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Autodock Vina generates docking poses using an iterated local search global optimizer [23] which consists in a succession of steps of stochastic mutations and local optimizations [18].
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In this article, a probability-based damage detection procedure is presented, in which the random factor method for non-homogeneous random field is developed and used as the forward propagation to analytically evaluate covariance matrices in each iteration step of stochastic model updating.
The number of descriptors M changed at each step of stochastic descriptor sampling was set to 1.
In our minimal model, reduction in the rate constant of the slow intermediate step of stochastic pathway generates slower activation with increased cell-to-cell variability and thus captures the signaling behavior in apoptosis with over-expressed Bcl-2 levels (Figure 5).
The next step of stochastic noise decomposition is to divided noise linearly into noise steaming from separate reactions.
The evolutionary model and branch lengths are estimated from all simulated sites as the first step of stochastic mapping inference (details in Materials and Methods).
We also propose a preconditioner for solving the linear systems of equations arising at each step of the stochastic (Galerkin) nonlinear iteration and demonstrate its effectiveness for solving a set of benchmark problems.
The mentioned measures are incorporated into the first step of proposed stochastic programming approach in this study.
Two steps of MSARC algorithm: stochastic alignment and iterative refinement follow the respective steps in Probalign [ 7].
Spatially explicit individual-based simulations (Monte-Carlo simulations, see Methods) explicitly describe the diffusive motion of each individual mRNA and protein molecules and emulate the reaction steps of (1) as stochastic processes whenever the concerned reactants encounter in space along their respective random walk (diffusion).
For r/ R<0.5, though, the average FZCA progressively decreases with increasing demixing, switching from oscillatory values (>0.1 million MC time steps) to values typical of stochastic fluctuations around a stationary state (<0.05 million MC time steps).
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