0000000000240494
AUTHOR
F. Brugè
Concurrent Molecular Dynamics Simulation of ST2 Water on a Transputer Array
Abstract A concurrent implementation of a Molecular Dynamics program for ST2 water molecules is presented, which exploits the great potentialities of the Transputer arrays for statistical mechanical calculations. High load-balance efficiency is obtained using a new task decomposition algorithm which evenly distributes particles and interaction calculations among the processors. This approach can also help to solve efficiently the more general problem of task distribution in parallel computing of symmetric pairwise system properties.
Demixing and polymerization in systems of anisotropic globular particles: A molecular dynamics simulation study
We report a first set of results of Molecular Dynamics simulations of phase separation in a two-dimensional system of identical particles bearing attachment sites at their surface. Morphology of regions of aggregation so obtained appear similar to images of biologically self-assembled structures. Also, they evidence the relevance of the region of thermodynamic instability and of the presence and range of interaction of specific attachment sites. Particles of our system are apt to represent indifferently, though grossly, globular proteins or rigid cells, bearing specific and fixed adhesion sites at their surface. Results illustrate some basic aspects of the origin of the morphology of extend…
One-dimensional hydrodynamic modeling of coronal plasmas on transputer arrays
Abstract We describe a concurrent implementation of the Palermo-Harvard hydrodynamic code on cost-effective and modularity expandable transputer arrays. We have tested the effectiveness of our approach by simulating an already well-studied compact solar-flare model on different transputer configurations and compared their performances with those of other machines. We have found that the speed of the concurrent program on a 16-T800 transputers array is ~1/9 of that of the equivalent code optimized for a CRAY X-MP/48. This work clearly shows that transputer-based arrays provide locally available high computing-power tools to extend the investigation of compact solar flares and similar astroph…
A molecular dynamics study of large-scale reversible aggregation of anisotropic particles
We report findings of 1000 ps molecular dynamics simulations of a bidimensional system of 4050 Lennard–Jones particles with electric dipoles, undergoing spinodal separation. This simple system is used to model the reversible aggregation of building blocks bearing specific and fixed adhesion sites at their surface. Aggregation regions so obtained resemble images of self-assembled biological structures. Statistical analyses of these regions evidence the interplay of thermodynamic instability and of interaction range between the attachment sites. They also illustrate some basic aspects of the morphogenesis of extended biomolecular/cellular structures, self-organized from initially homogeneous …
Concurrent molecular dynamics simulation of spinodal phase transition on transputer arrays
Abstract We describe a concurrent implementation on cost-effective transputer arrays of a molecular dynamics program to efficiently simulate physical systems consisting of thousands of mobile particles with an interaction range much shorter than the system dimensions. This program, which uses a geometric decomposition strategy and includes a distributed dynamic load balancer, has been extensively tested by simulating the two-dimensional spinodal phase separation of a large Lennard-Jones system.
Microscopic aspects of solute-solute interactions induced by the solvent
Nous presentons les plus importants resultats que nous ayons obtenus par des simulations etendues de dynamique moleculaire de solutions aqueuses contenant des modeles de solute hydrophiles et hydrophobes. Ces simulations determinent les forces induites par le solvant sur les solutes (SIFs) en fonction du type de solute, de la separation solute-solute et de leur orientation mutuelle. Les proprietes structurales et dynamiques du solvant autour des solutes ont ete analysees pour comprendre leur relation avec les SIFs. les presents resultats sont compares a des observations experimentales et precedentes stimulations sur des solutions aqueuses de biomolecules.
A distributed dynamic load balancer and its implementation on multi-transputer systems for molecular dynamics simulation
Abstract A new and efficient approach is described to the dynamic load-balancing problem which is central in concurrent computing. A transputer-based implementation is tested on a molecular dynamics simulation of spinodal phase separation.
A mixed geometric-systolic approach to parallel molecular dynamics simulations
We have developed a flexible and efficient method of performing molecular dynamics simulations on distributed memory parallel computers. The novel feature is to use simultaneously spatial partitioning and systolic loop approaches according to a strategy which, for a given simulation, adapts itself to the multiprocessor system, allowing to approach optimal performance. The method assures high efficiencies even in situations in which, due to the exceeding large number of processors, the usage of a pure spatial decomposition would be impossible. The algorithm provides as particular cases both the pure spatial partitioning and the pure systolic parallelization schemes, so that its adoption assu…