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"Education, in and of itself, is neither irrelevant nor outmoded. However, the current need to educate a planetary citizenry under conditions relevant to the living context of our planet is palpable. A new education para...

"In this paper we study the stability of nonlinear and time-varying switched systems under restricted switching. We approach the problem by decomposing the system dynamics into a nominal-like part and a perturbationlike ...

"We study the dynamics of self-organized systems when disturbed by shocks. For this purpose, we consider extensions of the “Bar Attendance Model” [1] (BAM), which provides a stylized setting for the analysis of the e...

"The use of information measures for model selection in geophysical models with subgrid parameterizations is examined. Although the resolved dynamical equations of atmospheric or oceanic global numerical models are well ...

"We study a modification of the Evolutionary Minority Game (EMG) in which agents are placed in the nodes of a regular or a random graph. A neighborhood for each agent can thus be defined and a modification of the usual r...

Materias / palabras clave: Cartesian coordinate system; Holonomic constraints; Verlet integration; Equations of motion; Constraint (computer-aided design); Numerical integration; Classical mechanics; Molecular dynamics; Motion (physics); Generaliz...

Abstract CHARMM ( C hemistry at HAR vard M acromolecular M echanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build struct...

A molecular dynamics simulation method which can generate configurations belonging to the canonical (T, V, N) ensemble or the constant temperature constant pressure (T, P, N) ensemble, is proposed. The physical system of...

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simu...

A new Lagrangian formulation is introduced. It can be used to make molecular dynamics (MD) calculations on systems under the most general, externally applied, conditions of stress. In this formulation the MD cell shape a...

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on lo...

We present a unified scheme that, by combining molecular dynamics and density-functional theory, profoundly extends the range of both concepts. Our approach extends molecular dynamics beyond the usual pair-potential appr...

In this paper we present a new mixed-variables symplectic tree code for planetesimal dynamics, which allows to use a very large number of particles in numerical simulations of planet disk interaction. Furthermore, we dis...

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, origi...

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological inte...

Abstract This book provides a practical guide to molecular dynamics and Monte Carlo simulation techniques used in the modelling of simple and complex liquids. Computer simulation is an essential tool in studying the chem...

This paper aims to bridge the gap between neurophysiology and automatic control methodologies by redefining the Wilson-Cowan (WC) model as a control-oriented linear parameter-varying (LPV) system. A novel approach is pre...

CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-g...