On practical applicability of the Jarzynski relation in statistical mechanics: a pedagogical example

We suggest and discuss a simple model of an ideal gas under the piston to gain an insight into the workings of the Jarzynski identity connecting the average exponential of the work over the non-equilibrium trajectories with the equilibrium free energy. We show that the Jarzynski identity is valid for our system due to the very rapid molecules belonging to the tail of the Maxwell distribution. For the most interesting extreme, when the system volume is large, while the piston is moving with large speed (compared to thermal velocity) for a very short time, the necessary number of independent experimental runs to obtain a reasonable approximation for the free energy from averaging the non-equilibrium work grows exponentially with the system size.Comment: 15 pages, 7 figures, submitted to JP

Topologically Driven Swelling of a Polymer Loop

Numerical studies of the average size of trivially knotted polymer loops with no excluded volume are undertaken. Topology is identified by Alexander and Vassiliev degree 2 invariants. Probability of a trivial knot, average gyration radius, and probability density distributions as functions of gyration radius are generated for loops of up to N=3000 segments. Gyration radii of trivially knotted loops are found to follow a power law similar to that of self avoiding walks consistent with earlier theoretical predictions.Comment: 6 pages, 4 figures, submitted to PNAS (USA) in Feb 200

Polymer translocation through a nanopore - a showcase of anomalous diffusion

The translocation dynamics of a polymer chain through a nanopore in the absence of an external driving force is analyzed by means of scaling arguments, fractional calculus, and computer simulations. The problem at hand is mapped on a one dimensional {\em anomalous} diffusion process in terms of reaction coordinate $s$ (i.e. the translocated number of segments at time $t$) and shown to be governed by an universal exponent $\alpha = 2/(2\nu+2-\gamma_1)$ whose value is nearly the same in two- and three-dimensions. The process is described by a {\em fractional} diffusion equation which is solved exactly in the interval $0 <s < N$ with appropriate boundary and initial conditions. The solution gives the probability distribution of translocation times as well as the variation with time of the statistical moments: $$, and $- < s(t)>^2$ which provide full description of the diffusion process. The comparison of the analytic results with data derived from extensive Monte Carlo (MC) simulations reveals very good agreement and proves that the diffusion dynamics of unbiased translocation through a nanopore is anomalous in its nature.Comment: 5 pages, 3 figures, accepted for publication in Phys. Rev.

Probability distributions of the work in the 2D-Ising model

Probability distributions of the magnetic work are computed for the 2D Ising model by means of Monte Carlo simulations. The system is first prepared at equilibrium for three temperatures below, at and above the critical point. A magnetic field is then applied and grown linearly at different rates. Probability distributions of the work are stored and free energy differences computed using the Jarzynski equality. Consistency is checked and the dynamics of the system is analyzed. Free energies and dissipated works are reproduced with simple models. The critical exponent $\delta$ is estimated in an usual manner.Comment: 12 pages, 6 figures. Comments are welcom

Model-based relative entropy stochastic search

Stochastic search algorithms are general black-box optimizers. Due to their ease of use and their generality, they have recently also gained a lot of attention in operations research, machine learning and policy search. Yet, these algorithms require a lot of evaluations of the objective, scale poorly with the problem dimension, are affected by highly noisy objective functions and may converge prematurely. To alleviate these problems, we introduce a new surrogate-based stochastic search approach. We learn simple, quadratic surrogate models of the objective function. As the quality of such a quadratic approximation is limited, we do not greedily exploit the learned models. The algorithm can be misled by an inaccurate optimum introduced by the surrogate. Instead, we use information theoretic constraints to bound the ‘distance’ between the new and old data distribution while maximizing the objective function. Additionally the new method is able to sustain the exploration of the search distribution to avoid premature convergence. We compare our method with state of art black-box optimization methods on standard uni-modal and multi-modal optimization functions, on simulated planar robot tasks and a complex robot ball throwing task. The proposed method considerably outperforms the existing approaches

Energetic changes caused by antigenic module insertion in a virus-like particle revealed by experiment and molecular dynamics simulations

The success of recombinant virus-like particles (VLPs) for human papillomavirus and hepatitis B demonstrates the potential of VLPs as safe and efficacious vaccines. With new modular designs emerging, the effects of antigen module insertion on the self-assembly and structural integrity of VLPs should be clarified so as to better enabling improved design. Previous work has revealed insights into the molecular energetics of a VLP subunit, capsomere, comparing energetics within various solution conditions known to drive or inhibit self-assembly. In the present study, molecular dynamics (MD) simulations coupled with the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method were performed to examine the molecular interactions and energetics in a modular capsomere of a murine polyomavirus (MPV) VLP designed to protect against influenza. Insertion of an influenza antigenic module is found to lower the binding energy within the capsomere, and a more active state is observed in Assembly Buffer as compared with that in Stabilization Buffer, which has been experimentally validated through measurements using differential scanning calorimetry. Further in-depth analysis based on free-energy decomposition indicates that destabilized binding can be attributed to electrostatic interaction induced by the chosen antigen module. These results provide molecular insights into the conformational stability of capsomeres and their abilities to be exploited for antigen presentation, and are expected to be beneficial for the biomolecular engineering of VLP vaccines.Lin Zhang, Ronghong Tang, Shu Bai, Natalie K. Connors, Linda H.L. Lua, Yap P. Chuan, Anton P.J. Middelberg, Yan Su

A Dual Spring Modeling Approach for Static and Fatigue Failure Assessments of Carbon/Epoxy Composite Sub-Elements

A dual spring model is developed for the static and fatigue damage predictions of laminates interface in composite structures. Stress concentrations can be induced by the defects formed in the fabrication or service process. A conventional S-N based fatigue damage model may not be accurate to predict the fatigue life of a structure with high stress concentration. With the dual spring model, static delamination failure can be simulated using springs of cohesive type material model while fatigue delamination development can be predicted using linear springs, where the crack driving force is computed based on virtual crack closure technique (VCCT). A Paris law type fatigue growth law with its mode mixity is applied for fatigue crack growth prediction. After verified using benchmark examples, including Double Cantilever Beam (DCB), End-Notched Flexure (ENF) and Mix-Mode Bending (MMB), the proposed dual spring model is applied in the static and fatigue damage prediction of NASA/Boeing sub-elements and UTC sub-elements

Abundance of unknots in various models of polymer loops

A veritable zoo of different knots is seen in the ensemble of looped polymer chains, whether created computationally or observed in vitro. At short loop lengths, the spectrum of knots is dominated by the trivial knot (unknot). The fractional abundance of this topological state in the ensemble of all conformations of the loop of $N$ segments follows a decaying exponential form, $\sim \exp (-N/N_0)$, where $N_0$ marks the crossover from a mostly unknotted (ie topologically simple) to a mostly knotted (ie topologically complex) ensemble. In the present work we use computational simulation to look closer into the variation of $N_0$ for a variety of polymer models. Among models examined, $N_0$ is smallest (about 240) for the model with all segments of the same length, it is somewhat larger (305) for Gaussian distributed segments, and can be very large (up to many thousands) when the segment length distribution has a fat power law tail.Comment: 13 pages, 6 color figure

Residence Time Statistics for Normal and Fractional Diffusion in a Force Field

We investigate statistics of occupation times for an over-damped Brownian particle in an external force field. A backward Fokker-Planck equation introduced by Majumdar and Comtet describing the distribution of occupation times is solved. The solution gives a general relation between occupation time statistics and probability currents which are found from solutions of the corresponding problem of first passage time. This general relationship between occupation times and first passage times, is valid for normal Markovian diffusion and for non-Markovian sub-diffusion, the latter modeled using the fractional Fokker-Planck equation. For binding potential fields we find in the long time limit ergodic behavior for normal diffusion, while for the fractional framework weak ergodicity breaking is found, in agreement with previous results of Bel and Barkai on the continuous time random walk on a lattice. For non-binding potential rich physical behaviors are obtained, and classification of occupation time statistics is made possible according to whether or not the underlying random walk is recurrent and the averaged first return time to the origin is finite. Our work establishes a link between fractional calculus and ergodicity breaking.Comment: 12 page