Vipin Sachdeva

Fully Integrated On-FPGA Molecular Dynamics Simulations

The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually...

Particle Mesh Ewald for Molecular Dynamics in OpenCL on an FPGA Cluster

Molecular Dynamics (MD) simulations play a central role in physics-driven drug discovery. MD applications often use the Particle Mesh Ewald (PME) algorithm to accelerate electrostatic force...

OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution

We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment --- simulating an entire mammal red blood cell lipid bilayer and...

A Memory and Time Scalable Parallelization of the Reptile Error-Correction Code

Mesh Interface Resolution and Ghost Exchange in a Parallel Mesh Representation

p_2Matlab: Productive Parallel Matlab for the Exascale

Parallelization of the Trinity Pipeline for De Novo Transcriptome Assembly

Exploring the Viability of the Cell Broadband Engine for Bioinformatics Applications

Exploring HPC-based scientific software as a service using CometCloud

Molecular Dynamics Range-Limited Force Evaluation Optimized for FPGAs

A Cache-Aware Parallel Implementation of the Push-Relabel Network Flow Algorithm and Experimental Evaluation of the Gap Relabeling Heuristic

Evaluating Cell/B.E software cache for ClustalW

Particle Mesh Ewald for Molecular Dynamics in OpenCL on an FPGA Cluster

Upgrade of FPGA Range-Limited Molecular Dynamics to Handle Hundreds of Processors

K-mer clustering algorithm using a MapReduce approach

Incorporating life sciences applications in the architectural optimizations of next-generation petaflop-system

Optimized Mappings for Symmetric Range-Limited Molecular Force Calculations on FPGAs

Fully integrated FPGA molecular dynamics simulations