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At least 73 records · Page 4Linked to original sources
arXiv2009

A middle option for choices in the Continuous Opinions and Discrete Actions model

Modeling the conditions for the emergence of extremism is a very important problem, with clear applications for describing the interaction among individuals. Traditional models either are not suited for the task, as in the case of discrete models, or, like Bounded Confidence models, are built with rules that make opinions tend to a common ground between agents or not change at all. Continuous Opinions and Discrete Actions (CODA) model allowed us to observe the emergence of extremist agents, even when every agent was initially a moderate, due to local influence effects. In this paper, the problem of emergence of extremism will be addressed by introducing a middle discrete option in the CODA model, making it similar to a Potts model. Different scenarios for the third option will be discussed: when it is equivalent to withholding judgment, when it is a real third option and when it is a real, middle option. The effects on the opinions will be studied and its effects on extremism discussed. Withholding judgment seems to have an unexpected effect, causing the diminishing of moderate opinions in the long run. For a central third opinion, we find that, under specific conditions, this new choice can act as a buffer between the extreme choices.

physics.soc-ph↗
arXiv2009

Ab initio investigation of the groundstate, electronic, and optical properties of polyyne and cumulene prototypes

We have investigated polyyne and cumulene prototypes based on the density-functional theory. Our independent-particle spectra show that the various carbynes can be distinguished by optical properties comparing the low-energy spectral structure as well as using very general considerations. The latter conclusion is supported by results based on the random-phase approximation including local-field effects.

physics.comp-ph↗
arXiv2011

Active transport and cluster formation on 2D networks

We introduce a model for active transport on inhomogeneous networks embedded in a diffusive environment and investigate the formation of particle clusters. In the presence of a hard-core interaction, cluster sizes exhibit an algebraically decaying distribution in a large parameter regime, indicating the existence of clusters on all scales. The results are compared with a diffusion limited aggregation model and active transport on a regular network. For both models we observe aggregation of particles to clusters which are characterized by a finite size-scale if the relevant time-scales and particle densities are considered.

physics.bio-ph↗
arXiv2010

Scientific Software Engineering in a Nutshell

Writing complex computer programs to study scientific problems requires careful planning and an in-depth knowledge of programming languages and tools. In this chapter the importance of using the right tool for the right problem is emphasized. Common tools to organize computer programs, as well as to debug and improve them are discussed, followed by simple data reduction strategies and visualization tools. Furthermore, some useful scientific libraries such as boost, GSL, LEDA and numerical recipes are outlined.

physics.comp-ph↗
arXiv2011

Introduction to Monte Carlo Methods

Monte Carlo methods play an important role in scientific computation, especially when problems have a vast phase space. In this lecture an introduction to the Monte Carlo method is given. Concepts such as Markov chains, detailed balance, critical slowing down, and ergodicity, as well as the Metropolis algorithm are explained. The Monte Carlo method is illustrated by numerically studying the critical behavior of the two-dimensional Ising ferromagnet using finite-size scaling methods. In addition, advanced Monte Carlo methods are described (e.g., the Wolff cluster algorithm and parallel tempering Monte Carlo) and illustrated with nontrivial models from the physics of glassy systems. Finally, we outline an approach to study rare events using a Monte Carlo sampling with a guiding function.

cond-mat.stat-mech↗
arXiv2009

EasyDD: A Program for Batch Processing and Visualization of Powder Diffraction Data

In this article we report the release of a new program for batch processing and visualization of powder diffraction data. The program, which is free-of-charge for non-commercial use and can be obtained with its detailed documentation from our website www.scienceware.net, is currently in use by a number of researchers in University College London, University of Manchester, Utrecht University in the Netherland, European Synchrotron Radiation Facility (ESRF), and Diamond Light Source. The software is designed for the treatment of large volume of powder diffraction data, especially those obtained from the new generation of synchrotron detectors. The program has a great potential for future development to be a workbench for powder diffraction work.

physics.comp-ph↗
arXiv2009

Random Number Generators: A Survival Guide for Large Scale Simulations

Monte Carlo simulations are an important tool in statistical physics, complex systems science, and many other fields. An increasing number of these simulations is run on parallel systems ranging from multicore desktop computers to supercomputers with thousands of CPUs. This raises the issue of generating large amounts of random numbers in a parallel application. In this lecture we will learn just enough of the theory of pseudo random number generation to make wise decisions on how to choose and how to use random number generators when it comes to large scale, parallel simulations.

cond-mat.stat-mech↗
arXiv2011

Structures and magnetic properties of ZnO nanoislands

Using first-principles calculations, we systematically study the atomic structures and electronic properties for two dimensional triangular ZnO nanoislands that are graphite-like with monolayer and bilayer thickness. We find that the monolayer ZnO nanoisland with O terminated zigzag edges is magnetic at its ground state, with the magnetism coming from the O edge states. The other monolayer and bilayer ZnO nanoislands with different edge structures are all nonmagnetic at their ground states. It is further revealed that for different ZnO nanoislands, their magnetic properties are quite dependent on their sizes, with larger nanoislands having larger magnetic moments.

cond-mat.mtrl-sci↗
arXiv2009

Von Neumann Turbulent Transport Model

I propose a simple model, based on an analogy to von Neumann artificial viscosity, of turbulent diffusion, heat diffusion and viscosity coefficients for use in modeling subgrid turbulent diffusivity in multi-phase numerical hydrodynamics and, more generally, in subgrid turbulent viscosity and thermal transport. In analogy to the von Neumann artificial viscosity, these coefficients explicitly contain the grid size and do not attempt a quantitative model of the unresolved turbulence. In order to address the problem that it is often not known a priori when and where a flow will become turbulent, the coefficients are set to zero when the flow is not expected to be turbulent on the basis of a Richardson/Rayleigh-Taylor stability criterion, in analogy to von Neumann's setting of artificial viscosity to zero in expanding flows.

physics.comp-ph↗
arXiv2010

An approach to the Riemann problem for SPH inviscid ideal flows

In the physically non viscous fluid dynamics, "shock capturing" methods adopt either an artificial viscosity contribution or an appropriate Riemann solver algorithm. These techniques are necessary to solve the strictly hyperbolic Euler equations if flow discontinuities (the Riemann problem) must be solved. A necessary dissipation is normally used in such cases. An explicit artificial viscosity contribution is normally adopted to smooth out spurious heating and to treat transport phenomena. Such a treatment of inviscid flows is also widely adopted in the Smooth Particle Hydrodynamics (SPH) finite volume free Lagrangian scheme. In other cases, the intrinsic dissipation of Godunov - type methods is implicitly useful. Instead "shock tracking" methods normally use the Rankine - Hugoniot jump conditions to solve such problem. A simple, effective solution of the Riemann problem in inviscid ideal gases is here proposed, based on an empirical reformulation of the equation of state (EoS) in the Euler equations in fluid dynamics, whose limit for a motionless gas coincides with the classical EoS of ideal gases. The application of such effective solution of the Riemann problem excludes any dependence, in the transport phenomena, on particle resolution length $h$ in non viscous SPH flows. Results on 1D shock tube tests are here shown.

physics.flu-dyn↗
arXiv2009

Diffusive Corrections to Pn Approximations

In this paper, we investigate moment methods from a general point of view using an operator notation. This theoretical approach lets us explore the moment closure problem in more detail. This gives rise to a new idea, proposed in [Levermore2005, Levermore2009], of how to improve the well-known Pn approximations. We systematically develop a diffusive correction to the Pn equations from the operator formulation - the so-called Dn approximation. We validate the new approach with numerical examples in one and two dimensions.

physics.comp-ph↗
arXiv2010

Asymptotic and factorial expansions of Euler series truncation errors via exponential polynomials

A detailed analysis of the remainder obtained by truncating the Euler series up to the $n$th-order term is presented. In particular, by using an approach recently proposed by Weniger, asymptotic expansions of the remainder, both in inverse powers and in inverse rising factorials of $n$, are obtained. It is found that the corresponding expanding coefficients are expressed, in closed form, in terms of exponential polynomials, well known in combinatorics, and in terms of associated Laguerre polynomials, respectively. A study of the divergence and/or of the convergence of the above expansions is also carried out for positive values of the Euler series argument.

physics.comp-ph↗
arXiv2009

Numerical modeling of fluid flow through porous media (Modelowanie numeryczne transportu plynow przez osrodki porowate)

The aim of the thesis is to present and analyze two particular problems of transport in porous media flow. The first of them is related to the process of saturation of porous building materials. Recently, M. Küntz and P. Lavalée, using a computer model of this process, have concluded that the anomalous diffusion assumption is correct. In this thesis I present an alternative explanation of this results without any refer to anomalous diffusion. The second part of the thesis covers the numerical analysis of the tortuosity of the flow -- one of a very interesting physical macroscopic variables characterizing transport in porous media. (in Polish)

physics.comp-ph↗
arXiv2010

Computational Estimates of Binding Affinities for Estrogen Receptor Isoforms in Rainbow Trout

Molecular dynamics simulations were used to determine the binding affinities between between the hormone 17 beta-estradiol (E2) and different estrogen receptor (ER) isoforms in the rainbow trout, Oncorhynchus mykiss. Previous phylogenetic analysis indicates that a whole genome duplication prior to the divergence of ray-finned fish led to two distinct ER beta isoforms, ER beta 1 and ER beta 2, and the recent whole genome duplication in the ancestral salmonid created two ER alpha isoforms, ER alpha 1 and ER alpha 2. The objective of our computational studies is to provide insight into the underlying evolutionary pressures on these isoforms. For the ER alpha subtype our results show that E2 binds preferentially to ER alpha 1 over ER alpha 2. Tests of lineage specific dN/dS ratios indicate that the ligand binding domain of the ER alpha 2 gene is evolving under relaxed selection relative to all other ER alpha genes. Comparison with the highly conserved DNA binding domain suggests that ER alpha 2 may be undergoing neofunctionalization possibly by binding to another ligand. By contrast, both ER beta 1 and ER beta 2 bind similarly to E2 and the best fitting model of selection indicates that the ligand binding domain of all ER beta genes are evolving under the same level of purifying selection, comparable to ER alpha 1.

physics.bio-ph↗
arXiv2010

Single-Species Weibel Instability of Radiationless Plasma

A Particle-in-Cell (PIC) numerical simulation of the electron Weibel instability is applied in a frame of Darwin (radiationless) approximation of the self-consistent fields of sparse plasma. As a result, we were able to supplement the classical picture of the instability and, in particular, to obtain the dependency of the basic characteristics (the time of development and the maximum field energy) of the thermal anisotropy parameter, to trace the dynamic restructuring of current filaments accompanying the nonlinear stage of the instability and to trace in detail the evolution of the initial anisotropy of the electron component of plasma.

physics.plasm-ph↗
arXiv2010

Rapid sampling of all-atom peptides using a library-based polymer-growth approach

We adapted existing polymer growth strategies for equilibrium sampling of peptides described by modern atomistic forcefields with implicit solvent. The main novel feature of our approach is the use of pre-calculated statistical libraries of molecular fragments. A molecule is sampled by combining fragment configurations -- of single residues in this study -- which are stored in the libraries. Ensembles generated from the independent libraries are reweighted to conform with the Boltzmann factor distribution of the forcefield describing the full molecule. In this way, high-quality equilibrium sampling of small peptides (4-8 residues) typically requires less than one hour of single-processor wallclock time and can be significantly faster than Langevin simulations. Furthermore, approximate but clash-free ensembles can be generated for larger peptides (e.g., 16 residues) in less than a minute of single-processor computing. We also describe an application to free energy calculation, a "multi-resolution" implementation of the growth procedure and application to fragment assembly protein-structure prediction protocols.

physics.bio-ph↗
arXiv2010

Hybrid modeling of plasmas

Here we present the mathematical and numerical details of a general hybrid model for plasmas. All grid quantities are stored at cell centers on the grid. The most common discretization of the fields in PIC solvers is to have the electric and magnetic fields staggered, introduced by Yee. This automatically ensures that div(B)=0, down to round-off errors. Here we instead present a cell centered discretization of the magnetic field. That the standard cell centered second order stencil for rot(E) in Faraday's law will preserve div(B)=0 was noted by Toth. The advantage of a cell centered discretization is ease of implementation, and the possibility to use available solvers that only handle cell centered variables. We also show that the proposed method has very good energy conservation for a simple test problem in three dimensions, when compared to a commonly used algorithm.

physics.space-ph↗