Abstract:We developed a software package (RedMD) to perform molecular dynamics simulations and normal mode analysis of reduced models of proteins, nucleic acids, and their complexes. With RedMD one can perform molecular dynamics simulations in a microcanonical ensemble, with Berendsen and Langevin thermostats, and with Brownian dynamics. We provide force field and topology generators which are based on the one-bead per residue/nucleotide elastic network model and its extensions. The user can change the force field parameters with the command line options that are passed to generators. Also, the generators can be modified, for example, to add new potential energy functions. Normal mode analysis tool is available for elastic or anisotropic network models. The program is written in C and C++ languages and the structure/topology of a molecule is based on an XML format. OpenMP technology for sharedmemory architectures was used for code parallelization. The code is distributed under GNU public licence and available at
We perform the stochastic analysis of a thermochemical system using a master equation which describes a chemical reaction and includes discrete and continuous temperature jumps. We study the time evolution of the system selecting the temperature of the thermostat as an easily tunable control parameter. Depending on the thermostat temperature, the system can be in an excitable, oscillatory, or stationary regime. Stochastic time series for the system temperature are generated and the distributions of interspike intervals are analyzed in the three dynamical regimes separated by a homoclinic bifurcation and a Hopf bifurcation. Different constructive roles of internal fluctuations are exhibited. A noise-induced transition is observed in the vicinity of the Hopf bifurcation. Coherence resonance and stochastic resonance are found in the oscillatory regime. In a range of thermostat temperatures, a nontrivial behavior of the highly nonlinear system is revealed by the existence of both a minimum and a maximum in the scaled standard deviation of interspike intervals as a function of particle number. This high sensitivity to system size illustrates that controlling dynamics in nanoreactors may remain a difficult task.
We show that Granger-type causality analysis can be applied to determine correlations between atomic motions. A multivariate autoregressive model and directed transfer functions were applied to analyze the causality in the dynamics of a linear chain of atoms and the malonaldehyde molecule. The presented methodology is promising, can be applied in post-processing of classical and quantum-classical molecular dynamics data, and to study the mechanisms of functioning of biomolecular systems.
ABSTRACT:We present a parallel version of a quantum dynamics (QD) algorithm in a wave function representation. The algorithm has been optimized for a Linux cluster as well as for Cray T3E, using a parallel version of a three-dimensional FFT library. We have applied this algorithm for solving the nonlinear Gross-Pitaevskii equation (GPE), which describes the evolution of Bose-Einstein condensates (BEC) in the mean field approximation. Our method reduces the computational time and allows the study of nonlinear quantum systems.
Reliable feasibility analysis of potential exploitation of a mining waste deposit poses a great challenge. One of the most crucial parts of this process is the approximation of the deposit volume. In this case study we propose a novel method of tailing pile volume estimation using open remote sensing and cartographic data. For selected piles, the difference between the proposed and classical approach reach 50% of the pile volume, which is a significant change in the potential value of the deposit.
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