Search results for "Statistical physics"
showing 10 items of 1402 documents
Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics
2013
Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers however from the same limitation, i.e. the non trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachadran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates. We illustrate the robustness of this …
Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field.
2010
Coarse-grained molecular dynamics simulations offer a dramatic extension of the time-scale of simulations compared to all-atom approaches. In this article, we describe the use of the physics-based united-residue (UNRES) force field, developed in our laboratory, in protein-structure simulations. We demonstrate that this force field offers about a 4000-times extension of the simulation time scale; this feature arises both from averaging out the fast-moving degrees of freedom and reduction of the cost of energy and force calculations compared to all-atom approaches with explicit solvent. With massively parallel computers, microsecond folding simulation times of proteins containing about 1000 r…
High-accuracy extrapolated ab initio thermochemistry. II. Minor improvements to the protocol and a vital simplification
2006
The recently developed high-accuracy extrapolated ab initio thermochemistry method for theoretical thermochemistry, which is intimately related to other high-precision protocols such as the Weizmann-3 and focal-point approaches, is revisited. Some minor improvements in theoretical rigor are introduced which do not lead to any significant additional computational overhead, but are shown to have a negligible overall effect on the accuracy. In addition, the method is extended to completely treat electron correlation effects up to pentuple excitations. The use of an approximate treatment of quadruple and pentuple excitations is suggested; the former as a pragmatic approximation for standard cas…
A Novel Non-Stationary Channel Model Utilizing Brownian Random Paths
2014
This paper proposes a non-stationary channel model in which real-time dynamics of the mobile station (MS) are taken into account. We utilize Brownian motion (BM) processes to model targeted and non-targeted dynamics of the MS. The proposed trajectory model consists of both drift and random components to capture both targeted and non-targeted motions of the MS. The Brownian trajectory model is then employed to provide a non-stationary channel model, in which the scattering effects of the propagation area are modelled by a non-centred one-ring geometric scattering model. The starting point of the motion is a fixed point in the propagation environment, whereas its terminating point is a random…
Quantum Entanglement and the Issue of Selective Influences in Psychology: An Overview
2012
Similar formalisms have been independently developed in psychology, to deal with the issue of selective influences (deciding which of several experimental manipulations selectively influences each of several, generally non-independent, response variables), and in quantum mechanics (QM), to deal with the EPR entanglement phenomena (deciding whether an EPR experiment allows for a "classical" account). The parallels between these problems are established by observing that any two noncommuting measurements in QM are mutually exclusive and can therefore be treated as analogs of different values of one and the same input. Both problems reduce to that of the existence of a jointly distributed syst…
Dynamics of closed ecosystems described by operators
2014
Abstract We adopt the so-called occupation number representation , originally used in quantum mechanics and recently adopted in the description of several classical systems, in the analysis of the dynamics of some models of closed ecosystems. In particular, we discuss two linear models, for which the solution can be found analytically, and a nonlinear system, for which we produce numerical results. We also discuss how a dissipative effect could be effectively implemented in the model.
Quantum walk on the line through potential barriers
2015
Quantum walks are well-known for their ballistic dispersion, traveling $\Theta(t)$ away in $t$ steps, which is quadratically faster than a classical random walk's diffusive spreading. In physical implementations of the walk, however, the particle may need to tunnel through a potential barrier to hop, and a naive calculation suggests this could eliminate the ballistic transport. We show by explicit calculation, however, that such a loss does not occur. Rather, the $\Theta(t)$ dispersion is retained, with only the coefficient changing, which additionally gives a way to detect and quantify the hopping errors in experiments.
Reply to 'The super-quadratic growth of high-harmonic signal as a function of pressure'
2010
Parameter Sensitivity and the Quality of Model Predictions
1994
Using SIM-PEL, a comprehensive model for the pelagic compartment of lake ecosystems, we analyse synergistic toxicant effects in lake ecosystems. We show, that — even for a rather simple model — model predictions may be strongly dependent on the time horizon of the prediction and on the quality of input parameters. For longer time spans, small errors in parameter estimation may lead to qualitatively wrong prediction of toxicant effects. Monte Carlo simulations allow to take errors in parameter estimation into account, but they need rather good estimates of parameter variance.
A method for fitting multi-component decay curves
1982
Abstract A generalization of a non-iterative method recently proposed by Mukoyama for the fitting of two-component decay curve is presented. Two modifications of the procedure are also suggested, by which the influence of the statistical fluctuations of the data may be reduced. Results of fairly good quality are obtained also for three- and, to a lesser extent, for four-component decay curves.