Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

To improve the performance of particle image velocimetry in measuring instantaneous velocity fields, direct cross-correlation of image fields can be used in place of auto-correlation methods of interrogation of double- or multiple-exposure recordings. With improved speed of photographic recording and increased resolution of video array detectors, cross-correlation methods of interrogation of successive single-exposure frames can be used to measure the separation of pairs of particle images between successive frames. By knowing the extent of image shifting used in a multiple-exposure and by a priori knowledge of the mean flow-field, the cross-correlation of different sized interrogation spots with known separation can be optimized in terms of spatial resolution, detection rate, accuracy and reliability.

Theory of cross-correlation analysis of PIV images : Image analysis as measuring technique in flows

Fluid dynamic turbulence is one of the most challenging computational physics problems because of the extremely wide range of time and space scales involved, the strong nonlinearity of the governing equations, and the many practical and important applications. While most linear fluid instabilities are well understood, the nonlinear interactions among them makes even the relatively simple limit of homogeneous isotropic turbulence difficult to treat physically, mathematically, and computationally. Turbulence is modeled computationally by a two-stage bootstrap process. The first stage, direct numerical simulation, attempts to resolve the relevant physical time and space scales but its application is limited to diffusive flows with a relatively small Reynolds number (Re). Using direct numerical simulation to provide a database, in turn, allows calibration of phenomenological turbulence models for engineering applications. Large eddy simulation incorporates a form of turbulence modeling applicable when the large-scale flows of interest are intrinsically time dependent, thus throwing common statistical models into question. A promising approach to large eddy simulation involves the use of high-resolution monotone computational fluid dynamics algorithms such as flux-corrected transport or the piecewise parabolic method which have intrinsic subgrid turbulence models coupled naturally to the resolved scales in the computed flow. The physical considerations underlying and evidence supporting this monotone integrated large eddy simulation approach are discussed.

New insights into large eddy simulation

ReviewFunction of alternative splicing

Hypoplastic Left Heart Syndrome : Current Considerations and Expectations

Time to cool off on a hot topic? Let's not forget about evidence when discussing heat-induced pump thrombogenesis.

To address the increasing number of failing Fontan patients, Penn State University and the Penn State Hershey Medical Center are developing a centrifugal blood pump for long-term mechanical support. Computational fluid dynamics (CFD) modeling of the Penn State Fontan Circulatory Assist Device (FCAD) was performed to understand hemodynamics within the pump and its potential for hemolysis and thrombosis. CFD velocity and pressure results were first validated against experimental data and found to be within the standard deviations of the velocities and within 5% of the pressures. Further simulations performed with a human blood model found that most of the fluid domain was subjected to low shear stress (<50 Pa), with areas of highest stress around the rotor blade tips that increased with pump flow rate and rotor speed (138–178 Pa). However, the stresses compared well to previous CFD studies of commercial blood pumps and remained mostly below common thresholds of hemolysis and platelet activation. Additionally, few regions of low shear rate were observed within the FCAD, signifying minimal potential for platelet adhesion. These results further emphasize the FCAD’s potential that has been observed previously in experimental and animal studies.

Computational Modeling of the Penn State Fontan Circulation Assist Device

/pdf/special-issue-on-professor-john-m-tarbell-s-contribution-to-2lng56s8ev.pdf

Special Issue on Professor John M. Tarbell's Contribution to Cardiovascular Engineering.

Approximately 5.7 million Americans are afflicted with heart disease, with a reported 670,000 new cases and 300,000 deaths each year [1]. While the success rate of transplantation procedures continues to improve, organ availability remains limited. Left ventricular assist devices (LVADs) function as a bridge to transplant for advanced staged heart failure patients awaiting a donor heart. The devices have also been used, more recently, as a bridge to recovery by helping to unload the native ventricle. Along with pharmacological intervention, LVADs can act to help reverse pathological hypertrophy and recover normal myocardial function [2].Copyright © 2012 by ASME

https://etda.libraries.psu.edu/files/final_submissions/7701

Keefe B. Manning

Papers

Time to cool off on a hot topic? Let's not forget about evidence when discussing heat-induced pump thrombogenesis.

Computational Modeling of the Penn State Fontan Circulation Assist Device

Special Issue on Professor John M. Tarbell's Contribution to Cardiovascular Engineering.

A Comparison of Thrombus Susceptibility for Two Pulsatile 50 CC Left Ventricular Assist Pumps

Use of computer and in vitro modeling techniques during the development of pediatric circulatory support devices (ASAIO Journal (2009) 55, (3-5))