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@article{Wood2002,
author = {Wood, V. and Gwilliam, R. and Rajandream, M.-A. and Lyne, M. and Lyne, R. and Stewart, A. and Sgouros, J. and Peat, N. and Hayles, J. and Baker, S. and Basham, D. and Bowman, S. and Brooks, K. and Brown, D. and Brown, S. and Chillingworth, T. and Churcher, C. and Collins, M. and Connor, R. and Cronin, A. and Davis, P. and Feltwell, T. and Fraser, A. and Gentles, S. and Goble, A. and Hamlin, N. and Harris, D. and Hidalgo, J. and Hodgson, G. and Holroyd, S. and Hornsby, T. and Howarth, S. and Huckle, E. J. and Hunt, S. and Jagels, K. and James, K. and Jones, L. and Jones, M. and Leather, S. and McDonald, S. and McLean, J. and Mooney, P. and Moule, S. and Mungall, K. and Murphy, L. and Niblett, D. and Odell, C. and Oliver, K. and O'Neil, S. and Pearson, D. and Quail, M. A. and Rabbinowitsch, E. and Rutherford, K. and Rutter, S. and Saunders, D. and Seeger, K. and Sharp, S. and Skelton, J. and Simmonds, M. and Squares, R. and Squares, S. and Stevens, K. and Taylor, K. and Taylor, R. G. and Tivey, A. and Walsh, S. and Warren, T. and Whitehead, S. and Woodward, J. and Volckaert, G. and Aert, R. and Robben, J. and Grymonprez, B. and Weltjens, I. and Vanstreels, E. and Rieger, M. and Sch{\"{a}}fer, M. and M{\"{u}}ller-Auer, S. and Gabel, C. and Fuchs, M. and Fritzc, C. and Holzer, E. and Moestl, D. and Hilbert, H. and Borzym, K. and Langer, I. and Beck, A. and Lehrach, H. and Reinhardt, R. and Pohl, T. M. and Eger, P. and Zimmermann, W. and Wedler, H. and Wambutt, R. and Purnelle, B. and Goffeau, A. and Cadieu, E. and Dr{\'{e}}ano, S. and Gloux, S. and Lelaure, V. and Mottier, S. and Galibert, F. and Aves, S. J. and Xiang, Z. and Hunt, C. and Moore, K. and Hurst, S. M. and Lucas, M. and Rochet, M. and Gaillardin, C. and Tallada, V. A. and Garzon, A. and Thode, G. and Daga, R. R. and Cruzado, L. and Jimenez, J. and S{\'{a}}nchez, M. and del Rey, F. and Benito, J. and Dom{\'{i}}nguez, A. and Revuelta, J. L. and Moreno, S. and Armstrong, J. and Forsburg, S. L. and Cerrutti, L. and Lowe, T. and McCombie, W. R. and Paulsen, I. and Potashkin, J. and Shpakovski, G. V. and Ussery, D. and Barrell, B. G. and Nurse, P.},
doi = {10.1038/nature724},
file = {:Users/wenwen/Documents/MendeleyRefs/Wood et al.{\_}Nature{\_}2002.pdf:pdf},
issn = {00280836},
journal = {Nature},
month = {feb},
number = {6874},
pages = {871--880},
publisher = {Nature Publishing Group},
title = {{The genome sequence of Schizosaccharomyces pombe}},
url = {http://www.nature.com/doifinder/10.1038/nature724},
volume = {415},
year = {2002}
}
@article{Leyva2012a,
author = {Leyva, I. and Sevilla-Escoboza, R. and Buld{\'{u}}, J. and Sendi{\~{n}}a-Nadal, I. and G{\'{o}}mez-Garde{\~{n}}es, J. and Arenas, a. and Moreno, Y. and G{\'{o}}mez, S. and Jaimes-Re{\'{a}}tegui, R. and Boccaletti, S.},
doi = {10.1103/PhysRevLett.108.168702},
file = {:Users/wenwen/Documents/MendeleyRefs/Leyva et al.{\_}Physical Review Letters{\_}2012.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {apr},
number = {16},
pages = {1--4},
title = {{Explosive First-Order Transition to Synchrony in Networked Chaotic Oscillators}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.108.168702},
volume = {108},
year = {2012}
}
@article{Popovych2011,
author = {Popovych, Oleksandr and Yanchuk, Serhiy and Tass, Peter},
doi = {10.1103/PhysRevLett.107.228102},
file = {::},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {nov},
number = {22},
pages = {1--5},
title = {{Delay- and Coupling-Induced Firing Patterns in Oscillatory Neural Loops}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.107.228102},
volume = {107},
year = {2011}
}
@article{Pinto2012,
author = {Pinto, Pedro and Thiran, Patrick and Vetterli, Martin},
doi = {10.1103/PhysRevLett.109.068702},
file = {::;::},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {aug},
number = {6},
pages = {1--5},
title = {{Locating the Source of Diffusion in Large-Scale Networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.109.068702},
volume = {109},
year = {2012}
}
@article{Do2012a,
author = {Do, Anne-Ly and Boccaletti, Stefano and Gross, Thilo},
doi = {10.1103/PhysRevLett.108.194102},
file = {:Users/wenwen/Documents/MendeleyRefs/Do, Boccaletti, Gross{\_}Physical Review Letters{\_}2012.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {may},
number = {19},
pages = {1--5},
title = {{Graphical Notation Reveals Topological Stability Criteria for Collective Dynamics in Complex Networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.108.194102},
volume = {108},
year = {2012}
}
@article{Melchionna2006,
author = {Melchionna, Simone and Succi, Sauro and Hansen, Jean-Pierre},
doi = {10.1103/PhysRevE.73.017701},
file = {:Users/wenwen/Documents/MendeleyRefs/Melchionna, Succi, Hansen{\_}Physical Review E{\_}2006.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
number = {1},
pages = {017701},
title = {{Simulation of single-file ion transport with the lattice Fokker-Planck equation}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.73.017701},
volume = {73},
year = {2006}
}
@article{Mukherji2008,
abstract = {We present a molecular dynamics study of a generic model for single polymer diffusion on surfaces, which have variable atomic-scale corrugation but no artificial, impenetrable obstacles. The diffusion coefficient D scales as D is proportional to (-3/2) with the degree of polymerization N for strongly adsorbed, linear polymers on solid substrates in good solvents. Weaker scaling, i.e., D is proportional to (-1), is found if (i) the substrate is a fluid, e.g., a membrane, (ii) the polymer is a ring polymer, and (iii) the polymer is commensurate with the substrate. In poor solvents, diffusion on solids slows exponentially fast with N. Reptation is not observed in any of the simulations presented here.},
author = {Mukherji, Debashish and Bartels, Guido and M{\"{u}}ser, Martin H.},
doi = {10.1103/PhysRevLett.100.068301},
file = {:Users/wenwen/Documents/MendeleyRefs/Mukherji, Bartels, M{\"{u}}ser{\_}Physical Review Letters{\_}2008.pdf:pdf},
issn = {00319007},
journal = {Phys. Rev. Lett.},
number = {February},
pages = {1--4},
pmid = {18352522},
title = {{Scaling laws of single polymer dynamics near attractive surfaces}},
volume = {100},
year = {2008}
}
@article{Bruna2014,
abstract = {Abstract The diffusion of finite-size hard-core interacting particles in two-or three- dimensional confined domains is considered in the limit that the confinement dimensions become comparable to the particle's dimensions. The result is a nonlinear diffusion ... $\backslash$n},
archivePrefix = {arXiv},
arxivId = {0809.0045},
author = {Bruna, Maria and Chapman, S. Jonathan},
doi = {10.1007/s11538-013-9847-0},
eprint = {0809.0045},
file = {:Users/wenwen/Documents/MendeleyRefs/Bruna, Chapman{\_}Bulletin of Mathematical Biology{\_}2014.pdf:pdf},
isbn = {1522-9602 (Electronic)$\backslash$r0092-8240 (Linking)},
issn = {15229602},
journal = {Bull. Math. Biol.},
keywords = {Brownian motion,Diffusion in confined geometries,Entropic effects,Fokker-Planck equation,Stochastic simulations},
number = {4},
pages = {947--982},
pmid = {23660951},
title = {{Diffusion of Finite-Size Particles in Confined Geometries}},
volume = {76},
year = {2014}
}
@article{Lin2015,
abstract = {During recombination, the DNA of parents exchange their genetic information to give rise to a genetically unique offspring. For recombination to occur, homologous chromosomes need to find each other and align with high precision. Fission yeast solves this problem by folding chromosomes in loops and pulling them through the viscous nucleoplasm. We propose a theory of pulled polymer loops to quantify the effect of drag forces on the alignment of chromosomes. We introduce an external force field to the concept of a Brownian bridge and thus solve for the statistics of loop configurations in space.},
author = {Lin, Yen Ting and Fr{\"{o}}mberg, Daniela and Huang, Wenwen and Delivani, Petrina and Chac{\'{o}}n, Mariola and Toli{\'{c}}, Iva M. and J{\"{u}}licher, Frank and Zaburdaev, Vasily},
doi = {10.1103/PhysRevLett.115.208102},
file = {:Users/wenwen/Documents/MendeleyRefs/Lin et al.{\_}Physical Review Letters{\_}2015.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {nov},
number = {20},
pages = {208102},
title = {{Pulled Polymer Loops as a Model for the Alignment of Meiotic Chromosomes}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.115.208102},
volume = {115},
year = {2015}
}
@book{M.D1986,
author = {Doi, M. and Edwards, S. F.},
file = {:Users/wenwen/Documents/MendeleyRefs/Doi, Edwards{\_}Unknown{\_}1986(2).pdf:pdf},
publisher = {Oxford University Press},
title = {{The Theory of Plymer Dynamics}},
year = {1986}
}
@article{Hegde2014,
author = {Hegde, Chaitra and Sabhapandit, Sanjib and Dhar, Abhishek},
doi = {10.1103/PhysRevLett.113.120601},
file = {:Users/wenwen/Documents/MendeleyRefs/Hegde, Sabhapandit, Dhar{\_}Physical Review Letters{\_}2014.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
number = {12},
pages = {120601},
title = {{Universal Large Deviations for the Tagged Particle in Single-File Motion}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.113.120601},
volume = {113},
year = {2014}
}
@article{Kalhor2012,
abstract = {We describe tethered conformation capture (TCC), a method for genome-wide mapping of chromatin interactions. By performing ligations on solid substrates rather than in solution, TCC substantially enhances the signal-to-noise ratio, thereby facilitating a detailed analysis of interactions within and between chromosomes. We identified a group of regions in each chromosome in human cells that account for the majority of interchromosomal interactions. These regions are marked by high transcriptional activity, suggesting that their interactions are mediated by transcriptional machinery. Each of these regions interacts with numerous other such regions throughout the genome in an indiscriminate fashion, partly driven by the accessibility of the partners. As a different combination of interactions is likely present in different cells, we developed a computational method to translate the TCC data into physical chromatin contacts in a population of three-dimensional genome structures. Statistical analysis of the resulting population demonstrates that the indiscriminate properties of interchromosomal interactions are consistent with the well-known architectural features of the human genome.},
author = {Kalhor, Reza and Tjong, Harianto and Jayathilaka, Nimanthi and Alber, Frank and Chen, Lin},
doi = {10.1038/nbt.2057},
file = {:Users/wenwen/Documents/MendeleyRefs/Kalhor et al.{\_}Nature Biotechnology{\_}2011.pdf:pdf},
issn = {1087-0156},
journal = {Nat. Biotechnol.},
month = {dec},
number = {1},
pages = {90--98},
pmid = {22198700},
publisher = {Nature Publishing Group},
title = {{Genome architectures revealed by tethered chromosome conformation capture and population-based modeling}},
url = {http://www.nature.com/doifinder/10.1038/nbt.2057},
volume = {30},
year = {2011}
}
@article{Youngren2014,
abstract = {At all but the slowest growth rates, Escherichia coli cell cycles overlap, and its nucleoid is segregated to daughter cells as a forked DNA circle with replication ongoing-a state fundamentally different from eukaryotes. We have solved the chromosome organization, structural dynamics, and segregation of this constantly replicating chromosome. It is locally condensed to form a branched donut, compressed so that the least replicated DNA spans the cell center and the newest DNA extends toward the cell poles. Three narrow zones at the cell center and quarters contain both the replication forks and nascent DNA and serve to segregate the duplicated chromosomal information as it flows outward. The overall pattern is smoothly self-replicating, except when the duplicated terminus region is released from the septum and recoils to the center of a sister nucleoid. In circular cross-section of the cell, the left and right arms of the chromosome form separate, parallel structures that lie in each cell half along the radial cell axis. In contrast, replication forks and origin and terminus regions are found mostly at the center of the cross section, balanced by the parallel chromosome arms. The structure is consistent with the model in which the nucleoid is a constrained ring polymer that develops by spontaneous thermodynamics. The ring polymer pattern extrapolates to higher growth rates and also provides a structural basis for the form of the chromosome during very slow growth.},
author = {Youngren, Brenda and Nielsen, Henrik J{\"{o}}rk and Jun, Suckjoon and Austin, Stuart},
doi = {10.1101/gad.231050.113},
file = {:Users/wenwen/Documents/MendeleyRefs/Youngren et al.{\_}Genes and Development{\_}2014.pdf:pdf},
issn = {08909369},
journal = {Genes Dev.},
keywords = {Bacterial cell cycle,Bacterial chromosome,Chromosome organization,Chromosome segregation multifork replication},
pages = {71--84},
pmid = {24395248},
title = {{The multifork Escherichia coli chromosome is a self-duplicating and self-segregating thermodynamic ring polymer}},
volume = {28},
year = {2014}
}
@article{Brangwynne2015,
author = {Brangwynne, Clifford P. and Tompa, Peter and Pappu, Rohit V.},
doi = {10.1038/nphys3532},
file = {:Users/wenwen/Documents/MendeleyRefs/Brangwynne, Tompa, Pappu{\_}Unknown{\_}2015.pdf:pdf},
issn = {1745-2473},
journal = {Nat. Phys.},
month = {nov},
number = {11},
pages = {899--904},
title = {{Polymer physics of intracellular phase transitions}},
url = {http://www.nature.com/doifinder/10.1038/nphys3532},
volume = {11},
year = {2015}
}
@article{Fakhri2010,
abstract = {The thermal motion of stiff filaments in a crowded environment is highly constrained and anisotropic; it underlies the behavior of such disparate systems as polymer materials, nanocomposites, and the cell cytoskeleton. Despite decades of theoretical study, the fundamental dynamics of such systems remains a mystery. Using near-infrared video microscopy, we studied the thermal diffusion of individual single-walled carbon nanotubes (SWNTs) confined in porous agarose networks. We found that even a small bending flexibility of SWNTs strongly enhances their motion: The rotational diffusion constant is proportional to the filament-bending compliance and is independent of the network pore size. The interplay between crowding and thermal bending implies that the notion of a filament?s stiffness depends on its confinement. Moreover, the mobility of SWNTs and other inclusions can be controlled by tailoring their stiffness.},
author = {Fakhri, Nikta and MacKintosh, Frederick C and Lounis, Brahim and Cognet, Laurent and Pasquali, Matteo},
doi = {10.1126/science.1197321},
file = {:Users/wenwen/Documents/MendeleyRefs/Fakhri et al.{\_}Science{\_}2010.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Fakhri et al.{\_}Science{\_}2010.pdf:pdf},
isbn = {1095-9203 (Electronic)$\backslash$r0036-8075 (Linking)},
issn = {1095-9203},
journal = {Science (80-. ).},
keywords = {Carbon,Carbon: chemistry,Diffusion,Microscopy,Nanotubes,Physicochemical Phenomena,Polymers,Polymers: chemistry,Sepharose,Temperature,Video},
month = {dec},
number = {6012},
pages = {1804--1807},
pmid = {21205665},
title = {{Brownian Motion of Stiff Filaments in a Crowded Environment}},
url = {http://www.sciencemag.org/content/330/6012/1804.abstract http://www.ncbi.nlm.nih.gov/pubmed/21205665},
volume = {330},
year = {2010}
}
@article{Klenin1998,
abstract = {For the interpretation of solution structural and dynamic data of linear and circular DNA molecules in the kb range, and for the prediction of the effect of local structural changes on the global conformation of such DNAs, we have developed an efficient and easy way to set up a program based on a second-order explicit Brownian dynamics algorithm. The DNA is modeled by a chain of rigid segments interacting through harmonic spring potentials for bending, torsion, and stretching. The electrostatics are handled using precalculated energy tables for the interactions between DNA segments as a function of relative orientation and distance. Hydrodynamic interactions are treated using the Rotne-Prager tensor. While maintaining acceptable precision, the simulation can be accelerated by recalculating this tensor only once in a certain number of steps.},
author = {Klenin, Konstantin and Merlitz, Holger and Langowski, J{\"{o}}rg},
doi = {10.1016/S0006-3495(98)74003-2},
file = {:Users/wenwen/Documents/MendeleyRefs/Klenin, Merlitz, Langowski{\_}Biophysical journal{\_}1998.pdf:pdf},
isbn = {4962214233},
issn = {00063495},
journal = {Biophys. J.},
month = {feb},
number = {2},
pages = {780--788},
pmid = {9533691},
title = {{A Brownian Dynamics Program for the Simulation of Linear and Circular DNA and Other Wormlike Chain Polyelectrolytes}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0006349598740032},
volume = {74},
year = {1998}
}
@article{Bird1981,
author = {Bird, R. Byron},
file = {:Users/wenwen/Documents/MendeleyRefs/Bird{\_}Chem. Eng. Commun.{\_}1981.pdf:pdf},
journal = {Chem. Eng. Commun.},
pages = {321--329},
title = {{The Kramers Chain Model for Polymers}},
volume = {9},
year = {1981}
}
@book{Bird1987b,
author = {Bird, R. Byron and Curtiss, Charles F. and Armstrong, Robert C. and Hassager, Ole},
edition = {2},
file = {:Users/wenwen/Documents/MendeleyRefs/Bird et al.{\_}Unknown{\_}1987.pdf:pdf},
publisher = {John Wiley {\&} Sons},
title = {{Dynamics of polymeric liquids}},
volume = {2},
year = {1987}
}
@article{Zdeborova2010,
author = {Zdeborov{\'{a}}, Lenka and Boettcher, Stefan},
doi = {10.1088/1742-5468/2010/02/P02020},
file = {:Users/wenwen/Documents/MendeleyRefs/Zdeborov{\'{a}}, Boettcher{\_}Journal of Statistical Mechanics Theory and Experiment{\_}2010.pdf:pdf},
issn = {1742-5468},
journal = {J. Stat. Mech. Theory Exp.},
month = {feb},
number = {02},
pages = {P02020},
title = {{A conjecture on the maximum cut and bisection width in random regular graphs}},
url = {http://stacks.iop.org/1742-5468/2010/i=02/a=P02020?key=crossref.a1065cb94bc7ebf52bab74064cac3580},
volume = {2010},
year = {2010}
}
@techreport{Zhao2011,
author = {Zhao, Yanxiang},
file = {:Users/wenwen/Documents/MendeleyRefs/Zhao{\_}Unknown{\_}2011.pdf:pdf},
title = {{Brief introduction to the thermostats}},
year = {2011}
}
@article{Boekelheide2011,
abstract = {We use quantized molecular dynamics simulations to characterize the role of enzyme vibrations in facilitating dihydrofolate reductase hydride transfer. By sampling the full ensemble of reactive trajectories, we are able to quantify and distinguish between statistical and dynamical correlations in the enzyme motion. We demonstrate the existence of nonequilibrium dynamical coupling between protein residues and the hydride tunneling reaction, and we characterize the spatial and temporal extent of these dynamical effects. Unlike statistical correlations, which give rise to nanometer-scale coupling between distal protein residues and the intrinsic reaction, dynamical correlations vanish at distances beyond 4-6 Å from the transferring hydride. This work finds a minimal role for nonlocal vibrational dynamics in enzyme catalysis, and it supports a model in which nanometer-scale protein fluctuations statistically modulate--or gate--the barrier for the intrinsic reaction.},
author = {Boekelheide, N. and Salomon-Ferrer, R. and Miller, T. F.},
doi = {10.1073/pnas.1106397108},
file = {:Users/wenwen/Documents/MendeleyRefs/Boekelheide, Salomon-Ferrer, Miller{\_}Proceedings of the National Academy of Sciences{\_}2011.pdf:pdf},
isbn = {1091-6490 (Electronic)$\backslash$r0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
number = {24},
pages = {16159--16163},
pmid = {21930950},
title = {{Dynamics and dissipation in enzyme catalysis}},
volume = {108},
year = {2011}
}
@article{Hsu2012,
abstract = {Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice (d = 3 dimensions) and square lattice (d = 2 dimensions), varying chain stiffness by an energy penalty $\epsilon$(b) for chain bending. In the absence of excluded volume interactions, the persistence length l(p) of the polymers would then simply be l(p) = l(b)(2d - 2)(-1)q(b) (-1) with q(b) = exp(-$\epsilon$(b)/k(B)T), the bond length l(b) being the lattice spacing, and k(B)T is the thermal energy. Using Monte Carlo simulations applying the pruned-enriched Rosenbluth method (PERM), both q(b) and the chain length N are varied over a wide range (0.005 ≤ q(b) ≤ 1, N ≤ 50,000), and also a stretching force f is applied to one chain end (fixing the other end at the origin). In the absence of this force, in d = 2 a single crossover from rod-like behavior (for contour lengths less than l(p)) to swollen coils occurs, invalidating the Kratky-Porod model, while in d = 3 a double crossover occurs, from rods to Gaussian coils (as implied by the Kratky-Porod model) and then to coils that are swollen due to the excluded volume interaction. If the stretching force is applied, excluded volume interactions matter for the force versus extension relation irrespective of chain stiffness in d = 2, while theories based on the Kratky-Porod model are found to work in d = 3 for stiff chains in an intermediate regime of chain extensions. While for q(b) ≪ 1 in this model a persistence length can be estimated from the initial decay of bond-orientational correlations, it is argued that this is not possible for more complex wormlike chains (e.g., bottle-brush polymers). Consequences for the proper interpretation of experiments are briefly discussed.},
archivePrefix = {arXiv},
arxivId = {1110.1410v2},
author = {Hsu, Hsiao-Ping and Binder, Kurt},
doi = {10.1063/1.3674303},
eprint = {1110.1410v2},
file = {:Users/wenwen/Documents/MendeleyRefs/Hsu, Binder{\_}The Journal of chemical physics{\_}2012.pdf:pdf},
issn = {1089-7690},
journal = {J. Chem. Phys.},
keywords = {Monte Carlo Method,Polymers,Polymers: chemistry},
number = {2012},
pages = {024901},
pmid = {22260610},
title = {{Stretching semiflexible polymer chains: evidence for the importance of excluded volume effects from Monte Carlo simulation.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22260610},
volume = {136},
year = {2012}
}
@book{Morgan2007,
author = {Morgan, D O},
isbn = {9780199206100},
publisher = {OUP/New Science Press},
series = {Primers in Biology},
title = {{The Cell Cycle: Principles of Control}},
url = {https://books.google.de/books?id=ScEuiD2V6GoC},
year = {2007}
}
@book{Binder1995,
author = {Binder, Kurt},
file = {:Users/wenwen/Documents/MendeleyRefs/Binder{\_}Unknown{\_}1995.pdf:pdf},
isbn = {0195094387},
publisher = {Oxford University Press},
title = {{Monte Carlo and Molecular Dymanics Simulations in Polymers Science}},
url = {http://medcontent.metapress.com/index/A65RM03P4874243N.pdf},
year = {1995}
}
@article{Hassager1974,
author = {Hassager, Ole},
doi = {10.1063/1.1681321},
file = {:Users/wenwen/Documents/MendeleyRefs/Hassager{\_}The Journal of Chemical Physics{\_}1974.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {May 2013},
pages = {2111},
title = {{Kinetic theory and rheology of bead-rod models for macromolecular solutions. I. Equilibrium and steady flow properties}},
url = {http://link.aip.org/link/?JCP/60/2111/1{\&}Agg=doi},
volume = {60},
year = {1974}
}
@article{Habuchi2010,
abstract = {Polymergewirr: Die Untersuchung einzelner synthetischer Ringpolymere mit einer fluoreszierenden Perylendiimid-Einheit (siehe Bild, orange) in einer Matrix aus linearen Polymeren ergab, dass ein heterogenes System vorliegt. Die cyclischen Polymere sind teilweise auf die linearen Polymere aufgef{\"{a}}delt.},
author = {Habuchi, Satoshi and Satoh, Norihiro and Yamamoto, Takuya and Tezuka, Yasuyuki and Vacha, Martin},
doi = {10.1002/anie.200904394},
file = {:Users/wenwen/Documents/MendeleyRefs/Habuchi et al.{\_}Angewandte Chemie - International Edition{\_}2010.pdf:pdf},
issn = {14337851},
journal = {Angew. Chemie Int. Ed.},
keywords = {Diffusion,Polymers,Single-molecule studies,Topological polymers},
month = {feb},
number = {8},
pages = {1418--1421},
pmid = {20084645},
title = {{Multimode Diffusion of Ring Polymer Molecules Revealed by a Single-Molecule Study}},
url = {http://doi.wiley.com/10.1002/anie.200904394},
volume = {49},
year = {2010}
}
@article{Meimaroglou2013,
abstract = {Monte Carlo (MC) is a term quite common in the research community but, quite surprisingly, it may possess a different meaning among researchers in different areas. This paradox is derived from the potential of the method to serve as a modeling tool of systems that belong to a very wide range of different areas in science, such as mathematics, biology, economics, and physics. Thus, depending on the nature of the system under study and the type of the calculated properties, a different variation of the MC method may be encountered. In the present work, an attempt is made to provide a short overview of some of the most important MC techniques and their applications. Special emphasis is placed on problems related to the polymer science, with a more persistent presentation of a specific class of MC methods that can be implemented to the different scales of a polymerization process in order to predict the dynamic evolution of key properties of the polymer in terms of the varying process conditions. The latest developments in this field have made it possible to relate the macroscopic characteristics of a process to the end-use properties and functionalities of the produced polymeric products, via a detailed tracking of the evolution of the microstructural characteristics of the polymer chains. The presentation of these MC techniques is accompanied by specific illustrative examples from the literature.},
author = {Meimaroglou, Dimitrios and Kiparissides, Costas},
file = {:Users/wenwen/Documents/MendeleyRefs/Meimaroglou, Kiparissides{\_}Industrial and Engineering Chemistry Research{\_}2013.pdf:pdf},
journal = {Ind. Eng. Chem. Res.},
pages = {8963--8979},
title = {{Review of Monte Carlo methods for the prediction of distributed molecular and morphological polymer properties}},
volume = {53},
year = {2013}
}
@article{Li2009,
abstract = {In this paper, synchronization between two discrete-time networks, called "outer synchronization" for brevity, is theoretically and numerically studied. First, a sufficient criterion for this outer synchronization between two coupled discrete-time networks which have the same connection topologies is derived analytically. Numerical examples are also given and they are in line with the theoretical analysis. Additionally, numerical investigations of two coupled networks which have different connection topologies are analyzed as well. The involved numerical results show that these coupled networks with different connection matrices can reach synchronization.},
author = {Li, Changpin and Xu, Congxiang and Sun, Weigang and Xu, Jian and Kurths, Jürgen},
doi = {10.1063/1.3068357},
file = {:Users/wenwen/Documents/MendeleyRefs/Li et al.{\_}Chaos An Interdisciplinary Journal of Nonlinear Science{\_}2009.pdf:pdf},
issn = {10541500},
journal = {Chaos An Interdiscip. J. Nonlinear Sci.},
keywords = {Acquired Immunodeficiency Syndrome,Acquired Immunodeficiency Syndrome: epidemiology,Algorithms,Animals,Birds,Computer Simulation,Disease Transmission,Humans,Infectious,Influenza in Birds,Influenza in Birds: epidemiology,Models,Neural Networks (Computer),Neurological,Nonlinear Dynamics,Theoretical,Zoonoses},
month = {mar},
number = {1},
pages = {013106},
pmid = {19334970},
title = {{Outer synchronization of coupled discrete-time networks}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19334970 http://scitation.aip.org/content/aip/journal/chaos/19/1/10.1063/1.3068357},
volume = {19},
year = {2009}
}
@article{Kyrylyuk2011,
abstract = {Carbon nanotube reinforced polymeric composites can have favourable electrical properties, which make them useful for applications such as flat-panel displays and photovoltaic devices. However, using aqueous dispersions to fabricate composites with specific physical properties requires that the processing of the nanotube dispersion be understood and controlled while in the liquid phase. Here, using a combination of experiment and theory, we study the electrical percolation of carbon nanotubes introduced into a polymer matrix, and show that the percolation threshold can be substantially lowered by adding small quantities of a conductive polymer latex. Mixing colloidal particles of different sizes and shapes (in this case, spherical latex particles and rod-like nanotubes) introduces competing length scales that can strongly influence the formation of the system-spanning networks that are needed to produce electrically conductive composites. Interplay between the different species in the dispersions leads to synergetic or antagonistic percolation, depending on the ease of charge transport between the various conductive components.},
author = {Kyrylyuk, Andriy V and Hermant, Marie Claire and Schilling, Tanja and Klumperman, Bert and Koning, Cor E and van der Schoot, Paul},
doi = {10.1038/nnano.2011.40},
file = {:Users/wenwen/Documents/MendeleyRefs/Kyrylyuk et al.{\_}Nature nanotechnology{\_}2011.pdf:pdf},
issn = {1748-3387},
journal = {Nat. Nanotechnol.},
keywords = {Carbon,Carbon: chemistry,Electric Conductivity,Electricity,Latex,Latex: chemistry,Monte Carlo Method,Nanocomposites,Nanocomposites: chemistry,Nanotechnology,Nanotechnology: instrumentation,Nanotubes,Particle Size,Polymers,Polymers: chemistry,Surface Properties},
month = {jun},
number = {6},
pages = {364--369},
pmid = {21478868},
publisher = {Nature Publishing Group},
title = {{Controlling electrical percolation in multicomponent carbon nanotube dispersions}},
url = {http://dx.doi.org/10.1038/nnano.2011.40 http://www.ncbi.nlm.nih.gov/pubmed/21478868 http://www.nature.com/doifinder/10.1038/nnano.2011.40},
volume = {6},
year = {2011}
}
@article{Guan2010,
author = {Guan, Shuguang and Gong, Xiaofeng and Li, Kun and Liu, Zonghua and Lai, C-H},
doi = {10.1088/1367-2630/12/7/073045},
file = {:Users/wenwen/Documents/MendeleyRefs/Guan et al.{\_}New Journal of Physics{\_}2010.pdf:pdf},
issn = {1367-2630},
journal = {New J. Phys.},
keywords = {ek laboratories,national university of singapore,singapore 117411},
month = {jul},
number = {7},
pages = {073045},
title = {{Characterizing generalized synchronization in complex networks}},
url = {http://stacks.iop.org/1367-2630/12/i=7/a=073045?key=crossref.a7440160796fc0bac4c68f7ff8114e6d},
volume = {12},
year = {2010}
}
@article{Fixman1974,
abstract = {A classical system of mass points subject to holonomic constraints has a kinetic energy dependent on the coordinates as well as the moments of the remaining degrees of freedom. Coordinate averages formed in the reduced space of unconstrained coordinates and their conjugate momenta then involve a metric determinant that may be difficult to evaluate. A theorem is derived that permits a relatively easy evaluation when the constraints are distances between particles, and an application is made to a Kramers type freely jointed chain.},
author = {Fixman, M.},
doi = {10.1073/pnas.71.8.3050},
file = {:Users/wenwen/Documents/MendeleyRefs/Fixman{\_}Proceedings of the National Academy of Sciences{\_}1974.pdf:pdf},
isbn = {1091-6490},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
number = {8},
pages = {3050--3053},
pmid = {16578718},
title = {{Classical Statistical Mechanics of Constraints: A Theorem and Application to Polymers}},
url = {http://www.pnas.org/content/71/8/3050},
volume = {71},
year = {1974}
}
@incollection{Forsburg2003,
abstract = {The fission yeast S. pombe provides an attractive alternative system to budding yeast S. cerevisiae for studies of fundamental cell biology. Fission yeast is a particularly powerful model for studies of cell cycle, chromosome dynamics, and polarity. Other areas of study are also expanding. Conceptually similar genetic tools are available in both systems, and both organisms have completely sequenced genomes.},
author = {Forsburg, Susan L},
booktitle = {Curr. Protoc. Mol. Biol.},
doi = {10.1002/0471142727.mb1314s64},
isbn = {1934-3647 (Electronic)$\backslash$r1934-3647 (Linking)},
issn = {1934-3647},
keywords = {Fungal,Genes,Genetics,Microbial,Microbial: methods,Mycology,Mycology: methods,Schizosaccharomyces,Schizosaccharomyces: cytology,Schizosaccharomyces: genetics,Schizosaccharomyces: metabolism},
pages = {Unit 13.14},
pmid = {18265318},
title = {{Overview of Schizosaccharomyces pombe}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18265318{\%}5Cnhttp://doi.wiley.com/10.1002/0471142727.mb1314s64},
volume = {Chapter 13},
year = {2003}
}
@article{JoanGubermanJudithSaksBarbaraShapiro2006,
abstract = {Based on courses held in 2002 and 2005 by the Burroughs Wellcome Fund and HHMI, this book is a collection of practical advice and experiences from seasoned biomedical investigators. The second edition contains three new chapters on laboratory leadership, project management, and teaching and course design.},
author = {{Joan Guberman, Judith Saks, Barbara Shapiro}, and Marion Torchia},
file = {:Users/wenwen/Documents/MendeleyRefs/Joan Guberman, Judith Saks, Barbara Shapiro{\_}Unknown{\_}2006.pdf:pdf},
isbn = {0908072345},
pages = {201--211},
title = {{Making the Right Moves A Practical Guide to Scientifıc Management Making the}},
volume = {Second Edi},
year = {2006}
}
@article{Sebastian2000,
author = {Sebastian, K L},
file = {:Users/wenwen/Documents/MendeleyRefs/Sebastian{\_}Unknown{\_}2000.pdf:pdf},
number = {1},
pages = {1128--1132},
title = {{Pulling a polymer out of a potential well and the mechanical unzipping of DNA}},
volume = {62},
year = {2000}
}
@article{Shimamura2001,
abstract = {It is nontrivial whether the average size of a ring polymer should become smaller or larger under a topological constraint. Making use of some knot invariants, we numerically evaluate the mean-square radius of gyration for ring polymers having a fixed knot type, where the ring polymers are given by self-avoiding polygons consisting of freely jointed hard cylinders. We obtain plots of the gyration radius versus the number of polygonal nodes for the trivial, trefoil, and figure-eight knots. We discuss possible asymptotic behaviors of the gyration radius under the topological constraint. In the asymptotic limit, the size of a ring polymer with a given knot is larger than that of no topological constraint when the polymer is thin, and the effective expansion becomes weak when the polymer is thick enough.},
archivePrefix = {arXiv},
arxivId = {cond-mat/0104022},
author = {Shimamura, Miyuki K and Deguchi, Tetsuo},
doi = {10.1103/PhysRevE.64.020801},
eprint = {0104022},
file = {:Users/wenwen/Documents/MendeleyRefs/Shimamura, Deguchi{\_}Physical Review E{\_}2001.pdf:pdf},
isbn = {1539-3755 (Print)$\backslash$r1539-3755 (Linking)},
issn = {1063-651X},
journal = {Phys. Rev. E},
month = {jul},
number = {2},
pages = {020801},
pmid = {11497553},
primaryClass = {cond-mat},
title = {{Gyration radius of a circular polymer under a topological constraint with excluded volume}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.64.020801},
volume = {64},
year = {2001}
}
@article{Medvinsky2001,
author = {Medvinsky, Alexander and Tikhonova, Irene and Aliev, Rubin and Li, Bai-Lian and Lin, Zhen-Shan and Malchow, Horst},
doi = {10.1103/PhysRevE.64.021915},
file = {:Users/wenwen/Documents/MendeleyRefs/Medvinsky et al.{\_}Physical Review E{\_}2001.pdf:pdf},
issn = {1063-651X},
journal = {Phys. Rev. E},
month = {jul},
number = {2},
pages = {1--7},
title = {{Patchy environment as a factor of complex plankton dynamics}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.64.021915},
volume = {64},
year = {2001}
}
@article{Berryman1992,
author = {Berryman, Alan A},
doi = {10.2307/1940005},
file = {:Users/wenwen/Documents/MendeleyRefs/Berryman{\_}Ecology{\_}1992.pdf:pdf},
isbn = {2646122373},
issn = {00129658},
journal = {Ecology},
month = {oct},
number = {5},
pages = {1530--1535},
title = {{The Orgins and Evolution of Predator-Prey Theory}},
url = {http://doi.wiley.com/10.2307/1940005},
volume = {73},
year = {1992}
}
@article{Rzehak1999,
author = {Rzehak, R and Kienle, D and Kawakatsu, T and Zimmermann, W},
doi = {10.1209/epl/i1999-00338-1},
file = {:Users/wenwen/Documents/MendeleyRefs/Rzehak et al.{\_}Europys. Lett.{\_}1999.pdf:pdf},
issn = {0295-5075},
journal = {Europhys. Lett.},
month = {jun},
number = {6},
pages = {821--826},
title = {{Partial draining of a tethered polymer in flow}},
url = {http://stacks.iop.org/0295-5075/46/i=6/a=821?key=crossref.f9aab2d74189bb5e382729ec469797ef},
volume = {46},
year = {1999}
}
@book{Meyer2004,
author = {Meyer, Cd},
isbn = {9780898714548},
title = {{Matrix Analysis and Applied Linear Algebra}},
url = {http://onlinelibrary.wiley.com/doi/10.1002/cbdv.200490137/abstract{\%}5Cnhttp://scholar.google.com/scholar?hl=en{\&}btnG=Search{\&}q=intitle:Matrix+Analysis+and+Applied+Linear+Algebra{\#}1{\%}5Cnhttp://scholar.google.com/scholar?hl=en{\&}btnG=Search{\&}q=intitle:Matrix+Analys},
year = {2004}
}
@article{Beygelzimer2005,
author = {Beygelzimer, Alina and Grinstein, Geoffrey and Linsker, Ralph and Rish, Irina},
doi = {10.1016/j.physa.2005.03.040},
file = {:Users/wenwen/Documents/MendeleyRefs/Beygelzimer et al.{\_}Physica A Statistical Mechanics and its Applications{\_}2005.pdf:pdf},
issn = {03784371},
journal = {Phys. A Stat. Mech. its Appl.},
keywords = {1 914 784 6071,1 914 784 6960,a,beygel,beygelzimer,com,complex networks,e-mail addresses,fax,g,ggrin,grinstein,i,ibm,largest connected component,linsker,r,rish,robustness,scale-free networks,tel,us,{\~{a}} corresponding author},
month = {nov},
number = {3-4},
pages = {593--612},
title = {{Improving network robustness by edge modification}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0378437105003523},
volume = {357},
year = {2005}
}
@misc{Munz1994,
abstract = {The evaluation of three-point crosses at the tetrad and random spore level leads to the conclusion that both chiasma and chromatid interference are absent in the fission yeast Schizosaccharomyces pombe.},
author = {Munz, P.},
booktitle = {Genetics},
isbn = {0016-6731 (Print)$\backslash$n0016-6731 (Linking)},
issn = {00166731},
number = {3},
pages = {701--707},
pmid = {8088515},
title = {{An analysis of interference in the fission yeast Schizosaccharomyces pombe}},
volume = {137},
year = {1994}
}
@article{Derrida1998,
abstract = {A number of exact results have been obtained recently for the one-dimensional asymmetric simple exclusion process, a model of particles which hop to their right at random times, on a one-dimensional lattice, provided that the target site is empty. Using either a matrix form for the steady-state weights or the Bethe ansatz, several steady-state properties can be calculated exactly: the current, the density profile for open boundary conditions, the diffusion constant of a tagged particle. The matrix form of the steady state can be extended to calculate exactly the steady state of systems of two species of particles and shock profiles. (C) 1998 Elsevier Science B.V. All rights reserved.},
author = {Derrida, B.},
doi = {10.1016/S0370-1573(98)00006-4},
file = {:Users/wenwen/Documents/MendeleyRefs/Derrida{\_}Physics Reports{\_}1998.pdf:pdf},
isbn = {0370-1573},
issn = {03701573},
journal = {Phys. Rep.},
number = {1-3},
pages = {65--83},
title = {{An exactly soluble non-equilibrium system: The asymmetric simple exclusion process}},
volume = {301},
year = {1998}
}
@article{Haber2000,
abstract = {Random walks have been used to describe a wide variety of systems ranging from cell colonies to polymers. Sixty-five years ago, Kuhn [Kuhn, W. (1934) Kolloid-Z. 68, 2-11] made the prediction, backed later by computer simulations, that the overall shape of a random-walk polymer is aspherical, yet no experimental work has directly tested Kuhn's general idea and subsequent computer simulations. By using fluorescence microscopy, we monitored the conformation of individual, long, random-walk polymers (fluorescently labeled DNA molecules) at equilibrium. We found that a polymer most frequently adopts highly extended, nonfractal structures with a strongly anisotropic shape. The ensemble-average ratio of the lengths of the long and short axes of the best-fit ellipse of the polymer was much larger than unity.},
author = {Haber, C and Ruiz, S a and Wirtz, D},
doi = {10.1073/pnas.190320097},
file = {:Users/wenwen/Documents/MendeleyRefs/Haber, Ruiz, Wirtz{\_}Proceedings of the National Academy of Sciences of the United States of America{\_}2000.pdf:pdf},
isbn = {0027-8424 (Print)$\backslash$r0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
month = {sep},
number = {20},
pages = {10792--10795},
pmid = {10984514},
title = {{Shape anisotropy of a single random-walk polymer}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.190320097},
volume = {97},
year = {2000}
}
@article{Rosenblum1996,
author = {Rosenblum, Mg and Pikovsky, As and Kurths, J},
file = {:Users/wenwen/Documents/MendeleyRefs/Rosenblum, Pikovsky, Kurths{\_}Physical review letters{\_}1996.pdf:pdf},
issn = {1079-7114},
journal = {Phys. Rev. Lett.},
month = {mar},
number = {11},
pages = {1804--1807},
pmid = {10060525},
title = {{Phase synchronization of chaotic oscillators.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10060525},
volume = {76},
year = {1996}
}
@article{Michels1982,
author = {Michels, J.P.J. and Wiegel, F.W.},
doi = {10.1016/0375-9601(82)90636-3},
file = {:Users/wenwen/Documents/MendeleyRefs/Michels, Wiegel{\_}Physics Letters A{\_}1982.pdf:pdf},
isbn = {0375-9601},
issn = {03759601},
journal = {Phys. Lett. A},
number = {7},
pages = {381--384},
title = {{Probability of knots in a polymer ring}},
volume = {90},
year = {1982}
}
@article{Sakaue2012a,
abstract = {We study the conformation and dynamics of a single polymer chain that$\backslash$nis pulled by a constant force applied at its one end with the other$\backslash$nend free. Such a situation is relevant to the growing technology$\backslash$nof manipulating individual macromolecules, which offers a paradigm$\backslash$nresearch for probing far-from-equilibrium responses of long flexible$\backslash$nbiological polymers. We first analyze the Rouse model for the Gaussian$\backslash$nchains for which the exact analytical results can be obtained. More$\backslash$nrealistic features such as the finite extensibility, the excluded$\backslash$nvolume, and the hydrodynamic interactions are taken into account$\backslash$nwith the help of the scaling argument, which leads to various nontrivial$\backslash$npredictions such as the force-dependent friction constants. We elucidate$\backslash$n(i) generalized dynamical equations of state describing extension$\backslash$nand friction laws in steady-state and (ii) the tension propagation$\backslash$nlaws in the transient process. We point out that the time evolutions$\backslash$nof the dynamic friction in the transient process crucially depend$\backslash$non the experimental protocol, i.e., either constant force or constant$\backslash$nvelocity ensemble. These predictions could be verified in experiments$\backslash$nusing giant DNAs and chromosomes.},
archivePrefix = {arXiv},
arxivId = {1203.4095},
author = {Sakaue, Takahiro and Saito, Takuya and Wada, Hirofumi},
doi = {10.1103/PhysRevE.86.011804},
eprint = {1203.4095},
file = {:Users/wenwen/Documents/MendeleyRefs/Sakaue, Saito, Wada{\_}Physical Review E - Statistical, Nonlinear, and Soft Matter Physics{\_}2012.pdf:pdf},
isbn = {1550-2376 (Electronic)$\backslash$r1539-3755 (Linking)},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {jul},
number = {1},
pages = {011804},
pmid = {23005445},
title = {{Dragging a polymer in a viscous fluid: Steady state and transient}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.86.011804},
volume = {86},
year = {2012}
}
@article{Somasi2002,
author = {Somasi, Madan and Khomami, Bamin and Woo, Nathanael J. and Hur, Joe S. and Shaqfeh, Eric S.G.},
doi = {10.1016/S0377-0257(02)00132-5},
file = {:Users/wenwen/Documents/MendeleyRefs/Somasi et al.{\_}Journal of Non-Newtonian Fluid Mechanics{\_}2002.pdf:pdf},
issn = {03770257},
journal = {J. Nonnewton. Fluid Mech.},
keywords = {1-314-935-6065,1-314-935-7211,algorithm,bead-rod model,bead-spring model,brownian dynamics,coarse graining,corresponding author,dilute polymer solution,extensional flow,fax,shear flow,tel},
month = {dec},
number = {1-3},
pages = {227--255},
title = {{Brownian dynamics simulations of bead-rod and bead-spring chains: numerical algorithms and coarse-graining issues}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0377025702001325},
volume = {108},
year = {2002}
}
@article{Tokuda2012,
abstract = {Eukaryotic genome is organized in a set of chromosomes each of which consists of a chain of DNA and associated proteins. Processes involving DNA such as transcription, duplication, and repair, therefore, should be intrinsically related to the three-dimensional organization of the genome. In this article, we develop a computational model of the three-dimensional organization of the haploid genome of interphase budding yeast by regarding chromosomes as chains moving under the constraints of nuclear structure and chromatin-chromatin interactions. The simulated genome structure largely fluctuates with the diffusive movement of chromosomes. This fluctuation, however, is not completely random, as parts of chromosomes distribute in characteristic ways to form "territories" in the nucleus. By suitably taking account of constraints arising from the data of the chromosome-conformation-capture measurement, the model explains the observed fluorescence data of chromosome distributions and motions.},
author = {Tokuda, Naoko and Terada, Tomoki P. and Sasai, Masaki},
doi = {10.1016/j.bpj.2011.12.005},
file = {:Users/wenwen/Documents/MendeleyRefs/Tokuda, Terada, Sasai{\_}Biophysical Journal{\_}2012.pdf:pdf},
isbn = {1542-0086 (Electronic)$\backslash$n0006-3495 (Linking)},
issn = {00063495},
journal = {Biophys. J.},
keywords = {Chromatin,Chromatin: chemistry,Chromatin: genetics,Chromatin: metabolism,Diffusion,Fungal,Fungal: genetics,Genome,Interphase,Interphase: genetics,Models,Molecular,Movement,Nuclear Envelope,Nuclear Envelope: metabolism,Saccharomycetales,Saccharomycetales: cytology,Saccharomycetales: genetics,Saccharomycetales: metabolism,Telomere,Telomere: genetics,Telomere: metabolism},
month = {jan},
number = {2},
pages = {296--304},
pmid = {22339866},
publisher = {Biophysical Society},
title = {{Dynamical Modeling of Three-Dimensional Genome Organization in Interphase Budding Yeast}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0006349511054014},
volume = {102},
year = {2012}
}
@incollection{Schadschneider2011j,
author = {Schadschneider, Andreas and Chowdhury, Debashish and Nishinari, Katsuhiro},
booktitle = {Stoch. Transp. Complex Syst.},
doi = {10.1016/B978-0-444-52853-7.00006-3},
file = {:Users/wenwen/Documents/MendeleyRefs/Schadschneider, Chowdhury, Nishinari{\_}Stochastic Transport in Complex Systems{\_}2011(4).pdf:pdf},
isbn = {9780444528537},
pages = {215--241},
publisher = {Elsevier},
title = {{Vehicular Traffic I: Empirical Facts}},
url = {http://linkinghub.elsevier.com/retrieve/pii/B9780444528537000063},
year = {2011}
}
@article{Wei1989,
author = {Wei, Gaoyuan},
doi = {10.1063/1.456394},
file = {:Users/wenwen/Documents/MendeleyRefs/Wei{\_}The Journal of Chemical Physics{\_}1989.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {1989},
pages = {5873},
title = {{Distribution function of the radius of gyration for Gaussian molecules}},
url = {http://scitation.aip.org/content/aip/journal/jcp/90/10/10.1063/1.456394},
volume = {90},
year = {1989}
}
@article{Lazarescu2015a,
abstract = {One of the main features of statistical systems out of equilibrium is the currents they exhibit in their stationary state: microscopic currents of probability between configurations, which translate into macroscopic currents of mass, charge, etc. Understanding the general behaviour of these currents is an important step towards building a universal framework for non-equilibrium steady states akin to the Gibbs-Boltzmann distribution for equilibrium systems. In this review, we consider one-dimensional bulk-driven particle gases, and in particular the asymmetric simple exclusion process (ASEP) with open boundaries, which is one of the most popular models of one-dimensional transport. We focus, in particular, on the current of particles flowing through the system in its steady state, and on its fluctuations. We show how one can obtain the complete statistics of that current, through its large deviation function, by combining results from various methods: exact calculation of the cumulants of the current, using the integrability of the model ; direct diagonalisation of a biased process in the limits of very high or low current ; hydrodynamic description of the model in the continuous limit using the macroscopic fluctuation theory (MFT). We give a pedagogical account of these techniques, starting with a quick introduction to the necessary mathematical tools, as well as a short overview of the existing works relating to the ASEP. We conclude by drawing the complete dynamical phase diagram of the current. We also remark on a few possible generalisations of these results.},
archivePrefix = {arXiv},
arxivId = {1507.04179},
author = {Lazarescu, Alexandre},
doi = {10.1088/1751-8113/48/50/503001},
eprint = {1507.04179},
file = {:Users/wenwen/Documents/MendeleyRefs/Lazarescu{\_}Journal of Physics A Mathematical and Theoretical{\_}2015.pdf:pdf},
issn = {1751-8113},
journal = {J. Phys. A Math. Theor.},
keywords = {02.50.Ga,05.40.-a,05.60.-k,asymmetric simple exclusion process,current fluctuations,dynamical phase transitions,large deviations,macroscopic fluctuation theory,one-dimensional transport},
month = {dec},
number = {50},
pages = {503001},
publisher = {IOP Publishing},
title = {{The physicist's companion to current fluctuations: one-dimensional bulk-driven lattice gases}},
url = {http://stacks.iop.org/1751-8121/48/i=50/a=503001?key=crossref.12e584f525b6ea69118036b04fadcd5e},
volume = {48},
year = {2015}
}
@article{Kennedy2013,
author = {Kennedy, Tom},
doi = {10.1103/PhysRevLett.111.165703},
file = {:Users/wenwen/Documents/MendeleyRefs/Kennedy{\_}Physical Review Letters{\_}2013.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {oct},
number = {16},
pages = {165703},
title = {{Conformal Invariance of the 3D Self-Avoiding Walk}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.111.165703},
volume = {111},
year = {2013}
}
@article{Lyulin1999,
author = {Lyulin, Alexey V and Adolf, David B and Davies, Geoffrey R},
doi = {10.1063/1.479355},
file = {:Users/wenwen/Documents/MendeleyRefs/Lyulin, Adolf, Davies{\_}The Journal of Chemical Physics{\_}1999.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {2},
pages = {758},
title = {{Brownian dynamics simulations of linear polymers under shear flow}},
url = {http://scitation.aip.org/content/aip/journal/jcp/111/2/10.1063/1.479355},
volume = {111},
year = {1999}
}
@article{Daido2004,
author = {Daido, Hiroaki and Nakanishi, Kenji},
doi = {10.1103/PhysRevLett.93.104101},
file = {:Users/wenwen/Documents/MendeleyRefs/Daido, Nakanishi{\_}Physical review letters{\_}2004.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {aug},
number = {10},
pages = {104101},
publisher = {APS},
title = {{Aging transition and universal scaling in oscillator networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.93.104101},
volume = {93},
year = {2004}
}
@article{Hatfield1999,
abstract = {Extended polymers are relevant in a variety of situations ranging from the classic coil-stretch problem to recent single molecule polymer experiments with DNA. We present theoretical calculations and computer simulations of the dynamic properties of extended single polymers. We discuss the effects of tension and hydrodynamics on t, the fundamental relaxation time of the polymer, and find that tension dominates the behavior of t. Furthermore, the symmetry breaking caused by extending the polymer splits t, leading to distinct longitudinal and transverse relaxation times. Our results are in agreement with recent experiments, and we discuss implications for the coil-stretch transition.},
author = {Hatfield, John and Quake, Stephen},
doi = {10.1103/PhysRevLett.82.3548},
file = {:Users/wenwen/Documents/MendeleyRefs/Hatfield, Quake{\_}Physical Review Letters{\_}1999.pdf:pdf},
isbn = {0031-9007},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
number = {17},
pages = {3548--3551},
title = {{Dynamic Properties of an Extended Polymer in Solution}},
volume = {82},
year = {1999}
}
@book{Lemons2002,
author = {Lemons, Ds},
file = {:Users/wenwen/Documents/MendeleyRefs/Lemons{\_}Unknown{\_}2002.pdf:pdf},
isbn = {0801868661},
pages = {124},
publisher = {The Johns Hopkins University Press},
title = {{An Introduction to Stochastic Processes in Physics}},
year = {2002}
}
@article{barabasi1999emergence,
author = {Barab{\'{a}}si, Albert-L{\'{a}}szl{\'{o}} and Albert, R{\'{e}}ka},
file = {:Users/wenwen/Documents/MendeleyRefs/Barab{\'{a}}si, Albert{\_}Science{\_}1999.pdf:pdf},
journal = {Science (80-. ).},
number = {5439},
pages = {509--512},
publisher = {American Association for the Advancement of Science},
title = {{Emergence of scaling in random networks}},
volume = {286},
year = {1999}
}
@article{Riordan2011,
abstract = {"Explosive percolation" is said to occur in an evolving network when a macroscopic connected component emerges in a number of steps that is much smaller than the system size. Recent predictions based on simulations suggested that certain Achlioptas processes (much-studied local modifications of the classical mean-field growth model of Erdős and R{\'{e}}nyi) exhibit this phenomenon, undergoing a phase transition that is discontinuous in the scaling limit. We show that, in fact, all Achlioptas processes have continuous phase transitions, although related models in which the number of nodes sampled may grow with the network size can indeed exhibit explosive percolation.},
author = {Riordan, Oliver and Warnke, Lutz},
doi = {10.1126/science.1206241},
file = {:Users/wenwen/Documents/MendeleyRefs/Riordan, Warnke{\_}Science (New York, N.Y.){\_}2011.pdf:pdf},
issn = {0036-8075},
journal = {Science (80-. ).},
month = {jul},
number = {6040},
pages = {322--324},
pmid = {21764743},
title = {{Explosive Percolation Is Continuous}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21764743 http://www.sciencemag.org/cgi/doi/10.1126/science.1206241},
volume = {333},
year = {2011}
}
@article{Halverson2014,
abstract = {We review pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells. For that purpose, we review, first, recent theoretical and computational findings in polymer physics related to concentrated, topologically simple (unknotted and unlinked) chains or a system of chains. Second, we review recent experimental discoveries related to genome folding. Understanding in these fields is far from complete, but we show how looking at them in parallel sheds new light on both.},
archivePrefix = {arXiv},
arxivId = {arXiv:1311.5262v1},
author = {Halverson, Jonathan D and Smrek, Jan and Kremer, Kurt and Grosberg, Alexander Y},
doi = {10.1088/0034-4885/77/2/022601},
eprint = {arXiv:1311.5262v1},
file = {:Users/wenwen/Documents/MendeleyRefs/Halverson et al.{\_}Reports on Progress in Physics{\_}2014.pdf:pdf},
isbn = {1361-6633 (Electronic)$\backslash$r0034-4885 (Linking)},
issn = {0034-4885},
journal = {Reports Prog. Phys.},
keywords = {chromatin,dna,genome,genome folding,polymer physics,protein folding},
month = {feb},
number = {2},
pages = {022601},
pmid = {24472896},
title = {{From a melt of rings to chromosome territories: the role of topological constraints in genome folding}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24472896 http://stacks.iop.org/0034-4885/77/i=2/a=022601?key=crossref.8e4861781671e664cd77eee1dfcbde57},
volume = {77},
year = {2014}
}
@article{Craig2005,
abstract = {We further develop the ring polymer molecular dynamics (RPMD) method for calculating chemical reaction rates [I. R. Craig and D. E. Manolopoulos, J. Chem. Phys. 122, 084106 (2005)]. We begin by showing how the rate coefficient we obtained before can be calculated in a more efficient way by considering the side functions of the ring-polymer centroids, rather than averaging over the side functions of the individual ring-polymer beads. This has two distinct advantages. First, the statistics of the phase-space average over the ring-polymer coordinates and momenta are greatly improved. Second, the resulting flux-side correlation function converges to its long-time limit much more rapidly. Indeed the short-time limit of this flux-side correlation function already provides a "quantum transition state theory" approximation to the final rate coefficient. In cases where transition state recrossing effects are negligible, and the transition state dividing surface is put in the right place, the RPMD rate is therefore obtained almost instantly. We then go on to show that the long-time limit of the new flux-side correlation function, and hence the fully converged RPMD reaction rate, is rigorously independent of the choice of the transition state dividing surface. This is especially significant because the optimum dividing surface can often be very difficult to determine for reactions in complex chemical systems.},
author = {Craig, Ian R and Manolopoulos, David E},
doi = {10.1063/1.1954769},
file = {:Users/wenwen/Documents/MendeleyRefs/Craig, Manolopoulos{\_}The Journal of chemical physics{\_}2005.pdf:pdf},
issn = {0021-9606},
journal = {J. Chem. Phys.},
number = {3},
pages = {34102},
pmid = {16080725},
title = {{A refined ring polymer molecular dynamics theory of chemical reaction rates.}},
volume = {123},
year = {2005}
}
@book{Hall2003,
address = {New York, NY},
author = {Hall, Brian C.},
doi = {10.1007/978-0-387-21554-9},
file = {:Users/wenwen/Documents/MendeleyRefs/Hall{\_}Unknown{\_}2003.pdf:pdf},
number = {1},
publisher = {Springer New York},
series = {Graduate Texts in Mathematics},
title = {{Lie Groups, Lie Algebras, and Representations}},
url = {http://link.springer.com/10.1007/978-0-387-21554-9},
volume = {222},
year = {2003}
}
@article{Donges2009,
author = {Donges, J. F. and Zou, Y. and Marwan, N. and Kurths, J.},
doi = {10.1140/epjst/e2009-01098-2},
file = {:Users/wenwen/Documents/MendeleyRefs/Donges et al.{\_}The European Physical Journal Special Topics{\_}2009.pdf:pdf},
issn = {1951-6355},
journal = {Eur. Phys. J. Spec. Top.},
month = {jul},
number = {1},
pages = {157--179},
title = {{Complex networks in climate dynamics}},
url = {http://www.springerlink.com/index/10.1140/epjst/e2009-01098-2},
volume = {174},
year = {2009}
}
@article{Rouse1953,
abstract = {The necessary coordination of the motions of different parts of a polymer molecule is made the basis of a theory of the linear viscoelastic properties of dilute solutions of coiling polymers. This is accomplished by use of the concept of the submolecule, a portion of polymer chain long enough for the separation of its ends to approximate a Gaussian probability distribution. The configuration of a submolecule is specified in terms of the vector which corresponds to its end‐to‐end separation. The configuration of a molecule which contains N submolecules is described by the corresponding set of N vectors.The action of a velocity gradient disturbs the distribution of configurations of the polymer molecules away from its equilibrium form, storing free energy in the system. The coordinated thermal motions of the segments cause the configurations to drift toward their equilibrium distribution. The coordination is taken into account by the mathematical requirement that motions of the atom which joins two submolecules change the configurations of both submolecules. By means of an orthogonal transformation of coordinates, the coordination of all the motions of the parts of a molecule is resolved into a series of modes. Each mode has a characteristic relaxation time. The theory produces equations by means of which the relaxation times, the components of the complex viscosity, and the components of the complex rigidity can be calculated from the steady flow viscosities of the solution and the solvent, the molecular weight and concentration of the polymer, and the absolute temperature.Limitations of the theory may arise from the exclusion from consideration of (1) very rapid relaxation processes involving segments shorter than the submolecule and (2) the obstruction of the motion of a segment by other segments with which it happens to be in contact. Another possible cause of disagreement between the theory and experimental data is the polydispersity of any actual polymer; this factor is important because the calculated relaxation times increase rapidly with increasing molecular weight.},
author = {Rouse, P. E.},
doi = {10.1063/1.1699180},
file = {:Users/wenwen/Documents/MendeleyRefs/Rouse{\_}The Journal of Chemical Physics{\_}1953.pdf:pdf},
isbn = {00219606},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {7},
pages = {1272},
title = {{A Theory of the Linear Viscoelastic Properties of Dilute Solutions of Coiling Polymers}},
url = {http://link.aip.org/link/?JCPSA6/21/1272/1},
volume = {21},
year = {1953}
}
@article{Sadhu2015,
abstract = {Diffusion of impenetrable particles in a crowded one-dimensional channel is referred as the single file diffusion. The particles do not pass each other and the displacement of each individual particle is sub-diffusive. We analyse a simple realization of this single file diffusion problem where one dimensional Brownian point particles interact only by hard-core repulsion. We show that the large deviation function which characterizes the displacement of a tracer at large time can be computed via a mapping to a problem of non-interacting Brownian particles. We confirm recently obtained results of the one time distribution of the displacement and show how to extend them to the multi-time correlations. The probability distribution of the tracer position depends on whether we take annealed or quenched averages. In the quenched case we notice an exact relation between the distribution of the tracer and the distribution of the current. This relation is in fact much more general and would be valid for arbitrary single file diffusion. It allows in particular to get the full statistics of the tracer position for the symmetric simple exclusion process (SSEP) at density 1/2 in the quenched case.},
archivePrefix = {arXiv},
arxivId = {1505.04572},
author = {Sadhu, Tridib and Derrida, Bernard},
doi = {10.1088/1742-5468/2015/09/P09008},
eprint = {1505.04572},
file = {:Users/wenwen/Documents/MendeleyRefs/Sadhu, Derrida{\_}Unknown{\_}2015.pdf:pdf},
issn = {1742-5468},
journal = {J. Stat. Mech. Theory Exp.},
month = {sep},
number = {9},
pages = {P09008},
title = {{Large deviation function of a tracer position in single file diffusion}},
url = {http://arxiv.org/abs/1505.04572 http://dx.doi.org/10.1088/1742-5468/2015/09/P09008 http://stacks.iop.org/1742-5468/2015/i=9/a=P09008?key=crossref.f677e6aba84117781a8dec3a652e748f},
volume = {2015},
year = {2015}
}
@article{Reis2012,
author = {Reis, Saulo D. S. and Moreira, Andr{\'{e}} a. and Andrade, Jos{\'{e}} S.},
doi = {10.1103/PhysRevE.85.041112},
file = {:Users/wenwen/Documents/MendeleyRefs/Reis, Moreira, Andrade{\_}Physical Review E{\_}2012.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {apr},
number = {4},
pages = {1--5},
title = {{Nonlocal product rules for percolation}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.85.041112},
volume = {85},
year = {2012}
}
@article{Vogel2009,
abstract = {Meiotic nuclear oscillations in the fission yeast Schizosaccharomyces pombe are crucial for proper chromosome pairing and recombination. We report a mechanism of these oscillations on the basis of collective behavior of dynein motors linking the cell cortex and dynamic microtubules that extend from the spindle pole body in opposite directions. By combining quantitative live cell imaging and laser ablation with a theoretical description, we show that dynein dynamically redistributes in the cell in response to load forces, resulting in more dynein attached to the leading than to the trailing microtubules. The redistribution of motors introduces an asymmetry of motor forces pulling in opposite directions, leading to the generation of oscillations. Our work provides the first direct in vivo observation of self-organized dynamic dynein distributions, which, owing to the intrinsic motor properties, generate regular large-scale movements in the cell.},
author = {Vogel, Sven K and Pavin, Nenad and Maghelli, Nicola and J{\"{u}}licher, Frank and Toli{\'{c}}-N{\o}rrelykke, Iva M},
doi = {10.1371/journal.pbio.1000087},
editor = {Schliwa, Manfred},
file = {:Users/wenwen/Documents/MendeleyRefs/Vogel et al.{\_}PLoS Biology{\_}2009.pdf:pdf},
issn = {1545-7885},
journal = {PLoS Biol.},
keywords = {Biological,Biological Clocks,Biological Clocks: physiology,Cell Nucleus,Cell Nucleus: physiology,Chromosomes,Chromosomes: physiology,Dyneins,Dyneins: physiology,Meiosis,Meiosis: physiology,Microtubules,Microtubules: physiology,Models,Physical Phenomena,Schizosaccharomyces,Schizosaccharomyces pombe Proteins,Schizosaccharomyces pombe Proteins: physiology,Schizosaccharomyces: genetics,Schizosaccharomyces: metabolism,Spindle Apparatus,Spindle Apparatus: physiology},
month = {apr},
number = {4},
pages = {e1000087},
pmid = {19385717},
title = {{Self-Organization of Dynein Motors Generates Meiotic Nuclear Oscillations}},
url = {http://dx.plos.org/10.1371/journal.pbio.1000087},
volume = {7},
year = {2009}
}
@article{Iatsenko2014,
abstract = {Large networks of coupled oscillators appear in many branches of science, so that the kinds of phenomena they exhibit are not only of intrinsic interest but also of very wide importance. In 1975, Kuramoto proposed an analytically tractable model to describe these systems, which has since been successfully applied in many contexts and remains a subject of intensive research. Some related problems, however, remain unclarified for decades, such as the existence and properties of the oscillator glass state. Here we present a detailed analysis of a very general form of the Kuramoto model. In particular, we find the conditions when it can exhibit glassy behaviour, which represents a kind of synchronous disorder in the present case. Furthermore, we discover a new and intriguing phenomenon that we refer to as super- relaxation where the oscillators feel no interaction at all while relaxing to incoherence. Our findings offer the possibility of creating glassy states and observing super-relaxation in real systems.},
archivePrefix = {arXiv},
arxivId = {1303.4453},
author = {Iatsenko, Dymtro and McClintock, P.V.E. and Stefanovska, Aneta},
doi = {10.1038/ncomms5118},
eprint = {1303.4453},
file = {:Users/wenwen/Documents/MendeleyRefs/Iatsenko, McClintock, Stefanovska{\_}Nature Communications{\_}2014.pdf:pdf},
issn = {2041-1723},
journal = {Nat. Commun.},
keywords = {Oscillators: coupled},
month = {jun},
number = {May},
pages = {1--11},
publisher = {Nature Publishing Group},
title = {{Glassy states and super-relaxation in populations of coupled phase oscillators}},
url = {http://www.nature.com/doifinder/10.1038/ncomms5118{\%}5Cnhttp://www.sciencedaily.com/releases/2014/06/140620120339.htm http://www.nature.com/doifinder/10.1038/ncomms5118},
volume = {5},
year = {2014}
}
@book{Schadschneider2011i,
author = {Schadschneider, Andreas and Chowdhury, Debashish and Nishinari, Katsuhiro},
booktitle = {Stoch. Transp. Complex Syst.},
doi = {10.1016/B978-0-444-52853-7.00003-8},
file = {:Users/wenwen/Documents/MendeleyRefs/Schadschneider, Chowdhury, Nishinari{\_}Stochastic Transport in Complex Systems{\_}2011(2).pdf:pdf},
isbn = {9780444528537},
pages = {71--108},
title = {{Particle-Hopping Models of Transport Far from Equilibrium}},
url = {http://linkinghub.elsevier.com/retrieve/pii/B9780444528537000038},
volume = {1},
year = {2011}
}
@article{Panyukov2001,
abstract = {We study the effects of thermal fluctuations on elastic rings. Analytical expressions are derived for correlation functions of Euler angles, mean-square distance between points on the ring contour, radius of gyration, and probability distribution of writhe fluctuations. Since fluctuation amplitudes diverge in the limit of vanishing twist rigidity, twist elasticity is essential for the description of fluctuating rings. We discover a crossover from a small scale regime in which the filament behaves as a straight rod, to a large scale regime in which spontaneous curvature is important and twist rigidity affects the spatial configurations of the ring. The fluctuation-dissipation relation between correlation functions of Euler angles and response functions, is used to study the deformation of the ring by external forces. The effects of inertia and dissipation on the relaxation of temporal correlations of writhe fluctuations, are analyzed using Langevin dynamics.},
archivePrefix = {arXiv},
arxivId = {cond-mat/0011222},
author = {Panyukov, Sergey and Rabin, Yitzhak},
doi = {10.1103/PhysRevE.64.011909},
eprint = {0011222},
file = {:Users/wenwen/Documents/MendeleyRefs/Panyukov, Rabin{\_}Physical review. E, Statistical, nonlinear, and soft matter physics{\_}2001.pdf:pdf},
issn = {1063-651X},
journal = {Phys. Rev. E},
month = {jun},
number = {1},
pages = {011909},
pmid = {11461290},
primaryClass = {cond-mat},
title = {{Fluctuating elastic rings: Statics and dynamics}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.64.011909},
volume = {64},
year = {2001}
}
@book{Fernandes2004,
address = {Berlin, Heidelberg},
author = {Kawakatsu, Toshihiro},
doi = {10.1007/978-3-662-10024-0},
file = {:Users/wenwen/Documents/MendeleyRefs/Kawakatsu{\_}Unknown{\_}2004.pdf:pdf},
isbn = {978-3-642-07786-9},
publisher = {Springer Berlin Heidelberg},
series = {Advanced Texts in Physics},
title = {{Statistical Physics of Polymers}},
url = {http://link.springer.com/10.1007/978-3-662-10024-0},
year = {2004}
}
@article{Reiss2011,
abstract = {Inspired by the topological organization of the circular Escherichia coli chromosome, which is compacted by separate domains, we study a polymer architecture consisting of a central ring to which either looped or linear side chains are grafted. A shape change from a spherical to a toroidal organization takes place as soon as the inner ring becomes large enough for the attached arms to fit within its circumference. Building up a torus, the system flattens, depending on the effective bending rigidity of the chain induced by entropic repulsion of the attached loops and, to a lesser extent, linear arms. Our results suggest that the natural formation of a toroidal structure with a decreased amount of writhe induced by a specific underlying topology could be one driving force, among others, that nature exploits to ensure proper packaging of the genetic material within a rod-shaped, bacterial envelope.},
author = {Reiss, Pascal and Fritsche, Miriam and Heermann, Dieter W.},
doi = {10.1103/PhysRevE.84.051910},
file = {:Users/wenwen/Documents/MendeleyRefs/Reiss, Fritsche, Heermann{\_}Physical Review E - Statistical, Nonlinear, and Soft Matter Physics{\_}2011.pdf:pdf},
isbn = {1550-2376 (Electronic)$\backslash$r1539-3755 (Linking)},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {nov},
number = {5},
pages = {051910},
pmid = {22181447},
title = {{Looped star polymers show conformational transition from spherical to flat toroidal shapes}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.84.051910},
volume = {84},
year = {2011}
}
@article{Veestraeten2004,
author = {Veestraeten, Dirk},
file = {:Users/wenwen/Documents/MendeleyRefs/Veestraeten{\_}Computational Economics{\_}2004.pdf:pdf},
journal = {Comput. Econ.},
pages = {185--207},
title = {{The conditional probability density function for a reflected Brownian motion}},
volume = {24},
year = {2004}
}
@article{Chae2012,
author = {Chae, Huiseung and Yook, Soon-Hyung and Kim, Yup},
doi = {10.1103/PhysRevE.85.051118},
file = {:Users/wenwen/Documents/MendeleyRefs/Chae, Yook, Kim{\_}Physical Review E{\_}2012.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {may},
number = {5},
pages = {5--8},
title = {{Explosive percolation on the Bethe lattice}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.85.051118},
volume = {85},
year = {2012}
}
@article{Frisch1988,
author = {Frisch, H L and Pistoor, N and Sariban, A and Binder, K and Fesjian, S},
doi = {10.1063/1.455609},
file = {:Users/wenwen/Documents/MendeleyRefs/Frisch et al.{\_}J. Chem. Phys.{\_}1988.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {8},
pages = {5194},
title = {{Polymer chain dynamics derived from the Kramers potential: A treatment of the Rouse model with and without excluded volume interaction}},
url = {http://scitation.aip.org/content/aip/journal/jcp/89/8/10.1063/1.455609},
volume = {89},
year = {1988}
}
@article{Pincus1976,
abstract = {The renormalized elastic theory for isolated flexible polymers developed by P. G. deGennes (1976) is extended to include strong elongation with Z/RF {\textgreater}{\textgreater}1 (Z = av. end-to-end length under uniform tension, RF is the excluded vol. Flory radius of a free coil). In this regime the elastic restoring force is nonlinear in distortion and varies with Z1.5 in 3 dimensions. The consequences of this behavior are discussed in relation to coil-stretch transition in strong shear flow and to elastic neutron scattering.},
author = {Pincus, P},
doi = {10.1021/ma60051a002},
file = {:Users/wenwen/Documents/MendeleyRefs/Pincus{\_}Macromolecules{\_}1976.pdf:pdf},
isbn = {0024-9297},
issn = {0024-9297},
journal = {Macromolecules},
keywords = {Chains (coil-stretch transition of,Polymers Role: PRP (Properties) (excluded vol. of,Volume (excluded,coil stretch transition polymer,e,neutron scattering polymer stretching,of polymers,polymer stretching excluded vol,stretching in relat},
pages = {386--388},
title = {{Excluded volume effects and stretched polymer chains}},
volume = {9},
year = {1976}
}
@book{Dutcher2005,
author = {Dutcher, John R. and Marangoni, Alejandro G.},
file = {:Users/wenwen/Documents/MendeleyRefs/Dutcher, Marangoni{\_}Unknown{\_}2005.pdf:pdf},
publisher = {Marcel Dekker},
title = {{Soft Materials}},
year = {2005}
}
@article{Kim2010,
author = {Kim, Yup and Yun, Yeo-kwang and Yook, Soon-Hyung},
doi = {10.1103/PhysRevE.82.061105},
file = {:Users/wenwen/Documents/MendeleyRefs/Kim, Yun, Yook{\_}Physical Review E{\_}2010.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {dec},
number = {6},
pages = {1--4},
title = {{Explosive percolation in a nanotube-based system}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.82.061105},
volume = {82},
year = {2010}
}
@article{Chen2009,
abstract = {This paper investigates the generalized synchronization (GS) of two typical complex dynamical networks, small-world networks and scale-free networks, in terms of impulsive control strategy. By applying the auxiliary-system approach to networks, we demonstrate theoretically that for any given coupling strength, GS can take place in complex dynamical networks consisting of nonidentical systems. Particularly, for Barabasi-Albert scale-free networks, we look into the relations between GS error and topological parameter m, which denotes the number of edges linking to a new node at each time step, and find out that GS speeds up with increasing m. And for Newman-Watts small-world networks, the time needed to achieve GS decreases as the probability of adding random edges increases. We further reveal how node dynamics affects GS speed on both small-world and scale-free networks. Finally, we analyze how the development of GS depends on impulsive control gains. Some abnormal but interesting phenomena regarding the GS process are also found in simulations.},
author = {Chen, Juan and Lu, Jun-An and Wu, Xiaoqun and Zheng, Wei Xing},
doi = {10.1063/1.3268587},
file = {:Users/wenwen/Documents/MendeleyRefs/Chen et al.{\_}Chaos An Interdisciplinary Journal of Nonlinear Science{\_}2009.pdf:pdf},
issn = {10541500},
journal = {Chaos An Interdiscip. J. Nonlinear Sci.},
keywords = {Algorithms,Computer Simulation,Feedback,Nonlinear Dynamics,Oscillometry,Oscillometry: methods},
month = {dec},
number = {4},
pages = {043119},
pmid = {20059215},
title = {{Generalized synchronization of complex dynamical networks via impulsive control}},
url = {http://scitation.aip.org/content/aip/journal/chaos/19/4/10.1063/1.3268587},
volume = {19},
year = {2009}
}
@article{Pecora1990,
author = {Pecora, Louis and Carroll, Thomas},
doi = {10.1103/PhysRevLett.64.821},
file = {:Users/wenwen/Documents/MendeleyRefs/Pecora, Carroll{\_}Physical Review Letters{\_}1990.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {feb},
number = {8},
pages = {821--824},
title = {{Synchronization in chaotic systems}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.64.821},
volume = {64},
year = {1990}
}
@book{Doi1988,
author = {Doi, M. and Edwards, S. F.},
file = {:Users/wenwen/Documents/MendeleyRefs/Doi, Edwards{\_}Unknown{\_}1988.pdf:pdf},
publisher = {Oxford University Press},
title = {{The theory of polymer dynamics}},
year = {1988}
}
@article{Bishop1985,
author = {Bishop, Marvin and Michels, J. P. J.},
doi = {10.1063/1.448949},
file = {:Users/wenwen/Documents/MendeleyRefs/Bishop, Michels{\_}The Journal of Chemical Physics{\_}1985.pdf:pdf},
isbn = {0021-9606},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {2},
pages = {1059},
title = {{The shape of ring polymers}},
url = {http://link.aip.org/link/JCPSA6/v82/i2/p1059/s1{\&}Agg=doi},
volume = {82},
year = {1985}
}
@article{Cho2009,
author = {Cho, Y. S. and Kim, J. S. and Park, J. and Kahng, B. and Kim, D.},
doi = {10.1103/PhysRevLett.103.135702},
file = {:Users/wenwen/Documents/MendeleyRefs/Cho et al.{\_}Physical Review Letters{\_}2009.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {sep},
number = {13},
pages = {1--4},
title = {{Percolation Transitions in Scale-Free Networks under the Achlioptas Process}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.103.135702},
volume = {103},
year = {2009}
}
@article{Orlandini2003,
abstract = {We study numerically the tightness of prime flat knots in a model of self-attracting polymers with excluded volume. We find that these knots are localized in the high temperature swollen regime, but become delocalized in the low temperature globular phase. Precisely at the collapse transition, the knots are weakly localized. Some of our results can be interpreted in terms of the theory of polymer networks, which allows one to conjecture exact exponents for the knot length probability distributions.},
archivePrefix = {arXiv},
arxivId = {cond-mat/0211259},
author = {Orlandini, E and Stella, a L and Vanderzande, C},
doi = {10.1103/PhysRevE.68.031804},
eprint = {0211259},
file = {:Users/wenwen/Documents/MendeleyRefs/Orlandini, Stella, Vanderzande{\_}Physical review. E, Statistical, nonlinear, and soft matter physics{\_}2003.pdf:pdf},
isbn = {1539-3755 (Print)$\backslash$r1539-3755 (Linking)},
issn = {1063-651X},
journal = {Phys. Rev. E},
month = {sep},
number = {3},
pages = {031804},
pmid = {14524795},
primaryClass = {cond-mat},
title = {{Polymer $\theta$-point as a knot delocalization transition}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.68.031804},
volume = {68},
year = {2003}
}
@article{Doyle1997,
abstract = {(Received 8 December 1995 and in revised form 3 October 1996) We present a study of the rheological and optical behaviour of Kramers beadrod chains in dilute solution using stochastic computer simulations. We consider two model linear ﬂows, steady shear and uniaxial extensional ﬂow, in which we calculate the non-Newtonian Brownian and viscous stress contribution of the polymers, their birefringence and a stress-optic coeﬃcient. We have developed a computer algorithm to diﬀerentiate the Brownian from the viscous stress contributions which also avoids the order ($\delta$t)1/2 noise associated with the Brownian forces. The strain or shear rate is made dimensionless with a molecular relaxation time determined by simulated relaxation of the birefringence and stress after a strong ﬂow is applied. The charac- teristic long relaxation time obtained from the birefringence and stress are equivalent and shown to scale with N 2 where N is the number of beads in the chain. For small shear or extension rates the viscous contribution to the eﬀective viscosity is constant and scales as N. We obtain an analytic expression which explains the scaling and magnitude of this viscous contribution. In uniaxial extensional ﬂow we ﬁnd an increase in the extensional viscosity with the dimensionless ﬂow strength up to a plateau value. Moreover, the Brownian stress also reaches a plateau and we develop an analytic expression which shows that the Brownian stress in an aligned beadrod chain scales as N 3 . Using scaling arguments we show that the Brownian stress dominates in steady uniaxial extensional ﬂow until large W i, W i 0.06N 2 , where W i is the chain Weissenberg number. In shear ﬂow the viscosity decays as W i1/2 and the ﬁrst normal stress as W i4/3 at moderate W i. We demonstrate that these scalings can be understood through a quasi-steady balance of shear forces with Brownian forces. For small W i (in shear and uniaxial extensional ﬂow) and for long times (in stress relaxation) the stress-optic law is found to be valid. We show that the rheology of the beadrod chain can be qualitatively described by an equivalent FENE dumbbell for small W i.},
author = {Doyle, Patrick S. and Shaqfeh, Eric S. G. and Gast, Alice P.},
doi = {10.1017/S0022112096004302},
file = {:Users/wenwen/Documents/MendeleyRefs/Doyle, Shaqfeh, Gast{\_}Journal of Fluid Mechanics{\_}1997.pdf:pdf},
isbn = {0022-1120},
issn = {00221120},
journal = {J. Fluid Mech.},
pages = {251--291},
title = {{Dynamic simulation of freely draining flexible polymers in steady linear flows}},
volume = {334},
year = {1997}
}
@article{Aslangul1989,
author = {Aslangul, C and Pottier, N and Aslangul, C and Pottier, N and Velocity, D Saint-james},
file = {:Users/wenwen/Documents/MendeleyRefs/Aslangul et al.{\_}J. Phys. France{\_}1989.pdf:pdf},
journal = {J. Phys. Fr.},
pages = {899--921},
title = {{Velocity and diffusion coefficient of a random asymmetric one-dimensional hopping model To cite this version : one-dimensional hopping model}},
volume = {50},
year = {1989}
}
@article{Arrese-Igor2014,
author = {Arrese-Igor, S. and Alegr{\'{i}}a, a. and Colmenero, J.},
doi = {10.1103/PhysRevLett.113.078302},
file = {:Users/wenwen/Documents/MendeleyRefs/Arrese-Igor, Alegr{\'{i}}a, Colmenero{\_}Physical Review Letters{\_}2014.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
number = {August},
pages = {078302},
title = {{Polymer Chain Dynamics: Evidence of Nonexponential Mode Relaxation Using Thermally Stimulated Depolarization Current Techniques}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.113.078302},
volume = {113},
year = {2014}
}
@book{E.Gurtin2010,
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {E.Gurtin, Morton and Fried, Eliot and Anand, Lallit},
doi = {10.1017/CBO9781107415324.004},
eprint = {arXiv:1011.1669v3},
isbn = {9788578110796},
issn = {1098-6596},
keywords = {Gurtin2010},
number = {9},
pmid = {25246403},
publisher = {Cambridge University Press},
title = {{The mechanics and thermodynamics of continua}},
volume = {53},
year = {2010}
}
@article{Chou2011,
author = {Chou, T and Mallick, K and Zia, R K P},
doi = {10.1088/0034-4885/74/11/116601},
file = {:Users/wenwen/Documents/MendeleyRefs/Chou, Mallick, Zia{\_}Reports on Progress in Physics{\_}2011.pdf:pdf},
issn = {0034-4885},
journal = {Reports Prog. Phys.},
month = {nov},
number = {11},
pages = {116601},
title = {{Non-equilibrium statistical mechanics: from a paradigmatic model to biological transport}},
url = {http://stacks.iop.org/0034-4885/74/i=11/a=116601?key=crossref.30bad238da74b623c0ecee856d37854f},
volume = {74},
year = {2011}
}
@article{Zhou2005,
author = {Zhou, Haijun},
doi = {10.1103/PhysRevLett.94.217203},
file = {:Users/wenwen/Documents/MendeleyRefs/Zhou{\_}Physical Review Letters{\_}2005.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {jun},
number = {21},
pages = {217203},
title = {{Long-Range Frustration in a Spin-Glass Model of the Vertex-Cover Problem}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.94.217203},
volume = {94},
year = {2005}
}
@article{Geyer2011,
abstract = {Background: Brownian Dynamics (BD) is a coarse-grained implicit-solvent simulation method that is routinely used to investigate binary protein association dynamics, but due to its efficiency in handling large simulation volumes and particle numbers it is well suited to also describe many-protein scenarios as they often occur in biological cells. Results: Here we introduce our "brownmove" simulation package which was designed to handle many-particle problems with varying particle numbers and allows for a very flexible definition of rigid and flexible protein and polymer models. Both a Brownian and a Langevin dynamics (LD) propagation scheme can be used and hydrodynamic interactions are treated efficiently with our recently introduced TEA-HI ansatz [Geyer, Winter, JCP 130 (2009) 114905]. With simulations of constrained polymers and flexible models of spherical proteins we demonstrate that it is crucial to include hydrodynamics when multi-bead models are used in BD or LD simulations. Only then both the translational and the rotational diffusion coefficients and the timescales of the internal dynamics can be reproduced correctly. In the third example project we show how constant density boundary conditions [Geyer et al, JCP 120 (2004) 4573] can be used to set up a non-equilibrium simulation of diffusional transport across an array of fixed obstacles. Finally, we demonstrate how the agglomeration dynamics of multiple particles with attractive patches can be analysed conveniently with the help of a dynamic interaction network. Conclusions: Combining BD and LD propagation, fast hydrodynamics, a flexible protein model, and interfaces for "open" simulation settings, our freely available "brownmove" simulation package constitutes a new platform for coarse-grained many-particle simulations of biologically relevant diffusion and transport processes.},
author = {Geyer, Tiham{\'{e}}r},
doi = {10.1186/2046-1682-4-7},
file = {:Users/wenwen/Documents/MendeleyRefs/Geyer{\_}BMC biophysics{\_}2011.pdf:pdf},
issn = {2046-1682},
journal = {BMC Biophys.},
number = {1},
pages = {7},
pmid = {21596002},
publisher = {BioMed Central Ltd},
title = {{Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package.}},
url = {http://www.biomedcentral.com/2046-1682/4/7},
volume = {4},
year = {2011}
}
@article{Helfand1979,
abstract = {Rigid constraints fix the value of some degrees of freedom, such as bond lengths or angles, in the allowed motion of a system. "Flexible constraints" is a term which describes the limit as the amplitudes of vibration in these coordinates are made to approach zero by infinitely increasing appropriate force constants. The statistical properties of flexibly and rigidly constrained systems are, in general, different. How the difference arises is illustrated in terms of a simple model. A suggestion of Fixman on how to compensate for the difference in terms of an effective potential is rederived for the statics of the model. This paper examines dynamical problems more deeply. The quantum mechanical case is also discussed.},
author = {Helfand, Eugene},
doi = {10.1063/1.438314},
file = {:Users/wenwen/Documents/MendeleyRefs/Reiss, Frisch, Lebowitz{\_}The Journal of Chemical Physics{\_}1959.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {12},
pages = {5000},
title = {{Flexible vs rigid constraints in statistical mechanics}},
url = {http://dx.doi.org/10.1063/1.438314{\%}5Cnhttp://scitation.aip.org/content/aip/journal/jcp/71/12?ver=pdfcov http://scitation.aip.org/content/aip/journal/jcp/31/2/10.1063/1.1730361 http://scitation.aip.org/content/aip/journal/jcp/71/12/10.1063/1.438314},
volume = {71},
year = {1979}
}
@techreport{Cooray2008,
abstract = {Synchronization phenomena in large populations of interacting units are the subject of intense research efforts in physical, biological, chemical and social systems. A successful approach to the problem of synchronization is to model each member of the population as a phase oscillator. Synchronization in the most representative model of coupled phase oscillators, the Kuramoto model, is extensively analyzed in this review. We present a rigorous mathematical treatment, specific numerical methods, and many variations and extensions of the original model that have appeared in the last years. Relevant applications of the model to understanding synchronization in different physical problems are also included.},
author = {Cooray, Gerald},
file = {:Users/wenwen/Documents/MendeleyRefs/Cooray{\_}Unknown{\_}2008.pdf:pdf},
number = {September},
title = {{The Kuramoto Model}},
url = {http://www.mendeley.com/research/kuramoto-model/},
year = {2008}
}
@article{Golinelli2006,
abstract = {The asymmetric simple exclusion process (ASEP) plays the role of a paradigm in non-equilibrium statistical mechanics. We review exact results for the ASEP obtained by the Bethe ansatz and put emphasis on the algebraic properties of this model. The Bethe equations for the eigenvalues of the Markov matrix of the ASEP are derived from the algebraic Bethe ansatz. Using these equations we explain how to calculate the spectral gap of the model and how global spectral properties such as the existence of multiplets can be predicted. An extension of the Bethe ansatz leads to an analytic expression for the large deviation function of the current in the ASEP that satisfies the Gallavotti-Cohen relation. Finally, we describe some variants of the ASEP that are also solvable by the Bethe ansatz.},
archivePrefix = {arXiv},
arxivId = {cond-mat/0611701},
author = {Golinelli, Olivier and Mallick, Kirone},
doi = {10.1088/0305-4470/39/41/S03},
eprint = {0611701},
file = {:Users/wenwen/Documents/MendeleyRefs/Golinelli, Mallick{\_}Journal of Physics A Mathematical and General{\_}2006.pdf:pdf},
isbn = {0305-4470},
issn = {0305-4470},
journal = {J. Phys. A. Math. Gen.},
keywords = {asep,bethe ansatz,integrable models,large deviations},
month = {oct},
number = {41},
pages = {12679--12705},
primaryClass = {cond-mat},
title = {{The asymmetric simple exclusion process: an integrable model for non-equilibrium statistical mechanics}},
url = {http://stacks.iop.org/0305-4470/39/i=41/a=S03?key=crossref.8aa95a4bce6fcab88cb3aa858056dea2},
volume = {39},
year = {2006}
}
@article{Hanney2006,
author = {Hanney, T and Stinchcombe, R B},
doi = {10.1088/0305-4470/39/47/001},
file = {:Users/wenwen/Documents/MendeleyRefs/Hanney, Stinchcombe{\_}Journal of Physics A Mathematical and General{\_}2006.pdf:pdf},
issn = {0305-4470},
journal = {J. Phys. A. Math. Gen.},
month = {nov},
number = {47},
pages = {14535--14544},
title = {{Real-space renormalization group approach to driven diffusive systems}},
url = {http://stacks.iop.org/0305-4470/39/i=47/a=001?key=crossref.6fd2c67e1d7d3bddca09e4639eefabbe},
volume = {39},
year = {2006}
}
@article{Witz2008,
abstract = {The conformation of circular DNA molecules of various lengths adsorbed in a 2D conformation on a mica surface is studied. The results confirm the conjecture that the critical exponent nu is topologically invariant and equal to the self-avoiding walk value (in the present case nu=3/4), and that the topology and dimensionality of the system strongly influence the crossover between the rigid regime and the self-avoiding regime at a scale L approximately 7l{\{}p{\}}. Additionally, the bond correlation function scales with the molecular length L as predicted. For molecular lengths L{\textless}or=5l{\{}p{\}}, circular DNA behaves like a stiff molecule with an approximately elliptic shape.},
archivePrefix = {arXiv},
arxivId = {0806.0514},
author = {Witz, Guillaume and Rechendorff, Kristian and Adamcik, Jozef and Dietler, Giovanni},
doi = {10.1103/PhysRevLett.101.148103},
eprint = {0806.0514},
file = {:Users/wenwen/Documents/MendeleyRefs/Witz et al.{\_}Physical Review Letters{\_}2008.pdf:pdf},
isbn = {0031-9007},
issn = {00319007},
journal = {Phys. Rev. Lett.},
number = {14},
pages = {3--6},
pmid = {18851579},
title = {{Conformation of circular DNA in two dimensions}},
volume = {101},
year = {2008}
}
@article{Rabin1985a,
author = {Rabin, Y. and Henyey, F. S. and Pathria, R. K.},
doi = {10.1103/PhysRevLett.55.201},
file = {:Users/wenwen/Documents/MendeleyRefs/Rabin, Henyey, Pathria{\_}Physical Review Letters{\_}1985.pdf:pdf},
issn = {00319007},
journal = {Phys. Rev. Lett.},
number = {2},
pages = {201--203},
title = {{Scaling behavior of dilute polymer solutions in elongational flows}},
volume = {55},
year = {1985}
}
@article{Shang2009,
author = {Shang, Yun and Chen, Maoyin and Kurths, J{\"{u}}rgen},
doi = {10.1103/PhysRevE.80.027201},
file = {:Users/wenwen/Documents/MendeleyRefs/Shang, Chen, Kurths{\_}Physical Review E{\_}2009.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {aug},
number = {2},
pages = {2--5},
title = {{Generalized synchronization of complex networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.80.027201},
volume = {80},
year = {2009}
}
@book{Driscoll2016,
author = {Driscoll, Michael},
file = {:Users/wenwen/Documents/MendeleyRefs/Driscoll{\_}Unknown{\_}2016.pdf:pdf},
pages = {1--244},
title = {{Python 201: Intermediate Python}},
url = {http://leanpub.com/python201},
year = {2016}
}
@article{Swope1991,
abstract = {Abstract 10.1002/jcc.540130508.abs We have derived alternative expressions for computing the energies and forces associated with angle bending and torsional energy terms commonly used in molecular mechanics and molecular dynamics computer programs. Our expressions address the problems of singularities that are intrinsic in popular angle energy functions and that occur from other chain rule derivations of force expressions. Most chain rule derivations of expressions for Cartesian forces due to angle energies make use of relations such as $\backslash$documentclass{\{}article{\}}$\backslash$pagestyle{\{}empty{\}}$\backslash$begin{\{}document{\}}{\$}{\$} $\backslash$frac{\{}{\{}$\backslash$partial E{\}}{\}}{\{}{\{}$\backslash$partial x{\}}{\}} = $\backslash$frac{\{}{\{}$\backslash$partial E{\}}{\}}{\{}{\{}$\backslash$partial $\backslash$phi {\}}{\}}$\backslash$frac{\{}{\{}$\backslash$partial $\backslash$phi {\}}{\}}{\{}{\{}$\backslash$partial $\backslash$cos $\backslash$phi {\}}{\}}$\backslash$frac{\{}{\{}$\backslash$partial $\backslash$cos $\backslash$phi {\}}{\}}{\{}{\{}$\backslash$partial x{\}}{\}} {\$}{\$}$\backslash$end{\{}document{\}} where ϕ is a bond or torsion angle, E(ϕ) is energy, and ∂/∂x represents a derivative with respect to some Cartesian coordinate. This expression leads to singularities from the middle term, −1/sin ϕ, when ϕ is 0 or $\pi$. This is a problem that prevents the use of torsional energy expressions that have phase angles, ϕ°, other than 0 or $\pi$, such as in E(ϕ) = $\kappa$[1 + cos(nϕ − phsi;°)]. Our derivations make use of a different, but equivalent, form of the chain rule: $\backslash$documentclass{\{}article{\}}$\backslash$pagestyle{\{}empty{\}}$\backslash$begin{\{}document{\}}{\$}{\$} $\backslash$frac{\{}{\{}$\backslash$partial E{\}}{\}}{\{}{\{}$\backslash$partial x{\}}{\}} = $\backslash$frac{\{}{\{}$\backslash$partial E{\}}{\}}{\{}{\{}$\backslash$partial $\backslash$phi {\}}{\}}$\backslash$frac{\{}{\{}$\backslash$partial $\backslash$phi {\}}{\}}{\{}{\{}$\backslash$partial x{\}}{\}} {\$}{\$}$\backslash$end{\{}document{\}} This form still possesses singularities for the bond angle forces since the last factor is undefined when ϕ is 0 or $\pi$. However, the alternate form may be used to great advantage for the torsional angle forces where no such problem arises. The new expressions are necessary if one desires the use of torsional energy expressions with general phase angles. Even for energy expressions in common use, i.e., with phase angles of 0 or $\pi$, our force expressions are as computationally efficient as the standard ones. The new expressions are applicable to all molecular simulations that employ restrained, or phase-shifted, torsional angle energy expressions.},
author = {Swope, William C and Ferguson, David M},
doi = {10.1002/jcc.540130508},
file = {:Users/wenwen/Documents/MendeleyRefs/Swope, Ferguson{\_}Journal of Computational Chemistry{\_}1992.pdf:pdf},
isbn = {1096-987X},
issn = {0192-8651},
journal = {J. Comput. Chem.},
month = {jun},
number = {5},
pages = {585--594},
title = {{Alternative expressions for energies and forces due to angle bending and torsional energy}},
url = {http://doi.wiley.com/10.1002/jcc.540130508},
volume = {13},
year = {1992}
}
@article{Wang2001,
author = {Wang, Xiaoling and Chatterjee, Avik P.},
doi = {10.1021/ma001241u},
file = {:Users/wenwen/Documents/MendeleyRefs/Wang, Chatterjee{\_}Macromolecules{\_}2001.pdf:pdf},
issn = {0024-9297},
journal = {Macromolecules},
month = {feb},
number = {4},
pages = {1118--1121},
title = {{Chain Orientation and Extension in Steady Shear Flow}},
url = {http://pubs.acs.org/doi/abs/10.1021/ma001241u},
volume = {34},
year = {2001}
}
@article{Coutinho2013,
abstract = {We study the Kuramoto model on complex networks, in which natural frequencies of phase oscillators and the vertex degrees are correlated. Using the annealed network approximation and numerical simulations we explore a special case in which the natural frequencies of the oscillators and the vertex degrees are linearly coupled. We find that in uncorrelated scale-free networks with the degree distribution exponent {\$}2 {\textless} \backslashgamma {\textless} 3{\$}, the model undergoes a first-order phase transition, while the transition becomes of the second order at {\$}\backslashgamma{\textgreater}3{\$}. If {\$}\backslashgamma=3{\$}, the phase synchronization emerges as a result of a hybrid phase transition that combines an abrupt emergence of synchronization, as in first-order phase transitions, and a critical singularity, as in second-order phase transitions. The critical fluctuations manifest themselves as avalanches in synchronization process. Comparing our analytical calculations with numerical simulations for Erd$\backslash$H{\{}o{\}}s--R$\backslash$'{\{}e{\}}nyi and scale-free networks, we demonstrate that the annealed network approach is accurate if the the mean degree and size of the network are sufficiently large. We also study analytically and numerically the Kuramoto model on star graphs and find that if the natural frequency of the central oscillator is sufficiently large in comparison to the average frequency of its neighbors, then synchronization emerges as a result of a first-order phase transition. This shows that oscillators sitting at hubs in a network may generate a discontinuous synchronization transition.},
archivePrefix = {arXiv},
arxivId = {1211.5690},
author = {Coutinho, B C and Goltsev, A V and Dorogovtsev, S N and Mendes, J F F},
doi = {10.1103/PhysRevE.87.032106},
eprint = {1211.5690},
file = {:Users/wenwen/Documents/MendeleyRefs/Coutinho et al.{\_}Physical Review E{\_}2013.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {mar},
number = {3},
pages = {032106},
title = {{Kuramoto model with frequency-degree correlations

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repo_name: huangww/chromosome