The dynamics of cargo driven by molecular motors in the context of asymmetric simple exclusion processes

We consider the dynamics of cargo driven by a collection of interacting molecular motors in the context of ail asymmetric simple exclusion process (ASEP). The model is formulated to account for (i) excluded-volume interactions, (ii) the observed asymmetry of the stochastic movement of individual motors and (iii) interactions between motors and cargo. Items (i) and (ii) form the basis of ASEP models and have already been considered to study the behavior of motor density profile [A. Parmeggiani. T. Franosch, E. Frey, Phase Coexistence in driven one-dimensional transport, Phys. Rev. Lett. 90 (2003) 086601-1-086601-4]. Item (iii) is new. It is introduced here as an attempt to describe explicitly the dependence of cargo movement on the dynamics of motors in this context. The steady-state Solutions Of the model indicate that the system undergoes a phase transition of condensation type as the motor density varies. We study the consequences of this transition to the behavior of the average cargo velocity. (C) 2009 Elsevier B.V. All rights reserved.

Percolation in a network with long-range connections: Implications for cytoskeletal structure and function

Cell shape, signaling, and integrity depend on cytoskeletal organization. In this study we describe the cytoskeleton as a simple network of filamentary proteins (links) anchored by complex protein structures (nodes). The structure of this network is regulated by a distance-dependent probability of link formation as P = p/d(s), where p regulates the network density and s controls how fast the probability for link formation decays with node distance (d). It was previously shown that the regulation of the link lengths is crucial for the mechanical behavior of the cells. Here we examined the ability of the two-dimensional network to percolate (i.e. to have end-to-end connectivity), and found that the percolation threshold depends strongly on s. The system undergoes a transition around s = 2. The percolation threshold of networks with s < 2 decreases with increasing system size L, while the percolation threshold for networks with s > 2 converges to a finite value. We speculate that s < 2 may represent a condition in which cells can accommodate deformation while still preserving their mechanical integrity. Additionally, we measured the length distribution of F-actin filaments from publicly available images of a variety of cell types. In agreement with model predictions, cells originating from more deformable tissues show longer F-actin cytoskeletal filaments. (C) 2008 Elsevier B.V. All rights reserved.

Finite temperature effective actions

We present, from first principles, a direct method for evaluating the exact fermion propagator in the presence of a general background held at finite temperature, which can be used to determine the finite temperature effective action for the system. As applications, we determine the complete one loop finite temperature effective actions for (0 + 1)-dimensional QED as well as the Schwinger model. These effective actions, which are derived in the real time (closed time path) formalism, generate systematically all the Feynman amplitudes calculated in thermal perturbation theory and also show that the retarded (advanced) amplitudes vanish in these theories. (C) 2009 Elsevier B.V. All rights reserved.

Quantum current algebra for the AdS(5) x S(5) superstring

The sigma model describing the dynamics of the superstring in the AdS(5) x S(5) background can be constructed using the coset PSU(2, 2 vertical bar 4)/SO(4, 1) x SO(5). A basic set of operators in this two dimensional conformal field theory is composed by the left invariant currents. Since these currents are not (anti) holomorphic, their OPE`s is not determined by symmetry principles and its computation should be performed perturbatively. Using the pure spinor sigma model for this background, we compute the one-loop correction to these OPE`s. We also compute the OPE`s of the left invariant currents with the energy momentum tensor at tree level and one loop.

The spectrum of an open vertex model based on the U(q)[SU(2)] algebra at roots of unity

We study the exact solution of an N-state vertex model based on the representation of the U(q)[SU(2)] algebra at roots of unity with diagonal open boundaries. We find that the respective reflection equation provides us one general class of diagonal K-matrices having one free-parameter. We determine the eigenvalues of the double-row transfer matrix and the respective Bethe ansatz equation within the algebraic Bethe ansatz framework. The structure of the Bethe ansatz equation combine a pseudomomenta function depending on a free-parameter with scattering phase-shifts that are fixed by the roots of unity and boundary variables. (C) 2010 Elsevier B.V. All rights reserved.

Number of particle creation and decoherence in the nonideal dynamical Casimir effect at finite temperature

In this work we investigate the dynamical Casimir effect in a nonideal cavity by deriving an effective Hamiltonian. We first compute a general expression for the average number of particle creation, applicable for any law of motion of the cavity boundary, under the only restriction of small velocities. We also compute a general expression for the linear entropy of an arbitrary state prepared in a selected mode, also applicable for any law of motion of a slow moving boundary. As an application of our results we have analyzed both the average number of particle creation and linear entropy within a particular oscillatory motion of the cavity boundary. On the basis of these expressions we develop a comprehensive analysis of the resonances in the number of particle creation in the nonideal dynamical Casimir effect. We also demonstrate the occurrence of resonances in the loss of purity of the initial state and estimate the decoherence times associated with these resonances. Since our results were obtained in the framework of the perturbation theory, they are restricted, under resonant conditions, to a short-time approximation. (C) 2009 Elsevier Inc. All rights reserved.

Transition to quantum turbulence in finite-size superfluids

A novel concept of quantum turbulence in finite size superfluids, such as trapped bosonic atoms, is discussed. We have used an atomic (87)Rb Bose-Einstein condensate (BEC) to study the emergence of this phenomenon. In our experiment, the transition to the quantum turbulent regime is characterized by a tangled vortex lines formation, controlled by the amplitude and time duration of the excitation produced by an external oscillating field. A simple model is suggested to account for the experimental observations. The transition from the non-turbulent to the turbulent regime is a rather gradual crossover. But it takes place in a sharp enough way, allowing for the definition of an effective critical line separating the regimes. Quantum turbulence emerging in a finite-size superfluid may be a new idea helpful for revealing important features associated to turbulence, a more general and broad phenomenon. [GRAPHICS] Amplitude versus elapsed time diagram of magnetically excited BEC superfluid, presenting the evolution from the non-turbulent regime, with well separated vortices, to the turbulent regimes, with tangled vortices (C) 2011 by Astro Ltd. Published exclusively by WILEY-VCH Verlag GmbH & Co. KGaA

On the lower bound on the exchange-correlation energy in two dimensions

We study the properties of the lower bound on the exchange-correlation energy in two dimensions. First we review the derivation of the bound and show how it can be written in a simple density-functional form. This form allows an explicit determination of the prefactor of the bound and testing its tightness. Next we focus on finite two-dimensional systems and examine how their distance from the bound depends on the system geometry. The results for the high-density limit suggest that a finite system that comes as close as possible to the ultimate bound on the exchange-correlation energy has circular geometry and a weak confining potential with a negative curvature. (c) 2009 Elsevier B.V. All rights reserved.

Friedel oscillations in one-dimensional metals: From Luttinger`s theorem to the Luttinger liquid

Charge density and magnetization density profiles of one-dimensional metals are investigated by two complementary many-body methods: numerically exact (Lanczos) diagonalization, and the Bethe-Ansatz local-density approximation with and without a simple self-interaction correction. Depending on the magnetization of the system, local approximations reproduce different Fourier components of the exact Friedel oscillations. (C) 2008 Elsevier B.V. All rights reserved.

Density-Profile Processes Describing Biological Signaling Networks: Almost Sure Convergence to Deterministic Trajectories

We introduce jump processes in R(k), called density-profile processes, to model biological signaling networks. Our modeling setup describes the macroscopic evolution of a finite-size spin-flip model with k types of spins with arbitrary number of internal states interacting through a non-reversible stochastic dynamics. We are mostly interested on the multi-dimensional empirical-magnetization vector in the thermodynamic limit, and prove that, within arbitrary finite time-intervals, its path converges almost surely to a deterministic trajectory determined by a first-order (non-linear) differential equation with explicit bounds on the distance between the stochastic and deterministic trajectories. As parameters of the spin-flip dynamics change, the associated dynamical system may go through bifurcations, associated to phase transitions in the statistical mechanical setting. We present a simple example of spin-flip stochastic model, associated to a synthetic biology model known as repressilator, which leads to a dynamical system with Hopf and pitchfork bifurcations. Depending on the parameter values, the magnetization random path can either converge to a unique stable fixed point, converge to one of a pair of stable fixed points, or asymptotically evolve close to a deterministic orbit in Rk. We also discuss a simple signaling pathway related to cancer research, called p53 module.

Predicting random effects with an expanded finite population mixed model

Prediction of random effects is an important problem with expanding applications. In the simplest context, the problem corresponds to prediction of the latent value (the mean) of a realized cluster selected via two-stage sampling. Recently, Stanek and Singer [Predicting random effects from finite population clustered samples with response error. J. Amer. Statist. Assoc. 99, 119-130] developed best linear unbiased predictors (BLUP) under a finite population mixed model that outperform BLUPs from mixed models and superpopulation models. Their setup, however, does not allow for unequally sized clusters. To overcome this drawback, we consider an expanded finite population mixed model based on a larger set of random variables that span a higher dimensional space than those typically applied to such problems. We show that BLUPs for linear combinations of the realized cluster means derived under such a model have considerably smaller mean squared error (MSE) than those obtained from mixed models, superpopulation models, and finite population mixed models. We motivate our general approach by an example developed for two-stage cluster sampling and show that it faithfully captures the stochastic aspects of sampling in the problem. We also consider simulation studies to illustrate the increased accuracy of the BLUP obtained under the expanded finite population mixed model. (C) 2007 Elsevier B.V. All rights reserved.

ENO adaptive method for solving one-dimensional conservation laws

In this work an efficient third order non-linear finite difference scheme for solving adaptively hyperbolic systems of one-dimensional conservation laws is developed. The method is based oil applying to the solution of the differential equation an interpolating wavelet transform at each time step, generating a multilevel representation for the solution, which is thresholded and a sparse point representation is generated. The numerical fluxes obtained by a Lax-Friedrichs flux splitting are evaluated oil the sparse grid by an essentially non-oscillatory (ENO) approximation, which chooses the locally smoothest stencil among all the possibilities for each point of the sparse grid. The time evolution of the differential operator is done on this sparse representation by a total variation diminishing (TVD) Runge-Kutta method. Four classical examples of initial value problems for the Euler equations of gas dynamics are accurately solved and their sparse solutions are analyzed with respect to the threshold parameters, confirming the efficiency of the wavelet transform as an adaptive grid generation technique. (C) 2008 IMACS. Published by Elsevier B.V. All rights reserved.

On automorphisms of finite abelian p-groups

Let A be a finitely generated abelian group. We describe the automorphism group Aut(A) using the rank of A and its torsion part p-part A(p). For a finite abelian p-group A of type (k(1),..., k(n)), simple necessary and sufficient conditions for an n x n-matrix over integers to be associated with an automorphism of A are presented. Then, the automorphism group Aut(A) for a finite p-group A of type (k(1), k(2)) is analyzed. (C) 2008 Mathematical Institute Slovak Academy of Sciences.

The smallest simple Moufang loop

We study the simple Moufang loop GLL(F(2)) and give a complete description of its lattice of subloops. (C) 2008 Elsevier Inc. All rights reserved.

Torsion theories induced from commutative subalgebras

We begin a study of torsion theories for representations of finitely generated algebras U over a field containing a finitely generated commutative Harish-Chandra subalgebra Gamma. This is an important class of associative algebras, which includes all finite W-algebras of type A over an algebraically closed field of characteristic zero, in particular, the universal enveloping algebra of gl(n) (or sl(n)) for all n. We show that any Gamma-torsion theory defined by the coheight of the prime ideals of Gamma is liftable to U. Moreover, for any simple U-module M, all associated prime ideals of M in Spec Gamma have the same coheight. Hence, the coheight of these associated prime ideals is an invariant of a given simple U-module. This implies the stratification of the category of U-modules controlled by the coheight of the associated prime ideals of Gamma. Our approach can be viewed as a generalization of the classical paper by Block (1981) [4]; it allows, in particular, to study representations of gl(n) beyond the classical category of weight or generalized weight modules. (C) 2011 Elsevier B.V. All rights reserved.