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https://www.readbyqxmd.com/read/28341132/stochastic-modeling-and-numerical-simulation-of-gene-regulatory-networks-with-protein-bursting
#1
Manuel Pájaro, Antonio A Alonso, Irene Otero-Muras, C Vázquez
Gene expression is inherently stochastic. Advanced single-cell microscopy techniques together with mathematical models for single gene expression led to important insights in elucidating the sources of intrinsic noise in prokaryotic and eukaryotic cells. In addition to the finite size effects due to low copy numbers, translational bursting is a dominant source of stochasticity in cell scenarios involving few short lived mRNA transcripts with high translational efficiency (as is typically the case for prokaryotes), causing protein synthesis to occur in random bursts...
March 21, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28320908/reaction-and-relaxation-at-surface-hotspots-using-molecular-dynamics-and-the-energy-grained-master-equation-to-describe-diamond-etching
#2
David R Glowacki, W J Rodgers, Robin Shannon, Struan H Robertson, Jeremy N Harvey
The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at 'hotspots' that form on the surface of diamond during the chemical vapour deposition process...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28306551/master-equations-and-the-theory-of-stochastic-path-integrals
#3
Markus F Weber, Erwin Frey
This review provides a pedagogic and self-contained introduction to master equations and to their representation by path integrals. Since the 1930s, master equations have served as a fundamental tool to understand the role of fluctuations in complex biological, chemical, and physical systems. Despite their simple appearance, analyses of master equations most often rely on low-noise approximations such as the Kramers-Moyal or the system size expansion, or require ad-hoc closure schemes for the derivation of low-order moment equations...
April 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/28301761/reaction-mechanisms-on-multiwell-potential-energy-surfaces-in-combustion-and-atmospheric-chemistry
#4
David L Osborn
Chemical reactions occurring on a potential energy surface with multiple wells are ubiquitous in low-temperature combustion and in the oxidation of volatile organic compounds in Earth's atmosphere. The rich variety of structural isomerizations that compete with collisional stabilization makes characterizing such complex-forming reactions challenging. This review describes recent experimental and theoretical advances that deliver increasingly complete views of their reaction mechanisms. New methods for creating reactive intermediates coupled with multiplexed measurements provide many experimental observables simultaneously...
March 15, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28268606/mechanisms-of-stochastic-focusing-and-defocusing-in-biological-reaction-networks-insight-from-accurate-chemical-master-equation-acme-solutions
#5
Gamze Gursoy, Anna Terebus, Youfang Cao, Jie Liang
Stochasticity plays important roles in regulation of biochemical reaction networks when the copy numbers of molecular species are small. Studies based on Stochastic Simulation Algorithm (SSA) has shown that a basic reaction system can display stochastic focusing (SF) by increasing the sensitivity of the network as a result of the signal noise. Although SSA has been widely used to study stochastic networks, it is ineffective in examining rare events and this becomes a significant issue when the tails of probability distributions are relevant as is the case of SF...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226785/mechanisms-of-stochastic-focusing-and-defocusing-in-biological-reaction-networks-insight-from-accurate-chemical-master-equation-acme-solutions
#6
Gamze Giirsoy, Anna Terebus, Youfang Cao, Jie Liang, Gamze Gursoy, Anna Terebus, Youfang Cao, Jie Liang, Gamze Gursoy, Youfang Cao, Anna Terebus, Jie Liang
Stochasticity plays important roles in regulation of biochemical reaction networks when the copy numbers of molecular species are small. Studies based on Stochastic Simulation Algorithm (SSA) has shown that a basic reaction system can display stochastic focusing (SF) by increasing the sensitivity of the network as a result of the signal noise. Although SSA has been widely used to study stochastic networks, it is ineffective in examining rare events and this becomes a significant issue when the tails of probability distributions are relevant as is the case of SF...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28199109/the-nucleotide-selectivity-at-a-pre-insertion-checkpoint-of-t7-rna-polymerase-transcription-elongation
#7
Chao E, Baogen Duan, Jin Yu
Nucleotide selection is crucial for transcription fidelity control, in particular, for viral T7 RNA polymerase (RNAP) lack of proofreading activity. It has been recognized that multiple kinetic checkpoints exist prior to full nucleotide incorporation. In this work, we implemented intensive atomistic molecular dynamics (MD) simulations to quantify how strong the nucleotide selection is at the initial checkpoint of an elongation cycle of T7 RNAP. The incoming nucleotides bind into a pre-insertion site where a critical tyrosine residue locates nearby to assist the nucleotide selection...
February 15, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28166778/markov-state-models-of-gene-regulatory-networks
#8
Brian K Chu, Margaret J Tse, Royce R Sato, Elizabeth L Read
BACKGROUND: Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understanding of network dynamics have the potential to guide cell-reprogramming strategies. Networks are often modeled by the stochastic Chemical Master Equation, but methods for systematic identification of key properties of the global dynamics are currently lacking. RESULTS: The method identifies the number, phenotypes, and lifetimes of long-lived states for a set of common gene regulatory network models...
February 6, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28156115/discussion-of-the-separation-of-chemical-and-relaxational-kinetics-of-chemically-activated-intermediates-in-master-equation-simulations
#9
Malte Döntgen, Kai Leonhard
Chemical activation of intermediates, such as hydrogen abstraction products, is emerging as a basis for a fully new reaction type: hot β-scission. While for thermally equilibrated intermediates chemical kinetics are typically orders of magnitude slower than relaxational kinetics, chemically activated intermediates raise the issue of inseparable chemical and relaxational kinetics. Here, this separation problem is discussed in the framework of master equation simulations, proposing three cases often encountered in chemistry: insignificant chemical activation, predominant chemical activation, and the transition between these two limits...
February 16, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28125716/numerical-simulations-reveal-randomness-of-cu-ii-induced-a%C3%AE-peptide-dimerization-under-conditions-present-in-glutamatergic-synapses
#10
Wojciech Goch, Wojciech Bal
The interactions between the Aβ1-40 molecules species and the copper ions (Cu(II)) were intensively investigated due to their potential role in the development of the Alzheimer Disease (AD). The rate and the mechanism of the Cu(II)-Aβ complexes formation determines the aggregation pathway of the Aβ species, starting from smaller but more cytotoxic oligomers and ending up in large Aβ plaques, being the main hallmark of the AD. In our study we exploit the existing knowledge on the Cu(II)-Aβ interactions and create the theoretical model of the initial phase of the copper- driven Aβ aggregation mechanism...
2017: PloS One
https://www.readbyqxmd.com/read/28088866/combined-experimental-and-computational-study-on-the-unimolecular-decomposition-of-jp-8-jet-fuel-surrogates-ii-n-dodecane-n-c12h26
#11
Long Zhao, Tao Yang, Ralf I Kaiser, Tyler P Troy, Musahid Ahmed, Joao Marcelo Ribeiro, Daniel Belisario-Lara, Alexander M Mebel
We investigated temperature-dependent products in the pyrolysis of helium-seeded n-dodecane, which represents a surrogate of the n-alkane fraction of Jet Propellant-8 (JP-8) aviation fuel. The experiments were performed in a high temperature chemical reactor over a temperature range of 1200 K to 1600 K at a pressure of 600 Torr, with in situ identification of the nascent products in a supersonic molecular beam using single photon vacuum ultraviolet (VUV) photoionization coupled with the analysis of the ions in a reflectron time-of-flight mass spectrometer (ReTOF)...
February 1, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28049303/anomalous-dielectric-relaxation-with-linear-reaction-dynamics-in-space-dependent-force-fields
#12
Tao Hong, Zhengming Tang, Huacheng Zhu
The anomalous dielectric relaxation of disordered reaction with linear reaction dynamics is studied via the continuous time random walk model in the presence of space-dependent electric field. Two kinds of modified reaction-subdiffusion equations are derived for different linear reaction processes by the master equation, including the instantaneous annihilation reaction and the noninstantaneous annihilation reaction. If a constant proportion of walkers is added or removed instantaneously at the end of each step, there will be a modified reaction-subdiffusion equation with a fractional order temporal derivative operating on both the standard diffusion term and a linear reaction kinetics term...
December 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27991440/simulating-charge-transport-in-organic-semiconductors-and-devices-a-review
#13
C Groves
Charge transport simulation can be a valuable tool to better understand, optimise and design organic transistors (OTFTs), photovoltaics (OPVs), and light-emitting diodes (OLEDs). This review presents an overview of common charge transport and device models; namely drift-diffusion, master equation, mesoscale kinetic Monte Carlo and quantum chemical Monte Carlo, and a discussion of the relative merits of each. This is followed by a review of the application of these models as applied to charge transport in organic semiconductors and devices, highlighting in particular the insights made possible by modelling...
December 19, 2016: Reports on Progress in Physics
https://www.readbyqxmd.com/read/27984171/stochastic-analysis-of-chemical-reaction-networks-using-linear-noise-approximation
#14
Luca Cardelli, Marta Kwiatkowska, Luca Laurenti
Stochastic evolution of Chemical Reactions Networks (CRNs) over time is usually analysed through solving the Chemical Master Equation (CME) or performing extensive simulations. Analysing stochasticity is often needed, particularly when some molecules occur in low numbers. Unfortunately, both approaches become infeasible if the system is complex and/or it cannot be ensured that initial populations are small. We develop a probabilistic logic for CRNs that enables stochastic analysis of the evolution of populations of molecular species...
October 28, 2016: Bio Systems
https://www.readbyqxmd.com/read/27959536/exact-product-formation-rates-for-stochastic-enzyme-kinetics
#15
Ramon Grima, André Leier
The rate of product formation is an important measure of the speed of enzyme reactions. Classical studies of enzyme reactions have been conducted in dilute solutions and under conditions that justified the substrate abundance assumption. However, such assumption is well-known to break down in the context of cellular biochemistry. Instead, the concentration of available substrate can become rate limiting. Here we use the chemical master equation to obtain expressions for the instantaneous and time averaged rate of product formation without invoking the conventional substrate abundance assumption...
December 27, 2016: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/27923064/sparse-regression-based-structure-learning-of-stochastic-reaction-networks-from-single-cell-snapshot-time-series
#16
Anna Klimovskaia, Stefan Ganscha, Manfred Claassen
Stochastic chemical reaction networks constitute a model class to quantitatively describe dynamics and cell-to-cell variability in biological systems. The topology of these networks typically is only partially characterized due to experimental limitations. Current approaches for refining network topology are based on the explicit enumeration of alternative topologies and are therefore restricted to small problem instances with almost complete knowledge. We propose the reactionet lasso, a computational procedure that derives a stepwise sparse regression approach on the basis of the Chemical Master Equation, enabling large-scale structure learning for reaction networks by implicitly accounting for billions of topology variants...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27911933/driving-cells-to-the-desired-state-in-a-bimodal-distribution-through-manipulation-of-internal-noise-with-biologically-practicable-approaches
#17
Che-Chi Shu, Chen-Chao Yeh, Wun-Sin Jhang, Shih-Chiang Lo
The stochastic nature of gene regulatory networks described by Chemical Master Equation (CME) leads to the distribution of proteins. A deterministic bistability is usually reflected as a bimodal distribution in stochastic simulations. Within a certain range of the parameter space, a bistable system exhibits two stable steady states, one at the low end and the other at the high end. Consequently, it appears to have a bimodal distribution with one sub-population (mode) around the low end and the other around the high end...
2016: PloS One
https://www.readbyqxmd.com/read/27816736/stochastic-analysis-of-chemical-reaction-networks-using-linear-noise-approximation
#18
Luca Cardelli, Marta Kwiatkowska, Luca Laurenti
Stochastic evolution of Chemical Reactions Networks (CRNs) over time is usually analyzed through solving the Chemical Master Equation (CME) or performing extensive simulations. Analysing stochasticity is often needed, particularly when some molecules occur in low numbers. Unfortunately, both approaches become infeasible if the system is complex and/or it cannot be ensured that initial populations are small. We develop a probabilistic logic for CRNs that enables stochastic analysis of the evolution of populations of molecular species...
November 2016: Bio Systems
https://www.readbyqxmd.com/read/27761104/accurate-chemical-master-equation-solution-using-multi-finite-buffers
#19
Youfang Cao, Anna Terebus, Jie Liang
The discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multi-scale nature of many networks where reaction rates have large disparity, directly solving dCMEs is intractable due to the exploding size of the state space. It is important to truncate the state space effectively with quantified errors, so accurate solutions can be computed. It is also important to know if all major probabilistic peaks have been computed. Here we introduce the Accurate CME (ACME) algorithm for obtaining direct solutions to dCMEs...
2016: Multiscale Modeling & Simulation: a SIAM Interdisciplinary Journal
https://www.readbyqxmd.com/read/27711478/observation-of-a-new-channel-the-production-of-ch3-in-the-abstraction-reaction-of-oh-radicals-with-acetaldehyde
#20
Neil U M Howes, James P A Lockhart, Mark A Blitz, Scott A Carr, Maria Teresa Baeza-Romero, Dwayne E Heard, Robin J Shannon, Paul W Seakins, T Varga
Using laser flash photolysis coupled to photo-ionization time-of-flight mass spectrometry (PIMS), methyl radicals (CH3) have been detected as primary products from the reaction of OH radicals with acetaldehyde (ethanal, CH3CHO) with a yield of ∼15% at 1-2 Torr of helium bath gas. Supporting measurements based on laser induced fluorescence studies of OH recycling in the OH/CH3CHO/O2 system are consistent with the PIMS study. Master equation calculations suggest that the origin of the methyl radicals is from prompt dissociation of chemically activated acetyl products and hence is consistent with previous studies which have shown that abstraction, rather than addition/elimination, is the sole route for the OH + acetaldehyde reaction...
September 29, 2016: Physical Chemistry Chemical Physics: PCCP
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