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ICCS
2004
Springer
15 years 11 months ago
Improved Sampling for Biological Molecules Using Shadow Hybrid Monte Carlo
Shadow Hybrid Monte Carlo (SHMC) is a new method for sampling the phase space of large biological molecules. It improves sampling by allowing larger time steps and system sizes in ...
Scott S. Hampton, Jesús A. Izaguirre
DCC
2007
IEEE
16 years 6 months ago
A Simple Statistical Algorithm for Biological Sequence Compression
This paper introduces a novel algorithm for biological sequence compression that makes use of both statistical properties and repetition within sequences. A panel of experts is ma...
Minh Duc Cao, Trevor I. Dix, Lloyd Allison, Chris ...
AB
2008
Springer
16 years 23 days ago
Algebraic Analysis of Bifurcation and Limit Cycles for Biological Systems
In this paper, we show how to analyze bifurcation and limit cycles for biological systems by using an algebraic approach based on triangular decomposition, Gr¨obner bases, discrim...
Wei Niu, Dongming Wang
ISMB
1998
15 years 7 months ago
BioSim: A New Qualitative Simulation Environment for Molecular Biology
Traditionally, biochemical systems are modelled usingkinetics anddifferential equationsin a quantitative simulator. However,for manybiological processes detailed quantitative info...
Karsten R. Heidtke, Steffen Schulze-Kremer
CMSB
2009
Springer
16 years 1 months ago
Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora crassa Circadian Network
Circadian clocks are biochemical networks, present in nearly all living organisms, whose function is to regulate the expression of specific mRNAs and proteins to synchronise rhyth...
Ozgur E. Akman, Federica Ciocchetta, Andrea Degasp...