhult",
	Title = "{Adsorption of core-shell nanoparticles at liquid-liquid interfaces}",
	Journal = "Soft Matter",
	Volume = "7",
	Pages = "7663–7675",
	collection = "nanoparticles",
	doi = "10.1039/c1sm05407d",
	keywords = "binary fluids; liquid interfaces; nanoparticle grafts",
	localfile = "nanoparticles/2011 - Adsorption of core-shell nanoparticles at liquid-liquid interfaces.pdf",
	methods = "PDT, QCM",
	rating = "2",
	read = "2012-04-27",
	systems = "Fe-PEG@n-decane/water",
	year = 2011
}

@Article{2011-Iyer-ZMCL,
	Author = "K. Swaminathan Iyer and Bogdan Zdyrko and Sergiy Malynych and George Chumanov and Igor Luzinov",
	Title = "{Reversible submergence of nanoparticles into ultrathin block copolymer films}",
	Journal = "Soft Matter",
	Volume = "7",
	Pages = "2538–2542",
	collection = "block copolymer nanocomposites",
	keywords = "block copolymers; nanospheres; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2011 - Reversible submergence of nanoparticles into ultrathin block copolymer films.pdf",
	methods = "AFM",
	year = 2011
}

@Article{2011-Jang-KDKLKH,
	Author = "Se Gyu Jang and Anzar Khan and Michael D. Dimitriou and Bumjoon J. Kim and Nathaniel A. Lynd and Edward J. Kramer and Craig J. Hawker",
	Title = "{Synthesis of thermaly stable Au-core-Pt-shell nanoparticles and their segregation behavior in diblock copolymer mixtures}",
	Journal = "Soft Matter",
	Volume = "7",
	Pages = "6255–6263",
	collection = "block copolymer nanocomposites",
	doi = "10.1039/c1sm05223c",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2011 - Synthesis of thermally stable Au-core-Pt-shell nanoparticles and their segregation behavior in diblock copolymer mixtures.pdf",
	methods = "TEM, NMR, XRD, UV-VIS",
	rating = "2",
	read = "2012-03-21",
	systems = "Au-Pt@PS-P2VP",
	year = 2011
}

@Article{2011-Jang-KHK,
	Author = "Se Gyu Jang and Bumjoon J. Kim and Craig J. Hawker and Edward J. Kramer",
	Title = "{Bicontinuous block copolymer morphologies produced by interfacially active, thermally stable nanoparticles}",
	Journal = "Macromolecules",
	Volume = "44",
	Number = "23",
	Pages = "9366–9373",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma201937z",
	keywords = "block copolymers; mesophase transitions; nanospheres; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2011 - Bicontinuous block copolymer morphologies produced by interfacially active, thermally stable nanoparticles.pdf",
	year = 2011
}

@Article{2011-Jessop-AMR,
	Author = "David M. Jessop and Sam E. Adams and Peter Murray-Rust",
	Title = "{Mining chemical information from open patents}",
	Journal = "J. Cheminf.",
	Volume = "3",
	Pages = "40",
	collection = "cheminformatics",
	doi = "10.1186/1758-2946-3-40",
	keywords = "open data; data mining; patents; chemical markup language",
	localfile = "cheminformatics/2011 - Mining chemical information from open patents.pdf",
	rating = "2",
	read = "2012-09-23",
	year = 2011
}

@Article{2011-Jessop-AWHMR,
	Author = "David M. Jessop and Sam E. Adams and Egon L. Willighagen and Lezan Hawizy and Peter Murray-Rust",
	Title = "{OSCAR4: a flexible architecture for chemical text-mining}",
	Journal = "Cheminformatics",
	Volume = "3",
	Pages = "41",
	collection = "informatics",
	doi = "10.1186/1758-2946-3-41",
	keywords = "data mining; parsing",
	localfile = "cheminformatics/2011 - OSCAR4: a flexible architecture for chemical text-mining.pdf",
	rating = "2",
	read = "2012-01-23",
	year = 2011
}

@Article{2011-Jiang-ZCY,
	Author = "X. C. Jiang and Q. H. Zeng and C. Y. Chen and A. B. Yu",
	Title = "{Self-assembly of particles: some thoughts and comments}",
	Journal = "J. Mater. Chem.",
	Volume = "21",
	Pages = "16797",
	Note = "Includes nice list of self-assembly techniques, their features and controlling forces; also several interesting remarks.",
	collection = "nanotechnology",
	doi = "10.1039/C1JM12213D",
	keywords = "self-assembly",
	localfile = "nanotechnology/2011 - Self-assembly of particles: some thoughts and comments.pdf",
	rating = "2",
	read = "2012-08-08",
	year = 2011
}

@Article{2011-Jones-HMHAJTWDBSC,
	Author = "James T. A. Jones and Daniel Holden and Tamoghna Mitra and Tom Hasell and Dave J. Adams and Kim E. Jelfs and Abbite Trewin and David J. Willock and Graeme M. Day and John Bacsa and Alexander Steiner and Andrew I. Cooper",
	Title = "{On-off porosity switching in a molecular organic solid}",
	Journal = "Angew. Chem. Int. Ed.",
	Volume = "50",
	Pages = "749–753",
	collection = "molecular crystals",
	doi = "10.1002/anie.201006030",
	keywords = "porosity; synthetic molecular network",
	localfile = "molecular crystals/2011 - On-off porosity switching in a molecular organic solid.pdf",
	rating = "2",
	read = "2012-02-16",
	year = 2011
}

@Article{2011-Kim-Cochran,
	Author = "Seung Ha Kim and Eric W. Cochran",
	Title = "{Localization of spherical nanoparticles within lamellar AB diblock copolymer melts through self-consistent theory}",
	Journal = "Polymer",
	Volume = "52",
	Pages = "2328–2339",
	Note = "Demonstrates nonmonotonic dependence of preferred NP position in BCP lamellas on NP concentration.",
	collection = "polymer nanocomposites",
	doi = "10.1016/j.polymer.2011.03.016",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "polymer nanocomposites/2011 - Localization of spherical nanoparticles within lamellar AB diblock copolymer melts through self-consistent field theory.pdf",
	methods = "SCFT",
	rating = "1",
	read = "2011-11-25",
	year = 2011
}

@Article{2011-Li-PMP,
	Author = "Li Li and Suzette A. Pabit and Steve P. Meisburger and Lois Pollack",
	Title = "{Double-stranded RNA resists condensation}",
	Journal = "Phys. Rev. Lett.",
	Volume = "106",
	Pages = "108101",
	Note = "Page 1: There is no universally accepted explanation of the physical origin of like-charge attraction.",
	collection = "nucleic acids",
	doi = "10.1103/PhysRevLett.106.108101",
	localfile = "nucleic acids/2011 - Double-stranded RNA resists condensation.pdf",
	rating = "2",
	read = "2012-08-13",
	year = 2011
}

@Article{2011-Lin-DAGW,
	Author = "Ying Lin and Vikram K. Daga and Eric R. Anderson and Samuel P. Gido and James J. Watkins",
	Title = "{Nanoparticle-driven assembly of block copolymers: a simple route to ordered hybrid materials}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "133",
	Pages = "6513–6516",
	abstract = "The addition of nanoparticles that selectively hydrogen bond with one of the segments of a block copolymer is shown to induce order in otherwise disordered systems. This enables the fabrication of well-ordered hybrid materials with spherical, cylindrical, or lamellar domains at particle loading of more than 40\%, as evidenced by TEM and SAXS. The approach described is simple and applicable to a wide range of nanoparticles and block copolymers, and it lays the groundwork for the design of cooperatively assembled functional devices.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ja2003632",
	keywords = "block copolymers; hydrogen bonding; mesophase transitions; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2011 - Nanoparticle-driven assembly of block copolymers: a simple route to ordered hybrid materials.pdf",
	methods = "SAXS, TEM",
	year = 2011
}

@Article{2011-Lindorff-Larsen-PDS,
	Author = "Kresten Lindorff-Larsen and Stefano Piana and Ron O. Dror and David E. Shaw",
	Title = "{How fast-folding protein fold}",
	Journal = "Science",
	Volume = "334",
	Pages = "517–520",
	Note = "Monitors the folding of a dozen different small protein using the same force field. In particular, transient native-like structures and major kinetic barriers.",
	collection = "protein structure",
	doi = "10.1126/science.1208351",
	keywords = "protein folding",
	localfile = "protein structure/2011 - How fast-folding proteins fold.pdf",
	rating = "3",
	read = "2012-04-25",
	year = 2011
}

@Article{2011-Liu-WSGZC,
	Author = "Jun Liu and Yan Wu and Jianxiang Shen and Yangyang Gao and Liqun Zhang and Dapeng Cao",
	Title = "{Polymer-nanoparticle interfacial behavior revisited: A molecular dynamics study}",
	Journal = "Phys. Chem. Chem. Phys.",
	Pages = "13058–13069",
	abstract = {By tuning the polymer-filler interaction, filler size and filler loading, we use a coarse-grained model-based molecular dynamics simulation to study the polymer-filler interfacial structural (the orientations at the bond, segment and chain length scales, chain size and conformation), dynamic and stress-strain properties. Simulated results indicate that the interfacial region is composed of partial segments of different polymer chains, which is consistent with the experimental results presented by Chen et al. {(Macromolecules,} 2010, 43, 1076). Moreover, it is found that the interfacial region is within one single chain size {(Rg)} range, irrespective of the polymer-filler interaction and the filler size, beyond which the bulk behavior appears. In the interfacial region, the orientation and dynamic behaviors are induced by the interfacial enthalpy, while the size and conformation of polymer chains near the filler are controlled by the configurational entropy. In the case of strong polymer-filler interaction (equivalent to the hydrogen bond), the innerest adsorbed polymer segments still undergo adsorption-desorption process, the transport of chain mass center in the interfacial region exhibits away from the glassy behavior, and no plastic-like yielding point appears in the stress-strain curve, which indicates that although the mobility of interfacial polymer chains is restricted, there exist no "polymer glassy layers" surrounding the filler. In addition, it is evidenced that the filler particle prefers selectively adsorbing the long polymer chains for attractive polymer-filler interaction, validating the experimental explanation of the change of the bound rubber {(BR).} In short, this work provides important information for further experimental and simulation studies of polymer-nanoparticle interfacial behavior.},
	collection = "polymer nanocomposites",
	doi = "10.1039/C0CP02952A",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2011 - Polymer-nanoparticle interfacial behavior revisited: a molecular dynamics study.pdf",
	year = 2011
}

@Article{2011-Liu-WZWC,
	Author = "Jun Liu and Sizhu Wu and Liqun Zhang and Wenchuan Wang and Dapeng Cao",
	Title = "{Molecular dynamics simulation for insight into microscopic mechanism of polymer reinformcement}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "13",
	Pages = "518–529",
	collection = "polymer nanocomposites",
	doi = "10.1039/c0cp00297f",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2011 - Molecular dynamics simulation for insight into microscopic mechanism of polymer reinforcement.pdf",
	year = 2011
}

@Article{2011-Lodola-CRCSDSMTPMM,
	Author = "Alessio Lodola and Luigi Capoferri and Silvia Rivara and Ewa Chudyk and Jitmapa Sirirak and Edyta Dyguda-Kazimierowicz and W. Andrzej Sokalski and Mauro Mileni and Giorgio Tarzia and Daniele Piomelli and Marco Mor and Adrian J. Mulholland",
	Title = "{Understanding the role of carbamate reactivity in fatty acid amide hydrolase nihibition by QM/MM mechanistic modelling}",
	Journal = "Chem. Commun.",
	Volume = "47",
	Pages = "2517–2519",
	collection = "enzymes",
	doi = "10.1039/c0cc04937a",
	localfile = "enzymes/2011 - Understanding the role of carbamate reactivity in fatty acid amide hydrolase inhibition by QMMM mechanistic modelling.pdf",
	year = 2011
}

@Article{2011-Ma-Li,
	Author = "Zengwei Ma and Robert K. Y. Li",
	Title = "{Effect of particle surface selectivity on composite nanostructures in nanoparticle/diblock copolymer mixture dilute solution}",
	Journal = "J. Coll. Int. Sci.",
	Volume = "363",
	Pages = "241–249",
	collection = "polymers",
	doi = "10.1016/j.jcis.2011.07.008",
	keywords = "block copolymers; nanospheres; polymer mixtures",
	localfile = "polymers/2011 - Effect of particle surface selectivity on composite nanostructures in nanoparticle-diblock copolymer mixtures dilute solution.pdf",
	methods = "SCFT",
	year = 2011
}

@Article{2011-Martin-SJ,
	Author = "Tyler B. Martin and Arezou Seifpour and Arthi Jayaraman",
	Title = "{Assembly of copolymer functionalized nanoparticles: a Monte Carlo simulation study}",
	Journal = "Soft Matter",
	Volume = "7",
	Pages = "5952",
	collection = "nanoparticles",
	doi = "10.1039/c1sm05179b",
	keywords = "block copolymers; nanoparticle grafts",
	localfile = "nanoparticles/2011 - Assembly of copolymer functionalized nanoparticles: a Monte Carlo simulation study.pdf",
	year = 2011
}

@Article{2011-McAllister-BK,
	Author = "Linda J. McAllister and Duncan W. Bruce and Peter B. Karadakov",
	Title = "{Halogen bonding interaction between fluorohalides and isocyanides}",
	Journal = "J. Phys. Chem. A",
	Volume = "115",
	Pages = "11079–11086",
	collection = "basis set superposition",
	doi = "10.1021/jp207119c",
	keywords = "halogen bonding",
	localfile = "basis set superposition/2011 - Halogen bonding interaction between fluorohalides and isocyanides.pdf",
	year = 2011
}

@Article{2011-Milano-SRCD,
	Author = "Giuseppe Milano and G. Santangel and F. Ragone and L. Cavallo and A. {Di Matteo}",
	Title = "{Gold nanoparticle/polymer interfaces: all atom structures fro molecular dynamics simulations}",
	Journal = "J. Phys. Chem. C",
	Volume = "115",
	Pages = "15154–15163",
	collection = "nanoparticles",
	doi = "10.1021/jp201374h",
	keywords = "nanoparticle grafts; nanospheres",
	localfile = "nanoparticles/2011 - Gold nanoparticle-polymer interfaces: all atom structures from molecular dynamics simulations.pdf",
	year = 2011
}

@Article{2011-Murray-Rust,
	Author = "Peter Murray-Rust",
	Title = "{Semantic science and its communication – a personal view}",
	Journal = "J. Cheminf.",
	Volume = "3",
	Pages = "48",
	Note = "An interesting point of view and historical backdrop for open chemical science.",
	collection = "cheminformatics",
	doi = "10.1186/1758-2946-3-48",
	keywords = "open data; semantic web",
	localfile = "cheminformatics/2011 - Semantic science and its communication - a personal view.pdf",
	rating = "3",
	read = "2012-09-02",
	url = "http://www.jcheminf.com/content/3/1/48",
	year = 2011
}

@Article{2011-Murray-Rust-ADWZ,
	Author = "Peter Murray-Rust and Sam E. Adams and Jim Downing and Joe A. Townsend and Yong Zhang",
	Title = "{The semantic architecture of the World-Wide Molecular Matrix (WWMM)}",
	Journal = "J. Cheminf.",
	Pages = "42",
	collection = "cheminformatics",
	doi = "10.1186/1758-2946-3-42",
	keywords = "semantic web",
	localfile = "cheminformatics/2011 - The semantic architecture of the World-Wide-Molecular-Matrix.pdf",
	rating = "2",
	read = "2013-05-11",
	url = "http://www.jcheminf.com/content/3/1/42",
	volme = "3",
	year = 2011
}

@Article{2011-Murray-Rust-Rzepa,
	Author = "Peter Murray-Rust and henry S. Rzepa",
	Title = "{CML: evolution and design}",
	Journal = "J. Cheminf.",
	Volume = "3",
	Pages = "44",
	Note = "Does not discuss the technical side of CML, but provides a nice historic perspective.",
	collection = "cheminformatics",
	doi = "10.1186/1758-2946-3-44",
	keywords = "chemical markup language; semantic web; open data",
	localfile = "cheminformatics/2011 - CML: evolution and design.pdf",
	rating = "2",
	read = "2012-09-10",
	url = "http://www.jcheminf.com/content/3/1/44",
	year = 2011
}

@Article{2011-Murray-Rust-TAPT,
	Author = "Peter Murray-Rust and Joe A. Townsend and Sam E. Adams and Weerapong Phadungsukanan and Jens Thomas",
	Title = "{The semantics of chemical markup langauge (CML): dictionaries and conventions}",
	Journal = "J. Cheminf.",
	Volume = "3",
	Pages = "43",
	Note = "Discusses the technicalities of CML semantics.",
	collection = "cheminformatics",
	doi = "10.1186/1758-2946-3-43",
	keywords = "chemical markup language",
	localfile = "cheminformatics/2011 - The semantics of chemical markup language (CML): dictionaries and conventions.pdf",
	rating = "1",
	read = "2013-05-10",
	url = "http://www.jcheminf.com/content/3/1/43",
	year = 2011
}

@Article{2011-Nair-WJ,
	Author = "Nitish Nair and Nathaniel Wentzel and Arthi Jayaraman",
	Title = "{Effect of bidispersity in grafted chain length on grafted chain conformations and potential of mean force between polymer grafted nanoparticles in a homopolymer matrix}",
	Journal = "J. Chem. Phys.",
	Volume = "134",
	Pages = "194906",
	collection = "nanoparticles",
	doi = "10.1063/1.3590275",
	keywords = "nanoparticle grafts; polydispersity",
	localfile = "nanoparticles/2011 - Effect of bidispersity in grafted chain length on grafted chain conformations and potential of mean force between polymer grafted nanoparticles in a homopolymer matrix.pdf",
	methods = "MC, PRISM",
	year = 2011
}

@Article{2011-Ndoro-VGTBM,
	Author = "Tinashe V. M. Ndoro and Evangelos Voyiatzis and Azadeh Ghanbari and Doros N. Theodorou and Michael C. Böhm and Florian Müller-Plathe",
	Title = "{Interface of grafted and ungrafted silica nanoparticle with a polystyrene matrix: atomistic molecular dynamics simulations}",
	Journal = "Macromolecules",
	Volume = "44",
	Pages = "2316–2327",
	collection = "nanoparticles",
	keywords = "nanoparticle grafts; nanospheres; polymer nanocomposites",
	localfile = "nanoparticles/2011 - Interface of grafted and ungrafted silica nanoparticles with a polystyrene matrix: atomistic molecular dynamics simulations.pdf",
	methods = "MD",
	year = 2011
}

@Article{2011-Neylon,
	Author = "Cameron Neylon",
	Title = "{Three stories about the conduct of science: Past, future, and present}",
	Journal = "J. Cheminf.",
	Volume = "3",
	Pages = "35",
	Note = "Manifest included: I want my work to make a difference. I will act to optimize te potential for my work to make a difference. I will persuade others to optimize the potential for their work to make a difference.",
	collection = "cheminformatics",
	keywords = "open data; semantic web",
	localfile = "cheminformatics/2011 - Three stories about the conduct of science.pdf",
	year = 2011
}

@Article{2011-Nicola-ZKRM,
	Author = "Antonio De Nicola and Ying Zhao and Toshihiro Kawakatsu and Danilo Roccatano and Giuseppe Milano",
	Title = "{Hybrid particle–field coarse-grained models for biological phospholipids}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "7",
	Pages = "2947–2962",
	abstract = "In the framework of a recently developed scheme for a hybrid particle-field simulation technique where self-consistent field theiry (SCF) and molecular dynamics (MD) are combined, specific coarse-grained models for phospholipids and water have been developed. We optimized the model parameters, which are necessary in evaluating the interactions between the particles and the dnesity fields, so that the coarse-grained model can reproduce the structural properties of the reference particle–particle simulations. The development of these specific coarse-grained models suitable for hybrid particle-field simulations opens the way toward simulations of large-scale systems employing models with chemical specificity, especially for biological systems.",
	collection = "lipid bilayers",
	doi = "10.1021/ct200132n",
	keywords = "coarse graining; lipid bilayers",
	localfile = "lipid bilayers/2011 - Hybrid particle-field coarse-grained models for biological phospholipids.pdf",
	rating = "2",
	year = 2011
}

@Article{2011-Orilall-Wiesner,
	Author = "M. Christopher Orilall and Ulrich Wiesner",
	Title = "{Block copolymer based composition and morphology control in nanostructured hybrid materials for energy conversion and storage: solar cells, batteries, and fuel cells}",
	Journal = "Chem. Soc. Rev.",
	Volume = "40",
	Pages = "520–535",
	collection = "block copolymer nanocomposites",
	doi = "10.1039/c0cs00034e",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2011 - Block copolymer based composition and morphology control in nanostructured hybrid materials for energy conversion and storage: colar cells, batteries, and fuel cells.pdf",
	type = "Review",
	year = 2011
}

@Article{2011-Pan-HZL,
	Author = "Zhengquan Pan and Linli He and Linxi Zhang and Haojun Liang",
	Title = "{The dynamic behaviors of diblock copolymer/nanorod mixtures under equilibrium and nonequilibrium conditions}",
	Journal = "Polymer",
	Volume = "52",
	Pages = "2711–2721",
	collection = "block copolymer nanocomposites",
	doi = "10.1016/j.polymer.2011.04.012",
	keywords = "block copolymers; nanorods; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2011 - The dynamic behaviors of diblock copolymer-nanorod mixtures under equilibrium and nonequilibrium conditions.pdf",
	methods = "DPD",
	year = 2011
}

@Article{2011-Pan-TZ,
	Author = "Qiangyong Pan and Chaohui Tong and Yuejin Zhu",
	Title = "{Self-consistent-field and hybrid particle-field theory simulation of confined copolymer and nanoparticle mixtures}",
	Journal = "ACS Nano",
	Volume = "51",
	Number = "1",
	Pages = "123–128",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/nn101886x",
	keywords = "block copolymers; mesophase transitions; nanospheres",
	localfile = "block copolymer nanocomposites/2011 - Self-consistent-field and hybrid particle-field theory simulation of confined copolymer and nanoparticle mixtures.pdf",
	methods = "SCFT",
	rating = "1",
	read = "2011-11-25",
	year = 2011
}

@Article{2011-Park-Boker,
	Author = "Sungjune Park and Alexander Böker",
	Title = "{Ceramic nanowrinkles {\it via} a facile replication process}",
	Journal = "J. Mater. Chem.",
	Volume = "21",
	Pages = "11734",
	abstract = "Wrinkled ceramic nanopatters were fabricated via a molding a replication process. Wrinkled PDMS stamps generated in a lithography-free way were used as masters fro structure replication onto pre-ceramic polymer films. The resulting structures of the ceramic precursor obtained from photopolymerization were converted to a ceramic material by pyrolysis at 800C in a nitrogen atmosphere.",
	collection = "nanotechnology",
	doi = "10.1039/c1jm12007g",
	localfile = "nanotechnology/2011 - Ceramic nanowrinkles via a facile replication process.pdf",
	year = 2011
}

@Article{2011-Pavan-Shenhar,
	Author = "Mariela J. Pavan and Roy Shenhar",
	Title = "{Two-dimensional nanoparticle organization using block copolymer thin films as templates}",
	Journal = "J. Mater. Chem.",
	Volume = "21",
	Pages = "2028–2040",
	collection = "block copolymer nanocomposites",
	doi = "10.1039/c0jm02853c",
	localfile = "block copolymer nanocomposites/2011 - Two-dimensional nanoparticle organization using block copolymer thin films as templates.pdf",
	rating = "2",
	read = "2012-10-10",
	year = 2011
}

@Article{2011-Pester-RSSLRSHCMUB,
	Author = "Christian W. Pester and Markus Ruppel and Heiko G. Schoberth and Kristin Schmidt and Clemens Liedel and Patrick {van Rijn} and Kerstin A. Schindler and Stephanie Hiltl and Thomas Czubak and Jimmy Mays and Volker S. Urban and Alexander Böker",
	Title = "{Piezoelectric properties of non-polar block copolymers}",
	Journal = "Adv. Mater.",
	Volume = "23",
	Pages = "4047–4052",
	collection = "block copolymers",
	doi = "10.1002/adma.201102192",
	localfile = "block copolymers/2011 - Piezoelectric properties of non-polar block copolymers.pdf",
	year = 2011
}

@Article{2011-Pinna-PZ,
	Author = "Marco Pinna and Ignacio Pagonabarraga and Andrei V. Zvelindovsky",
	Title = "{Modeling of block copolymer/colloid hybrid composite materials}",
	Journal = "Macromol. Theory Simul.",
	Volume = "20",
	Number = "8",
	Pages = "769–779",
	abstract = "The interaction between a diblock copolymer and nanoscopic particles can lead to highly organized hybrid materials. The morphology of such hybrid materials depends on the polymer compositions as well on the shapes, sizes, and surface treatment of the particles. A hybrid mesoscopic approach to study the dynamics of nanocomposites composed from a block copolymer melt and a suspension of colloids is proposed. A collective description of the polymer dynamics is combined with the individual resolution of the colloids. The implementation of the method in two and three dimensions is described and the method is tested for different particle sizes, diblock copolymer compositions and polymer/colloid interactions.",
	collection = "block copolymer nanocomposites",
	doi = "10.1002/mats.201100047",
	keywords = "block copolymers; mesophase transitions; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2011 - Modeling of block copolymer-colloid hybrid composite materials.pdf",
	methods = "CDS/BD",
	year = 2011
}

@Article{2011-Potts-DBR,
	Author = "Jeffrey R. Potts and Daniel R. Dreyer and Christopher W. Bielawski and Rodney S. Ruoff",
	Title = "{Graphene-based polymer nanocomposites}",
	Journal = "Polymer",
	Volume = "52",
	Pages = "5–25",
	collection = "polymer nanocomposites",
	doi = "10.1016/j.polymer.2010.11.042",
	keywords = "graphene; polymer nanocomposites",
	localfile = "polymer nanocomposites/2011 - Graphene-based polymer nanocomposites.pdf",
	type = "Review",
	year = 2011
}

@Article{2011-Pross,
	Author = "Addy Pross",
	Title = "{Toward a general theory of evolution: extending Darwinian theory to inanimate matter}",
	Journal = "J. Systems Chem.",
	Volume = "2",
	Pages = "1",
	collection = "evolution",
	doi = "10.1186/1759-2208-2-1",
	keywords = "kinetics",
	localfile = "evolution/2011 - Toward a general theory of evolution: extending Darwinian theory to inanimate matter.pdf",
	rating = "2",
	read = "2015-02-10",
	year = 2011
}

@Article{2011-Qiao-DPB,
	Author = "Rui Qiao and Hua Deng and Karl W. Putz and L. Catherine Brinson",
	Title = "{Effect of particle agglomeration and interphase on the glass transition temperature of polymer nanocomposites}",
	Journal = "J. Polym. Sci. Pt. B-Polym. Phys.",
	Volume = "49",
	Pages = "740–748",
	collection = "polymer nanocomposites",
	doi = "10.1002/polb.22236",
	keywords = "nanoparticle aggregation; polymer nanocomposites",
	localfile = "polymer nanocomposites/2011 - Effect of particle agglomeration and interphase on the glass transition temperature of polymer nanocomposites.pdf",
	methods = "FE",
	rating = "2",
	year = 2011
}

@Article{2011-Reynwar-Deserno,
	Author = "Benedict J. Reynwar and Markus Deserno",
	Title = "{Membrane-mediated interactions between circular particles in teh strongly curved regime}",
	Journal = "Soft Matter",
	Volume = "7",
	Pages = "8567–8575",
	collection = "lipid bilayers",
	doi = "10.1039/c1sm05358b",
	keywords = "biological nanocomposites; lipid bilayers; nanospheres",
	localfile = "lipid bilayers/2011 - Membrane-mediated interactions between circular praticles in the strongly curved regime.pdf",
	methods = "CG MD",
	year = 2011
}

@Article{2011-Rezac-RH,
	Author = "Jan Řezáč and Kevin E. Riley and Pavel Hobza",
	Title = "{S66: A well-balanced databse of benchmark interaction energies relevant to biomolecular structures}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "7",
	Pages = "2427–2438",
	collection = "molecular interactions",
	doi = "10.1021/ct2002946",
	localfile = "molecular interactions/2011 - S66: A well-balanced database of benchmark interaction energies relevant to biomolecular structures.pdf",
	rating = "3",
	year = 2011
}

@Article{2011-Rezac-RH1,
	Author = "Jan Řezáč and Kevin E. Riley and Pavel Hobza",
	Title = "{Extensions of the S66 Data Set: More Accurate Interaction Energies and Angular-Displaced Nonequilibrium Geometries}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "7",
	Number = "11",
	Pages = "3466–3470",
	abstract = "We present two extensions of the recently published S66 data set [řezáč, Riley, Hobza; DOI: 10.1021/ct2002946]. Interaction energies for the equilibrium geometry complexes have been recalculated using a triple-ζ basis set for the CCSD(T) term in the CCSD(T)/CBS scheme. This allows for the extrapolation of this term to the complete basis set limit, improving accuracy by almost 1 order of magnitude compared to the scheme previously used for the S66 set. Now, we estimate the largest error in the set to be about 1\%. Validation of several methods against the new data indicates the exceptional robustness and accuracy of the SCS-MI-CCSD method. The second extension improves the coverage of nonequilibrium geometries. We introduce a new data set, S66a8, that samples intermolecular angular degrees of freedom in the S66 complexes. For each of the 66 complexes, eight displaced geometries have been constructed, systematically sampling possible rotations of the monomers. Interaction energies in this set are calculated at the CCSD(T)/CBS level consistently with the earlier introduced S66x8 data set that samples the intermolecular distance.",
	collection = "molecular interactions",
	doi = "10.1021/ct200523a",
	localfile = "molecular interactions/2011 - Extension of the S66 data set: more eccurate interaction energies and angular-displaced nonequilibrium geometries.pdf",
	rating = "2",
	systems = "S66",
	year = 2011
}

@Article{2011-Shan-KEDSS,
	Author = "Yibing Shan and Eric T. Kim and Michael P. Eastwood and Ron O. Dror and Markus A. Seeliger and David E. Shaw",
	Title = "{How does a drug molecule find its target binding site?}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "133",
	Pages = "9181–9183",
	Note = "Shows unguided docking of ligand and inhibitor to PP1 protein.",
	collection = "molecular docking",
	doi = "10.1021/ja202726y",
	keywords = "molecular docking",
	localfile = "enzymes/2011 - How does a drug molecule find its target binding site.pdf",
	methods = "MD",
	rating = "3",
	read = "2012-03-05",
	systems = "dasatinib@Src, PP1@Src",
	year = 2011
}

@Article{2011-Vijay-SS,
	Author = "Dolly Vijay and Hidehiro Sakurai and Narahari Sastry",
	Title = "{The impact of basis set superposition error on the structure of pi-pi dimers}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "111",
	Number = "9",
	Pages = "1893–1901",
	collection = "basis set superposition",
	localfile = "basis set superposition/2011 - The impact of basis set superposition error on the structure of pi-pi dimers.pdf",
	rating = "2",
	read = "2012-08-01",
	year = 2011
}

@Article{2011-Vogiatzis-VT,
	Author = "Georgios G. Vogiatzis and Evangelos Voyiatzis and Doros N. Theodorou",
	Title = "{Monte Carlo simulations of a coarse grained model for an athermal all-polystyrene nanocomposite system}",
	Journal = "Eur. Polym. J.",
	Volume = "47",
	Pages = "699–712",
	collection = "polymer nanocomposites",
	doi = "10.1016/j.eurpolymj.2010.09.017",
	keywords = "nanospheres; polymer conformations; polymer nanocomposites",
	localfile = "polymer nanocomposites/2011 - Monte Carlo simulations of a coarse grained model for an athermal all-polystyrene nanocomposite system.pdf",
	methods = "MC with mean fields",
	rating = "2",
	read = "2011-11-26",
	systems = "PS(cross-linked)@PS",
	year = 2011
}

@Article{2011-Vorselaars-KCFM,
	Author = "Bart Vorselaars and Jaeup U. Kim and Tanya L. Chantawansri and Glenn H. Fredrickson and Mark W. Matsen",
	Title = "{Self-consistent field theory for diblock copolymers grafted to a sphere}",
	Journal = "Soft Matter",
	Volume = "7",
	Pages = "5128–5137",
	collection = "nanoparticles",
	doi = "10.1039/c0sm01242d",
	keywords = "nanoparticle grafts",
	localfile = "nanoparticles/2011 - Self-consistent

repository: langner/library

repo_name: langner/library

branch_name: refs/heads/master