Stochastic simulation of multiscale complex systems with PISKaS: A rule-based approach.
Sign Up to like & getrecommendations! Published in 2018 at "Biochemical and biophysical research communications"
DOI: 10.1016/j.bbrc.2017.11.138
Abstract: Computational simulation is a widely employed methodology to study the dynamic behavior of complex systems. Although common approaches are based either on ordinary differential equations or stochastic differential equations, these techniques make several assumptions which,… read more here.
Keywords: stochastic simulation; rule based; complex systems; simulation ... See more keywords
Stochastic Simulation of Isotopic Exchange Mechanisms for Fe(II)-Catalyzed Recrystallization of Goethite.
Sign Up to like & getrecommendations! Published in 2017 at "Environmental science & technology"
DOI: 10.1021/acs.est.7b01491
Abstract: Understanding Fe(II)-catalyzed transformations of Fe(III)-(oxyhydr)oxides is critical for correctly interpreting stable isotopic distributions and for predicting the fate of metal ions in the environment. Recent Fe isotopic tracer experiments have shown that goethite undergoes rapid… read more here.
Keywords: recrystallization; stochastic simulation; exchange; simulation isotopic ... See more keywords
A Comparison of Weighted Stochastic Simulation Methods for the Analysis of Genetic Circuits.
Sign Up to like & getrecommendations! Published in 2022 at "ACS synthetic biology"
DOI: 10.1021/acssynbio.2c00553
Abstract: Rare events are of particular interest in synthetic biology because rare biochemical events may be catastrophic to a biological system by, for example, triggering irreversible events such as off-target drug delivery. To estimate the probability… read more here.
Keywords: weighted stochastic; comparison; simulation methods; simulation ... See more keywords
RSSALib: a library for stochastic simulation of complex biochemical reactions
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa602
Abstract: Abstract Motivation Stochastic chemical kinetics is an essential mathematical framework for investigating the dynamics of biological processes, especially when stochasticity plays a vital role in their development. Simulation is often the only option for the… read more here.
Keywords: library stochastic; stochastic simulation; biochemical reactions; reactions rssalib ... See more keywords
Block Search Stochastic Simulation Algorithm (BlSSSA): A Fast Stochastic Simulation Algorithm for Modeling Large Biochemical Networks.
Sign Up to like & getrecommendations! Published in 2021 at "IEEE/ACM transactions on computational biology and bioinformatics"
DOI: 10.1109/tcbb.2021.3070123
Abstract: Stochastic simulation algorithms are extensively used for exploring stochastic behavior of biochemical pathways/networks. Computational cost of these algorithms is high in simulating real biochemical systems due to their large size, complex structure and stiffness. In… read more here.
Keywords: simulation algorithm; stochastic simulation; block search; algorithm blsssa ... See more keywords
TemporalGSSA: A numerically robust R-wrapper to facilitate computation of a metabolite-specific and simulation time-dependent trajectory from stochastic simulation algorithm (SSA)-generated datasets
Sign Up to like & getrecommendations! Published in 2022 at "Journal of bioinformatics and computational biology"
DOI: 10.1142/s0219720022500184
Abstract: Whilst data on biochemical networks has increased several-fold, our comprehension of the underlying molecular biology is incomplete and inadequate. Simulation studies permit data collation from disparate time points and the imputed trajectories can provide valuable… read more here.
Keywords: time; ssa generated; simulation; stochastic simulation ... See more keywords
Stochastic simulation in reservoir sedimentation estimation: application in a PCH.
Sign Up to like & getrecommendations! Published in 2022 at "Anais da Academia Brasileira de Ciencias"
DOI: 10.1590/0001-3765202220211573
Abstract: In reservoir projects it is important to estimate when the accumulated sediments will start to interfere with their functions. However, predicting silting is difficult because the processes involved have some uncertainties. Thus, the study is… read more here.
Keywords: estimation application; reservoir sedimentation; simulation reservoir; reservoir ... See more keywords
Topographic uncertainty quantification for flow-like landslide models via stochastic simulations
Sign Up to like & getrecommendations! Published in 2020 at "Natural Hazards and Earth System Sciences"
DOI: 10.5194/nhess-20-1441-2020
Abstract: Abstract. Digital elevation models (DEMs) representing topography are an essential input for computational models capable of simulating the run-out of flow-like landslides. Yet, DEMs are often subject to error, a fact that is mostly overlooked… read more here.
Keywords: stochastic simulation; flow like; uncertainty; topographic uncertainty ... See more keywords
Stochastic simulation of destruction processes in self-irradiated materials
Sign Up to like & getrecommendations! Published in 2017 at "Condensed Matter Physics"
DOI: 10.5488/cmp.20.33003
Abstract: Self-irradiation damages resulting from fission processes are common phenomena observed in nuclear fuel containing (NFC) materials. Numerous $\alpha$-decays lead to local structure transformations in NFC materials. The damages appearing due to the impacts of heavy… read more here.
Keywords: simulation destruction; stochastic simulation; destruction processes; material ... See more keywords