text:
chromosomes III, IV, XII, and XIV of Saccharomyces cerevisiae over an extended temporal range spanning more than four orders of magnitude (10(-2)-10(3) sec). Spatial fluctuations appear to be characterized by an anomalous diffusive behavior, which is homogeneous in the time domain, for all sites analyzed. We show that this response is consistent with the Rouse polymer model, and we confirm the relevance of the model with Brownian dynamics simulations and the analysis of the statistical properties of the trajectories. Moreover, the analysis of the amplitude of fluctuations by the Rouse model shows that yeast chromatin is highly flexible, its persistence length being qualitatively estimated to {\textless}30 nm. Finally, we show that the Rouse model is also relevant to analyze chromosome motion in mutant cells depleted of proteins that bind to or assemble chromatin, and suggest that it provides a consistent framework to study chromatin dynamics. We discuss the implications of our findings for yeast genome architecture and for target search mechanisms in the nucleus.},
author = {Hajjoul, Houssam and Mathon, Julien and Ranchon, Hubert and Goiffon, Isabelle and Mozziconacci, Julien and Albert, Benjamin and Carrivain, Pascal and Victor, Jean-Marc and Gadal, Olivier and Bystricky, Kerstin and Bancaud, Aur{\'{e}}lien},
doi = {10.1101/gr.157008.113},
file = {:Users/wenwen/Documents/MendeleyRefs/Hajjoul et al.{\_}Genome research{\_}2013.pdf:pdf},
isbn = {1549-5469 (Electronic)$\backslash$r1088-9051 (Linking)},
issn = {1549-5469},
journal = {Genome Res.},
keywords = {Cell Nucleus,Cell Nucleus: genetics,Chromatin,Chromatin: metabolism,Chromosomes, Fungal,Genetic Loci,Genome, Fungal,High-Throughput Screening Assays,Models, Molecular,Molecular Dynamics Simulation,Saccharomyces cerevisiae,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Telomere,Telomere: genetics},
number = {11},
pages = {1829--38},
pmid = {24077391},
title = {{High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome.}},
url = {http://genome.cshlp.org/content/23/11/1829.full},
volume = {23},
year = {2013}
}
@book{Grimmett1999,
author = {Bollobas, Bela and Riordan, Oliver},
file = {:Users/wenwen/Documents/MendeleyRefs/Bollobas, Riordan{\_}Unknown{\_}2006.pdf:pdf},
isbn = {0521872324},
publisher = {Cambridge University Press},
title = {{Percolation}},
year = {2006}
}
@article{DeGier2008d,
abstract = {We analyze the Bethe ansatz equations describing the complete spectrum of the transition matrix of the partially asymmetric exclusion process on a finite lattice and with the most general open boundary conditions. We extend results obtained recently for totally asymmetric diffusion [J. de Gier and F.H.L. Essler, J. Stat. Mech. P12011 (2006)] to the case of partial symmetry. We determine the finite-size scaling of the spectral gap, which characterizes the approach to stationarity at large times, in the low and high density regimes and on the coexistence line. We observe boundary induced crossovers and discuss possible interpretations of our results in terms of effective domain wall theories.},
archivePrefix = {arXiv},
arxivId = {0806.3493},
author = {de Gier, Jan and Essler, Fabian H L},
doi = {10.1088/1751-8113/41/48/485002},
eprint = {0806.3493},
file = {:Users/wenwen/Documents/MendeleyRefs/de Gier, Essler{\_}Journal of Physics A Mathematical and Theoretical{\_}2008.pdf:pdf},
issn = {1751-8113},
journal = {J. Phys. A Math. Theor.},
month = {dec},
number = {48},
pages = {485002},
title = {{Slowest relaxation mode of the partially asymmetric exclusion process with open boundaries}},
url = {http://stacks.iop.org/1751-8121/41/i=48/a=485002?key=crossref.4e33dcc71d451f09ef22bc683e0d718b},
volume = {41},
year = {2008}
}
@article{Kim2012,
author = {Kim, Jaeup U. and Yang, Yong Biao and Lee, Won Bo},
doi = {10.1021/ma202583y},
file = {:Users/wenwen/Documents/MendeleyRefs/Kim, Yang, Lee{\_}Macromolecules{\_}2012.pdf:pdf},
issn = {00249297},
journal = {Macromolecules},
number = {7},
pages = {3263--3269},
title = {{Self-consistent field theory of gaussian ring polymers}},
volume = {45},
year = {2012}
}
@article{Liu1989,
author = {Liu, Tony W.},
doi = {10.1063/1.456389},
file = {:Users/wenwen/Documents/MendeleyRefs/Liu{\_}The Journal of Chemical Physics{\_}1989.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {10},
pages = {5826},
title = {{Flexible polymer chain dynamics and rheological properties in steady flows}},
url = {http://link.aip.org/link/JCPSA6/v90/i10/p5826/s1{\&}Agg=doi},
volume = {90},
year = {1989}
}
@article{Wells2006,
author = {Wells, Jennifer L. and Pryce, David W. and McFarlane, Ramsay J.},
doi = {10.1002/yea.1403},
file = {:Users/wenwen/Documents/MendeleyRefs/Wells, Pryce, McFarlane{\_}Yeast{\_}2006.pdf:pdf},
issn = {0749503X},
journal = {Yeast},
keywords = {Schizosaccharomyces pombe,centromeres,homologous chromosome pairing,linear elements,meiosis,meiotic bouquet,recombination,telomeres},
month = {oct},
number = {13},
pages = {977--989},
publisher = {John Wiley {\&} Sons, Ltd.},
title = {{Homologous chromosome pairing inSchizosaccharomyces pombe}},
url = {http://doi.wiley.com/10.1002/yea.1403},
volume = {23},
year = {2006}
}
@article{Rosa2014b,
abstract = {The conformational statistics of ring polymers in melts or dense solutions is strongly affected by their quenched microscopic topological state. The effect is particularly strong for nonconcatenated unknotted rings, which are known to crumple and segregate and which have been implicated as models for the generic behavior of interphase chromosomes. Here we use a computationally efficient multiscale approach to show that melts of rings of total contour length L-r can be quantitatively mapped onto melts of interacting lattice trees with gyration radii {\textless} R-g(2) (L-r){\textgreater} proportional to L-r(2 nu) and nu = 0.32 +/- 0.01.},
archivePrefix = {arXiv},
arxivId = {arXiv:1310.7641v1},
author = {Rosa, Angelo and Everaers, Ralf},
doi = {10.1103/PhysRevLett.112.118302},
eprint = {arXiv:1310.7641v1},
file = {:Users/wenwen/Documents/MendeleyRefs/Rosa, Everaers{\_}Physical Review Letters{\_}2014.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Rosa, Everaers{\_}Physical Review Letters{\_}2014.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Rosa, Everaers{\_}Physical Review Letters{\_}2014.pdf:pdf},
isbn = {0031-9007},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {mar},
number = {11},
pages = {118302},
title = {{Ring Polymers in the Melt State: The Physics of Crumpling}},
url = {http://arxiv.org/abs/1310.7641 http://link.aps.org/doi/10.1103/PhysRevLett.112.118302},
volume = {112},
year = {2014}
}
@book{Alberts2014,
abstract = {Discusses fundamental processes in the cell and provides insights into current research},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Alberts, Bruce and Johnson, Alexander and Lewis, Julian and Morgan, David and Raff, Martin and Roberts, Keith and Walter, Peter},
doi = {10.1002/1521-3773(20010316)40:6<9823::AID-ANIE9823>3.3.CO;2-C},
eprint = {arXiv:1011.1669v3},
isbn = {1136844422},
issn = {14337851},
number = {6},
pages = {1465},
pmid = {2998816},
publisher = {Garland Science},
title = {{Molecular Biology of the Cell}},
volume = {6},
year = {2014}
}
@article{Bick2011,
author = {Bick, Christian and Timme, Marc and Paulikat, Danilo and Rathlev, Dirk and Ashwin, Peter},
doi = {10.1103/PhysRevLett.107.244101},
file = {:Users/wenwen/Documents/MendeleyRefs/Bick et al.{\_}Physical Review Letters{\_}2011.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {dec},
number = {24},
pages = {1--4},
title = {{Chaos in Symmetric Phase Oscillator Networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.107.244101},
volume = {107},
year = {2011}
}
@techreport{Hayden,
author = {Hayden, R A},
file = {:Users/wenwen/Documents/MendeleyRefs/Hayden{\_}Unknown{\_}Unknown.pdf:pdf},
pages = {1--26},
title = {{On the application of tensor products of vector spaces to the representation theory of finite groups}}
}
@article{Marwan2009,
author = {Marwan, Norbert and Donges, Jonathan F. and Zou, Yong and Donner, Reik V. and Kurths, J{\"{u}}rgen},
doi = {10.1016/j.physleta.2009.09.042},
file = {:Users/wenwen/Documents/MendeleyRefs/Marwan et al.{\_}Physics Letters A{\_}2009.pdf:pdf},
issn = {03759601},
journal = {Phys. Lett. A},
month = {nov},
number = {46},
pages = {4246--4254},
publisher = {Elsevier B.V.},
title = {{Complex network approach for recurrence analysis of time series}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0375960109011852},
volume = {373},
year = {2009}
}
@article{Fantes2016,
author = {Fantes, Peter A. and Hoffman, Charles S.},
doi = {10.1534/genetics.116.189407},
issn = {0016-6731},
journal = {Genetics},
month = {jun},
number = {2},
pages = {621--629},
title = {{A Brief History of Schizosaccharomyces pombe Research: A Perspective Over the Past 70 Years}},
url = {http://www.genetics.org/cgi/doi/10.1534/genetics.116.189407},
volume = {203},
year = {2016}
}
@article{Brattain2015,
abstract = {The asymmetric simple exclusion process (ASEP) for N particles on a ring with L sites may be analyzed using the Bethe ansatz. In this paper, we provide a rigorous proof that the Bethe ansatz is complete for the periodic ASEP. More precisely, we show that for all but finitely many values of the hopping rate, the solutions of the Bethe ansatz equations do indeed yield all L choose N eigenstates. The proof follows ideas of Langlands and Saint-Aubin, which draw upon a range of techniques from algebraic geometry, topology and enumerative combinatorics.},
archivePrefix = {arXiv},
arxivId = {1511.03762},
author = {Brattain, Eric and Do, Norman and Saenz, Axel},
eprint = {1511.03762},
file = {:Users/wenwen/Documents/MendeleyRefs/Brattain, Do, Saenz{\_}Unknown{\_}2015.pdf:pdf},
month = {nov},
pages = {1--36},
title = {{The completeness of the Bethe ansatz for the periodic ASEP}},
url = {http://arxiv.org/abs/1511.03762},
year = {2015}
}
@article{Motter2002,
author = {Motter, Adilson and Lai, Ying-Cheng},
doi = {10.1103/PhysRevE.66.065102},
file = {:Users/wenwen/Documents/MendeleyRefs/Motter, Lai{\_}Physical Review E{\_}2002.pdf:pdf},
issn = {1063-651X},
journal = {Phys. Rev. E},
month = {dec},
number = {6},
pages = {065102},
title = {{Cascade-based attacks on complex networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.66.065102},
volume = {66},
year = {2002}
}
@article{Meiners2000,
abstract = {We studied the thermal fluctuations of single DNA molecules with a novel optical tweezer based force spectroscopy technique. This technique combines femtonewton sensitivity with millisecond time resolution, surpassing the sensitivity of previous force measurements in aqueous solution with comparable bandwidth by a hundredfold. Our data resolve long-standing questions concerning internal hydrodynamics of the polymer and anisotropy in the molecular relaxation times and friction coefficients. The dynamics at high extension show interesting nonlinear behavior.},
author = {Meiners, Jens-Christian and Quake, Stephen R},
doi = {10.1103/PhysRevLett.84.5014},
file = {:Users/wenwen/Documents/MendeleyRefs/Meiners, Quake{\_}Physical Review Letters{\_}2000.pdf:pdf},
isbn = {0031-9007 (Print)$\backslash$r0031-9007 (Linking)},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {may},
number = {21},
pages = {5014--5017},
pmid = {10990855},
title = {{Femtonewton Force Spectroscopy of Single Extended DNA Molecules}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.84.5014},
volume = {84},
year = {2000}
}
@article{Holme2002,
author = {Holme, Petter and Kim, Beom and Yoon, Chang and Han, Seung},
doi = {10.1103/PhysRevE.65.056109},
file = {:Users/wenwen/Documents/MendeleyRefs/Holme et al.{\_}Physical Review E{\_}2002.pdf:pdf},
issn = {1063-651X},
journal = {Phys. Rev. E},
month = {may},
number = {5},
pages = {1--14},
title = {{Attack vulnerability of complex networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.65.056109},
volume = {65},
year = {2002}
}
@article{Brown1998a,
author = {Brown, Scott and Szamel, Grzegorz},
doi = {10.1063/1.475927},
file = {:Users/wenwen/Documents/MendeleyRefs/Brown, Szamel{\_}The Journal of Chemical Physics{\_}1998.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {12},
pages = {4705},
title = {{Structure and dynamics of ring polymers}},
url = {http://scitation.aip.org/content/aip/journal/jcp/108/12/10.1063/1.475927},
volume = {108},
year = {1998}
}
@article{Sugihara2012,
abstract = {Identifying causal networks is important for effective policy and management recommendations on climate, epidemiology, financial regulation, and much else. We introduce a method, based on nonlinear state space reconstruction, that can distinguish causality from correlation. It extends to nonseparable weakly connected dynamic systems (cases not covered by the current Granger causality paradigm). The approach is illustrated both by simple models (where, in contrast to the real world, we know the underlying equations/relations and so can check the validity of our method) and by application to real ecological systems, including the controversial sardine-anchovy-temperature problem.},
author = {Sugihara, G. and May, R. and Ye, H. and Hsieh, C.-h. and Deyle, E. and Fogarty, M. and Munch, S.},
doi = {10.1126/science.1227079},
file = {:Users/wenwen/Documents/MendeleyRefs/Sugihara et al.{\_}Science{\_}2012.pdf:pdf},
isbn = {1095-9203},
issn = {0036-8075},
journal = {Science (80-. ).},
month = {oct},
number = {6106},
pages = {496--500},
pmid = {22997134},
title = {{Detecting Causality in Complex Ecosystems}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1227079},
volume = {338},
year = {2012}
}
@article{Larson1999,
abstract = {The unraveling dynamics of long, isolated, molecules of DNA subjected to an extensional flow in a crossed-slot device ?T. T. Perkins, D. E. Smith, and S. Chu, ‘‘Single polymer dynamics in an elongational flow,'' Science 276, 2016–2021 ?1997?; D. E. Smith and S. Chu, ‘‘Response of Flexible Polymers to a Sudden Elongational Flow,'' Science 281, 1335–1340 ?1998?? are predicted by Brownian dynamics simulations using measured elastic and viscous properties of the DNA as the only inputs. Quantitative agreement is obtained both in the percentages of various unraveling states, such as ‘‘folds,'' ‘‘kinks,'' ‘‘dumbbells,'' half-dumbbells,'' and ‘‘coils,'' and in the ensemble-averaged stretch and rate of stretch. Under fast flows (De ? 10), unraveling is initially nearly affine, but for fractional stretch greater than ? 1/3, stretching is delayed to an extent that varies widely from molecule to molecule by flow-induced folded states, which are far-from-equilibrium kinetic hindrances not predicted by dumbbell models. From the computer simulations, the source of the high molecule-to-molecule heterogeneity in the experiments is traced to variability in the initial polymer configuration, which sets the unraveling path the molecule must take at De ? 10. Formation of folds and kinks during unraveling can be predicted fairly reliably just by examining the initial state. The high-De unraveling behavior is consistent with the predictions of one-dimensional ‘‘kink dynamics'' simulations.},
author = {Larson, R. G. and Hu, Hua and Smith, D. E. and Chu, S.},
doi = {10.1122/1.550991},
file = {:Users/wenwen/Documents/MendeleyRefs/Larson et al.{\_}Journal of Rheology{\_}1999.pdf:pdf},
issn = {01486055},
journal = {J. Rheol. (N. Y. N. Y).},
number = {2},
pages = {267},
title = {{Brownian dynamics simulations of a DNA molecule in an extensional flow field}},
url = {http://scitation.aip.org/content/sor/journal/jor2/43/2/10.1122/1.550991},
volume = {43},
year = {1999}
}
@article{Li2012,
author = {Li, Nianbei and Ren, Jie and Wang, Lei and Zhang, Gang and H{\"{a}}nggi, Peter and Li, Baowen},
doi = {10.1103/RevModPhys.84.1045},
file = {:Users/wenwen/Documents/MendeleyRefs/Li et al.{\_}Reviews of Modern Physics{\_}2012.pdf:pdf},
issn = {0034-6861},
journal = {Rev. Mod. Phys.},
month = {jul},
number = {3},
pages = {1045--1066},
title = {{Colloquium: Phononics: Manipulating heat flow with electronic analogs and beyond}},
url = {http://link.aps.org/doi/10.1103/RevModPhys.84.1045},
volume = {84},
year = {2012}
}
@misc{Ferziger2002,
author = {{Ferziger Joel H.; Peric}, Milovan},
file = {:Users/wenwen/Documents/MendeleyRefs/Ferziger Joel H. Peric{\_}Unknown{\_}2002.pdf:pdf},
publisher = {Springer},
title = {{Computational Methods for Fluid Dynamics}},
year = {2002}
}
@article{Zhang,
abstract = {While social network is becoming more and more im- portant in our everyday life, it is becoming huger and huger. How to partition a social network is one of the most fundamental and important problems in social network. In recent years, a lot of partition algorithms have been proposed for social networks. But none of them could achieve good partition results as they were in random graphs, which gives a small global cut be- tween partitions. A natural question is: Does there really exist partition methods for social network? This report takes a small step towards this question. Using the preferential attachment model, the lower and upper bound of the expectation of cut when partitioning the graph into two parts have been presented in this report. Based on preferential attachment model, we propose a partition growth model. The intuition behind it is that, when a new vertex adds into the network, it ﬁrstly connects with several vertices by preferential attachment, then it adds into either partition. By the recursively doing so, we can get a good approximation of the expectation of cut between the two partitions. This report mainly serve as a course project ﬁnal report for CS290D at 2011 spring quarter. Author is Yuanyang Zhang, who is a ﬁrst year Ph.D. student. The advisor is Xifeng Yan, who is the professor of the course CS290D.},
author = {Zhang, Yuanyang and Yan, Xifeng},
file = {:Users/wenwen/Documents/MendeleyRefs/Zhang, Yan{\_}Cs.Ucsb.Edu{\_}Unknown.pdf:pdf},
journal = {Cs.Ucsb.Edu},
title = {{Analysis of Partition in Scale-free Network}},
url = {http://www.cs.ucsb.edu/{~}yuanyang/papers/CS290dFinalReportYuanyangZhang.pdf}
}
@article{Schaeffer2007a,
abstract = {In this survey we overview the definitions and methods for graph clustering, that is, finding sets of "related" vertices in graphs. We review the many definitions for what is a cluster in a graph and measures of cluster quality. Then we present global algorithms for producing a clustering for the entire vertex set of an input graph, after which we discuss the task of identifying a cluster for a specific seed vertex by local computation. Some ideas on the application areas of graph clustering algorithms are given. We also address the problematics of evaluating clusterings and benchmarking cluster algorithms. {\textcopyright} 2007 Elsevier Ltd. All rights reserved.},
author = {Schaeffer, Satu Elisa},
doi = {10.1016/j.cosrev.2007.05.001},
file = {:Users/wenwen/Documents/MendeleyRefs/Schaeffer{\_}Computer Science Review{\_}2007.pdf:pdf},
isbn = {1574-0137},
issn = {15740137},
journal = {Comput. Sci. Rev.},
keywords = {- see front matter,001,05,10,1016,1574-0137,2007,all rights reserved,ap 126-f,c 2007 elsevier ltd,ciudad universitaria,com,cosrev,doi,e-mail address,elisa,garza,gmail,j,mexico,nl 66450,pisis,san nicol{\'{a}}s de los,schaeffer},
month = {aug},
number = {1},
pages = {27--64},
pmid = {12952885},
title = {{Graph clustering}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1574013707000020},
volume = {1},
year = {2007}
}
@article{Moreira2010,
author = {Moreira, a. a. and Oliveira, E. a. and Reis, S. D. S. and Herrmann, H. J. and Andrade, J. S.},
doi = {10.1103/PhysRevE.81.040101},
file = {:Users/wenwen/Documents/MendeleyRefs/Moreira et al.{\_}Physical Review E{\_}2010.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {apr},
number = {4},
pages = {1--4},
title = {{Hamiltonian approach for explosive percolation}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.81.040101},
volume = {81},
year = {2010}
}
@article{Chapman2014,
author = {Chapman, Cole D and Robertson-Anderson, Rae M},
doi = {10.1103/PhysRevLett.113.098303},
file = {:Users/wenwen/Documents/MendeleyRefs/Chapman, Robertson-Anderson{\_}Physical Review Letters{\_}2014.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {aug},
number = {9},
pages = {098303},
title = {{Nonlinear Microrheology Reveals Entanglement-Driven Molecular-Level Viscoelasticity of Concentrated DNA}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.113.098303},
volume = {113},
year = {2014}
}
@article{Sakaue2011,
abstract = {We propose a simple mean-field theory for the structure of ring polymer melts. By combining the notion of topological volume fraction and a classical van der Waals theory of fluids, we take into account many-body effects of topological origin in dense systems. We predict that although the compact statistics with the Flory exponent $\nu$=1/3 is realized for very long chains, most practical cases fall into the crossover regime with the apparent exponent $\nu$≃2/5 during which the system evolves toward a topological dense-packed limit.},
archivePrefix = {arXiv},
arxivId = {1104.1008},
author = {Sakaue, Takahiro},
doi = {10.1103/PhysRevLett.106.167802},
eprint = {1104.1008},
file = {:Users/wenwen/Documents/MendeleyRefs/Sakaue{\_}Physical Review Letters{\_}2011.pdf:pdf},
issn = {00319007},
journal = {Phys. Rev. Lett.},
number = {April},
pages = {1--4},
pmid = {21599414},
title = {{Ring polymers in melts and solutions: Scaling and crossover}},
volume = {106},
year = {2011}
}
@book{Breu2008,
author = {Jiawei, H and Kamber, Micheline},
doi = {10.1002/1521-3773(20010316)40:6<9823::AID-ANIE9823>3.3.CO;2-C},
isbn = {9780123814791},
issn = {14337851},
pmid = {13951627},
publisher = {Pearson Education},
title = {{C++ Primer Plus}},
url = {http://scholar.google.com/scholar?hl=en{\&}btnG=Search{\&}q=intitle:Data+mining+concepts+and+techniques{\#}1{\%}5Cnhttp://scholar.google.com/scholar?hl=en{\&}btnG=Search{\&}q=intitle:Data+mining:+concepts+and+techniques{\#}1},
year = {2001}
}
@misc{Phillips,
author = {Phillips, Nelson},
file = {:Users/wenwen/Documents/MendeleyRefs/Phillips{\_}Unknown{\_}Unknown.pdf:pdf},
title = {{生物物理学：能量、信息、生命+（美）菲利普{\textperiodcentered}纳尔逊着.Pdf}}
}
@article{Polymers1991,
abstract = {We represent ring polymers in free space with the rod-bead model and show through unbiased computer simulations that the probability of observing a trivial self-entanglement (P) has a decreasing exponential dependence on the contour length (N) of the polymer, or that P=exp(-N/N0). The characteristic length (N0) varies by many orders of magnitude depending on chain flexibility and solvent quality. We also suggest that sufficiently large knots are always composite, not prime.},
author = {Koniaris, Kleanthes and Muthukumar, M.},
doi = {10.1103/PhysRevLett.66.2211},
file = {:Users/wenwen/Documents/MendeleyRefs/Koniaris, Muthukumar{\_}Physical Review Letters{\_}1991.pdf:pdf},
issn = {00319007},
journal = {Phys. Rev. Lett.},
number = {17},
pages = {2211--2214},
pmid = {10043425},
title = {{Knottedness in ring polymers}},
volume = {66},
year = {1991}
}
@article{Rzehak2000,
abstract = {The decay of correlations in the conformational fluctuations of a tethered polymer subjected to a uniform flow is analyzed in terms of relaxation times and associated normal modes. These quantities are calculated numerically from Brownian dynamics simulations of several bead spring polymer models. In this way, the influence of different effects like a finite extensibility of the springs and excluded-volume as well as hydrodynamic interactions between the beads on the decay of fluctuations is identified. Moreover, by comparison of the simulation results to analytically tractable blob models with corresponding assumptions, the capability of the tensile-blob picture to predict relaxation times and modes is assessed. For excluded-volume and hydrodynamic interactions a crossover to Rouse-like behavior occurs when the flow velocity and hence the polymer deformation exceeds a certain value. For finitely extensible springs, in contrast, the relaxation times decrease monotonically with increasing polymer deformation. This latter behavior differs from assumptions often used in rheological modeling by dumbbells and is not captured by the blob model.},
author = {Rzehak, R and Kromen, W},
doi = {10.1140/epje/i2003-10021-y},
file = {:Users/wenwen/Documents/MendeleyRefs/Rzehak, Kromen{\_}The European Physical {\ldots}{\_}2000.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Rzehak, Kromen{\_}The European Physical {\ldots}{\_}2000.pdf:pdf},
isbn = {1292-8941 (Print)$\backslash$r1292-8941 (Linking)},
issn = {1292-8941},
journal = {Eur. Phys. {\ldots}},
pages = {3--30},
pmid = {15011036},
title = {{Deformation of a tethered polymer in uniform flow}},
url = {http://link.springer.com/article/10.1007/s101890050036},
volume = {30},
year = {2000}
}
@article{King1983,
abstract = {Stresses generated by a solution of Rouse macromolecules in planar and axisymmetric sink flow were analyzed by solving the momentum equation together with the constitutive relation corresponding to the Rouse model (i.e., the generalized convected Maxwell equation). The results show that the additional normal stress in the radial direction is of order [77]C when compared with the corresponding Newtonian viscous stress. However, in the high Reynolds number range where sink flow conditions are valid, the additional stress must be compared with inertial stresses, and in that case the results show that the ratio of non-Newtonian to Newtonian hydrodynamic stresses is of order [77 ]c/Re, where Re is the Reynolds number. Since experimental data exceed this small ratio by two orders of magnitude, a new molecular model was developed to accommodate limited molecular extension. The model presumes that, in a converging flow, a molecule initially deforms as a Rouse molecule and then its configuration is frozen after a certain amount of extension. This "frozen-necklace" model consequently provides an estimate of hydrodynamic effects caused by finite extension, as might be created by intramolecular entanglements. Non-Newtonian stresses predicted by the model are compared with available data for strictly dilute solutions and agree to the same order of magnitude.},
author = {King, D. H. and James, D. F.},
doi = {10.1063/1.445274},
file = {:Users/wenwen/Documents/MendeleyRefs/King, James{\_}The Journal of Chemical Physics{\_}1983.pdf:pdf},
isbn = {0021-9606},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {7},
pages = {4749},
title = {{Analysis of the Rouse model in extensional flow. II. Stresses generated in sink flow by flexible macromolecules and by finitely extended macromolecules}},
url = {http://scitation.aip.org/content/aip/journal/jcp/78/7/10.1063/1.445274},
volume = {78},
year = {1983}
}
@book{Athreya2006,
author = {Athreya, Krishna B. and Lahiri, Soumendra N.},
file = {:Users/wenwen/Documents/MendeleyRefs/Athreya, Lahiri{\_}Unknown{\_}2006.pdf:pdf},
isbn = {9780387329031},
publisher = {Springer},
title = {{Measure Theory and Probability Theory}},
year = {2006}
}
@article{Crampe2014b,
abstract = {We study the matrix ansatz in the quantum group framework, applying integrable systems techniques to statistical physics models. We start by reviewing the two approaches, and then show how one can use the former to get new insight on the latter. We illustrate our method by solving a model of reaction-diffusion. An eigenvector for the transfer matrix for the XXZ spin chain with non-diagonal boundary is also obtained using a matrix ansatz.},
archivePrefix = {arXiv},
arxivId = {1408.5357},
author = {Crampe, N and Ragoucy, E and Vanicat, M},
doi = {10.1088/1742-5468/2014/11/P11032},
eprint = {1408.5357},
file = {:Users/wenwen/Documents/MendeleyRefs/Crampe, Ragoucy, Vanicat{\_}Journal of Statistical Mechanics Theory and Experiment{\_}2014.pdf:pdf},
issn = {1742-5468},
journal = {J. Stat. Mech. Theory Exp.},
number = {11},
pages = {P11032},
title = {{Integrable approach to simple exclusion processes with boundaries. Review and progress}},
url = {http://arxiv.org/abs/1408.5357},
volume = {2014},
year = {2014}
}
@article{Pasquali2002,
abstract = {The dynamical behavior and equilibrium distribution of linear bead-rod and bead-spring polymers differ even in the limit of infinitely stiff springs. Imposing metric pseudopotential forces on the bead-rod chains yields the behavior of bead-spring chains in Langevin and Brownian Dynamics simulations. Here we present a simple, compact, and efficient algorithm for computing the required metric correction forces at minimal computational cost.},
author = {Pasquali, Matteo and Morse, David C.},
doi = {10.1063/1.1428747},
file = {:Users/wenwen/Documents/MendeleyRefs/Pasquali, Morse{\_}The Journal of Chemical Physics{\_}2002.pdf:pdf},
isbn = {00219606},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {5},
pages = {1834},
title = {{An efficient algorithm for metric correction forces in simulations of linear polymers with constrained bond lengths}},
url = {http://scitation.aip.org/content/aip/journal/jcp/116/5/10.1063/1.1428747},
volume = {116},
year = {2002}
}
@article{Aoki2009,
author = {Aoki, Takaaki and Aoyagi, Toshio},
doi = {10.1103/PhysRevLett.102.034101},
file = {:Users/wenwen/Documents/MendeleyRefs/Aoki, Aoyagi{\_}Physical Review Letters{\_}2009.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {jan},
number = {3},
pages = {1--4},
title = {{Co-evolution of Phases and Connection Strengths in a Network of Phase Oscillators}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.102.034101},
volume = {102},
year = {2009}
}
@article{Kyrylyuk2008,
abstract = {We apply continuum connectedness percolation theory to realistic carbon nanotube systems and predict how bending flexibility, length polydispersity, and attractive interactions between them influence the percolation threshold, demonstrating that it can be used as a predictive tool for designing nanotube-based composite materials. We argue that the host matrix in which the nanotubes are dispersed controls this threshold through the interactions it induces between them during processing and through the degree of connectedness that must be set by the tunneling distance of electrons, at least in the context of conductivity percolation. This provides routes to manipulate the percolation threshold and the level of conductivity in the final product. We find that the percolation threshold of carbon nanotubes is very sensitive to the degree of connectedness, to the presence of small quantities of longer rods, and to very weak attractive interactions between them. Bending flexibility or tortuosity, on the other hand, has only a fairly weak impact on the percolation threshold.},
author = {Kyrylyuk, Andriy V and van der Schoot, Paul},
doi = {10.1073/pnas.0711449105},
file = {:Users/wenwen/Documents/MendeleyRefs/Kyrylyuk, van der Schoot{\_}Proceedings of the National Academy of Sciences of the United States of America{\_}2008.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
month = {jun},
number = {24},
pages = {8221--8226},
pmid = {18550818},
title = {{Continuum percolation of carbon nanotubes in polymeric and colloidal media}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2448818{\&}tool=pmcentrez{\&}rendertype=abstract http://www.pnas.org/cgi/doi/10.1073/pnas.0711449105},
volume = {105},
year = {2008}
}
@article{Barabasi2011,
author = {Barab{\'{a}}si, Albert-L{\'{a}}szl{\'{o}}},
doi = {10.1038/nphys2188},
file = {:Users/wenwen/Documents/MendeleyRefs/Barab{\'{a}}si{\_}Nature Physics{\_}2011.pdf:pdf},
issn = {1745-2473},
journal = {Nat. Phys.},
month = {dec},
number = {1},
pages = {14--16},
publisher = {Nature Publishing Group},
title = {{The network takeover}},
url = {http://www.nature.com/doifinder/10.1038/nphys2188},
volume = {8},
year = {2011}
}
@article{Arenas2008,
annote = {From Duplicate 2 (

Synchronization in complex networks

- Arenas, Alex; D{\'{i}}az-Guilera, Albert; Kurths, Jurgen; Moreno, Yamir; Zhou, Changsong )

},
author = {Arenas, Alex and D{\'{i}}az-Guilera, Albert and Kurths, Jurgen and Moreno, Yamir and Zhou, Changsong and Albert, D},
doi = {10.1016/j.physrep.2008.09.002},
file = {:Users/wenwen/Documents/MendeleyRefs/Arenas et al.{\_}Physics Reports{\_}2008.pdf:pdf},
issn = {03701573},
journal = {Phys. Rep.},
month = {dec},
number = {3},
pages = {93--153},
publisher = {Elsevier B.V.},
title = {{Synchronization in complex networks}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0370157308003384},
volume = {469},
year = {2008}
}
@article{Marwan2007,
author = {Marwan, N and Carmenromano, M and Thiel, M and Kurths, J},
doi = {10.1016/j.physrep.2006.11.001},
file = {:Users/wenwen/Documents/MendeleyRefs/Marwan et al.{\_}Physics Reports{\_}2007.pdf:pdf},
issn = {03701573},
journal = {Phys. Rep.},
keywords = {data analysis,nonlinear dynamics,recurrence plot},
month = {jan},
number = {5-6},
pages = {237--329},
title = {{Recurrence plots for the analysis of complex systems}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0370157306004066},
volume = {438},
year = {2007}
}
@article{Nepomechie2002,
abstract = {We consider the open XXZ quantum spin chain with nondiagonal boundary terms. For bulk anisotropy value ?? = i??/p+1, p = 1, 2, ..., we propose an exact (p + 1)-order functional relation for the transfer matrix, which implies Bethe-ansatz-like equations for the corresponding eigenvalues. The key observation is that the fused spin-p+1/2 transfer matrix can be expressed in terms of a lower-spin transfer matrix, resulting in the truncation of the fusion hierarchy. ?? 2002 Elsevier Science B.V. All rights reserved.},
archivePrefix = {arXiv},
arxivId = {hep-th/0304092},
author = {Nepomechie, Rafael I.},
doi = {10.1016/S0550-3213(01)00585-5},
eprint = {0304092},
file = {:Users/wenwen/Documents/MendeleyRefs/Nepomechie{\_}Nuclear Physics B{\_}2002.pdf:pdf},
issn = {05503213},
journal = {Nucl. Phys. B},
month = {feb},
number = {3},
pages = {615--632},
primaryClass = {hep-th},
title = {{Solving the open XXZ spin chain with nondiagonal boundary terms at roots of unity}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0550321301005855},
volume = {622},
year = {2002}
}
@article{Dernburg2012,
author = {Dernburg, Abby F},
doi = {10.1126/science.1222647},
file = {:Users/wenwen/Documents/MendeleyRefs/Dernburg{\_}Science{\_}2012.pdf:pdf},
issn = {0036-8075},
journal = {Science (80-. ).},
keywords = {Chromosome Pairing,Chromosomes,Fungal,Fungal: physiology,Meiosis,RNA,Schizosaccharomyces,Schizosaccharomyces: genetics,Untranslated,Untranslated: genetics},
month = {may},
number = {6082},
pages = {681--682},
pmid = {22582252},
title = {{RNA Plays Meiotic Matchmaker}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22582252 http://www.sciencemag.org/cgi/doi/10.1126/science.1222647},
volume = {336},
year = {2012}
}
@article{Barkema2015,
abstract = {Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the absence of hydrodynamic interactions. The dsDNA is modelled with one bead-spring element per basepair, and the polymer dynamics is described by the Langevin equation. The key to efficiency is that we describe the equations of motion for the polymer in terms of the amplitudes of the polymer's fluctuation modes, as opposed to the use of the physical positions of the beads. We show that, within an accuracy tolerance level of {\$}5\backslash{\%}{\$} of several key observables, the model allows for single Langevin time steps of {\$}\backslashapprox1.6{\$}, 8, 16 and 16 ps for a dsDNA model-chain consisting of 64, 128, 256 and 512 basepairs (i.e., chains of 0.55, 1.11, 2.24 and 4.48 persistence lengths) respectively. Correspondingly, in one hour, a standard desktop computer can simulate 0.23, 0.56, 0.56 and 0.26 ms of these dsDNA chains respectively. We compare our results to those obtained from other methods, in particular, the (inextensible discretised) WLC model. Importantly, we demonstrate that at the same level of discretisation, i.e., when each discretisation element is one basepair long, our algorithm gains about 5-6 orders of magnitude in the size of time steps over the inextensible WLC model. Further, we show that our model can be mapped one-on-one to a discretised version of the extensible WLC model; implying that the speed-up we achieve in our model must hold equally well for the latter. We also demonstrate the use of the method by simulating efficiently the tumbling behaviour of a dsDNA segment in a shear flow.},
archivePrefix = {arXiv},
arxivId = {1411.3487},
author = {Panja, Debabrata and Barkema, Gerard T and van Leeuwen, J. M. J.},
doi = {10.1103/PhysRevE.92.032603},
eprint = {1411.3487},
file = {:Users/wenwen/Documents/MendeleyRefs/Panja, Barkema, van Leeuwen{\_}Physical Review E{\_}2015.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {sep},
number = {3},
pages = {032603},
title = {{Efficient simulation of semiflexible polymers}},
url = {http://arxiv.org/abs/1411.3487 http://dx.doi.org/10.1103/PhysRevE.92.032603 http://link.aps.org/doi/10.1103/PhysRevE.92.032603},
volume = {92},
year = {2015}
}
@article{Zimm1949,
abstract = {Formulas for the mean square radii of various branched and ringed polymer molecules are developed under the assumptions regarding the statistics of chain configuration. For brancehd molecules, the mean square radii vary less rapidly with molecular weight than for strictly lineal molecules, while for systems containing only rings and unbranched chains the variation is more rapid than for the linear case. These results show that in principle the quantity of branches or of rings can be determined from light scattering measurements.},
author = {Zimm, Bruno H. and Stockmayer, Walter H.},
doi = {10.1063/1.1747157},
file = {:Users/wenwen/Documents/MendeleyRefs/Zimm, Stockmayer{\_}The Journal of chemical physics{\_}1949.pdf:pdf},
isbn = {0021-9606},
issn = {00219606},
journal = {J. Chem. Phys.},
keywords = {Branching,branched architecture},
number = {12},
pages = {1301--1314},
title = {{The Dimensions of Chain Molecules Containing Branches and Rings}},
volume = {17},
year = {1949}
}
@article{Gonzalez2008,
abstract = {Despite their importance for urban planning, traffic forecasting and the spread of biological and mobile viruses, our understanding of the basic laws governing human motion remains limited owing to the lack of tools to monitor the time-resolved location of individuals. Here we study the trajectory of 100,000 anonymized mobile phone users whose position is tracked for a six-month period. We find that, in contrast with the random trajectories predicted by the prevailing L{\'{e}}vy flight and random walk models, human trajectories show a high degree of temporal and spatial regularity, each individual being characterized by a time-independent characteristic travel distance and a significant probability to return to a few highly frequented locations. After correcting for differences in travel distances and the inherent anisotropy of each trajectory, the individual travel patterns collapse into a single spatial probability distribution, indicating that, despite the diversity of their travel history, humans follow simple reproducible patterns. This inherent similarity in travel patterns could impact all phenomena driven by human mobility, from epidemic prevention to emergency response, urban planning and agent-based modelling.},
archivePrefix = {arXiv},
arxivId = {0806.1256},
author = {Gonz{\'{a}}lez, Marta C and Hidalgo, C{\'{e}}sar a and Barab{\'{a}}si, Albert-L{\'{a}}szl{\'{o}}},
doi = {10.1038/nature06958},
eprint = {0806.1256},
file = {:Users/wenwen/Documents/MendeleyRefs/Gonz{\'{a}}lez, Hidalgo, Barab{\'{a}}si{\_}Nature{\_}2008.pdf:pdf},
isbn = {1476-4687 (Electronic)$\backslash$r0028-0836 (Linking)},
issn = {0028-0836},
journal = {Nature},
number = {7196},
pages = {779--782},
pmid = {18528393},
title = {{Understanding individual human mobility patterns.}},
volume = {453},
year = {2008}
}
@article{Wang2003,
author = {Wang, XF and Chen, Guanrong},
file = {:Users/wenwen/Documents/MendeleyRefs/Wang, Chen{\_}Circuits and Systems Magazine, IEEE{\_}2003.pdf:pdf},
journal = {Circuits Syst. Mag. IEEE},
number = {1},
pages = {6----20},
title = {{Complex networks: small-world, scale-free and beyond}},
url = {http://ieeexplore.ieee.org/xpls/abs{\_}all.jsp?arnumber=1228503},
volume = {3},
year = {2003}
}
@article{Valente2004,
author = {Valente, Andr{\'{e}} and Sarkar, Abhijit and Stone, Howard},
doi = {10.1103/PhysRevLett.92.118702},
file = {:Users/wenwen/Documents/MendeleyRefs/Valente, Sarkar, Stone{\_}Physical Review Letters{\_}2004.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {mar},
number = {11},
pages = {1--4},
title = {{Two-Peak and Three-Peak Optimal Complex Networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.92.118702},
volume = {92},
year = {2004}
}
@article{Michieletto2014,
abstract = {We perform large scale three-dimensional molecular dynamics simulations of unlinked and un-knotted ring polymers diffusing through a background gel, here a three-dimensional cubic lattice. Taking advantage of this architecture, we propose a new method to unambiguously identify and quantify inter-ring threadings (penetrations) and to relate these to the slow dynamics of the ring polymers. We find both that the number and the persistence time of the threadings increase with the length of the chains, ultimately leading to a percolating network of inter-ring penetrations. We discuss the implications of these findings for the possible emergence of a {\{}$\backslash$em topological glass{\}} of very long rings.},
archivePrefix = {arXiv},
arxivId = {arXiv:1306.4965v1},
author = {Michieletto, Davide and Marenduzzo, Davide and Orlandini, Enzo and Alexander, Gareth P. and Turner, Matthew S.},
doi = {10.1021/mz500060c},
eprint = {arXiv:1306.4965v1},
file = {:Users/wenwen/Documents/MendeleyRefs/Michieletto et al.{\_}ACS Macro Letters{\_}2014.pdf:pdf},
isbn = {1086627555},
issn = {21611653},
journal = {ACS Macro Lett.},
pages = {255--259},
title = {{Threading dynamics of ring polymers in a gel}},
volume = {3},
year = {2014}
}
@article{Rosa2010,
abstract = {Fluorescence in-situ hybridization (FISH) and chromosome conformation capture (3C) are two powerful techniques for investigating the three-dimensional organization of the genome in interphase nuclei. The use of these techniques provides complementary information on average spatial distances (FISH) and contact probabilities (3C) for specific genomic sites. To infer the structure of the chromatin fiber or to distinguish functional interactions from random colocalization, it is useful to compare experimental data to predictions from statistical fiber models. The current estimates of the fiber stiffness derived from FISH and 3C differ by a factor of 5. They are based on the wormlike chain model and a heuristic modification of the Shimada-Yamakawa theory of looping for unkinkable, unconstrained, zero-diameter filaments. Here, we provide an extended theoretical and computational framework to explain the currently available experimental data for various species on the basis of a unique, minimal model of decondensing chromosomes: a kinkable, topologically constraint, semiflexible polymer with the (FISH) Kuhn length of l(K) = 300 nm, 10 kinks per Mbp, and a contact distance of 45 nm. In particular: 1), we reconsider looping of finite-diameter filaments on the basis of an analytical approximation (novel, to our knowledge) of the wormlike chain radial density and show that unphysically large contact radii would be required to explain the 3C data based on the FISH estimate of the fiber stiffness; 2), we demonstrate that the observed interaction frequencies at short genomic lengths can be explained by the presence of a low concentration of curvature defects (kinks); and 3), we show that the most recent experimental 3C data for human chromosomes are in quantitative agreement with interaction frequencies extracted from our simulations of topologically confined model chromosomes.},
author = {Rosa, Angelo and Becker, Nils B and Everaers, Ralf},
doi = {10.1016/j.bpj.2010.01.054},
file = {:Users/wenwen/Documents/MendeleyRefs/Rosa, Becker, Everaers{\_}Biophysical journal{\_}2010.pdf:pdf},
issn = {1542-0086},
journal = {Biophys. J.},
keywords = {Algorithms,Chromatin,Chromatin: chemistry,Chromosomes,Chromosomes: chemistry,DNA,DNA: chemistry,Elasticity,Humans,In Situ Hybridization, Fluorescence,Interphase,Interphase: genetics,Models, Genetic,Molecular Dynamics Simulation,Nucleic Acid Conformation,Probability,Yeasts,Yeasts: genetics},
month = {jun},
number = {11},
pages = {2410--9},
pmid = {20513384},
publisher = {Biophysical Society},
title = {{Looping probabilities in model interphase chromosomes.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2877331{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {98},
year = {2010}
}
@article{Achlioptas2009,
abstract = {Networks in which the formation of connections is governed by a random process often undergo a percolation transition, wherein around a critical point, the addition of a small number of connections causes a sizable fraction of the network to suddenly become linked together. Typically such transitions are continuous, so that the percentage of the network linked together tends to zero right above the transition point. Whether percolation transitions could be discontinuous has been an open question. Here, we show that incorporating a limited amount of choice in the classic Erd{\"{o}}s-R{\'{e}}nyi network formation model causes its percolation transition to become discontinuous.},
author = {Achlioptas, Dimitris and D'Souza, Raissa M and Spencer, Joel},
doi = {10.1126/science.1167782},
file = {:Users/wenwen/Documents/MendeleyRefs/Achlioptas, D'Souza, Spencer{\_}Science (New York, N.Y.){\_}2009.pdf:pdf},
issn = {0036-8075},
journal = {Science (80-. ).},
month = {mar},
number = {5920},
pages = {1453--1455},
pmid = {19286548},
title = {{Explosive Percolation in Random Networks}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19286548 http://www.sciencemag.org/cgi/doi/10.1126/science.1167782},
volume = {323},
year = {2009}
}
@article{Centres2010,
author = {Centres, P. M. and Bustingorry, S.},
doi = {10.1103/PhysRevE.81.061101},
file = {:Users/wenwen/Documents/MendeleyRefs/Centres, Bustingorry{\_}Physical Review E{\_}2010.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
number = {6},
pages = {061101},
title = {{Effective Edwards-Wilkinson equation for single-file diffusion}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.81.061101},
volume = {81},
year = {2010}
}
@article{Wenczel2002,
abstract = {We consider a polymer chain confined by a harmonic potential in theta solvents using the Zimm and Rouse model to elucidate the chain relaxation behavior in weak and strong fields, respectively. We investigate a case in which the center of the field is tuned to match the center of mass of the polymer at the instant when the field is switched on. The closed-form expressions are obtained for these models. When the field strength is weak enough so that the chain conformation is close to ideal Gaussian, the Zimm model predicts that the chain molecule would fluctuate within the confined space induced by the applied field. Moreover, the molecular rotation relaxes faster than the translational motion of the center of mass of the polymer molecule. However, under a strong field, the polymer molecule contracts continuously from a random coil to a collapsed conformation after the field is switched on. The Rouse model makes predictions that the center of mass of the confined polymer molecule would achieve its equilibrium state first. After the relaxation of the center of mass, the polymer molecule reaches the equilibrium chain conformation, followed by the molecular rotation. Furthermore, the Rouse model also predicts that in the presence of a strong field, the Rouse time is predominated by the field strength only. (C) 2002 American Institute of Physics.},
author = {Wenczel, Rob and Shew, Chwen-Yang},
doi = {10.1063/1.1468217},
file = {:Users/wenwen/Documents/MendeleyRefs/Wenczel, Shew{\_}The Journal of Chemical Physics{\_}2002.pdf:pdf},
isbn = {0021-9606},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {21},
pages = {9537},
title = {{Extension of the Zimm and Rouse model to a polymer chain confined by a harmonic potential in $\theta$-solvent conditions}},
url = {http://scitation.aip.org/content/aip/journal/jcp/116/21/10.1063/1.1468217},
volume = {116},
year = {2002}
}
@article{Qi2015a,
abstract = {Homologous recombination (HR) mediates the exchange of genetic information between sister or homologous chromatids. During HR, members of the RecA/Rad51 family of recombinases must somehow search through vast quantities of DNA sequence to align and pair single-strand DNA (ssDNA) with a homologous double-strand DNA (dsDNA) template. Here, we use single-molecule imaging to visualize Rad51 as it aligns and pairs homologous DNA sequences in real time. We show that Rad51 uses a length-based recognition mechanism while interrogating dsDNA, enabling robust kinetic selection of 8-nucleotide (nt) tracts of microhomology, which kinetically confines the search to sites with a high probability of being a homologous target. Successful pairing with a ninth nucleotide coincides with an additional reduction in binding free energy, and subsequent strand exchange occurs in precise 3-nt steps, reflecting the base triplet organization of the presynaptic complex. These findings provide crucial new insights into the physical and evolutionary underpinnings of DNA recombination.},
author = {Qi, Zhi and Redding, Sy and Lee, Ja Yil Yil and Gibb, Bryan and Kwon, YoungHo and Niu, Hengyao and Gaines, William A. A. and Sung, Patrick and Greene, Eric C. C.},
doi = {10.1016/j.cell.2015.01.029},
file = {:Users/wenwen/Documents/MendeleyRefs/Qi et al.{\_}Cell{\_}2015.pdf:pdf},
isbn = {1097-4172 (Electronic)$\backslash$r0092-8674 (Linking)},
issn = {10974172},
journal = {Cell},
number = {5},
pages = {856--869},
pmid = {25684365},
publisher = {Elsevier Inc.},
title = {{DNA sequence alignment by microhomology sampling during homologous recombination}},
url = {http://dx.doi.org/10.1016/j.cell.2015.01.029 http://linkinghub.elsevier.com/retrieve/pii/S0092867415000720},
volume = {160},
year = {2015}
}
@article{Minato1977,
abstract = {The characteristic function of the distribution function of the square radius of gyration S2 of an unperturbed ring chain represented by the Feynman path integral is exactly evaluated. The Fourier transform of the characteristic function is performed analytically and numerically in one-, two-, and three-dimensional spaces. Rigorous expressions of the distribution function valid for small and large S2 are given by the contour integrations.},
author = {Minato, Takao and Hatano, Akira},
file = {:Users/wenwen/Documents/MendeleyRefs/Minato, Hatano{\_}Journal of the Physical Society of Japan{\_}1977.{\%}3:{\%}3},
journal = {J. Phys. Soc. Japan},
number = {6},
pages = {1992--1996},
title = {{On the distribution function of the square radius of gyration of a ring chain}},
volume = {42},
year = {1977}
}
@article{McKee2004,
abstract = {Pairing of homologous chromosomes is an essential feature of meiosis, acting to promote high levels of recombination and to ensure segregation of homologs. However, homologous pairing also occurs in somatic cells, most regularly in Dipterans such as Drosophila, but also to a lesser extent in other organisms, and it is not known how mitotic and meiotic pairing relate to each other. In this article, I summarize results of recent molecular studies of pairing in both mitosis and meiosis, focusing especially on studies using fluorescent in situ hybridization (FISH) and GFP-tagging of single loci, which have allowed investigators to assay the pairing status of chromosomes directly. These approaches have permitted the demonstration that pairing occurs throughout the cell cycle in mitotic cells in Drosophila, and that the transition from mitotic to meiotic pairing in spermatogenesis is accompanied by a dramatic increase in pairing frequency. Similar approaches in mammals, plants and fungi have established that with few exceptions, chromosomes enter meiosis unpaired and that chromosome movements involving the telomeric, and sometimes centromeric, regions often precede the onset of meiotic pairing. The possible roles of proteins involved in homologous recombination, synapsis and sister chromatid cohesion in homolog pairing are discussed with an emphasis on those for which mutant phenotypes have permitted an assessment of effects on homolog pairing. Finally, I consider the question of the distribution and identity of chromosomal pairing sites, using recent data to evaluate possible relationships between pairing sites and other chromosomal sites, such as centromeres, telomeres, promoters and heterochromatin. I cite evidence that may point to a relationship between matrix attachment sites and homologous pairing sites. ?? 2004 Elsevier B.V. All rights reserved.},
author = {McKee, Bruce D.},
doi = {10.1016/j.bbaexp.2003.11.017},
file = {:Users/wenwen/Documents/MendeleyRefs/McKee{\_}Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression{\_}2004.pdf:pdf},
isbn = {0006-3002 (Print)},
issn = {01674781},
journal = {Biochim. Biophys. Acta - Gene Struct. Expr.},
keywords = {Chromosome pairing,Cohesion,Meiosis,Mitosis,Nuclear matrix,Recombination},
month = {mar},
number = {1-3},
pages = {165--180},
pmid = {15020057},
title = {{Homologous pairing and chromosome dynamics in meiosis and mitosis}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0167478103003075},
volume = {1677},
year = {2004}
}
@book{Jaynes1995,
author = {Jaynes, E. T.},
file = {:Users/wenwen/Documents/MendeleyRefs/Jaynes{\_}Unknown{\_}1995.pdf:pdf},
title = {{Probability theory: the logic of science}},
year = {1995}
}
@article{Bystricky2004,
abstract = {Little is known about how chromatin folds in its native state. Using optimized in situ hybridization and live imaging techniques have determined compaction ratios and fiber flexibility for interphase chromatin in budding yeast. Unlike previous studies, ours examines nonrepetitive chromatin at intervals short enough to be meaningful for yeast chromosomes and functional domains in higher eukaryotes. We reconcile high-resolution fluorescence in situ hybridization data from intervals of 14-100 kb along single chromatids with measurements of whole chromosome arms (122-623 kb in length), monitored in intact cells through the targeted binding of bacterial repressors fused to GFP derivatives. The results are interpreted with a flexible polymer model and suggest that interphase chromatin exists in a compact higher-order conformation with a persistence length of 170-220 nm and a mass density of approximately 110-150 bp/nm. These values are equivalent to 7-10 nucleosomes per 11-nm turn within a 30-nm-like fiber structure. Comparison of long and short chromatid arm measurements demonstrates that chromatin fiber extension is also influenced by nuclear geometry. The observation of this surprisingly compact chromatin structure for transcriptionally competent chromatin in living yeast cells suggests that the passage of RNA polymerase II requires a very transient unfolding of higher-order chromatin structure.},
author = {Bystricky, Kerstin and Heun, Patrick and Gehlen, Lutz and Langowski, J{\"{o}}rg and Gasser, Susan M},
doi = {10.1073/pnas.0402766101},
file = {:Users/wenwen/Documents/MendeleyRefs/Bystricky et al.{\_}Proceedings of the National Academy of Sciences{\_}2004.pdf:pdf},
isbn = {0027-8424 (Print)$\backslash$n0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
month = {nov},
number = {47},
pages = {16495--16500},
pmid = {15545610},
publisher = {National Academy of Sciences},
title = {{Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15545610 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC534505 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=534505{\&}tool=pmcentrez{\&}rendertype=abstract http://www.pnas.org/cgi/doi/10.1073/pnas.04},
volume = {101},
year = {2004}
}
@article{Flomenbom2008,
author = {Flomenbom, O. and Taloni, A.},
doi = {10.1209/0295-5075/83/20004},
file = {:Users/wenwen/Documents/MendeleyRefs/Flomenbom, Taloni{\_}EPL (Europhysics Letters){\_}2008.pdf:pdf},
issn = {0295-5075},
journal = {EPL (Europhysics Lett.},
month = {jul},
number = {2},
pages = {20004},
title = {{On single-file and less dense processes}},
url = {http://stacks.iop.org/0295-5075/83/i=2/a=20004?key=crossref.d11534f82fceedaa80f8b3b6d93f2677},
volume = {83},
year = {2008}
}
@article{Suarez2013,
author = {Su{\'{a}}rez, Gonzalo and Hoyuelos, Miguel and M{\'{a}}rtin, H{\'{e}}ctor O.},
doi = {10.1103/PhysRevE.88.022131},
file = {:Users/wenwen/Documents/MendeleyRefs/Su{\'{a}}rez, Hoyuelos, M{\'{a}}rtin{\_}Physical Review E{\_}2013.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
number = {2},
pages = {022131},
title = {{Evolution equation for tagged-particle density and correlations in single-file diffusion}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.88.022131},
volume = {88},
year = {2013}
}
@article{Araujo2011,
author = {Ara{\'{u}}jo, Nuno and Andrade, Jos{\'{e}} and Ziff, Robert and Herrmann, Hans},
doi = {10.1103/PhysRevLett.106.095703},
file = {:Users/wenwen/Documents/MendeleyRefs/Ara{\'{u}}jo et al.{\_}Physical Review Letters{\_}2011.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {mar},
number = {9},
pages = {4--7},
title = {{Tricritical Point in Explosive Percolation}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.106.095703},
volume = {106},
year = {2011}
}
@article{Gao2011,
author = {Gao, Jianxi and Buldyrev, Sergey V. and Stanley, H. Eugene and Havlin, Shlomo},
doi = {10.1038/nphys2180},
file = {:Users/wenwen/Documents/MendeleyRefs/Gao et al.{\_}Nature Physics{\_}2011.pdf:pdf},
issn = {1745-2473},
journal = {Nat. Phys.},
month = {dec},
number = {1},
pages = {40--48},
publisher = {Nature Publishing Group},
title = {{Networks formed from interdependent networks}},
url = {http://www.nature.com/doifinder/10.1038/nphys2180},
volume = {8},
year = {2011}
}
@article{Linetsky2005,
abstract = {Diffusion models in economics, finance, queueing, mathematical biology, and electrical engineering often involve reflecting barriers. In this paper, we study the analytical representation of transition densities for reflected one-dimensional diffusions in terms of their associated Sturm-Liouville spectral expansions. In particular, we provide explicit analytical expressions for transition densities of Brownian motion with drift, the Ornstein-Uhlenbeck process, and affine (square-root) diffusion with one or two reflecting barriers. The results are easily implementable on a personal computer and should prove useful in applications.},
author = {Linetsky, Vadim},
doi = {10.1239/aap/1118858633},
file = {:Users/wenwen/Documents/MendeleyRefs/Linetsky{\_}Advances in Applied Probability{\_}2005.pdf:pdf},
issn = {0001-8678},
journal = {Adv. Appl. Probab.},
keywords = {Currency target zone,Heavy traffic,Reflected Brownian motion,Reflected Ornstein-Uhlenbeck process,Reflected affine process,Reflected diffusion,Spectral expansion},
month = {jun},
number = {2},
pages = {435--460},
title = {{On the transition densities for reflected diffusions}},
url = {http://projecteuclid.org/Dienst/getRecord?id=euclid.aap/1118858633/},
volume = {37},
year = {2005}
}
@article{Rohden2012,
author = {Rohden, Martin and Sorge, Andreas and Timme, Marc and Witthaut, Dirk},
doi = {10.1103/PhysRevLett.109.064101},
file = {:Users/wenwen/Documents/MendeleyRefs/Rohden et al.{\_}Physical Review Letters{\_}2012.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {aug},
number = {6},
pages = {1--5},
title = {{Self-Organized Synchronization in Decentralized Power Grids}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.109.064101},
volume = {109},
year = {2012}
}
@article{Underhill2005,
abstract = {A method for generating coarse-grained models of polymers was evaluated. The resulting models consist of bead-spring chains with the spring force law taken from the force-extension behavior in the const. extension ensemble. This method, called the polymer ensemble transformation method, is applied to the freely jointed chain. The resulting model illustrates why current bead-spring chain models are insufficient in describing polymer behavior at high discretization. Applying the method to the freely jointed chain with unequal rod lengths showed the effect of varying flexibility in the chain. The method was also used to generate a bead-spring model of F-actin, which shows how the method is not restricted to one mol. model and can even be applied to exptl. data. The current limitations of the method are discussed, including the need for approx. bending potentials to model the worm-like chain with a bead-spring chain. Practical issues are discussed, such as using the bead-spring models in Brownian dynamics simulations and a simple spring force law was developed that can accurately represent a freely jointed chain with only a few rods per spring. Because of the functional form of this new force law, existing computer simulations can be easily modified. [on SciFinder(R)]},
author = {Underhill, Patrick T. and Doyle, Patrick S.},
doi = {10.1122/1.2008294},
file = {:Users/wenwen/Documents/MendeleyRefs/Underhill, Doyle{\_}Journal of Rheology{\_}2005.pdf:pdf},
isbn = {0148-6055},
issn = {01486055},
journal = {J. Rheol. (N. Y. N. Y).},
pages = {963},
title = {{Development of bead-spring polymer models using the constant extension ensemble}},
volume = {49},
year = {2005}
}
@article{Gooßen2015,
author = {Goo{\ss}en, Sebastian and Krutyeva, Margarita and Sharp, Melissa and Feoktystov, Artem and Allgaier, J{\"{u}}rgen and Pyckhout-Hintzen, Wim and Wischnewski, Andreas and Richter, Dieter},
doi = {10.1103/PhysRevLett.115.148302},
file = {:Users/wenwen/Documents/MendeleyRefs/Goo{\ss}en et al.{\_}Physical Review Letters{\_}2015.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
number = {14},
pages = {148302},
title = {{Sensing Polymer Chain Dynamics through Ring Topology: A Neutron Spin Echo Study}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.115.148302 http://physics.aps.org/articles/v8/93},
volume = {115},
year = {2015}
}
@article{Doi1976,
abstract = {The second quantization method is applied to classical many-particle systems. Statistical quantities such as free energy and time correlation functions are expressed in terms of creation and annihilation operators. The method is especially useful for the system in which the number of the composite molecules changes with time, e.g. the system including chemical reaction.},
author = {Doi, Masao},
doi = {10.1088/0305-4470/9/9/008},
file = {:Users/wenwen/Documents/MendeleyRefs/Doi{\_}Journal of Physics A Mathematical and General{\_}1976.pdf:pdf},
isbn = {0305-4470},
issn = {0305-4470},
journal = {J. Phys. A. Math. Gen.},
month = {sep},
number = {9},
pages = {1465--1477},
title = {{Second quantization representation for classical many-particle system}},
url = {http://stacks.iop.org/0305-4470/9/i=9/a=008?key=crossref.3636aa95c9b44032951fe37e8bc6282d},
volume = {9},
year = {1976}
}
@phdthesis{Spakowitz2004,
author = {Spakowitz, Andrew James},
file = {:Users/wenwen/Documents/MendeleyRefs/Spakowitz{\_}Unknown{\_}2004.pdf:pdf},
school = {California Institute of Technology},
title = {{Semiflexible Polymers : Fundamental Theory and Applications in DNA Packaging}},
year = {2004}
}
@article{Krapivsky2015a,
author = {Krapivsky, P. L. and Mallick, Kirone and Sadhu, Tridib},
doi = {10.1007/s10955-015-1291-0},
file = {:Users/wenwen/Documents/MendeleyRefs/Krapivsky, Mallick, Sadhu{\_}Journal of Statistical Physics{\_}2015.pdf:pdf},
issn = {0022-4715},
journal = {J. Stat. Phys.},
keywords = {Anomalous diffusion,Large deviations,Macroscopic fluctuation theory,Single-file diffusion,anomalous diffusion,macroscopic fluctuation theory,single-file diffusion},
number = {4},
pages = {885--925},
publisher = {Springer US},
title = {{Tagged Particle in Single-File Diffusion}},
url = {http://link.springer.com/10.1007/s10955-015-1291-0},
volume = {160},
year = {2015}
}
@article{Pincus1977,
author = {Pincus, P.},
doi = {10.1021/ma60055a042},
file = {:Users/wenwen/Documents/MendeleyRefs/Pincus{\_}Macromolecules{\_}1977.pdf:pdf},
issn = {0024-9297},
journal = {Macromolecules},
month = {jan},
number = {1},
pages = {210--213},
title = {{Dynamics of Stretched Polymer Chains}},
url = {http://pubs.acs.org/doi/abs/10.1021/ma60055a042},
volume = {10},
year = {1977}
}
@article{Carlson2002,
abstract = {Highly optimized tolerance (HOT) was recently introduced as a conceptual framework to study fundamental aspects of complexity. HOT is motivated primarily by systems from biology and engineering and emphasizes, (i) highly structured, nongeneric, self-dissimilar internal configurations, and (ii) robust yet fragile external behavior. HOT claims these are the most important features of complexity and not accidents of evolution or artifices of engineering design but are inevitably intertwined and mutually reinforcing. In the spirit of this collection, our paper contrasts HOT with alternative perspectives on complexity, drawing on real-world examples and also model systems, particularly those from self-organized criticality.},
author = {Carlson, J M and Doyle, John},
doi = {10.1073/pnas.012582499},
file = {:Users/wenwen/Documents/MendeleyRefs/Carlson, Doyle{\_}Proceedings of the National Academy of Sciences of the United States of America{\_}2002.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
month = {feb},
number = {Supplement 1},
pages = {2538--2545},
pmid = {11875207},
title = {{Complexity and robustness}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=128573{\&}tool=pmcentrez{\&}rendertype=abstract http://www.pnas.org/cgi/doi/10.1073/pnas.012582499},
volume = {99},
year = {2002}
}
@article{Lin2015a,
author = {Lin, Yen Ting},
file = {:Users/wenwen/Documents/MendeleyRefs/Lin{\_}Unknown{\_}2015.pdf:pdf},
number = {6},
title = {{Finite-dimeionsal Fermionic statistics and polymer conformation : behind the scene}},
year = {2015}
}
@book{Ryabov2016,
address = {Cham},
author = {Ryabov, Artem},
doi = {10.1007/978-3-319-27188-0},
file = {:Users/wenwen/Documents/MendeleyRefs/Ryabov{\_}Unknown{\_}2016.pdf:pdf},
isbn = {978-3-319-27187-3},
publisher = {Springer International Publishing},
series = {Springer Theses},
title = {{Stochastic Dynamics and Energetics of Biomolecular Systems}},
url = {http://link.springer.com/10.1007/978-3-319-27188-0},
year = {2016}
}
@article{Wang2012,
author = {Wang, Lei and Hu, Bambi and Li, Baowen},
doi = {10.1103/PhysRevE.86.040101},
file = {:Users/wenwen/Documents/MendeleyRefs/Wang, Hu, Li{\_}Physical Review E{\_}2012.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {oct},
number = {4},
pages = {1--5},
title = {{Logarithmic divergent thermal conductivity in two-dimensional nonlinear lattices}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.86.040101},
volume = {86},
year = {2012}
}
@article{Duan2010,
abstract = {Layered on top of information conveyed by DNA sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes. Interphase chromosomes are not positioned randomly within the nucleus, but instead adopt preferred conformations. Disparate DNA elements co-localize into functionally defined aggregates or 'factories' for transcription and DNA replication. In budding yeast, Drosophila and many other eukaryotes, chromosomes adopt a Rabl configuration, with arms extending from centromeres adjacent to the spindle pole body to telomeres that abut the nuclear envelope. Nonetheless, the topologies and spatial relationships of chromosomes remain poorly understood. Here we developed a method to globally capture intra- and inter-chromosomal interactions, and applied it to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae. The map recapitulates known features of genome organization, thereby validating the method, and identifies new features. Extensive regional and higher order folding of individual chromosomes is observed. Chromosome XII exhibits a striking conformation that implicates the nucleolus as a formidable barrier to interaction between DNA sequences at either end. Inter-chromosomal contacts are anchored by centromeres and include interactions among transfer RNA genes, among origins of early DNA replication and among sites where chromosomal breakpoints occur. Finally, we constructed a three-dimensional model of the yeast genome. Our findings provide a glimpse of the interface between the form and function of a eukaryotic genome.},
author = {Duan, Zhijun and Andronescu, Mirela and Schutz, Kevin and McIlwain, Sean and Kim, Yoo Jung and Lee, Choli and Shendure, Jay and Fields, Stanley and Blau, C Anthony and Noble, William S},
doi = {10.1038/nature08973},
file = {:Users/wenwen/Documents/MendeleyRefs/Duan et al.{\_}Nature{\_}2010.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Cell Nucleolus,Cell Nucleolus: genetics,Cell Nucleolus: metabolism,Cell Nucleus,Cell Nucleus: genetics,Cell Nucleus: metabolism,Centromere,Centromere: genetics,Centromere: metabolism,Chromosome Breakpoints,Chromosome Positioning,Chromosome Positioning: physiology,Chromosomes, Fungal,Chromosomes, Fungal: genetics,Chromosomes, Fungal: metabolism,DNA Replication,Genome, Fungal,Haploidy,Imaging, Three-Dimensional,Intranuclear Space,Intranuclear Space: metabolism,RNA, Transfer,RNA, Transfer: genetics,Replication Origin,Replication Origin: genetics,Saccharomyces cerevisiae,Saccharomyces cerevisiae: cytology,Saccharomyces cerevisiae: genetics},
month = {may},
number = {7296},
pages = {363--7},
pmid = {20436457},
publisher = {Nature Publishing Group},
title = {{A three-dimensional model of the yeast genome.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2874121{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {465},
year = {2010}
}
@article{Jimbo1989a,
abstract = {The Yang-Baxter equation first appeared in theoretical physics, in a paper by the Nobel laureate C. N. Yang, and in statistical mechanics, in R. J. Baxter's work. Later, it turned out that this equation plays a crucial role in: quantum groups, knot theory, braided categories, analysis of integrable systems, quantum mechanics, non-commutative descent theory, quantum computing, non-commutative geometry, etc. Many scientists have found solutions for the Yang-Baxter equation, obtaining qualitative results (using the axioms of various algebraic structures) or quantitative results (usually using computer calculations). However, the full classification of its solutions remains an open problem. In this paper, we present the (set-theoretical) Yang-Baxter equation, we sketch the proof of a new theorem, we state some problems, and discuss about directions for future research.},
author = {Jimbo, MICHIO},
doi = {10.1142/S0217751X89001503},
file = {:Users/wenwen/Documents/MendeleyRefs/Jimbo{\_}International Journal of Modern Physics A{\_}1989.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Jimbo{\_}International Journal of Modern Physics A{\_}1989(2).pdf:pdf},
issn = {0217-751X},
journal = {Int. J. Mod. Phys. A},
month = {sep},
number = {15},
pages = {3759--3777},
title = {{Introduction To the Yang-Baxter Equation}},
url = {http://www.worldscientific.com/doi/abs/10.1142/S0217751X89001503},
volume = {04},
year = {1989}
}
@article{Coppersmith2004,
author = {Coppersmith, Don and Gamarnik, David and Hajiaghayi, MohammadTaghi and Sorkin, Gregory B.},
doi = {10.1002/rsa.20015},
file = {:Users/wenwen/Documents/MendeleyRefs/Coppersmith et al.{\_}Random Structures and Algorithms{\_}2004.pdf:pdf},
issn = {1042-9832},
journal = {Random Struct. Algorithms},
month = {jul},
number = {4},
pages = {502--545},
title = {{Random MAX SAT, random MAX CUT, and their phase transitions}},
url = {http://doi.wiley.com/10.1002/rsa.20015},
volume = {24},
year = {2004}
}
@article{Pham2008,
abstract = {The effect of solvent on the collapse dynamics of homopolymers is investigated with Brownian dynamics simulations of a non-linear bead-spring chain model incorporating implicit hydrodynamic interactions. Our simulations suggest that the polymer collapse takes place via a three-stage mechanism, namely, formation of pearls, coarsening of pearls and the formation of a compact globule. The collapse pathways from a good solvent state to a poor solvent state are found to be independent of hydrodynamic interactions. On the other hand, hydrodynamic interaction is found to speed up the collapse rate. At a large quench depth (the depth of the Lennard-Jones potential), independent of the presence of hydrodynamic interaction, polymer molecules are found to be trapped in metastable states for long periods before acquiring their native globular state. The exponents characterizing the decay of various properties such as the radius of gyration are determined and compared with the values reported in the literature.},
author = {Pham, Tri Thanh and Bajaj, Mohit and Prakash, J. Ravi},
doi = {10.1039/b717350d},
file = {:Users/wenwen/Documents/MendeleyRefs/Pham, Bajaj, Prakash{\_}Soft Matter{\_}2008.pdf:pdf},
issn = {1744-683X},
journal = {Soft Matter},
pages = {1196},
title = {{Brownian dynamics simulation of polymer collapse in a poor solvent: influence of implicit hydrodynamic interactions}},
volume = {4},
year = {2008}
}
@article{Jose2008,
author = {Jose, Prasanth P and Szamel, Grzegorz},
doi = {10.1063/1.2937912},
file = {:Users/wenwen/Documents/MendeleyRefs/Jose, Szamel{\_}The Journal of Chemical Physics{\_}2008.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {22},
pages = {224910},
title = {{Single-chain dynamics in a semidilute polymer solution under steady shear}},
url = {http://scitation.aip.org/content/aip/journal/jcp/128/22/10.1063/1.2937912},
volume = {128},
year = {2008}
}
@article{Guan2006,
author = {Guan, Shuguang and Wang, Xingang and Lai, C.-H.},
doi = {10.1016/j.physleta.2006.01.067},
file = {:Users/wenwen/Documents/MendeleyRefs/Guan, Wang, Lai{\_}Physics Letters A{\_}2006.pdf:pdf},
issn = {03759601},
journal = {Phys. Lett. A},
keywords = {117508 singapore,117543 singapore,20 january 2006,5 sports drive 2,accepted 27 january 2006,b beijing,c department of physics,ek laboratories,hong kong,national university of singapore,nonlinear and complex systems,received 11 november 2005,received in revised form,singapore,singapore joint center of},
month = {jun},
number = {4},
pages = {298--304},
title = {{Frequency locking by external force from a dynamical system with strange nonchaotic attractor}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0375960106001563},
volume = {354},
year = {2006}
}
@article{Rodenbeck1998,
author = {R{\"{o}}denbeck, Christian and K{\"{a}}rger, J{\"{o}}rg and Hahn, Karsten},
doi = {10.1103/PhysRevE.57.4382},
file = {:Users/wenwen/Documents/MendeleyRefs/R{\"{o}}denbeck, K{\"{a}}rger, Hahn{\_}Physical Review E{\_}1998.pdf:pdf},
issn = {1063-651X},
journal = {Phys. Rev. E},
number = {4},
pages = {4382--4397},
title = {{Calculating exact propagators in single-file systems via the reflection principle}},
url = {http://pre.aps.org/abstract/PRE/v57/i4/p4382{\_}1{\%}5Cnhttp://link.aps.org/doi/10.1103/PhysRevE.57.4382},
volume = {57},
year = {1998}
}
@article{Hu2011,
archivePrefix = {arXiv},
arxivId = {arXiv:0907.0894},
author = {Hu, Yanqing and Ksherim, Baruch and Cohen, Reuven and Havlin, Shlomo},
doi = {10.1103/PhysRevE.84.066116},
eprint = {arXiv:0907.0894},
file = {:Users/wenwen/Documents/MendeleyRefs/Hu et al.{\_}Physical Review E{\_}2011.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {dec},
number = {6},
pages = {066116},
title = {{Percolation in interdependent and interconnected networks: Abrupt change from second- to first-order transitions}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.84.066116},
volume = {84},
year = {2011}
}
@article{Nepomechie2003a,
abstract = {There is an approach due to Bazhanov and Reshetikhin for solving integrable RSOS models which consists of solving the functional relations which result from the truncation of the fusion hierarchy. We demonstrate that this is also an effective means of solving integrable vertex models. Indeed, we use this method to recover the known Bethe Ansatz solutions of both the closed and open XXZ quantum spin chains with U(1) symmetry. Moreover, since this method does not rely on the existence of a pseudovacuum state, we also use this method to solve a special case of the open XXZ chain with nondiagonal boundary terms.},
archivePrefix = {arXiv},
arxivId = {hep-th/0211001},
author = {Nepomechie, Rafael I.},
doi = {10.1023/A:1023016602955},
eprint = {0211001},
file = {:Users/wenwen/Documents/MendeleyRefs/Nepomechie{\_}Journal of Statistical Physics{\_}2003.pdf:pdf},
issn = {00224715},
journal = {J. Stat. Phys.},
keywords = {Bethe Ansatz,Boundary sine-Gordon model,Functional relations,Fusion hierarchy,Integrable quantum spin chain,Yang-Baxter equation,boundary terms},
number = {5/6},
pages = {1363--1376},
primaryClass = {hep-th},
title = {{Functional Relations and Bethe Ansatz for the XXZ Chain}},
url = {http://link.springer.com/10.1023/A:1023016602955},
volume = {111},
year = {2003}
}
@article{Nagler2011,
archivePrefix = {arXiv},
arxivId = {arXiv:1103.0922v1},
author = {Nagler, Jan and Levina, Anna and Timme, Marc},
doi = {10.1038/nphys1860},
eprint = {arXiv:1103.0922v1},
file = {:Users/wenwen/Documents/MendeleyRefs/Nagler, Levina, Timme{\_}Nature Physics{\_}2011.pdf:pdf},
issn = {1745-2473},
journal = {Nat. Phys.},
month = {jan},
number = {3},
pages = {265--270},
publisher = {Nature Publishing Group},
title = {{Impact of single links in competitive percolation}},
url = {http://www.nature.com/doifinder/10.1038/nphys1860},
volume = {7},
year = {2011}
}
@article{Curro1987,
author = {Curro, John G. and Schweizer, Kenneth S.},
doi = {10.1063/1.453197},
file = {:Users/wenwen/Documents/MendeleyRefs/Curro, Schweizer{\_}The Journal of Chemical Physics{\_}1987.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {1987},
pages = {1842},
title = {{Equilibrium theory of polymer liquids: Linear chains}},
url = {http://scitation.aip.org/content/aip/journal/jcp/87/3/10.1063/1.453197},
volume = {87},
year = {1987}
}
@article{Cremer1975,
abstract = {A unique mean plane is defined for a general monocyclic puckered ring. The geometry of the puckering relative to this plane is described by amplitude and phase coordinates which are generalizations of those introduced for cyclopentane by Kilpatrick, Pitzer, and Spitzer. Unlike earlier treatments based on torsion angles, no mathematical approximations are involved. A short treatment of the four-, five-, and six-membered ring demonstrates the usefulness oexample is given of the analysis of crystallographic structural data in terms of these coordinates.},
author = {Cremer, D and Pople, J a},
doi = {10.1021/ja00839a011},
file = {:Users/wenwen/Documents/MendeleyRefs/Cremer, Pople{\_}Journal of the American Chemical Society{\_}1975.pdf:pdf},
isbn = {0002-7863},
issn = {0002-7863},
journal = {J. Am. Chem. Soc.},
number = {6},
pages = {1354--1358},
title = {{A General definition of ring puckering coordinates}},
url = {http://pubs.acs.org/doi/abs/10.1021/ja00839a011},
volume = {97},
year = {1975}
}
@article{LopezCascales1992a,
author = {{Lopez Cascales}, J. J. and Navarro, S. and {Garcia de la Torre}, J.},
doi = {10.1021/ma00039a042},
file = {:Users/wenwen/Documents/MendeleyRefs/Lopez Cascales, Navarro, Garcia de la Torre{\_}Macromolecules{\_}1992.pdf:pdf},
isbn = {0024929719},
issn = {0024-9297},
journal = {Macromolecules},
number = {13},
pages = {3574--3580},
title = {{Deformation, orientation, and scattering from polymer chains in shear flow. A Brownian dynamics simulation study}},
url = {http://dx.doi.org/10.1021/ma00039a042},
volume = {25},
year = {1992}
}
@article{Dimarzio1978,
author = {Dimarzio, Edmund A. and Bubin, Robert J.},
file = {:Users/wenwen/Documents/MendeleyRefs/Dimarzio, Bubin{\_}Journal of Polymer Science{\_}1978.pdf:pdf},
journal = {J. Polym. Sci.},
pages = {456--466},
title = {{Dynamics of a Polymer Attached to a Surface: Bead ans Spring Model}},
volume = {16},
year = {1978}
}
@phdthesis{Zhang2011,
author = {Zhang, Yu},
file = {:Users/wenwen/Documents/MendeleyRefs/Zhang{\_}Unknown{\_}2011.pdf:pdf},
pages = {1--179},
school = {University of Wisconsin-Madison},
title = {{Brownian Dynamics Simulation of DNA in Complex Geometries}},
year = {2011}
}
@article{Carl1995,
abstract = {The configurational and rheological properties of multiple-twisted ring polymers, modelled as long cyclic finitely extensible bead-spring chains with internal distance constraints, have been calculated. This model corresponds to chemically cross-linked Rouse chains. The calculations were carried out for equilibrium and steady shear flow. The mean-square radius of gyration in equilibrium depends on the number of loops. In shear flow, non-Newtonian flow behaviour arises. The shear viscosity and the first normal stress coefficient decrease with increasing shear rate. The second normal stress coefficient is negative and much smaller than the first normal stress coefficient. Since the mean-square radius of gyration, shear viscosity and the first and second normal stress coefficients depend on the number of loops, the latter can be determined by four independent experiments.},
author = {Carl, Wilfried},
file = {:Users/wenwen/Documents/MendeleyRefs/Carl{\_}J. Chem. Soc. Farday Trans.{\_}1995.pdf:pdf},
journal = {J. Chem. Soc. Farday Trans.},
keywords = {ring},
number = {16},
pages = {2525--2530},
title = {{Configurational and rheological properties of cyclic polymers}},
url = {citeulike-article-id:5805903{\%}5Cnhttp://dx.doi.org/10.1039/ft9959102525},
volume = {91},
year = {1995}
}
@article{Liu2008,
abstract = {An effective bead-spring model combining the advantages of large time steps of traditional bead-rod models and computational rigor of traditional bead-spring models is proposed to simulate the dynamic behaviors of flexible polymer chains with arbitrary longitudinal stiffness. The proposed model can be used to simulate many types of polymer chains or networks with different chain elasticity via a unified integration scheme with reasonably large time steps. ?? 2007 Elsevier Inc. All rights reserved.},
author = {Liu, Bin and Wang, Jizeng and Fan, Xiaojun and Kong, Yong and Gao, Huajian},
doi = {10.1016/j.jcp.2007.11.012},
file = {:Users/wenwen/Documents/MendeleyRefs/Liu et al.{\_}Journal of Computational Physics{\_}2008.pdf:pdf},
isbn = {9781932078800},
issn = {00219991},
journal = {J. Comput. Phys.},
keywords = {Bead-rod model,Bead-spring model,Brownian dynamic simulations,Flexible polymer,Freely jointed chain model,Polymer dynamics},
number = {5},
pages = {2794--2807},
title = {{An effective bead-spring model for polymer simulation}},
volume = {227},
year = {2008}
}
@article{Arnaudon2004,
abstract = {We present an "algebraic treatment" of the analytical Bethe Ansatz. For this purpose, we introduce abstract monodromy and transfer matrices which provide an algebraic framework for the analytical Bethe Ansatz. It allows us to deal with a generic gl(n)-spin chain possessing on each site an arbitrary gl(n)-representation. For open spin chains, we use the classification of the reflection matrices to treat all the diagonal boundary cases. As a result, we obtain the Bethe equations in their full generality for closed and open spin chains. The classifications of finite dimensional irreducible representations for the Yangian (closed spin chains) and for the reflection algebras (open spin chains) are directly linked to the calculation of the transfer matrix eigenvalues. As examples, we recover the usual closed and open spin chains, we treat the alternating spin chains and the closed spin chain with impurity.},
archivePrefix = {arXiv},
arxivId = {math-ph/math-ph/0411021},
author = {Arnaudon, Daniel and Crampe, Nicolas and Doikou, Anastasia and Frappat, Luc and Ragoucy, Eric},
doi = {10.1088/1742-5468/2005/02/P02007},
eprint = {math-ph/0411021},
file = {:Users/wenwen/Documents/MendeleyRefs/Arnaudon et al.{\_}Journal of Statistical Mechanics Theory and Experiment{\_}2004.pdf:pdf},
issn = {17425468},
journal = {J. Stat. Mech. Theory Exp.},
keywords = {algebraic structures of integrable,bethe ansatz,integrable spin chains,models,quantum integrability,symmetries of integrable,vertex models},
number = {2},
pages = {7},
primaryClass = {math-ph},
title = {{Analytical Bethe Ansatz for closed and open gl(n)-spin chains in any representation}},
url = {http://arxiv.org/abs/math-ph/0411021},
volume = {0502},
year = {2004}
}
@article{DeGennes1974,
abstract = {Because the hydrodynamic interactions are reduced by stretching, a solutepolymer coil should unwind abruptly when a certain critical value of the velocity gradient is reached. Depending on the details of the velocity field (``longitudinal{\&}apos;{\&}apos;, or ``transverse{\&}apos;{\&}apos;, or more complex gradients) this coil ↔ stretch transition may be continuous (``second order{\&}apos;{\&}apos;) or discontinuous (``first order{\&}apos;{\&}apos;). In the latter case hysteresis should often be observed; a qualitative discussion of the associated relaxation times is given. Simple shear flow is an exceptional case, with no sharp transition. Some expected effects of the C↔S transition on the mechanical behavior, on optical properties, and on chemical degradation in flow are briefly analyzed.},
author = {{De Gennes}, P. G.},
doi = {10.1063/1.1681018},
file = {:Users/wenwen/Documents/MendeleyRefs/De Gennes{\_}The Journal of Chemical Physics{\_}1974.pdf:pdf},
isbn = {doi:10.1063/1.1681018},
issn = {00219606},
journal = {J. Chem. Phys.},
number = {12},
pages = {5030--5042},
title = {{Coil-stretch transition of dilute flexible polymers under ultrahigh velocity gradients}},
url = {http://scitation.aip.org/content/aip/journal/jcp/60/12/10.1063/1.1681018},
volume = {60},
year = {1974}
}
@book{John1996,
author = {Lakos, John},
file = {:Users/wenwen/Documents/MendeleyRefs/Lakos{\_}Unknown{\_}1996.pdf:pdf},
publisher = {Addison Wesley Longman},
title = {{Large-Scale C++ Software Design.pdf}},
year = {1996}
}
@article{Jun2010a,
abstract = {We present a new physical biology approach to understanding the relationship between the organization and segregation of bacterial chromosomes. We posit that replicated Escherichia coli daughter strands will spontaneously demix as a result of entropic forces, despite their strong confinement within the cell; in other words, we propose that entropy can act as a primordial physical force which drives chromosome segregation under the right physical conditions. Furthermore, proteins implicated in the regulation of chromosome structure and segregation may in fact function primarily in supporting such an entropy-driven segregation mechanism by regulating the physical state of chromosomes. We conclude that bacterial chromosome segregation is best understood in terms of spontaneous demixing of daughter strands. Our concept may also have important implications for chromosome segregation in eukaryotes, in which spindle-dependent chromosome movement follows an extended period of sister chromatid demixing and compaction.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Jun, Suckjoon and Wright, Andrew},
doi = {10.1038/nrmicro2391},
eprint = {NIHMS150003},
file = {:Users/wenwen/Documents/MendeleyRefs/Jun, Wright{\_}Nature Reviews Microbiology{\_}2010.pdf:pdf},
isbn = {1740-1526$\backslash$r1740-1534},
issn = {1740-1526},
journal = {Nat. Rev. Microbiol.},
number = {8},
pages = {600--607},
pmid = {20634810},
publisher = {Nature Publishing Group},
title = {{Entropy as the driver of chromosome segregation}},
url = {http://www.nature.com/nrmicro/journal/v8/n8/full/nrmicro2391.html{\%}5Cnhttp://www.nature.com/nrmicro/journal/v8/n8/pdf/nrmicro2391.pdf},
volume = {8},
year = {2010}
}
@article{Swift1991a,
author = {Gwa, Leh-Hun and Spohn, Herbert},
file = {:Users/wenwen/Documents/MendeleyRefs/Gwa, Spohn{\_}Physical Review A{\_}1992.pdf:pdf},
journal = {Phys. Rev. A},
number = {2},
pages = {884},
title = {{Bethe solution for the dynamical-scaling exponent of the noisy Burgers equation}},
volume = {46},
year = {1992}
}
@article{Yamamoto2001,
abstract = {During meiotic prophase in fission yeast, the nucleus migrates back and forth between the two ends of the cell, led by the spindle pole body (SPB). This nuclear oscillation is dependent on astral microtubules radiating from the SPB and a microtubule motor, cytoplasmic dynein. Here we have examined the dynamic behavior of astral microtubules labeled with the green fluorescent protein during meiotic prophase with the use of optical sectioning microscopy. During nuclear migrations, the SPB mostly follows the microtubules that extend toward the cell cortex. SPB migrations start when these microtubules interact with the cortex and stop when they disappear, suggesting that these microtubules drive nuclear migrations. The microtubules that are followed by the SPB often slide along the cortex and are shortened by disassembly at their ends proximal to the cortex. In dynein-mutant cells, where nuclear oscillations are absent, the SPB never migrates by following microtubules, and microtubule assembly/disassembly dynamics is significantly altered. Based on these observations, together with the frequent accumulation of dynein at a cortical site where the directing microtubules interact, we propose a model in which dynein drives nuclear oscillation by mediating cortical microtubule interactions and regulating the dynamics of microtubule disassembly at the cortex.},
author = {Yamamoto, A and Tsutsumi, C and Kojima, H and Oiwa, K and Hiraoka, Y},
doi = {10.1091/mbc.12.12.3933},
file = {:Users/wenwen/Documents/MendeleyRefs/Yamamoto et al.{\_}Molecular Biology of the Cell{\_}2001.pdf:pdf},
issn = {1059-1524},
journal = {Mol. Biol. Cell},
month = {dec},
number = {12},
pages = {3933--3946},
pmid = {11739791},
publisher = {American Society for Cell Biology},
title = {{Dynamic Behavior of Microtubules during Dynein-dependent Nuclear Migrations of Meiotic Prophase in Fission Yeast}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11739791 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC60766 http://www.molbiolcell.org/cgi/doi/10.1091/mbc.12.12.3933},
volume = {12},
year = {2001}
}
@article{Ziff2009,
author = {Ziff, Robert M.},
doi = {10.1103/PhysRevLett.103.045701},
file = {:Users/wenwen/Documents/MendeleyRefs/Ziff{\_}Physical Review Letters{\_}2009.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {jul},
number = {4},
pages = {1--4},
title = {{Explosive Growth in Biased Dynamic Percolation on Two-Dimensional Regular Lattice Networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.103.045701},
volume = {103},
year = {2009}
}
@book{Vetterling2007a,
abstract = {From Preface: “I was just going to say, when I was interrupted:::” begins Oliver Wendell Holmes in the second series of his famous essays, The Autocrat of the Breakfast Table. The interruption referred towas a gap of 25 years. In our case, as the autocrats of Numerical Recipes, the gap between our second and third editions has been “only” 15 years. Scientific computing has changed enormously in that time. The first edition of Numerical Recipes was roughly coincident with the first commercial success of the personal computer. The second edition came at about the time that the Internet, as we know it today, was created. Now, as we launch the third edition, the practice of science and engineering, and thus scientific computing, has been profoundly altered by the mature Internet and Web. It is no longer difficult to find somebody's algorithm, and usually free code, for almost any conceivable scien- tific application. The critical questions have instead become, “How does it work?” and “Is it any good?” Correspondingly, the second edition of Numerical Recipes has come to be valued more and more for its text explanations, concise mathematical derivations, critical judgments, and advice, and less for its code implementations per se. Recognizing the change, we have expanded and improved the text in many places in this edition and addedmany completely newsections. We seriously consid- ered leaving the code out entirely, or making it available only on theWeb. However, in the end, we decided that without code, it wouldn't be Numerical Recipes.That is, without code you, the reader, could never know whether our advice was in fact hon- est, implementable, and practical. Many discussions of algorithms in the literature and on the Web omit crucial details that can only be uncovered by actually coding (our job) or reading compilable code (your job). Also, we needed actual code to teach and illustrate the large number of lessons about object-oriented programming that are implicit and explicit in this edition.},
author = {Vetterling, William T. and Teukolsky, Saul a. and Press, William H. and Flannery, Brian P. and Teukolsky, Saul a. and Vetterling, William T. and Flannery, Brian P.},
file = {:Users/wenwen/Documents/MendeleyRefs/Vetterling et al.{\_}Unknown{\_}2007.pdf:pdf},
isbn = {9780521880688},
issn = {0036-1445},
keywords = {n/a},
pages = {1256},
title = {{Numerical recipes}},
year = {2007}
}
@article{Davis2001,
abstract = {In most organisms homologous recombination is vital for the proper segregation of chromosomes during meiosis, the formation of haploid sex cells from diploid precursors. This review compares meiotic recombination and chromosome segregation in the fission yeast Schizosaccharomyces pombe and the distantly related budding yeast Saccharomyces cerevisiae, two especially tractable microorganisms. Certain features, such as the occurrence of DNA breaks associated with recombination, appear similar, suggesting that these features may be common in eukaryotes. Other features, such as the role of these breaks and the ability of chromosomes to segregate faithfully in the absence of recombination, appear different, suggesting multiple solutions to the problems faced in meiosis.},
author = {Davis, L and Smith, G R},
doi = {10.1073/pnas.121005598},
file = {:Users/wenwen/Documents/MendeleyRefs/Davis, Smith{\_}Proceedings of the National Academy of Sciences{\_}2001.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
month = {jul},
number = {15},
pages = {8395--8402},
pmid = {11459981},
publisher = {National Academy of Sciences},
title = {{Meiotic recombination and chromosome segregation in Schizosaccharomyces pombe}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11459981 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC37449 http://www.pnas.org/cgi/doi/10.1073/pnas.121005598},
volume = {98},
year = {2001}
}
@article{Wu2009,
abstract = {In this paper, the problem of generalized outer synchronization between two completely different complex dynamical networks is investigated. With a nonlinear control scheme, a sufficient criterion for this generalized outer synchronization is derived based on Barbalat's lemma. Two corollaries are also obtained, which contains the situations studied in two lately published papers as special cases. Numerical simulations further demonstrate the feasibility and effectiveness of the theoretical results.},
author = {Wu, Xiaoqun and Zheng, Wei Xing and Zhou, Jin},
doi = {10.1063/1.3072787},
file = {:Users/wenwen/Documents/MendeleyRefs/Wu, Zheng, Zhou{\_}Chaos (Woodbury, N.Y.){\_}2009.pdf:pdf},
issn = {10541500},
journal = {Chaos An Interdiscip. J. Nonlinear Sci.},
keywords = {Algorithms,Animals,Biological Evolution,Computer Simulation,Food Chain,Humans,Models,Neural Networks (Computer),Nonlinear Dynamics,Predatory Behavior,Reproducibility of Results,Statistical,Systems Theory,Theoretical,Time Factors},
month = {mar},
number = {1},
pages = {013109},
pmid = {19334973},
title = {{Generalized outer synchronization between complex dynamical networks}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19334973 http://scitation.aip.org/content/aip/journal/chaos/19/1/10.1063/1.3072787},
volume = {19},
year = {2009}
}
@article{Chen2011,
author = {Chen, Wei and D'Souza, Raissa},
doi = {10.1103/PhysRevLett.106.115701},
file = {:Users/wenwen/Documents/MendeleyRefs/Chen, D'Souza{\_}Physical Review Letters{\_}2011.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {mar},
number = {11},
pages = {1--4},
title = {{Explosive Percolation with Multiple Giant Components}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.106.115701},
volume = {106},
year = {2011}
}
@book{DeGennes1979,
author = {de Gennes, Pierre-Gilles},
file = {:Users/wenwen/Documents/MendeleyRefs/de Gennes{\_}Unknown{\_}1979.pdf:pdf},
publisher = {Cornell University Press},
title = {{Scaling Concepts in Polymer Physics}},
year = {1979}
}
@article{Liu2007,
author = {Liu, Zonghua and Li, Baowen},
doi = {10.1103/PhysRevE.76.051118},
file = {:Users/wenwen/Documents/MendeleyRefs/Liu, Li{\_}Physical Review E{\_}2007.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {nov},
number = {5},
pages = {1--6},
title = {{Heat conduction in simple networks: The effect of interchain coupling}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.76.051118},
volume = {76},
year = {2007}
}
@article{Chikashige1994,
abstract = {The movement of chromosomes that precedes meiosis was observed in living cells of fission yeast by fluorescence microscopy. Further analysis by in situ hybridization revealed that the telomeres remain clustered at the leading end of premeiotic chromosome movement, unlike mitotic chromosome movement in which the centromere leads. Once meiotic chromosome segregation starts, however, centromeres resume the leading position in chromosome movement, as they do in mitosis. Although the movement of the telomere first has not been observed before, the clustering of telomeres is reminiscent of the bouquet structure of meiotic-prophase chromosomes observed in higher eukaryotes, which suggests that telomeres perform specific functions required for premeiotic chromosomal events generally in eukaryotes.},
author = {Chikashige, Y and Ding, D. and Funabiki, H and Haraguchi, T and Mashiko, S and Yanagida, M and Hiraoka, Y},
doi = {10.1126/science.8146661},
isbn = {0036-8075 (Print)$\backslash$r0036-8075 (Linking)},
issn = {0036-8075},
journal = {Science (80-. ).},
month = {apr},
number = {5156},
pages = {270--273},
pmid = {8146661},
title = {{Telomere-led premeiotic chromosome movement in fission yeast}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.8146661},
volume = {264},
year = {1994}
}
@book{Feynman2011b,
author = {Feynman, Richard P and Leighton, Robert B and Sands, Matthew},
file = {:Users/wenwen/Documents/MendeleyRefs/Feynman, Leighton, Sands{\_}Unknown{\_}2010.pdf:pdf},
publisher = {California Institute of Technology},
title = {{The Feynman Lectures on Physics, Vol. I}},
year = {2010}
}
@article{Huang2012,
abstract = {The end-over-end tumbling dynamics of individual polymers in dilute and semidilute solutions is studied under shear flow by large-scale mesoscale hydrodynamic simulations. End-to-end vector relaxation times are determined along the flow, gradient, and vorticity directions. Along the flow and gradient directions, the correlation functions decay exponentially with sinusoidal modulations at short times. In dilute solution, the decay times of the various directions are very similar. However, in semidilute solutions, the relaxation behaviors are rather different along the various directions, with the longest relaxation time in the vorticity direction and the shortest time in the flow direction. The various relaxation times exhibit a power-law shear-rate dependence with the exponent  - 2/3 at high shear rates. Quantitatively, the relaxation times are equal to the tumbling times extracted from cross-correlation functions of fluctuations of radius-of-gyration components along the flow and gradient direction.},
author = {Huang, Chien-Cheng and Gompper, Gerhard and Winkler, Roland G},
doi = {10.1088/0953-8984/24/28/284131},
file = {:Users/wenwen/Documents/MendeleyRefs/Huang, Gompper, Winkler{\_}Journal of physics. Condensed matter an Institute of Physics journal{\_}2012.pdf:pdf},
issn = {1361-648X},
journal = {J. Phys. Condens. Matter},
keywords = {Hydrodynamics,Models, Molecular,Molecular Conformation,Pol

repository: huangww/chromosome

repo_name: huangww/chromosome