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Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. He...

The parallel computing model used in this paper, the Collective Computing Model (CCM), is a variant of the well-known Bulk Synchronous Parallel (BSP) model. The synchronicity imposed by the BSP model restricts the set of...

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...

New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (b...

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...

The parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and a...

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...

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...

Materias / palabras clave: numerical methods, computational mathematics, computer networks, computational modeling, computational methodology, computational simulation; Science: Mathematics

Materias / palabras clave: computational engineering, physical modeling, civil engineering, mechanical engineering, materials science, simulation; Technology: Electrical engineering. Electronics. Nuclear engineering: Electronics: Computer engineer...

Materias / palabras clave: materials modeling and theory, novel materials, computational methods, theoretical simulation; Technology: Electrical engineering. Electronics. Nuclear engineering: Materials of engineering and construction. Mechanics of...

Materias / palabras clave: partial differential equations, monte carlo and quasi-monte carlo simulation, soft computing, computational chemistry and physic, energy conversion and transfer in systems, optimization of civil structures and structural...

Materias / palabras clave: mathematical biophysics, computational biophysics, mathematical molecular bioscience, biomolecular simulations, biomolecular data deep leaning, rational drug discovery; Technology: Chemical technology: Biotechnology; Sci...

Materias / palabras clave: computational mechanics, numerical analysis, engineering simulation, complex models; Technology: Engineering (General). Civil engineering (General): Mechanics of engineering. Applied mechanics; Technology: Engineering (G...

Materias / palabras clave: computer simulation, computational methods, process control, instrumentation, multiscale experiments; Science: Mathematics: Instruments and machines: Electronic computers. Computer science: Computer software