Fluctuation spectrum of quasispherical membranes with force-dipole activity

The fluctuation spectrum of a quasi-spherical vesicle with active membrane proteins is calculated. The activity of the proteins is modeled as the proteins pushing on their surroundings giving rise to non-local force distributions. Both the contributions from the thermal fluctuations of the active protein densities and the temporal noise in the individual active force distributions of the proteins are taken into account. The noise in the individual force distributions is found to become significant at short wavelengths.Comment: 9 pages, 2 figures, minor changes and addition

Entropy Production of Brownian Macromolecules with Inertia

We investigate the nonequilibrium steady-state thermodynamics of single Brownian macromolecules with inertia under feedback control in isothermal ambient fluid. With the control being represented by a velocity-dependent external force, we find such open systems can have a negative entropy production rate and we develop a mesoscopic theory consistent with the second law. We propose an equilibrium condition and define a class of external forces, which includes a transverse Lorentz force, leading to equilibrium.Comment: 10 pages, 1 figur

Can kinomics and proteomics bridge the gap between pediatric cancers and newly designed kinase inhibitors?

status: publishe

Compositionality, stochasticity and cooperativity in dynamic models of gene regulation

We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a ``gene gate'' and defines an input/output-relationship corresponding to the binding and production of transcription factors. The proposed reaction kinetics of the gene gates can be mapped onto stochastic processes and the standard ode-description. While the ode-approach requires fixing the system's topology before its correct implementation, expressing them in stochastic pi-calculus leads to a fully compositional scheme: network elements become autonomous and only the input/output relationships fix their wiring. The modularity of our approach allows to pass easily from a basic first-level description to refined models which capture more details of the biological system. As an illustrative application we present the stochastic repressilator, an artificial cellular clock, which oscillates readily without any cooperative effects.Comment: 15 pages, 8 figures. Accepted by the HFSP journal (13/09/07

Cluster approximations for infection dynamics on random networks

In this paper, we consider a simple stochastic epidemic model on large regular random graphs and the stochastic process that corresponds to this dynamics in the standard pair approximation. Using the fact that the nodes of a pair are unlikely to share neighbors, we derive the master equation for this process and obtain from the system size expansion the power spectrum of the fluctuations in the quasi-stationary state. We show that whenever the pair approximation deterministic equations give an accurate description of the behavior of the system in the thermodynamic limit, the power spectrum of the fluctuations measured in long simulations is well approximated by the analytical power spectrum. If this assumption breaks down, then the cluster approximation must be carried out beyond the level of pairs. We construct an uncorrelated triplet approximation that captures the behavior of the system in a region of parameter space where the pair approximation fails to give a good quantitative or even qualitative agreement. For these parameter values, the power spectrum of the fluctuations in finite systems can be computed analytically from the master equation of the corresponding stochastic process.Comment: the notation has been changed; Ref. [26] and a new paragraph in Section IV have been adde

Dynamic Mean-Field Glass Model with Reversible Mode Coupling and Trivial Hamiltonian

Often the current mode coupling theory (MCT) of glass transitions is compared with mean field theories. We explore this possible correspondence. After showing a simple-minded derivation of MCT with some difficulties we give a concise account of our toy model developed to gain more insight into MCT. We then reduce this toy model by adiabatically eliminating rapidly varying velocity-like variables to obtain a Fokker-Planck equation for the slowly varying density-like variables where diffusion matrix can be singular. This gives a room for nonergodic stationary solutions of the above equation.Comment: 9 pages, contribution to the Proceedings of the Merida Satellite Meeting to STATPHYS21 (Merida, Mexico, July 9-14, 2001). To appear in J. Phys. Condens. Matte

Information spreading and development of cultural centers

The historical interplay between societies are governed by many factors, including in particular spreading of languages, religion and other symbolic traits. Cultural development, in turn, is coupled to emergence and maintenance of information spreading. Strong centralized cultures exist thanks to attention from their members, which faithfulness in turn relies on supply of information. Here, we discuss a culture evolution model on a planar geometry that takes into account aspects of the feedback between information spreading and its maintenance. Features of model are highlighted by comparing it to cultural spreading in ancient and medieval Europe, where it in particular suggests that long lived centers should be located in geographically remote regions.Comment: 7 pages, 5 figure

Mapping between dissipative and Hamiltonian systems

Theoretical studies of nonequilibrium systems are complicated by the lack of a general framework. In this work we first show that a transformation introduced by Ao recently (J. Phys. A {\bf 37}, L25 (2004)) is related to previous works of Graham (Z. Physik B {\bf 26}, 397 (1977)) and Eyink {\it et al.} (J. Stat. Phys. {\bf 83}, 385 (1996)), which can also be viewed as the generalized application of the Helmholtz theorem in vector calculus. We then show that systems described by ordinary stochastic differential equations with white noise can be mapped to thermostated Hamiltonian systems. A steady-state of a dissipative system corresponds to the equilibrium state of the corresponding Hamiltonian system. These results provides a solid theoretical ground for corresponding studies on nonequilibrium dynamics, especially on nonequilibrium steady state. The mapping permits the application of established techniques and results for Hamiltonian systems to dissipative non-Hamiltonian systems, those for thermodynamic equilibrium states to nonequilibrium steady states. We discuss several implications of the present work.Comment: 18 pages, no figure. final version for publication on J. Phys. A: Math & Theo

Conservation Laws and Integrability of a One-dimensional Model of Diffusing Dimers

We study a model of assisted diffusion of hard-core particles on a line. The model shows strongly ergodicity breaking : configuration space breaks up into an exponentially large number of disconnected sectors. We determine this sector-decomposion exactly. Within each sector the model is reducible to the simple exclusion process, and is thus equivalent to the Heisenberg model and is fully integrable. We discuss additional symmetries of the equivalent quantum Hamiltonian which relate observables in different sectors. In some sectors, the long-time decay of correlation functions is qualitatively different from that of the simple exclusion process. These decays in different sectors are deduced from an exact mapping to a model of the diffusion of hard-core random walkers with conserved spins, and are also verified numerically. We also discuss some implications of the existence of an infinity of conservation laws for a hydrodynamic description.Comment: 39 pages, with 5 eps figures, to appear in J. Stat. Phys. (March 1997

Mobility and stochastic resonance in spatially inhomogeneous system

The mobility of an overdamped particle, in a periodic potential tilted by a constant external field and moving in a medium with periodic friction coefficient is examined. When the potential and the friction coefficient have the same periodicity but have a phase difference, the mobility shows many interesting features as a function of the applied force, the temperature, etc. The mobility shows stochastic resonance even for constant applied force, an issue of much recent interest. The mobility also exhibits a resonance like phenomenon as a function of the field strength and noise induced slowing down of the particle in an appropriate parameter regime.Comment: 14 pages, 12 figures. Submitted to Phys. Rev.