text:
00},
journal = {Chaos An Interdiscip. J. Nonlinear Sci.},
keywords = {Action Potentials,Action Potentials: physiology,Algorithms,Animals,Biological Clocks,Biological Clocks: physiology,Computer Simulation,Humans,Models,Nerve Net,Nerve Net: physiology,Neurological,Neurons,Neurons: physiology,Nonlinear Dynamics,Statistical,Synaptic Transmission,Synaptic Transmission: physiology,Time Factors},
month = {mar},
number = {1},
pages = {015105},
pmid = {16599771},
title = {{Synchronization in complex networks with a modular structure}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16599771 http://scitation.aip.org/content/aip/journal/chaos/16/1/10.1063/1.2154881},
volume = {16},
year = {2006}
}
@article{Brochard-Wyart1994a,
abstract = {PACS. 36.20 -Macromolecules and polymer molecules. PACS. 46.90 -Other topics in mechanics, elasticity, and rheology. PACS. 87.10 -General, theoretical, and mathematical biophysics (inc. logic of biosystems, quantum biology and relevant aspects of thermodynamics, information theory, cybernetics, and bionics). Abstract. -With optical tweezers plus fluorescent labels it is now possible to force, and to observe, the stretching and the relaxation of a single polymer chain. We calculate here the unwinding of a tethered, flexible, chain (N monomers) immersed in a solvent if, at time t = 0 start-ing from rest, one imposes either a flow (V) of the solvent, or an external force f on the free end.},
author = {Brochard-Wyart, F and Hervet, H and Pincus, P},
doi = {10.1209/0295-5075/26/7/006},
file = {:Users/wenwen/Documents/MendeleyRefs/Brochard-Wyart, Hervet, Pincus{\_}Europhysics Letters (EPL){\_}1994.pdf:pdf},
isbn = {0295-5075},
issn = {0295-5075},
journal = {Europhys. Lett.},
month = {jun},
number = {7},
pages = {511--516},
title = {{Unwinding of Polymer Chains under Forces or Flows}},
url = {http://iopscience.iop.org/0295-5075/26/7/006},
volume = {26},
year = {1994}
}
@article{Toan2007,
abstract = {We investigate the kinetics of loop formation in flexible ideal polymer chains (Rouse model), and polymers in good and poor solvents. We show for the Rouse model, using a modification of the theory of Szabo, Schulten, and Schulten, that the time scale for cyclization is taucsim tau0 N 2 (where tau0 is a microscopic time scale and N is the number of monomers), provided the coupling between the relaxation dynamics of the end-to-end vector and the looping dynamics is taken into account. The resulting analytic expression fits the simulation results accurately when a, the capture radius for contact formation, exceeds b, the average distance between two connected beads. Simulations also show that, when a {\textless} b, taucsim N alphatau, where {\$}1.5{\textless}alphataule 2 in the range {\$}7{\textless}N{\textless}200 used in the simulations. By using a diffusion coefficient that is dependent on the length scales a and b (with a{\textless}b), which captures the two-stage mechanism by which looping occurs when a {\textless} b, we obtain an analytic expression for tauc that fits the simulation results well. The kinetics of contact formation between the ends of the chain are profoundly affected when interactions between monomers are taken into account. Remarkably, for N {\textless} 100 the values of tauc decrease by more than two orders of magnitude when the solvent quality changes from good to poor. Fits of the simulation data for tauc to a power law in N (taucsim N alphatau) show that alphatau varies from about 2.4 in a good solvent to about 1.0 in poor solvents. Loop formation in poor solvents, in which the polymer adopts dense, compact globular conformations, occurs by a reptation-like mechanism of the ends of the chain.},
author = {Toan, Ngo Minh and Morrison, Greg and Hyeon, Changbong and Thirumalai, D.},
doi = {10.1021/jp076510y},
file = {:Users/wenwen/Documents/MendeleyRefs/Toan et al.{\_}The Journal of Physical Chemistry B{\_}2008.pdf:pdf},
isbn = {1520-6106},
issn = {1520-6106},
journal = {J. Phys. Chem. B},
keywords = {computer simulation,cyclization,diffusion,kinetics,polymers,polymers chemistry,solvents,time factors},
month = {may},
number = {19},
pages = {6094--6106},
pmid = {18269274},
title = {{Kinetics of Loop Formation in Polymer Chains}},
url = {http://arxiv.org/abs/0708.2077 http://pubs.acs.org/doi/abs/10.1021/jp076510y},
volume = {112},
year = {2008}
}
@article{Sing2011,
abstract = {In the present article, we use simulation and theory to understand the case of flexible and semiflexible tethered polymers in the limit of high shear flows and consequently near-full extension of the chains. We adopt a random-walk picture along the axis of the polymer, which in combination with a statistical mechanical description of perturbations along the chain contour allows us to fully characterize the geometry of the polymer chain without any fit parameters. Incorporation of hydrodynamic interactions is also investigated, with the hydrodynamic lift force inducing changes in the chain equilibrium structure near the tether point that could have implications for adsorption and desorption kinetics.},
author = {Sing, Charles E. and Alexander-Katz, Alfredo},
doi = {10.1021/ma201808c},
file = {:Users/wenwen/Documents/MendeleyRefs/Sing, Alexander-Katz{\_}Macromolecules{\_}2011.pdf:pdf},
isbn = {0024-9297},
issn = {00249297},
journal = {Macromolecules},
number = {22},
pages = {9020--9028},
title = {{Theory of tethered polymers in shear flow: The strong stretching limit}},
volume = {44},
year = {2011}
}
@article{Krapivsky2015,
abstract = {We study the statistics of a tagged particle in single-file diffusion, a one-dimensional interacting infinite-particle system in which the order of particles never changes. We compute the two-time correlation function for the displacement of the tagged particle for an arbitrary single-file system. We also discuss single-file analogs of the arcsine law and the law of the iterated logarithm characterizing the behavior of Brownian motion. Using a macroscopic fluctuation theory we devise a formalism giving the cumulant generating functional. In principle, this functional contains the full statistics of the tagged particle trajectory---the full single-time statistics, all multiple-time correlation functions, etc. are merely special cases.},
archivePrefix = {arXiv},
arxivId = {1505.01287},
author = {Krapivsky, P. L. and Mallick, Kirone and Sadhu, Tridib},
doi = {10.1088/1742-5468/2015/09/P09007},
eprint = {1505.01287},
file = {:Users/wenwen/Documents/MendeleyRefs/Krapivsky, Mallick, Sadhu{\_}Unknown{\_}2015.pdf:pdf},
issn = {1742-5468},
journal = {J. Stat. Mech. Theory Exp.},
keywords = {a special issue of,arcsine law,ecole,j stat,law of,macroscopic fluctuation theory,mech,philippe meyer institute for,physics department,present address,single-file diffusion,submitted to,tagged particle,the iterated logarithm,theoretical physics},
month = {sep},
number = {9},
pages = {P09007},
title = {{Dynamical properties of single-file diffusion}},
url = {http://arxiv.org/abs/1505.01287 http://stacks.iop.org/1742-5468/2015/i=9/a=P09007?key=crossref.eb4f21a01722e2023393d091ce1a6174},
volume = {2015},
year = {2015}
}
@article{Schutz1997,
author = {Sch{\"{u}}tz, Gunter M.},
doi = {10.1007/BF02183623},
file = {:Users/wenwen/Documents/MendeleyRefs/Sch{\"{u}}tz{\_}Journal of Statistical Physics{\_}1997(2).pdf:pdf},
issn = {0022-4715},
journal = {J. Stat. Phys.},
month = {mar},
number = {5-6},
pages = {1265--1287},
title = {{Duality relations for asymmetric exclusion processes}},
url = {http://link.springer.com/10.1007/BF02183623},
volume = {86},
year = {1997}
}
@article{Saxena2012,
author = {Saxena, Garima and Prasad, Awadhesh and Ramaswamy, Ram},
doi = {10.1016/j.physrep.2012.09.003},
file = {:Users/wenwen/Documents/MendeleyRefs/Saxena, Prasad, Ramaswamy{\_}Physics Reports{\_}2012.pdf:pdf},
issn = {03701573},
journal = {Phys. Rep.},
month = {sep},
publisher = {Elsevier B.V.},
title = {{Amplitude death: The emergence of stationarity in coupled nonlinear systems}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0370157312002645},
year = {2012}
}
@article{Newman2001,
author = {Newman, M. E. J. and Strogatz, S. H. and Watts, D. J.},
doi = {10.1103/PhysRevE.64.026118},
file = {:Users/wenwen/Documents/MendeleyRefs/Newman, Strogatz, Watts{\_}Physical Review E{\_}2001.pdf:pdf},
issn = {1063-651X},
journal = {Phys. Rev. E},
month = {jul},
number = {2},
pages = {026118},
title = {{Random graphs with arbitrary degree distributions and their applications}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.64.026118},
volume = {64},
year = {2001}
}
@article{Sheng1997a,
abstract = {The static and nonequilibrium dynamic properties of a single linear polymer chain under a traction force f is studied by Monte Carlo simulations using a continuous model and by scaling calculations. Chain lengths from N=10 to 100 are considered. For the static results, our simulation data show that the averaged end-to-end distance {\textless}Rf{\textgreater}{\~{}}N2 nu f at weak tension forces and for strong forces {\textless}Rf{\textgreater}{\~{}}Nf1/ nu -1, which are consistent with previous studies. The nonequilibrium relaxation behavior is studied for an initially stretched polymer chain, when the stretching force is removed. Detail chain configurations during the relaxation process are analyzed from the simulation data. Different relaxation dynamics are found for three regions: the linear, Pincus, and model-dependent regimes. The nonequilibrium relaxation time tau is derived in the linear ( tau {\~{}}N1+2 nu ), Pincus ( tau {\~{}}N2f1/ nu -2), and model-dependent regimes. These results are compared with our Monte Carlo data and recent experiments, and are discussed in the light of scaling theories.},
author = {Sheng, Yu-Jane and Lai, Pik-Yin and Tsao, Heng-Kwong},
doi = {10.1103/PhysRevE.56.1900},
file = {:Users/wenwen/Documents/MendeleyRefs/Sheng, Lai, Tsao{\_}Physical Review E{\_}1997.pdf:pdf},
issn = {1063-651X},
journal = {Phys. Rev. E},
number = {2},
pages = {1900--1909},
title = {{Nonequilibrium relaxation of a stretched polymer chain}},
volume = {56},
year = {1997}
}
@article{Daniels2005,
abstract = {Global synchronization of oscillators is found abundantly in nature, emerging in fields from physics to biology. The Kuramoto model describes the synchronization behavior of a generalized systemof interacting oscillators. With a large number of oscillators with different natural frequencies, the Kuramoto model predicts that, if they are allowed to interact strongly enough, they will all start oscillating at the same rate. The model provides a mathematical basis for studying the conditions under which synchronization can occur. For example, it is possible to solve for the critical amount of coupling needed among the oscillators to have synchronization. My research involved studying the basics of Kuramotos analysis and then investigating how the synchronization behavior is affected by random noise. Numerical simulations were run with and without noise to supplement and verify the analytical results.},
author = {Daniels, Bryan C},
file = {:Users/wenwen/Documents/MendeleyRefs/Daniels{\_}Analysis{\_}2005.pdf:pdf},
journal = {Analysis},
pages = {1--54},
title = {{Synchronization of Globally Coupled Nonlinear Oscillators : the Rich Behavior of the Kuramoto Model}},
url = {http://www.stanford.edu/group/brainsinsilicon/documents/kuramoto{\_}paper{\_}lab6.pdf},
year = {2005}
}
@article{Huang,
author = {Huang, Kerson},
file = {:Users/wenwen/Documents/MendeleyRefs/Huang{\_}Unknown{\_}2001.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Huang{\_}Unknown{\_}2001.pdf:pdf},
publisher = {Taylor{\&}Francis},
title = {{Introduction to Statistical Physics}},
year = {2001}
}
@article{Fiasconaro2010,
author = {Fiasconaro, Alessandro and Mazo, Juan Jos{\'{e}} and Falo, Fernando},
doi = {10.1103/PhysRevE.82.031803},
file = {:Users/wenwen/Documents/MendeleyRefs/Fiasconaro, Mazo, Falo{\_}Physical Review E{\_}2010.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {sep},
number = {3},
pages = {031803},
title = {{Translocation time of periodically forced polymer chains}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.82.031803},
volume = {82},
year = {2010}
}
@article{Ragoucy2009,
abstract = {We present in a unified and detailed way the nested Bethe ansatz for open spin chains based on$\backslash$n{\#}{\#}IMG{\#}{\#} [http://ej.iop.org/images/1751-8121/42/20/205203/jpa308910ieqn1.gif] {\{}{\{}$\backslash$cal Y{\}}(gl({\{}$\backslash$mathfrak$\backslash$nn{\}})), {\{}$\backslash$cal Y{\}}(gl({\{}$\backslash$mathfrak m{\}}|{\{}$\backslash$mathfrak n{\}})), $\backslash$wh{\{}$\backslash$cal U{\}}{\_}{\{}q{\}}(gl({\{}$\backslash$mathfrak n{\}})){\}} or {\#}{\#}IMG{\#}{\#}$\backslash$n[http://ej.iop.org/images/1751-8121/42/20/205203/jpa308910ieqn2.gif] {\{}$\backslash$wh{\{}$\backslash$cal U{\}}{\_}{\{}q{\}}(gl({\{}$\backslash$mathfrak$\backslash$nm{\}}|{\{}$\backslash$mathfrak n{\}})){\}} (super)algebras, with arbitrary representations (i.e., 'spins') on each site of$\backslash$nthe chain and diagonal boundary matrices ( K + ( u ), K − ( u )). The nested Bethe ansatz applies$\backslash$nfor a general K − ( u ), but a particular form of the K + ( u ) matrix. The construction extends and$\backslash$nunifies the results already obtained for open spin chains based on the fundamental representation$\backslash$nand for some particular super-spin chains. We give the eigenvalues, Bethe equations and the explicit$\backslash$nform of the Bethe vectors for the corresponding models. The Bethe vectors are also expressed using a$\backslash$ntrace formula.},
archivePrefix = {arXiv},
arxivId = {0902.0321},
author = {Belliard, S and Ragoucy, E},
doi = {10.1088/1751-8113/42/20/205203},
eprint = {0902.0321},
file = {:Users/wenwen/Documents/MendeleyRefs/Belliard, Ragoucy{\_}Journal of Physics A Mathematical and Theoretical{\_}2009.pdf:pdf},
issn = {1751-8113},
journal = {J. Phys. A Math. Theor.},
month = {may},
number = {20},
pages = {205203},
title = {{The nested Bethe ansatz for ‘all' open spin chains with diagonal boundary conditions}},
url = {http://stacks.iop.org/1751-8121/42/i=20/a=205203?key=crossref.1fd9ed47e22b2ec879dbd0ad7a30e9bc},
volume = {42},
year = {2009}
}
@article{Fritsche2011,
abstract = {We investigate the conformational properties of a semiflexible ring polymer in confined spaces. Taking into account the competing interplay between configurational entropy, bending energy and excluded volume, we elucidate the role that different geometrical constraints can play in shaping the spatial organization of biopolymers. While elongated, rod-like geometries reduce the amount of chain overcrossings and induce a pronounced ordering with respect to the long axis of the surrounding envelope, there exists no preferred orientational axis in the case of spherical confinement. Upon increasing the system density and the rigidity of the chain, the polymer migrates from the center of the accessible space towards the surrounding surface, forming a spool-like structure known for DNA condensation within viral capsids. The existence of distinguished loop sizes for different confining geometries might influence co-localization in biopolymers necessary for the genome-wide coordination of gene expression. Thus, the advantages of certain geometric constraints, such as spherical confinement of viral DNA in a capsid or the rod-shaped envelope of the circular chromosome in Escherichia coli could be one driving force for controlling proper biological functioning. {\textcopyright} 2011 The Royal Society of Chemistry.},
author = {Fritsche, Miriam and Heermann, Dieter W.},
doi = {10.1039/c1sm05445g},
file = {:Users/wenwen/Documents/MendeleyRefs/Fritsche, Heermann{\_}Soft Matter{\_}2011.pdf:pdf},
isbn = {4962215493},
issn = {1744-683X},
journal = {Soft Matter},
pages = {6906},
title = {{Confinement driven spatial organization of semiflexible ring polymers: Implications for biopolymer packaging}},
volume = {7},
year = {2011}
}
@article{Choi2011,
author = {Choi, Woosik and Yook, Soon-Hyung and Kim, Yup},
doi = {10.1103/PhysRevE.84.020102},
file = {:Users/wenwen/Documents/MendeleyRefs/Choi, Yook, Kim{\_}Physical Review E{\_}2011.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {aug},
number = {2},
pages = {1--4},
title = {{Explosive site percolation with a product rule}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.84.020102},
volume = {84},
year = {2011}
}
@inproceedings{Ding2001,
author = {Ding, CHQ and He, Xiaofeng and Zha, Hongyuan and Gu, Ming and Simon, Horst D.},
booktitle = {Data Mining, 2001. ICDM 2001, Proc. IEEE Int. Conf.},
file = {:Users/wenwen/Documents/MendeleyRefs/Ding et al.{\_}Data Mining, 2001. ICDM 2001, Proceedings IEEE International Conference on{\_}2001.pdf:pdf},
pages = {107--114},
title = {{A min-max cut algorithm for graph partitioning and data clustering}},
url = {http://ieeexplore.ieee.org/xpls/abs{\_}all.jsp?arnumber=989507},
year = {2001}
}
@article{Santalla2014,
abstract = {We consider the Kardar-Parisi-Zhang (KPZ) equation for a circular interface in two dimensions, unconstrained by the standard small-slopes and no-overhang approximations. Numerical simulations using an adaptive scheme allow us to elucidate the complete time evolution as a crossover between a short-time regime with the interface fluctuations of a self-avoiding ring or 2D vesicle, and a long-time regime governed by the Tracy-Widom distribution expected for this geometry. For small noise amplitudes, scaling behavior is only of the latter type. Large noise is also seen to renormalize the bare physical parameters of the ring, akin to analogous parameter renormalization for equilibrium 3D membranes. Our results bear particular importance on the relation between relevant universality classes of scale-invariant systems in two dimensions.},
archivePrefix = {arXiv},
arxivId = {1312.7696},
author = {Santalla, Silvia N. and Rodr{\'{i}}guez-Laguna, Javier and Cuerno, Rodolfo},
doi = {10.1103/PhysRevE.89.010401},
eprint = {1312.7696},
file = {:Users/wenwen/Documents/MendeleyRefs/Santalla, Rodr{\'{i}}guez-Laguna, Cuerno{\_}Physical Review E - Statistical, Nonlinear, and Soft Matter Physics{\_}2014.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
keywords = {05.10.Gg,68.35.Ct,81.15.Aa,82.35.Gh},
month = {jan},
number = {1},
pages = {010401},
title = {{Circular Kardar-Parisi-Zhang equation as an inflating, self-avoiding ring polymer}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.89.010401},
volume = {89},
year = {2014}
}
@book{Rozanov1969,
author = {Rozanov, Y.A.},
file = {:Users/wenwen/Documents/MendeleyRefs/Rozanov{\_}Unknown{\_}1969.pdf:pdf},
publisher = {Richard A. Silverman},
title = {{Probability Theory: A Concise Course}},
year = {1969}
}
@article{Lang2014b,
abstract = {Polymers exposed to shear flow exhibit a remarkably rich tumbling dynamics. While rigid rods rotate on Jeffery orbits, a flexible polymer stretches and coils up during tumbling. Theoretical results show that in both of these asymptotic regimes the corresponding tumbling frequency fc in a linear shear flow of strength $\gamma$ scales as a power law Wi2/3 in the Weissenberg number Wi=$\gamma$$\tau$, where $\tau$ is a characteristic time of the polymer's relaxational dynamics. For a flexible polymer these theoretical results are well confirmed by a large body of experimental single molecule studies. However, for the intermediate semiflexible regime, especially relevant for cytoskeletal filaments like F-actin and microtubules, the situation is less clear. While recent experiments on single F-actin filaments are still interpreted within the classical Wi2/3 scaling law, theoretical results indicated deviations from it. Here we perform extensive Brownian dynamics simulations to explore the tumbling dynamics of semiflexible polymers over a broad range of shear strength and the polymer's persistence length lp. We find that the Weissenberg number alone does not suffice to fully characterize the tumbling dynamics, and the classical scaling law breaks down. Instead, both the polymer's stiffness and the shear rate are relevant control parameters. Based on our Brownian dynamics simulations we postulate that in the parameter range most relevant for cytoskeletal filaments there is a distinct scaling behavior with fc$\tau$∗=Wi3/4fˆc(x) with Wi=$\gamma$$\tau$∗ and the scaling variable x=(lp/L)(Wi)−1/3; here $\tau$∗ is the time the polymer's center of mass requires to diffuse its own contour length L. Comparing these results with experimental data on F-actin we find that the Wi3/4 scaling law agrees quantitatively significantly better with the data than the classical Wi2/3 law. Finally, we extend our results to single ring polymers in shear flow, and find similar results as for linear polymers with slightly different power laws.},
archivePrefix = {arXiv},
arxivId = {arXiv:1402.3441v2},
author = {Lang, Philipp S. and Obermayer, Benedikt and Frey, Erwin},
doi = {10.1103/PhysRevE.89.022606},
eprint = {arXiv:1402.3441v2},
file = {:Users/wenwen/Documents/MendeleyRefs/Lang, Obermayer, Frey{\_}Physical Review E{\_}2014.pdf:pdf},
isbn = {1539-3755},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {feb},
number = {2},
pages = {022606},
title = {{Dynamics of a semiflexible polymer or polymer ring in shear flow}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.89.022606},
volume = {89},
year = {2014}
}
@article{Nepomechie2003,
abstract = {A Bethe Ansatz solution of the open spin-1/2 XXZ quantum spin chain with nondiagonal boundary terms has recently been proposed. Using a numerical procedure developed by McCoy et al., we find significant evidence that this solution can yield the complete set of eigenvalues for generic values of the bulk and boundary parameters satisfying one linear relation. Moreover, our results suggest that this solution is practical for investigating the ground state of this model in the thermodynamic limit.},
archivePrefix = {arXiv},
arxivId = {hep-th/0307095},
author = {Nepomechie, Rafael I. and Ravanini, Francesco},
doi = {10.1088/0305-4470/36/45/003},
eprint = {0307095},
file = {:Users/wenwen/Documents/MendeleyRefs/Nepomechie, Ravanini{\_}Journal of Physics A Mathematical and General{\_}2003.pdf:pdf},
issn = {0305-4470},
journal = {J. Phys. A. Math. Gen.},
month = {nov},
number = {45},
pages = {11391--11401},
primaryClass = {hep-th},
title = {{Completeness of the Bethe Ansatz solution of the open XXZ chain with nondiagonal boundary terms}},
url = {http://stacks.iop.org/0305-4470/36/i=45/a=003?key=crossref.0fbc952062fef6e262710224ce3fb77a},
volume = {36},
year = {2003}
}
@article{Coelho2013,
author = {Coelho, Miguel and Dereli, Ayg{\"{u}}l and Haese, Anett and K{\"{u}}hn, Sebastian and Malinovska, Liliana and DeSantis, Morgan E. and Shorter, James and Alberti, Simon and Gross, Thilo and Toli{\'{c}}-N{\o}rrelykke, Iva M.},
doi = {10.1016/j.cub.2013.07.084},
issn = {09609822},
journal = {Curr. Biol.},
month = {oct},
number = {19},
pages = {1844--1852},
title = {{Fission Yeast Does Not Age under Favorable Conditions, but Does So after Stress}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982213009731},
volume = {23},
year = {2013}
}
@article{Gerton2005,
abstract = {Proper chromosome segregation is crucial for preventing fertility problems, birth defects and cancer. During mitotic cell divisions, sister chromatids separate from each other to opposite poles, resulting in two daughter cells that each have a complete copy of the genome. Meiosis poses a special problem in which homologous chromosomes must first pair and then separate at the first meiotic division before sister chromatids separate at the second meiotic division. So, chromosome interactions between homologues are a unique feature of meiosis and are essential for proper chromosome segregation. Pairing and locking together of homologous chromosomes involves recombination interactions in some cases, but not in others. Although all organisms must match and lock homologous chromosomes to maintain genome integrity throughout meiosis, recent results indicate that the underlying mechanisms vary in different organisms.},
author = {Gerton, Jennifer L and Hawley, R Scott},
doi = {10.1038/nrg1614},
file = {:Users/wenwen/Documents/MendeleyRefs/Gerton, Hawley{\_}Nature Reviews Genetics{\_}2005.pdf:pdf},
isbn = {1471-0056 (Print)$\backslash$n1471-0056 (Linking)},
issn = {1471-0056},
journal = {Nat. Rev. Genet.},
month = {jun},
number = {6},
pages = {477--487},
pmid = {15931171},
title = {{Homologous chromosome interactions in meiosis: diversity amidst conservation}},
url = {http://www.nature.com/doifinder/10.1038/nrg1614},
volume = {6},
year = {2005}
}
@article{P.W.Anderson1972,
author = {Anderson, P. W.},
doi = {10.1126/science.177.4047.393},
file = {:Users/wenwen/Documents/MendeleyRefs/P. W. Anderson{\_}Science (New York, N.Y.){\_}1972.pdf:pdf},
issn = {0036-8075},
journal = {Science (80-. ).},
month = {aug},
number = {4047},
pages = {393--396},
title = {{More Is Different}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.177.4047.393},
volume = {177},
year = {1972}
}
@book{Simmonds1994,
address = {New York, NY},
author = {Simmonds, James G.},
doi = {10.1007/978-1-4419-8522-4},
file = {:Users/wenwen/Documents/MendeleyRefs/Simmonds{\_}Unknown{\_}1994.pdf:pdf},
isbn = {978-1-4612-6424-8},
keywords = {contact lens,friction,hydrogel,microtribometer,mucin},
publisher = {Springer New York},
series = {Undergraduate Texts in Mathematics},
title = {{A Brief on Tensor Analysis}},
url = {http://link.springer.com/10.1007/978-1-4419-8522-4},
year = {1994}
}
@article{Sakaue2013,
author = {Sakaue, Takahiro},
doi = {10.1103/PhysRevE.87.040601},
file = {:Users/wenwen/Documents/MendeleyRefs/Sakaue{\_}Physical Review E{\_}2013.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {apr},
number = {4},
pages = {040601},
title = {{Memory effect and fluctuating anomalous dynamics of a tagged monomer}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.87.040601},
volume = {87},
year = {2013}
}
@article{DeMenezes2004,
author = {de Menezes, M. and a.-L. Barab{\'{a}}si},
doi = {10.1103/PhysRevLett.92.028701},
file = {:Users/wenwen/Documents/MendeleyRefs/de Menezes, Barab{\'{a}}si{\_}Physical Review Letters{\_}2004.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {jan},
number = {2},
pages = {1--4},
title = {{Fluctuations in Network Dynamics}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.92.028701},
volume = {92},
year = {2004}
}
@article{Tanizawa2010,
abstract = {We have comprehensively mapped long-range associations between chromosomal regions throughout the fission yeast genome using the latest genomics approach that combines next generation sequencing and chromosome conformation capture (3C). Our relatively simple approach, referred to as enrichment of ligation products (ELP), involves digestion of the 3C sample with a 4 bp cutter and self-ligation, achieving a resolution of 20 kb. It recaptures previously characterized genome organizations and also identifies new and important interactions. We have modeled the 3D structure of the entire fission yeast genome and have explored the functional relationships between the global genome organization and transcriptional regulation. We find significant associations among highly transcribed genes. Moreover, we demonstrate that genes co-regulated during the cell cycle tend to associate with one another when activated. Remarkably, functionally defined genes derived from particular gene ontology groups tend to associate in a statistically significant manner. Those significantly associating genes frequently contain the same DNA motifs at their promoter regions, suggesting that potential transcription factors binding to these motifs are involved in defining the associations among those genes. Our study suggests the presence of a global genome organization in fission yeast that is functionally similar to the recently proposed mammalian transcription factory.},
author = {Tanizawa, Hideki and Iwasaki, Osamu and Tanaka, Atsunari and Capizzi, Joseph R and Wickramasinghe, Priyankara and Lee, Mihee and Fu, Zhiyan and Noma, K.-i.},
doi = {10.1093/nar/gkq955},
file = {:Users/wenwen/Documents/MendeleyRefs/Tanizawa et al.{\_}Nucleic Acids Research{\_}2010.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Res.},
keywords = {Cell Cycle,Cell Cycle: genetics,DNA,Fluorescence,Fungal,Fungal: chemistry,Gene Expression Regulation,Genetic,Genetic Loci,Genome,Genomics,Genomics: methods,In Situ Hybridization,Models,Molecular,Physical Chromosome Mapping,Retroelements,Schizosaccharomyces,Schizosaccharomyces: genetics,Schizosaccharomyces: metabolism,Terminal Repeat Sequences,Transcription},
month = {dec},
number = {22},
pages = {8164--8177},
pmid = {21030438},
title = {{Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation}},
url = {https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkq955},
volume = {38},
year = {2010}
}
@article{Pan2011,
author = {Pan, Raj and Kivel{\"{a}}, Mikko and Saram{\"{a}}ki, Jari and Kaski, Kimmo and Kert{\'{e}}sz, J{\'{a}}nos},
doi = {10.1103/PhysRevE.83.046112},
file = {:Users/wenwen/Documents/MendeleyRefs/Pan et al.{\_}Physical Review E{\_}2011.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {apr},
number = {4},
pages = {1--6},
title = {{Using explosive percolation in analysis of real-world networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.83.046112},
volume = {83},
year = {2011}
}
@misc{Chandrasekhar1943,
abstract = {Not Available},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Chandrasekhar, S.},
booktitle = {Rev. Mod. Phys.},
doi = {10.1103/RevModPhys.15.1},
eprint = {arXiv:1011.1669v3},
file = {:Users/wenwen/Documents/MendeleyRefs/Chandrasekhar{\_}Reviews of Modern Physics{\_}1943.pdf:pdf},
isbn = {0034-6861},
issn = {00346861},
number = {1},
pages = {1--89},
pmid = {20958214},
title = {{Stochastic problems in physics and astronomy}},
volume = {15},
year = {1943}
}
@article{Cruz2012,
abstract = {Kinetic theory is a mathematical framework intended to relate directly the most relevant characteristics of the molecular structure to the rheological behavior of the bulk system. In other words, kinetic theory is a micro-to-macro approach for solving the flow of complex fluids that circumvents the use of closure relations and offers a better physical description of the phenomena involved in the flow processes. Cornerstone models in kinetic theory employ beads, rods and springs for mimicking the molecular structure of the complex fluid. The generalized bead-rod-spring chain includes the most basic models in kinetic theory: the freely jointed bead-spring chain and the freely-jointed bead-rod chain. Configuration of simple coarse-grained models can be represented by an equivalent Fokker-Planck (FP) diffusion equation, which describes the evolution of the configuration distribution function in the physical and configurational spaces. FP equation can be a complex mathematical object, given its multidimensionality, and solving it explicitly can become a difficult task. Even more, in some cases, obtaining an equivalent FP equation is not possible given the complexity of the coarse-grained molecular model. Brownian dynamics can be employed as an alternative extensive numerical method for approaching the configuration distribution function of a given kinetic-theory model that avoid obtaining and/or resolving explicitly an equivalent FP equation. The validity of this discrete approach is based on the mathematical equivalence between a continuous diffusion equation and a stochastic differential equation as demonstrated by It{\^{o}} in the 1940s. This paper presents a review of the fundamental issues in the BD simulation of the linear viscoelastic behavior of bead-rod-spring coarse grained models in dilute solution. In the first part of this work, the BD numerical technique is introduced. An overview of the mathematical framework of the BD and a review of the scope of applications are presented. Subsequently, the links between the rheology of complex fluids, the kinetic theory and the BD technique are established at the light of the stochastic nature of the bead-rod-spring models. Finally, the pertinence of the present state-of-the-art review is explained in terms of the increasing interest for the stochastic micro-to-macro approaches for solving complex fluids problems. In the second part of this paper, a detailed description of the BD algorithm used for simulating a small-amplitude oscillatory deformation test is given. Dynamic properties are employed throughout this work to characterise the linear viscoelastic behavior of bead-rod-spring models in dilute solution. In the third and fourth part of this article, an extensive discussion about the main issues of a BD simulation in linear viscoelasticity of diluted suspensions is tackled at the light of the classical multi-bead-spring chain model and the multi-bead-rod chain model, respectively. Kinematic formulations, integration schemes and expressions to calculate the stress tensor are revised for several classical models: Rouse and Zimm theories in the case of multi-bead-spring chains, and Kramers chain and semi-flexible filaments in the case of multi-bead-rod chains. The implemented BD technique is, on the one hand, validated in front of the analytical or exact numerical solutions known of the equivalent FP equations for those classic kinetic theory models; and, on the other hand, is control-set thanks to the analysis of the main numerical issues involved in a BD simulation. Finally, the review paper is closed by some concluding remarks.},
author = {Cruz, C. and Chinesta, F. and R{\'{e}}gnier, G.},
doi = {10.1007/s11831-012-9072-2},
file = {:Users/wenwen/Documents/MendeleyRefs/Cruz, Chinesta, R{\'{e}}gnier{\_}Archives of Computational Methods in Engineering{\_}2012.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Cruz, Chinesta, R{\'{e}}gnier{\_}Archives of Computational Methods in Engineering{\_}2012.pdf:pdf},
issn = {1134-3060},
journal = {Arch. Comput. Methods Eng.},
month = {jun},
number = {2},
pages = {227--259},
title = {{Review on the Brownian Dynamics Simulation of Bead-Rod-Spring Models Encountered in Computational Rheology}},
url = {http://link.springer.com/10.1007/s11831-012-9072-2},
volume = {19},
year = {2012}
}
@article{Otten2009,
author = {Otten, Ronald H. J. and van der Schoot, Paul},
doi = {10.1103/PhysRevLett.103.225704},
file = {:Users/wenwen/Documents/MendeleyRefs/Otten, van der Schoot{\_}Physical Review Letters{\_}2009.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {nov},
number = {22},
pages = {1--4},
title = {{Continuum Percolation of Polydisperse Nanofillers}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.103.225704},
volume = {103},
year = {2009}
}
@article{F.Brochard-Wyart1993a,
abstract = {1. We describe first the non-uniform stretching of one long flexible tethered chain (N monomers) immersed in a good solvent moving at velocity V. In strong flows the extension L is predicted to increase quadratically with velocity (L approximately N3V2). The chain can be pictured as a sequence of blobs of size y decreasing as x-1 (x being the distance measured from the chain end). 2. We extend this analysis to the stretching of a few grafted chains ({\{}"{\}}mushroom{\{}"{\}} regime) when a shear flow (rate s) of the solvent is imposed near the wall. Here the elongation L approximately N3/2 s1/2 and the blob size decreases as y approximately x -1/2 . 3. Finally we discuss a chain confined in a slit. We find L approximately N4/3V1/3 and blobs sizes y approximately x-3/4. In all these cases, the deformation is progressive and we expect no sharp coil stretch transitions.},
author = {Brochard-Wyart, F},
doi = {10.1209/0295-5075/23/2/005},
file = {:Users/wenwen/Documents/MendeleyRefs/Brochard-Wyart{\_}Europhysics Letters (EPL){\_}1993.pdf:pdf},
issn = {0295-5075},
journal = {Europhys. Lett.},
keywords = {Chain under tension},
month = {jul},
number = {2},
pages = {105--111},
title = {{Deformations of One Tethered Chain in Strong Flows}},
url = {http://stacks.iop.org/0295-5075/23/i=2/a=005?key=crossref.ed7029c9602de10dadc40be400807ae3},
volume = {23},
year = {1993}
}
@article{Ikonen2012,
abstract = {We present a Brownian dynamics model of driven polymer translocation, in which nonequilibrium memory effects arising from tension propagation (TP) along the cis side subchain are incorporated as a time-dependent friction. To solve the effective friction, we develop a finite chain length TP formalism, based on the idea suggested by Sakaue [Phys. Rev.E76,021803(2007)].We validate themodel by numerical comparisonswith high-accuracy molecular dynamics simulations, showing excellent agreement in a wide range of parameters. Our results show that the dynamics of driven translocation is dominated by the nonequilibrium TP along the cis side subchain. Furthermore, by solving themodel for chain lengths up to 1010 monomers,we showthat the chain lengths probed by experiments and simulations are typically orders ofmagnitude below the asymptotic limit. This explains both the considerable scatter in the observed scaling of translocation time with respect to chain length, and some of the shortcomings of present theories. Our study shows that for a quantitative theory of polymer translocation, explicit consideration of finite chain length effects is required.},
archivePrefix = {arXiv},
arxivId = {1111.4782},
author = {Ikonen, T. and Bhattacharya, A. and Ala-Nissila, T. and Sung, W.},
doi = {10.1103/PhysRevE.85.051803},
eprint = {1111.4782},
file = {:Users/wenwen/Documents/MendeleyRefs/Ikonen et al.{\_}Physical Review E - Statistical, Nonlinear, and Soft Matter Physics{\_}2012.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {may},
number = {5},
pages = {051803},
title = {{Unifying model of driven polymer translocation}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.85.051803},
volume = {85},
year = {2012}
}
@article{Li2012a,
author = {Li, Wei and Bashan, Amir and Buldyrev, Sergey V. and Stanley, H. Eugene and Havlin, Shlomo},
doi = {10.1103/PhysRevLett.108.228702},
file = {:Users/wenwen/Documents/MendeleyRefs/Li et al.{\_}Physical Review Letters{\_}2012.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {may},
number = {22},
pages = {228702},
title = {{Cascading Failures in Interdependent Lattice Networks: The Critical Role of the Length of Dependency Links}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.108.228702},
volume = {108},
year = {2012}
}
@inproceedings{Zhu2013a,
abstract = {Motivated by applications of large-scale graph clustering, we study random-walk-based local algorithms whose running times depend only on the size of the output cluster, rather than the entire graph. In particular, we develop a method with better theoretical guarantee compared to all previous work, both in terms of the clustering accuracy and the conductance of the output set. We also prove that our analysis is tight, and perforin empirical evaluation to support our theory on both synthetic and real data. More specifically, our method outperforms prior work when the cluster is well-connected. In fact, the better it is well-connected inside, the more significant improvement we can obtain. Our results shed light on why in practice some random-walk-based algorithms perform better than its previous theory, and help guide future research about local clustering. Copyright 2013 by the author(s).},
archivePrefix = {arXiv},
arxivId = {1304.8132},
author = {Zhu, Zeyuan A and Lattanzi, Silvio and Mirrokni, Vahab},
booktitle = {Proc. 30th Int. Conf. Mach. Learn.},
eprint = {1304.8132},
file = {:Users/wenwen/Documents/MendeleyRefs/Zhu, Lattanzi, Mirrokni{\_}Proceedings of the 30th International Conference on Machine Learning (ICML-13){\_}2013.pdf:pdf},
keywords = {Local clustering,PageRank,Random walk},
pages = {396--404},
title = {{A local algorithm for finding well-connected clusters}},
volume = {28},
year = {2013}
}
@article{Liu2010,
author = {Liu, Zonghua and Wu, Xiang and Yang, Huijie and Gupte, Neelima and Li, Baowen},
doi = {10.1088/1367-2630/12/2/023016},
file = {:Users/wenwen/Documents/MendeleyRefs/Liu et al.{\_}New Journal of Physics{\_}2010.pdf:pdf},
issn = {1367-2630},
journal = {New J. Phys.},
month = {feb},
number = {2},
pages = {023016},
title = {{Heat flux distribution and rectification of complex networks}},
url = {http://stacks.iop.org/1367-2630/12/i=2/a=023016?key=crossref.bfd8ca4d2200cb67ed3a23ea7d8a4057},
volume = {12},
year = {2010}
}
@article{Clisby2010,
abstract = {The pivot algorithm for self-avoiding walks has been implemented in a manner which is dramatically faster than previous implementations, enabling extremely long walks to be efficiently simulated. We explicitly describe the data structures and algorithms used, and provide a heuristic argument that the mean time per attempted pivot for {\$}N{\$}-step self-avoiding walks is {\$}O(1){\$} for the square and simple cubic lattices. Numerical experiments conducted for self-avoiding walks with up to 268 million steps are consistent with {\$}o(\backslashlog N){\$} behavior for the square lattice and {\$}O(\backslashlog N){\$} behavior for the simple cubic lattice. Our method can be adapted to other models of polymers with short-range interactions, on the lattice or in the continuum, and hence promises to be widely useful.},
archivePrefix = {arXiv},
arxivId = {1005.1444},
author = {Clisby, Nathan},
doi = {10.1007/s10955-010-9994-8},
eprint = {1005.1444},
file = {:Users/wenwen/Documents/MendeleyRefs/Clisby{\_}Journal of Statistical Physics{\_}2010.pdf:pdf},
issn = {00224715},
journal = {J. Stat. Phys.},
keywords = {Monte Carlo,Pivot algorithm,Polymer,Self-avoiding walk},
pages = {349--392},
pmid = {20366773},
title = {{Efficient implementation of the pivot algorithm for self-avoiding walks}},
volume = {140},
year = {2010}
}
@article{Toba2006,
abstract = {Structural differences between dynein and kinesin suggest a unique molecular mechanism of dynein motility. Measuring the mechanical properties of a single molecule of dynein is crucial for revealing the mechanisms underlying its movement. We measured the step size and force produced by single molecules of active cytoplasmic dynein by using an optical trap and fluorescence imaging with a high temporal resolution. The velocity of dynein movement, 800 nm/s, is consistent with that reported in cells. The maximum force of 7-8 pN was independent of the ATP concentration and similar to that of kinesin. Dynein exhibited forward and occasional backwards steps of approximately 8 nm, independent of load. It is suggested that the large dynein heads take 16-nm steps by using an overlapping hand-over-hand mechanism.},
author = {Toba, Shiori and Watanabe, Tomonobu M and Yamaguchi-Okimoto, Lisa and Toyoshima, Yoko Yano and Higuchi, Hideo},
doi = {10.1073/pnas.0508511103},
file = {:Users/wenwen/Documents/MendeleyRefs/Toba et al.{\_}Proceedings of the National Academy of Sciences{\_}2006.pdf:pdf},
isbn = {0027-8424 (Print)},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
month = {apr},
number = {15},
pages = {5741--5745},
pmid = {16585530},
publisher = {National Academy of Sciences},
title = {{Overlapping hand-over-hand mechanism of single molecular motility of cytoplasmic dynein}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16585530 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC1424663 http://www.pnas.org/cgi/doi/10.1073/pnas.0508511103},
volume = {103},
year = {2006}
}
@article{Tubiana2011,
abstract = {The interplay of geometrical and topological entanglement in semiflexible knotted polymer rings inside a spherical cavity is investigated using advanced numerical methods. By using stringent and robust algorithms for locating knots, we characterize how the knot length, lk, depends on the ring contour length, Lc and the radius of the confining sphere, Rc. In the no- and strong-confinement cases we observe weak knot localization and complete knot delocalization, respectively. We show that the complex interplay of lk, Lc and Rc that seamlessly bridges these two limits can be encompassed by a simple scaling argument based on deflection theory. The same argument is used to rationalise the multiscale character of the entanglement that emerges with increasing confinement.},
archivePrefix = {arXiv},
arxivId = {1106.1872},
author = {Tubiana, Luca and Orlandini, Enzo and Micheletti, Cristian},
doi = {10.1103/PhysRevLett.107.188302},
eprint = {1106.1872},
file = {:Users/wenwen/Documents/MendeleyRefs/Tubiana, Orlandini, Micheletti{\_}Physical Review Letters{\_}2011.pdf:pdf},
isbn = {0031-9007$\backslash$n1079-7114},
issn = {00319007},
journal = {Phys. Rev. Lett.},
number = {October},
pages = {1--4},
pmid = {22107680},
title = {{Multiscale entanglement in ring polymers under spherical confinement}},
volume = {107},
year = {2011}
}
@article{Diehl1988,
author = {Diehl, H W and Eisenriegler, E},
file = {:Users/wenwen/Documents/MendeleyRefs/Diehl, Eisenriegler{\_}J. Phys. A Math. Gen.{\_}1988.pdf:pdf},
journal = {J. Phys. A Math. Gen.},
pages = {L87--L91},
title = {{Universal shape ratios for open and closed random walks: exact results for add d}},
volume = {22},
year = {1988}
}
@article{Rzehak2002,
abstract = {Bead spring models for polymers in solution are nonlinear if either the finite extensibility of the polymer, excluded-volume effects or hydrodynamic interactions between polymer segments are taken into account. For such models we use a powerful method for the determination of the complete relaxation spectrum of fluctuations at steady state. In general, the spectrum and modes differ significantly from those of the linear Rouse model. For a tethered polymer in uniform flow the differences are mainly caused by an inhomogeneous distribution of tension along the chain and are most pronounced due to the finite chain extensibility. Beyond the dynamics of steady-state fluctuations we also investigate the nonlinear response of the polymer to a large sudden change in the flow. This response exhibits several distinct regimes with characteristic decay laws and shows features which are beyond the scope of single-mode theories such as the dumb-bell model.},
archivePrefix = {arXiv},
arxivId = {cond-mat/0210322},
author = {Rzehak, R and Zimmermann, W},
doi = {10.1209/epl/i2002-00194-y},
eprint = {0210322},
file = {:Users/wenwen/Documents/MendeleyRefs/Rzehak, Zimmermann{\_}Europhysics Letters{\_}2002.pdf:pdf},
isbn = {0295-5075},
issn = {0295-5075},
journal = {Europhys. Lett.},
keywords = {Chains,Dna Molecule,Flow,Simulation,Tethered Polymer},
number = {5},
pages = {779--785},
primaryClass = {cond-mat},
title = {{Dynamics of strongly deformed polymers in solution}},
url = {papers://8d0de5a1-e8b7-4a12-aaa3-152761650b49/Paper/p188},
volume = {59},
year = {2002}
}
@article{Montesi2005a,
abstract = {A model of semiflexible bead-rod chain with anisotropic friction can mimic closely the hydrodynamics of a slender filament. We present an efficient algorithm for Brownian dynamics simulations of this model with configuration dependent anisotropic bead friction coefficients. The algorithm is an extension of that given previously for the case of configuration independent isotropic friction coefficients by Grassia and Hinch [J. Fluid Mech. 308, 255 (1996)]. We confirm that the algorithm yields predicted values for various equilibrium properties. We also present a stochastic algorithm for evaluation of the stress tensor, and we show that in the limit of stiff chains the algorithm recovers the results of Kirkwood and Plock [J. Chem. Phys. 24, 665 (1956)] for rigid rods with hydrodynamic interactions.},
author = {Montesi, Alberto and Morse, David C. and Pasquali, Matteo},
doi = {10.1063/1.1848511},
file = {:Users/wenwen/Documents/MendeleyRefs/Montesi, Morse, Pasquali{\_}The Journal of Chemical Physics{\_}2005.pdf:pdf},
issn = {00219606},
journal = {J. Chem. Phys.},
month = {feb},
number = {8},
pages = {084903},
pmid = {15836088},
title = {{Brownian dynamics algorithm for bead-rod semiflexible chain with anisotropic friction}},
url = {http://scitation.aip.org/content/aip/journal/jcp/122/8/10.1063/1.1848511},
volume = {122},
year = {2005}
}
@article{Bressloff2013,
abstract = {A number of exact results have been obtained recently for the one-dimensional asymmetric simple exclusion process, a model of particles which hop to their right at random times, on a one-dimensional lattice, provided that the target site is empty. Using either a matrix form for the steady-state weights or the Bethe ansatz, several steady-state properties can be calculated exactly: the current, the density profile for open boundary conditions, the diffusion constant of a tagged particle. The matrix form of the steady state can be extended to calculate exactly the steady state of systems of two species of particles and shock profiles. (C) 1998 Elsevier Science B.V. All rights reserved.},
author = {Bressloff, Paul C. and Newby, Jay M. and Derrida, B.},
doi = {10.1103/RevModPhys.85.135},
file = {:Users/wenwen/Documents/MendeleyRefs/Bressloff, Newby, Derrida{\_}Reviews of Modern Physics{\_}2013.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Derrida{\_}Physics Reports{\_}1998.pdf:pdf},
isbn = {0370-1573},
issn = {03701573},
journal = {Rev. Mod. Phys.},
number = {1-3},
pages = {135--196},
title = {{Stochastic models of intracellular transport}},
url = {http://link.aps.org/doi/10.1103/RevModPhys.85.135{\%}5Cnhttp://rmp.aps.org/pdf/RMP/v85/i1/p135{\_}1},
volume = {301},
year = {2013}
}
@article{Richter2015,
author = {Richter, D. and Goo{\ss}en, S. and Wischnewski, A.},
doi = {10.1039/C5SM01994J},
file = {:Users/wenwen/Documents/MendeleyRefs/Richter, Goo{\ss}en, Wischnewski{\_}Soft Matter{\_}2015.pdf:pdf},
issn = {1744-683X},
journal = {Soft Matter},
pages = {8535--8549},
title = {{Celebrating Soft Matter's 10th Anniversary: Topology matters: structure and dynamics of ring polymers}},
url = {http://xlink.rsc.org/?DOI=C5SM01994J},
year = {2015}
}
@article{Obukhov1994,
abstract = {Dynamics of a in a Gel. Sergei P We present a simple scaling theory of the dynamics of a in a gel. In the},
author = {Obukhov, Sergei P. and Rubinstein, Michael and Duke, Thomas},
doi = {10.1103/PhysRevLett.73.1263},
file = {:Users/wenwen/Documents/MendeleyRefs/Obukhov, Rubinstein, Duke{\_}Physical Review Letters{\_}1994.pdf:pdf},
isbn = {0031-9007},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {aug},
number = {9},
pages = {1263--1266},
title = {{Dynamics of a Ring Polymer in a Gel}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.73.1263},
volume = {73},
year = {1994}
}
@article{Schrenk2011,
author = {Schrenk, K. and Ara{\'{u}}jo, N. and Herrmann, H.},
doi = {10.1103/PhysRevE.84.041136},
file = {:Users/wenwen/Documents/MendeleyRefs/Schrenk, Ara{\'{u}}jo, Herrmann{\_}Physical Review E{\_}2011.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {oct},
number = {4},
pages = {2--7},
title = {{Gaussian model of explosive percolation in three and higher dimensions}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.84.041136},
volume = {84},
year = {2011}
}
@article{Reigh2013,
abstract = {The concentration dependence of the conformations of ring polymers is investigated by lattice Monte Carlo simulations and compared with that of linear polymers. The relative radii of gyration of linear polymers follow a universal master curve as a function of the scaled concentration for various chain lengths, with a scaling relationship ?Rg2? ? ??0.25, which is consistent with scaling theory and neutron scattering experiments. Ring polymers of different lengths also follow a universal behavior with a broad crossover to a scaling behavior ?Rg2? ? ??0.59 for long chains. The scaling relationship between the concentration dependence and the chain-length dependence of the radius of gyration implies ?Rg2? ? N0.72, indicating highly collapsed conformations for long-chain ring polymers in the melt. The concentration dependence of the conformations of ring polymers is investigated by lattice Monte Carlo simulations and compared with that of linear polymers. The relative radii of gyration of linear polymers follow a universal master curve as a function of the scaled concentration for various chain lengths, with a scaling relationship ?Rg2? ? ??0.25, which is consistent with scaling theory and neutron scattering experiments. Ring polymers of different lengths also follow a universal behavior with a broad crossover to a scaling behavior ?Rg2? ? ??0.59 for long chains. The scaling relationship between the concentration dependence and the chain-length dependence of the radius of gyration implies ?Rg2? ? N0.72, indicating highly collapsed conformations for long-chain ring polymers in the melt.},
author = {Reigh, Shang Yik and Yoon, Do Y.},
doi = {10.1021/mz300587v},
file = {:Users/wenwen/Documents/MendeleyRefs/Reigh, Yoon{\_}ACS Macro Letters{\_}2013.pdf:pdf},
issn = {21611653},
journal = {ACS Macro Lett.},
pages = {296--300},
title = {{Concentration dependence of ring polymer conformations from Monte Carlo simulations}},
volume = {2},
year = {2013}
}
@article{DeGier2005,
author = {de Gier, Jan and Essler, Fabian H. L.},
doi = {10.1103/PhysRevLett.95.240601},
file = {:Users/wenwen/Documents/MendeleyRefs/Crampe et al.{\_}Journal of Statistical Mechanics Theory and Experiment{\_}2009(7).pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {dec},
number = {24},
pages = {240601},
title = {{Bethe Ansatz Solution of the Asymmetric Exclusion Process with Open Boundaries}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.95.240601},
volume = {95},
year = {2005}
}
@article{Lizana2010,
abstract = {In this study we derive a single-particle equation of motion, from first principles, starting out with a microscopic description of a tracer particle in a one-dimensional many-particle system with a general two-body interaction potential. Using a harmonization technique, we show that the resulting dynamical equation belongs to the class of fractional Langevin equations, a stochastic framework which has been proposed in a large body of works as a means of describing anomalous dynamics. Our work sheds light on the fundamental assumptions of these phenomenological models and a relation derived by Kollmann.},
archivePrefix = {arXiv},
arxivId = {0909.0881},
author = {Lizana, Ludvig and Ambj{\"{o}}rnsson, Tobias and Taloni, Alessandro and Barkai, Eli and Lomholt, Michael A},
doi = {10.1103/PhysRevE.81.051118},
eprint = {0909.0881},
file = {:Users/wenwen/Documents/MendeleyRefs/Lizana et al.{\_}Physical Review E{\_}2010.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {may},
number = {5},
pages = {051118},
pmid = {20866196},
title = {{Foundation of fractional Langevin equation: Harmonization of a many-body problem}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.81.051118},
volume = {81},
year = {2010}
}
@article{Parshani2010,
author = {Parshani, Roni and Buldyrev, Sergey V. and Havlin, Shlomo},
doi = {10.1103/PhysRevLett.105.048701},
file = {:Users/wenwen/Documents/MendeleyRefs/Parshani, Buldyrev, Havlin{\_}Physical Review Letters{\_}2010.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {jul},
number = {4},
pages = {048701},
title = {{Interdependent Networks: Reducing the Coupling Strength Leads to a Change from a First to Second Order Percolation Transition}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.105.048701},
volume = {105},
year = {2010}
}
@book{Sander2009,
author = {Sander, L M},
isbn = {9780521872904},
publisher = {Cambridge University Press},
title = {{Advanced Condensed Matter Physics}},
url = {https://books.google.de/books?id={\_}A7FexiuAm8C},
year = {2009}
}
@phdthesis{Wong2001,
author = {Wong, Wesley Philip},
file = {:Users/wenwen/Documents/MendeleyRefs/Wong{\_}Unknown{\_}2001.pdf:pdf},
school = {The University of British Columbia},
title = {{Modelling a Tethed Polymer Loop: Shape and thickness compressibility}},
year = {2001}
}
@article{Kapnistos2008,
abstract = {After many years of intense research, most aspects of the motion of entangled polymers have been understood. Long linear and branched polymers have a characteristic entanglement plateau and their stress relaxes by chain reptation or branch retraction, respectively. In both mechanisms, the presence of chain ends is essential. But how do entangled polymers without ends relax their stress? Using properly purified high-molar-mass ring polymers, we demonstrate that these materials exhibit self-similar dynamics, yielding a power-law stress relaxation. However, trace amounts of linear chains at a concentration almost two decades below their overlap cause an enhanced mechanical response. An entanglement plateau is recovered at higher concentrations of linear chains. These results constitute an important step towards solving an outstanding problem of polymer science and are useful for manipulating properties of materials ranging from DNA to polycarbonate. They also provide possible directions for tuning the rheology of entangled polymers.},
author = {Kapnistos, M and Lang, M and Vlassopoulos, D and Pyckhout-Hintzen, W and Richter, D and Cho, D and Chang, T and Rubinstein, M},
doi = {10.1038/nmat2292},
file = {:Users/wenwen/Documents/MendeleyRefs/Kapnistos et al.{\_}Nature Materials{\_}2008.pdf:pdf},
isbn = {1476-1122},
issn = {1476-1122},
journal = {Nat. Mater.},
month = {dec},
number = {12},
pages = {997--1002},
pmid = {18953345},
title = {{Unexpected power-law stress relaxation of entangled ring polymers}},
url = {http://www.nature.com/doifinder/10.1038/nmat2292},
volume = {7},
year = {2008}
}
@article{Iatsenko2013,
author = {Iatsenko, D. and Petkoski, S. and McClintock, P. V. E. and Stefanovska, a.},
doi = {10.1103/PhysRevLett.110.064101},
file = {:Users/wenwen/Documents/MendeleyRefs/Iatsenko et al.{\_}Physical Review Letters{\_}2013.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {feb},
number = {6},
pages = {064101},
title = {{Stationary and Traveling Wave States of the Kuramoto Model with an Arbitrary Distribution of Frequencies and Coupling Strengths}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.110.064101},
volume = {110},
year = {2013}
}
@article{Antal2005,
abstract = {We study the excited random walk, in which a walk that is at a site that contains cookies eats one cookie and then hops to the right with probability p and to the left with probability q = 1-p. If the walk hops onto an empty site, there is no bias. For the 1-excited walk on the half-line (one cookie initially at each site), the probability of first returning to the starting point at time t scales as t(-(2-p)). Although the average return time to the origin is infinite for all p, the walk eats, on average, only a finite number of cookies until this first return when p {\textless} 1/2. For the infinite line, the probability distribution for the 1-excited walk has an unusual anomaly at the origin. The positions of the leftmost and rightmost uneaten cookies can be accurately estimated by probabilistic arguments and their corresponding distributions have power-law singularities. The 2-excited walk on the infinite line exhibits peculiar features in the regime p {\textgreater} 3/4, where the walk is transient, including a mean displacement that grows as t(v), with v {\textgreater} 1 dependent on p, and a breakdown of scaling for the probability distribution of the walk.},
archivePrefix = {arXiv},
arxivId = {math/0412407},
author = {Antal, T and Redner, S},
doi = {10.1088/0305-4470/38/12/002},
eprint = {0412407},
file = {:Users/wenwen/Documents/MendeleyRefs/Antal, Redner{\_}Journal of Physics A Mathematical and General{\_}2005.pdf:pdf},
isbn = {0305-4470},
issn = {0305-4470},
journal = {J. Phys. A. Math. Gen.},
keywords = {bond repulsion,reinforced random-walk,self-avoiding walk},
month = {mar},
number = {12},
pages = {2555--2577},
primaryClass = {math},
title = {{The excited random walk in one dimension}},
url = {http://stacks.iop.org/0305-4470/38/i=12/a=002?key=crossref.b5ba9065ba55c5317c6bff184b1901ec},
volume = {38},
year = {2005}
}
@article{Dong2013,
author = {Dong, Yan and Huang, Wenwen and Liu, Zonghua and Guan, Shuguang},
doi = {10.1016/j.physa.2012.10.014},
file = {:Users/wenwen/Documents/MendeleyRefs/Dong et al.{\_}Physica A Statistical Mechanics and its Applications{\_}2013.pdf:pdf},
issn = {03784371},
journal = {Phys. A Stat. Mech. its Appl.},
month = {feb},
number = {4},
pages = {967--973},
publisher = {Elsevier B.V.},
title = {{Network analysis of time series under the constraint of fixed nearest neighbors}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0378437112009107},
volume = {392},
year = {2013}
}
@article{Zhang2006,
author = {Zhang, J. and Small, M.},
doi = {10.1103/PhysRevLett.96.238701},
file = {:Users/wenwen/Documents/MendeleyRefs/Zhang, Small{\_}Physical Review Letters{\_}2006.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {jun},
number = {23},
pages = {3--6},
title = {{Complex Network from Pseudoperiodic Time Series: Topology versus Dynamics}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.96.238701},
volume = {96},
year = {2006}
}
@article{Rosa2008,
abstract = {During interphase chromosomes decondense, but fluorescent in situ hybridization experiments reveal the existence of distinct territories occupied by individual chromosomes inside the nuclei of most eukaryotic cells. We use computer simulations to show that the existence and stability of territories is a kinetic effect that can be explained without invoking an underlying nuclear scaffold or protein-mediated interactions between DNA sequences. In particular, we show that the experimentally observed territory shapes and spatial distances between marked chromosome sites for human, Drosophila, and budding yeast chromosomes can be reproduced by a parameter-free minimal model of decondensing chromosomes. Our results suggest that the observed interphase structure and dynamics are due to generic polymer effects: confined Brownian motion conserving the local topological state of long chain molecules and segregation of mutually unentangled chains due to topological constraints.},
author = {Rosa, Angelo and Everaers, Ralf},
doi = {10.1371/journal.pcbi.1000153},
editor = {Henikoff, Steven},
file = {:Users/wenwen/Documents/MendeleyRefs/Rosa, Everaers{\_}PLoS Computational Biology{\_}2008.pdf:pdf},
issn = {1553-7358},
journal = {PLoS Comput. Biol.},
month = {aug},
number = {8},
pages = {e1000153},
pmid = {18725929},
title = {{Structure and Dynamics of Interphase Chromosomes}},
url = {http://dx.plos.org/10.1371/journal.pcbi.1000153},
volume = {4},
year = {2008}
}
@article{Usatenko2014,
abstract = {Summary : Application of the massive field theory approach in a fixed space dimensions d = 3 up to one loop order for investigation of the elastic properties of a real polymer chain immersed in a good solvent and anchored by one end to the surface and with other end being under tension of the external applied force as it is usually takes place in the single - mol. force spectroscopy expts.  The obtained results include calcns. of the dependence of the applied force upon stretching of a real polymer chain in a good solvent on the distance from the repulsive and inert surfaces.  Besides, the obtained results are in good qual. and quant. agreement with previous theor. investigations, results of D. Functional Theory (DFT) and Monte Carlo (MC) simulations and have important practical applications for understanding of the elastic properties of the individual macromols., networks, gels and brush layers. [on SciFinder(R)]},
author = {Usatenko, Zoryana.},
doi = {10.1002/masy.201400029},
file = {:Users/wenwen/Documents/MendeleyRefs/Usatenko{\_}Macromolecular Symposia{\_}2014.pdf:pdf},
issn = {1022-1360},
journal = {Macromol. Symp.},
keywords = {adsorption,afm,atomic force microscopy,macromonomers,theory},
number = {1},
pages = {14--21},
title = {{Stretching of Anchored to the Surface a Real Polymer Chain in a Good Solvent: The Massive Field Theory Approach.}},
volume = {346},
year = {2014}
}
@article{rubinov2010complex,
abstract = {Brain connectivity datasets comprise networks of brain regions connected by anatomical tracts or by functional associations. Complex network analysis-a new multidisciplinary approach to the study of complex systems-aims to characterize these brain networks with a small number of neurobiologically meaningful and easily computable measures. In this article, we discuss construction of brain networks from connectivity data and describe the most commonly used network measures of structural and functional connectivity. We describe measures that variously detect functional integration and segregation, quantify centrality of individual brain regions or pathways, characterize patterns of local anatomical circuitry, and test resilience of networks to insult. We discuss the issues surrounding comparison of structural and functional network connectivity, as well as comparison of networks across subjects. Finally, we describe a Matlab toolbox (http://www.brain-connectivity-toolbox.net) accompanying this article and containing a collection of complex network measures and large-scale neuroanatomical connectivity datasets.},
author = {Rubinov, Mikail and Sporns, Olaf},
doi = {10.1016/j.neuroimage.2009.10.003},
issn = {10538119},
journal = {Neuroimage},
keywords = {Brain,Brain: physiology,Models,Nerve Net,Nerve Net: physiology,Neural Networks (Computer),Neurological},
month = {sep},
number = {3},
pages = {1059--1069},
pmid = {19819337},
publisher = {Elsevier},
title = {{Complex network measures of brain connectivity: Uses and interpretations}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S105381190901074X},
volume = {52},
year = {2010}
}
@article{Liu2014,
abstract = {Consider anomalous energy spread in solid phases, i.e., {\textless}$\Delta$x(2)(t){\textgreater}E≡∫(x-{\textless}x{\textgreater}E)(2)$\rho$E(x,t)dx∝t($\beta$), as induced by a small initial excess energy perturbation distribution $\rho$E(x,t=0) away from equilibrium. The second derivative of this variance of the nonequilibrium excess energy distribution is shown to rigorously obey the intriguing relation d(2){\textless}$\Delta$x(2)(t){\textgreater}E/dt2=2CJJ(t)/(kBT(2)c), where CJJ(t) equals the thermal equilibrium total heat flux autocorrelation function and c is the specific volumetric heat capacity. Its integral assumes a time-local Helfand-like relation. Given that the averaged nonequilibrium heat flux is governed by an anomalous heat conductivity, the energy diffusion scaling determines a corresponding anomalous thermal conductivity scaling behavior.},
archivePrefix = {arXiv},
arxivId = {1306.3167},
author = {Liu, Sha and H{\"{a}}nggi, Peter and Li, Nianbei and Ren, Jie and Li, Baowen},
doi = {10.1103/PhysRevLett.112.040601},
eprint = {1306.3167},
file = {:Users/wenwen/Documents/MendeleyRefs/Liu et al.{\_}Physical Review Letters{\_}2014.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {jan},
number = {4},
pages = {040601},
pmid = {24580429},
title = {{Anomalous Heat Diffusion}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.112.040601},
volume = {112},
year = {2014}
}
@article{Halverson2012,
abstract = {Ring polymers remain a challenge to our understanding of polymer dynamics. Experiments are difficult to interpret because of the uncertainty in the purity and dispersity of the sample. Using both equilibrium and nonequilibrium molecular dynamics simulations we have investigated the structure, dynamics, and rheology of perfectly controlled ring-linear polymer blends of chains of up to about 14 entanglements per chain, comparable to experimental systems. Linear contaminants increase the zero-shear viscosity of a ring polymer melt by about 10{\%} around one-fifth of their overlap concentration. For equal concentrations of linear and ring polymers, the blend viscosity is about twice that of the pure linear melt. The diffusion coefficient of the rings decreases dramatically, while the linear polymers are mostly unaffected. Our results are supported by a primitive path analysis. {\textcopyright} 2012 American Physical Society.},
archivePrefix = {arXiv},
arxivId = {1112.3519},
author = {Halverson, Jonathan D. and Grest, Gary S. and Grosberg, Alexander Y. and Kremer, Kurt},
doi = {10.1103/PhysRevLett.108.038301},
eprint = {1112.3519},
file = {:Users/wenwen/Documents/MendeleyRefs/Halverson et al.{\_}Physical Review Letters{\_}2012.pdf:pdf},
issn = {00319007},
journal = {Phys. Rev. Lett.},
number = {January},
pages = {1--5},
title = {{Rheology of ring polymer melts: From linear contaminants to ring-linear blends}},
volume = {108},
year = {2012}
}
@article{vespignani2010complex,
author = {Vespignani, Alessandro},
file = {:Users/wenwen/Documents/MendeleyRefs/Vespignani{\_}Nature{\_}2010.pdf:pdf},
journal = {Nature},
number = {7291},
pages = {984--985},
publisher = {Nature Publishing Group},
title = {{Complex networks: The fragility of interdependency}},
volume = {464},
year = {2010}
}
@article{Daido2007,
author = {Daido, Hiroaki and Nakanishi, Kenji},
doi = {10.1103/PhysRevE.75.056206},
file = {:Users/wenwen/Documents/MendeleyRefs/Daido, Nakanishi{\_}Physical Review E{\_}2007.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {may},
number = {5},
pages = {056206},
title = {{Aging and clustering in globally coupled oscillators}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.75.056206},
volume = {75},
year = {2007}
}
@book{ZhangPython2012,
author = {张若愚},
file = {:Users/wenwen/Documents/MendeleyRefs/张若愚{\_}Unknown{\_}2012.pdf:pdf},
publisher = {清华大学出版社},
title = {{Python 科学计算}},
year = {2012}
}
@article{Fixman1986,
author = {Fixman, Marshall},
doi = {10.1021/ma00158a042},
file = {:Users/wenwen/Documents/MendeleyRefs/Fixman{\_}Macromolecules{\_}1986.pdf:pdf},
issn = {0024-9297},
journal = {Macromolecules},
pages = {1195--1204},
title = {{Implicit algorithm for Brownian dynamics of polymers}},
url = {http://pubs.acs.org/doi/pdf/10.1021/ma00158a042{\%}5Cnhttp://pubs.acs.org/doi/abs/10.1021/ma00158a042},
volume = {19},
year = {1986}
}
@article{Shibuya2014,
author = {Shibuya, Hiroki and Morimoto, Akihiro and Watanabe, Yoshinori},
doi = {10.1371/journal.pgen.1004821},
file = {:Users/wenwen/Documents/MendeleyRefs/Shibuya, Morimoto, Watanabe{\_}PLoS Genetics{\_}2014.pdf:pdf},
issn = {1553-7404},
journal = {PLoS Genet.},
number = {12},
pages = {e1004821},
title = {{The Dissection of Meiotic Chromosome Movement in Mice Using an In Vivo Electroporation Technique}},
url = {http://dx.plos.org/10.1371/journal.pgen.1004821},
volume = {10},
year = {2014}
}
@article{Vaisburd1997,
author = {Hoeycutt, Rebecca L.},
file = {:Users/wenwen/Documents/MendeleyRefs/Hoeycutt{\_}Physical Review A{\_}1991.pdf:pdf},
journal = {Phys. Rev. A},
number = {2},
pages = {600--603},
title = {{Stochastic Runge-Kutta algorithms}},
volume = {45},
year = {1991}
}
@article{Zhang2012,
abstract = {We have studied the dynamics of a flexible polymer chain in constrained dumb-bell-shape geometry subject to a periodic force and external noise along the longitudinal direction. It is found that the system exhibits a feature of entropic stochastic resonance (ESR), i.e., the temporal coherence of the polymer motion can reach a maximum level for an optimal noise intensity. We demonstrate that the occurrence of ESR is robust to the change of chain length, while the bottleneck width should be properly chosen. A gravity force in the vertical direction is not necessary for the ESR here, however, the elastic coupling between polymer beads is crucial.},
author = {Zhang, Zhen and Chen, Hanshuang and Hou, Zhonghuai},
doi = {10.1063/1.4737638},
file = {:Users/wenwen/Documents/MendeleyRefs/Zhang, Chen, Hou{\_}The Journal of chemical physics{\_}2012.pdf:pdf},
issn = {1089-7690},
journal = {J. Chem. Phys.},
keywords = {Entropy,Polymers,Polymers: chemistry,Stochastic Processes},
month = {jul},
number = {4},
pages = {044904},
pmid = {22852652},
title = {{Entropic stochastic resonance of a flexible polymer chain in a confined system.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22852652},
volume = {137},
year = {2012}
}
@article{Newman2003,
author = {Newman, MEJ},
file = {:Users/wenwen/Documents/MendeleyRefs/Newman{\_}SIAM review{\_}2003.pdf:pdf},
journal = {SIAM Rev.},
title = {{The structure and function of complex networks}},
url = {http://epubs.siam.org/doi/pdf/10.1137/S003614450342480},
year = {2003}
}
@article{Yang2008,
author = {Yang, Yue and Yang, Huijie},
doi = {10.1016/j.physa.2007.10.055},
file = {:Users/wenwen/Documents/MendeleyRefs/Yang, Yang{\_}Physica A Statistical Mechanics and its Applications{\_}2008.pdf:pdf},
issn = {03784371},
journal = {Phys. A Stat. Mech. its Appl.},
keywords = {1,achievements in this field,applications of physical theories,attracts special attention due,biology and society,complex networks,have led to fruitful,network construction,of the basic origins,of the ideas and,physiology,the complexity,the methods,theoretical importance in physics,theoretical physics is one,time series analysis,to cite an example,to its practical and},
month = {feb},
number = {5-6},
pages = {1381--1386},
title = {{Complex network-based time series analysis}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0378437107011235},
volume = {387},
year = {2008}
}
@article{Majumdar2004,
author = {Majumdar, Satya N. and Comtet, Alain},
doi = {10.1103/PhysRevLett.92.225501},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {jun},
number = {22},
pages = {225501},
publisher = {American Physical Society},
title = {{Exact Maximal Height Distribution of Fluctuating Interfaces}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.92.225501},
volume = {92},
year = {2004}
}
@article{Feller2008,
author = {Kovalenko, I.N.},
doi = {10.1016/0041-5553(68)90030-X},
isbn = {ISBN 0-471-25709-5},
issn = {00415553},
journal = {USSR Comput. Math. Math. Phys.},
month = {jan},
number = {1},
pages = {353--355},
publisher = {Wiley},
title = {{An introduction to probability theory and its applications. Vol. II}},
url = {http://linkinghub.elsevier.com/retrieve/pii/004155536890030X},
volume = {8},
year = {1968}
}
@article{Wirtz1995,
abstract = {A fluorescently labeled DNA molecule is end tethered to a small magnetic bead and pulled by a calibrated magnetic force through a solution of unlabeled DNA molecules to monitor the transport coefficients of the chain. From the force velocity diagram F-V, we report the first direct measurement of the friction coefficient zeta = F/V of a single DNA molecule. zeta is found to be highly velocity dependent due to sharp conformational transitions for increasing velocities in agreement with a recent model by Ajdari et al.},
author = {Wirtz, D},
file = {:Users/wenwen/Documents/MendeleyRefs/Wirtz{\_}Physical Review Letters{\_}1995.pdf:pdf},
isbn = {0031-9007},
journal = {Phys. Rev. Lett.},
keywords = {CHAINS},
number = {12},
pages = {2436--2439},
title = {{Direct Measurement of the Transport-Properties of a Single DNA Molecule}},
volume = {75},
year = {1995}
}
@article{Nishikawa2010,
abstract = {Synchronization, in which individual dynamical units keep in pace with each other in a decentralized fashion, depends both on the dynamical units and on the properties of the interaction network. Yet, the role played by the network has resisted comprehensive characterization within the prevailing paradigm that interactions facilitating pairwise synchronization also facilitate collective synchronization. Here we challenge this paradigm and show that networks with best complete synchronization, least coupling cost, and maximum dynamical robustness, have arbitrary complexity but quantized total interaction strength, which constrains the allowed number of connections. It stems from this characterization that negative interactions as well as link removals can be used to systematically improve and optimize synchronization properties in both directed and undirected networks. These results extend the recently discovered compensatory perturbations in metabolic networks to the realm of oscillator networks and demonstrate why "less can be more" in network synchronization.},
author = {Nishikawa, Takashi and Motter, Adilson E},
doi = {10.1073/pnas.0912444107},
file = {:Users/wenwen/Documents/MendeleyRefs/Nishikawa, Motter{\_}Proceedings of the National Academy of Sciences of the United States of America{\_}2010.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
month = {jun},
number = {23},
pages = {10342--10347},
pmid = {20489183},
title = {{Network synchronization landscape reveals compensatory structures, quantization, and the positive effect of negative interactions}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2890837{\&}tool=pmcentrez{\&}rendertype=abstract http://www.pnas.org/cgi/doi/10.1073/pnas.0912444107},
volume = {107},
year = {2010}
}
@techreport{Noh2014,
author = {Noh, Jae Dong},
file = {:Users/wenwen/Documents/MendeleyRefs/Noh{\_}Unknown{\_}2014.pdf:pdf},
title = {{Exactly Solvable Many-Body Stochastic Processes}},
year = {2014}
}
@article{Zhang2008,
author = {Zhang, Jie and Sun, Junfeng and Luo, Xiaodong and Zhang, Kai and Nakamura, Tomomichi and Small, Michael},
doi = {10.1016/j.physd.2008.05.008},
file = {:Users/wenwen/Documents/MendeleyRefs/Zhang et al.{\_}Physica D Nonlinear Phenomena{\_}2008.pdf:pdf},
issn = {01672789},
journal = {Phys. D Nonlinear Phenom.},
keywords = {chaos,complex network transformation,nonlinear time series analysis,pseudoperiodic signal,unstable periodic orbits},
month = {nov},
number = {22},
pages = {2856--2865},
publisher = {Elsevier B.V.},
title = {{Characterizing pseudoperiodic time series through the complex network approach}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0167278908001930},
volume = {237},
year = {2008}
}
@article{Underhill2004,
abstract = {We present a study of the coarse-graining of polymers into bead-spring chains using statistical mechanics. The force-extension behavior is examined at different levels of coarse-graining. A direct result of the springs being decoupled is that the force-extension behavior depends only on the number of flexibility lengths (e.g. persistence or Kuhn lengths) represented by each spring. This dimensionless parameter is found to govern the fluctuations around the mean extension, analogous to the conventional role of temperature. The use of an effective flexibility length to correct the model behavior is analyzed, and we have calculated bounds on the choices of this correction factor. The analytic nature of the statistical mechanical framework has also allowed for the calculation of asymptotic and universal behavior. The zero Weissenberg number rheological behavior is examined using the retarded-motion expansion coefficients of bead-spring chains at different levels of coarse-graining. The results show the trade-off between using too few or too many springs. The general framework to analyze the force-extension and rheological behavior is applied to the worm-like chain, FENE, and Fraenkel models. We introduce a new method for coarse-graining a polymer into a bead-spring chain called the Polymer Ensemble Transformation (PET) method. Application to the freely jointed chain polymer yields a set of spring force-laws called the Random Walk Spring (RWS) model. This new method illustrates why the previous spring force-laws cannot be used to finely discretize polymers and also provides new insight into how to rationally proceed in the coarse-graining of polymers into bead-spring chains. {\textcopyright} Elsevier B.V. All rights reserved.},
author = {Underhill, Patrick T. and Doyle, Patrick S.},
doi = {10.1016/j.jnnfm.2003.10.006},
file = {:Users/wenwen/Documents/MendeleyRefs/Underhill, Doyle{\_}Journal of Non-Newtonian Fluid Mechanics{\_}2004.pdf:pdf},
isbn = {0377-0257},
issn = {03770257},
journal = {J. Nonnewton. Fluid Mech.},
keywords = {Bead-spring models,Coarse-graining,Statistical mechanics},
number = {October 2003},
pages = {3--31},
title = {{On the coarse-graining of polymers into bead-spring chains}},
volume = {122},
year = {2004}
}
@article{Belitsky2015,
abstract = {We consider a two-component asymmetric simple exclusion process (ASEP) on a finite lattice with reflecting boundary conditions. For this process, which is equivalent to the ASEPwith second-class particles, we construct the repre- sentation matrices of the quantum algebraUq[gl(3)] that commute with the genera- tor. As a byproductwe prove reversibility and obtain in explicit form the reversible measure. A review of the algebraic techniques used in the proofs is given.},
archivePrefix = {arXiv},
arxivId = {arXiv:1504.06958v1},
author = {Belitsky, V. and Sch??tz, G. M.},
doi = {10.1007/s10955-015-1363-1},
eprint = {arXiv:1504.06958v1},
file = {:Users/wenwen/Documents/MendeleyRefs/Belitsky, Schtz{\_}Journal of Statistical Physics{\_}2015.pdf:pdf},
issn = {00224715},
journal = {J. Stat. Phys.},
keywords = {Asymmetric simple exclusion process,Quantum algebras,Second class particles},
number = {4},
pages = {821--842},
title = {{Quantum Algebra Symmetry of the ASEP with Second-Class Particles}},
volume = {161},
year = {2015}
}
@article{Lee2011,
archivePrefix = {arXiv},
arxivId = {arXiv:1103.4439v3},
author = {Lee, Hyun Keun and Kim, Beom Jun and Park, Hyunggyu},
doi = {10.1103/PhysRevE.84.020101},
eprint = {arXiv:1103.4439v3},
file = {:Users/wenwen/Documents/MendeleyRefs/Lee, Kim, Park{\_}Physical Review E{\_}2011.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {aug},
number = {2},
pages = {2--5},
title = {{Continuity of the explosive percolation transition}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.84.020101},
volume = {84},
year = {2011}
}
@book{DeGennes1979,
abstract = {Author index.},
author = {de Gennes, P G},
doi = {10.1016/0032-3861(81)90183-X},
file = {:Users/wenwen/Documents/MendeleyRefs/de Gennes{\_}Unknown{\_}1979.pdf:pdf},
isbn = {9780801412035},
issn = {00323861},
number = {4},
pages = {565},
pmid = {1320465},
publisher = {Cornell University Press},
title = {{Scaling Concepts in Polymer Physics}},
url = {https://books.google.de/books?id=ApzfJ2LYwGUC http://linkinghub.elsevier.com/retrieve/pii/003238618190183X},
volume = {22},
year = {1979}
}
@phdthesis{Jain2008,
author = {Jain, Semant},
file = {:Users/wenwen/Documents/MendeleyRefs/Jain{\_}Unknown{\_}2008.pdf:pdf},
school = {The University of Michigan},
title = {{Brownian Dynamics Simulation of Dilute Polymer Chains}},
year = {2008}
}
@article{Stauffer1979,
author = {Stauffer, D},
file = {:Users/wenwen/Documents/MendeleyRefs/Stauffer{\_}Physics Reports{\_}1979.pdf:pdf},
journal = {Phys. Rep.},
number = {1},
pages = {1--74},
title = {{Scaling theory of percolation clusters}},
volume = {54},
year = {1979}
}
@article{Son2011,
author = {Son, Seung-Woo and Grassberger, Peter and Paczuski, Maya},
doi = {10.1103/PhysRevLett.107.195702},
file = {:Users/wenwen/Documents/MendeleyRefs/Son, Grassberger, Paczuski{\_}Physical Review Letters{\_}2011.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {nov},
number = {19},
pages = {1--5},
title = {{Percolation Transitions Are Not Always Sharpened by Making Networks Interdependent}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.107.195702},
volume = {107},
year = {2011}
}
@article{Zidovska2013,
abstract = {Chromatin structure and dynamics control all aspects of DNA biology yet are poorly understood, especially at large length scales. We developed an approach, displacement correlation spectroscopy based on time-resolved image correlation analysis, to map chromatin dynamics simultaneously across the whole nucleus in cultured human cells. This method revealed that chromatin movement was coherent across large regions (4-5 µm) for several seconds. Regions of coherent motion extended beyond the boundaries of single-chromosome territories, suggesting elastic coupling of motion over length scales much larger than those of genes. These large-scale, coupled motions were ATP dependent and unidirectional for several seconds, perhaps accounting for ATP-dependent directed movement of single genes. Perturbation of major nuclear ATPases such as DNA polymerase, RNA polymerase II, and topoisomerase II eliminated micron-scale coherence, while causing rapid, local movement to increase; i.e., local motions accelerated but became uncoupled from their neighbors. We observe similar trends in chromatin dynamics upon inducing a direct DNA damage; thus we hypothesize that this may be due to DNA damage responses that physically relax chromatin and block long-distance communication of forces.},
author = {Zidovska, Alexandra and Weitz, David a and Mitchison, Timothy J},
doi = {10.1073/pnas.1220313110},
file = {:Users/wenwen/Documents/MendeleyRefs/Zidovska, Weitz, Mitchison{\_}Proceedings of the National Academy of Sciences of the United States of America{\_}2013.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
keywords = {Chromatin,Chromatin: metabolism,Green Fluorescent Proteins,Green Fluorescent Proteins: metabolism,HeLa Cells,Histones,Histones: metabolism,Humans,Interphase,Models,Molecular,Spectrum Analysis},
month = {sep},
number = {39},
pages = {15555--15560},
pmid = {24019504},
title = {{Micron-scale coherence in interphase chromatin dynamics}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24019504 http://www.pnas.org/cgi/doi/10.1073/pnas.1220313110},
volume = {110},
year = {2013}
}
@article{Paschek2001,
author = {Paschek, D. and Krishna, R.},
doi = {10.1039/b101982l},
file = {:Users/wenwen/Documents/MendeleyRefs/Paschek, Krishna{\_}Physical Chemistry Chemical Physics{\_}2001.pdf:pdf},
isbn = {14639076},
issn = {14639076},
journal = {Phys. Chem. Chem. Phys.},
number = {15},
pages = {3185--3191},
title = {{Kinetic Monte Carlo simulations of transport diffusivities of binary mixtures in zeolites}},
volume = {3},
year = {2001}
}
@article{Hsu2011,
abstract = {In this review, we describe applications of the pruned-enriched Rosenbluth method (PERM), a sequential Monte Carlo algorithm with resampling, to various problems in polymer physics. PERM produces samples according to any given prescribed weight distribution, by growing configurations step by step with controlled bias, and correcting "bad" configurations by "population control". The latter is implemented, in contrast to other population based algorithms like e.g. genetic algorithms, by depth-first recursion which avoids storing all members of the population at the same time in computer memory. The problems we discuss all concern single polymers (with one exception), but under various conditions: Homopolymers in good solvents and at the {\$}\backslashTheta{\$} point, semi-stiff polymers, polymers in confining geometries, stretched polymers undergoing a forced globule-linear transition, star polymers, bottle brushes, lattice animals as a model for randomly branched polymers, DNA melting, and finally -- as the only system at low temperatures, lattice heteropolymers as simple models for protein folding. PERM is for some of these problems the method of choice, but it can also fail. We discuss how to recognize when a result is reliable, and we discuss also some types of bias that can be crucial in guiding the growth into the right directions.},
archivePrefix = {arXiv},
arxivId = {1107.1214},
author = {Hsu, Hsiao Ping and Grassberger, Peter},
doi = {10.1007/s10955-011-0268-x},
eprint = {1107.1214},
file = {:Users/wenwen/Documents/MendeleyRefs/Hsu, Grassberger{\_}Journal of Statistical Physics{\_}2011.pdf:pdf},
issn = {00224715},
journal = {J. Stat. Phys.},
keywords = {Chain growth,Lattice animals,Phase transitions,Polymers,Population control,Protein folding},
pages = {597--637},
title = {{A Review of Monte Carlo Simulations of Polymers with PERM}},
volume = {144},
year = {2011}
}
@article{Bonilla1992,
author = {Bonilla, Luis L. and Neu, John C. and Spigler, Renato},
doi = {10.1007/BF01049037},
file = {:Users/wenwen/Documents/MendeleyRefs/Bonilla, Neu, Spigler{\_}Journal of Statistical Physics{\_}1992.pdf:pdf},
issn = {0022-4715},
journal = {J. Stat. Phys.},
keywords = {1,a long-standing intellectual aspiration,bifurcation,bimodal distribution,i n t r,in m a n,is to under-,mean-field model,nonlinear oscillators,nonlinear stability,o d u c,synchronization,t i o n,y fields of science},
month = {apr},
number = {1-2},
pages = {313--330},
title = {{Nonlinear stability of incoherence and collective synchronization in a population of coupled oscillators}},
url = {http://www.springerlink.com/index/10.1007/BF01049037},
volume = {67},
year = {1992}
}
@article{Pazo2006,
author = {Paz{\'{o}}, Diego and Montbri{\'{o}}, Ernest},
doi = {10.1103/PhysRevE.73.055202},
file = {:Users/wenwen/Documents/MendeleyRefs/Paz{\'{o}}, Montbri{\'{o}}{\_}Physical Review E{\_}2006.pdf:pdf},
issn = {1539-3755},
journal = {Phys. Rev. E},
month = {may},
number = {5},
pages = {055202},
title = {{Universal behavior in populations composed of excitable and self-oscillatory elements}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.73.055202},
volume = {73},
year = {2006}
}
@incollection{Ronceret2007,
abstract = {Somatic embryogenesis is a complex developmental program in which somatic cells are induced for a commitment towards forming totipotent embryogenic cells capable of becoming complete plants. Plant somatic embryogenesis has been the choice model system to explore the earliest regulatory and morphogenetic events in the life of the plant. Somatic embryos are similar to zygotic embryos and undergo almost the same developmental stages except for the acquisition of embryogenic competence. Common regulatory mechanisms probably operate in the early stages in both types of embryogenesis and hence it is possible to investigate somatic embryogenesis either by analysis of the expression of genes (isolated and characterized in zygotic embryos) in somatic embryos or by analyzing the differential expression of genes in embryogenic and nonembryogenic tissues. Studies have been conducted either to identify the genes expressed and gene products that accumulate specifically during different stages of embryogenesis or to analyze the expression of a variety of genes that probably have some role in the embryogenic pathway. More often this has involved the comparison of somatic embryos, embryogenic callus or cells and embryos at an early stage. This review will cover the aspects outlined above and discuss current information.},
author = {Ronceret, Arnaud and Sheehan, Moira J. and Pawlowski, Wojciech P.},
booktitle = {Somat. Embryog.},
doi = {10.1007/7089_2007_124},
file = {:Users/wenwen/Documents/MendeleyRefs/Ronceret, Sheehan, Pawlowski{\_}Somatic Embryogenesis{\_}2007.pdf:pdf},
isbn = {9783540734864},
issn = {10010602},
number = {October},
pages = {103--124},
pmid = {17148785},
title = {{Chromosome Dynamics in Meiosis}},
url = {http://link.springer.com/10.1007/7089{\_}2007{\_}124},
year = {2007}
}
@article{Radicchi2009,
author = {Radicchi, Filippo and Fortunato, Santo},
doi = {10.1103/PhysRevLett.103.168701},
file = {:Users/wenwen/Documents/MendeleyRefs/Radicchi, Fortunato{\_}Physical Review Letters{\_}2009.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {oct},
number = {16},
pages = {1--4},
title = {{Explosive Percolation in Scale-Free Networks}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.103.168701},
volume = {103},
year = {2009}
}
@article{Physics1994,
abstract = {Brownian systems with stiff elastic bonds of nearly constant length, such as long chain polymer molecules, behave differently when the stiff bonds are replaced by rigid bonds of exactly constant length, i.e. in statistical mechanics real stiff systems cannot be idealized by theoretical rigid ones. It is shown that a potential force can be applied to the rigidly constrained system in order to make it behave like the limit of a very stiff elastic system. A simple explicit expression for the required potential, suitable for computer simulations of the Brownian motion, is given for general constraints and also in the particular case of a trumbbell or trimer.},
author = {Hinch, E. J.},
doi = {10.1017/S0022112094001746},
file = {:Users/wenwen/Documents/MendeleyRefs/Hinch{\_}Journal of Fluid Mechanics{\_}1994.pdf:pdf;:Users/wenwen/Documents/MendeleyRefs/Hinch{\_}Journal of Fluid Mechanics{\_}1994.pdf:pdf},
isbn = {0022-1120},
issn = {0022-1120},
journal = {J. Fluid Mech.},
pages = {219},
title = {{Brownian motion with stiff bonds and rigid constraints}},
url = {http://journals.cambridge.org/abstract{\_}S0022112094001746},
volume = {271},
year = {1994}
}
@article{Crampe2010c,
abstract = {We present a generalization of the coordinate Bethe ansatz that allows us to solve integrable open XXZ and ASEP models with non-diagonal boundary matrices, provided their parameters obey some relations. These relations extend the ones already known in the literature in the context of algebraic or functional Bethe ansatz. The eigenvectors are represented as sums over cosets of the {\$}BC{\_}n{\$} Weyl group.},
archivePrefix = {arXiv},
arxivId = {1009.4119},
author = {Cramp{\'{e}}, Nicolas and Ragoucy, Eric and Simon, Damien},
doi = {10.1088/1742-5468/2010/11/P11038},
eprint = {1009.4119},
file = {:Users/wenwen/Documents/MendeleyRefs/Cramp{\'{e}}, Ragoucy, Simon{\_}Journal of Statistical Mechanics Theory and Experiment{\_}2010.pdf:pdf},
issn = {1742-5468},
journal = {J. Stat. Mech. Theory Exp.},
number = {11},
pages = {P11038},
title = {{Eigenvectors of open XXZ and ASEP models for a class of non-diagonal boundary conditions}},
url = {http://arxiv.org/abs/1009.4119},
volume = {2010},
year = {2010}
}
@article{Candu2013,
author = {Candu, Constantin},
file = {:Users/wenwen/Documents/MendeleyRefs/Candu{\_}Unknown{\_}2013.pdf:pdf},
pages = {1--17},
title = {{Introduction to integrability}},
year = {2013}
}
@article{Friedman2009,
author = {Friedman, Eric J. and Landsberg, Adam S.},
doi = {10.1103/PhysRevLett.103.255701},
file = {:Users/wenwen/Documents/MendeleyRefs/Friedman, Landsberg{\_}Physical Review Letters{\_}2009.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {dec},
number = {25},
pages = {1--4},
title = {{Construction and Analysis of Random Networks with Explosive Percolation}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.103.255701},
volume = {103},
year = {2009}
}
@article{Jung2012,
author = {Jung, Youngkyun and Jeon, Chanil and Kim, Juin and Jeong, Hawoong and Jun, Suckjoon and Ha, Bae-Yeun},
doi = {10.1039/c1sm05706e},
file = {:Users/wenwen/Documents/MendeleyRefs/Jung et al.{\_}Soft Matter{\_}2012.pdf:pdf},
issn = {1744-683X},
journal = {Soft Matter},
number = {i},
pages = {2095},
title = {{Ring polymers as model bacterial chromosomes: confinement, chain topology, single chain statistics, and how they interact}},
volume = {8},
year = {2012}
}
@article{Stinchcombe1995,
abstract = {Algebraic manipulations are used to reduce a new description of stochastic dynamics and quantum spin chains involving two nonlocal operators C,D. For the symmetric hopping of hard-core particles, and its associated Heisenberg chain, the operator algebra may be written in the reduced form 2Ḋ = [[C,D],C-1], 2D2 = CDC-1D+DC-1DC. These equations are shown to describe diffusive dynamics and phase change on interchange, respectively, and to lead to Bethe ansatz equations for the spectrum of the isotropic Heisenberg chain with symmetry-breaking boundary fields. This yields new exact results for the dynamics of boundary-driven systems.},
author = {Stinchcombe, R. B. and Sch{\"{u}}tz, G. M.},
doi = {10.1103/PhysRevLett.75.140},
file = {:Users/wenwen/Documents/MendeleyRefs/Stinchcombe, Sch{\"{u}}tz{\_}Physical Review Letters{\_}1995.pdf:pdf},
issn = {0031-9007},
journal = {Phys. Rev. Lett.},
month = {jul},
number = {1},
pages = {140--143},
title = {{Application of Operator Algebras to Stochastic Dynamics and the Heisenberg Chain}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.75.140},
volume = {75},
year = {1995}
}
@article{Holme2003,
author = {Holme, Petter and Liljeros, Fredrik and Edling, Christofer and Kim, Beom},
doi = {10.1103/PhysRevE.68.056107},
file = {:Users/wenwen/Documents/MendeleyRefs/Holme et al.{\_}Physical Review E{\_}2003.pdf:pdf},
issn = {1063-651X},
journal = {Phys. Rev. E},
month = {nov},
number = {5},
pages = {056107},
title = {{Network bipartivity}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.68.056107},
volume = {68},
year = {2003}
}
@article{VanKampen1984,
author = {van Kampen, N. G.},
doi = {10.1119/1.13647},
file = {:Users/wenwen/Documents/MendeleyRefs/van Kampen{\_}American Journal of Physics{\_}1984.pdf:pdf},
issn = {00029505},
journal = {Am. J. Phys.},
number = {5},
pages = {419},
title = {{Constraints}},
url = {http://link.aip.org/link/?AJP/52/419/1{\&}Agg=doi},
volume = {52},
year = {1984}
}
@article{Wegener1980a,
abstract = {The mechanism by which homologous chromosomes pair during meiosis, as a prelude to recombination, has long been mysterious. At meiosis, the telomeres in many organisms attach to the nuclear envelope and move together to form the telomere bouquet, perhaps to facilitate the homologous search. It is believed that diffusion alone is not sufficient to account for the formation of the bouquet, and that some directed movement is also required. Here we consider the formation of the telomere bouquet in a wheat-rye hybrid both experimentally and using mathematical modelling. The large size of the wheat nucleus and wheat's commercial importance make chromosomal pairing in wheat a particularly interesting and important process, which may well shed light on pairing in other organisms. We show that, prior to bouquet formation, sister chromatid telomeres are always attached to a hemisphere of the nuclear membrane and tend to associate in pairs. We study a mutant lacking the Ph1 locus, a locus ensuring correct homologous chromosome pairing, and discover that bouquet formation is delayed in the wild type compared to the mutant. Further, we develop a mathematical model of bouquet formation involving diffusion and directed movement, where we show that directed movement alone is sufficient to explain bouquet formation dynamics.},
address = {Berlin, Heidelberg},
author = {Richards, David M. and Greer, Emma and Martin, Azahara C. and Moore, Graham and Shaw, Peter J. and Howard, Martin},
doi = {10.1371/journal.pcbi.1002812},
editor = {Noble, William Stafford},
isbn = {0021-9533 (Print)$\backslash$n0021-9533 (Linking)},
issn = {1553-7358},
journal = {PLoS Comput. Biol.},
keywords = {CELLBIO,CELLCYCLE,DIFFUSIO,FLEXIBILITY,MACROMOLECULES,SHAPE,SIZE,bouquet,chromosome,meiosis,telomere clustering},
month = {dec},
number = {12},
pages = {e1002812},
pmid = {23236272},
publisher = {Springer Berlin Heidelberg},
title = {{Quantitative Dynamics of Telomere Bouquet Formation}},
url = {http://dx.plos.org/10.1371/journal.pcbi.1002812},
volume = {8},
year = {2012}
}
@article{Tanaka2012,
author = {Tanaka, G and Morino, K and Aihara, K},
journal = {Sci. Rep.},
number = {2},
pages = {232},
title = {{Dynamical robustness in complex networks: the crucial role of low-degree nodes}},
url = {http://www.nature.com/srep/2012/120125/srep00232/full/srep00232.html?WT.mc{\_}id=FBK{\_}SciReports},
year = {2012}
}
@book{Wittenburg1977,
address = {Wiesbaden},
author = {Wittenburg, Jens},
doi = {10.1007/978-3-322-90942-8},
file = {:Users/wenwen/Documents/MendeleyRefs/Wittenburg{\_}Unknown{\_}1977.pdf:pdf},
isbn = {978-3-322-90943-5},
pages = {224},
publisher = {Vieweg+Teubner Verlag},
title = {{Dynamics of Systems of Rigid Bodies}},
url = {http://link.springer.com/10.1007/978-3-322-90942-8},
year = {1977}
}
@article{Boccaletti2006,
author = {Boccaletti, S and Latora, V and Moreno, Y and Chavez, M and Hwang, D},
doi = {10.1016/j.physrep.2005.10.009},
file = {:Users/wenwen/Documents/MendeleyRefs/Boccaletti et al.{\_}Physics Reports{\_}2006.pdf:pdf},
issn = {03701573},
journal = {Phys. Rep.},
month = {feb},
number = {4-5},
pages = {175--308},
title = {{Complex networks: Structure and dynamics}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S037015730500462X},
volume = {424},
year = {2006}
}
@article{Wiest1987,
author = {Wiest, John M. and Burdette, Steven R. Burdette and Liu, Tony W. and Bird, R. Byron},
file = {:Users/wenwen/Documents/MendeleyRefs/Wiest et al.{\_}Journal of Non-Newtonian Fluid Mechanics{\_}1987.pdf:pdf},
journal = {J. Nonnewton. Fluid Mech.},
pages = {279--295},
title = {{Effect of ring closure on rheological behavior}},
volume = {24},
year = {1987}
}
@article{Fitz2016a,
author = {Fitz, Veronika and Shin, Jaeoh and Ehrlich, Christoph and Farnung, Lucas and Cramer, Patrick and Zaburdaev, Vasily and Grill, Stephan W.},
doi = {10.1073/pnas.1602764113},
file = {:Users/wenwen/Documents/MendeleyRefs/Fitz et al.{\_}Proceedings of the National Academy of Sciences{\_}2016.pdf:pdf},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci.},
pages = {201602764},
pmid = {27791062},
title = {{Nucleosomal arrangement affects single-molecule transcription dynamics}},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1602764113},
year = {2016}
}
@article{Hajjoul2013,
abstract = {Chromosome dynamics are recognized to be intimately linked to genomic transactions, yet the physical principles governing spatial fluctuations of chromatin are still a matter of debate. Using high-throughput single-particle tracking, we recorded the movements of nine fluorescently labeled chromosome loci located on

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