Data-Driven Method for Efficient Characterization of Rare Event Probabilities in Biochemical Systems
Sign Up to like & getrecommendations! Published in 2018 at "Bulletin of Mathematical Biology"
DOI: 10.1007/s11538-018-0509-0
Abstract: As mathematical models and computational tools become more sophisticated and powerful to accurately depict system dynamics, numerical methods that were previously considered computationally impractical started being utilized for large-scale simulations. Methods that characterize a rare… read more here.
Keywords: driven method; dwssa; rare event; data driven ... See more keywords
Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems
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DOI: 10.1093/bioinformatics/bty171
Abstract: Motivation: Biological cells operate in a noisy regime influenced by intrinsic, extrinsic and external noise, which leads to large differences of individual cell states. Stochastic effects must be taken into account to characterize biochemical kinetics… read more here.
Keywords: biochemical systems; intrinsic extrinsic; external noise; efficient simulation ... See more keywords
Summation Laws in Control of Biochemical Systems
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DOI: 10.3390/math11112473
Abstract: Dynamic variables in the non-equilibrium systems of life are determined by catalytic activities. These relate to the expression of the genome. The extent to which such a variable depends on the catalytic activity defined by… read more here.
Keywords: biochemical systems; control biochemical; laws control; control ... See more keywords
GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems
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DOI: 10.3390/molecules28031277
Abstract: Metadynamics calculations of large chemical systems with ab initio methods are computationally prohibitive due to the extensive sampling required to simulate the large degrees of freedom in these systems. To address this computational bottleneck, we… read more here.
Keywords: enhanced dftb; biochemical systems; free energy; gpu enhanced ... See more keywords