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

Mechanical heart valve cavitation fluid mechanics

Background:Both pulsatile and continuous flow ventricular assist devices are being developed for pediatric congenital heart defect patients. Pulsatile devices are often operated asynchronously with...

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Asynchronous Pumping of a Pulsatile Ventricular Assist Device in a Pediatric Anastomosis Model

Thrombosis and thromboembolism still plague cardiovascular prosthetic devices. While it is known that areas of stasis and stagnation will result in thrombus formation, the potential for embolization remains unknown. The local fluid dynamics, in particular, the local shear stress, play an integral role with embolization. A backward facing step model was used to investigate thrombus formation and embolization. Through the use of an in vitro blood loop with radiolabeled platelets, high and low Reynolds number flows were investigated. In addition, computational fluid dynamics (CFD) simulations under the same conditions and the same model dimensions were executed with an added simulation involving a clot formed beyond the step to understand how clot growth affects the local flow. The results indicate that areas of high Reynolds number flow produce substantial thrombus with both techniques. The low Reynolds number flow with the blood loop showed no visible thrombus, but the simulations illustrated a recirculation zone suggesting potential for thrombus formation. The simulated CFD clot formation showed a change in the local flow with an increase in shear stress suggesting embolization might occur. Further refinement in the CFD and more blood studies at higher Reynolds number are required to induce embolization. This work is an initial step towards understanding how thromboembolization and the local fluid dynamics are related.

A Novel Approach to the Correlation of Fluid Dynamics and Thromboembolism Associated with Cardiovascular Prosthetic Devices

Deep vein thrombosis (DVT) is a life-threatening blood clotting condition that, if undetected, can cause deadly pulmonary embolisms. Critical to its clinical management is the ability to rapidly detect, monitor, and treat thrombosis. However, current diagnostic imaging modalities lack the resolution required to precisely localize vessel occlusions and enable clot monitoring in real time. Here, we rationally design fibrinogen-mimicking fluoropeptide nanoemulsions, or nanopeptisomes (NPeps), that allow contrast-enhanced ultrasound imaging of thrombi and synchronous inhibition of clot growth. The theranostic duality of NPeps is imparted via their intrinsic binding to integrins overexpressed on platelets activated during coagulation. The platelet-bound nanoemulsions can be vaporized and oscillate in an applied acoustic field to enable contrast-enhanced Doppler ultrasound detection of thrombi. Concurrently, nanoemulsions bound to platelets competitively inhibit secondary platelet-fibrinogen binding to disrupt further clot growth. Continued development of this synchronous theranostic platform may open new opportunities for image-guided, non-invasive, interventions for DVT and other vascular diseases.

Ultrasound-Responsive Nanopeptisomes Enable Synchronous Spatial Imaging and Inhibition of Clot Growth in Deep Vein Thrombosis

Transcatheter aortic valve replacements (TAVRs) provide minimally invasive delivery of bioprosthetic heart valves (BHVs) for the treatment of aortic valve disease. While surgical BHVs show efficacy for 8-10 years, long-term TAVR durability remains unknown. Pre-clinical testing evaluates BHV durability in an ISO:5840 compliant accelerated wear tester (AWT), yet, the design and development of AWTs and their accuracy in predicting in vivo performance, is unclear. As a result of limited knowledge on AWT environment and BHV loading, durability assessment of candidate valves remains fundamentally empirical. For the first time, high-speed particle image velocimetry quantified an ISO:5840 compliant downstream AWT velocity field, Reynolds stresses, and turbulence intensity. TAVR enface imaging quantified the orifice area and estimated the flow rate. When valve area and flow rate were at their maximum during peak systole (1.49 cm2 and 16.05 L/min, respectively), central jet velocity, Reynolds normal and shear stress, and turbulence intensity grew to 0.50 m/s, 265.1 Pa, 124.6 Pa, and 37.3%, respectively. During diastole, unique AWT recirculation produced retrograde flow and the directional changes created eddies. These novel AWT findings demonstrated a substantially reduced valve fully loaded period and pressure not matching in vivo or in vitro studies, despite the comparable fluid environment and TAVR motion.

Keefe B. Manning

Papers

Mechanical heart valve cavitation fluid mechanics

Asynchronous Pumping of a Pulsatile Ventricular Assist Device in a Pediatric Anastomosis Model

A Novel Approach to the Correlation of Fluid Dynamics and Thromboembolism Associated with Cardiovascular Prosthetic Devices

Ultrasound-Responsive Nanopeptisomes Enable Synchronous Spatial Imaging and Inhibition of Clot Growth in Deep Vein Thrombosis

Transcatheter Heart Valve Downstream Fluid Dynamics in an Accelerated Evaluation Environment