4,911 research outputs found
Efficient Parallel Algorithm for Statistical Ion Track Simulations in Crystalline Materials
We present an efficient parallel algorithm for statistical Molecular Dynamics
simulations of ion tracks in solids. The method is based on the Rare Event
Enhanced Domain following Molecular Dynamics (REED-MD) algorithm, which has
been successfully applied to studies of, e.g., ion implantation into
crystalline semiconductor wafers. We discuss the strategies for parallelizing
the method, and we settle on a host-client type polling scheme in which a
multiple of asynchronous processors are continuously fed to the host, which, in
turn, distributes the resulting feed-back information to the clients. This
real-time feed-back consists of, e.g., cumulative damage information or
statistics updates necessary for the cloning in the rare event algorithm. We
finally demonstrate the algorithm for radiation effects in a nuclear oxide
fuel, and we show the balanced parallel approach with high parallel efficiency
in multiple processor configurations.Comment: 17 pages, seven figures, four table
DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism
Inverted repeat (IR) sequences in DNA can form non-canonical cruciform
structures to relieve torsional stress. We use Monte Carlo simulations of a
recently developed coarse-grained model of DNA to demonstrate that the
nucleation of a cruciform can proceed through a cooperative mechanism. Firstly,
a twist-induced denaturation bubble must diffuse so that its midpoint is near
the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must
be large enough to allow one of the arms to form a small number of hairpin
bonds. Once the first arm is partially formed, the second arm can rapidly grow
to a similar size. Because bubbles can twist back on themselves, they need
considerably fewer bases to resolve torsional stress than the final cruciform
state does. The initially stabilised cruciform therefore continues to grow,
which typically proceeds synchronously, reminiscent of the S-type mechanism of
cruciform formation. By using umbrella sampling techniques we calculate, for
different temperatures and superhelical densities, the free energy as a
function of the number of bonds in each cruciform along the correlated but
non-synchronous nucleation pathways we observed in direct simulations.Comment: 12 pages main paper + 11 pages supplementary dat
Improving the scalability of parallel N-body applications with an event driven constraint based execution model
The scalability and efficiency of graph applications are significantly
constrained by conventional systems and their supporting programming models.
Technology trends like multicore, manycore, and heterogeneous system
architectures are introducing further challenges and possibilities for emerging
application domains such as graph applications. This paper explores the space
of effective parallel execution of ephemeral graphs that are dynamically
generated using the Barnes-Hut algorithm to exemplify dynamic workloads. The
workloads are expressed using the semantics of an Exascale computing execution
model called ParalleX. For comparison, results using conventional execution
model semantics are also presented. We find improved load balancing during
runtime and automatic parallelism discovery improving efficiency using the
advanced semantics for Exascale computing.Comment: 11 figure
A bibliography on parallel and vector numerical algorithms
This is a bibliography of numerical methods. It also includes a number of other references on machine architecture, programming language, and other topics of interest to scientific computing. Certain conference proceedings and anthologies which have been published in book form are listed also
Asynchronous Variational Contact Mechanics
An asynchronous, variational method for simulating elastica in complex
contact and impact scenarios is developed. Asynchronous Variational Integrators
(AVIs) are extended to handle contact forces by associating different time
steps to forces instead of to spatial elements. By discretizing a barrier
potential by an infinite sum of nested quadratic potentials, these extended
AVIs are used to resolve contact while obeying momentum- and
energy-conservation laws. A series of two- and three-dimensional examples
illustrate the robustness and good energy behavior of the method
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