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» Scalable Molecular Dynamics for Large Biomolecular Systems
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CGF
2010
143views more  CGF 2010»
13 years 7 months ago
Coherent Culling and Shading for Large Molecular Dynamics Visualization
Molecular dynamics simulations are a principal tool for studying molecular systems. Such simulations are used to investigate molecular structure, dynamics, and thermodynamical pro...
Sebastian Grottel, Guido Reina, Carsten Dachsbache...
IPPS
2006
IEEE
14 years 1 months ago
Achieving strong scaling with NAMD on Blue Gene/L
NAMD is a scalable molecular dynamics application, which has demonstrated its performance on several parallel computer architectures. Strong scaling is necessary for molecular dyn...
Sameer Kumar, Chao Huang, George Almási, La...
BMCBI
2010
141views more  BMCBI 2010»
13 years 7 months ago
BioPhysConnectoR: Connecting Sequence Information and Biophysical Models
Background: One of the most challenging aspects of biomolecular systems is the understanding of the coevolution in and among the molecule(s). A complete, theoretical picture of th...
Franziska Hoffgaard, Philipp Weil, Kay Hamacher
ICPPW
2009
IEEE
13 years 4 months ago
A Scalable Parallel Approach for Peptide Identification from Large-Scale Mass Spectrometry Data
Identifying peptides, which are short polymeric chains of amino acid residues in a protein sequence, is of fundamental importance in systems biology research. The most popular appr...
Gaurav Ramesh Kulkarni, Ananth Kalyanaraman, Willi...
FCCM
2004
IEEE
143views VLSI» more  FCCM 2004»
13 years 10 months ago
Reconfigurable Molecular Dynamics Simulator
Current high-performance applications are typically implemented on large-scale general-purpose distributed or multiprocessing systems often based on commodity microprocessors. Fie...
Navid Azizi, Ian Kuon, Aaron Egier, Ahmad Darabiha...