A General Algorithm for Sampling Rare Events in Non-Equilibrium and Non-Stationary Systems

Although many computational methods for rare event sampling exist, this type of calculation is not usually practical for general nonequilibrium conditions, with macroscopically irreversible dynamics and away from both stationary and metastable states. A novel method for calculating the time-series of the probability of a rare event is presented which is designed for these conditions. The method is validated for the cases of the Glauber-Ising model under time-varying shear flow, the Kawasaki-Ising model after a quench into the region between nucleation dominated and spinodal decomposition dominated phase change dynamics, and the parallel open asymmetric exclusion process (p-o ASEP). The method requires a subdivision of the phase space of the system: it is benchmarked and found to scale well for increasingly fine subdivisions, meaning that it can be applied without detailed foreknowledge of the physically important reaction pathways.Comment: 11 pages, 6 figure

Crystal nucleation mechanism in melts of short polymer chains under quiescent conditions and under shear flow

We present a molecular dynamics simulation study of crystal nucleation from undercooled melts of n-alkanes, and we identify the molecular mechanism of homogeneous crystal nucleation under quiescent conditions and under shear flow. We compare results for n-eicosane(C20) and n-pentacontahectane(C150), i.e. one system below the entanglement length and one above. Under quiescent conditions, we observe that entanglement does not have an effect on the nucleation mechanism. For both chain lengths, the chains first align and then straighten locally. Then the local density increases and finally positional ordering sets in. At low shear rates the nucleation mechanism is the same as under quiescent conditions, while at high shear rates the chains align and straighten at the same time. We report on the effects of shear rate and temperature on the nucleation rates and estimate the critical shear rates, beyond which the nucleation rates increase with the shear rate. We show that the viscosity of the system is not affected by the crystalline nuclei.Comment: 9 page

The Early Crystal Nucleation Process in Hard Spheres shows Synchronised Ordering and Densification

We investigate the early part of the crystal nucleation process in the hard sphere fluid using data produced by computer simulation. We find that hexagonal order manifests continuously in the overcompressed liquid, beginning approximately one diffusion time before the appearance of the first `solid-like' particle of the nucleating cluster, and that a collective influx of particles towards the nucleation site occurs simultaneously to the ordering process: the density increases leading to nucleation are generated by the same individual particle displacements as the increases in order. We rule out the presence of qualitative differences in the early nucleation process between medium and low overcompressions, and also provide evidence against any separation of translational and orientational order on the relevant lengthscales

Free Energies by Thermodynamic Integration Relative to an Exact Solution, Used to Find the Handedness-Switching Salt Concentration for DNA

Sets of free energy differences are useful for finding the equilibria of chemical reactions, while absolute free energies have little physical meaning. However finding the relative free energy between two macrostates by subtraction of their absolute free energies is a valuable strategy in certain important cases. We present calculations of absolute free energies of biomolecules, using a combination of the well-known Einstein Molecule method (for treating the solute) with a conceptually related method of recent genesis for computing free energies of liquids (to treat the solvent and counterions). The approach is based on thermodynamic integration from a detailed atomistic model to one which is simplified but analytically solvable, thereby giving the absolute free energy as that of the tractable model plus a correction term found numerically. An example calculation giving the free energy with respect to salt concentration for the B- and Z-isomers of all-atom duplex DNA in explicit solvent and counterions is presented. The coexistence salt concentration is found with unprecedented accuracy.Comment: Supplementary derivations and convergence data were uploaded as two pdf file

A case-matched study of neurophysiological correlates to attention /working memory in people with somatic hypervigilance

Accepted 14 June 2016Somatic hypervigilance describes a clinical presentation in which people report more, and more intense, bodily sensations than is usual. Most explanations of somatic hypervigilance implicate altered information processing, but strong empirical data are lacking. Attention and working memory are critical for information processing, and we aimed to evaluate brain activity during attention/working memory tasks in people with and without somatic hypervigilance. Method: Data from 173 people with somatic hypervigilance and 173 controls matched for age, gender, handedness, and years of education were analyzed. Event-related potential (ERP) data, extracted from the continuous electroencephalograph recordings obtained during performance of the Auditory Oddball task, and the Two In A Row (TIAR) task, for N1, P2, N2, and P3, were used in the analysis. Between-group differences for P3 amplitude and N2 amplitude and latency were assessed with two-tailed independent t tests. Between-group differences for N1 and P2 amplitude and latency were assessed using mixed, repeated measures analyses of variance (ANOVAs) with group and Group × Site factors. Linear regression analysis investigated the relationship between anxiety and depression and any outcomes of significance. Results: People with somatic hypervigilance showed smaller P3 amplitudes—Auditory Oddball task: t(285) = 2.32, 95% confidence interval, CI [3.48, 4.47], p = .026, d = 0.27; Two-In-A-Row (TIAR) task: t(334) = 2.23, 95% CI [2.20; 3.95], p = .021, d = 0.24—than case-matched controls. N2 amplitude was also smaller in people with somatic hypervigilance—TIAR task: t(318) = 2.58, 95% CI [0.33, 2.47], p = .010, d = 0.29—than in case-matched controls. Neither depression nor anxiety was significantly associated with any outcome. Conclusion: People with somatic hypervigilance demonstrated an event-related potential response to attention/working memory tasks that is consistent with altered information processing.Carolyn Berryman, Vikki Wise, Tasha R. Stanton, Alexander McFarlane and G. Lorimer Mosele

Agency in Transport Service: Implications of Traveller Mode Choice Objective and Latent Attributes Using Random Parameter Logit Model

Abstract: This paper explains how principal-agent theory (PAT) can be used as an analytical tool to understand the traveller-Transport for NSW (TfNSW) relationship and minimise the agency problem in the relationship by examining traveller preferences for mode choices. The paper emphasises latent variables (LVs) and traditional objective attributes (TOAs) together during the choice process within the agency relationship, as a method by which the utility of the principal (traveller) can be maximised and evaluated using a discrete choice experiment, i.e. random parameter logit (RPL) model. The probability of car use is significantly higher than public transport, which indicates that an agency problem exists in the relationship and incorporating traveller preferences in the transport projects may minimise this problem. Citation: Anwar, A.H.M., Tieu, K., Gibson, P., Win, K.T. & Berryman, M.J. (2014). Agency in Transport Service: Implications of Traveller Mode Choice Objective and Latent Attributes Using Ransom Parameter Logit Model. In: Campbell P. and Perez P. (Eds), Proceedings of the International Symposium of Next Generation Infrastructure, 1-4 October 2013, SMART Infrastructure Facility, University of Wollongong, Australia

Factor structure of the autonomy preference index in people with severe mental illness

People vary in the amount of control they want to exercise over decisions about their healthcare. Given the importance of patient-centered care, accurate measurement of these autonomy preferences is critical. This study aimed to assess the factor structure of the Autonomy Preference Index (API), used widely in general healthcare, in individuals with severe mental illness. Data came from two studies of people with severe mental illness (N=293) who were receiving mental health and/or primary care/integrated care services. Autonomy preferences were assessed with the API regarding both psychiatric and primary care services. Confirmatory factor analysis was used to evaluate fit of the hypothesized two-factor structure of the API (decision-making autonomy and information-seeking autonomy). Results indicated the hypothesized structure for the API did not adequately fit the data for either psychiatric or primary care services. Three problematic items were dropped, resulting in adequate fit for both types of treatment. These results suggest that with relatively minor modifications the API has an acceptable factor structure when asking people with severe mental illness about their preferences to be involved in decision-making. The modified API has clinical and research utility for this population in the burgeoning field of autonomy in patient-centered healthcare

Production cross sections from 82Se fragmentation as indications of shell effects in neutron-rich isotopes close to the drip-line

Production cross sections for neutron-rich nuclei from the fragmentation of a 82Se beam at 139 MeV/u were measured. The longitudinal momentum distributions of 126 neutron-rich isotopes of elements 11 <= Z <= 32 were scanned using an experimental approach of varying the target thickness. Production cross sections with beryllium and tungsten targets were determined for a large number of nuclei including several isotopes first observed in this work. These are the most neutron-rich nuclides of the elements 22 <= Z <= 25 (64Ti, 67V, 69Cr, 72Mn). One event was registered consistent with 70Cr, and another one with 75Fe. The production cross sections are correlated with Qg systematics to reveal trends in the data. The results presented here confirm our previous result from a similar measurement using a 76Ge beam, and can be explained with a shell model that predicts a subshell closure at N = 34 around Z = 20. This is demonstrated by systematic trends and calculations with the Abrasion-Ablation model that are sensitive to separation energies.Comment: 13 pages, 11 figures, accepted to Phys.Rev.