http://pre.aps.org/ Recently published articles in Phys. Rev. E in the Table of Content section "Biological physics" en-us Copyright (c) 2008 The American Physical Society 2008-05-07T08:06:23-04:00 assocpub@aps.org rss@aps.org hourly 4 2008-05-07T08:06:23-04:00 rss@aps.org http://link.aps.org/doi/10.1103/PhysRevE.77.051903 Author(s): Joseph Rudnick and Tatiana Kuriabova<br/>We discuss the effects of external stress on the thermal denaturation of homogeneous DNA. Pulling double-stranded DNA at each end exerts a profound effect on the thermal denaturation, or melting, of a long segment of this molecule. We discuss the effects on this transition of a stretching force appl...<br/>[Phys. Rev. E 77, 051903] Published Mon May 05, 2008 Joseph Rudnick and Tatiana Kuriabova 2008-05-05T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.051903 Phys. Rev. E 77, 051903 text/html article Physical Review E 77 5 2008-05-05T00:00:00-04:00 051903 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.051902 Author(s): Ranjan V. Mannige and Charles L. Brooks<br/>Virus capsids are highly specific assemblies that are formed from a large number of often chemically identical capsid subunits. In the present paper we ask to what extent these structures can be viewed as mathematically tilable objects using a single two-dimensional tile. We find that spherical viru...<br/>[Phys. Rev. E 77, 051902] Published Thu May 01, 2008 Ranjan V. Mannige and Charles L. Brooks 2008-05-01T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.051902 Phys. Rev. E 77, 051902 text/html article Physical Review E 77 5 2008-05-01T00:00:00-04:00 051902 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.051901 Author(s): Sergey A. Akimov, Vladimir A. Frolov, Peter I. Kuzmin, Joshua Zimmerberg, Yuri A. Chizmadzhev, and Fredric S. Cohen<br/>Formation of rafts and other domains in cell membranes is considered as wetting of proteins by lipids. The membrane is modeled as a continuous elastic medium. Thermodynamic functions of the lipid films that wet proteins are calculated using a mean-field theory of liquid crystals as adapted to biomem...<br/>[Phys. Rev. E 77, 051901] Published Thu May 01, 2008 Sergey A. Akimov, Vladimir A. Frolov, Peter I. Kuzmin, Joshua Zimmerberg, Yuri A. Chizmadzhev, and Fredric S. Cohen 2008-05-01T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.051901 Phys. Rev. E 77, 051901 text/html article Physical Review E 77 5 2008-05-01T00:00:00-04:00 051901 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041919 Author(s): György Szabó, Attila Szolnoki, and István Borsos<br/>Formation and competition of associations are studied in a six-species ecological model where each species has two predators and two prey. Each site of a square lattice is occupied by an individual belonging to one of the six species. The evolution of the spatial distribution of species is governed ...<br/>[Phys. Rev. E 77, 041919] Published Tue Apr 29, 2008 György Szabó, Attila Szolnoki, and István Borsos 2008-04-29T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041919 Phys. Rev. E 77, 041919 text/html article Physical Review E 77 4 2008-04-29T00:00:00-04:00 041919 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041918 Author(s): Sashi Marella and G. Bard Ermentrout<br/>We describe the relationship between the shape of the phase-resetting curve (PRC) and the degree of stochastic synchronization observed between a pair of uncoupled general oscillators receiving partially correlated Poisson inputs in addition to inputs from independent sources. We use perturbation me...<br/>[Phys. Rev. E 77, 041918] Published Tue Apr 29, 2008 Sashi Marella and G. Bard Ermentrout 2008-04-29T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041918 Phys. Rev. E 77, 041918 text/html article Physical Review E 77 4 2008-04-29T00:00:00-04:00 041918 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.042902 Author(s): H. Sakaguchi and P. Woafo<br/>We study a two-dimensional reaction-diffusion equation for calcium oscillation with a pacemaker region. When the pacemaker entrains the whole system, circular waves are observed as a target pattern. However, if the pace of the pacemaker is too fast, the pulse propagation to the outer region sometime...<br/>[Phys. Rev. E 77, 042902] Published Wed Apr 23, 2008 H. Sakaguchi and P. Woafo 2008-04-23T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.042902 Phys. Rev. E 77, 042902 text/html article Physical Review E 77 4 2008-04-23T00:00:00-04:00 042902 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041917 Author(s): David Lepzelter and Jin Wang<br/>We investigated the spatial-dependent stochastic effects originating from the finite number of bicoid proteins in Drosophila melanogaster, which are crucial to cell development. We obtained an exact solution to the spatial-dependent stochastic chemical master equation and recovered the usual reactio...<br/>[Phys. Rev. E 77, 041917] Published Tue Apr 22, 2008 David Lepzelter and Jin Wang 2008-04-22T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041917 Phys. Rev. E 77, 041917 text/html article Physical Review E 77 4 2008-04-22T00:00:00-04:00 041917 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041916 Author(s): Masayo Inoue and Kunihiko Kaneko<br/>We have numerically studied chemotactic aggregation of microorganisms by introducing a model consisting of elements with intracellular dynamics, random walks with a state-dependent turnover rate, and secretion of attractant. Three phases with and without aggregation, as well as partial aggregation, ...<br/>[Phys. Rev. E 77, 041916] Published Mon Apr 21, 2008 Masayo Inoue and Kunihiko Kaneko 2008-04-21T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041916 Phys. Rev. E 77, 041916 text/html article Physical Review E 77 4 2008-04-21T00:00:00-04:00 041916 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041915 Author(s): Aaditya V. Rangan, Gregor Kovačič, and David Cai<br/>We present a kinetic theory for all-to-all coupled networks of identical, linear, integrate-and-fire, excitatory point neurons in which a fast and a slow excitatory conductance are driven by the same spike train in the presence of synaptic failure. The maximal-entropy principle guides us in deriving...<br/>[Phys. Rev. E 77, 041915] Published Fri Apr 18, 2008 Aaditya V. Rangan, Gregor Kovačič, and David Cai 2008-04-18T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041915 Phys. Rev. E 77, 041915 text/html article Physical Review E 77 4 2008-04-18T00:00:00-04:00 041915 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041914 Author(s): Jens Prusseit and Klaus Lehnertz<br/>We propose a data-driven approach to measure interdependences between dissipative dynamical systems under the influence of noise. We estimate drift and diffusion coefficients of a Fokker-Planck equation and derive measures that allow one to quantify the asymmetry in coupling in a fully automated and...<br/>[Phys. Rev. E 77, 041914] Published Fri Apr 18, 2008 Jens Prusseit and Klaus Lehnertz 2008-04-18T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041914 Phys. Rev. E 77, 041914 text/html article Physical Review E 77 4 2008-04-18T00:00:00-04:00 041914 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041913 Author(s): Lars Wolff and Benjamin Lindner<br/>Neurons are subject to synaptic inputs from many other cells. These inputs consist of spikes changing the conductivity of the target cell, i.e., they enter the neural dynamics as multiplicative shot noise. Up to now, only for simplified models like current-based (additive-noise) point neurons or mod...<br/>[Phys. Rev. E 77, 041913] Published Thu Apr 17, 2008 Lars Wolff and Benjamin Lindner 2008-04-17T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041913 Phys. Rev. E 77, 041913 text/html article Physical Review E 77 4 2008-04-17T00:00:00-04:00 041913 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041912 Author(s): Daniel J. Lacks<br/>The signal transfer from nerve to muscle occurs by diffusion across the neuromuscular junction. The continuum level analysis of diffusion processes is based on the diffusion equation, which in one dimension is ∂c∕∂t=D(∂^{2} c∕∂x^{2} ) , where c is the molecular concentration and D is the...<br/>[Phys. Rev. E 77, 041912] Published Thu Apr 17, 2008 Daniel J. Lacks 2008-04-17T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041912 Phys. Rev. E 77, 041912 text/html article Physical Review E 77 4 2008-04-17T00:00:00-04:00 041912 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041911 Author(s): Y. Wu and W. Q. Zhu<br/>A stochastic Lotka-Volterra model, a so-called pulse-type model, for the interaction between two species and their random natural environment is investigated. The effect of a random environment is modeled as random pulse trains in the birth rate of the prey and the death rate of the predator. The ge...<br/>[Phys. Rev. E 77, 041911] Published Thu Apr 17, 2008 Y. Wu and W. Q. Zhu 2008-04-17T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041911 Phys. Rev. E 77, 041911 text/html article Physical Review E 77 4 2008-04-17T00:00:00-04:00 041911 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.040901 Author(s): Max N. Artyomov, Alexander Yu. Morozov, and Anatoly B. Kolomeisky<br/>Dynamics of molecular motors that move along linear lattices and interact with them via reversible destruction of specific lattice bonds is investigated theoretically by analyzing exactly solvable discrete-state “burnt-bridge” models. Molecular motors are viewed as diffusing particles that can a...<br/><img src="http://prola.aps.org/graphics/rapid30x30.gif" width="30" height="30" alt="Rapid Communication"/><br/>[Phys. Rev. E 77, 040901] Published Thu Apr 17, 2008 Max N. Artyomov, Alexander Yu. Morozov, and Anatoly B. Kolomeisky 2008-04-17T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.040901 Phys. Rev. E 77, 040901 text/html article Physical Review E 77 4 2008-04-17T00:00:00-04:00 040901 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041910 Author(s): Eric E. Keaveny and Martin R. Maxey<br/>The artificial microswimmer [R. Dreyfus , Nature (London) 437, 862 (2005)] whose mechanism of propulsion is the magnetically driven undulation of a flagellum-like tail composed of chemically linked paramagnetic beads can be used as a physical model with which to study low-Reynolds-number swimming. U...<br/>[Phys. Rev. E 77, 041910] Published Wed Apr 16, 2008 Eric E. Keaveny and Martin R. Maxey 2008-04-16T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041910 Phys. Rev. E 77, 041910 text/html article Physical Review E 77 4 2008-04-16T00:00:00-04:00 041910 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041909 Author(s): Y. Morishita and Y. Iwasa<br/>During development, cells grow, differentiate, divide, and die according to their spatial positions, yet the positional information given to cells by morphogens (diffusive chemicals) includes considerable noises from various origins. In this paper, we examine a relationship between fluctuations in m...<br/>[Phys. Rev. E 77, 041909] Published Wed Apr 16, 2008 Y. Morishita and Y. Iwasa 2008-04-16T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041909 Phys. Rev. E 77, 041909 text/html article Physical Review E 77 4 2008-04-16T00:00:00-04:00 041909 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041908 Author(s): Xiao-Qin Cao, Jia Zeng, and Hong Yan<br/>The capacity of transcription factors to activate gene expression is encoded in the promoter sequences, which are composed of short regulatory motifs that function as transcription factor binding sites (TFBSs) for specific proteins. To the best of our knowledge, the structural property of TFBSs that...<br/>[Phys. Rev. E 77, 041908] Published Tue Apr 15, 2008 Xiao-Qin Cao, Jia Zeng, and Hong Yan 2008-04-15T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041908 Phys. Rev. E 77, 041908 text/html article Physical Review E 77 4 2008-04-15T00:00:00-04:00 041908 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041907 Author(s): Hu Chen and Jie Yan<br/>We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible polymer model. The defects discussed are kinks and flexible hinges...<br/>[Phys. Rev. E 77, 041907] Published Tue Apr 15, 2008 Hu Chen and Jie Yan 2008-04-15T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041907 Phys. Rev. E 77, 041907 text/html article Physical Review E 77 4 2008-04-15T00:00:00-04:00 041907 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041906 Author(s): Hristina Popova and Andrey Milchev<br/>Using a continuum bead-spring Monte Carlo model, we study the anomalous diffusion dynamics of a self-avoiding tethered membrane by means of extensive computer simulations. We focus on the subdiffusive stochastic motion of the membrane’s central node in the regime of flat membranes at temperatures ...<br/>[Phys. Rev. E 77, 041906] Published Tue Apr 15, 2008 Hristina Popova and Andrey Milchev 2008-04-15T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041906 Phys. Rev. E 77, 041906 text/html article Physical Review E 77 4 2008-04-15T00:00:00-04:00 041906 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041905 Author(s): Carl Franck, Wui Ip, Albert Bae, Nathan Franck, Elijah Bogart, and Thanhbinh Thi Le<br/>In cell culture, when cells are inoculated into fresh media, there can be a period of slow (or lag phase) growth followed by a transition to exponential growth. This period of slow growth is usually attributed to the cells’ adaptation to a new environment. However, we argue that, based on observat...<br/>[Phys. Rev. E 77, 041905] Published Fri Apr 11, 2008 Carl Franck, Wui Ip, Albert Bae, Nathan Franck, Elijah Bogart, and Thanhbinh Thi Le 2008-04-11T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041905 Phys. Rev. E 77, 041905 text/html article Physical Review E 77 4 2008-04-11T00:00:00-04:00 041905 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.042901 Author(s): Pavel Gorodetsky and Emmanuel Tannenbaum<br/>This Brief Report studies the quasispecies dynamics of a population capable of genetic repair evolving on a time-dependent fitness landscape. We develop a model that considers an asexual population of single-stranded, conservatively replicating genomes, whose only source of genetic variation is due ...<br/>[Phys. Rev. E 77, 042901] Published Thu Apr 10, 2008 Pavel Gorodetsky and Emmanuel Tannenbaum 2008-04-10T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.042901 Phys. Rev. E 77, 042901 text/html article Physical Review E 77 4 2008-04-10T00:00:00-04:00 042901 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041904 Author(s): C. B. Korn and U. S. Schwarz<br/>Motivated by rolling adhesion of white blood cells in the vasculature, we study how cells move in linear shear flow above a wall to which they can adhere via specific receptor-ligand bonds. Our computer simulations are based on a Langevin equation accounting for hydrodynamic interactions, thermal fl...<br/>[Phys. Rev. E 77, 041904] Published Thu Apr 10, 2008 C. B. Korn and U. S. Schwarz 2008-04-10T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041904 Phys. Rev. E 77, 041904 text/html article Physical Review E 77 4 2008-04-10T00:00:00-04:00 041904 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041903 Author(s): Eldon Emberly<br/>In multicellular organisms, the initial patterns of gene expression are regulated by spatial gradients of biochemical factors, known as morphogen gradients. Because of biochemical noise in the morphogen gradients there are associated spatial errors in the positions of target gene patterns. Using a s...<br/>[Phys. Rev. E 77, 041903] Published Tue Apr 08, 2008 Eldon Emberly 2008-04-08T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041903 Phys. Rev. E 77, 041903 text/html article Physical Review E 77 4 2008-04-08T00:00:00-04:00 041903 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041902 Author(s): Stefan P. Hau-Riege and Henry N. Chapman<br/>Atomic-resolution diffraction imaging of biological particles using x-ray free-electron lasers (XFELs) at 1 Å wavelength requires a detailed understanding of the photon-induced damage processes. We discuss how several aspects of existing continuum damage models can be tested during early operation ...<br/>[Phys. Rev. E 77, 041902] Published Tue Apr 01, 2008 Stefan P. Hau-Riege and Henry N. Chapman 2008-04-01T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041902 Phys. Rev. E 77, 041902 text/html article Physical Review E 77 4 2008-04-01T00:00:00-04:00 041902 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.041901 Author(s): Diana Clausznitzer, Benjamin Lindner, Frank Jülicher, and Pascal Martin<br/>Hair cells perform the mechanoelectrical transduction of sound signals in the auditory and vestibular systems of vertebrates. The part of the hair cell essential for this transduction is the so-called hair bundle. In vitro experiments on hair cells from the sacculus of the American bullfrog have sho...<br/>[Phys. Rev. E 77, 041901] Published Tue Apr 01, 2008 Diana Clausznitzer, Benjamin Lindner, Frank Jülicher, and Pascal Martin 2008-04-01T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.041901 Phys. Rev. E 77, 041901 text/html article Physical Review E 77 4 2008-04-01T00:00:00-04:00 041901 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.032901 Author(s): F. de los Santos, Omar Al Hammal, and Miguel A. Muñoz<br/>A simple Langevin approach is used to study stationary properties of the Peyrard-Bishop-Dauxois model for DNA, allowing known properties to be recovered in an easy way. Results are shown for the denaturation transition in homogeneous samples, for which some implications, so far overlooked, of an ana...<br/>[Phys. Rev. E 77, 032901] Published Mon Mar 31, 2008 F. de los Santos, Omar Al Hammal, and Miguel A. Muñoz 2008-03-31T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.032901 Phys. Rev. E 77, 032901 text/html article Physical Review E 77 3 2008-03-31T00:00:00-04:00 032901 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.031924 Author(s): Steven P. Mielke, Niels Grønbech-Jensen, and Craig J. Benham<br/>Numerical models of mesoscale DNA dynamics relevant to in vivo scenarios require methods that incorporate important features of the intracellular environment, while maintaining computational tractability. Because the explicit inclusion of ions leads to electrostatic calculations that scale as the sq...<br/>[Phys. Rev. E 77, 031924] Published Mon Mar 31, 2008 Steven P. Mielke, Niels Grønbech-Jensen, and Craig J. Benham 2008-03-31T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.031924 Phys. Rev. E 77, 031924 text/html article Physical Review E 77 3 2008-03-31T00:00:00-04:00 031924 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.031923 Author(s): Changhui Li, Manojit Pramanik, Geng Ku, and Lihong V. Wang<br/>We report an intrinsic image distortion in microwave-induced thermoacoustic tomography. The distortion, due to microwave diffraction in the object to be imaged, leads to nonuniform excitation of acoustic pressure during microwave illumination. Both numerical simulations and phantom experiments demon...<br/>[Phys. Rev. E 77, 031923] Published Fri Mar 28, 2008 Changhui Li, Manojit Pramanik, Geng Ku, and Lihong V. Wang 2008-03-28T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.031923 Phys. Rev. E 77, 031923 text/html article Physical Review E 77 3 2008-03-28T00:00:00-04:00 031923 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.031922 Author(s): Bo Han and Jin Wang<br/>From a study of the budding yeast cell cycle, we found that the cellular network evolves to have the least cost for realizing its biological function. We quantify the cost in terms of the dissipation or heat loss characterized through the steady-state properties: the underlying landscape and the ass...<br/>[Phys. Rev. E 77, 031922] Published Thu Mar 27, 2008 Bo Han and Jin Wang 2008-03-27T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.031922 Phys. Rev. E 77, 031922 text/html article Physical Review E 77 3 2008-03-27T00:00:00-04:00 031922 Biological physics Biological physics http://link.aps.org/doi/10.1103/PhysRevE.77.031921 Author(s): Tatiana Kuriabova and Alex J. Levine<br/>We study the microrheology of nanoparticle shells [A. D. Dinsmore , Science 298, 1006 (2002)] and viral capsids [I. L. Ivanovska , Proc. Natl. Acad. Sci. U.S.A. 101, 7600 (2004)] by computing the mechanical response function and thermal fluctuation spectrum of a viscoelastic spherical shell that is ...<br/>[Phys. Rev. E 77, 031921] Published Thu Mar 27, 2008 Tatiana Kuriabova and Alex J. Levine 2008-03-27T00:00:00-04:00 Personal use only, all commercial or other reuse prohibited 10.1103/PhysRevE.77.031921 Phys. Rev. E 77, 031921 text/html article Physical Review E 77 3 2008-03-27T00:00:00-04:00 031921 Biological physics Biological physics