Structure and stability of helices in square-well homopolymers

Recently, it has been demonstrated [Magee et al., Phys. Rev. Lett. 96, 207802 (2006)] that isolated, square-well homopolymers can spontaneously break chiral symmetry and freeze into helical structures at sufficiently low temperatures. This behavior is interesting because the square-well homopolymer is itself achiral. In this work, we use event-driven molecular dynamics, combined with an optimized parallel tempering scheme, to study this polymer model over a wide range of parameters. We examine the conditions where the helix structure is stable and determine how the interaction parameters of the polymer govern the details of the helix structure. The width of the square well (proportional to lambda) is found to control the radius of the helix, which decreases with increasing well width until the polymer forms a coiled sphere for sufficiently large wells. The helices are found to be stable for only a window of molecular weights. If the polymer is too short, the helix will not form. If the polymer is too long, the helix is no longer the minimum energy structure, and other folded structures will form. The size of this window is governed by the chain stiffness, which in this model is a function of the ratio of the monomer size to the bond length. Outside this window, the polymer still freezes into a locked structure at low temperature, however, unless the chain is sufficiently stiff, this structure will not be unique and is similar to a glassy state.Comment: Submitted to Physical Review

Exact on-event expressions for discrete potential systems

The properties of systems composed of atoms interacting though discrete potentials are dictated by a series of events which occur between pairs of atoms. There are only four basic event types for pairwise discrete potentials and the square-well/shoulder systems studied here exhibit them all. Closed analytical expressions are derived for the on-event kinetic energy distribution functions for an atom, which are distinct from the Maxwell-Boltzmann distribution function. Exact expressions are derived that directly relate the pressure and temperature of equilibrium discrete potential systems to the rates of each type of event. The pressure can be determined from knowledge of only the rate of core and bounce events. The temperature is given by the ratio of the number of bounce events to the number of disassociation/association events. All these expressions are validated with event-driven molecular dynamics simulations and agree with the data within the statistical precision of the simulations

Movers and shakers: Granular damping in microgravity

The response of an oscillating granular damper to an initial perturbation is studied using experiments performed in microgravity and granular dynamics mulations. High-speed video and image processing techniques are used to extract experimental data. An inelastic hard sphere model is developed to perform simulations and the results are in excellent agreement with the experiments. The granular damper behaves like a frictional damper and a linear decay of the amplitude is bserved. This is true even for the simulation model, where friction forces are absent. A simple expression is developed which predicts the optimal damping conditions for a given amplitude and is independent of the oscillation frequency and particle inelasticities.Comment: 9 pages, 9 figure

Thermodynamic and dynamical properties of the hard sphere system revisited by molecular dynamics simulation

Acknowledgements Some of the MD calculations were performed at the Poznan Supercomputing and Networking Center (PCSS). DMH would like to thank Dr. T. Crane (Department of Physics, Royal Holloway, University of London, UK) for helpful software support.Peer reviewedPostprin

Transport properties of highly asymmetric hard-sphere mixtures

The static and dynamic properties of binary mixtures of hard spheres with a diameter ratio of sigma(B)/sigma(A)= 0.1 and a mass ratio of m(B)/m(A)= 0.001 are investigated using event driven molecular dynamics. The contact values of the pair correlation functions are found to compare favorably with recently proposed theoretical expressions. The transport coefficients of the mixture, determined from simulation, are compared to the predictions of the revised Enskog theory using both a third-order Sonine expansion and direct simulation Monte Carlo. Overall, the Enskog theory provides a fairly good description of the simulation data, with the exception of systems at the smallest mole fraction of larger spheres (x(A)=0.01) examined. A "fines effect" was observed at higher packing fractions, where adding smaller spheres to a system of large spheres decreases the viscosity of the mixture; this effect is not captured by the Enskog theory

Mapping continuous potentials to discrete forms

The optimal conversion of a continuous inter-particle potential to a discrete equivalent is considered here. Existing and novel algorithms are evaluated to determine the best technique for creating accurate discrete forms using the minimum number of discontinuities. This allows the event-driven molecular dynamics technique to be efficiently applied to the wide range of continuous force models available in the literature, and facilitates a direct comparison of event-driven and time-driven molecular dynamics. The performance of the proposed conversion techniques are evaluated through application to the Lennard-Jones model. A surprising linear dependence of the computational cost on the number of discontinuities is found, allowing accuracy to be traded for speed in a controlled manner. Excellent agreement is found for static and dynamic properties using a relatively low number of discontinuities. For the Lennard-Jones potential, the optimized discrete form outperforms the original continuous form at gas densities but is significantly slower at higher densities

A Role for Dorsal and Ventral Hippocampus in Inter-Temporal Choice Cost-Benefit Decision Making

Previous studies suggest a preferential role for dorsal hippocampus (dHPC) in spatial memory tasks, whereas ventral hippocampus (vHPC) has been implicated in aspects of fear and/or anxiety. In this study, we tested the hypothesis that vHPC may be a critical subregion for performance on a delay-based, cost-benefit decision making task. Rats chose between the two goal arms of a T maze, one containing an immediately available small reward, the other containing a larger reward that was only accessible after a delay. dHPC, vHPC, and complete hippocampal (cHPC) lesions all reduced choice of the delayed high reward (HR) in favor of the immediately available low reward (LR). The deficits were not due to a complete inability to remember which reward size was associated with which arm of the maze. When an equivalent 10-s delay was introduced in both goal arms, all rats chose the HR arm on nearly all trials. The deficit was, however, reinstated when the inequality was reintroduced. Our results suggest an important role for both dHPC and vHPC in the extended neural circuitry that underlies intertemporal choice

Stereotypic wheel running decreases cortical activity in mice

Prolonged wakefulness is thought to gradually increase sleep need' and influence subsequent sleep duration and intensity, but the role of specific waking behaviours remains unclear. Here we report the effect of voluntary wheel running during wakefulness on neuronal activity in the motor and somatosensory cortex in mice. We find that stereotypic wheel running is associated with a substantial reduction in firing rates among a large subpopulation of cortical neurons, especially at high speeds. Wheel running also has longer-term effects on spiking activity across periods of wakefulness. Specifically, cortical firing rates are significantly higher towards the end of a spontaneous prolonged waking period. However, this increase is abolished when wakefulness is dominated by running wheel activity. These findings indicate that wake-related changes in firing rates are determined not only by wake duration, but also by specific waking behaviours