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CIBCB
2007
IEEE
16 years 28 days ago
Modeling protein-DNA binding time in Stochastic Discrete Event Simulation of Biological Processes
Abstract— This paper presents a parametric model to estimate the DNA-protein binding time using the DNA and protein structures and details of the binding site. To understand the ...
Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal K. ...
ICCS
2007
Springer
16 years 22 days ago
High Quality Surface Mesh Generation for Multi-physics Bio-medical Simulations
Abstract. Manual surface reconstruction is still an everyday practice in applications involving complex irregular domains necessary for modeling biological systems. Rapid developme...
Dominik Szczerba, Robert H. P. McGregor, Gá...
PPOPP
2006
ACM
16 years 16 days ago
Performance characterization of molecular dynamics techniques for biomolecular simulations
Large-scale simulations and computational modeling using molecular dynamics (MD) continues to make significant impacts in the field of biology. It is well known that simulations...
Sadaf R. Alam, Jeffrey S. Vetter, Pratul K. Agarwa...
AGILEDC
2003
IEEE
15 years 12 months ago
YP and Urban Simulation: Applying an Agile Programming Methodology in a Politically Tempestuous Domain
YP is an agile programming methodology that has evolved over the past 15 years. Many of its features are common to other agile methodologies; its novel features include using a hi...
Bjørn N. Freeman-Benson, Alan Borning
ACSAC
2004
IEEE
15 years 10 months ago
Using Predators to Combat Worms and Viruses: A Simulation-Based Study
Large-scale attacks generated by fast-spreading or stealthy malicious mobile code, such as flash worms and e-mail viruses, demand new approaches to patch management and disinfecti...
Ajay K. Gupta 0002, Daniel C. DuVarney