Showing papers by "Nicolae Goga published in 2012"

Efficient Algorithms for Langevin and DPD Dynamics.

Abstract: In this article, we present several algorithms for stochastic dynamics, including Langevin dynamics and different variants of Dissipative Particle Dynamics (DPD), applicable to systems with or without constraints. The algorithms are based on the impulsive application of friction and noise, thus avoiding the computational complexity of algorithms that apply continuous friction and noise. Simulation results on thermostat strength and diffusion properties for ideal gas, coarse-grained (MARTINI) water, and constrained atomic (SPC/E) water systems are discussed. We show that the measured thermal relaxation rates agree well with theoretical predictions. The influence of various parameters on the diffusion coefficient is discussed.

GPU-SD and DPD parallelization for Gromacs tools for molecular dynamics simulations

Abstract: This article presents the GPU parallelization of new algorithms SD and DPD types for molecular dynamics systems developed by the Molecular Dynamics Group, University of Groningen, the Netherlands One should note that molecular dynamics simulations are time-consuming simulations of systems, running time ranging from days to weeks and months Therefore parallelization is a key issue for the well-running and use of MD software The paper presents the main ingredients of GPU parallelization of the new algorithms and simulation results It can be concluded that the parallelization through the use of graphical cards improves the performances of the runs as compared to the serial version of the code

Methods for multiscale modeling of membranes

Abstract: Multiscale modeling is a recent approach to simulating molecular systems, such as membranes and liposomes, in which different levels of detail are combined. By using distinct models, it is often possible to speed up or enrich the sampling of a given system. Examples are the use in molecular dynamics simulations of both coarse-grained and fine-grained representations, either simultaneously or alternating in time or space domains. Another possible example is the combination of Monte Carlo and molecular dynamics simulations. This chapter reviews the existing proposed methods of multiscale modeling and simulation and also presents new insights into this fascinating new trend.

Using TTCN-3 for testing the interoperability of HL7v3 based applications

Abstract: HL7v3 standard was designed to facilitate communication between all types of eHealth applications, regardless of the domain of activity. The exibility of the HL7v3 messages led, however, to proprietary denitions of HL7v3 messages and structures. In order to unify the communication in dierent domains, proles have been developed and standardized. In this context, testing plays an important role in assuring interoperability, as well. This paper presents a method to test the interoperability of HL7v3 applications, using the standardized TTCN-3 test scripting language and its corresponding TTCN-3 test system. The full testing process is described, highlighting all the components involved and providing guidelines for implementing them. This approach requires testers to be familiar to the TTCN-3 environment.