http://www.bibsonomy.org/burst/user/statphys23/molecularBibSonomy BuRST Feed for /user/statphys23/molecular2008-07-21T01:42:28+02:00http://www.bibsonomy.org/bibtex/2fbf9edf2d04659a3f50ace0a4a169e0b/statphys23statphys232007-06-20T10:16:09+02:00kinetic dynamics boltzmann molecular coefficients topic-7 restitution gases theory statphys23 granular equation <span style="color:#555555;">N.V. <a href="http://www.bibsonomy.org/author/Brilliantov">Brilliantov</a> and T. <a href="http://www.bibsonomy.org/author/Poeschel">Poeschel</a> and W.T. <a href="http://www.bibsonomy.org/author/Kranz">Kranz</a> and A. <a href="http://www.bibsonomy.org/author/Zippelius">Zippelius</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyTranslations and Rotations Are Correlated in Granular Gases2007kinetic dynamics boltzmann molecular coefficients topic-7 restitution gases theory statphys23 granular equation In a granular gas of rough particles the axis of rotation is shown to be correlated with the translational velocity of the particles. The average relative orientation of angular and linear velocities depends on the restitution coefficients -- the parameters which characterize the dissipative nature of the collision [1,2]. Using the Boltzmann equation and pseudo-Liouville operator technique [1,3] we derive a simple analytical theory for these correlations. We also perform numerical simulations for a wide range of coefficients of normal and tangential restitution. Two different numerical methods were used: Direct simulation Monte Carlo (DSMC) [4] and event-driven molecular dynamics (MD). Surprisingly, the limit of smooth spheres was found to be singular: even an arbitrarily small roughness of the particles gives rise to orientational correlations. The results of the analytical theory are in a good agreement with the numerical simulations [5]. 1) N.V. Brilliantov and T. Poeschel, Kinetic Theory of Granular Gases (Oxford University Press, Oxford, 2004).\\ 2) T. Poeschel, and N.V. Brilliantov (Eds.), Granular Gas Dynamics, Lecture Notes in Physics, vol. 624, Springer (2003).\\ 3) T. Aspelmeier, M. Huthmann, and A. Zippelius, in Granular Gases, S. Luding and T. Poeschel (Eds), Lecture Notes in Physics vol. 425, Springer, Berlin, (2000), p. 680.\\ 4) T. Poeschel and T. Schwager, Computational Granular Dynamics (Springer, New York, 2005).\\ 5) N.V. Brilliantov, T. Poeschel, W.T. Kranz, and A. Zippelius, Phys. Rev. Lett., 98, (2007) 128001.http://www.bibsonomy.org/bibtex/2923a24d50839e1869fc99f92073b5eb2/statphys23statphys232007-06-20T10:16:09+02:00statphys23 dynamin motors molecular protein-membrane interaction topic-10 <span style="color:#555555;">M. <a href="http://www.bibsonomy.org/author/Lenz">Lenz</a> and J.F. <a href="http://www.bibsonomy.org/author/Joanny">Joanny</a> and J. <a href="http://www.bibsonomy.org/author/Prost">Prost</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyDynamin as a molecular motor: a thermodynamic study2007statphys23 dynamin motors molecular protein-membrane interaction topic-10 Dynamin is a GTPase implicated in the severing of cell membrane during endocytosis. Recent in vitro experiments have shown that it is a molecular motor: when polymerized in a helical shape around a membrane nanotube, it can drag a polystyrene bead along with its rotation and form supercoils. We model the dynamin-membrane assembly in order to extract information from this and future experimental data about the mechanical mode of action of dynamin, a topic still under debate. Our first results concern the long dynamin/membrane tubes used in in vitro experiments: their dynamics is dominated by the relaxation of the membrane and dynamin helix deformations through helix-membrane friction. Little is known about this mechanism on the molecular level, but our coarse-grained out-of-equilibrium thermodynamical approach allows us to characterize it. This model and data from ongoing experiments in Institut Curie should allow us to know more about the role of dynamin in endocytosis.http://www.bibsonomy.org/bibtex/23607e7ca13743104cc53691e751730df/statphys23statphys232007-06-20T10:16:09+02:00motors statphys23 non-markovian molecular topic-10 exclusion process effects <span style="color:#555555;">T. <a href="http://www.bibsonomy.org/author/Antal">Antal</a> and P.L. <a href="http://www.bibsonomy.org/author/Krapivsky">Krapivsky</a> and K. <a href="http://www.bibsonomy.org/author/Mallick">Mallick</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyExactly solvable models of molecular spiders2007motors statphys23 non-markovian molecular topic-10 exclusion process effects Molecular spiders are synthetic bio-molecular systems with ``legs'' made of short single-stranded segments of DNA. Spiders move on a surface covered by single-stranded DNA segments complementary to the legs, and the legs can attach to them. When a leg detaches from a segment on the surface, it can attach to a neighboring segment, and the spider moves. The motion of the legs is modeled by particles hopping to nearest neighbor sites on a one or two dimensional lattice. In addition to particle exclusion, we consider two types of constraints: either any two neighboring legs (local rule), or any two legs (global rule) have to stay within a given distance to each other. In one dimension, the spiders can be mapped exactly to the Exclusion Process for both local and global constraints. These mappings lead to simple exact results for the speed and the diffusion coefficient of the spiders. In experiments, each site is altered when first visited by a leg, and the legs leave these sites faster at subsequent visits. Hence the proper description of the spider's motion requires the knowledge of its entire trajectory. Even in this non-Markovian case, for certain types of spiders we obtained exact results for the experimentally interesting number of visited sites as a function of time. Interesting phenomena associated with driven spiders, asymmetric gaits, interacting and two dimensional spiders will also be discussed.http://www.bibsonomy.org/bibtex/2268992c81f0c024a85085ce438d68cd0/statphys23statphys232007-06-20T10:16:09+02:00statphys23 lucas-washburn filling capillary molecular equation dynamics topic-6 <span style="color:#555555;">D.I. <a href="http://www.bibsonomy.org/author/Dimitrov">Dimitrov</a> and A. <a href="http://www.bibsonomy.org/author/Milchev">Milchev</a> and K. <a href="http://www.bibsonomy.org/author/Binder">Binder</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyCapillary Rise in Nanopores: Molecular Dynamics Evidence for the Lucas-Washburn Equation2007statphys23 lucas-washburn filling capillary molecular equation dynamics topic-6 When a capillary is inserted into a liquid, the liquid will rapidly flow into it. This phenomenon, well studied and understood on the macroscale, is investigated by Molecular Dynamics simulations for coarse-grained models of nanotubes. Both a simple Lennard-Jones fluid and a model for a polymer melt are considered. In both cases after a transient period (of a few nanoseconds) the meniscus rises according to a square-root-of-time law. For the polymer melt, however, we find that the capillary flow exhibits a slip length, comparable in size with the nanotube radius R. We show that a consistent description of the imbibition process in nanotubes is only possible upon modification of the Lucas-Washburn law which takes explicitly into account the slip length. We also demonstrate that the velocity field of the rising fluid close to the interface is not a simple diffusive spreading.http://www.bibsonomy.org/bibtex/29db770b3e327cd9b24156428f3aceb2b/statphys23statphys232007-06-20T10:16:09+02:00one-molecule thermodynamics model maxwell demon statphys23 state topic-1 equation molecular motors szilard paradox <span style="color:#555555;">T. <a href="http://www.bibsonomy.org/author/Hondou">Hondou</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyEquation of state in a small system: Violation of an assumption of Maxwell's demon2007one-molecule thermodynamics model maxwell demon statphys23 state topic-1 equation molecular motors szilard paradox An equation of state for an ideal gas with a small number of particles is studied. The equation of state is a basis both for studies of Maxwell's demon paradox [since Szilard (1929), including Landauer's principle] and for the proper interpretation and modeling of one-molecule experiment in biophysics. It has been assumed, even for the studies in Maxwell's demon, conventional equation of state, $PV=nRT$ holds for systems of small number of particles (for review, see {\em Maxwell's Demon 2} by Leff and Rex, IOP Publishing, 2003). We study the validity of the equation of state in small systems toward the construction of one-molecule thermodynamics. We consider a one-dimensional piston in thermal equilibrium, where the dynamical variables are $N$ thermal particles and a movable piston on one side (Figure 1). In systems of small number of particles, coarse-grained variable, $P$ (pressure) in the equation of state is no longer well-defined. Thus we discuss the validity of the equation of state in the following form, $f X=N k_{\rm B} T$, in which $f$, $X$ are a mechanical force externally exerted on the movable piston and a distance between the bottom and the movable piston, respectively (Fig. 1). In order to discuss the validity of the equation of state, we first discuss the extreme case of one thermal molecule in the piston, where the total energy of the system is written as $E=\frac{p_{\rm t}^{2}}{2m} + \frac{p_{\rm p}^{2}}{2M} + f X$, where $m (p_{\rm t}) $ and $M (p_{\rm p})$ are the masses (momenta) of the thermal particle and the piston, respectively. To keep the system isothermal, a thermal wall is introduced. The particle is reflected with a positive random velocity according to Maxwell's velocity distribution at the bottom of the piston. One naively expects that the equation of state for one molecule should be obtained by replacing $N$ by $1$ in the reference equation $f X = N k_{\rm B} T$; namely $f X = k_{\rm B} T$. The extension of conventional thermodynamics into those of one molecule has been naively performed since Szilard (Z. Phys. {\bf 53} p.840, 1929) until now. We found through numerical simulation, however, that the equation of state for one molecule is in fact $f \langle X \rangle = 2 k_{\rm B} T $, where the angular brackets indicate an average value. This result is obviously different from that which is conventionally assumed. We obtained the same analytical result using the Master equation of the distribution function in a phase space, which consists of Liouville terms and collision terms. A stochastic boundary condition is applied for the system at one end, which corresponds to the thermal wall in the numerical simulation. From straightforward calculation, one obtains a stationary solution, $\rho (x, p_{\rm t}, X, p_{\rm p}) = \frac{f^2}{2 \pi (k_{\rm B} T)^3 \sqrt{mM}} \exp\{-(\frac{p_{\rm t}^{2}/2m + p_{\rm p}^2 /2M + f X }{k_{\rm B} T}) \} \theta (X-x) ,$ where $\theta$ is a Heaviside step function. From this equation, we again obtain the same equation of state as by the numerical simulation. The result is independent of the masses of both the thermal particle and the movable piston, which is in contrast to the result by Hatano-Sasa (Prog. Theor. Phys. {\bf 100} p.695, 1998). Although we introduced a thermal wall and, correspondingly, a stochastic boundary condition, one may obtain the same generalized result for any number of thermal particles, N, without applying such boundary conditions, but instead using conventional Gibbs' statistical mechanics. The result is found to be the same as the conventional equation of state in the thermodynamic limit ($N \rightarrow \infty$). Impact of our finding on the studies of Maxwell's demon (Szilard's and the followers', including Landauer's) and on one-molecule experiments in biophysics will be discussed in the conference.http://www.bibsonomy.org/bibtex/2f390b2941dc3dc16c361970c437de17d/statphys23statphys232007-06-20T10:16:09+02:00statphys23 dynamics self-condensation polyelectrolyte topic-7 counterion interaction simulations molecular electrostatic condensation <span style="color:#555555;">H. <a href="http://www.bibsonomy.org/author/Takano">Takano</a> and I. <a href="http://www.bibsonomy.org/author/Baba">Baba</a> and D. <a href="http://www.bibsonomy.org/author/Kubota">Kubota</a> and S. <a href="http://www.bibsonomy.org/author/Miyashita">Miyashita</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyCounterion Condensation and Self-Condensation of Single Polyelectrolytes2007statphys23 dynamics self-condensation polyelectrolyte topic-7 counterion interaction simulations molecular electrostatic condensation \par For a highly charged polyelectrolyte, counterions are known to condense onto the polyelectrolyte. Moreover, under certain conditions, the polyelectrolyte itself condenses. In this study, the relation between the the counterion condensation and the conditions for the self-condensation of single polyelectrolytes is studied by performing molecular dynamics simulations of a single flexible polyelectrolyte. We consider a system consisting of a polyelectrolyte with $N_{\rm m}$ monomers, which is represented by a bead-spring model, and $N_{\rm c}$ counterions. The charge of each monomer is $-{e}<0$ and that of each counterion is $z_{\rm c}{e}>0$. We choose $N_{\rm m}=z_{\rm c}N_{\rm c}$. The Manning ratio $\lambda_{\rm M}=e^2/(\varepsilon ak_{\rm B}T)$ describes the strength of the electrostatic interaction relative to the thermal energy. Here, $\varepsilon$, $a$, $k_{\rm B}$ and $T$ are the dielectric constant of the solvent, the distance between two consecutive monomers, the Boltzmann constant and the temperature of the system, respectively. Note that $\lambda_{\rm M}=0$ corresponds to the case of the neutral polymer. The simulations are performed for various values of $\varepsilon$ at a constant temperature $T$ by using the Langevin-type equations of motion, where $N_{\rm m}=24,48$ and $96$ and $z_{\rm c}=1,2,3$ and $4$. \par As $\lambda_{\rm M}$ is increased from zero, the mean square average $\langle R_{\rm e}^2 \rangle$ of the end-to-end distance of the polyelectrolyte first increases and then decreases after reaching a maximum value. See Fig.\ 1. The increase is due to the increase of the strength of the repulsive electrostatic interaction between the monomers. Screening of this repulsive interaction by the counterions condensed onto the polyelectrolyte causes the decrease in $\langle R_{\rm e}^2\rangle$. For large values of $\lambda_{\rm M}$, $\langle R_{\rm e}^2\rangle$ is smaller than that for $\lambda_{\rm M}=0$, which signals the self-condensation of the polyelectrolyte. Note that the self-condensation can occur independent of the counterion valence. The self-condensation implies the existence of an effective attractive interaction among the monomers. If the repulsive interaction between the monomers is counterbalanced with the effective attractive interaction, the polyelectrolyte is expected to behave as an ideal chain, where the ratio of $\langle R_{\rm e}^2\rangle$ to the the mean square average $\langle R_{\rm g}^2\rangle$ of the radius of gyration becomes 6. By determining the onset of the self-condensation by the condition $\langle R_{\rm e}^2\rangle /\langle R_{\rm g}^2\rangle =6$, it is found that the self-condensation occurs when about 90\% of the charge of the polyelectrolyte is neutralized by the condensed counterions, which agrees with the experimental fact. It is also found that $\langle R_{\rm e}^2\rangle$ takes its maximum value when about 13\% of the charge of the polyelectrolyte is neutralized.http://www.bibsonomy.org/bibtex/2385216219fee94c168b82eb7987bbb1b/statphys23statphys232007-06-20T10:16:09+02:00simulations statphys23 interfaces topic-7 dynamics polymeric nonequilibrium microfluidics molecular <span style="color:#555555;">C. <a href="http://www.bibsonomy.org/author/Pastorino">Pastorino</a> and K. <a href="http://www.bibsonomy.org/author/Binder">Binder</a> and M. <a href="http://www.bibsonomy.org/author/Mueller">Mueller</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyMolecular dynamics study of the flow properties of a polymeric liquid confined by a soft substrate2007simulations statphys23 interfaces topic-7 dynamics polymeric nonequilibrium microfluidics molecular We studied the flow properties of a polymer melt confined between polymer brush layers, by means of molecular dynamics simulations. The brush serves as a model of a soft, deformable and elastic substrate whose properties are tuned in the simulation changing the grafting density. Brush and polymer melt are composed of bead-spring chains of identical chemical identity and modeled with well-established coarse-grained potentials that retain the main properties of the chains. The temperature is held constant with a Dissipative Particle Dynamics thermostat that keeps the hydrodynamic correlations in the system. Moving the confining walls at constant velocity or applying an external volume force, Couette and Poiseuille flows are imposed to the system and the velocity and density profiles are obtained from the simulations, as a function of shear rate or external force. Boundary conditions (slip length and velocity) of this non-newtonian liquid are measured directly from the simulations, as function of the grafting density of the brush layer. The characteristics of the brush-melt interface, morphology and dynamics of the chains are also obtained. We observe an interesting inversion of the flow velocity in the vicinity of the brush-melt interface, due to non-trivial cyclic dynamics of the grafted chains.http://www.bibsonomy.org/bibtex/2bdcb6d6c6d0f9475e9cac263a67b7b48/statphys23statphys232007-06-20T10:16:09+02:00topic-10 statphys23 folding discrete alzheimer protein molecular dynamics disease amyloid <span style="color:#555555;">A.R. <a href="http://www.bibsonomy.org/author/Lam">Lam</a> and B. <a href="http://www.bibsonomy.org/author/Urbanc">Urbanc</a> and H.E. <a href="http://www.bibsonomy.org/author/Stanley">Stanley</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 July{\bf In Silico} Studies of Alzheimer $\beta$-protein A$\beta$ Folding2007topic-10 statphys23 folding discrete alzheimer protein molecular dynamics disease amyloid Pathological folding and oligomerization of amyloid $\beta$-protein (A$\beta$) are widely perceived as central to Alzheimer's disease (AD). A$\beta$ exists in two alloforms, A$\beta$40 and A$\beta$42, of which A$\beta$42 is linked particularly strongly to AD. Here we apply a discrete molecular dynamics approach and a four-bead protein model with backbone hydrogen bonding and residue-specific effective hydropathic and electrostatic interactions (EIs) to study temperature dependence of A$\beta$40 and A$\beta$42 folding at different strengths of EIs. Our results show that at low temperatures both A$\beta$40 and A$\beta$42 monomers adopt a predominantly collapsed--coil conformation with a small $\alpha$-helical component. At higher temperatures, the $\beta$-strand structure becomes more prominent in both alloform. A$\beta$42 monomer conformation is characterized by a larger number of $\beta$-strands than A$\beta$40 conformation. The temperature dependence of the A$\beta$ folded structure is in a good agreement with recent experimental findings. At all temperatures, folded structures of A$\beta$40 and A$\beta$42 show differences in the N-terminal and C-terminal regions. The folded A$\beta$42 monomer has an additional turn structure at the C-terminus not present in A$\beta$40, consistent with recent {\it in vitro} findings. By varying the strength of EIs, we examine the A$\beta$40 and A$\beta$42 conformational changes due to a change in pH. At the highest strength of EIs, the folded structures of A$\beta$40 and A$\beta$42 have the highest amount of $\beta$-strand structure, while more globular conformations are observed at the lowest strength of EIs. Our results demonstrate that A$\beta$ folding is strongly sensitive to both temperature and pH variations, suggesting a possibility of different aggregation pathways at slightly different external conditions.http://www.bibsonomy.org/bibtex/22534175dd73fa36e16e7ef8a81b5ecd2/statphys23statphys232007-06-20T10:16:09+02:00liquids glass energy statphys23 molecular dynamics transition supercooled landscape topic-9 <span style="color:#555555;">D. <a href="http://www.bibsonomy.org/author/Coslovich">Coslovich</a> and G. <a href="http://www.bibsonomy.org/author/Pastore">Pastore</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyFragility of supercooled Lennard-Jones mixtures at constant pressure: role of locally preferred structures and energy landscape2007liquids glass energy statphys23 molecular dynamics transition supercooled landscape topic-9 Molecular Dynamics simulations of supercooled Lennard-Jones liquids continue to provide a useful benchmark for theories and paradigms of the glass transition. A minimal exploration of the field of parameters of the Lennard-Jones potential for binary mixtures reveals a rich phenomenology. In particular, we find systematic variations of fragility in different mixtures, i.e. a varying degree of super-Arrhenius behaviour of dynamical properties. Employing a Voronoi construction, we show that fragile behaviour in binary Lennard-Jones mixtures is associated to the growth upon supercooling of slow domains characterized by distinct microstructural features. The more fragile is the mixture, the more rapid is the increase of particles forming locally preferred structures. This behaviour is consistent with the predictions of the frustration-limited domains theory (1), in which fragility arises from the interplay between stability and frustration of locally preferred structures. Schematic models of the Potential Energy Surface are also often invoked to explain the behaviour of supercooled liquids. We adopt a simple, non-topographic approach and analyse some statistical properties of the PES, with particular focus on high-order stationary points (2). Notwithstanding the role of metabasins in the PES (3), an increase of energy barriers between single saddles appears to be a simple possible mechanism for super-Arrhenius behaviour of dynamical properties in fragile glass-formers. Further connections between fragility, vibrational properties and localization of unstable modes (4) are discussed. The two approaches together provide a simple picture of the fragile vs. strong behaviour of glass-formers, bridging the ideas of frustration in supercooled liquids and roughness of the energy landscape. (1) G. Tarjus et al., J. Phys.: Condens. Matter 17, R1182 (2005) (2) L. Angelani et al., J. Chem. Phys. 119, 2120 (2003) (3) B. Doliwa and A. Heuer, Phys. Rev. Lett. 91, 235501 (2003) (4) D. Coslovich and G. Pastore, Europhys. Lett. 75, 784 (2006)http://www.bibsonomy.org/bibtex/2abc6e217d562b64163da79b8c1d2e9aa/statphys23statphys232007-06-20T10:16:09+02:00self-driven particles motors two statphys23 topic-2 species molecular <span style="color:#555555;">R. <a href="http://www.bibsonomy.org/author/Harris">Harris</a> and H. <a href="http://www.bibsonomy.org/author/Grzeschik">Grzeschik</a> and L. <a href="http://www.bibsonomy.org/author/Santen">Santen</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyTwo species models of intracellular transport2007self-driven particles motors two statphys23 topic-2 species molecular Systems of self-driven particles combine a stochastic motion with a directional bias. This type of particle dynamics is generic for a wide range of applications including vehicular traffic and intracellular transport. In the latter case the active particles, i.e. molecular motors, perform a stepwise motion along the cellular filament network. Besides the directional bias it is important to take the finite processivity of the molecular motors into account. This realised by introducing bulk reservoirs exchanging particles with given rates. Motivated by experimental results on the interplay between molecular motors and ?-proteins we discuss the influence of a second species of particles, which does not influence the particle dynamics on the filaments but alters locally the attach rates of the motor proteins.http://www.bibsonomy.org/bibtex/20dc4311d8ce374c86367833f8c582447/statphys23statphys232007-06-20T10:16:09+02:00diffusion structural density anomaly topic-6 dynamics water statphys23 molecular <span style="color:#555555;">A.B. <a href="http://www.bibsonomy.org/author/De Oliveira">De Oliveira</a> and P.A. <a href="http://www.bibsonomy.org/author/Netz">Netz</a> and T. <a href="http://www.bibsonomy.org/author/Colla">Colla</a> and M.C. <a href="http://www.bibsonomy.org/author/Barbosa">Barbosa</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyWater anomalies and isotropic potentials2007diffusion structural density anomaly topic-6 dynamics water statphys23 molecular Water is ubiquitous in nature, however many of its characteristics are not well undestood. Molecular models have been proposed to represent the anomalies present in water. They have been successful in reproducing some of its anomalous behaviour but they have been unable to discribe the main physical machanism responsible for the anomalies. We propose a simple effective model that is able to capture the thermodynamic, dynamic, and structural anomalies present in water. From the analysis of this simple potential, we derive a prescription for potentials to exhibit thermodynamic and dynamic anomalies.http://www.bibsonomy.org/bibtex/24cec383c30fdc9345609c12c11555037/statphys23statphys232007-06-20T10:16:09+02:00behavior colloidal crystals liquid phase theory topic-7 molecular statphys23 simulation diffusion functional density dynamics <span style="color:#555555;">G. <a href="http://www.bibsonomy.org/author/Cinacchi">Cinacchi</a> and L. <a href="http://www.bibsonomy.org/author/De Gaetani">De Gaetani</a> and Y. <a href="http://www.bibsonomy.org/author/Martinez-raton">Martinez-raton</a> and L. <a href="http://www.bibsonomy.org/author/Mederos">Mederos</a> and E. <a href="http://www.bibsonomy.org/author/Velasco">Velasco</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyTheory and computer simulation of model colloidal liquid crystals2007behavior colloidal crystals liquid phase theory topic-7 molecular statphys23 simulation diffusion functional density dynamics Since the work of Onsager, anisotropic shape is known to be the major driving force for the formation of liquid-crystalline systems, particularly lyotropic liquid crystals. In this communication, recent results on several repulsive models of colloidal liquid crystals are presented. Molecular Dynamics computer simulations have been used to trace the phase boundaries of pure systems of worm-like, semiflexible rods, as a function of an internal flexibility parameter. Attention has been given to the evolution of the phase transitions taking place, most notably to the smectic-nematic and nematic-isotropic ones. Couplings between phase structure and particle conformation have been revealed, as well as an unexpected behaviour of the diffusion coefficients with the degree of flexibility observed. Density functional theory has been used to calculate the phase diagram of a number of binary mixtures of hard rods. Smectic phases have been included in the calculations, besides the usual isotropic and nematic phases.ones. Interesting phenomena have been observed, which include competing de-mixing transitions, micro-separated smectic phases, triple, critical and azeotropic points. All results presented should be of basic relevance to the field of lyotropic liquid crystals of both mineral and biological origin.http://www.bibsonomy.org/bibtex/2b9bf4d09b2991f454686692cec175f32/statphys23statphys232007-06-20T10:16:09+02:00statphys23 topic-10 molecular brownian kinesins motors effects cooperative force-velocity curves <span style="color:#555555;">J. <a href="http://www.bibsonomy.org/author/Brugu\&#039;es">Brugu'es</a> and J. <a href="http://www.bibsonomy.org/author/Casademunt">Casademunt</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyEnhanced cooperativity and collective force-velocity curves of interacting molecular motors2007statphys23 topic-10 molecular brownian kinesins motors effects cooperative force-velocity curves We study the collective behavior of ensembles of weakly coupled processive molecular motors subject to an external force. In the framework of a general two-state model, we demonstrate that if the external force is unequally loaded to the motors, they can generically cooperate constructively to perform more efficiently than separately. We show that, given a specific type of motor and an interaction potential, it is possible to define a limiting collective force-velocity curve which is extensive with the number of motors but may significantly differ from that of a single motor if interactions are short-ranged. For small ensembles of motors, collective force-velocity curves may exhibit surprising non-monotonic behavior. The effects and predictions are well understood with the help of exact analytical calculations and extensive numerical simulation. They are relevant in the general context of Browninan motors, but may be particularly useful to biological motors, in particular to monomeric kinesins.http://www.bibsonomy.org/bibtex/241673db51d70e3d66a64501af5651cef/statphys23statphys232007-06-20T10:16:09+02:00scales liquid spatial topic-6 statphys23 size dynamics cluster molecular temporal lennard-jones <span style="color:#555555;">R. <a href="http://www.bibsonomy.org/author/Orlik">Orlik</a> and A.C. <a href="http://www.bibsonomy.org/author/Mitus">Mitus</a> and A.Z. <a href="http://www.bibsonomy.org/author/Patashinski">Patashinski</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyTemporal and spatial scales in twodimensional Lennard-Jones liquid2007scales liquid spatial topic-6 statphys23 size dynamics cluster molecular temporal lennard-jones The time and spatial scales of solid-like atoms in two dimensional Lennard-Jones liquid are analyzed. Molecular simulation in NVE ensemble for a system of N=2500 and N=16384 particles are used. The main topic of temporal analysis are neighborhood relations in coexistence regime. Spatial analysis concentrates on distribution and shapes of cluster of solid-like atoms.http://www.bibsonomy.org/bibtex/24136a92b1337bc5b060b7e79b2f73ea9/statphys23statphys232007-06-20T10:16:09+02:00power topic-10 statphys23 motors molecular figure efficiency chemical engines merit <span style="color:#555555;">K. <a href="http://www.bibsonomy.org/author/Sasaki">Sasaki</a> and R. <a href="http://www.bibsonomy.org/author/Kanada">Kanada</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyOptimizing the Efficiency and Power of Molecular Chemical Engines2007power topic-10 statphys23 motors molecular figure efficiency chemical engines merit Biological molecular motors are chemical engines which convert the free energy released by a chemical reaction into mechanical work. The efficiency $\eta$ of energy transduction and the power (work done per unit time) $p$ are important quantities to evaluate the performance of such molecular chemical engines. However, these quantities are conflicting: high efficiencies are realized when the engine operates slowly (i.e. with low power), while the efficiency tends to be low when the machine produces high power. An engine working with (moderately) large values of \textit{both} efficiency and power may be considered as being of high performance, and we would like to propose $q = \eta p$ as a \textit{figure of merit} to measure the performance of the molecular chemical engine. The purpose of the present work is to investigate the conditions for optimizing the figure of merit $q$. We work with a simple ratchet-type model for a molecular chemical engine studied by us [K. Sasaki, R. Kanada, and S. Amari, J. Phys. Soc. Jpn. \textbf{76} (2007) 023003]; this model takes into account the binding and release of both reactant and product molecules to and from the engine, and hence enables us to study the effects of the concentrations $\rho_A$ and $\rho_B$ of these molecules as well as the load torque $L$ against which the engine does work. Once the design of the engine is specified, the set of parameters $\rho_A$, $\rho_B$, and $L$ that maximizes $q$ is searched. (The figure shows an example of the dependence of $q$ on $\rho_A$ and $\rho_B$ as a contour plot for a certain value of $L$.) This set of parameters provides the optimal condition for a given design of the engine. The maximum value, $q_{\rm max}$, of $q$ depends on the design of the engine. It is found that for a well designed engine, i.e. an engine with large $q_{\rm max}$, we have $\eta \approx 2/3$ and $p \approx (8/9)p_{\rm max}$ under the condition that $q_{\rm max}$ is realized, where $p_{\rm max}$ is the upper limit of power which the engine of a given design can produce. The present study also indicates that the F$_1$ motor (the F$_1$-ATPase) is a well designed engine in this sense, and that the condition in the cell is likely to be close to optimal one.http://www.bibsonomy.org/bibtex/2c0ef6959df8a65b1905bca077bbd3004/statphys23statphys232007-06-20T10:16:09+02:00green-kubo conduction statphys23 nonlinear long-time tails lattice molecular topic-3 dynamics simulation formula heat <span style="color:#555555;">H. <a href="http://www.bibsonomy.org/author/Shiba">Shiba</a> and S. <a href="http://www.bibsonomy.org/author/Yukawa">Yukawa</a> and N. <a href="http://www.bibsonomy.org/author/Ito">Ito</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyAnomalous Heat Conduction in Three-dimensional Nonlinear Lattices2007green-kubo conduction statphys23 nonlinear long-time tails lattice molecular topic-3 dynamics simulation formula heat Recently, heat conduction in one-dimensional nonlinear oscillator chains has been investigated. Many strenuous studies have elucidated that thermal conductivity of such a system with momentum conservation depends on the size of the system as $\kappa\sim N^\alpha$ where the exponent $\alpha$ takes values near 0.4. This property seems to hold in many nonlinear lattice systems with nonintegrability such as FPU chains, diatomic Toda lattices, etc. The results mean that thermal conductivity of such systems does not have any finite value in the thermodynamic limit $N\rightarrow\infty$. The anomalous behavior is thought to originate in a slow decay of the equilibrium autocorrelation function of heat flux, called ''long-time tails''. This decay is typically represented by a power-law function as \[ \langle J(t)\cdot J(0)\rangle \sim t^{-d/2}.\qquad \] Here, $J(t)$ is the total heat flux and $d$ is the dimensionality of the system. This type of decay is known to widely hold in dense gases and liquids, and momentum conservation is thought to play an important role for such a slow decay. In this paper, we investigate heat conduction in simple three-dimensional extensions of three-dimensional nonlinear lattices. When $d=3$, the usual long-time tails will predict some finite conductivity through Green-Kubo formula. Our starting point is a simple three-dimensional model of which the Hamiltonian is given by \[ H = \sum_{i=1}^N \frac{\vec{p}_i^2}{2m} +\sum_{\langle i,j\rangle} \left[ \frac{k}{2}|\vec{r}_i-\vec{r}_j |^2 +\frac{g}{4} |\vec{r}_i-\vec{r}_j|^4 \right] . \] We will present that the three-dimensional lattices have diverging thermal conductivity, contrary to a naive expectation. The conductivity seems to show power-law divergence as $\kappa\sim N_z^\alpha$, and the long-time tail of the heat flux autocorrelation function is of a completely different type from the conventional ones. This anomalous behavior is so robust that the conductivity diverges with its size even when the system contains disorders in the mass, etc. Our results evidence that such divergence of thermal conductivity is a robust and universal nature of three-dimensional model insulators. We think that our results is the first case that anomalous conductivity is essentially found in three-dimensional cases, and that the result arises an important problem about what is the origin of finite conductivity which we usually observe in three-dimensional insulators. 1. S. Lepri, R. Livi, and A. Politi: Phys. Rep. 377, 1 (2003), and references therein. 2. H. Shiba, S. Yukawa, and N. Ito: J. Phys. Soc. Jpn. 75, 103001 (2006). We have reported logarithmic divergence of thermal conductivityin this paper. However, our current notion is that the divergence is not of a logarithmic but a weak power-law type. 3. H. Shiba and N. Ito: in preparation.http://www.bibsonomy.org/bibtex/2c5f54be75706f54dae376733403abd64/statphys23statphys232007-06-20T10:16:09+02:00molecular liquid study topic-9 dynamics statphys23 monatomic simple <span style="color:#555555;">T. <a href="http://www.bibsonomy.org/author/Mizuguchi">Mizuguchi</a> and J. <a href="http://www.bibsonomy.org/author/Matsui">Matsui</a> and T. <a href="http://www.bibsonomy.org/author/Odagaki">Odagaki</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyGlass transition in a simple monatomic liquid2007molecular liquid study topic-9 dynamics statphys23 monatomic simple We present a molecular dynamics study of a simple monatomic liquid in two dimensions, where atoms interact with other atoms through a potential of the form $\displaystyle V(r)=4(1/r^{12}-1/r^6)-\epsilon_0\exp(-(r-r_0)^2/2\delta^2)$ which is called Lennard-Jones-Gauss (LJG) potential ([M.Engel and H.-R. Trebin. preprint]). This potential has three parameters, the position of the second well $r_0$, the depth $\epsilon_0$, the width $\delta$. We change $r_0,\epsilon_0$ with fixed $\delta$ and observe the change of the particle configulation. As a result, in a certain range of parameters of the LJG potential, we find that the system can be supercooled without crystallization and be turned into a glassy state. We confirm a glassy state by the static structure factor. The characteristics of the transition is investigated through thermodynamic properties such as the specific heat and dynamic properties such as the dynamical structure factor and the non-Gaussian parameter. We show that the simple monatomic liquid share the same characteristic with binary softspheres or binary Lennard-Jones liquids. Figure 1 shows the temperature dependence of the specific heat, where we can see the sudden decrease of the specific heat at the glass transition temperature $T_g=0.34\epsilon/k$.http://www.bibsonomy.org/bibtex/2c70a9439b8b4d2f34f2b56f2a23cafad/statphys23statphys232007-06-20T10:16:09+02:00hydrodynamics dynamics topic-6 molecular theory capillary density functional waves statphys23 time-dependent <span style="color:#555555;">T.H. <a href="http://www.bibsonomy.org/author/Hiester">Hiester</a> and K. <a href="http://www.bibsonomy.org/author/Mecke">Mecke</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyDynamics of liquid-vapor interfaces on nanometer scales2007hydrodynamics dynamics topic-6 molecular theory capillary density functional waves statphys23 time-dependent On nanometer scales, the dynamics of liquid-vapor interfaces is expected to behave differently from hydrodynamical predictions, which are valid in the limit of long wavelengths and time scales. However, recent experimental studies [PRL 98 096104 (2007)] have started to explore the coupling between bulk and surface dynamical modes on small length and time scales. Thus, a more detailed understanding of the relevant processes at those scales is mandatory. We apply a dynamical density functional theory (DDFT) as a microscopic description of fluid interfaces. In the corresponding dispersion relation a wavevector-dependent surface energy instead of the constant surface tension is obtained by taking additionally into account the local curvature of the fluctuating interface. In particular, the influence of the static height-height fluctuation spectrum of capillary waves can be identified. Since various competing density functionals and dynamical models for the time evolution of fluid interfaces exist, we provide here a comparison between the corresponding results in order to elucidate capillary wave dynamics on different length and time scales.http://www.bibsonomy.org/bibtex/2bfaa5c34bc321fca6778f119ffb274b3/statphys23statphys232007-06-20T10:16:09+02:00molecular topic-6 statphys23 dynamics nanodroplet <span style="color:#555555;">Y. <a href="http://www.bibsonomy.org/author/Jung">Jung</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyDynamics of Nanodroplets on Curved Surfaces2007molecular topic-6 statphys23 dynamics nanodroplet The dynamical behavior of nanometer-sized polymer droplets on a curved surface is studied using molecular dynamics simulations. We address how the curved nature of the substrate affects the spreading dynamics of the nanoscale droplet. Large hemispherical drops consisting of chains of lengths 2, 10, and 50 are simulated using a bead-spring model. We compare our results with those obtained on flat surfaces.http://www.bibsonomy.org/bibtex/227123f2244a61a8725f163136336046b/statphys23statphys232007-06-20T10:16:09+02:00statphys23 molecular microtubule topic-11 rna motor dna <span style="color:#555555;">D. <a href="http://www.bibsonomy.org/author/Chowdhury">Chowdhury</a> </span><em>Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, </em><em>Genova, Italy, </em><em>9-13 July2007. </em>Wed Jun 20 10:16:09 CEST 2007Genova, ItalyAbstract Book of the XXIII IUPAP International Conference on Statistical Physics9-13 JulyIntra-cellular traffic: bio-molecular motors on filamentary tracks2007statphys23 molecular microtubule topic-11 rna motor dna Molecular motors are macromolecular complexes which use some form of input energy to perform mechanical work. The filamentary tracks, on which these motors move, are made of either proteins (e.g., microtubules) or nucleic acids (DNA or RNA). Often, many such motors move simultaneously on the same track and their collective properties have several superficial similarities with vehicular traffic on highways. After introducing the fundamental physical principles underlying the mechanisms of operation of individual motors, I'll consider a few specific examples of molecular motor traffic. The models we have developed [1-6] provide ``unified'' description: in the low-density limit, a model captures the transport properties of a single motor while, at higher densities the same model accounts for the collective spatio-temporal dynamics of interacting motors. We show how the intra-cellular molecular motor traffic phenomena depend on the mechano-chemistry of the corresponding individual motors [7]. 1) A. Basu and D. Chowdhury, Phys. Rev. E, 75, 021902 (2007). \\ 2) A. Basu and D. Chowdhury, submitted for publication (e-print: physics/0702149).\\ 3) A. Basu, D. Chowdhury, A. Garai and T.V. Ramakrishnan, to be published (2007).\\ 4) T. Tripathi and D. Chowdhury, submitted for publication (2007).\\ 5) K. Nishinari, Y. Okada, A. Schadschneider and D. Chowdhury, Phys. Rev. Lett. 95, 118101 (2005).\\ 6) P. Greulich, A. Garai, K. Nishinari, A. Schadschneider and D. Chowdhury, accepted for publication in Phys. Rev. E (2007).\\ 7) D. Chowdhury, P.K. Mishra, K. Nishinari and A. Schadschneider, to be published, (2007).