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APBC
2004
122views Bioinformatics» more  APBC 2004»
13 years 11 months ago
Integrating Biopathway Databases for Large-scale Modeling and Simulation
Biopathway databases have been developed, such as KEGG and EcoCyc, that compile interaction structures of biopathways together with biological annotations. However, these biopathw...
Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Sato...
JCC
2006
110views more  JCC 2006»
13 years 10 months ago
Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm
: This article describes a method for solving the geometric closure problem for simplified models of nucleic acid structures by using the constant bond lengths approximation. The r...
Heinz Sklenar, Daniel Wüstner, Remo Rohs
WABI
2009
Springer
117views Bioinformatics» more  WABI 2009»
14 years 4 months ago
A Simulation Study Comparing Supertree and Combined Analysis Methods Using SMIDGen
Background: Supertree methods comprise one approach to reconstructing large molecular phylogenies given multi-marker datasets: trees are estimated on each marker and then combined...
M. Shel Swenson, François Barbançon,...
DAGSTUHL
2010
13 years 11 months ago
Visual Simulation of Flow
We have adopted a numerical method from computational fluid dynamics, the Lattice Boltzmann Method (LBM), for real-time simulation and visualization of flow and amorphous phenomen...
Arie E. Kaufman, Ye Zhao
BMCBI
2010
156views more  BMCBI 2010»
13 years 10 months ago
Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes
Background: An adaptive coarse-grained (kinetic) Monte Carlo (ACGMC) simulation framework is applied to reaction and diffusion dynamics in inhomogeneous domains. The presented mod...
Stuart Collins, Michail Stamatakis, Dionisios G. V...