109 research outputs found
Message-Passing Multi-Cell Molecular Dynamics on the Connection Machine 5
We present a new scalable algorithm for short-range molecular dynamics
simulations on distributed memory MIMD multicomputer based on a message-passing
multi-cell approach. We have implemented the algorithm on the Connection
Machine 5 (CM-5) and demonstrate that meso-scale molecular dynamics with more
than particles is now possible on massively parallel MIMD computers.
Typical runs show single particle update-times of in 2 dimensions
(2D) and approximately in 3 dimensions (3D) on a 1024 node CM-5
without vector units, corresponding to more than 1.8 GFlops overall
performance. We also present a scaling equation which agrees well with actually
observed timings.Comment: 17 pages, Uuencoded compressed PostScript fil
Mixed quantum-classical dynamics of an amide-I vibrational excitation in a protein a-helix
Adenosine triphosphate sATPd is known to be the main energy currency of the living cell, and is used as a coenzyme to generate energy for many cellular processes through hydrolysis to adenosine diphosphate sADPd,although the mechanism of energy transfer is not well understood. It has been proposed that following hydrolysis of the ATP cofactor bound to a protein, up to two quanta of amide-I vibrational energy are excited and utilized to bring about important structural changes in the protein. To study whether, and how, amide-I vibrational excitations are capable of leading to protein structural changes, we have added components arising from quantum-mechanical amide-I vibrational excitations to the total energy and force terms within a moleculardynamics simulation. This model is applied to helical deca-alanine as a test case to investigate how its dynamics differs in the presence or absence of an amide-I excitation. We find that the presence of an amide-I excitation can bias the structure toward a more helical state
Soliton motion in a parametrically ac-driven damped Toda lattice
We demonstrate that a staggered parametric ac driving term can support stable
progressive motion of a soliton in a Toda lattice with friction, while an
unstaggered drivng force cannot. A physical context of the model is that of a
chain of anharmonically coupled particles adsorbed on a solid surface of a
finite size. The ac driving force models a standing acoustic wave excited on
the surface. Simulations demonstrate that the state left behind the moving
soliton, with the particles shifted from their equilibrium positions, gradually
relaxes back to the equilibrium state that existed before the passage of the
soliton. Perturbation theory predicts that the ac-driven soliton exists if the
amplitude of the drive exceeds a certain threshold. The analytical prediction
for the threshold is in reasonable agreement with that found numerically.
Collisions between two counter propagating solitons were also simulated,
demonstrating that the collisions are, essentially fully elastic
A reduced model for shock and detonation waves. II. The reactive case
We present a mesoscopic model for reactive shock waves, which extends a
previous model proposed in [G. Stoltz, Europhys. Lett. 76 (2006), 849]. A
complex molecule (or a group of molecules) is replaced by a single
mesoparticle, evolving according to some Dissipative Particle Dynamics.
Chemical reactions can be handled in a mean way by considering an additional
variable per particle describing a rate of reaction. The evolution of this rate
is governed by the kinetics of a reversible exothermic reaction. Numerical
results give profiles in qualitative agreement with all-atom studies
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