text:
$hat{\{}l{\}}{\^{}}2){\^{}}{\{}-1/2{\}}). The dominant physical processes occurring in these separate short, long and intermediate time regimes are identified.},
author = {Grassia, P. and Hinch, EJ J.},
doi = {10.1017/S0022112096001474},
file = {:Users/wenwen/Documents/MendeleyRefs/Grassia, Hinch{\_}Journal of Fluid Mechanics{\_}1996.pdf:pdf},
issn = {0022-1120},
journal = {J. Fluid Mech.},
month = {feb},
number = {-1},
pages = {255},
title = {{Computer simulations of polymer chain relaxation via Brownian motion}},
url = {http://www.journals.cambridge.org/abstract{\_}S0022112096001474},
volume = {308},
year = {1996}
}
@article{DSouza2010,
author = {D'Souza, Raissa M. and Mitzenmacher, Michael},
doi = {10.1103/PhysRevLett.104.195702},
file = {:Users/wenwen/Documents/MendeleyRefs/D'Souza, Mitzenmacher{\_}Physical Review Letters{\_}2010.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {may},
number = {19},
pages = {195702},
title = {{Local Cluster Aggregation Models of Explosive Percolation}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.104.195702},
volume = {104},
year = {2010}
}
@article{Cohen2000,
abstract = {A common property of many large networks, including the Internet, is that the connectivity of the various nodes follows a scale-free power-law distribution, P(k) = ck(-alpha). We study the stability of such networks with respect to crashes, such as random removal of sites. Our approach, based on percolation theory, leads to a general condition for the critical fraction of nodes, p(c), that needs to be removed before the network disintegrates. We show analytically and numerically that for alpha{\textless}/=3 the transition never takes place, unless the network is finite. In the special case of the physical structure of the Internet (alpha approximately 2.5), we find that it is impressively robust, with p(c){\textgreater}0.99.},
author = {Cohen, R and Erez, K and Ben-Avraham, D and Havlin, S},
file = {:Users/wenwen/Documents/MendeleyRefs/Cohen et al.{\_}Physical Review Letters{\_}2000.pdf:pdf},
issn = {1079-7114},
journal = {Phys. Rev. Lett.},
month = {nov},
number = {21},
pages = {4626--8},
pmid = {11082612},
title = {{Resilience of the internet to random breakdowns}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11082612},
volume = {85},
year = {2000}
}
@article{Ziff2010,
author = {Ziff, Robert},
doi = {10.1103/PhysRevE.82.051105},
file = {:Users/wenwen/Documents/MendeleyRefs/Ziff{\_}Physical Review E{\_}2010.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {nov},
number = {5},
pages = {1--8},
title = {{Scaling behavior of explosive percolation on the square lattice}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.82.051105},
volume = {82},
year = {2010}
}
@article{Schtz1997,
abstract = {Using the Bethe ansatz, we obtain the exact solution of the master equation for the totally asymmetric exclusion process on an infinite one-dimensional lattice. We derive explicit expressions for the conditional probabilities P(x{\_}1, ... ,x{\_}N;t|y{\_}1, ... ,y{\_}N;0) of finding N particles on lattice sites x{\_}1, ... ,x{\_}N at time t with initial occupation y{\_}1, ... ,y{\_}N at time t=0.},
archivePrefix = {arXiv},
arxivId = {cond-mat/9701019},
author = {Sch{\"{u}}tz, Gunter M.},
doi = {10.1007/BF02508478},
eprint = {9701019},
file = {:Users/wenwen/Documents/MendeleyRefs/Sch{\"{u}}tz{\_}Journal of Statistical Physics{\_}1997.pdf:pdf},
issn = {0022-4715},
journal = {J. Stat. Phys.},
keywords = {1,asymmetric exclusion process,bethe ansatz,driven lattice gases and,i n t r,o d u c,particularly the one-dimensional asymmetric,t i o n},
month = {jul},
number = {1-2},
pages = {427--445},
primaryClass = {cond-mat},
title = {{Exact solution of the master equation for the asymmetric exclusion process}},
url = {http://arxiv.org/abs/cond-mat/9701019{\%}5Cnhttp://dx.doi.org/10.1007/bf02508478 http://link.springer.com/10.1007/BF02508478},
volume = {88},
year = {1997}
}
@article{Gao2011,
author = {Gao, Jianxi and Buldyrev, Sergey and Havlin, Shlomo and Stanley, H.},
doi = {10.1103/PhysRevLett.107.195701},
file = {:Users/wenwen/Documents/MendeleyRefs/Gao et al.{\_}Physical Review Letters{\_}2011.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {nov},
number = {19},
pages = {1--5},
title = {{Robustness of a Network of Networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.107.195701},
volume = {107},
year = {2011}
}
@book{Chandler1987,
author = {{David Chandler}},
file = {:Users/wenwen/Documents/MendeleyRefs/David Chandler{\_}Unknown{\_}1987.pdf:pdf},
publisher = {Oxford University Press},
title = {{Introduction to modern statistical mechanics.}},
volume = {1},
year = {1987}
}
@article{Aranson2007,
abstract = {The dynamics of polymer collapse with a fixed distance between endpoints is studied analytically and numerically by the Nos{\&}{\#}233;-Hoover algorithm. We find that at the pearling stage of the collapse the number of pearls decays as t[?]1/2 leading to anomalously long collapse time. To understand the effect of Stokes drag we reduced the problem of long-polymer-chain collapse to the one-dimensional diffusion-limited coalescence of particles with the mass-dependent mobility. In this case the number of pearls decays slower, as t[?]3/7.},
author = {Aranson, I. S and Tsimring, L. S},
doi = {10.1209/epl/i2003-00450-8},
file = {:Users/wenwen/Documents/MendeleyRefs/Aranson, Tsimring{\_}Europhysics Letters (EPL){\_}2007.pdf:pdf},
issn = {0295-5075},
journal = {Europhys. Lett.},
pages = {848--854},
title = {{Dynamics of the constrained polymer collapse}},
volume = {62},
year = {2007}
}
@article{Zhang2014,
abstract = {Spatial patterning is a ubiquitous feature of biological systems. Meiotic crossovers provide an interesting example, defined by the classic phenomenon of crossover interference. Here we identify a molecular pathway for interference by analysing crossover patterns in budding yeast. Topoisomerase II plays a central role, thus identifying a new function for this critical molecule. SUMOylation (of topoisomerase II and axis component Red1) and ubiquitin-mediated removal of SUMOylated proteins are also required. The findings support the hypothesis that crossover interference involves accumulation, relief and redistribution of mechanical stress along the protein/DNA meshwork of meiotic chromosome axes, with topoisomerase II required to adjust spatial relationships among DNA segments.},
author = {Zhang, Liangran and Wang, Shunxin and Yin, Shen and Hong, Soogil and Kim, Keun P. and Kleckner, Nancy},
doi = {10.1038/nature13442},
file = {:Users/wenwen/Documents/MendeleyRefs/Zhang et al.{\_}Nature{\_}2014.pdf:pdf},
isbn = {1476-4687},
issn = {0028-0836},
journal = {Nature},
number = {7511},
pages = {551--556},
pmid = {25043020},
publisher = {Nature Publishing Group},
title = {{Topoisomerase II mediates meiotic crossover interference}},
url = {http://www.nature.com/doifinder/10.1038/nature13442},
volume = {511},
year = {2014}
}
@article{Morino2011,
author = {Morino, Kai and Tanaka, Gouhei and Aihara, Kazuyuki},
doi = {10.1103/PhysRevE.83.056208},
file = {:Users/wenwen/Documents/MendeleyRefs/Morino, Tanaka, Aihara{\_}Physical Review E{\_}2011.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {may},
number = {5},
pages = {056208},
title = {{Robustness of multilayer oscillator networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.83.056208},
volume = {83},
year = {2011}
}
@article{Perkins1995a,
abstract = {The stretching of single, tethered DNA molecules by a flow was directly visualized with fluorescence microscopy. Molecules ranging in length (L) from 22 to 84 micrometers were held stationary against the flow by the optical trapping of a latex microsphere attached to one end. The fractional extension x/L is a universal function of eta vL(0.54+/-0.05), where eta and v are the viscosity and velocity of the flow, respectively. This relation shows that the DNA is not ''free-draining'' (that is, hydrodynamic coupling within the chain is not negligible) even near full extension (similar to 80 percent). This function has the same form over a lone range as the fractional extension versus force applied at the ends of a worm-like chain. For small deformations ({\textless}30 percent of full extension), the extension increases with velocity as x similar to v(0.70+/-0.08). The relative size of fluctuations in extension decreases as sigma(x)/x congruent to 0.42 exp(-4.9 x/L). Video images of the fluctuating chain have a cone-like envelope and show as sharp increase in intensity at the free end.},
author = {Perkins, Thomas and Smith, Douglas and Larson, Ronald and Chu, Steven},
doi = {10.1126/science.7701345},
file = {:Users/wenwen/Documents/MendeleyRefs/Perkins et al.{\_}Science{\_}1995(2).pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Perkins et al.{\_}Science{\_}1995.pdf:pdf},
isbn = {0036-8075 FIELD Publ},
issn = {0036-8075},
journal = {Science (80-. ).},
month = {apr},
number = {5207},
pages = {83--87},
pmid = {7701345},
title = {{Stretching of a single tethered polymer in a uniform flow}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.7701345},
volume = {268},
year = {1995}
}
@article{Ding2011,
author = {Ding, DaQiao},
doi = {10.1007/s11434-011-4800-9},
file = {:Users/wenwen/Documents/MendeleyRefs/Ding{\_}Chinese Science Bulletin{\_}2011.pdf:pdf},
issn = {1001-6538},
journal = {Chinese Sci. Bull.},
month = {nov},
number = {33},
pages = {3500--3503},
title = {{A rush hour towards sexual reproduction: The chromosome dynamics during meiosis}},
url = {http://link.springer.com/10.1007/s11434-011-4800-9},
volume = {56},
year = {2011}
}
@article{Varghese2013,
archivePrefix = {arXiv},
arxivId = {arXiv:1405.0594v1},
author = {Varghese, Anoop and Vemparala, Satyavani and Rajesh, R.},
doi = {10.1103/PhysRevE.88.022134},
eprint = {arXiv:1405.0594v1},
file = {:Users/wenwen/Documents/MendeleyRefs/Varghese, Vemparala, Rajesh{\_}Physical Review E{\_}2013.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
number = {2},
pages = {022134},
title = {{Force fluctuations in stretching a tethered polymer}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.88.022134},
volume = {88},
year = {2013}
}
@article{Burchard1980,
abstract = {The influence of hydrodynamic pre-averaging on the first cumulant $\Gamma$ of the dynamic structure factor of Gaussian ring molecules has been calculated. Similar to star-branched macromolecules, the relative error Image introduced by the pre-average approximation exhibits a maximum at intermediate Image sin Image which does not ocour for the corresponding linear chain. This maximum is related to the increase of segment density by ring formation. The static structure factor also shows a maximum in the Kratky plot (q2left angle bracketS2right-pointing angle bracketP(q) against q2) and has an asymptote at large q which is half that of linear chains. Furthermore, the S:R ratio (Image ), which can be determined from combined integrated and quasi-elastic scattering, proves to be significantly lower than for the linear chain. Thus, ring molecules and open chains can easily be distinguished from combined integrated and quasi-elastic light scattering, without comparison with linear chains as has been necessary hitherto. The accuracy will be particularly high with instruments which allow the recording of both types of scattering measurements simultaneously.},
author = {Burchard, W and Schmidt, M},
doi = {10.1016/0032-3861(80)90289-X},
file = {:Users/wenwen/Documents/MendeleyRefs/Burchard, Schmidt{\_}Polymer{\_}1980.pdf:pdf},
issn = {00323861},
journal = {Polymer (Guildf).},
number = {7},
pages = {745--749},
title = {{Static and dynamic structure factors calculated for flexible ring macromolecules}},
volume = {21},
year = {1980}
}
@article{Simonsen2008,
author = {Simonsen, Ingve and Buzna, Lubos and Peters, Karsten and Bornholdt, Stefan and Helbing, Dirk},
doi = {10.1103/PhysRevLett.100.218701},
file = {:Users/wenwen/Documents/MendeleyRefs/Simonsen et al.{\_}Physical Review Letters{\_}2008.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {may},
number = {21},
pages = {1--4},
title = {{Transient Dynamics Increasing Network Vulnerability to Cascading Failures}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.100.218701},
volume = {100},
year = {2008}
}
@article{Brummitt2012,
abstract = {Understanding how interdependence among systems affects cascading behaviors is increasingly important across many fields of science and engineering. Inspired by cascades of load shedding in coupled electric grids and other infrastructure, we study the Bak-Tang-Wiesenfeld sandpile model on modular random graphs and on graphs based on actual, interdependent power grids. Starting from two isolated networks, adding some connectivity between them is beneficial, for it suppresses the largest cascades in each system. Too much interconnectivity, however, becomes detrimental for two reasons. First, interconnections open pathways for neighboring networks to inflict large cascades. Second, as in real infrastructure, new interconnections increase capacity and total possible load, which fuels even larger cascades. Using a multitype branching process and simulations we show these effects and estimate the optimal level of interconnectivity that balances their trade-offs. Such equilibria could allow, for example, power grid owners to minimize the largest cascades in their grid. We also show that asymmetric capacity among interdependent networks affects the optimal connectivity that each prefers and may lead to an arms race for greater capacity. Our multitype branching process framework provides building blocks for better prediction of cascading processes on modular random graphs and on multitype networks in general.},
author = {Brummitt, Charles D and D'Souza, Raissa M and Leicht, E a},
doi = {10.1073/pnas.1110586109},
file = {:Users/wenwen/Documents/MendeleyRefs/Brummitt, D'Souza, Leicht{\_}Proceedings of the National Academy of Sciences{\_}2012.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
month = {mar},
number = {12},
pages = {E680--E689},
pmid = {22355144},
title = {{Suppressing cascades of load in interdependent networks}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1110586109},
volume = {109},
year = {2012}
}
@article{Mohan2007,
author = {Mohan, Aruna and Doyle, Patrick S},
doi = {10.1021/ma070050p},
file = {:Users/wenwen/Documents/MendeleyRefs/Mohan, Doyle{\_}Macromolecules{\_}2007.pdf:pdf},
issn = {0024-9297},
journal = {Macromolecules},
month = {jun},
number = {12},
pages = {4301--4312},
title = {{Unraveling of a Tethered Polymer Chain in Uniform Solvent Flow}},
url = {papers2://publication/uuid/EA4038ED-69E3-40BD-A779-CE1BBDD22E1D http://pubs.acs.org/doi/abs/10.1021/ma070050p},
volume = {40},
year = {2007}
}
@article{Do2012,
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{Zaburdaev2015,
abstract = {Random walk is a fundamental concept with applications ranging from quantum physics to econometrics. Remarkably, one specific model of random walks appears to be ubiquitous across many fields as a tool to analyze transport phenomena in which the dispersal process is faster than dictated by Brownian diffusion. The L{\'{e}}vy-walk model combines two key features, the ability to generate anomalously fast diffusion and a finite velocity of a random walker. Recent results in optics, Hamiltonian chaos, cold atom dynamics, biophysics, and behavioral science demonstrate that this particular type of random walk provides significant insight into complex transport phenomena. This review gives a self-consistent introduction to L{\'{e}}vy walks, surveys their existing applications, including latest advances, and outlines further perspectives.},
archivePrefix = {arXiv},
arxivId = {arXiv:1410.5100},
author = {Zaburdaev, V. and Denisov, S. and Klafter, J.},
doi = {10.1103/RevModPhys.87.483},
eprint = {arXiv:1410.5100},
file = {:Users/wenwen/Documents/MendeleyRefs/Zaburdaev, Denisov, Klafter{\_}Reviews of Modern Physics{\_}2015.pdf:pdf},
issn = {0034-6861},
journal = {Rev. Mod. Phys.},
month = {jun},
number = {2},
pages = {483--530},
title = {{L{\'{e}}vy walks}},
url = {http://link.aps.org/doi/10.1103/RevModPhys.87.483},
volume = {87},
year = {2015}
}
@article{Barkai2010,
abstract = {We study the diffusion of tagged hard-core interacting Brownian point particles under the influence of an external force field in one dimension. Using the Jepsen line we map this many-particle problem onto a single particle one. We obtain general equations for the distribution and the mean-square displacement {\textless}(x{\_}T){\^{}}2{\textgreater} of the tagged center particle valid for rather general external force fields and initial conditions. The case of symmetric distribution of initial conditions around the initial position of the tagged particle on x=0 and symmetric potential fields V(x)=V(-x) yields zero drift {\textless}x{\_}T{\textgreater}=0 and is investigated in detail. We find {\textless}(x{\_}T){\^{}}2{\textless}=R(1-R)/2Nr2 where 2N is the (large) number of particles in the system. R is a single particle reflection coeffi- cient, i.e., the probability that a particle free of collisions starts on x0{\textgreater}0 and remains in x{\textgreater}0 while r is the probability density of noninteracting particles on the origin. We show that this equation is related to the mathematical theory of order statistics and it can be used to find {\textless}(x{\_}T){\^{}}2{\textgreater} even when the motion between collision events is not Brownian (e.g., it might be ballistic or anomalous diffusion). As an example we derive the Percus relation for non-Gaussian diffusion. A wide range of physical behaviors emerge which are very different than the classical single file subdiffusion {\textless}(x{\_}T){\^{}}2{\textgreater}{\~{}}t{\^{}}{\{}1/2{\}} found for uniformly distributed particles in an infinite space and in the absence of force fields},
archivePrefix = {arXiv},
arxivId = {arXiv:1001.0732v1},
author = {Barkai, E and Silbey, R},
doi = {10.1103/PhysRevE.81.041129},
eprint = {arXiv:1001.0732v1},
file = {:Users/wenwen/Documents/MendeleyRefs/Barkai, Silbey{\_}Physical Review E - Statistical, Nonlinear, and Soft Matter Physics{\_}2010.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {apr},
number = {4},
pages = {041129},
pmid = {20481699},
title = {{Diffusion of tagged particle in an exclusion process}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.81.041129},
volume = {81},
year = {2010}
}
@article{Qian2010,
author = {Qian, Yu and Huang, Xiaodong and Hu, Gang and Liao, Xuhong},
doi = {10.1103/PhysRevE.81.036101},
file = {:Users/wenwen/Documents/MendeleyRefs/Qian et al.{\_}Physical Review E{\_}2010.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {mar},
number = {3},
pages = {1--8},
title = {{Structure and control of self-sustained target waves in excitable small-world networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.81.036101},
volume = {81},
year = {2010}
}
@article{Doyle1998,
abstract = {We present a study of the rheology and optical properties during the start-up of uniaxial extensional and shear flow for freely-draining, Kramers bead-rod chains using Brownian dynamics simulations. The viscous and elastic contributions to the polymer stress are unambiguously determined via methods developed in our previous publication [1]. The elastic contribution to the polymer stress is much larger than the viscous contribution beyond a time of 5.3?1 /N2 where N is the number of beads in the chain and ?1 is the longest relaxation time of the chain. For small Wi (at arbitrary strains) and for small strains (at arbitrary Wi) the stress-optic law is found to be valid. The stress-optic coefficients based on the shear stress and first normal stress difference are equal for all Wi (even when the stress-optic law is not valid) suggesting the stress-optic coefficient is in general a scalar quantity rather than its most general form as a fourth order tensor. We show that a multimode FENE-PM or Rouse model describes the rheology of the bead-rod chains at small strains, while the FENE dumbbell is an accurate model at larger strains. We compare the FENE-PM and FENE model to experimental extensional stress data of dilute polystyrene solutions and find that a multimode FENE-PM with a Zimm relaxation spectrum describes the data well at small strains while a FENE dumbbell with a conformation dependent drag is in quantitative agreement at larger strains.},
author = {Doyle, Patrick S. and Shaqfeh, Eric S. G.},
doi = {10.1016/S0377-0257(97)00112-2},
file = {:Users/wenwen/Documents/MendeleyRefs/Doyle, Shaqfeh{\_}Journal of Non-Newtonian Fluid Mechanics{\_}1998.pdf:pdf},
isbn = {0377-0257},
issn = {03770257},
journal = {J. Nonnewton. Fluid Mech.},
keywords = {bead-rod chains,extensional flow,shear flow},
number = {1-3},
pages = {43--78},
title = {{Dynamic simulation of freely-draining, flexible bead-rod chains: Start-up of extensional and shear flow}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0377025797001122},
volume = {76},
year = {1998}
}
@article{Faddeev1996,
abstract = {I study the technique of Algebraic Bethe Ansatz for solving integrable models and show how it works in detail on the simplest example of spin 1/2 XXX magnetic chain. Several other models are treated more superficially, only the specific details are given. Several parameters, appearing in these generalizations: spin {\$}s{\$}, anisotropy parameter {\$}\backslashga{\$}, shift {\$}\backslashom{\$} in the alternating chain, allow to include in our treatment most known examples of soliton theory, including relativistic model of Quantum Field Theory.},
archivePrefix = {arXiv},
arxivId = {hep-th/9605187},
author = {Faddeev, L. D.},
eprint = {9605187},
file = {:Users/wenwen/Documents/MendeleyRefs/Faddeev{\_}Arxiv{\_}1996.pdf:pdf},
journal = {Arxiv},
month = {may},
pages = {59},
primaryClass = {hep-th},
title = {{How Algebraic Bethe Ansatz works for integrable model}},
url = {http://arxiv.org/abs/hep-th/9605187},
year = {1996}
}
@book{Lawler2010,
address = {Cambridge},
author = {Lawler, Gregory F and Limic, Vlada},
doi = {10.1017/CBO9780511750854},
file = {:Users/wenwen/Documents/MendeleyRefs/Lawler, Limic{\_}Unknown{\_}2010.pdf:pdf},
isbn = {9780511750854},
publisher = {Cambridge University Press},
title = {{Random Walk: A Modern Introduction}},
url = {http://ebooks.cambridge.org/ref/id/CBO9780511750854},
year = {2010}
}
@article{Schlitz1999,
abstract = {We present a brief tutorial introduction into the quantum Hamiltonian formalism for stochastic many-body systems which are defined in terms of a master equation. These models describe interacting classical particle systems where particles hop on a lattice and may undergo reactions. In the quantum Hamiltonian formalism the generator of the stochastic process is reformulated as the Hamiltonian of some generalized quantum spin system. This correspondance is par-ticularly useful if the quantum Hamiltonian associated to the process has continuous global symmetries or if it is integrable, i.e . has an infinite set of conservation laws . This is demon-strated in the case of the one-dimensional exclusion process for which we derive various duality relations and some explicit results on the dynamics of shocks. The time evolution of many systems encountered in nature is most appropriately described by stochastic laws rather than by deterministic equations as in Newto-nian mechanics for classical physics. The randomness of the time evolution leads to the description of the process in terms of random variables and to the con-nection of the theory with measurements in terms of expectation values. Rather than predicting the actual value of some observable in a given measurement, one calculates e.g. the mean value of the observable as obtained by repeating the same measurement many times, starting from the same initial state. Despite the ran-domness of the motion , complex systems of many interacting particles [1, 2, 3, 4] may exhibit very interesting patterns of collective behaviour, including various types of phase transitions, development of spatially stable shocks, or coarsening phenomena. The purpose of these lecture notes is to review a framework for the study of such systems which uses ideas and techniques borrowed from many-body quantum mechanics. There are various approaches to a stochastic description [5] such as the Lan-gevin or Fokker-Plank equations. Here we adopt the strategy of describing the system by a probability distribution, the time evolution of which is governed by a master equation. Solving the master equation, which is a first-order linear dif-ferential equation in the time variable, yields the probability of finding any given state the system may take given that it started from some initial state. One can 1 Research partially supported by Capes / Probal 047/97 and Fapesp 98 / 04422-5 .},
author = {Schlitz, Gunter M},
file = {:Users/wenwen/Documents/MendeleyRefs/Schlitz{\_}Resenhas IME-USP{\_}1999.pdf:pdf},
journal = {Resenhas IME-USP},
number = {1},
pages = {17--43},
title = {{Stochastic many-body systems and quantum spin chains}},
volume = {4},
year = {1999}
}
@article{Yamashita2005,
abstract = {Formin proteins are key regulators of eukaryotic actin filament assembly and elongation, and many species possess multiple formin isoforms. A nomenclature system based on fundamental features would be desirable, to aid the rapid identification and characterization of novel formins. In this article, we attempt to systematize the formin family by performing phylogenetic analyses of the formin homology 2 (FH2) domain, an independently folding region common to all formins, which alone can influence actin dynamics. Through database searches, we identify 101 FH2 domains from 26 eukaryotic species, including 15 in mice. Sequence alignments reveal a highly conserved yeast-specific insert in the "knob loop" region of the FH2 domain, with unknown functional consequences. Phylogenetic analysis using minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML) algorithms strongly supports the existence of seven metazoan groups. Yeast FH2 domains segregate from all other eukaryotes, including metazoans, other fungi, plants, and protists. Sequence comparisons of non-FH2 regions support relationships between three metazoan groups (Dia, DAAM, and FRL) and examine previously identified coiled-coil and Diaphanous auto-regulatory domain sequences. This analysis allows for a formin nomenclature system based on sequence relationships, as well as suggesting strategies for the determination of biochemical and cellular activities of these proteins.},
author = {Yamashita, Akira},
doi = {10.1091/mbc.E04-10-0859},
file = {:Users/wenwen/Documents/MendeleyRefs/Yamashita{\_}Molecular Biology of the Cell{\_}2005.pdf:pdf},
isbn = {1059-1524 (Print)},
issn = {1059-1524},
journal = {Mol. Biol. Cell},
month = {jan},
number = {3},
pages = {1378--1395},
pmid = {15509653},
title = {{The Roles of Fission Yeast Ase1 in Mitotic Cell Division, Meiotic Nuclear Oscillation, and Cytokinesis Checkpoint Signaling}},
url = {http://www.molbiolcell.org/cgi/doi/10.1091/mbc.E04-10-0859},
volume = {16},
year = {2005}
}
@article{Patriciu2004,
abstract = {It is well known that mass-metric tensor determinants det(G(s)) influence the equilibrium statistics and the rates of conformational transitions for polymers with constrained bond lengths and bond angles. It is now standard practice to include a Fixman-style compensating potential of the form U(c)(q(s)) proportional, variant(-k(B)T/2)ln[det(G(s))] as part of algorithms for torsional space molecular dynamics. This elegant strategy helps eliminate unwarranted biases that arise due to the imposition of holonomic constraints. However, the precise nature and extent of variation of det(G(s)) and hence ln[det(G(s))] with chain conformation and chain length has never been quantified. This type of analysis is crucial for understanding the nature of the conformational bias that the introduction of a Fixman potential aims to eliminate. Additionally, a detailed analysis of the conformational dependence of det(G(s)) will help resolve ambiguities regarding suggestions for incorporating terms related to det(G(s)) in the design of move sets in torsional space Monte Carlo simulations. In this work, we present results from a systematic study of the variation of det(G(s)) for a serial polymer with fixed bond lengths and bond angles as a function of chain conformation and chain length. This analysis requires an algorithm designed for rapid computation of det(G(s)) which simultaneously allows for a physical/geometric interpretation of the conformational dependence of det(G(s)). Consequently, we provide a detailed discussion of our adaptation of an O(n) algorithm from the robotics literature, which leads to simple recursion relations for direct evaluation of det(G(s)). Our analysis of the conformational dependence of det(G(s)) yields the following insights. (1) det(G(s)) is maximized for spatial conformers and minimized for planar conformations. (2) Previous work suggests that it is logical to expect that the conformational dependence of det(G(s)) becomes more pronounced with increase in chain length. Confirming this expectation, we provide systematic quantification of the nature of this dependency and show that the difference in det(G(s)) between spatial and planar conformers, i.e., between the maxima and minima of det(G(s)) grows systematically with chain length. Finally, we provide a brief discussion of implications of our analysis for the design of move sets in Monte Carlo simulations.},
author = {Patriciu, Alexandru and Chirikjian, Gregory S and Pappu, Rohit V},
doi = {10.1063/1.1821492},
file = {:Users/wenwen/Documents/MendeleyRefs/Patriciu, Chirikjian, Pappu{\_}The Journal of chemical physics{\_}2004.pdf:pdf},
issn = {0021-9606},
journal = {J. Chem. Phys.},
month = {dec},
number = {24},
pages = {12708--20},
pmid = {15606297},
title = {{Analysis of the conformational dependence of mass-metric tensor determinants in serial polymers with constraints.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15606297},
volume = {121},
year = {2004}
}
@article{Adjarei1995a,
author = {Adjarei, A and Brochardt-Wyart, F and de Gennes, P G},
file = {:Users/wenwen/Documents/MendeleyRefs/Adjarei, Brochardt-Wyart, de Gennes{\_}J. Phys. II France{\_}1995.pdf:pdf},
journal = {J. Phys. II Fr.},
pages = {491},
title = {{Drag on a Tethered Chain in a Polymer Melt.}},
volume = {5},
year = {1995}
}
@article{Altaner2012,
author = {Altaner, B. and Grosskinsky, S. and Herminghaus, S. and Katth{\"{a}}n, L. and Timme, M. and Vollmer, J.},
doi = {10.1103/PhysRevE.85.041133},
file = {:Users/wenwen/Documents/MendeleyRefs/Altaner et al.{\_}Physical Review E{\_}2012.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {apr},
number = {4},
pages = {1--8},
title = {{Network representations of nonequilibrium steady states: Cycle decompositions, symmetries, and dominant paths}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.85.041133},
volume = {85},
year = {2012}
}
@article{Villeneuve2001a,
abstract = {Sexual reproduction predominates among eukaryotic organisms on our planet. While debate continues over why this should be so, burgeoning genomic and functional information now allows us to begin to think reasonably about some of the events that may have occurred to make sex possible in the first place.},
author = {Villeneuve, a M and Hillers, K J},
doi = {10.1016/S0092-8674(01)00500-1},
file = {:Users/wenwen/Documents/MendeleyRefs/Villeneuve, Hillers{\_}Cell{\_}2001.pdf:pdf},
isbn = {0092-8674 (Print)$\backslash$n0092-8674 (Linking)},
issn = {0092-8674},
journal = {Cell},
number = {6},
pages = {647--650},
pmid = {11572770},
title = {{Whence meiosis?}},
volume = {106},
year = {2001}
}
@book{Feynman2010a,
author = {Feynman, Richard},
file = {:Users/wenwen/Documents/MendeleyRefs/Feynman{\_}Unknown{\_}2010.pdf:pdf},
isbn = {9780465079988},
publisher = {California Institute of Technology},
title = {{The Feynman Lectures on Physics; Vol. II}},
year = {2010}
}
@article{Saadat2014,
abstract = {Excluded volume and hydrodynamic interactions play a central role in macromolecular dynamics under equilibrium and non-equilibrium settings. The high computational cost of incorporating the influence of hydrodynamic interaction in meso-scale simulation of polymer dynamics has motivated much research on development of high fidelity and cost efficient techniques. Among them, the Chebyshev polynomial based techniques and the Krylov subspace methods are most promising. To this end, in this study we have developed a series of semi-implicit predictor-corrector Brownian dynamics algorithms for bead-spring chain micromechanical model of polymers that utilizes either the Chebyshev or the Krylov framework. The efficiency and fidelity of these new algorithms in equilibrium (radius of gyration and diffusivity) and non-equilibrium conditions (transient planar extensional flow) are demonstrated with particular emphasis on the new enhancements of the Chebyshev polynomial and the Krylov subspace methods. In turn, the algorithm with the highest efficiency and fidelity, namely, the Krylov subspace method, is used to simulate dilute solutions of high molecular weight polystyrene in uniaxial extensional flow. Finally, it is demonstrated that the bead-spring Brownian dynamics simulation with appropriate inclusion of excluded volume and hydrodynamic interactions can quantitatively predict the observed extensional hardening of polystyrene dilute solutions over a broad molecular weight range.},
author = {Saadat, Amir and Khomami, Bamin},
doi = {10.1063/1.4873999},
file = {:Users/wenwen/Documents/MendeleyRefs/Saadat, Khomami{\_}Journal of Chemical Physics{\_}2014.pdf:pdf},
isbn = {1089-7690 (Electronic)$\backslash$r0021-9606 (Linking)},
issn = {00219606},
journal = {J. Chem. Phys.},
pmid = {24832302},
title = {{Computationally efficient algorithms for incorporation of hydrodynamic and excluded volume interactions in Brownian dynamics simulations: A comparative study of the Krylov subspace and Chebyshev based techniques}},
volume = {140},
year = {2014}
}
@article{Gomez-Gardenes2011,
author = {G{\'{o}}mez-Garde{\~{n}}es, Jes{\'{u}}s and G{\'{o}}mez, Sergio and Arenas, Alex and Moreno, Yamir},
doi = {10.1103/PhysRevLett.106.128701},
file = {:Users/wenwen/Documents/MendeleyRefs/G{\'{o}}mez-Garde{\~{n}}es et al.{\_}Physical Review Letters{\_}2011.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {mar},
number = {12},
pages = {128701},
title = {{Explosive Synchronization Transitions in Scale-Free Networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.106.128701},
volume = {106},
year = {2011}
}
@article{Callaway2000,
abstract = {Recent work on the internet, social networks, and the power grid has addressed the resilience of these networks to either random or targeted deletion of network nodes. Such deletions include, for example, the failure of internet routers or power transmission lines. Percolation models on random graphs provide a simple representation of this process, but have typically been limited to graphs with Poisson degree distribution at their vertices. Such graphs are quite unlike real world networks, which often possess power-law or other highly skewed degree distributions. In this paper we study percolation on graphs with completely general degree distribution, giving exact solutions for a variety of cases, including site percolation, bond percolation, and models in which occupation probabilities depend on vertex degree. We discuss the application of our theory to the understanding of network resilience.},
archivePrefix = {arXiv},
arxivId = {cond-mat/0007300},
author = {Callaway, Duncan S and Newman, M E J and Strogatz, Steven H and Watts, Duncan J},
doi = {10.1103/PhysRevLett.85.5468},
eprint = {0007300},
file = {:Users/wenwen/Documents/MendeleyRefs/Callaway et al.{\_}Physical Review Letters{\_}2000.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {dec},
number = {25},
pages = {5468--5471},
primaryClass = {cond-mat},
title = {{Network Robustness and Fragility: Percolation on Random Graphs}},
url = {http://arxiv.org/abs/cond-mat/0007300 http://link.aps.org/doi/10.1103/PhysRevLett.85.5468},
volume = {85},
year = {2000}
}
@article{Grassberger2011,
author = {Grassberger, Peter and Christensen, Claire and Bizhani, Golnoosh and Son, Seung-Woo and Paczuski, Maya},
doi = {10.1103/PhysRevLett.106.225701},
file = {:Users/wenwen/Documents/MendeleyRefs/Grassberger et al.{\_}Physical Review Letters{\_}2011.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {may},
number = {22},
pages = {1--4},
title = {{Explosive Percolation is Continuous, but with Unusual Finite Size Behavior}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.106.225701},
volume = {106},
year = {2011}
}
@article{Acebron2005,
author = {Acebr{\'{o}}n, Juan JA and Bonilla, L. LL and {P{\'{e}}rez Vicente}, Conrad and Ritort, F{\'{e}}lix and Spigler, Renato and Vicente, CJP},
doi = {10.1103/RevModPhys.77.137},
file = {:Users/wenwen/Documents/MendeleyRefs/Acebr{\'{o}}n et al.{\_}Reviews of Modern Physics{\_}2005.pdf:pdf},
issn = {0034-6861},
journal = {Rev. Mod. Phys.},
month = {apr},
number = {January},
pages = {137--185},
title = {{The Kuramoto model: A simple paradigm for synchronization phenomena}},
url = {http://rmp.aps.org/abstract/RMP/v77/i1/p137{\_}1 http://link.aps.org/doi/10.1103/RevModPhys.77.137},
volume = {77},
year = {2005}
}
@article{Brochard-Wyart1995,
abstract = {Under a constant flow velocity V, a flexible polymer (in steady state) is expected to display three types of conformation: 1) unperturbed at low V; 2) ''trumpet'': partly stretched, with certain scaling laws (F. Brochard-Wyart, Europhys. Lett., 23 (1993) 105) at intermediate V; 3) ''stem and flower'' with a completely stretched portion (the stem) at high V. We discuss regime 3) here. We also consider transients where (starting from regime 3)) the flow is abruptly suppressed and the resulting decay law for the stem is of the Rouse type.},
author = {Brochard-Wyart, F.},
doi = {10.1209/0295-5075/30/7/002},
file = {:Users/wenwen/Documents/MendeleyRefs/Brochard-Wyart{\_}Europhys. Lett{\_}1995.pdf:pdf},
isbn = {0295-5075},
issn = {0295-5075},
journal = {Europhys. Lett.},
month = {jun},
number = {7},
pages = {387--392},
title = {{Polymer Chains Under Strong Flows: Stems and Flowers}},
url = {http://stacks.iop.org/0295-5075/30/i=7/a=002?key=crossref.66f60541055fe8e9518a47ca6207ff89},
volume = {30},
year = {1995}
}
@article{Black-schaffer2012,
author = {Black-schaffer, David},
doi = {10.1016/B978-0-12-405894-1.00002-4},
file = {:Users/wenwen/Documents/MendeleyRefs/Black-schaffer{\_}Unknown{\_}2012.pdf:pdf},
isbn = {0415183723},
pages = {1--14},
title = {{Introduction to OpenCL}},
year = {2012}
}
@article{Li2000a,
abstract = {Using Brownian dynamics simulations, we predict the deformation of a polymer coil in dilute solution and compare the results to direct measurements for DNA molecules and for polystyrene. For DNA, optical microscopy measurements of Smith and Chu yield measurements of the average projected length of the molecule onto the flow direction as a function of shear rate, while for dilute polystyrene solutions, light scattering experiments yield the root-mean-square radius of gyration. Both measurements of deformation are obtained from the simulations using input parameters required to match the molecular characteristics of both the DNA and the polystyrene solutions used in the experiments. We find that while the agreement between the simulations and the measurements of coil deformation for DNA is excellent, for polystyrene the measured deformation is much less than predicted.},
author = {Li, Lei and Larson, Ronald G},
doi = {10.1021/ma991090z},
file = {:Users/wenwen/Documents/MendeleyRefs/Li, Larson{\_}Macromolecules{\_}2000.pdf:pdf},
isbn = {0024-9297$\backslash$r1520-5835},
issn = {00249297},
journal = {Macromolecules},
number = {4},
pages = {1411--1415},
title = {{Comparison of Brownian dynamics simulations with microscopic and light-scattering measurements of polymer deformation under flow}},
volume = {33},
year = {2000}
}
@book{Revuz2004,
abstract = {{\{}From the reviews: "This is a magnificent book! Its purpose is to describe in considerable detail a variety of techniques used by probabilists in the investigation of problems concerning Brownian motion. The great strength of Revuz and Yor is the enormous variety of calculations carried out both in the main text and also (by implication) in the exercises. ... This is THE book for a capable graduate student starting out on research in probability: the effect of working through it is as if the authors are sitting beside one, enthusiastically explaining the theory, presenting further developments as exercises, and throwing out challenging remarks about areas awaiting further research..." Bull.L.M.S. 24, 4 (1992) Since the first edition in 1991, an impressive variety of advances has been made in relation to the material of this book, and these are reflected in the successive editions.{\}}},
author = {Revuz, Daniel and Yor, Marc},
booktitle = {Stochastics An Int. J. Probab. Stoch. Process.},
doi = {10.1007/978-3-662-06400-9},
isbn = {3540643257},
title = {{Continuous Martingales and Brownian Motion (Grundlehren der mathematischen Wissenschaften)}},
url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20{\&}path=ASIN/3540643257{\%}5Cnhttp://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21{\&}path=ASIN/3540643257{\%}5Cnhttp://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21{\&}path=ASIN/35},
volume = {42},
year = {2004}
}
@article{Coriell1967,
author = {Coriell, S R and Jackson, J L},
doi = {10.1063/1.1705344},
file = {:Users/wenwen/Documents/MendeleyRefs/Coriell, Jackson{\_}Journal of Mathematical Physics{\_}1967.pdf:pdf},
issn = {00222488},
journal = {J. Math. Phys.},
number = {1967},
pages = {1276},
title = {{Probability Distribution of the Radius of Gyration of a Flexible Polymer}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=276958018238633604related:hFbPptnz1wMJ},
volume = {8},
year = {1967}
}
@article{Marko2009,
abstract = {The Gauss linking number ?Ca? of two flexible polymer rings which are tethered to one another is investi- gated. For ideal random walks, mean linking-squared varies with the square root of polymer length while for self-avoiding walks, linking-squared increases logarithmically with polymer length. The free-energy cost of linking of polymer rings is therefore strongly dependent on degree of self-avoidance, i.e., on intersegment excluded volume. Scaling arguments and numerical data are used to determine the free-energy cost of fixed linking number in both the fluctuation and large-Ca regimes; for ideal random walks, for ?Ca??N1/4, the free energy of catenation is found to grow ??Ca/N1/4?4/3.When excluded volume interactions between segments are present, the free energy rapidly approaches a linear dependence on Gauss linking ?dF/dCa?3.7kBT?, sugges- tive of a novel “catenation condensation” effect. These results are used to show that condensation of long entangled polymers along their length, so as to increase excluded volume while decreasing number of statis- tical segments, can drive disentanglement if a mechanism is present to permit topology change. For chromo- somal DNA molecules, lengthwise condensation is therefore an effective means to bias topoisomerases to eliminate catenations between replicated chromatids. The results for mean-square catenation are also used to provide a simple approximate estimate for the “knotting length,” or number of segments required to have a knot along a single circular polymer, explaining why the knotting length ranges from ?300 for an ideal random walk to 106 for a self-avoiding walk.},
author = {Marko, John F},
doi = {10.1103/PhysRevE.79.051905},
file = {:Users/wenwen/Documents/MendeleyRefs/Marko{\_}Physical Review E{\_}2009.pdf:pdf},
isbn = {1539-3755 (Print)$\backslash$r1539-3755 (Linking)},
issn = {1539-3755},
journal = {Phys. Rev. E},
pages = {051905 (1--16)},
pmid = {19518478},
title = {{Linking topology of tethered polymer rings with applications to chromosome segregation and estimation of the knotting length}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.79.051905},
volume = {79},
year = {2009}
}
@article{Simon2009,
abstract = {The asymmetric simple exclusion process with open boundaries, which is a very simple model of out-of-equilibrium statistical physics, is known to be integrable. In particular, its spectrum can be described in terms of Bethe roots. The large deviation function of the current can be obtained as well by diagonalizing a modified transition matrix, that is still integrable: the spectrum of this new matrix can be also described in terms of Bethe roots for special values of the parameters. However, due to the algebraic framework used to write the Bethe equations in the previous works, the nature of the excitations and the full structure of the eigenvectors were still unknown. This paper explains why the eigenvectors of the modified transition matrix are physically relevant, gives an explicit expression for the eigenvectors and applies it to the study of atypical currents. It also shows how the coordinate Bethe Ansatz developped for the excitations leads to a simple derivation of the Bethe equations and of the validity conditions of this Ansatz. All the results obtained by de Gier and Essler are recovered and the approach gives a physical interpretation of the exceptional points The overlap of this approach with other tools such as the matrix Ansatz is also discussed. The method that is presented here may be not specific to the asymmetric exclusion process and may be applied to other models with open boundaries to find similar exceptional points.},
archivePrefix = {arXiv},
arxivId = {0903.4968},
author = {Simon, Damien},
doi = {10.1088/1742-5468/2009/07/P07017},
eprint = {0903.4968},
file = {:Users/wenwen/Documents/MendeleyRefs/Simon{\_}Journal of Statistical Mechanics Theory and Experiment{\_}2009.pdf:pdf},
issn = {1742-5468},
journal = {J. Stat. Mech. Theory Exp.},
keywords = {00,09,1742-5468,28,30,bethe ansatz,c 2009 iop publishing,current fluctuations,exact,ltd and sissa,p07017,quantum integrability,results,solvable lattice models},
number = {07},
pages = {P07017},
title = {{Construction of a Coordinate Bethe Ansatz for the asymmetric simple exclusion process with open boundaries}},
url = {http://arxiv.org/abs/0903.4968},
volume = {2009},
year = {2009}
}
@article{Ding2004,
abstract = {Pairing of homologous chromosomes is important for homologous recombination and correct chromosome segregation during meiosis. It has been proposed that telomere clustering, nuclear oscillation, and recombination during meiotic prophase facilitate homologous chromosome pairing in fission yeast. Here we examined the contributions of these chromosomal events to homologous chromosome pairing, by directly observing the dynamics of chromosomal loci in living cells of fission yeast. Homologous loci exhibited a dynamic process of association and dissociation during the time course of meiotic prophase. Lack of nuclear oscillation reduced association frequency for both centromeric and arm regions of the chromosome. Lack of telomere clustering or recombination reduced association frequency at arm regions, but not significantly at centromeric regions. Our results indicate that homologous chromosomes are spatially aligned by oscillation of telomere-bundled chromosomes and physically linked by recombination at chromosome arm regions; this recombination is not required for association of homologous centromeres. ?? 2004 by Cell Press.},
author = {Ding, Da-Qiao and Yamamoto, Ayumu and Haraguchi, Tokuko and Hiraoka, Yasushi},
doi = {10.1016/S1534-5807(04)00059-0},
file = {:Users/wenwen/Documents/MendeleyRefs/Ding et al.{\_}Developmental Cell{\_}2004.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Ding et al.{\_}Developmental Cell{\_}2004.pdf:pdf},
journal = {Dev. Cell},
month = {mar},
number = {3},
pages = {329--341},
title = {{Dynamics of Homologous Chromosome Pairing during Meiotic Prophase in Fission Yeast}},
url = {http://www.sciencedirect.com/science/article/pii/S1534580704000590 http://linkinghub.elsevier.com/retrieve/pii/S1534580704000590},
volume = {6},
year = {2004}
}
@article{Newman2011,
author = {Newman, M. E. J.},
doi = {10.1038/nphys2162},
file = {:Users/wenwen/Documents/MendeleyRefs/Newman{\_}Nature Physics{\_}2011.pdf:pdf},
issn = {1745-2473},
journal = {Nat. Phys.},
month = {dec},
number = {1},
pages = {25--31},
publisher = {Nature Publishing Group},
title = {{Communities, modules and large-scale structure in networks}},
url = {http://www.nature.com/doifinder/10.1038/nphys2162},
volume = {8},
year = {2011}
}
@article{Lacasa2008,
abstract = {In this work we present a simple and fast computational method, the visibility algorithm, that converts a time series into a graph. The constructed graph inherits several properties of the series in its structure. Thereby, periodic series convert into regular graphs, and random series do so into random graphs. Moreover, fractal series convert into scale-free networks, enhancing the fact that power law degree distributions are related to fractality, something highly discussed recently. Some remarkable examples and analytical tools are outlined to test the method's reliability. Many different measures, recently developed in the complex network theory, could by means of this new approach characterize time series from a new point of view.},
author = {Lacasa, Lucas and Luque, B. and Ballesteros, Fernando and Luque, Jordi and Nuno, J. C.},
doi = {10.1073/pnas.0709247105},
file = {:Users/wenwen/Documents/MendeleyRefs/Lacasa et al.{\_}Proceedings of the National Academy of Sciences of the United States of America{\_}2008.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
month = {apr},
number = {13},
pages = {4972--4975},
pmid = {18362361},
title = {{From time series to complex networks: The visibility graph}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2278201{\&}tool=pmcentrez{\&}rendertype=abstract http://www.pnas.org/cgi/doi/10.1073/pnas.0709247105},
volume = {105},
year = {2008}
}
@article{Tead1992,
abstract = {S. F. ' and EJ  Department of Materials Science and Engineering, Bard Hall, Cornell University, Ithaca, New York 14853-1501 G. Hadziioannou },
author = {Tead, Sf and Kramer, Ej},
doi = {10.1021/ma00041a017},
file = {:Users/wenwen/Documents/MendeleyRefs/Tead, Kramer{\_}Macromolecules{\_}1992.pdf:pdf},
isbn = {0024929719},
issn = {0024-9297},
journal = {Macromolecules},
pages = {3942--3947},
title = {{Polymer topology and diffusion: A comparison of diffusion in linear and cyclic macromolecules}},
url = {http://pubs.acs.org/doi/abs/10.1021/ma00041a017},
volume = {25},
year = {1992}
}
@article{Daqing2011,
author = {Daqing, Li and Kosmidis, Kosmas and Bunde, Armin and Havlin, Shlomo},
doi = {10.1038/nphys1932},
file = {:Users/wenwen/Documents/MendeleyRefs/Daqing et al.{\_}Nature Physics{\_}2011.pdf:pdf},
issn = {1745-2473},
journal = {Nat. Phys.},
month = {feb},
number = {6},
pages = {481--484},
publisher = {Nature Publishing Group},
title = {{Dimension of spatially embedded networks}},
url = {http://www.nature.com/doifinder/10.1038/nphys1932},
volume = {7},
year = {2011}
}
@book{Liggett2005,
author = {Liggett, Thomas M.},
file = {:Users/wenwen/Documents/MendeleyRefs/Liggett{\_}Unknown{\_}2005.pdf:pdf},
publisher = {Springer Berlin Heidelberg},
title = {{Interacting Particle System}},
year = {2005}
}
@article{Sugiyama2003,
author = {Sugiyama, Hiroyuki and Escalona, Jos{\'{e}} L. and Shabana, Ahmed A.},
file = {:Users/wenwen/Documents/MendeleyRefs/Sugiyama, Escalona, Shabana{\_}Nonlinear Dynamics{\_}2003.pdf:pdf},
journal = {Nonlinear Dyn.},
number = {2},
pages = {167--195},
title = {{Formulation of three-dimensional joint constraints using the absolute nodal coordinates}},
volume = {31},
year = {2003}
}
@article{Corteel2007,
abstract = {The partially asymmetric exclusion process (PASEP) is an important model from statistical mechanics which describes a system of interacting particles hopping left and right on a one-dimensional lattice of n sites. It is partially asymmetric in the sense that the probability of hopping left is q times the probability of hopping right. Additionally, particles may enter from the left with probability ?? and exit from the right with probability ??. In this paper we prove a close connection between the PASEP and the combinatorics of permutation tableaux. (These tableaux come indirectly from the totally nonnegative part of the Grassmannian, via work of Postnikov, and were studied in a paper of Steingr??msson and the second author.) Namely, we prove that in the long time limit, the probability that the PASEP is in a particular configuration ?? is essentially the generating function for permutation tableaux of shape ?? (??) enumerated according to three statistics. The proof of this result uses a result of Derrida, Evans, Hakim, and Pasquier on the matrix ansatz for the PASEP model. As an application, we prove some monotonicity results for the PASEP. We also derive some enumerative consequences for permutations enumerated according to various statistics such as weak excedence set, descent set, crossings, and occurrences of generalized patterns. ?? 2006 Elsevier Inc. All rights reserved.},
archivePrefix = {arXiv},
arxivId = {math/0602109},
author = {Corteel, Sylvie and Williams, Lauren K.},
doi = {10.1016/j.aam.2006.08.002},
eprint = {0602109},
file = {:Users/wenwen/Documents/MendeleyRefs/Corteel, Williams{\_}Advances in Applied Mathematics{\_}2007.pdf:pdf},
issn = {01968858},
journal = {Adv. Appl. Math.},
keywords = {Asymmetric exclusion process,Eulerian numbers,Generalized patterns,Matrix ansatz,Permutation tableaux},
number = {3},
pages = {293--310},
primaryClass = {math},
title = {{Tableaux combinatorics for the asymmetric exclusion process}},
volume = {39},
year = {2007}
}
@article{Cates1986,
abstract = {We present some conjectures concerning the equilibrium statistics and dynamics of ring polymers. We argue that unconcatenated ring polymers in the melt may have statistics intermediate between those of collapsed and Gaussian chains. An extremely crude (Flory-like) treatment suggests that the radius R of such a ring scales with its polymerization index N as R N 2/5. In contrast, a ring in a melt of long linear chains (of the same chemical species) should be swollen. Moreover, rings of one chemical species (A) can be compatible with linear chains of another (B), even when linear chains of A and B are not compatible. Rings in a network of fixed obstacles are also discussed. A simple analysis of their dynamics shows that the diffusion constant D of such a ring (in three dimensions) scales with its polymerization index N as D N-2. This prediction is confirmed by computer simulations. Finally, we consider a knotted ring formed irreversibly in a theta solvent, and argue that, under appropriate formation conditions, such a ring may remain Gaussian when placed in a good solvent.},
author = {Cates, M.E. and Deutsch, J.M.},
doi = {10.1051/jphys:0198600470120212100},
file = {:Users/wenwen/Documents/MendeleyRefs/Cates, Deutsch{\_}Journal de Physique{\_}1986.pdf:pdf},
issn = {0302-0738},
journal = {J. Phys.},
number = {12},
pages = {2121--2128},
title = {{Conjectures on the statistics of ring polymers}},
url = {http://www.edpsciences.org/10.1051/jphys:0198600470120212100},
volume = {47},
year = {1986}
}
@article{Dorogovtsev2008,
author = {Dorogovtsev, S. and Goltsev, a. and Mendes, J.},
doi = {10.1103/RevModPhys.80.1275},
file = {:Users/wenwen/Documents/MendeleyRefs/Dorogovtsev, Goltsev, Mendes{\_}Reviews of Modern Physics{\_}2008.pdf:pdf},
issn = {0034-6861},
journal = {Rev. Mod. Phys.},
month = {oct},
number = {4},
pages = {1275--1335},
title = {{Critical phenomena in complex networks}},
url = {http://link.aps.org/doi/10.1103/RevModPhys.80.1275},
volume = {80},
year = {2008}
}
@article{Cho2010a,
author = {Cho, Y. and Kim, S.-W. and Noh, J. and Kahng, B. and Kim, D.},
doi = {10.1103/PhysRevE.82.042102},
file = {:Users/wenwen/Documents/MendeleyRefs/Cho et al.{\_}Physical Review E{\_}2010.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {oct},
number = {4},
pages = {2--5},
title = {{Finite-size scaling theory for explosive percolation transitions}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.82.042102},
volume = {82},
year = {2010}
}
@article{Bohman2009,
author = {Bohman, Tom},
doi = {10.1126/science.1171297},
file = {:Users/wenwen/Documents/MendeleyRefs/Bohman{\_}Science (New York, N.Y.){\_}2009.pdf:pdf},
issn = {0036-8075},
journal = {Science (80-. ).},
month = {mar},
number = {5920},
pages = {1438--1439},
pmid = {19286543},
title = {{MATHEMATICS: Emergence of Connectivity in Networks}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1171297},
volume = {323},
year = {2009}
}
@article{Albert2000,
abstract = {Many complex systems display a surprising degree of tolerance against errors. For example, relatively simple organisms grow, persist and reproduce despite drastic pharmaceutical or environmental interventions, an error tolerance attributed to the robustness of the underlying metabolic network. Complex communication networks display a surprising degree of robustness: although key components regularly malfunction, local failures rarely lead to the loss of the global information-carrying ability of the network. The stability of these and other complex systems is often attributed to the redundant wiring of the functional web defined by the systems' components. Here we demonstrate that error tolerance is not shared by all redundant systems: it is displayed only by a class of inhomogeneously wired networks, called scale-free networks, which include the World-Wide Web, the Internet, social networks and cells. We find that such networks display an unexpected degree of robustness, the ability of their nodes to communicate being unaffected even by unrealistically high failure rates. However, error tolerance comes at a high price in that these networks are extremely vulnerable to attacks (that is, to the selection and removal of a few nodes that play a vital role in maintaining the network's connectivity). Such error tolerance and attack vulnerability are generic properties of communication networks.},
author = {Albert, R and Jeong, H and Barabasi, Al},
doi = {10.1038/35019019},
file = {:Users/wenwen/Documents/MendeleyRefs/Albert, Jeong, Barabasi{\_}Nature{\_}2000.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
month = {jul},
number = {6794},
pages = {378--82},
pmid = {10935628},
title = {{Error and attack tolerance of complex networks}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10935628},
volume = {406},
year = {2000}
}
@article{Osmanovic2012,
abstract = {Polymer-coated pores play a crucial role in nucleo-cytoplasmic transport and in a number of biomimetic and nanotechnological applications. Here we present Monte Carlo and Density Functional Theory approaches to identify different collective phases of end-grafted polymers in a nanopore and to study their relative stability as a function of intermolecular interactions. Over a range of system parameters that is relevant for nuclear pore complexes, we observe two distinct phases: one with the bulk of the polymers condensed at the wall of the pore, and the other with the polymers condensed along its central axis. The relative stability of these two phases depends on the interpolymer interactions. The existence the two phases suggests a transport mechanism in which marginal changes in these interactions, possibly induced by nuclear transport receptors, cause the pore to transform between open and closed configurations.},
archivePrefix = {arXiv},
arxivId = {1109.0419},
author = {Osmanovic, Dino and Bailey, Joe and Harker, Anthony H. and Fassati, Ariberto and Hoogenboom, Bart W. and Ford, Ian J.},
doi = {10.1103/PhysRevE.85.061917},
eprint = {1109.0419},
file = {:Users/wenwen/Documents/MendeleyRefs/Osmanovic et al.{\_}Physical Review E - Statistical, Nonlinear, and Soft Matter Physics{\_}2012.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {jun},
number = {6},
pages = {061917},
title = {{Bistable collective behavior of polymers tethered in a nanopore}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.85.061917},
volume = {85},
year = {2012}
}
@article{Lei2010,
abstract = {In this paper, we present a new approach to study the probability distribution of the radius of gyration of freely jointed chains. In this approach, we study the joint distribution P(N)(R(g) (2),R(G)), where R(g) is the radius of gyration and R(G) is the vector from the first bead to the center of the chain. We derive an iteration relation between the probability distributions of chains with lengths N and N+1. When the chain length is large, the iteration relation can be approximated by an evolution equation with integral determining condition. The equation is solved to obtain the probability distribution function, which yields the known result obtained by Fixman [J. Chem. Phys. 36, 306 (1962)] using the integral method. We hope the iteration method in this paper could be used to study the probability distribution of the structure factor of polymer molecules.},
author = {Lei, Jinzhi},
doi = {10.1063/1.3479040},
file = {:Users/wenwen/Documents/MendeleyRefs/Lei{\_}Journal of Chemical Physics{\_}2010.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {10},
pmid = {20849188},
title = {{Probability distribution of the radius of gyration of freely jointed chains}},
volume = {133},
year = {2010}
}
@article{Leibovich2013,
abstract = {We study the dynamics of a tagged particle in an environment of point Brownian particles with hard-core interactions in an infinite one dimensional channel (a single-file model). In particular we examine the influence of initial conditions on the dynamic of the tagged particle. We compare two initial conditions: equal distances between particles and uniform density distribution. The effect is shown by the differences of mean-square-displacement and correlation function for the two ensembles of initial conditions. We discuss the violation of Einstein relation, and its dependence on the initial condition, and the difference between time and ensemble averaging. More specifically, using the Jepsen line, we will discuss how transport coefficients, like diffusivity, depend on the initial state. Our work shows that initial conditions determine the long time limit of the dynamic, and in this sense the system never forgets its initial state in complete contrast with thermal systems (i.e a closed system which attains equilibrium independent of the initial state).},
archivePrefix = {arXiv},
arxivId = {1304.7462},
author = {Leibovich, N and Barkai, E},
doi = {10.1103/PhysRevE.88.032107},
eprint = {1304.7462},
file = {:Users/wenwen/Documents/MendeleyRefs/Leibovich, Barkai{\_}Physical Review E{\_}2013.pdf:pdf},
isbn = {1550-2376 (Electronic)$\backslash$r1539-3755 (Linking)},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {sep},
number = {3},
pages = {032107},
pmid = {24125214},
title = {{Everlasting effect of initial conditions on single-file diffusion}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.88.032107},
volume = {88},
year = {2013}
}
@article{Li2011,
abstract = {Axial rotational diffusion of rodlike polymers is important in processes such as microtubule filament sliding and flagella beating. By imaging the motion of small kinks along the backbone of chains of DNA-linked colloids, we produce a direct and systematic measurement of axial rotational diffusivity of rods both in bulk solution and near a wall. The measured diffusivities decrease linearly with the chain length, irrespective of the distance from a wall, in agreement with slender-body hydrodynamics theory. Moreover, the presence of small kinks does not affect the chain's axial diffusivity. Our system and measurements provide insights into fundamental axial diffusion processes of slender objects, which encompass a wide range of entities including biological filaments and linear polymer chains.},
author = {Li, Dichuan and Fakhri, Nikta and Pasquali, Matteo and Biswal, Sibani Lisa},
doi = {10.1103/PhysRevLett.106.188302},
file = {:Users/wenwen/Documents/MendeleyRefs/Li et al.{\_}Physical Review Letters{\_}2011.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {may},
number = {18},
pages = {188302},
title = {{Axial Thermal Rotation of Slender Rods}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.106.188302},
volume = {106},
year = {2011}
}
@article{Vigolo2005,
abstract = {Percolation is a statistical concept that describes the formation of an infinite cluster of connected particles or pathways. Lowering the percolation threshold is a critical issue to achieve light and low-cost conductive composites made of an insulating matrix loaded with conductive particles. This has interest for applications where charge dissipation and electrical conductivity are sought in films, coatings, paints, or composite materials. One route to decreasing the loading required for percolation is to use rod-like particles. Theoretical predictions indicate that this may also be achieved by altering the interaction potential between the particles. Although percolation may not always respond monotonically to interactions, the use of adhesive rods can be expected to be an ideal combination. By using a system made of carbon nanotubes in an aqueous surfactant solution, we find that very small attraction can markedly lower the percolation threshold. The strength of this effect can thereby have direct technological interest and explain the large variability of experimental results in the literature dealing with the electrical behavior of composites loaded with conducting rods.},
author = {Vigolo, B},
doi = {10.1126/science.1112835},
file = {:Users/wenwen/Documents/MendeleyRefs/Vigolo et al.{\_}Science (New York, N.Y.){\_}2005.pdf:pdf},
issn = {0036-8075},
journal = {Science (80-. ).},
month = {aug},
number = {5736},
pages = {920--923},
pmid = {16081733},
title = {{An Experimental Approach to the Percolation of Sticky Nanotubes}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16081733 http://www.sciencemag.org/cgi/doi/10.1126/science.1112835},
volume = {309},
year = {2005}
}
@article{Agmon1985,
author = {Agmon, Noam},
doi = {10.1063/1.448468},
file = {:Users/wenwen/Documents/MendeleyRefs/Agmon{\_}The Journal of Chemical Physics{\_}1985.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {2},
pages = {935},
title = {{Relaxation times in diffusion processes}},
url = {http://scitation.aip.org/content/aip/journal/jcp/82/2/10.1063/1.448468},
volume = {82},
year = {1985}
}
@article{Buldyrev2010,
abstract = {Complex networks have been studied intensively for a decade, but research still focuses on the limited case of a single, non-interacting network. Modern systems are coupled together and therefore should be modelled as interdependent networks. A fundamental property of interdependent networks is that failure of nodes in one network may lead to failure of dependent nodes in other networks. This may happen recursively and can lead to a cascade of failures. In fact, a failure of a very small fraction of nodes in one network may lead to the complete fragmentation of a system of several interdependent networks. A dramatic real-world example of a cascade of failures ('concurrent malfunction') is the electrical blackout that affected much of Italy on 28 September 2003: the shutdown of power stations directly led to the failure of nodes in the Internet communication network, which in turn caused further breakdown of power stations. Here we develop a framework for understanding the robustness of interacting networks subject to such cascading failures. We present exact analytical solutions for the critical fraction of nodes that, on removal, will lead to a failure cascade and to a complete fragmentation of two interdependent networks. Surprisingly, a broader degree distribution increases the vulnerability of interdependent networks to random failure, which is opposite to how a single network behaves. Our findings highlight the need to consider interdependent network properties in designing robust networks.},
archivePrefix = {arXiv},
arxivId = {0907.1182},
author = {Buldyrev, Sergey V and Parshani, Roni and Paul, Gerald and Stanley, H Eugene and Havlin, Shlomo},
doi = {10.1038/nature08932},
eprint = {0907.1182},
file = {:Users/wenwen/Documents/MendeleyRefs/Buldyrev et al.{\_}Nature{\_}2010.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
month = {apr},
number = {7291},
pages = {1025--8},
pmid = {20393559},
publisher = {Nature Publishing Group},
title = {{Catastrophic cascade of failures in interdependent networks}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20393559 http://arxiv.org/abs/0907.1182},
volume = {464},
year = {2010}
}
@article{Dierl2013,
abstract = {We study stochastic particle transport between two reservoirs along a channel, where the particles are pumped against a bias by a traveling wave potential. It is shown that phase transitions of period-averaged densities or currents occur inside the channel when exclusion interactions between the particles are taken into account. These transitions reflect those known for the asymmetric simple exclusion process (ASEP). We argue that their occurrence is a generic feature of Brownian motors operating in open systems.},
archivePrefix = {arXiv},
arxivId = {arXiv:1402.0220v1},
author = {Dierl, Marcel and Dieterich, Wolfgang and Einax, Mario and Maass, Philipp},
doi = {http://dx.doi.org/10.1103/PhysRevLett.112.150601},
eprint = {arXiv:1402.0220v1},
file = {:Users/wenwen/Documents/MendeleyRefs/Dierl et al.{\_}Physical Review Letters{\_}2013.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
number = {April},
pages = {4},
title = {{Phase Transitions in Brownian Pumps}},
url = {http://arxiv.org/abs/1402.0220{\%}5Cnhttp://link.aps.org/doi/10.1103/PhysRevLett.112.150601},
volume = {112},
year = {2013}
}
@article{Satyanarayana2004a,
abstract = {We have investigated the shape, size, and motility of a minimal model of an adherent biological cell using the Monte Carlo method. The cell is modeled as a two dimensional ring polymer on the square lattice enclosing continuously polymerizing and depolymerizing actin networks. Our lattice model is an approximate representation of a real cell at a resolution of one actin molecule, 5 nm. The polymerization kinetics for the actin network are controlled by appropriate reaction probabilities which correspond to the correct experimental reaction rates. Using the simulation data we establish various scaling laws relating the size of the model cell to the concentration of polymerized and unpolymerized actin molecules and the length of the enclosing membrane. The computed drift velocities, which characterize the motility of the cell, exhibit a maximum at a certain fraction of polymerized actin which agrees with physiological fractions observed in experiments. The appearance of the maximum is related to the competition between the polymerization-induced protrusion of the membrane and the concomitant suppression of membrane fluctuations.},
author = {Satyanarayana, S. V M and Baumgaertner, A.},
doi = {10.1063/1.1778151},
file = {:Users/wenwen/Documents/MendeleyRefs/Satyanarayana, Baumgaertner{\_}The Journal of Chemical Physics{\_}2004.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {9},
pages = {4255},
pmid = {15332973},
title = {{Shape and motility of a model cell: A computational study}},
url = {http://scitation.aip.org/content/aip/journal/jcp/121/9/10.1063/1.1778151},
volume = {121},
year = {2004}
}
@article{Ruttor2004,
abstract = {Reflecting boundary conditions cause two one-dimensional random walks to synchronize if a common direction is chosen in each step. The mean synchronization time and its standard deviation are calculated analytically. Both quantities are found to increase proportional to the square of the system size. Additionally, the probability of synchronization in a given step is analysed, which converges to a geometric distribution for long synchronization times. From this asymptotic behaviour the number of steps required to synchronize an ensemble of independent random walk pairs is deduced. Here the synchronization time increases with the logarithm of the ensemble size. The results of this model are compared to those observed in neural synchronization.},
author = {Ruttor, Andreas and Reents, Georg and Kinzel, Wolfgang},
doi = {10.1088/0305-4470/37/36/003},
file = {:Users/wenwen/Documents/MendeleyRefs/Ruttor, Reents, Kinzel{\_}Journal of Physics A Mathematical and General{\_}2004.pdf:pdf},
issn = {0305-4470},
journal = {J. Phys. A. Math. Gen.},
month = {sep},
number = {36},
pages = {8609--8618},
title = {{Synchronization of random walks with reflecting boundaries}},
url = {http://stacks.iop.org/0305-4470/37/i=36/a=003?key=crossref.f7f15ab767f2e1541aa9caef6e905563},
volume = {37},
year = {2004}
}
@article{Doyle2000,
abstract = {The dynamics of a single polymer tethered to a solid surface in a shear flow was observed using fluorescently labeled DNA chains. Dramatic shear enhanced temporal fluctuations in the chain extension were observed. The rate of these fluctuations initially decreased for increasing shear rate gamma; and increased above a critical gamma;. Simulations revealed that these anomalous dynamics arise from a continual recirculating motion of the chain or cyclic dynamics. These dynamics arise from a coupling of the chain velocity in the flow direction to thermally driven fluctuations of the chain in the shear gradient direction.},
author = {Doyle, P S and Ladoux, B and Viovy, J L},
doi = {10.1103/PhysRevLett.84.4769},
file = {:Users/wenwen/Documents/MendeleyRefs/Doyle, Ladoux, Viovy{\_}Physical Review letters{\_}2000.pdf:pdf},
isbn = {0031-9007},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
number = {20},
pages = {4769--4772},
pmid = {10990792},
title = {{Dynamics of a tethered polymer in shear flow.}},
volume = {84},
year = {2000}
}
@article{Krapivsky2014,
author = {Krapivsky, P. L. and Mallick, Kirone and Sadhu, Tridib},
doi = {10.1103/PhysRevLett.113.078101},
file = {:Users/wenwen/Documents/MendeleyRefs/Krapivsky, Mallick, Sadhu{\_}Physical Review Letters{\_}2014.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
number = {7},
pages = {078101},
title = {{Large Deviations in Single-File Diffusion}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.113.078101},
volume = {113},
year = {2014}
}
@article{Galina1983,
author = {Galina, Henryk},
file = {:Users/wenwen/Documents/MendeleyRefs/Galina{\_}Macromolecules{\_}1983.pdf:pdf},
issn = {00249297},
journal = {Macromolecules},
pages = {1479--1483},
title = {{Mean Square Radii of Gyration for Gaussian Comblike and Cyclic Polymers}},
volume = {16},
year = {1983}
}
@article{Wang2002,
author = {{Xiao Fan Wang} and {Guanrong Chen}},
doi = {10.1109/81.974874},
file = {:Users/wenwen/Documents/MendeleyRefs/Xiao Fan Wang, Guanrong Chen{\_}IEEE Transactions on Circuits and Systems I Fundamental Theory and Applications{\_}2002.pdf:pdf},
isbn = {9040565570},
issn = {10577122},
journal = {IEEE Trans. Circuits Syst. I Fundam. Theory Appl.},
number = {1},
pages = {54--62},
title = {{Synchronization in scale-free dynamical networks: robustness and fragility}},
url = {http://ieeexplore.ieee.org/document/974874/},
volume = {49},
year = {2002}
}
@article{Daido2012,
author = {Daido, Hiroaki},
doi = {10.1016/j.piutam.2012.06.029},
file = {:Users/wenwen/Documents/MendeleyRefs/Daido{\_}Procedia IUTAM{\_}2012.pdf:pdf},
issn = {22109838},
journal = {Procedia IUTAM},
keywords = {active oscillators,aging transition,critical coupling strength,critical ratio,inactive oscillators,robustness against defects},
month = {jan},
pages = {220--226},
title = {{Dynamics of Large Ensembles of Coupled Active and Inactive Oscillators}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S2210983812000892},
volume = {5},
year = {2012}
}
@article{DeGier2008c,
abstract = {We analyze the Bethe ansatz equations describing the complete spectrum of the transition matrix of the partially asymmetric exclusion process on a finite lattice and with the most general open boundary conditions. We extend results obtained recently for totally asymmetric diffusion [J. de Gier and F.H.L. Essler, J. Stat. Mech. P12011 (2006)] to the case of partial symmetry. We determine the finite-size scaling of the spectral gap, which characterizes the approach to stationarity at large times, in the low and high density regimes and on the coexistence line. We observe boundary induced crossovers and discuss possible interpretations of our results in terms of effective domain wall theories.},
archivePrefix = {arXiv},
arxivId = {0806.3493},
author = {de Gier, Jan and Essler, Fabian H L},
doi = {10.1088/1742-5468/2006/12/P12011},
eprint = {0806.3493},
file = {:Users/wenwen/Documents/MendeleyRefs/Gier, Essler{\_}Journal of Statistical Mechanics Theory and Experiment{\_}2006.pdf:pdf},
issn = {1742-5468},
journal = {J. Stat. Mech. Theory Exp.},
month = {dec},
number = {12},
pages = {P12011--P12011},
title = {{Exact spectral gaps of the asymmetric exclusion process with open boundaries}},
volume = {2006},
year = {2006}
}
@article{Funaya2012,
abstract = {BACKGROUND: Vigorous chromosome movements driven by cytoskeletal assemblies are a widely conserved feature of sexual differentiation to facilitate meiotic recombination. In fission yeast, this process involves the dramatic conversion of arrays of cytoplasmic microtubules (MTs), generated from multiple MT organizing centers (MTOCs), into a single radial MT (rMT) array associated with the spindle pole body (SPB), the major MTOC during meiotic prophase. The rMT is then dissolved upon the onset of meiosis I when a bipolar spindle emerges to conduct chromosome segregation. Structural features and molecular mechanisms that govern these dynamic MT rearrangements are poorly understood. RESULTS: Electron tomography of the SPBs showed that the rMT emanates from a newly recognized amorphous structure, which we term the rMTOC. The rMTOC, which resides at the cytoplasmic side of the SPB, is highly enriched in $\gamma$-tubulin reminiscent of the pericentriolar material of higher eukaryotic centrosomes. Formation of the rMTOC depends on Hrs1/Mcp6, a meiosis-specific SPB component that is located at the rMTOC. At the onset of meiosis I, Hrs1/Mcp6 is subject to strict downregulation by both proteasome-dependent degradation and phosphorylation leading to complete inactivation of the rMTOC. This ensures rMT dissolution and bipolar spindle formation. CONCLUSIONS: Our study reveals the molecular basis for the transient generation of a novel MTOC, which triggers a program of MT rearrangement that is required for meiotic differentiation.},
author = {Funaya, Charlotta and Samarasinghe, Shivanthi and Pruggnaller, Sabine and Ohta, Midori and Connolly, Yvonne and M{\"{u}}ller, Jan and Murakami, Hiroshi and Grallert, Agnes and Yamamoto, Masayuki and Smith, Duncan and Antony, Claude and Tanaka, Kayoko},
doi = {10.1016/j.cub.2012.02.042},
file = {:Users/wenwen/Documents/MendeleyRefs/Funaya et al.{\_}Current Biology{\_}2012.pdf:pdf},
issn = {09609822},
journal = {Curr. Biol.},
keywords = {Cell Nucleus,Cell Nucleus: physiology,Fluorescence,Meiosis,Microscopy,Microtubule-Organizing Center,Microtubule-Organizing Center: metabolism,Microtubules,Microtubules: metabolism,Schizosaccharomyces,Schizosaccharomyces pombe Proteins,Schizosaccharomyces pombe Proteins: metabolism,Schizosaccharomyces: metabolism,Spindle Apparatus,Spindle Apparatus: metabolism,Tubulin,Tubulin: metabolism},
month = {apr},
number = {7},
pages = {562--574},
pmid = {22425159},
title = {{Transient Structure Associated with the Spindle Pole Body Directs Meiotic Microtubule Reorganization in S. pombe}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982212001935},
volume = {22},
year = {2012}
}
@article{Henkel2003,
abstract = {This is a pedagogical account on reaction-diffusion systems and their relationship with integrable quantum spin chains. Reaction-diffusion systems are paradigmatic examples of non-equilibrium systems. Their long-time behaviour is strongly influenced through fluctuation effects in low dimensions which renders the habitual mean-field cinetic equations inapplicable. Starting from the master equation rewritten as a Schr$\backslash$"odinger equation with imaginary time, the associated quantum hamiltonian of certain one-dimensional reaction-diffusion models is closely related to integrable magnetic chains. The relationship with the Hecke algebra and its quotients allows to identify integrable reaction-diffusion models and, through the Baxterization procedure, relate them to the solutions of Yang-Baxter equations which can be solved via the Bethe ansatz. Methods such as spectral and partial integrability, free fermions, similarity transformations or diffusion algebras are reviewed, with several concrete examples treated explicitly. An outlook on how the recently-introduced concept of local scale invariance might become useful in the description of non-equilibrium ageing phenomena is presented, with particular emphasis on the kinetic Ising model with Glauber dynamics.},
archivePrefix = {arXiv},
arxivId = {cond-mat/0303512},
author = {Henkel, Malte},
eprint = {0303512},
file = {:Users/wenwen/Documents/MendeleyRefs/Henkel{\_}Unknown{\_}2003.pdf:pdf},
keywords = {High Energy Physics - Theory,Mathematical Physics,Statistical Mechanics},
month = {mar},
number = {Bristol 2003},
pages = {38},
primaryClass = {cond-mat},
title = {{Reaction-diffusion processes and their connection with integrable quantum spin chains}},
url = {http://arxiv.org/abs/cond-mat/0303512},
year = {2003}
}
@article{Slade2009,
author = {Slade, Gordon},
file = {:Users/wenwen/Documents/MendeleyRefs/Slade{\_}Surveys in Stochastic Processes{\_}2009.pdf:pdf},
journal = {Surv. Stoch. Process.},
keywords = {critical exponents,lace expan-,renormalisation group,self-avoiding walks},
pages = {181----199},
title = {{The Self-Avoiding Walk : A Brief Survey}},
year = {2009}
}
@article{Giorgetti2014,
abstract = {A new level of chromosome organization, topologically associating domains (TADs), was recently uncovered by chromosome conformation capture (3C) techniques. To explore TAD structure and function, we developed a polymer model that can extract the full repertoire of chromatin conformations within TADs from population-based 3C data. This model predicts actual physical distances and to what extent chromosomal contacts vary between cells. It also identifies interactions within single TADs that stabilize boundaries between TADs and allows us to identify and genetically validate key structural elements within TADs. Combining the model's predictions with high-resolution DNA FISH and quantitative RNA FISH for TADs within the X-inactivation center (Xic), we dissect the relationship between transcription and spatial proximity to cis-regulatory elements. We demonstrate that contacts between potential regulatory elements occur in the context of fluctuating structures rather than stable loops and propose that such fluctuations may contribute to asymmetric expression in the Xic during X inactivation.},
author = {Giorgetti, Luca and Galupa, Rafael and Nora, Elph{\`{e}}ge P and Piolot, Tristan and Lam, France and Dekker, Job and Tiana, Guido and Heard, Edith},
doi = {10.1016/j.cell.2014.03.025},
file = {:Users/wenwen/Documents/MendeleyRefs/Giorgetti et al.{\_}Cell{\_}2014.pdf:pdf},
issn = {1097-4172},
journal = {Cell},
month = {may},
number = {4},
pages = {950--63},
pmid = {24813616},
title = {{Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24813616},
volume = {157},
year = {2014}
}
@article{Jagodzinski1992,
author = {Jagodzinski, O. and Eisenriegler, E. and Kremer, K.},
file = {:Users/wenwen/Documents/MendeleyRefs/Jagodzinski, Eisenriegler, Kremer{\_}J. Phys. I France{\_}1992.pdf:pdf},
journal = {J. Phys. I Fr.},
pages = {2243--2279},
title = {{Universal shape properties of open and closed polymer chains: renormalization group analysis and Monte Carlo experiments}},
volume = {2},
year = {1992}
}
@article{Bras2011b,
author = {Br{\'{a}}s, Ana R. and Pasquino, Rossana and Koukoulas, Thanasis and Tsolou, Georgia and Holderer, Olaf and Radulescu, Aurel and Allgaier, J{\"{u}}rgen and Mavrantzas, Vlasis G. and Pyckhout-Hintzen, Wim and Wischnewski, Andreas and Vlassopoulos, Dimitris and Richter, Dieter},
doi = {10.1039/c1sm06257c},
file = {:Users/wenwen/Documents/MendeleyRefs/Br{\'{a}}s et al.{\_}Soft Matter{\_}2011.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Br{\'{a}}s et al.{\_}Soft Matter{\_}2011.pdf:pdf},
issn = {1744-683X},
journal = {Soft Matter},
pages = {11169},
title = {{Structure and dynamics of polymer rings by neutron scattering: breakdown of the Rouse model}},
volume = {7},
year = {2011}
}
@article{Higham.2001,
abstract = {A practical and accessible introduction to numerical methods for stochastic differential equations is given. The reader is assumed to be familiar with Euler's method for deterministic differential equations and to have at least an intuitive feel for the concept of a random variable; however, no knowledge of advanced probability theory or stochastic processes is assumed. The article is built around {\$}10{\$} MATLAB programs, and the topics covered include stochastic integration, the Euler--Maruyama method, Milstein's method, strong and weak convergence, linear stability, and the stochastic chain rule.},
author = {Higham., Desmond J.},
doi = {10.1137/S0036144500378302},
file = {:Users/wenwen/Documents/MendeleyRefs/Higham.{\_}SIAM Review{\_}2001.pdf:pdf},
issn = {0036-1445},
journal = {SIAM Rev.},
keywords = {65C20,65C30,Euler--Maruyama method,MATLAB,Milstein method,Monte Carlo,stochastic simulation,strong and weak convergence},
number = {3},
pages = {525--546},
pmid = {7962225527038909018},
title = {{An Algorithmic Introduction to Numerical Simulation of Stochastic Differential Equations}},
url = {http://epubs.siam.org/doi/abs/10.1137/S0036144500378302},
volume = {43},
year = {2001}
}
@article{Wynne2012,
abstract = {Meiotic chromosome segregation requires homologue pairing, synapsis, and crossover recombination, which occur during meiotic prophase. Telomere-led chromosome motion has been observed or inferred to occur during this stage in diverse species, but its mechanism and function remain enigmatic. In Caenorhabditis elegans, special chromosome regions known as pairing centers (PCs), rather than telomeres, associate with the nuclear envelope (NE) and the microtubule cytoskeleton. In this paper, we investigate chromosome dynamics in living animals through high-resolution four-dimensional fluorescence imaging and quantitative motion analysis. We find that chromosome movement is constrained before meiosis. Upon prophase onset, constraints are relaxed, and PCs initiate saltatory, processive, dynein-dependent motions along the NE. These dramatic motions are dispensable for homologous pairing and continue until synapsis is completed. These observations are consistent with the idea that motions facilitate pairing by enhancing the search rate but that their primary function is to trigger synapsis. This quantitative analysis of chromosome dynamics in a living animal extends our understanding of the mechanisms governing faithful genome inheritance.},
author = {Wynne, David J. and Rog, Ofer and Carlton, Peter M. and Dernburg, Abby F.},
doi = {10.1083/jcb.201106022},
isbn = {1540-8140 (Electronic)$\backslash$r0021-9525 (Linking)},
issn = {00219525},
journal = {J. Cell Biol.},
number = {1},
pages = {47--64},
pmid = {22232701},
title = {{Dynein-dependent processive chromosome motions promote homologous pairing in C. elegans meiosis}},
volume = {196},
year = {2012}
}
@article{Kampen1981,
author = {Kampen, N. G.},
doi = {10.1007/BF00382618},
file = {:Users/wenwen/Documents/MendeleyRefs/Kampen{\_}Applied Scientific Research{\_}1981.pdf:pdf},
issn = {0003-6994},
journal = {Appl. Sci. Res.},
number = {1-2},
pages = {67--75},
title = {{Statistical mechanics of trimers}},
url = {http://link.springer.com/10.1007/BF00382618},
volume = {37},
year = {1981}
}
@article{Casassa1965,
author = {Casassa, Ef},
file = {:Users/wenwen/Documents/MendeleyRefs/Casassa{\_}Journal of Polymer Science Part A General {\ldots}{\_}1965.pdf:pdf},
journal = {J. Polym. Sci. Part A Gen. {\ldots}},
pages = {605--614},
title = {{Some statistical properties of flexible ring polymers}},
url = {http://onlinelibrary.wiley.com/doi/10.1002/pol.1965.100030217/full},
volume = {3},
year = {1965}
}
@article{Simon1970,
author = {Simon, Eliot},
doi = {10.1063/1.1673586},
file = {:Users/wenwen/Documents/MendeleyRefs/Simon{\_}The Journal of Chemical Physics{\_}1970.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {8},
pages = {3879},
title = {{Dynamic Model for Locally Stiff Ring and Straight Chain Polymers}},
url = {http://link.aip.org/link/?JCP/52/3879/1{\&}Agg=doi},
volume = {52},
year = {1970}
}
@article{Li2007,
author = {Li, Changpin and Sun, Weigang and Kurths, J{\"{u}}rgen},
doi = {10.1103/PhysRevE.76.046204},
file = {:Users/wenwen/Documents/MendeleyRefs/Li, Sun, Kurths{\_}Physical Review E{\_}2007.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {oct},
number = {4},
pages = {1--6},
title = {{Synchronization between two coupled complex networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.76.046204},
volume = {76},
year = {2007}
}
@article{Xu2008,
abstract = {We introduce a transformation from time series to complex networks and then study the relative frequency of different subgraphs within that network. The distribution of subgraphs can be used to distinguish between and to characterize different types of continuous dynamics: periodic, chaotic, and periodic with noise. Moreover, although the general types of dynamics generate networks belonging to the same superfamily of networks, specific dynamical systems generate characteristic dynamics. When applied to discrete (map-like) data this technique distinguishes chaotic maps, hyperchaotic maps, and noise data.},
author = {Xu, Xiaoke and Zhang, Jie and Small, Michael},
doi = {10.1073/pnas.0806082105},
file = {:Users/wenwen/Documents/MendeleyRefs/Xu, Zhang, Small{\_}Proceedings of the National Academy of Sciences{\_}2008.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
month = {dec},
number = {50},
pages = {19601--19605},
pmid = {19064916},
title = {{Superfamily phenomena and motifs of networks induced from time series}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2604928{\&}tool=pmcentrez{\&}rendertype=abstract http://www.pnas.org/cgi/doi/10.1073/pnas.0806082105},
volume = {105},
year = {2008}
}
@article{Ladoux2000a,
abstract = {We discuss the stretching oftethered chains subject to a shear flow. Fluores- cence microscopy measurements ofthe extension ofsheared tethered DNA, “model polymers”, ofvarious lengths are presented. The tethered chains approach full extension as the flow rate is increased, but very slowly. We show that a general theory to understand the large defor- mation ofany sheared tethered chain must include both the correct nonlinear force-extension relation and chain fluctuations transverse to the flow direction, which themselves depend on the nonlinear elasticity ofthe chain. Direct comparison ofderived scaling laws to simulations and experiments support our theory. Introduction.},
author = {Ladoux, B and Doyle, P S},
doi = {10.1209/epl/i2000-00467-y},
file = {:Users/wenwen/Documents/MendeleyRefs/Ladoux, Doyle{\_}Europhysics Letters (EPL){\_}2000.pdf:pdf},
isbn = {0295-5075},
issn = {0295-5075},
journal = {Europhys. Lett.},
month = {dec},
number = {5},
pages = {511--517},
title = {{Stretching tethered DNA chains in shear flow}},
url = {http://stacks.iop.org/0295-5075/52/i=5/a=511?key=crossref.7bcfad469700af4ced21e8fb396fc0f2},
volume = {52},
year = {2000}
}
@article{Quake1997a,
abstract = {The behaviour of an isolated polymer floating in a solvent forms the basis of our understanding of polymer dynamics. Classical theories describe the motion of a polymer with linear equations of motion, which yield a set of 'normal modes', analogous to the fundamental frequency and the harmonics of a vibrating violin string. But hydrodynamic interactions make polymer dynamics inherently nonlinear, and the linearizing approximations required for the normal-mode picture have therefore been questioned. Here we test the normal-mode theory by measuring the fluctuations of single molecules of DNA held in a partially extended state with optical tweezers. We find that the motion of the DNA can be described by linearly independent normal modes, and we have experimentally determined the eigenstates of the system. Furthermore, we show that the spectrum of relaxation times obeys a power law.},
author = {Quake, S R and Babcock, H and Chu, S},
doi = {10.1038/40588},
file = {:Users/wenwen/Documents/MendeleyRefs/Quake, Babcock, Chu{\_}Nature{\_}1997.pdf:pdf},
isbn = {0028-0836 (Print)$\backslash$r0028-0836 (Linking)},
issn = {0028-0836},
journal = {Nature},
keywords = {Biopolymers,Biopolymers: chemistry,DNA,DNA: chemistry,Image Processing, Computer-Assisted,Microscopy, Video,Models, Chemical,Motion,Solutions,Video Recording},
number = {July},
pages = {151--4},
pmid = {9217154},
title = {{The dynamics of partially extended single molecules of DNA.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9217154},
volume = {388},
year = {1997}
}
@article{Mon2003,
author = {Mon, K. K. and Percus, J. K.},
doi = {10.1063/1.1591179},
file = {:Users/wenwen/Documents/MendeleyRefs/Mon, Percus{\_}The Journal of Chemical Physics{\_}2003.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {6},
pages = {3343},
title = {{Molecular dynamics simulation of anomalous self-diffusion for single-file fluids}},
url = {http://scitation.aip.org/content/aip/journal/jcp/119/6/10.1063/1.1591179},
volume = {119},
year = {2003}
}
@article{Barabasi2003,
author = {Barab{\'{a}}si, Albert-L{\'{a}}szl{\'{o}} and Bonabeau, Eric},
file = {:Users/wenwen/Documents/MendeleyRefs/Barab{\'{a}}si, Bonabeau{\_}Scientific American{\_}2003.pdf:pdf},
journal = {Sci. Am.},
number = {May},
pages = {60--69},
title = {{Scale-free networks}},
volume = {288},
year = {2003}
}
@article{Kalinina2013,
abstract = {During cell division, spindle microtubules attach to chromosomes through kinetochores, protein complexes on the chromosome. The central question is how microtubules find kinetochores. According to the pioneering idea termed search-and-capture, numerous microtubules grow from a centrosome in all directions and by chance capture kinetochores. The efficiency of search-and-capture can be improved by a bias in microtubule growth towards the kinetochores, by nucleation of microtubules at the kinetochores and at spindle microtubules, by kinetochore movement, or by a combination of these processes. Here we show in fission yeast that kinetochores are captured by microtubules pivoting around the spindle pole, instead of growing towards the kinetochores. This pivoting motion of microtubules is random and independent of ATP-driven motor activity. By introducing a theoretical model, we show that the measured random movement of microtubules and kinetochores is sufficient to explain the process of kinetochore capture. Our theory predicts that the speed of capture depends mainly on how fast microtubules pivot, which was confirmed experimentally by speeding up and slowing down microtubule pivoting. Thus, pivoting motion allows microtubules to explore space laterally, as they search for targets such as kinetochores.},
author = {Kalinina, Iana and Nandi, Amitabha and Delivani, Petrina and Chac{\'{o}}n, Mariola R. and Klemm, Anna H. and Ramunno-Johnson, Damien and Krull, Alexander and Lindner, Benjamin and Pavin, Nenad and Toli{\'{c}}-N{\o}rrelykke, Iva M.},
doi = {10.1038/ncb2640},
file = {:Users/wenwen/Documents/MendeleyRefs/Kalinina et al.{\_}Nature Cell Biology{\_}2012.pdf:pdf},
isbn = {doi:10.1038/ncb2640},
issn = {1465-7392},
journal = {Nat. Cell Biol.},
month = {dec},
number = {1},
pages = {82--87},
pmid = {23222841},
publisher = {Nature Research},
title = {{Pivoting of microtubules around the spindle pole accelerates kinetochore capture}},
url = {http://www.nature.com/doifinder/10.1038/ncb2640},
volume = {15},
year = {2012}
}
@article{Sato1996,
author = {Sato, Tetsuya},
doi = {10.1063/1.871666},
file = {:Users/wenwen/Documents/MendeleyRefs/Sato{\_}Physics of Plasmas{\_}1996.pdf:pdf},
issn = {1070664X},
journal = {Phys. Plasmas},
keywords = {abstract,and methods of the,complex systems,emergence,in a non-technical manner,multi-agent systems,networks,non-linearity,of the main concepts,science,self-organization,self-organizing systems and networks,studying complex,this article introduces some,unpredictability},
number = {5},
pages = {2135},
title = {{Complexity in plasma: From self-organization to geodynamo}},
url = {http://link.aip.org/link/PHPAEN/v3/i5/p2135/s1{\&}Agg=doi},
volume = {3},
year = {1996}
}
@article{Ravoori2011,
author = {Ravoori, Bhargava and Cohen, Adam and Sun, Jie and Motter, Adilson and Murphy, Thomas and Roy, Rajarshi},
doi = {10.1103/PhysRevLett.107.034102},
file = {:Users/wenwen/Documents/MendeleyRefs/Ravoori et al.{\_}Physical Review Letters{\_}2011.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {jul},
number = {3},
pages = {1--4},
title = {{Robustness of Optimal Synchronization in Real Networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.107.034102},
volume = {107},
year = {2011}
}
@article{Cui2000a,
abstract = {Single chicken erythrocyte chromatin fibers were stretched and released at room temperature with force-measuring laser tweezers. In low ionic strength, the stretch-release curves reveal a process of continuous deformation with little or no internucleosomal attraction. A persistence length of 30 nm and a stretch modulus of approximately 5 pN is determined for the fibers. At forces of 20 pN and higher, the fibers are modified irreversibly, probably through the mechanical removal of the histone cores from native chromatin. In 40-150 mM NaCl, a distinctive condensation-decondensation transition appears between 5 and 6 pN, corresponding to an internucleosomal attraction energy of approximately 2.0 kcal/mol per nucleosome. Thus, in physiological ionic strength the fibers possess a dynamic structure in which the fiber locally interconverting between "open" and "closed" states because of thermal fluctuations.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Cui, Y and Bustamante, C},
doi = {10.1073/pnas.97.1.127},
eprint = {NIHMS150003},
file = {:Users/wenwen/Documents/MendeleyRefs/Cui, Bustamante{\_}Proceedings of the National Academy of Sciences{\_}2000.pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
month = {jan},
number = {1},
pages = {127--132},
pmid = {10618382},
publisher = {National Academy of Sciences},
title = {{Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10618382 http://www.pnas.org/cgi/doi/10.1073/pnas.97.1.127},
volume = {97},
year = {2000}
}
@article{Brown1998,
abstract = {We study the equilibrium structure and dynamics of unconcatenated unknotted polymer rings in the melt. In accordance with earlier studies we find that rings in the melt are more compact than linear chains. We show that rings interpenetrate less and, perhaps as a result, diffuse faster than linear chains. Ring diffusion is faster for all ring sizes studied, the largest ring having numbers of monomers approximately ten times greater than the entanglement crossover of linear chains. {\textcopyright} 1998 American Institute of Physics. S0021-96069852112-5},
author = {Brown, Scott and Szamel, Grzegorz},
doi = {10.1063/1.477247},
file = {:Users/wenwen/Documents/MendeleyRefs/Brown, Szamel{\_}Journal of Chemical Physics{\_}1998.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {14},
pages = {6184--6192},
title = {{Computer simulation study of the structure and dynamics of ring polymers}},
volume = {109},
year = {1998}
}
@article{Hunter2014,
author = {Hunter, Gary L. and Edmond, Kazem V. and Weeks, Eric R.},
doi = {10.1103/PhysRevLett.112.218302},
file = {:Users/wenwen/Documents/MendeleyRefs/Hunter, Edmond, Weeks{\_}Physical Review Letters{\_}2014.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {may},
number = {21},
pages = {218302},
title = {{Boundary Mobility Controls Glassiness in Confined Colloidal Liquids}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.112.218302},
volume = {112},
year = {2014}
}
@article{Fixman1962,
abstract = {The probability distribution of the radius of gyration of unbranched polymer chains is discussed. The characteristic function of the distribution is presented in closed form, and calculations are the made of the semi‐invariants, moments, and behavior of the probability at very large and very small values of the radius of gyration.},
author = {Fixman, Marshall},
doi = {10.1063/1.1732501},
file = {:Users/wenwen/Documents/MendeleyRefs/Fixman{\_}The Journal of Chemical Physics{\_}1962.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {2},
pages = {306},
title = {{Radius of Gyration of Polymer Chains}},
url = {http://scitation.aip.org/content/aip/journal/jcp/36/2/10.1063/1.1732501},
volume = {36},
year = {1962}
}
@article{Kirkpatrick1973,
author = {Kirkpatrick, Scott},
doi = {10.1103/RevModPhys.45.574},
file = {:Users/wenwen/Documents/MendeleyRefs/Kirkpatrick{\_}Reviews of Modern Physics{\_}1973.pdf:pdf},
issn = {0034-6861},
journal = {Rev. Mod. Phys.},
month = {oct},
number = {4},
pages = {574--588},
title = {{Percolation and Conduction}},
url = {http://link.aps.org/doi/10.1103/RevModPhys.45.574},
volume = {45},
year = {1973}
}
@article{Haydukivska2014,
author = {Haydukivska, K. and Blavatska, V.},
doi = {10.1063/1.4894278},
file = {:Users/wenwen/Documents/MendeleyRefs/Haydukivska, Blavatska{\_}The Journal of Chemical Physics{\_}2014.pdf:pdf},
issn = {0021-9606},
journal = {J. Chem. Phys.},
number = {9},
pages = {094906},
title = {{Ring polymers in crowded environment: Conformational properties}},
url = {http://scitation.aip.org/content/aip/journal/jcp/141/9/10.1063/1.4894278},
volume = {141},
year = {2014}
}
@article{Park2006,
abstract = {Networks with a community (or modular) structure arise in social and biological sciences. In such a network individuals tend to form local communities, each having dense internal connections. The linkage among the communities is, however, much more sparse. The dynamics on modular networks, for instance synchronization, may be of great social or biological interest. (Here by synchronization we mean some synchronous behavior among the nodes in the network, not, for example, partially synchronous behavior in the network or the synchronizability of the network with some external dynamics.) By using a recent theoretical framework, the master-stability approach originally introduced by Pecora and Carroll in the context of synchronization in coupled nonlinear oscillators, we address synchronization in complex modular networks. We use a prototype model and develop scaling relations for the network synchronizability with respect to variations of some key network structural parameters. Our results indicate that random, long-range links among distant modules is the key to synchronization. As an application we suggest a viable strategy to achieve synchronous behavior in social networks.},
author = {Park, Kwangho and Lai, Ying-Cheng and Gupte, Saurabh and Kim, Jong-Won},
doi = {10.1063/1.2154881},
file = {:Users/wenwen/Documents/MendeleyRefs/Park et al.{\_}Chaos (Woodbury, N.Y.){\_}2006.pdf:pdf},
issn = {105415

repository: huangww/chromosome

repo_name: huangww/chromosome