text:
on complex networks}},
url = {http://arxiv.org/abs/1211.5690 http://dx.doi.org/10.1103/PhysRevE.87.032106 http://link.aps.org/doi/10.1103/PhysRevE.87.032106},
volume = {87},
year = {2013}
}
@article{Woglar2014,
author = {Woglar, Alexander and Jantsch, Verena},
doi = {10.1007/s00412-013-0436-7},
file = {:Users/wenwen/Documents/MendeleyRefs/Woglar, Jantsch{\_}Chromosoma{\_}2014.pdf:pdf},
issn = {0009-5915},
journal = {Chromosoma},
month = {mar},
number = {1-2},
pages = {15--24},
title = {{Chromosome movement in meiosis I prophase of Caenorhabditis elegans}},
url = {http://link.springer.com/10.1007/s00412-013-0436-7},
volume = {123},
year = {2014}
}
@article{Carl1996,
abstract = {We present a study of various properties of bead spring chains in steady flows. The Langevin equation of the normal modes of the chain is solved by Fourier transformation. From the resulting power spectrum, the autocorrelation functions of all configuration-dependent quantities can be calculated. In equilibrium, the influence of the bead masses on the short-time dynamics is discussed. The influence of different flow fields (shear, elongational and Kramers potential flow) on the mean- square chain dimension is calculated. A comparison with results obtained from non-equilibrium molecular dynamics and Monte Carlo calculations is made. Finally, the influence of shear flow on the configurational and rheological properties of cyclic polymers and on the excluded volume behaviour of linear chains is examined.},
author = {Carl, W.},
file = {:Users/wenwen/Documents/MendeleyRefs/Carl{\_}Macromolecular Theory and Simulations{\_}1996.pdf:pdf},
issn = {10221344},
journal = {Macromol. Theory Simulations},
number = {1},
pages = {1--27},
title = {{Some aspects of theory and simulations of polymers in steady flows}},
volume = {5},
year = {1996}
}
@article{Gillespie1976,
abstract = {An exact method is presented for numerically calculating, within the framework of the stochastic formulation of chemical kinetics, the time evolution of any spatially homogeneous mixture of molecular species which interreact through a specified set of coupled chemical reaction channels. The method is a compact, computer-oriented, Monte Carlo simulation procedure. It should be particularly useful for modeling the transient behavior of well-mixed gas-phase systems in which many molecular species participate in many highly coupled chemical reactions. For “ordinary” chemical systems in which fluctuations and correlations play no significant role, the method stands as an alternative to the traditional procedure of numerically solving the deterministic reaction rate equations. For nonlinear systems near chemical instabilities, where fluctuations and correlations may invalidate the deterministic equations, the method constitutes an efficient way of numerically examining the predictions of the stochastic master equation. Although fully equivalent to the spatially homogeneous master equation, the numerical simulation algorithm presented here is more directly based on a newly defined entity called “the reaction probability density function.” The purpose of this article is to describe the mechanics of the simulation algorithm, and to establish in a rigorous, a priori manner its physical and mathematical validity; numerical applications to specific chemical systems will be presented in subsequent publications.},
author = {Gillespie, Daniel T.},
doi = {10.1016/0021-9991(76)90041-3},
file = {:Users/wenwen/Documents/MendeleyRefs/Gillespie{\_}Journal of Computational Physics{\_}1976.pdf:pdf},
isbn = {0021-9991},
issn = {00219991},
journal = {J. Comput. Phys.},
number = {4},
pages = {403--434},
pmid = {20387305},
title = {{A general method for numerically simulating the stochastic time evolution of coupled chemical reactions}},
url = {http://www.sciencedirect.com/science/article/pii/0021999176900413},
volume = {22},
year = {1976}
}
@article{Forsling2014,
author = {Forsling, Robin and Sanders, Lloyd P. and Ambj{\"{o}}rnsson, Tobias and Lizana, Ludvig},
doi = {10.1063/1.4894117},
file = {:Users/wenwen/Documents/MendeleyRefs/Forsling et al.{\_}The Journal of Chemical Physics{\_}2014.pdf:pdf},
issn = {0021-9606},
journal = {J. Chem. Phys.},
number = {9},
pages = {094902},
title = {{Non-Markovian effects in the first-passage dynamics of obstructed tracer particle diffusion in one-dimensional systems}},
url = {http://scitation.aip.org/content/aip/journal/jcp/141/9/10.1063/1.4894117},
volume = {141},
year = {2014}
}
@article{Rzehak2003,
abstract = {We discuss relaxation of conformational fluctuations around deformed polymer states. To this end, Brownian dynamics simulations of bead-spring models including a finite extensibility of the springs as well as excluded volume and hydrodynamic interactions between the beads have been performed. Complete spectra of relaxation times as well as corresponding relaxation modes are obtained from the simulation data by applying the static dynamics formalism, which rigorously describes the initial decay of correlations between the bead positions. As shown here, this procedure amounts to using a generalized Rouse-Zimm-like model which is governed by linear effective equations of motion having the same initial decay of correlations as the full nonlinear bead-spring model used in the simulations. In thermal equilibrium, the well-known scaling laws in the presence of excluded volume and hydrodynamic interactions between the beads are recovered, but, in addition, the static dynamics method also yields numeric values for the nonuniversal prefactors of the respective laws. The method is equally applicable to a broad range of problems, where the polymer is deformed by the action of flows or forces. Two examples of recent interest are considered: a tethered polymer pulled at its free end and one which is stretched by a uniform flow. It is shown that in both cases, the relaxation process is dominated by a finite extensibility of the springs.},
author = {Rzehak, Roland and Zimmermann, Walter},
doi = {10.1103/PhysRevE.68.021804},
file = {:Users/wenwen/Documents/MendeleyRefs/Rzehak, Zimmermann{\_}Physical review. E, Statistical, nonlinear, and soft matter physics{\_}2003.pdf:pdf},
isbn = {1539-3755 (Print)$\backslash$r1539-3755 (Linking)},
issn = {1063-651X},
journal = {Phys. Rev. E},
month = {aug},
number = {2},
pages = {021804},
pmid = {14524998},
title = {{Static dynamics approach to relaxation modes and times for deformed polymers}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.68.021804},
volume = {68},
year = {2003}
}
@book{Andrews1998,
author = {Andrews, G E},
isbn = {9780521637664},
publisher = {Cambridge University Press},
series = {Cambridge mathematical library},
title = {{The Theory of Partitions}},
url = {https://books.google.de/books?id=Sp7z9sK7RNkC},
year = {1998}
}
@article{Li2003,
abstract = {We establish a connection between anomalous heat conduction and anomalous diffusion in one dimensional systems. It is shown that if the mean square of the displacement of the particle is {\$}{\textless}\backslashDelta x{\^{}}2{\textgreater} =2Dt{\^{}}{\{}\backslashalpha{\}} (0{\textless}\backslashalpha\backslashle 2){\$}, then the thermal conductivity can be expressed in terms of the system size {\$}L{\$} as {\$}\backslashkappa = cL{\^{}}{\{}\backslashbeta{\}}{\$} with {\$}\backslashbeta=2-2/\backslashalpha{\$}. This result predicts that a normal diffusion ({\$}\backslashalpha =1{\$}) implies a normal heat conduction obeying the Fourier law ({\$}\backslashbeta=0{\$}), a superdiffusion ({\$}\backslashalpha{\textgreater}1{\$}) implies an anomalous heat conduction with a divergent thermal conductivity ({\$}\backslashbeta{\textgreater}0{\$}), and more interestingly, a subdiffusion ({\$}\backslashalpha {\textless}1{\$}) implies an anomalous heat conduction with a convergent thermal conductivity ({\$}\backslashbeta{\textless}0{\$}), consequently, the system is a thermal insulator in the thermodynamic limit. Existing numerical data support our results.},
archivePrefix = {arXiv},
arxivId = {cond-mat/0306554},
author = {Li, Baowen and Wang, Jiao},
doi = {10.1103/PhysRevLett.91.044301},
eprint = {0306554},
file = {:Users/wenwen/Documents/MendeleyRefs/Li, Wang{\_}Unknown{\_}2003.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
keywords = {and anomalous diffusion in,between anomalous heat conduction,dimensional systems,ek laboratories,if the mean square,it is shown that,national university of singapore,of the displacement of,one-,published 24 july 2003,received 18 december 2002,republic of singapore,singapore 119260,the particle is h,we establish a connection,x 2 i},
month = {jul},
number = {4},
pages = {044301},
primaryClass = {cond-mat},
title = {{Anomalous Heat Conduction and Anomalous Diffusion in One-Dimensional Systems}},
url = {http://arxiv.org/abs/cond-mat/0306554 http://link.aps.org/doi/10.1103/PhysRevLett.91.044301},
volume = {91},
year = {2003}
}
@article{Alim2007,
abstract = {The shape of semiflexible polymer rings is studied over their whole range of flexibility. Investigating the joint distribution of asphericity and the nature of asphericity as well as their respective averages, we find two distinct shape regimes depending on the flexibility of the polymer. For a small perimeter to persistence length the fluctuating rings exhibit only planar, elliptical configurations. At higher flexibilities three-dimensional, crumpled structures arise. Analytic calculations confirm the qualitative behavior of the averaged shape parameters and the elliptical shape in the stiff regime.},
archivePrefix = {arXiv},
arxivId = {q-bio/0703049},
author = {Alim, Karen and Frey, Erwin},
doi = {10.1103/PhysRevLett.99.198102},
eprint = {0703049},
file = {:Users/wenwen/Documents/MendeleyRefs/Alim, Frey{\_}Physical Review Letters{\_}2007.pdf:pdf},
isbn = {0031-9007},
issn = {00319007},
journal = {Phys. Rev. Lett.},
number = {November},
pages = {1--4},
pmid = {18233119},
primaryClass = {q-bio},
title = {{Shapes of semiflexible polymer rings}},
volume = {99},
year = {2007}
}
@phdthesis{Lazarescu2013a,
archivePrefix = {arXiv},
arxivId = {1311.7370},
author = {Lazarescu, Alexandre},
eprint = {1311.7370},
file = {:Users/wenwen/Documents/MendeleyRefs/Lazarescu{\_}Unknown{\_}2013.pdf:pdf},
pages = {198},
school = {Universite Pierre et Marie Curie},
title = {{Exact Large Deviations of the Current in the Asymmetric Simple Exclusion Process with Open Boundaries}},
url = {http://arxiv.org/abs/1311.7370},
year = {2013}
}
@article{Balasubramanian2004,
abstract = {Cytokinesis is a temporally and spatially regulated process through which the cellular constituents of the mother cell are partitioned into two daughter cells, permitting an increase in cell number. When cytokinesis occurs in a polarized cell it can create daughters with distinct fates. In eukaryotes, cytokinesis is carried out by the coordinated action of a cortical actomyosin contractile ring and targeted membrane deposition. Recent use of model organisms with facile genetics and improved light-microscopy methods has led to the identification and functional characterization of many proteins involved in cytokinesis. To date, this analysis indicates that some of the basic components involved in cytokinesis are conserved from yeast to humans, although their organization into functional machinery that drives cytokinesis and the associated regulatory mechanisms bear species-specific features. Here, we briefly review the current status of knowledge of cytokinesis in the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe and animal cells, in an attempt to highlight both the common and the unique features. Although these organisms diverged from a common ancestor about a billion years ago, there are eukaryotes that are far more divergent. To evaluate the overall evolutionary conservation of cytokinesis, it will be necessary to include representatives of these divergent branches. Nevertheless, the three species discussed here provide substantial mechanistic diversity.},
author = {Balasubramanian, Mohan K and Bi, Erfei and Glotzer, Michael},
doi = {10.1016/j.cub.2004.09.022},
file = {:Users/wenwen/Documents/MendeleyRefs/Balasubramanian, Bi, Glotzer{\_}Current Biology{\_}2004.pdf:pdf},
issn = {09609822},
journal = {Curr. Biol.},
keywords = {Animals,Biological,Biological Evolution,Cell Cycle Proteins,Cell Cycle Proteins: physiology,Cell Membrane,Cell Membrane: physiology,Cytokinesis,Cytokinesis: physiology,Cytoskeletal Proteins,Cytoskeletal Proteins: physiology,Eukaryotic Cells,Eukaryotic Cells: physiology,Genes,Models,Myosin Type II,Myosin Type II: physiology,Saccharomyces cerevisiae,Schizosaccharomyces,cdc,cdc: physiology},
month = {sep},
number = {18},
pages = {R806--R818},
pmid = {15380095},
title = {{Comparative Analysis of Cytokinesis in Budding Yeast, Fission Yeast and Animal Cells}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15380095 http://linkinghub.elsevier.com/retrieve/pii/S0960982204006980},
volume = {14},
year = {2004}
}
@book{Taylor1998,
author = {Taylor, H.M. and Karlin, S.},
edition = {3},
file = {:Users/wenwen/Documents/MendeleyRefs/Taylor, Karlin{\_}Unknown{\_}1998.pdf:pdf},
publisher = {Academic Press},
title = {{An introduction to stochastic modeling}},
year = {1998}
}
@article{Li2015a,
author = {Li, Bing and Sun, Zhao-Yan Yan and An, Li-Jia Jia},
doi = {10.1063/1.4926775},
file = {:Users/wenwen/Documents/MendeleyRefs/Li, Sun, An{\_}Journal of Chemical Physics{\_}2015.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {2},
pages = {024908},
title = {{Effects of topology on the adsorption of singly tethered ring polymers to attractive surfaces}},
url = {http://dx.doi.org/10.1063/1.4926775 http://scitation.aip.org/content/aip/journal/jcp/143/2/10.1063/1.4926775},
volume = {143},
year = {2015}
}
@article{Kroeger,
author = {Kroeger, Martin},
doi = {10.1016/j.physrep.2003.10.014},
file = {:Users/wenwen/Documents/MendeleyRefs/Kroeger{\_}Physics Reports{\_}2004.pdf:pdf},
issn = {03701573},
journal = {Phys. Rep.},
keywords = {brownian dynamics,computer simulation,constitutive equation,dynamics,elongated particle,ferro uid,flow,kinetic theory,liquid crystal,mesoscopic models,microscopic models,molecular dynamics,network,non-newtonian rheology,order parameter,orientation,path,polymer,primitive,semi exible chain,stochastic di erential equation,structure,tube model,viscosities},
month = {feb},
number = {6},
pages = {453--551},
title = {{Simple models for complex nonequilibrium fluids}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0370157303003958},
volume = {390},
year = {2004}
}
@article{Kreer2004a,
abstract = {We present a comparison between results, obtained from different simulation models, for the static properties of end-tethered polymer layers in good solvent. Our analysis includes data from two previous studies--the bond fluctuation model of Wittmer et al. [J. Chem. Phys. 101, 4379 (1994)] and the off-lattice bead-spring model of Grest and Murat [Macromolecules 26, 3108 (1993)]. Additionally, we explore the properties of a similar off-lattice model simulated close to the Theta temperature. We show that the data for the bond fluctuation and the Grest-Murat model can be analyzed in terms of scaling theory because chains are swollen inside the Pincus blob. In the vicinity of the Theta point the structure of the chains is essentially Gaussian in the Pincus blob. Therefore, the data for the second off-lattice model can be compared quantitatively to the self-consistent field theory. Different ways to determine the parameters of the self-consistent field theory are discussed.},
author = {Kreer, T. and Metzger, S. and M{\"{u}}ller, M. and Binder, K. and Baschnagel, J.},
doi = {10.1063/1.1642615},
file = {:Users/wenwen/Documents/MendeleyRefs/Kreer et al.{\_}Journal of Chemical Physics{\_}2004.pdf:pdf},
isbn = {0021-9606 (Print)
0021-9606 (Linking)},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {8},
pages = {4012--4023},
pmid = {15268567},
title = {{Static properties of end-tethered polymers in good solution: A comparison between different models}},
volume = {120},
year = {2004}
}
@article{Abarbanel1993,
author = {Abarbanel, Henry and Brown, Reggie and Sidorowich, John and Tsimring, Lev},
doi = {10.1103/RevModPhys.65.1331},
file = {:Users/wenwen/Documents/MendeleyRefs/Abarbanel et al.{\_}Reviews of Modern Physics{\_}1993.pdf:pdf},
issn = {0034-6861},
journal = {Rev. Mod. Phys.},
month = {oct},
number = {4},
pages = {1331--1392},
title = {{The analysis of observed chaotic data in physical systems}},
url = {http://link.aps.org/doi/10.1103/RevModPhys.65.1331},
volume = {65},
year = {1993}
}
@article{Isichenko1992,
author = {Isichenko, MB},
file = {:Users/wenwen/Documents/MendeleyRefs/Isichenko{\_}Reviews of Modern Physics{\_}1992.pdf:pdf},
journal = {Rev. Mod. Phys.},
number = {4},
title = {{Percolation, statistical topography, and transport in random media}},
url = {http://rmp.aps.org/abstract/RMP/v64/i4/p961{\_}1},
volume = {64},
year = {1992}
}
@article{Macdonald1968,
author = {MacDonald, Carolyn T. and Gibbs, Julian H. and Pipkin, Allen C.},
file = {:Users/wenwen/Documents/MendeleyRefs/MacDonald, Gibbs, Pipkin{\_}Biopolymers{\_}1968.pdf:pdf},
journal = {Biopolymers},
pages = {1--25},
title = {{Kinetics of Biopolymerization}},
volume = {6},
year = {1968}
}
@article{Chikashige1997,
abstract = {In fission yeast meiotic prophase, telomeres are clustered near the spindle pole body (SPB; a centrosome-equivalent structure in fungi) and take the leading position in chromosome movement, while centromeres are separated from the SPB. This telomere position contrasts with mitotic nuclear organization, in which centromeres remain clustered near the SPB and lead chromosome movement. Thus, nuclear reorganization switching the position of centromeres and telomeres must take place upon entering meiosis. In this report, we analyze the nuclear location of centromeres and telomeres in genetically well-characterized meiotic mutant strains. An intermediate structure for telomere-centromere switching was observed in haploid cells induced to undergo meiosis by synthetic mating pheromone; fluorescence in situ hybridization revealed that in these cells, both telomeres and centromeres were clustered near the SPB. Further analyses in a series of mutants showed that telomere-centromere switching takes place in two steps; first, association of telomeres with the SPB and, second, dissociation of centromeres from the SPB. The first step can take place in the haploid state in response to mating pheromone, but the second step does not take place in haploid cells and probably depends on conjugation-related events. In addition, a linear minichromosome was also co-localized with authentic telomeres instead of centromeres, suggesting that telomere clustering plays a role in organizing chromosomes within a meiotic prophase nucleus.},
author = {Chikashige, Yuji and Ding, Da Qiao and Imai, Yoshiyuki and Yamamoto, Masayuki and Haraguchi, Tokuko and Hiraoka, Yasushi},
doi = {10.1093/emboj/16.1.193},
isbn = {0261-4189 (Print)$\backslash$r0261-4189 (Linking)},
issn = {02614189},
journal = {EMBO J.},
keywords = {Chromosome dynamics,Fission yeast,Fluorescence microscopy,Meiosis,Telomere},
number = {1},
pages = {193--202},
pmid = {9009280},
title = {{Meiotic nuclear reorganization: Switching the position of centromeres and telomeres in the fission yeast Schizosaccharomyces pombe}},
volume = {16},
year = {1997}
}
@article{Agmon1986,
author = {Agmon, N},
doi = {Doi 10.1007/Bf01020652},
file = {:Users/wenwen/Documents/MendeleyRefs/Agmon{\_}Journal of Statistical Physics{\_}1986.pdf:pdf},
isbn = {0022-4715},
journal = {J. Stat. Phys.},
number = {3-4},
pages = {537--559},
title = {{Diffusion with Random Traps: Transient One-Dimensional Kinetics in a Linear Potential}},
volume = {43},
year = {1986}
}
@article{Pasquino2013,
author = {Pasquino, Rossana and Vasilakopoulos, Thodoris C. and Jeong, Youn Cheol and Lee, Hyojoon and Rogers, Simon and Sakellariou, George and Allgaier, J{\"{u}}rgen and Takano, Atsushi and Br{\'{a}}s, Ana R. and Chang, Taihyun and Goo{\ss}en, Sebastian and Pyckhout-Hintzen, Wim and Wischnewski, Andreas and Hadjichristidis, Nikos and Richter, Dieter and Rubinstein, Michael and Vlassopoulos, Dimitris},
doi = {10.1021/mz400344e},
file = {:Users/wenwen/Documents/MendeleyRefs/Pasquino et al.{\_}ACS Macro Letters{\_}2013.pdf:pdf},
issn = {21611653},
journal = {ACS Macro Lett.},
pages = {874--878},
title = {{Viscosity of ring polymer melts}},
volume = {2},
year = {2013}
}
@article{Leyva2012,
author = {Leyva, I. and Sevilla-Escoboza, R. and Buld{\'{u}}, J. and Sendi{\~{n}}a-Nadal, I. and G{\'{o}}mez-Garde{\~{n}}es, J. and Arenas, a. and Moreno, Y. and G{\'{o}}mez, S. and Jaimes-Re{\'{a}}tegui, R. and Boccaletti, S.},
doi = {10.1103/PhysRevLett.108.168702},
file = {:Users/wenwen/Documents/MendeleyRefs/Leyva et al.{\_}Physical Review Letters{\_}2012.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {apr},
number = {16},
pages = {1--4},
title = {{Explosive First-Order Transition to Synchrony in Networked Chaotic Oscillators}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.108.168702},
volume = {108},
year = {2012}
}
@book{Rippe2012,
author = {Rippe, Karsten},
file = {:Users/wenwen/Documents/MendeleyRefs/Rippe{\_}Unknown{\_}2012.pdf:pdf},
publisher = {Wiley-VCH},
title = {{Genome organization and function in the cell nucleus}},
year = {2012}
}
@article{Grosberg1996,
abstract = {A mean field theory of the effect of knots on the statistical mechanics of ring polymers is presented. We introduce a topological invariant which is related to the primitive path in the "polymer in the lattice of obstacles" model and use it to estimate the entropic contribution to the free energy of a nonphantom ring polymer. The theory predicts that the volume of the maximally knotted ring polymer is independent of solvent quality and that the presence of knots suppresses both the swelling of the ring in a good solvent and its collapse in a poor solvent. The probability distribution of the degree of knotting is estimated and it is shown that the most probable degree of knotting upon random closure of the chain grows dramatically with chain compression. The theory also predicts some unexpected phenomena such as "knot segregation" in a swollen polymer ring, when the bulk of the ring expels all the entanglements and swells freely, with all the knots concentrated in a relatively small and compact part of the polymer.},
author = {Grosberg, Alexander and Feigel, Alexander and Rabin, Yitzhak},
doi = {10.1103/PhysRevE.54.6618},
file = {:Users/wenwen/Documents/MendeleyRefs/Grosberg, Feigel, Rabin{\_}Physical Review E{\_}1996.pdf:pdf},
issn = {1063-651X},
journal = {Phys. Rev. E},
number = {6},
pages = {6618--6622},
pmid = {9965887},
title = {{Flory-type theory of a knotted ring polymer}},
volume = {54},
year = {1996}
}
@article{Lizana2009,
author = {Lizana, L. and Ambj{\"{o}}rnsson, T.},
doi = {10.1103/PhysRevE.80.051103},
file = {:Users/wenwen/Documents/MendeleyRefs/Lizana, Ambj{\"{o}}rnsson{\_}Physical Review E{\_}2009.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
number = {5},
pages = {051103},
title = {{Diffusion of finite-sized hard-core interacting particles in a one-dimensional box: Tagged particle dynamics}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.80.051103},
volume = {80},
year = {2009}
}
@phdthesis{Streek2005,
author = {Streek, Martin Andreas},
file = {:Users/wenwen/Documents/MendeleyRefs/Streek{\_}Unknown{\_}2005.pdf:pdf},
school = {University Bielefeld},
title = {{Brownian Dynamics Simulation of Migration of DNA in structured Microchannels}},
year = {2005}
}
@article{Batchelor2007,
abstract = {A 1931 result that lay in obscurity for decades, Bethe's solution to a quantum mechanical model now finds its way into everything from superconductors to string theory.},
author = {Batchelor, Murray T.},
doi = {10.1063/1.2709557},
file = {:Users/wenwen/Documents/MendeleyRefs/Batchelor{\_}Physics Today{\_}2007.pdf:pdf},
issn = {00319228},
journal = {Phys. Today},
keywords = {Physics Today January 2007, page  36-40},
number = {1},
pages = {36--40},
title = {{The Bethe ansatz after 75 years}},
volume = {60},
year = {2007}
}
@article{Barabasi2009,
abstract = {For decades, we tacitly assumed that the components of such complex systems as the cell, the society, or the Internet are randomly wired together. In the past decade, an avalanche of research has shown that many real networks, independent of their age, function, and scope, converge to similar architectures, a universality that allowed researchers from different disciplines to embrace network theory as a common paradigm. The decade-old discovery of scale-free networks was one of those events that had helped catalyze the emergence of network science, a new research field with its distinct set of challenges and accomplishments.},
author = {Barabasi, A.-L.},
doi = {10.1126/science.1173299},
file = {:Users/wenwen/Documents/MendeleyRefs/Barabasi{\_}Science{\_}2009.pdf:pdf},
issn = {0036-8075},
journal = {Science (80-. ).},
keywords = {Models,Systems Theory,Theoretical},
month = {jul},
number = {5939},
pages = {412--413},
pmid = {19628854},
title = {{Scale-Free Networks: A Decade and Beyond}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1173299},
volume = {325},
year = {2009}
}
@article{Cao2003a,
abstract = {By using a set of gauge transformations (face-vertex correspondence relations), the XXZ spin chain with both transverse and longitudinal magnetic boundary fields is studied. The corresponding reflection boundary matrices therefore have non-diagonal elements. The Bethe ansatz equations, the eigenvalues and the eigenstates of the transfer matrix and the Hamiltonian of the system are obtained in the framework of algebraic Bethe ansatz method. The ground states for different couplings are derived. ?? 2003 Elsevier B.V. All rights reserved.},
archivePrefix = {arXiv},
arxivId = {cond-mat/0212163},
author = {Cao, Junpeng and Lin, Hai Qing and Shi, Kang Jie and Wang, Yupeng},
doi = {10.1016/S0550-3213(03)00372-9},
eprint = {0212163},
file = {:Users/wenwen/Documents/MendeleyRefs/Cao et al.{\_}Nuclear Physics B{\_}2003.pdf:pdf},
issn = {05503213},
journal = {Nucl. Phys. B},
keywords = {Bethe ansatz,Gauge transformation,Reflection equation,XXZ spin chain},
number = {3},
pages = {487--519},
primaryClass = {cond-mat},
title = {{Exact solution of XXZ spin chain with unparallel boundary fields}},
volume = {663},
year = {2003}
}
@article{Alvarez-Llamoza2008,
author = {Alvarez-Llamoza, O. and Cosenza, M.},
doi = {10.1103/PhysRevE.78.046216},
file = {:Users/wenwen/Documents/MendeleyRefs/Alvarez-Llamoza, Cosenza{\_}Physical Review E{\_}2008.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {oct},
number = {4},
pages = {1--6},
title = {{Generalized synchronization of chaos in autonomous systems}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.78.046216},
volume = {78},
year = {2008}
}
@incollection{Papoulis1965,
abstract = {Not Available},
author = {Papoulis, Athanasios},
edition = {3},
file = {:Users/wenwen/Documents/MendeleyRefs/Papoulis{\_}Unknown{\_}1965.pdf:pdf},
isbn = {0073660116},
publisher = {McGraw-Hill},
title = {{Probability, random variables, and stochastic processes}},
year = {1965}
}
@article{Winkler1999,
author = {Winkler, Roland},
doi = {10.1103/PhysRevLett.82.1843},
file = {:Users/wenwen/Documents/MendeleyRefs/Winkler{\_}Physical Review Letters{\_}1999.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
number = {9},
pages = {1843--1846},
title = {{Analytical Calculation of the Relaxation Dynamics of Partially Stretched Flexible Chain Molecules: Necessity of a Wormlike Chain Description}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.82.1843},
volume = {82},
year = {1999}
}
@article{Sachs1995,
abstract = {Fluorescence in situ hybridization data on distances between defined genomic sequences are used to construct a quantitative model for the overall geometric structure of a human chromosome. We suggest that the large-scale geometry during the G0/G1 part of the cell cycle may consist of flexible chromatin loops, averaging approximately 3 million bp, with a random-walk backbone. A fully explicit, three-parametric polymer model of this random-walk/giant-loop structure can account well for the data. More general models consistent with the data are briefly discussed.},
author = {Sachs, R K and van den Engh, G and Trask, B and Yokota, H and Hearst, J E},
doi = {10.1073/pnas.92.7.2710},
file = {:Users/wenwen/Documents/MendeleyRefs/Sachs et al.{\_}Proceedings of the National Academy of Sciences{\_}1995.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
keywords = {Base Composition,Chromatin,Chromatin: ultrastructure,Chromosomes,Fluorescence,Genetic,Human,Human: physiology,Human: ultrastructure,Humans,In Situ Hybridization,Interphase,Models,Polymers,Random Allocation,Theoretical},
month = {mar},
number = {7},
pages = {2710--2714},
pmid = {7708711},
title = {{A random-walk/giant-loop model for interphase chromosomes.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=42288{\&}tool=pmcentrez{\&}rendertype=abstract http://www.pnas.org/cgi/doi/10.1073/pnas.92.7.2710},
volume = {92},
year = {1995}
}
@article{Wong2013,
abstract = {Biological functions including gene expression and DNA repair are affected by the 3D architecture of the genome, but the underlying mechanisms are still unknown. Notably, it remains unclear to what extent nuclear architecture is driven by generic physical properties of polymers or by specific factors such as proteins binding particular DNA sequences. The budding yeast nucleus has been intensely studied by imaging and biochemical techniques, resulting in a large quantitative data set on locus positions and DNA contact frequencies. We recently described a quantitative model of the interphase yeast nucleus in which chromosomes are represented as passively moving polymer chains. This model ignores the DNA sequence information except for specific constraints at the centromeres, telomeres, and the ribosomal DNA (rDNA). Despite its simplicity, the model accounts for a large majority of experimental data, including absolute and relative locus positions and contact frequency patterns at chromosomal and subchromosomal scales. Here, we also illustrate the model's ability to reproduce observed features of chromatin movements. Our results strongly suggest that the dynamic large-scale architecture of the yeast nucleus is dominated by statistical properties of randomly moving polymers with a few sequence-specific constraints, rather than by a large number of DNA-specific factors or epigenetic modifications. In addition, we show that our model accounts for recently measured variations in homologous recombination efficiency, illustrating its potential for quantitatively understanding functional consequences of nuclear architecture.},
author = {Wong, Hua and Arbona, Jean-michel and Zimmer, Christophe},
doi = {10.4161/nucl.26226},
file = {:Users/wenwen/Documents/MendeleyRefs/Wong, Arbona, Zimmer{\_}Nucleus{\_}2013.pdf:pdf},
issn = {1949-1034},
journal = {Nucleus},
keywords = {bination,chro-,chromosome structure,computational,genome architecture,homologous recom-,model,mosome dynamics,nucleolus,polymer physics},
month = {sep},
number = {5},
pages = {361--366},
pmid = {23974728},
title = {{How to build a yeast nucleus}},
url = {http://www.tandfonline.com/doi/abs/10.4161/nucl.26226},
volume = {4},
year = {2013}
}
@article{Arai2010,
abstract = {In eukaryotic cells, the nuclear envelope partitions the nucleus from the cytoplasm. The fission yeast Schizosaccharomyces pombe undergoes closed mitosis in which the nuclear envelope persists rather than being broken down, as in higher eukaryotic cells [1]. It is therefore assumed that nucleocytoplasmic transport continues during the cell cycle [2]. Here we show that nuclear transport is, in fact, abolished specifically during anaphase of the second meiotic nuclear division. During that time, both nucleoplasmic and cytoplasmic proteins disperse throughout the cell, reminiscent of the open mitosis of higher eukaryotes, but the architecture of the S. pombe nuclear envelope itself persists. This functional alteration of the nucleocytoplasmic barrier is likely induced by spore wall formation, because ectopic induction of sporulation signaling leads to premature dispersion of nucleoplasmic proteins. A photobleaching assay demonstrated that nuclear envelope permeability increases abruptly at the onset of anaphase of the second meiotic division. The permeability was not altered when sporulation was inhibited by blocking the trafficking of forespore-membrane vesicles from the endoplasmic reticulum to the Golgi. The evidence indicates that yeast gametogenesis produces vesicle transport-mediated forespore membranes by inducing nuclear envelope permeabilization. {\textcopyright} 2010 Elsevier Ltd. All rights reserved.},
author = {Arai, Kunio and Sato, Masamitsu and Tanaka, Kayoko and Yamamoto, Masayuki},
doi = {10.1016/j.cub.2010.09.004},
file = {:Users/wenwen/Documents/MendeleyRefs/Arai et al.{\_}Current Biology{\_}2010.pdf:pdf},
isbn = {1879-0445 (Electronic)$\backslash$r0960-9822 (Linking)},
issn = {09609822},
journal = {Curr. Biol.},
number = {21},
pages = {1913--1918},
pmid = {20970334},
publisher = {Elsevier Ltd},
title = {{Nuclear compartmentalization is abolished during fission yeast meiosis}},
url = {http://dx.doi.org/10.1016/j.cub.2010.09.004},
volume = {20},
year = {2010}
}
@article{Cho2010,
author = {Cho, Y. S. and Kahng, B. and Kim, D.},
doi = {10.1103/PhysRevE.81.030103},
file = {:Users/wenwen/Documents/MendeleyRefs/Cho, Kahng, Kim{\_}Physical Review E{\_}2010.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {mar},
number = {3},
pages = {4--7},
title = {{Cluster aggregation model for discontinuous percolation transitions}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.81.030103},
volume = {81},
year = {2010}
}
@article{Mallick2011,
archivePrefix = {arXiv},
arxivId = {arXiv:1101.2849v1},
author = {Mallick, Kirone},
doi = {10.1088/1742-5468/2011/01/P01024},
eprint = {arXiv:1101.2849v1},
file = {:Users/wenwen/Documents/MendeleyRefs/Mallick{\_}Journal of Statistical Mechanics Theory and Experiment{\_}2011.pdf:pdf},
issn = {1742-5468},
journal = {J. Stat. Mech. Theory Exp.},
keywords = {asep,bethe ansatz,large deviations,matrix ansatz,non-equilibrium statistical physics},
month = {jan},
number = {01},
pages = {P01024},
title = {{Some exact results for the exclusion process}},
url = {http://iopscience.iop.org/1742-5468/2011/01/P01024 http://stacks.iop.org/1742-5468/2011/i=01/a=P01024?key=crossref.c0cd9b1fac13ddb79c3e5ed7553f3370},
volume = {2011},
year = {2011}
}
@book{Habershon2013,
abstract = {This article reviews the ring-polymer molecular dynamics model for condensed-phase quantum dynamics. This model, which involves classical evolution in an extended ring-polymer phase space, provides a practical approach to approximating the effects of quantum fluctuations on the dynamics of condensed-phase systems. The review covers the theory, implementation, applications, and limitations of the approximation.},
author = {Habershon, Scott and Manolopoulos, David E and Markland, Thomas E and Miller, Thomas F},
booktitle = {Annu. Rev. Phys. Chem.},
doi = {10.1146/annurev-physchem-040412-110122},
file = {:Users/wenwen/Documents/MendeleyRefs/Habershon et al.{\_}Annual review of physical chemistry{\_}2013.pdf:pdf},
isbn = {0404121101},
issn = {1545-1593},
keywords = {path integral,quantum dynamics,semiclassical theory,time-correlation function,tunneling,zero-point energy},
pages = {387--413},
pmid = {23298242},
title = {{Ring-polymer molecular dynamics: quantum effects in chemical dynamics from classical trajectories in an extended phase space.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23298242},
volume = {64},
year = {2013}
}
@article{Restrepo2005,
author = {Restrepo, Juan and Ott, Edward and Hunt, Brian},
doi = {10.1103/PhysRevE.71.036151},
file = {:Users/wenwen/Documents/MendeleyRefs/Restrepo, Ott, Hunt{\_}Physical Review E{\_}2005.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {mar},
number = {3},
pages = {1--12},
title = {{Onset of synchronization in large networks of coupled oscillators}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.71.036151},
volume = {71},
year = {2005}
}
@article{Watts1998,
abstract = {Networks of coupled dynamical systems have been used to model biological oscillators, Josephson junction arrays, excitable media, neural networks, spatial games, genetic control networks and many other self-organizing systems. Ordinarily, the connection topology is assumed to be either completely regular or completely random. But many biological, technological and social networks lie somewhere between these two extremes. Here we explore simple models of networks that can be tuned through this middle ground: regular networks 'rewired' to introduce increasing amounts of disorder. We find that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs. We call them 'small-world' networks, by analogy with the small-world phenomenon (popularly known as six degrees of separation. The neural network of the worm Caenorhabditis elegans, the power grid of the western United States, and the collaboration graph of film actors are shown to be small-world networks. Models of dynamical systems with small-world coupling display enhanced signal-propagation speed, computational power, and synchronizability. In particular, infectious diseases spread more easily in small-world networks than in regular lattices.},
author = {Watts, D J and Strogatz, S H},
doi = {10.1038/30918},
file = {:Users/wenwen/Documents/MendeleyRefs/Watts, Strogatz{\_}Nature{\_}1998.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
keywords = {Animals,Caenorhabditis elegans,Caenorhabditis elegans: physiology,Communicable Diseases,Communicable Diseases: transmission,Games, Experimental,Models, Biological,Models, Neurological,Models, Theoretical,Nerve Net},
month = {jun},
number = {6684},
pages = {440--2},
pmid = {9623998},
title = {{Collective dynamics of 'small-world' networks.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9623998},
volume = {393},
year = {1998}
}
@article{Hsieh2006,
abstract = {A very stiff finitely extensible nonlinear elastic (FENE)-Fraenkel spring is proposed to replace the rigid rod in the bead-rod model. This allows the adoption of a fast predictor-corrector method so that large time steps can be taken in Brownian dynamics (BD) simulations without over- or understretching the stiff springs. In contrast to the simple bead-rod model, BD simulations with beads and FENE-Fraenkel (FF) springs yield a random-walk configuration at equilibrium. We compare the simulation results of the free-draining bead-FF-spring model with those for the bead-rod model in relaxation, start-up of uniaxial extensional, and simple shear flows, and find that both methods generate nearly identical results. The computational cost per time step for a free-draining BD simulation with the proposed bead-FF-spring model is about twice as high as the traditional bead-rod model with the midpoint algorithm of Liu [J. Chem. Phys. 90, 5826 (1989)]. Nevertheless, computations with the bead-FF-spring model are as efficient as those with the bead-rod model in extensional flow because the former allows larger time steps. Moreover, the Brownian contribution to the stress for the bead-FF-spring model is isotropic and therefore simplifies the calculation of the polymer stresses. In addition, hydrodynamic interaction can more easily be incorporated into the bead-FF-spring model than into the bead-rod model since the metric force arising from the non-Cartesian coordinates used in bead-rod simulations is absent from bead-spring simulations. Finally, with our newly developed bead-FF-spring model, existing computer codes for the bead-spring models can trivially be converted to ones for effective bead-rod simulations merely by replacing the usual FENE or Cohen spring law with a FENE-Fraenkel law, and this convertibility provides a very convenient way to perform multiscale BD simulations.},
author = {Hsieh, Chih Chen CC and Jain, Semant and Larson, RG Ronald G.},
doi = {10.1063/1.2161210},
file = {:Users/wenwen/Documents/MendeleyRefs/Hsieh, Jain, Larson{\_}The Journal of chemical physics{\_}2006.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Hsieh, Jain, Larson{\_}The Journal of chemical physics{\_}2006.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
pages = {1--10},
pmid = {16460216},
title = {{Brownian dynamics simulations with stiff finitely extensible nonlinear elastic-Fraenkel springs as approximations to rods in bead-rod models}},
url = {http://scitation.aip.org/content/aip/journal/jcp/124/4/10.1063/1.2161210},
volume = {124},
year = {2006}
}
@article{Lui2013,
abstract = {Homolog pairing and crossing over during meiosis I prophase is required for accurate chromosome segregation to form euploid gametes. The repair of Spo11-induced double-strand breaks (DSB) using a homologous chromosome template is a major driver of pairing in many species, including fungi, plants, and mammals. Inappropriate pairing and crossing over at ectopic loci can lead to chromosome rearrangements and aneuploidy. How (or if) inappropriate ectopic interactions are disrupted in favor of allelic interactions is not clear. Here we used an in vivo "collision" assay in budding yeast to test the contributions of cohesion and the organization and motion of chromosomes in the nucleus on promoting or antagonizing interactions between allelic and ectopic loci at interstitial chromosome sites. We found that deletion of the cohesin subunit Rec8, but not other chromosome axis proteins (e.g. Red1, Hop1, or Mek1), caused an increase in homolog-nonspecific chromosome interaction, even in the absence of Spo11. This effect was partially suppressed by expression of the mitotic cohesin paralog Scc1/Mdc1, implicating Rec8's role in cohesion rather than axis integrity in preventing nonspecific chromosome interactions. Disruption of telomere-led motion by treating cells with the actin polymerization inhibitor Latrunculin B (Lat B) elevated nonspecific collisions in rec8$\Delta$ spo11$\Delta$. Next, using a visual homolog-pairing assay, we found that the delay in homolog pairing in mutants defective for telomere-led chromosome motion (ndj1$\Delta$ or csm4$\Delta$) is enhanced in Lat B-treated cells, implicating actin in more than one process promoting homolog juxtaposition. We suggest that multiple, independent contributions of actin, cohesin, and telomere function are integrated to promote stable homolog-specific interactions and to destabilize weak nonspecific interactions by modulating the elastic spring-like properties of chromosomes.},
author = {Lui, Doris Y and Cahoon, Cori K and Burgess, Sean M},
doi = {10.1371/journal.pgen.1003197},
file = {:Users/wenwen/Documents/MendeleyRefs/Lui, Cahoon, Burgess{\_}PLoS genetics{\_}2013.pdf:pdf},
issn = {1553-7404},
journal = {PLoS Genet.},
keywords = {Cell Cycle Proteins,Cell Cycle Proteins: genetics,Cell Cycle Proteins: metabolism,Cell Nucleus,Cell Nucleus: genetics,Chromosomal Proteins, Non-Histone,Chromosomal Proteins, Non-Histone: genetics,Chromosomal Proteins, Non-Histone: metabolism,Chromosome Pairing,Chromosome Pairing: genetics,Chromosome Segregation,Chromosome Segregation: genetics,DNA Breaks, Double-Stranded,Endodeoxyribonucleases,Endodeoxyribonucleases: genetics,Endodeoxyribonucleases: metabolism,Meiosis,Meiotic Prophase I,Meiotic Prophase I: genetics,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Telomere,Telomere: genetics,Telomere: metabolism},
month = {jan},
number = {1},
pages = {e1003197},
pmid = {23341780},
title = {{Multiple opposing constraints govern chromosome interactions during meiosis.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3547833{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {9},
year = {2013}
}
@article{Hoffman2015,
author = {Hoffman, Charles S. and Wood, Valerie and Fantes, Peter A.},
doi = {10.1534/genetics.115.181503},
issn = {0016-6731},
journal = {Genetics},
month = {oct},
number = {2},
pages = {403--423},
title = {{An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System}},
url = {http://www.genetics.org/cgi/doi/10.1534/genetics.115.181503},
volume = {201},
year = {2015}
}
@article{Phani2006,
abstract = {Plane wave propagation in infinite two-dimensional periodic lattices is investigated using Floquet-Bloch principles. Frequency bandgaps and spatial filtering phenomena are examined in four representative planar lattice topologies: hexagonal honeycomb, Kagom{\'{e}} lattice, triangular honeycomb, and the square honeycomb. These topologies exhibit dramatic differences in their long-wavelength deformation properties. Long-wavelength asymptotes to the dispersion curves based on homogenization theory are in good agreement with the numerical results for each of the four lattices. The slenderness ratio of the constituent beams of the lattice (or relative density) has a significant influence on the band structure. The techniques developed in this work can be used to design lattices with a desired band structure. The observed spatial filtering effects due to anisotropy at high frequencies (short wavelengths) of wave propagation are consistent with the lattice symmetries.},
author = {Phani, a Srikantha and Woodhouse, J and Fleck, N a},
doi = {10.1121/1.2179748},
file = {:Users/wenwen/Documents/MendeleyRefs/Phani, Woodhouse, Fleck{\_}The Journal of the Acoustical Society of America{\_}2006.pdf:pdf},
isbn = {0001-4966},
issn = {00014966},
journal = {J. Acoust. Soc. Am.},
number = {4},
pages = {1995},
pmid = {16642813},
title = {{Wave propagation in two-dimensional periodic lattices}},
url = {http://scitation.aip.org/content/asa/journal/jasa/119/4/10.1121/1.2179748},
volume = {119},
year = {2006}
}
@article{DONNER2011b,
abstract = {Complex networks are an important paradigm of modern complex systems sciences which allows quantitatively assessing the structural properties of systems composed of different interacting entities. During the last years, intensive efforts have been spent on applying network-based concepts also for the analysis of dynamically relevant higher-order statistical properties of time series. Notably, many corresponding approaches are closely related with the concept of recurrence in phase space. In this paper, we review recent methodological advances in time series analysis based on complex networks, with a special emphasis on methods founded on recurrence plots. The potentials and limitations of the individual methods are discussed and illustrated for paradigmatic examples of dynamical systems as well as for real-world time series. Complex network measures are shown to provide information about structural features of dynamical systems that are complementary to those characterized by other methods of time series analysis and, hence, substantially enrich the knowledge gathered from other existing (linear as well as nonlinear) approaches.},
archivePrefix = {arXiv},
arxivId = {1010.6032},
author = {DONNER, REIK V. and SMALL, MICHAEL and DONGES, JONATHAN F. and MARWAN, NORBERT and ZOU, YONG and XIANG, RUOXI and KURTHS, J{\"{U}}RGEN},
doi = {10.1142/S0218127411029021},
eprint = {1010.6032},
file = {:Users/wenwen/Documents/MendeleyRefs/DONNER et al.{\_}International Journal of Bifurcation and Chaos{\_}2011.pdf:pdf},
issn = {0218-1274},
journal = {Int. J. Bifurc. Chaos},
keywords = {complex networks,recurrence plots,time series analysis},
month = {apr},
number = {04},
pages = {1019--1046},
title = {{RECURRENCE-BASED TIME SERIES ANALYSIS BY MEANS OF COMPLEX NETWORK METHODS}},
url = {http://www.worldscientific.com/doi/abs/10.1142/S0218127411029021},
volume = {21},
year = {2011}
}
@article{Strogatz2000,
author = {Strogatz, Steven H.},
doi = {10.1016/S0167-2789(00)00094-4},
file = {:Users/wenwen/Documents/MendeleyRefs/Strogatz{\_}Physica D Nonlinear Phenomena{\_}2000.pdf:pdf},
issn = {01672789},
journal = {Phys. D Nonlinear Phenom.},
keywords = {coupled oscillators,kinetic theory,kuramoto model,plasma physics},
month = {sep},
number = {1-4},
pages = {1--20},
title = {{From Kuramoto to Crawford: exploring the onset of synchronization in populations of coupled oscillators}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0167278900000944},
volume = {143},
year = {2000}
}
@book{Iachello2006,
author = {Iachello, Francesco},
doi = {10.1007/b11785361},
file = {:Users/wenwen/Documents/MendeleyRefs/Iachello{\_}Unknown{\_}2006.pdf:pdf},
publisher = {Springer-Verlag Berlin Heidelberg},
title = {{Lie Algebras and Applications}},
year = {2006}
}
@article{Memmesheimer2012,
abstract = {Despite the current debate about the computational role of experimentally observed precise spike patterns it is still theoretically unclear under which conditions and how they may emerge in neural circuits. Here, we study spiking neural networks with non-additive dendritic interactions that were recently uncovered in single-neuron experiments. We show that supra-additive dendritic interactions enable the persistent propagation of synchronous activity already in purely random networks without superimposed structures and explain the mechanism underlying it. This study adds a novel perspective on the dynamics of networks with nonlinear interactions in general and presents a new viable mechanism for the occurrence of patterns of precisely timed spikes in recurrent networks.},
author = {Memmesheimer, Raoul-Martin and Timme, Marc},
doi = {10.1371/journal.pcbi.1002384},
file = {:Users/wenwen/Documents/MendeleyRefs/Memmesheimer, Timme{\_}PLoS computational biology{\_}2012.pdf:pdf},
issn = {1553-7358},
journal = {PLoS Comput. Biol.},
month = {apr},
number = {4},
pages = {e1002384},
pmid = {22532791},
title = {{Non-additive coupling enables propagation of synchronous spiking activity in purely random networks.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3330086{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {8},
year = {2012}
}
@article{Wang2005,
abstract = {This paper is aimed to develop a Brownian dynamics simulation method for strongly confined semiflexible polymers where numerical simulation plays an indispensable role in complementing theory and experiments. A wormlike chain under strong confinement is modeled as a string of virtual spherical beads connected by inextensible rods with length varying according to the confinement intensity of the chain measured by the Odijk deflection length. The model takes hydrodynamic interactions into account. The geometrical constraints associated with the inextensible rods are realized by the so-called linear constraint solver. The model parameters are studied by quantitatively comparing the simulated properties of a double-stranded DNA chain with available experimental data and theoretical predictions.},
author = {Wang, Jizeng and Gao, Huajian},
doi = {10.1063/1.2008233},
file = {:Users/wenwen/Documents/MendeleyRefs/Wang, Gao{\_}Journal of Chemical Physics{\_}2005.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {8},
pmid = {16164329},
title = {{A generalized bead-rod model for Brownian dynamics simulations of wormlike chains under strng confinement}},
volume = {123},
year = {2005}
}
@article{Liggett2002,
author = {Liggett, Tm},
file = {:Users/wenwen/Documents/MendeleyRefs/Liggett{\_}Unknown{\_}2002.pdf:pdf},
title = {{Interacting particle systems-An introduction}},
year = {2002}
}
@article{Schrenk2012,
author = {Schrenk, K. and Felder, A. and Deflorin, S. and Ara{\'{u}}jo, N. a. and D'Souza, R. and Herrmann, H.},
doi = {10.1103/PhysRevE.85.031103},
file = {:Users/wenwen/Documents/MendeleyRefs/Schrenk et al.{\_}Physical Review E{\_}2012.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {mar},
number = {3},
pages = {1--9},
title = {{Bohman-Frieze-Wormald model on the lattice, yielding a discontinuous percolation transition}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.85.031103},
volume = {85},
year = {2012}
}
@article{Koszul2009a,
abstract = {Dramatic chromosome motion is a characteristic of mid-prophase of meiosis that is observed across broadly divergent eukaryotic phyla. Although the specific mechanisms underlying chromosome motions vary among organisms studied to date, the outcome is similar in all cases: vigorous back-and-forth movement (as fast as ???1 ??m/sec for budding yeast), led by chromosome ends (or near-end regions), and directed by cytoskeletal components via direct association through the nuclear envelope. The exact role(s) of these movements remains unknown, although an idea gaining currency is that movement serves as a stringency factor, eliminating unwanted inter-chromosomal associations or entanglements that have arisen as part of the homolog pairing process and, potentially, unwanted associations of chromatin with the nuclear envelope. Turbulent chromosome movements observed during bipolar orientation of chromosomes for segregation could also serve similar roles during mitosis. Recent advances shed light on the contribution of protein complexes involved in the meiotic movements in chromosome dynamics during the mitotic program. ?? 2009 Elsevier Ltd. All rights reserved.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Koszul, Romain and Kleckner, Nancy},
doi = {10.1016/j.tcb.2009.09.007},
eprint = {NIHMS150003},
file = {:Users/wenwen/Documents/MendeleyRefs/Koszul, Kleckner{\_}Trends in Cell Biology{\_}2009.pdf:pdf},
isbn = {1879-3088 (Electronic)$\backslash$r0962-8924 (Linking)},
issn = {09628924},
journal = {Trends Cell Biol.},
number = {12},
pages = {716--724},
pmid = {19854056},
title = {{Dynamic chromosome movements during meiosis: a way to eliminate unwanted connections?}},
volume = {19},
year = {2009}
}
@article{Araujo2010,
author = {Ara{\'{u}}jo, N. and Herrmann, H.},
doi = {10.1103/PhysRevLett.105.035701},
file = {:Users/wenwen/Documents/MendeleyRefs/Ara{\'{u}}jo, Herrmann{\_}Physical Review Letters{\_}2010.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {jul},
number = {3},
pages = {2--5},
title = {{Explosive Percolation via Control of the Largest Cluster}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.105.035701},
volume = {105},
year = {2010}
}
@book{Baschnagel2004,
abstract = {A coarse-grained simulation model eliminates microscopic degrees of freedom and represents a polymer by a simplified structure. A priori, two classes of coarse-grained models may be distinguished: those which are designed for a specific polymer and reflect the underlying atomistic details to some extent, and those which retain only the most basic features of a polymer chain (chain connectivity, short-range excluded-volume interactions, etc.). In this review we mainly focus on the second class of generic polymer models, while the first class of specific coarse-grained models is only touched upon briefly.},
archivePrefix = {arXiv},
arxivId = {cond-mat/0407717},
author = {Baschnagel, J and Wittmer, J. P. and Meyer, Hendrik},
booktitle = {Comput. Soft Matter},
eprint = {0407717},
file = {:Users/wenwen/Documents/MendeleyRefs/Baschnagel, Wittmer, Meyer{\_}Computational Soft Matter{\_}2004.pdf:pdf},
isbn = {3000126414},
pages = {57},
primaryClass = {cond-mat},
title = {{Monte Carlo SImulation of Polymers: Coarse-Grained Models}},
url = {http://arxiv.org/abs/cond-mat/0407717},
volume = {23},
year = {2004}
}
@article{Baumgrtner1984,
author = {Baumgrtner, A},
doi = {10.1146/annurev.physchem.35.1.419},
file = {:Users/wenwen/Documents/MendeleyRefs/Baumgrtner{\_}Annual Review of Physical Chemistry{\_}1984.pdf:pdf},
isbn = {0066-426X},
issn = {0066426X},
journal = {Annu. Rev. Phys. Chem.},
month = {jan},
number = {1},
pages = {419--435},
title = {{Simulation of Polymer Motion}},
url = {http://physchem.annualreviews.org/cgi/doi/10.1146/annurev.physchem.35.1.419},
volume = {35},
year = {1984}
}
@article{Croxton1999b,
abstract = {The iterative convolution (IC) technique previously reported for linear self-avoiding sequences is extended to the description of nonintersecting rings of hard-sphere segments. The principal geometrical features of rings of N=20, 40 and 62 segments are determined, including the intersegmental spatial distribution functions, the mean-square intersegmental separations, the radius of gyration, bond correlation function and segment density distribution function. These quantities are compared with independent Monte Carlo estimates, and the results are found to be generally in good quantitative agreement. A sum rule for the bond correlation function is proposed for rings, whilst the segment density distribution is found to exhibit serrations which are unresolved in the Monte Carlo data scatter. These serrations, moreover, occur at integral multiples of the segment diameter and are attributed to entropic processes associated with ring closure.},
author = {Croxton, C a},
doi = {10.1088/0305-4470/18/6/021},
file = {:Users/wenwen/Documents/MendeleyRefs/Croxton{\_}Journal of Physics A Mathematical and General{\_}1999.pdf:pdf},
issn = {0305-4470},
journal = {J. Phys. A. Math. Gen.},
month = {apr},
number = {6},
pages = {995--1005},
title = {{Statistics of self-avoiding ring polymers}},
url = {http://stacks.iop.org/0305-4470/18/i=6/a=021?key=crossref.529be173817b3e0ba02916f0ab92161f},
volume = {18},
year = {1985}
}
@article{Radicchi2010,
author = {Radicchi, Filippo and Fortunato, Santo},
doi = {10.1103/PhysRevE.81.036110},
file = {:Users/wenwen/Documents/MendeleyRefs/Radicchi, Fortunato{\_}Physical Review E{\_}2010.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {mar},
number = {3},
pages = {1--10},
title = {{Explosive percolation: A numerical analysis}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.81.036110},
volume = {81},
year = {2010}
}
@article{Witz2011,
abstract = {The combination of ring closure and spatial constraints has a fundamental effect on the statistics of semiflexible polymers such as DNA. However, studies of the interplay between circularity and constraints are scarce and single-molecule experimental data concerning polymer conformations are missing. By means of atomic force microscopy we probe the conformation of circular DNA molecules in two dimensions and in the concentrated regime (above the overlap concentration c*). Molecules in this regime experience a collapse, and their statistical properties agree very well with those of simulated vesicles under pressure. Some circular molecules also create confining regions in which other molecules are trapped. Thus we show further that spatially confined molecules fold into specific conformations close to those found for linear chains, and strongly dependent on the size of the confining box.},
author = {Witz, G. and Rechendorff, K. and Adamcik, J. and Dietler, G.},
doi = {10.1103/PhysRevLett.106.248301},
file = {:Users/wenwen/Documents/MendeleyRefs/Witz et al.{\_}Physical Review Letters{\_}2011.pdf:pdf},
issn = {00319007},
journal = {Phys. Rev. Lett.},
number = {June},
pages = {2--5},
pmid = {21770605},
title = {{Conformation of ring polymers in 2D constrained environments}},
volume = {106},
year = {2011}
}
@article{Alexander1991,
abstract = {Before forming a monopolar attachment to the closest spindle pole, chromosomes attaching in newt (Taricha granulosa) pneumocytes generally reside in an optically clear region of cytoplasm that is largely devoid of cytoskeletal components, organelles, and other chromosomes. We have previously demonstrated that chromosome attachment in these cells occurs when an astral microtubule contacts one of the kinetochores (Hayden, J., S. S. Bowser, and C. L. Rieder. 1990. J. Cell Biol. 111:1039-1045), and that once this association is established the chromosome can be transported poleward along the surface of the microtubule (Rieder, C. L., and S. P. Alexander. 1990. J. Cell Biol. 110:81-95). In the study reported here we used video enhanced differential interference contrast light microscopy and digital image processing to compare, at high spatial and temporal resolution (0.1 microns and 0.93 s, respectively), the microtubule-mediated poleward movement of attaching chromosomes and poleward moving particles on the spindle. The results of this analysis demonstrate obvious similarities between minus end-directed particle motion on the newt pneumocyte spindle and the motion of attaching chromosomes. This is consistent with the hypothesis that both are driven by a similar force-generating mechanism. We then used the Brownian displacements of particles in the vicinity of attaching chromosomes to calculate the apparent viscosity of cytoplasm through which the chromosomes were moving. From these data, and that from our kinetic analyses and previous work, we calculate the force-producing potential of nascent kinetochore fibers in newt pneumocytes to be approximately 0.1-7.4 x 10(-6) dyn/microtubule) This is essentially equivalent to that calculated by Nicklas (Nicklas, R.B. 1988. Annu. Rev. Biophys. Biophys. Chem. 17:431-449) for prometaphase (4 x 10(-6) dyn/microtubule) and anaphase (5 x 10(-6) dyn/microtubule) chromosomes in Melanoplus. Thus, within the limits of experimental error, there appears to be a remarkable consistency in force production per microtubule throughout the various stages of mitosis and between groups of diverse taxonomic affinities.},
author = {Alexander, S P and Rieder, C L},
doi = {10.1083/jcb.113.4.805},
isbn = {0021-9525 (Print)$\backslash$r0021-9525 (Linking)},
issn = {00219525},
journal = {J. Cell Biol.},
number = {4},
pages = {805--815},
pmid = {2026651},
title = {{Chromosome motion during attachment to the vertebrate spindle: Initial saltatory-like behavior of chromosomes and quantitative analysis of force production by nascent kinetochore fibers}},
volume = {113},
year = {1991}
}
@incollection{Schadschneider2011a,
author = {Schadschneider, Andreas and Chowdhury, Debashish and Nishinari, Katsuhiro},
booktitle = {Stoch. Transp. Complex Syst.},
doi = {10.1016/B978-0-444-52853-7.00010-5},
file = {:Users/wenwen/Documents/MendeleyRefs/Schadschneider, Chowdhury, Nishinari{\_}Stochastic Transport in Complex Systems{\_}2011(3).pdf:pdf},
isbn = {9780444528537},
pages = {383--405},
publisher = {Elsevier},
title = {{Transport on Networks}},
url = {http://linkinghub.elsevier.com/retrieve/pii/B9780444528537000105},
year = {2011}
}
@article{Cohen2001,
author = {Cohen, Reuven and Erez, Keren and Ben-Avraham, Daniel and Havlin, Shlomo},
doi = {10.1103/PhysRevLett.86.3682},
file = {:Users/wenwen/Documents/MendeleyRefs/Cohen et al.{\_}Physical Review Letters{\_}2001.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {apr},
number = {16},
pages = {3682--3685},
title = {{Breakdown of the Internet under Intentional Attack}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.86.3682},
volume = {86},
year = {2001}
}
@article{Wong2012,
abstract = {BACKGROUND: Despite the absence of internal membranes, the nucleus of eukaryotic cells is spatially organized, with chromosomes and individual loci occupying dynamic, but nonrandom, spatial positions relative to nuclear landmarks and to each other. These positional preferences correlate with gene expression and DNA repair, recombination, and replication. Yet the principles that govern nuclear organization remain poorly understood and detailed predictive models are lacking. RESULTS: We present a computational model of dynamic chromosome configurations in the interphase yeast nucleus that is based on first principles and is able to statistically predict the positioning of any locus in nuclear space. Despite its simplicity, the model agrees with extensive previous and new measurements on locus positioning and with genome-wide DNA contact frequencies. Notably, our model recapitulates the position and morphology of the nucleolus, the observed variations in locus positions, and variations in contact frequencies within and across chromosomes, as well as subchromosomal contact features. The model is also able to correctly predict nuclear reorganization accompanying a reduction in ribosomal DNA transcription, and sites of chromosomal rearrangements tend to occur where the model predicted high contact frequencies. CONCLUSIONS: Our results suggest that large-scale yeast nuclear architecture can be largely understood as a consequence of generic properties of crowded polymers rather than of specific DNA-binding factors and that configurations of chromosomes and DNA contacts are dictated mainly by genomic location and chromosome lengths. Our model provides a quantitative framework to understand and predict large-scale spatial genome organization and its interplay with functional processes.},
author = {Wong, Hua and Marie-Nelly, Herv{\'{e}} and Herbert, S{\'{e}}bastien and Carrivain, Pascal and Blanc, Herv{\'{e}} and Koszul, Romain and Fabre, Emmanuelle and Zimmer, Christophe},
doi = {10.1016/j.cub.2012.07.069},
file = {:Users/wenwen/Documents/MendeleyRefs/Wong et al.{\_}Current Biology{\_}2012.pdf:pdf},
issn = {09609822},
journal = {Curr. Biol.},
month = {oct},
number = {20},
pages = {1881--1890},
pmid = {22940469},
title = {{A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22940469},
volume = {22},
year = {2012}
}
@article{Hooyberghs2011,
author = {Hooyberghs, Hans and {Van Schaeybroeck}, Bert},
doi = {10.1103/PhysRevE.83.032101},
file = {:Users/wenwen/Documents/MendeleyRefs/Hooyberghs, Van Schaeybroeck{\_}Physical Review E{\_}2011.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {mar},
number = {3},
pages = {1--3},
title = {{Criterion for explosive percolation transitions on complex networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.83.032101},
volume = {83},
year = {2011}
}
@article{Sandow1994,
author = {Sandow, S. and Sch{\"{u}}tz, G},
doi = {10.1209/0295-5075/26/1/002},
file = {:Users/wenwen/Documents/MendeleyRefs/Sandow, Sch{\"{u}}tz{\_}Europhys. Lett.{\_}1994.pdf:pdf},
issn = {0295-5075},
journal = {Europhys. Lett.},
month = {apr},
number = {1},
pages = {7--12},
title = {{On U q [ SU (2)]-Symmetric Driven Diffusion}},
url = {http://stacks.iop.org/0295-5075/26/i=1/a=002?key=crossref.1fd864b5be9d6af97953f733740aa775},
volume = {26},
year = {1994}
}
@book{Press1987,
abstract = {SUMMARY: The example books published as part of the Numerical Recipes second edition series contain source programs that exercise and demonstrate all of the Numerical Recipes subroutines. Each example program contains comments and is prefaced by a short description of what it does. The books contain all of the old material from the original edition as well as new material from the second edition. They will be valuable for readers who wish to incorporate procedures and subroutines into their own source programs. They are available in both FORTRAN and C.},
author = {Press, William H. and Teukolsky, Saul A. and Vetterling, William T. and Flannery, Brian P.},
doi = {10.2307/1269484},
edition = {3},
file = {:Users/wenwen/Documents/MendeleyRefs/Press et al.{\_}Unknown{\_}1987.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Press et al.{\_}Unknown{\_}1987.pdf:pdf},
isbn = {0521431085},
issn = {00401706},
month = {mar},
pages = {501},
publisher = {Cambridge university press},
title = {{Numerical recipes: the art of scientific computing.}},
url = {http://www.jstor.org/stable/1269484?origin=crossref},
volume = {29},
year = {1987}
}
@article{Gooßen2014,
author = {Goo{\ss}en, S and Br{\'{a}}s, ARE and Krutyeva, M and Sharp, M and Falus, P and Feoktystov, A and Gasser, U and Pyckhout-Hintzen, W. and Wischnewski, A and Richter, D},
doi = {10.1103/PhysRevLett.113.168302},
file = {:Users/wenwen/Documents/MendeleyRefs/Goo{\ss}en et al.{\_}Phys. Rev. Lett.{\_}2014.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {oct},
number = {16},
pages = {168302},
title = {{Molecular Scale Dynamics of Large Ring Polymers}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.113.168302},
volume = {113},
year = {2014}
}
@article{Sakaue2012,
abstract = {We present a detailed account of a recently proposed phenomenological theory for noncatenated ring polymer melts [Sakaue, Phys. Rev. Lett. 106, 167802 (2011)]. A basic assumption lies in the implementation of the noncatenation constraint via the effective excluded-volume effect, from which a geometrical picture of melts emerges. The result captures many of the salient features observed so far, including (i) the overall spatial size of rings, (ii) the coordinate number, i.e., the number of rings surrounding a given ring, (iii) the topological length scale as a function of the molecular weight, and (iv) the effect of the chain stiffness and concentration. We also suggest a geometrical interpretation of the topological length scale, which may shed some light on the entanglement concept in polymeric systems.},
archivePrefix = {arXiv},
arxivId = {arXiv:1202.1890v1},
author = {Sakaue, Takahiro},
doi = {10.1103/PhysRevE.85.021806},
eprint = {arXiv:1202.1890v1},
file = {:Users/wenwen/Documents/MendeleyRefs/Sakaue{\_}Physical Review E - Statistical, Nonlinear, and Soft Matter Physics{\_}2012.pdf:pdf},
isbn = {1550-2376 (Electronic)$\backslash$r1539-3755 (Linking)},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {feb},
number = {2},
pages = {021806},
pmid = {22463235},
title = {{Statistics and geometrical picture of ring polymer melts and solutions}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.85.021806},
volume = {85},
year = {2012}
}
@book{Knill2011,
author = {Knill, Oliver},
file = {:Users/wenwen/Documents/MendeleyRefs/Knill{\_}Unknown{\_}2011.pdf:pdf},
title = {{Probability and stochastic processes with applications}},
url = {http://www.math.harvard.edu/{~}knill/oldtexas/Teaching/MA144/all.ps},
year = {2011}
}
@article{Dai2013a,
abstract = {The similarities and differences between geo- metric and tensile constraints on polymers have not been fully investigated. Here we use theory (blob models) and simulations to present a comprehensive comparison between polymers in these two situations. For a polymer in good solvent, the effect of tensile force f on extension in the Pincus regime is similar to the effect of cylindrical confinement in the de Gennes regime after mapping the characteristic length kBT/ f to the cylindrical diameter D, where kBT is the thermal energy. However, the comparison of the effects of tension and confinement on extension is lacking when kBT/f and D are less than the thermal blob size b, referred to as extended Pincus regime and extended de Gennes regime, respectively. In the extended Pincus regime, force can still segregate the ideal-coils with the size of ∼kBT/f, resulting in the scaling of extension L∥ ∼ (kBT/f)−1. In the extended de Gennes regime, excluded volume interaction is not sufficient to segregate the ideal-coils with the size of D, resulting in the scaling L∥ ∼ D−2/3 different from the scaling in the extended Pincus regime. In addition to the scaling of extension, the scaling of fluctuation in extension $\sigma$ is also compared in the extended Pincus or extended de Gennes regime. It is found that $\sigma$ is independent of f and D, which reflects the ideal-chain behavior. All of the above scaling relations are validated by Monte Carlo simulations. Simulation and scaling results are also used to determine the experimental conditions needed to access the extended de Gennes and de Gennes regimes in various single molecule experiments.},
author = {Dai, Liang and Doyle, Patrick S.},
doi = {10.1021/ma400674q},
file = {:Users/wenwen/Documents/MendeleyRefs/Dai, Doyle{\_}Macromolecules{\_}2013.pdf:pdf},
isbn = {0024-9297},
issn = {00249297},
journal = {Macromolecules},
number = {15},
pages = {6336--6344},
title = {{Comparisons of a polymer in confinement versus applied force}},
volume = {46},
year = {2013}
}
@article{Boettcher2012,
abstract = {Percolation on a one-dimensional lattice and fractals, such as the Sierpinski gasket, is typically considered to be trivial, because they percolate only at full bond density. By dressing up such lattices with small-world bonds, a novel percolation transition with explosive cluster growth can emerge at a non-trivial critical point. There, the usual order parameter, describing the probability of any node to be part of the largest cluster, jumps instantly to a finite value. Here we provide a simple example in the form of a small-world network consisting of a one-dimensional lattice which, when combined with a hierarchy of long-range bonds, reveals many features of this transition in a mathematically rigorous manner.},
archivePrefix = {arXiv},
arxivId = {1110.4288},
author = {Boettcher, Stefan and Singh, Vijay and Ziff, Robert M},
doi = {10.1038/ncomms1774},
eprint = {1110.4288},
file = {:Users/wenwen/Documents/MendeleyRefs/Boettcher, Singh, Ziff{\_}Nature Communications{\_}2012.pdf:pdf},
issn = {2041-1723},
journal = {Nat. Commun.},
month = {apr},
number = {2},
pages = {787},
pmid = {22510692},
title = {{Ordinary percolation with discontinuous transitions}},
url = {http://arxiv.org/abs/1110.4288 http://www.ncbi.nlm.nih.gov/pubmed/22510692 http://www.nature.com/doifinder/10.1038/ncomms1774},
volume = {3},
year = {2012}
}
@article{Verdier1970,
author = {Verdier, Peter H.},
doi = {10.1063/1.1672818},
file = {:Users/wenwen/Documents/MendeleyRefs/Verdier{\_}The Journal of Chemical Physics{\_}1970.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {11},
pages = {5512},
title = {{Relaxation Behavior of the Freely Jointed Chain}},
url = {http://scitation.aip.org/content/aip/journal/jcp/52/11/10.1063/1.1672818},
volume = {52},
year = {1970}
}
@article{Ryabov2011,
abstract = {We study one-dimensional diffusion of N hard-core interacting Brownian particles driven by the space- and time-dependent external force. We give the exact solution of the N-particle Smoluchowski diffusion equation. In particular, we investigate the nonequilibrium energetics of two interacting particles under the time-periodic driving. The hard-core interaction induces entropic repulsion which differentiates the energetics of the two particles. We present exact time-asymptotic results which describe the mean energy, the accepted work and heat, and the entropy production of interacting particles, and we contrast these quantities against the corresponding ones for the noninteracting particles.},
author = {Ryabov, Artem and Chvosta, Petr},
doi = {10.1103/PhysRevE.83.020106},
file = {:Users/wenwen/Documents/MendeleyRefs/Ryabov, Chvosta{\_}Physical Review E{\_}2011.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {feb},
number = {2},
pages = {020106},
pmid = {21405804},
title = {{Single-file diffusion of externally driven particles}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.83.020106},
volume = {83},
year = {2011}
}
@article{Wilking2012,
abstract = {Many bacteria on earth exist in surface-attached communities known as biofilms. These films are responsible for manifold problems, including hospital-acquired infections and biofouling, but they can also be beneficial. Biofilm growth depends on the transport of nutrients and waste, for which diffusion is thought to be the main source of transport. However, diffusion is ineffective for transport over large distances and thus should limit growth. Nevertheless, biofilms can grow to be very large. Here we report the presence of a remarkable network of well-defined channels that form in wild-type Bacillus subtilis biofilms and provide a system for enhanced transport. We observe that these channels have high permeability to liquid flow and facilitate the transport of liquid through the biofilm. In addition, we find that spatial variations in evaporative flux from the surface of these biofilms provide a driving force for the flow of liquid in the channels. These channels offer a remarkably simple system for liquid transport, and their discovery provides insight into the physiology and growth of biofilms.},
author = {Wilking, James N and Zaburdaev, Vasily and {De Volder}, Michael and Losick, Richard and Brenner, Michael P and Weitz, David a},
doi = {10.1073/pnas.1216376110},
file = {:Users/wenwen/Documents/MendeleyRefs/Wilking et al.{\_}Proceedings of the National Academy of Sciences{\_}2013.pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
month = {jan},
number = {3},
pages = {848--852},
pmid = {23271809},
title = {{Liquid transport facilitated by channels in Bacillus subtilis biofilms}},
url = {http://www.pnas.org/content/110/3/848.short http://www.pnas.org/content/early/2012/12/26/1216376110.short http://www.pnas.org/cgi/doi/10.1073/pnas.1216376110},
volume = {110},
year = {2013}
}
@book{Doi1996a,
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Doi, M},
booktitle = {Oxford Univ. Press},
doi = {10.1016/S0097-8485(97)00027-2},
eprint = {arXiv:1011.1669v3},
file = {:Users/wenwen/Documents/MendeleyRefs/Doi{\_}Oxford University Press{\_}1996.pdf:pdf},
isbn = {0198517890},
issn = {00978485},
pages = {273},
pmid = {803720},
publisher = {Oxford University Press},
title = {{Introduction to polymer physics}},
volume = {21},
year = {1996}
}
@article{Cho2011,
author = {Cho, Y. and Kahng, B.},
doi = {10.1103/PhysRevLett.107.275703},
file = {:Users/wenwen/Documents/MendeleyRefs/Cho, Kahng{\_}Physical Review Letters{\_}2011.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {dec},
number = {27},
pages = {1--5},
title = {{Suppression Effect on Explosive Percolation}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.107.275703},
volume = {107},
year = {2011}
}
@article{Barkai2009,
author = {Barkai, E. and Silbey, R.},
doi = {10.1103/PhysRevLett.102.050602},
file = {:Users/wenwen/Documents/MendeleyRefs/Barkai, Silbey{\_}Physical Review Letters{\_}2009.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
number = {5},
pages = {050602},
title = {{Theory of Single File Diffusion in a Force Field}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.102.050602},
volume = {102},
year = {2009}
}
@book{Sternberg1994,
author = {Sternberg, S.},
file = {:Users/wenwen/Documents/MendeleyRefs/Sternberg{\_}Unknown{\_}1994.pdf:pdf},
publisher = {Cambridge University Press},
title = {{Group Theory and Physics}},
year = {1994}
}
@article{Crawford1991,
author = {Crawford, John David},
file = {:Users/wenwen/Documents/MendeleyRefs/Crawford{\_}Reviews of Modern Physics{\_}1991.pdf:pdf},
journal = {Rev. Mod. Phys.},
number = {4},
pages = {991},
title = {{Introduction to bifurcation theory}},
url = {http://rmp.aps.org/abstract/RMP/v63/i4/p991{\_}1},
volume = {63},
year = {1991}
}
@article{Manka2007,
author = {Manka, Anna and Malarz, Krzysztof and KULAKOWSKI, KRZYSZTOF},
file = {:Users/wenwen/Documents/MendeleyRefs/Manka, Malarz, KULAKOWSKI{\_}International Journal of {\ldots}{\_}2007.pdf:pdf},
journal = {Int. J. {\ldots}},
number = {11},
pages = {1765--1773},
title = {{Clusterization, frustration and collectivity in random networks}},
url = {http://www.worldscientific.com/doi/abs/10.1142/S0129183107011728},
volume = {18},
year = {2007}
}
@article{Arnaudon2006a,
abstract = {We consider the N-site U{\_}{\{}q{\}}(gl(N)) integrable spin chain with periodic and open diagonal soliton-preserving boundary conditions. By employing analytical Bethe ansatz techniques we are able to determine the spectrum and the corresponding Bethe ansatz equations for the general case, where each site of the spin chain is associated to any representation of U{\_}{\{}q{\}}(gl(N)). In the case of open spin chain, we study finite dimensional representations of the quantum reflection algebra, and prove in full generality that the pseudo-vacuum is a highest weight of the monodromy matrix. For these two types of spin chain, we study the (generalized) "algebraic" fusion procedures, which amount to construct the quantum contraction and the Sklyanin determinant for the affine U{\_}{\{}q{\}}(gl(N)) and quantum reflection algebras. We also determine the symmetry algebra of these two types of spin chains, including general K and K{\^{}}+ diagonal matrices for the open case. The case of open spin chains with soliton non-preserving boundary conditions is also presented in the framework of quantum twisted Yangians. The symmetry algebra of this spin chains is studied. We also give an exhaustive classification of the invertible matricial solutions to the corresponding reflection equation.},
archivePrefix = {arXiv},
arxivId = {math-ph/0512037},
author = {Arnaudon, Daniel and Cramp{\'{e}}, N. and Doikou, Anastasia and Frappat, Luc and Ragoucy, Eric},
doi = {10.1007/s00023-006-0280-x},
eprint = {0512037},
file = {:Users/wenwen/Documents/MendeleyRefs/Arnaudon et al.{\_}Annales Henri Poincar{\'{e}}{\_}2006.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Arnaudon et al.{\_}Annales Henri Poincar{\'{e}}{\_}2006(2).pdf:pdf},
issn = {1424-0637},
journal = {Ann. Henri Poincar{\'{e}}},
month = {dec},
number = {7-8},
pages = {1217--1268},
primaryClass = {math-ph},
title = {{Spectrum and Bethe Ansatz Equations for the {\$}{\$}U{\_}{\{}q{\}} {\{}$\backslash$left( {\{}gl($\backslash$mathcal{\{}N{\}}){\}} $\backslash$right){\}}{\$}{\$} Closed and Open Spin Chains in any Representation}},
url = {http://link.springer.com/10.1007/s00023-006-0280-x http://dx.doi.org/10.1007/s00023-006-0280-x},
volume = {7},
year = {2006}
}
@article{Ha2015,
abstract = {How confinement or a physical constraint modifies polymer chains is not only a classical problem in polymer physics but also relevant in a variety of contexts such as single-molecule manipulations, nanofabrication in narrow pores, and modelling of chromosome organization. Here, we review recent progress in our understanding of polymers in a confined (and crowded) space. To this end, we highlight converging views of these systems from computational, experimental, and theoretical approaches, and then clarify what remains to be clarified. In particular, we focus on exploring how cylindrical confinement reshapes individual chains and induces segregation forces between them – by pointing to the relationships between intra-chain organization and chain segregation. In the presence of crowders, chain molecules can be entropically phase-separated into a condensed state. We include a kernel of discussions on the nature of chain compaction by crowders, especially in a confined space. Finally, we discuss the relevance of confined polymers for the nucleoid, an intracellular space in which the bacterial chromosome is tightly packed, in part by cytoplasmic crowders.},
author = {Ha, Bae-Yeun and Jung, Youngkyun},
doi = {10.1039/C4SM02734E},
file = {:Users/wenwen/Documents/MendeleyRefs/Ha, Jung{\_}Soft Matter{\_}2015.pdf:pdf},
issn = {1744-683X},
journal = {Soft Matter},
number = {12},
pages = {2333--2352},
pmid = {25710099},
publisher = {Royal Society of Chemistry},
title = {{Polymers under confinement: single polymers, how they interact, and as model chromosomes}},
url = {http://pubs.rsc.org.globalproxy.cvt.dk/en/content/articlehtml/2015/sm/c4sm02734e},
volume = {11},
year = {2015}
}
@article{Schilling2007,
author = {Schilling, T. and Jungblut, S. and Miller, Mark},
doi = {10.1103/PhysRevLett.98.108303},
file = {:Users/wenwen/Documents/MendeleyRefs/Schilling, Jungblut, Miller{\_}Physical Review Letters{\_}2007.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {mar},
number = {10},
pages = {1--4},
title = {{Depletion-Induced Percolation in Networks of Nanorods}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.98.108303},
volume = {98},
year = {2007}
}
@book{Risken1989,
address = {Berlin, Heidelberg},
author = {Risken, Hannes},
doi = {10.1007/978-3-642-61544-3},
file = {:Users/wenwen/Documents/MendeleyRefs/Risken{\_}Unknown{\_}1989.pdf:pdf},
isbn = {978-3-540-61530-9},
issn = {1098-6596},
pmid = {25246403},
publisher = {Springer Berlin Heidelberg},
series = {Springer Series in Synergetics},
title = {{The Fokker-Planck Equation}},
url = {http://link.springer.com/10.1007/978-3-642-61544-3},
volume = {18},
year = {1989}
}
@book{Ottinger2008,
address = {Berlin, Heidelberg},
author = {{\"{O}}ttinger, Hans Christian},
doi = {10.1007/978-3-642-58290-5},
file = {:Users/wenwen/Documents/MendeleyRefs/{\"{O}}ttinger{\_}Unknown{\_}1996.pdf:pdf},
isbn = {978-3-540-58353-0},
publisher = {Springer Berlin Heidelberg},
title = {{Stochastic Processes in Polymeric Fluids}},
url = {http://link.springer.com/10.1007/978-3-642-58290-5},
year = {1996}
}
@article{Gao2012,
author = {Gao, Jianxi and Buldyrev, S. V. and Havlin, S. and Stanley, H. E.},
doi = {10.1103/PhysRevE.85.066134},
file = {:Users/wenwen/Documents/MendeleyRefs/Gao et al.{\_}Physical Review E{\_}2012.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {jun},
number = {6},
pages = {066134},
title = {{Robustness of a network formed by n interdependent networks with a one-to-one correspondence of dependent nodes}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.85.066134},
volume = {85},
year = {2012}
}
@book{Liggett1999,
address = {Berlin, Heidelberg},
author = {Liggett, Thomas M.},
doi = {10.1007/978-3-662-03990-8},
file = {:Users/wenwen/Documents/MendeleyRefs/Liggett{\_}Unknown{\_}1999.pdf:pdf},
isbn = {978-3-642-08529-1},
publisher = {Springer Berlin Heidelberg},
series = {Grundlehren der mathematischen Wissenschaften},
title = {{Stochastic Interacting Systems: Contact, Voter and Exclusion Processes}},
url = {http://link.springer.com/10.1007/978-3-662-03990-8},
volume = {324},
year = {1999}
}
@article{Jin2009,
author = {Gao, Zhongke and Jin, Ningde},
doi = {10.1063/1.3227736},
issn = {10541500},
journal = {Chaos An Interdiscip. J. Nonlinear Sci.},
number = {3},
pages = {033137},
title = {{Complex network from time series based on phase space reconstruction}},
url = {http://scitation.aip.org/content/aip/journal/chaos/19/3/10.1063/1.3227736},
volume = {19},
year = {2009}
}
@article{Golinelli2004a,
abstract = {We present a new derivation of the spectral gap of the totally asymmetric exclusion process on a half-filled ring of size L by using the Bethe Ansatz. We show that, in the large L limit, the Bethe equations reduce to a simple transcendental equation involving the polylogarithm, a classical special function. By solving that equation, the gap and the dynamical exponent are readily obtained. Our method can be extended to a system with an arbitrary density of particles. Keywords: ASEP, Bethe Ansatz, Dynamical Exponent, Spectral Gap.},
archivePrefix = {arXiv},
arxivId = {cond-mat/0312371},
author = {Golinelli, O. and Mallick, K.},
doi = {10.1088/0305-4470/37/10/001},
eprint = {0312371},
file = {:Users/wenwen/Documents/MendeleyRefs/Golinelli, Mallick{\_}Journal of Physics A Mathematical and General{\_}2004.pdf:pdf},
issn = {0305-4470},
journal = {J. Phys. A. Math. Gen.},
keywords = {asep,bethe ansatz,dynamical exponent,spectral},
month = {mar},
number = {10},
pages = {3321--3331},
primaryClass = {cond-mat},
title = {{Bethe ansatz calculation of the spectral gap of the asymmetric exclusion process}},
url = {http://arxiv.org/abs/cond-mat/0312371 http://stacks.iop.org/0305-4470/37/i=10/a=001?key=crossref.05f97b7bbb40aa69497f733ea65cf9e7},
volume = {37},
year = {2004}
}
@article{Koniaris1991,
author = {Koniaris, Kleanthes and Muthukumar, M.},
doi = {10.1063/1.460889},
file = {:Users/wenwen/Documents/MendeleyRefs/Koniaris, Muthukumar{\_}The Journal of Chemical Physics{\_}1991.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {4},
pages = {2873},
title = {{Self-entanglement in ring polymers}},
url = {http://scitation.aip.org/content/aip/journal/jcp/95/4/10.1063/1.460889},
volume = {95},
year = {1991}
}
@article{Dorier2009,
abstract = {Using freely jointed polymer model we compare equilibrium properties of crowded polymer chains whose segments are either permeable or not permeable for other segments to pass through. In particular, we addressed the question whether non-permeability of long chain molecules, in the absence of excluded volume effect, is sufficient to compartmentalize highly crowded polymer chains, similarly to what happens during formation of chromosomal territories in interphase nuclei. Our results indicate that even polymers without excluded volume compartmentalize and show strongly reduced intermingling when they are mutually non-permeable. Judging from the known fact that chromatin fibres originating from different chromosomes show very limited intermingling in interphase nuclei, we propose that regular chromatin fibres during chromosome decondensation can hardly serve as a substrate of cellular type II DNA topoisomerases.},
author = {Dorier, Julien and Stasiak, Andrzej},
doi = {10.1093/nar/gkp702},
file = {:Users/wenwen/Documents/MendeleyRefs/Dorier, Stasiak{\_}Nucleic Acids Research{\_}2009.pdf:pdf},
isbn = {1362-4962 (Electronic)$\backslash$r0305-1048 (Linking)},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
month = {oct},
number = {19},
pages = {6316--6322},
pmid = {19726582},
title = {{Topological origins of chromosomal territories}},
url = {https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkp702},
volume = {37},
year = {2009}
}
@article{Zhang2006a,
author = {Zhang, J. and Luo, X. and Small, M.},
doi = {10.1103/PhysRevE.73.016216},
file = {:Users/wenwen/Documents/MendeleyRefs/Zhang, Luo, Small{\_}Physical Review E{\_}2006.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {jan},
number = {1},
pages = {1--5},
title = {{Detecting chaos in pseudoperiodic time series without embedding}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.73.016216},
volume = {73},
year = {2006}
}
@article{Brown2001b,
abstract = {We report a computer simulation study of the influence of topological constraints on the statics and dynamics of single ring polymers and ring polymers in the melt. We show that single rings have identical static and dynamic scaling behavior regardless of the presence of topological constraints. For rings in the melt we find that the scaling behavior is significantly influenced by the presence of topological constraints.},
author = {Brown, Scott and Lenczycki, Tim and Szamel, Grzegorz},
doi = {10.1103/PhysRevE.63.052801},
file = {:Users/wenwen/Documents/MendeleyRefs/Brown, Lenczycki, Szamel{\_}Physical Review E{\_}2001.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Brown, Lenczycki, Szamel{\_}Physical Review E{\_}2001.pdf:pdf},
issn = {1063-651X},
journal = {Phys. Rev. E},
month = {apr},
number = {5},
pages = {052801},
pmid = {11414945},
title = {{Influence of topological constraints on the statics and dynamics of ring polymers}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.63.052801},
volume = {63},
year = {2001}
}
@incollection{Schutz2001,
author = {Sch{\"{u}}tz, G.M.},
booktitle = {Phase Transitions Crit. Phenom.},
doi = {10.1016/S1062-7901(01)80015-X},
file = {:Users/wenwen/Documents/MendeleyRefs/Sch{\"{u}}tz{\_}Phase Transitions and Critical Phenomena{\_}2001.pdf:pdf},
isbn = {1062-7901},
issn = {10627901},
number = {C},
pages = {1--251},
publisher = {Academic Press},
title = {{Exactly Solvable Models for Many-Body Systems Far from Equilibrium}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S106279010180015X},
volume = {19},
year = {2001}
}
@article{Pedley1997,
author = {Pedley, T J},
file = {:Users/wenwen/Documents/MendeleyRefs/Pedley{\_}Unknown{\_}1997.pdf:pdf},
keywords = {added mass,boundary layers,drag,fluid dynamics,fundamental laws and equations,geostrophic flow,hydrodynamic instability,hydrostatics,internal waves,kinematics,lift,mass conservation,navier-stokes equations,reynolds number,vorticity,water waves},
number = {1},
pages = {7--24},
title = {{Introduction to Fluid Dynamics}},
url = {http://scholar.google.com/scholar?hl=en{\&}btnG=Search{\&}q=intitle:Introduction+to+Fluid+Dynamics+*{\#}3},
volume = {61},
year = {1997}
}
@article{Blavatska2010a,
abstract = {We study the influence of structural obstacles in a disordered environment on the size and shape characteristics of long flexible polymer macromolecules. We use the model of self-avoiding random walks on diluted regular lattices at the percolation threshold in space dimensions d=2 and d=3. Applying the pruned-enriched Rosenbluth method, we numerically estimate rotationally invariant universal quantities such as the averaged asphericity {\textless}A(d){\textgreater} and prolateness {\textless}S{\textgreater} of polymer chain configurations. Our results quantitatively reveal the extent of anisotropy of macromolecules due to the presence of structural defects.},
archivePrefix = {arXiv},
arxivId = {1009.4358},
author = {Blavatska, Viktoria and Janke, Wolfhard},
doi = {10.1063/1.3501368},
eprint = {1009.4358},
file = {:Users/wenwen/Documents/MendeleyRefs/Blavatska, Janke{\_}Journal of Chemical Physics{\_}2010.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Blavatska, Janke{\_}Journal of Chemical Physics{\_}2010.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {18},
pages = {1--7},
pmid = {21073228},
title = {{Shape anisotropy of polymers in disordered environment}},
volume = {133},
year = {2010}
}
@article{Ding2006,
abstract = {The meiotic cohesin Rec8 is required for the stepwise segregation of chromosomes during the two rounds of meiotic division. By directly measuring chromosome compaction in living cells of the fission yeast Schizosaccharomyces pombe, we found an additional role for the meiotic cohesin in the compaction of chromosomes during meiotic prophase. In the absence of Rec8, chromosomes were decompacted relative to those of wild-type cells. Conversely, loss of the cohesin-associated protein Pds5 resulted in hypercompaction. Although this hypercompaction requires Rec8, binding of Rec8 to chromatin was reduced in the absence of Pds5, indicating that Pds5 promotes chromosome association of Rec8. To explain these observations, we propose that meiotic prophase chromosomes are organized as chromatin loops emanating from a Rec8-containing axis: the absence of Rec8 disrupts the axis, resulting in disorganized chromosomes, whereas reduced Rec8 loading results in a longitudinally compacted axis with fewer attachment points and longer chromatin loops.},
author = {Ding, Da Qiao and Sakurai, Nobuko and Katou, Yuki and Itoh, Takehiko and Shirahige, Katsuhiko and Haraguchi, Tokuko and Hiraoka, Yasushi},
doi = {10.1083/jcb.200605074},
isbn = {0021-9525 (Print)$\backslash$r0021-9525 (Linking)},
issn = {00219525},
journal = {J. Cell Biol.},
number = {4},
pages = {499--508},
pmid = {16893973},
title = {{Meiotic cohesins modulate chromosome compaction during meiotic prophase in fission yeast}},
volume = {174},
year = {2006}
}
@article{Zhou2012,
author = {Zhou, Di and Stanley, H. Eugene and D'Agostino, Gregorio and Scala, Antonio},
doi = {10.1103/PhysRevE.86.066103},
file = {:Users/wenwen/Documents/MendeleyRefs/Zhou et al.{\_}Physical Review E{\_}2012.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {dec},
number = {6},
pages = {066103},
title = {{Assortativity decreases the robustness of interdependent networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.86.066103},
volume = {86},
year = {2012}
}
@article{Boccaletti2002,
author = {Boccaletti, S and Kurths, J and Osipov, G and Valladares, D.L. and Zhou, C.S.},
doi = {10.1016/S0370-1573(02)00137-0},
file = {:Users/wenwen/Documents/MendeleyRefs/Boccaletti et al.{\_}Physics Reports{\_}2002.pdf:pdf},
issn = {03701573},
journal = {Phys. Rep.},
month = {aug},
number = {1-2},
pages = {1--101},
title = {{The synchronization of chaotic systems}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0370157302001370},
volume = {366},
year = {2002}
}
@article{Bastas2011,
author = {Bastas, Nikolaos and Kosmidis, Kosmas and Argyrakis, Panos},
doi = {10.1103/PhysRevE.84.066112},
file = {:Users/wenwen/Documents/MendeleyRefs/Bastas, Kosmidis, Argyrakis{\_}Physical Review E{\_}2011.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {dec},
number = {6},
pages = {1--6},
title = {{Explosive site percolation and finite-size hysteresis}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.84.066112},
volume = {84},
year = {2011}
}
@inproceedings{Rzehak2000,
author = {Rzehak, R and Kienle, D and Kawakatsu, T and Zimmermann, W},
booktitle = {Work. Mol. Dyn. Parallel Comput.},
file = {:Users/wenwen/Documents/MendeleyRefs/Rzehak et al.{\_}Workshop on Molecular Dynamics on Parallel Computers{\_}2000.pdf:pdf},
pages = {120},
title = {{Brownian Dynamics of tethered polymers in flow}},
year = {2000}
}
@article{Butler2009,
abstract = {We demonstrate that demographic noise can induce persistent spatial pattern formation and temporal oscillations in the Levin-Segel predator-prey model for plankton-herbivore population dynamics. Although the model exhibits a Turing instability in mean-field theory, demographic noise greatly enlarges the region of parameter space where pattern formation occurs. To distinguish between patterns generated by fluctuations and those present at the mean-field level in real ecosystems, we calculate the power spectrum in the noise-driven case and predict the presence of fat tails not present in the mean-field case. These results may account for the prevalence of large-scale ecological patterns, beyond that expected from traditional nonstochastic approaches.},
archivePrefix = {arXiv},
arxivId = {0906.5535},
author = {Butler, Thomas and Goldenfeld, Nigel},
doi = {10.1103/PhysRevE.80.030902},
eprint = {0906.5535},
isbn = {1063-651X},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {sep},
number = {3},
pages = {030902},
pmid = {19905053},
title = {{Robust ecological pattern formation induced by demographic noise}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.80.030902},
volume = {80},
year = {2009}
}
@article{Ding1998,
abstract = {Using a computerized fluorescence microscope system to observe fluorescently stained cellular structures in vivo, we have examined the dynamics of chromosomes and microtubules during the process of meiosis in the fission yeast Schizosaccharomyces pombe. Fission yeast meiotic prophase is characterized by a distinctive type of nuclear movement that is led by telomeres clustered at the spindle-pole body (the centrosome-equivalent structure in fungi): the nucleus oscillates back and forth along the cell axis, moving continuously between the two ends of the cell for some hours prior to the meiotic divisions. To obtain a dynamic view of this oscillatory nuclear movement in meiotic prophase, we visualized microtubules and chromosomes in living cells using jellyfish green fluorescent protein fused with alpha-tubulin and a DNA-specific fluorescent dye, Hoechst 33342, respectively. Continuous observation of chromosomes and microtubules in these cells demonstrated that the oscillatory nuclear movement is mediated by dynamic reorganization of astral microtubules originating from the spindle-pole body. During each half-oscillatory period, the microtubules extending rearward from the leading edge of the nucleus elongate to drive the nucleus to one end of the cell. When the nucleus reversed direction, its motion during the second half of the oscillation was not driven by the same microtubules that drove its motion during the first half, but rather by newly assembled microtubules. Reversible inhibition of nuclear movement by an inhibitor of microtubule polymerization, thiabendazole, confirmed the involvement of astral microtubules in oscillatory nuclear movement. The speed of the movement fluctuated within a range 0 to 15 micron/minute, with an average of about 5 microm/minute. We propose a model in which the oscillatory nuclear movement is mediated by dynamic instability and selective stabilization of astral microtubules.},
author = {Ding, D Q and Chikashige, Y and Haraguchi, T and Hiraoka, Y},
issn = {0021-9533},
journal = {J. Cell Sci.},
month = {mar},
pages = {701--12},
pmid = {9471999},
title = {{Oscillatory nuclear movement in fission yeast meiotic prophase is driven by astral microtubules, as revealed by continuous observation of chromosomes and microtubules in living cells}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9471999},
volume = {111 ( Pt 6},
year = {1998}
}
@article{Grassia1996b,
abstract = {ABSTRACT Numerical simulations are employed to study the Brownian motion of a bead-rod polymer chain dissolved in a solvent. An investigation is conducted of the relaxation of the stress for an initially straight chain as it begins to coil.For a numerical time step {\&}delta;t in the simulations, conventional formulae for the stress involve averaging large {\&}plusmn;O(1{\&}soGrassia, P., {\&} Hinch, E. J. (1996). Computer simulations of polymer chain relaxation via Brownian motion. Journal of Fluid Mechanics, 308(May 2009), 255. doi:10.1017/S0022112096001474l;({\&}delta;t)1{\&}sol;2) contributions over many realizations, in order to yield an O(1) average. An alternative formula for the stress is derived which only contains O(1) contributions, thereby improving the quality of the statistics.For a chain consisting of n rods in a solvent at temperature T, the component of the bulk stress along the initial chain direction arising from tensions in the rods at the initial instant is k$\backslash$hat{\{}T{\}}$\backslash$times n($\backslash$frac{\{}1{\}}{\{}3{\}}n{\^{}}2 + n +$\backslash$frac{\{}2{\}}{\{}3{\}}). Thus the bead-rod model yields results very different from other polymer models, such as the entropic spring of Flory (1969), which would assign an infinite stress to a fully aligned chain. For rods of length l and beads of friction factor $\backslash$hat{\{}$\backslash$zeta{\}} the stress decays at first on O($\backslash$hat{\{}$\backslash$zeta{\}}$\backslash$hat{\{}l{\}}{\^{}}2/k$\backslash$hat{\{}T{\}}$\backslash$times 1/n{\^{}}2) time scales. On longer time scales, this behaviour gives way to a more gradual stress decay, characterized by an O(k$\backslash$hat{\{}T{\}}$\backslash$times n) stress following a simple exponential decay with an O(k$\backslash$hat{\{}T{\}}/$\backslash$hat{\{}$\backslash$zeta{\}}$\backslash$hat{\{}l{\}}{\^{}}2$\backslash$times 1/n{\^{}}2) rate. Matching these two limiting regimes, a power law decay in time t is found with stress O(k$\backslash$hat{\{}T{\}}$\backslash$times n{\^{}}2$\backslash$times (k$\backslash$hat{\{}T{\}}$\backslash$hat{\{}t{\}}/$\backslash$hat{\{}$\backslash$zeta{\}}$\backslash

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib