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A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are…

Biomolecules · Quantitative Biology 2017-07-13 Akira R. Kinjo

We numerically investigate the long-time behavior of the density-density auto-correlation function in driven lattice gases with particle exclusion and periodic boundary conditions in one, two, and three dimensions using precise Monte Carlo…

Statistical Mechanics · Physics 2011-05-06 George L. Daquila , Uwe C. Tauber

Biased diffusion of two species with conserved dynamics on a 2xL periodic lattice is studied via Monte Carlo simulations. In contrast to its simple one-dimensional version on a ring, this quasi one-dimensional model surprisingly exhibits…

Statistical Mechanics · Physics 2009-10-31 G. Korniss , B. Schmittmann , R. K. P. Zia

The behavior of confined cylindrical micelle-forming surfactants under the influence of shear has been investigated using Monte Carlo simulations. The surfactants are modeled as coarse-grained lattice polymers, while the Monte Carlo shear…

Soft Condensed Matter · Physics 2009-11-10 Gaurav Arya , Athanassios Z. Panagiotopoulos

We present a new method for investigating first-order phase transitions using Monte Carlo simulations. It relies on the multiple-histogram method and uses solely histograms of individual phases. In addition, we extend the method to include…

adap-org · Physics 2009-10-28 Martin Ebeling , Walter Nadler

We study weak localization effects in the ballistic regime as induced by man-made scatterers. Specular reflection of the electrons off these scatterers results into backscattered trajectories which interfere with their time-reversed path…

Mesoscale and Nanoscale Physics · Physics 2009-10-31 K. L. Janssens , F. M. Peeters

Polymers confined to a narrow channel are subject to strong entropic forces that tend to drive the molecules apart. In this study, we use Monte Carlo computer simulations to study the segregation behavior of two flexible hard-sphere…

Soft Condensed Matter · Physics 2021-01-27 James M. Polson , Qinxin Zhu

We study an induced dynamics in the space of energy of single-spin-flip Monte Carlo algorithm. The method gives an efficient reweighting technique. This dynamics is shown to have relaxation times proportional to the specific heat. Thus, it…

Statistical Mechanics · Physics 2009-10-31 Jian-Sheng Wang , Tien Kiat Tay , Robert H. Swendsen

We propose an efficient Monte Carlo algorithm for simulating a ``hardly-relaxing" system, in which many replicas with different temperatures are simultaneously simulated and a virtual process exchanging configurations of these replica is…

Condensed Matter · Physics 2009-10-28 Koji Hukushima , Koji Nemoto

Based upon kinetic Monte Carlo simulations of crystallization in a simple polymer model we present a new picture of the mechanism by which the thickness of lamellar polymer crystals is constrained to a value close to the minimum…

Condensed Matter · Physics 2007-05-23 Jonathan Doye , Daan Frenkel

Ordering processes in fcc-alloys with composition A_3B (like Cu_3Au, Cu_3Pd, CoPt_3 etc.) are investigated by Monte Carlo simulation within a class of lattice models based on nearest-neighbor (NN) and second-neighbor (NNN) interactions.…

Statistical Mechanics · Physics 2015-06-24 Michael Kessler , Wolfgang Dieterich , Andrzej Majhofer

Dynamic Monte Carlo simulations are used to study coupled transport (co-transport) through sub-nanometer-diameter pores. In this classic Hodgkin-Keynes mechanism, an ion species uses the large flux of an abundant ion species to move against…

Soft Condensed Matter · Physics 2013-11-27 Dezső Boda , Éva Csányi , Dirk Gillespie , Tamás Kristóf

In this article, we briefly review the studies on magnetic relaxation behaviours. The theoretical as well as experimental investigations are reported briefly. A major part of this article is devoted to the recent Monte Carlo investigations…

Statistical Mechanics · Physics 2023-11-21 Ishita Tikader , Muktish Acharyya

The nature of freezing and melting transitions for a system of model colloids interacting by a DLVO potential in a spatially periodic external potential is studied using extensive Monte Carlo simulations. Detailed finite size scaling…

Statistical Mechanics · Physics 2009-11-07 W. Strepp , S. Sengupta , P. Nielaba

The effect of a random surface field, within the bimodal distribution, on the layering transitions in a spin-1/2 Ising thin film is investigated, using Monte Carlo simulations. It is found that the layering transitions depend strongly on…

Statistical Mechanics · Physics 2009-11-10 H. Ez-Zahraouy , L. Bahmad , A. Benyoussef

While kinetic Monte Carlo simulations can provide long-time simulations of the dynamics of physical and chemical systems, it is not yet possible in general to identify the inverse Monte Carlo attempt frequency with a physical timescale.…

Materials Science · Physics 2007-05-23 I. Abou Hamad , P. A. Rikvold , G. Brown

We present data of Monte Carlo simulations for monodisperse linear polymer chains in dense melts with degrees of polymerization between N=16 and N=512. The aim of this study is to investigate the crossover from Rouse-like dynamics for short…

Soft Condensed Matter · Physics 2009-10-31 T. Kreer , J. Baschnagel , M. Mueller , K. Binder

Motivated by recent experimental results in ultra-thin helimagnetic Holmium films, we have performed an extensive classical Monte Carlo simulation of films of different thickness, assuming a Hamiltonian with six inter-layer exchange…

Statistical Mechanics · Physics 2015-05-13 Fabio Cinti , Alessandro Cuccoli , Angelo Rettori

We modified the recently proposed multicanonical MC algorithm for the case of a magnetic field driven order--order phase transition. We test this {\it multimagnetic} Monte Carlo algorithm for the D=2 Ising model at $\beta=0.5$ and simulate…

High Energy Physics - Lattice · Physics 2007-05-23 U. Hansmann , B. A. Berg , T. Neuhaus

Most realistic, off-lattice surface simulations are done canonically--- conserving particles. For some applications, however, such as studying the thermal behavior of rare gas solid surfaces, these constitute bad working conditions. Surface…

Materials Science · Physics 2009-10-30 Franck Celestini , Daniele Passerone , Furio Ercolessi , Erio Tosatti