Distribution of Random Streams for Simulation Practitioners

International audienceThere is an increasing interest in the distribution of parallel random number streamsin the high-performance computing community particularly, with the manycore shift. Even ifwe have at our disposal statistically sound random number generators according to the latestand thorough testing libraries, their parallelization can still be a delicate problem. Indeed, aset of recent publications shows it still has to be mastered by the scientific community. Withthe arrival of multi-core and manycore processor architectures on the scientist desktop, modelerswho are non-specialists in parallelizing stochastic simulations need help and advice in distributingrigorously their experimental plans and replications according to the state of the art in pseudo-random numbers parallelization techniques. In this paper, we discuss the different partitioningtechniques currently in use to provide independent streams with their corresponding software. Inaddition to the classical approaches in use to parallelize stochastic simulations on regular processors,this paper also presents recent advances in pseudo-random number generation for general-purposegraphical processing units. The state of the art given in this paper is written for simulationpractitioners

Zinterhof Sequences in GRID-Based Numerical Integration

The appropriateness of Zinterhof sequences to be used in GRID-based QMC integration is discussed. Theoretical considerations as well as experimental investigations are conducted comparing and assessing different strategies for an efficient and reliable usage. The high robustness and ease of construction exhibited by those sequences qualifies them as excellent QMC point set candidates for heterogeneous environments like the GRID

Computational modelling of the vortex state in high-temperature superconductors

The vortex state in high temperature superconductors is investigated using computer simulations. Vortices are represented as particles and we employ Langevin dynamics to study the statics and dynamics of the system.We show that the long-range nature of the vortex-vortex interaction can result in numerical artefacts, and provide two techniques to overcome these problems: (i) using a ‘smooth’ cut-off which reduces the interaction force near the cut-off smoothly to zero, and (ii) an infinite lattice summation technique applicable for a K0-Bessel function interaction potential.Using these methods, we investigate a two-dimensional vortex system driven over a weak random potential. We observe the moving Bragg glass regime, and study the recently predicted critical transverse force. Our results agree with and extend other theoretical and numerical works, and provide important confirmation for the moving glass theory. We investigate the critical transverse force as a function of system size, temperature, driving force and disorder strength. We provide numerical estimates to assist experimentalists in verifying its existence.We study vortex matter in three-dimensional layered superconductors in the limit of zero Josephson coupling. The long-range nature of the electromagnetic interaction between pancake vortices in the c-direction allows us to employ a meanfield method: all attractive inter-layer interactions are described by a substrate potential, which pancakes experience in addition to the in-layer pancake repulsion. Using an averaged pancake-density, we iteratively re-compute the substrate potential. The self-consistent method converges, depending on temperature, either to a pancake lattice or a pancake liquid. We investigate different methods to perform these simulation efficiently, and compute the instability line for the transition from solid to liquid, the melting line and the entropy jump across the transition

Molecular Dynamics Studies on Structure and Phase Transitions of Nanoconfined Water

The goal of this dissertation was to understand the structure and dynamics of quasi–1D and quasi–2D water confined in low dimensional carbon materials by the use of molecular dynamics simulation methods combined with enhanced sampling strategies. For this goal, a first step was to derive simple but reliable LJ potential models for the interaction between water and carbon sheets of different curvature. These effective models then can be used to carry out a series of MD investigations on water confined inside CNTs and graphene capillaries, comprising the variation of the water model

Stochastic modelling of eukaryotic cell cycle

Stochastic models are developed to capture the inherent stochasticity of the biochemical networks associated to many biological processes. The objective of the present thesis is to present a detailed picture of stochastic approach for the mathematical modeling of eukaryotic cell cycle, to demonstrate an important application of such model in chemotherapy and to present a methodology for selecting the model parameters. The stochastic cell cycle model, developed using stochastic chemical kinetics approach, leads to the formation of an infinite dimensional differential equation in probabilities of system being in a specific state. Using Monte Carlo simulations of this model, dynamics of populations of eukaryotic cells such as yeasts or mammalian cells are obtained. Simulations are stochastic in nature and therefore exhibit variability among cells that is similar to the variability observed in natural populations. The model’s capability to predict heterogeneities in cell populations is used as a basis to implement it in a chemotherapic modeling framework to demonstrate how the model can be used to assist in the drug development stage by investigating drug administration strategies that can have different killing effect on cancer cells and healthy cells. Finally, basic cell cycle model is refined in a systematic way to make it more suitable for describing the population characteristics of budding yeast. Selection of model parameters using an evolutionary optimization strategy referred to as insilico evolution is described. The benefits of this approach lie in the fact that it generates an initial guess of reasonable set of parameters which in turn can be used in the least squares fitting of model to the steady state distributions obtained from flow cytometry measurements. The Insilco evolution algorithm serves as a tool for sensitivity analysis of the model parameters and leads to a synergistic approach of model and experiments guiding each other. To conclude, the stochastic model based on single cell kinetics will be useful for predicting the population distribution on whole organism level. Such models find applications in wide areas of biological and biomedical applications. Evolutionary optimization strategies can be used in parameter estimation methods based on steady state distributions

Computational Studies of Complex Systems in Condensed Matter Physics

Physic

Ring Polymers as a Model for Cellular Organization

A number of experimental studies have been reported on the spatial organization and collective motion of living cells during the past few decades. To explain the experimentally observed results, we propose a novel approach, in which the cells are modeled as semi-flexible ring polymers. We found that the basic physical properties of the polymer rings, such as average area per cell, elongation, and orientation highly depend on the areal polymer density. Investigations of systems composed of two types of ring polymers with different bending rigidities show that multi-component ring-polymer systems exhibit microphase separation. Simulations of the ring polymers on a unidirectional patterned substrate show that the polymers tend to orient along the direction of the substrate pattern. Simulations of the cells in the presence of non-equilibrium motile forces show that driven cell motility leads to aggregation of the cells with strong correlations in the velocity field

A Magneto-Gravitational Neutron Trap for the Measurement of the Neutron Lifetime

Thesis (Ph.D.) - Indiana University, Physics, 2015Neutron decay is the simplest example of nuclear beta-decay. The mean decay lifetime is a key input for predicting the abundance of light elements in the early universe. A precise measurement of the neutron lifetime, when combined with other neutron decay observables, can test for physics beyond the standard model in a way that is complimentary to, and potentially competitive with, results from high energy collider experiments. Many previous measurements of the neutron lifetime used ultracold neutrons (UCN) confined in material bottles. In a material bottle experiment, UCN are loaded into the apparatus, stored for varying times, and the surviving UCN are emptied and counted. These measurements are in poor agreement with experiments that use neutron beams, and new experiments are needed to resolve the discrepancy and precisely determine the lifetime. Here we present an experiment that uses a bowl-shaped array of NdFeB magnets to confine neutrons without material wall interactions. The trap shape is designed to rapidly remove higher energy UCN that might slowly leak from the top of the trap, and can facilitate new techniques to count surviving UCN within the trap. We review the scientific motivation for a precise measurement of the neutron lifetime, and present the commissioning of the trap. Data are presented using a vanadium activation technique to count UCN within the trap, providing an alternative method to emptying neutrons from the trap and into a counter. Potential systematic effects in the experiment are then discussed and estimated using analytical and numerical techniques. We also investigate solid nitrogen-15 as a source of UCN using neutron time-of-flight spectroscopy. We conclude with a discussion of forthcoming research and development for UCN detection and UCN sources

Atomistic Simulations and Computations of Clay Minerals at Geologic Carbon Sequestration Conditions

Classical atomistic simulations are carried out to study carbon sequestration at deep underground formations. In classical simulations, formulas and equations are inherently different from those used in continuum and quantum calculations. Here, in contrast to continuum approaches such as the finite element method, interactions of atomic particles are computed, and unlike quantum techniques such as the density functional theory, calculations are not restricted to a limited number of atoms, therefore a balance between accuracy and computational cost makes classical atomistic techniques the best candidate to study layered materials in numerous situations. The success of CO2 sequestration depends on diverse parameters related to the depth and type of the underground formations. In this work, chemical, physical, and geometrical characteristics of formations are investigated. Different types of interlayer cation (Na+ and Ca2+), intercalated molecule (water and CO2), and clay structure (montmorillonite (MMT) and beidellite (BEI), and pyrophyllite (PPT)) are investigated as chemical parameters. Rotational degree of layers, pressure, temperature and chemical potential are considered as geometrical and physical variables. Using free energy calculations, stable energy states due to the intercalation of water and carbon dioxide to smectite structures are predicted. For hydrated systems, three states consisting of interlayer spacing values 9-10, 11.5-12.5 and 14.5-15.5 A, respectively called 0W, 1W and 2W hydration state are found. For systems including mixed H2O-CO2 intercalation, the amount of adsorbed CO2 alters and reaches its peak at the sub-first hydration levels. Another fascinating result emerges by simulating the binary MMT-CO2 system. The global minimum is found at the dry (0W) state which explains why there is no experimental observation of pure CO2 adsorption on the MMT surface. Finally, ternary smectite-H2O-CO2 simulations show that the amount of adsorbed CO2 in the clay phase is higher than that of bulk phase suggesting that the underground formation is a proper option to store extensive volumes of the green house gas carbon dioxide

Institute of Safety Research; Annual Report 1993

The report gives an overview on the scientific work of the Institute of Safety Research in 1993