keyword
MENU ▼
Read by QxMD icon Read
search

Chemical master equation

keyword
https://www.readbyqxmd.com/read/29133841/nanopore-electric-snapshots-of-an-rna-tertiary-folding-pathway
#1
Xinyue Zhang, Dong Zhang, Chenhan Zhao, Kai Tian, Ruicheng Shi, Xiao Du, Andrew J Burcke, Jing Wang, Shi-Jie Chen, Li-Qun Gu
The chemical properties and biological mechanisms of RNAs are determined by their tertiary structures. Exploring the tertiary structure folding processes of RNA enables us to understand and control its biological functions. Here, we report a nanopore snapshot approach combined with coarse-grained molecular dynamics simulation and master equation analysis to elucidate the folding of an RNA pseudoknot structure. In this approach, single RNA molecules captured by the nanopore can freely fold from the unstructured state without constraint and can be programmed to terminate their folding process at different intermediates...
November 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29098989/an-application-of-the-krylov-fsp-ssa-method-to-parameter-fitting-with-maximum-likelihood
#2
Khanh N Dinh, Roger B Sidje
Monte Carlo methods such as the stochastic simulation algorithm (SSA) have traditionally been employed in gene regulation problems. However, there has been increasing interest to directly obtain the probability distribution of the molecules involved by solving the chemical master equation (CME). This requires addressing the curse of dimensionality that is inherent in most gene regulation problems. The finite state projection (FSP) seeks to address the challenge and there have been variants that further reduce the size of the projection or that accelerate the resulting matrix exponential...
November 3, 2017: Physical Biology
https://www.readbyqxmd.com/read/29064498/ephemeral-collision-complexes-mediate-chemically-termolecular-transformations-that-affect-system-chemistry
#3
Michael P Burke, Stephen J Klippenstein
Termolecular association reactions involve ephemeral collision complexes-formed from the collision of two molecules-that collide with a third and chemically inert 'bath gas' molecule that simply transfers energy to/from the complex. These collision complexes are generally not thought to react chemically on collision with a third molecule in the gas-phase systems of combustion and planetary atmospheres. Such 'chemically termolecular' reactions, in which all three molecules are involved in bond making and/or breaking, were hypothesized long ago in studies establishing radical chain branching mechanisms, but were later concluded to be unimportant...
November 2017: Nature Chemistry
https://www.readbyqxmd.com/read/29057418/the-reaction-of-criegee-intermediates-with-acids-and-enols
#4
L Vereecken
The reaction of CH2OO, the smallest carbonyl oxide (Criegee intermediate, CI), with several acids was investigated using the CCSD(T)/aug-cc-pVTZ//M06-2X/aug-cc-pVTZ quantum chemical method, as well as microvariational transition state theory and RRKM master equation theoretical kinetic methodologies. For oxoacids HNO3 and HCOOH, a 1,4-insertion mechanism allows for barrierless reactions with high rate coefficients, in agreement with literature experimental data. This mechanism relies on the presence of a double bond in the α-position to the acidic OH group...
November 1, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29055349/a-finite-state-projection-algorithm-for-the-stationary-solution-of-the-chemical-master-equation
#5
Ankit Gupta, Jan Mikelson, Mustafa Khammash
The chemical master equation (CME) is frequently used in systems biology to quantify the effects of stochastic fluctuations that arise due to biomolecular species with low copy numbers. The CME is a system of ordinary differential equations that describes the evolution of probability density for each population vector in the state-space of the stochastic reaction dynamics. For many examples of interest, this state-space is infinite, making it difficult to obtain exact solutions of the CME. To deal with this problem, the Finite State Projection (FSP) algorithm was developed by Munsky and Khammash [J...
October 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29040384/selansi-a-toolbox-for-simulation-of-stochastic-gene-regulatory-networks
#6
Manuel Pájaro, Irene Otero-Muras, Carlos Vázquez, Antonio A Alonso
Motivation: Gene regulation is inherently stochastic. In many applications concerning Systems and Synthetic Biology such as the reverse engineering and the de novo design of genetic circuits, stochastic effects (yet potentially crucial) are often neglected due to the high computational cost of stochastic simulations. With advances in these fields there is an increasing need of tools providing accurate approximations of the stochastic dynamics of gene regulatory networks (GRNs) with reduced computational effort...
October 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28976756/barrierless-reactions-with-loose-transition-states-govern-the-yields-and-lifetimes-of-organic-nitrates-derived-from-isoprene
#7
Ivan R Piletic, Edward O Edney, Libero J Bartolotti
The chemical reaction mechanism of NO addition to two β and δ isoprene hydroxy-peroxy radical isomers is examined in detail using density functional theory, coupled cluster methods, and the energy resolved master equation formalism to provide estimates of rate constants and organic nitrate yields. At the M06-2x/aug-cc-pVTZ level, the potential energy surfaces of NO reacting with β-(1,2)-HO-IsopOO(•) and δ-Z-(1,4)-HO-IsopOO(•) possess barrierless reactions that produce alkoxy radicals/NO2 and organic nitrates...
October 20, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28938803/hybrid-models-for-chemical-reaction-networks-multiscale-theory-and-application-to-gene-regulatory-systems
#8
Stefanie Winkelmann, Christof Schütte
Well-mixed stochastic chemical kinetics are properly modeled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded. The classical model reduction approach uniformly rescales the overall dynamics to obtain deterministic systems characterized by ordinary differential equations, the well-known mass action reaction rate equations...
September 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28886641/length-and-sequence-relaxation-of-copolymers-under-recombination-reactions
#9
Alex Blokhuis, David Lacoste
We describe the kinetics and thermodynamics of copolymers undergoing recombination reactions, which are important for prebiotic chemistry. We use two approaches: the first one, based on chemical rate equations and the mass-action law describes the infinite size limit, while the second one, based on the chemical master equation, describes systems of finite size. We compare the predictions of both approaches for the relaxation of thermodynamic quantities towards equilibrium. We find that for some choice of initial conditions, the entropy of the sequence distribution can be lowered at the expense of increasing the entropy of the length distribution...
September 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28881987/efficient-simulation-of-intrinsic-extrinsic-and-external-noise-in-biochemical-systems
#10
Dennis Pischel, Kai Sundmacher, Robert J Flassig
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 accurately. Since the exact solution of the chemical master equation, which governs the underlying stochastic process, cannot be derived for most biochemical systems, approximate methods are used to obtain a solution. Results: In this study, a method to efficiently simulate the various sources of noise simultaneously is proposed and benchmarked on several examples...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28862457/reaction-paths-and-chemical-activation-reactions-of-2-methyl-5-furanyl-radical-with-3-o2
#11
Jason M Hudzik, Joseph W Bozzelli
Interest in high-energy substituted furans has been increasing due to their occurrence in biofuel production and their versatility in conversion to other useful products. Methylfurans are the simplest substituted furans and understanding their reaction pathways, thermochemical properties, including intermediate species stability, and chemical kinetics would aid in the study of larger furans. Furan ring C-H bonds have been shown to be extremely strong, approximately 120 kcal mol(-1), due in part to the placement of the oxygen atom and aromatic-like resonance, both within the ring...
September 26, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28799405/the-spatiotemporal-master-equation-approximation-of-reaction-diffusion-dynamics-via-markov-state-modeling
#12
Stefanie Winkelmann, Christof Schütte
Accurate modeling and numerical simulation of reaction kinetics is a topic of steady interest. We consider the spatiotemporal chemical master equation (ST-CME) as a model for stochastic reaction-diffusion systems that exhibit properties of metastability. The space of motion is decomposed into metastable compartments, and diffusive motion is approximated by jumps between these compartments. Treating these jumps as first-order reactions, simulation of the resulting stochastic system is possible by the Gillespie method...
December 7, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28789554/adaptive-coarse-graining-method-for-energy-transfer-and-dissociation-kinetics-of-polyatomic-species
#13
A Sahai, B Lopez, C O Johnston, M Panesi
A novel reduced-order method is presented for modeling reacting flows characterized by strong non-equilibrium of the internal energy level distribution of chemical species in the gas. The approach seeks for a reduced-order representation of the distribution function by grouping individual energy states into macroscopic bins, and then reconstructing state population using the maximum entropy principle. This work introduces an adaptive grouping methodology to identify and lump together groups of states that are likely to equilibrate faster with respect to each other...
August 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28789553/rrkm-and-master-equation-kinetic-analysis-of-parallel-addition-reactions-of-isomeric-radical-intermediates-in-hydrocarbon-flames
#14
Pierre M Winter, Michael Rheaume, Andrew L Cooksy
We have calculated the temperature-dependent rate coefficients of the addition reactions of butadien-2-yl (C4H5) and acroylyl (C3H3O) radicals with ethene (C2H4), carbon monoxide (CO), formaldehyde (H2CO), hydrogen cyanide (HCN), and ketene (H2CCO), in order to explore the balance between kinetic and thermodynamic control in these combustion-related reactions. For the C4H5 radical, the 1,3-diene form of the addition products is more stable than the 1,2-diene, but the 1,2-diene form of the radical intermediate is stabilized by an allylic delocalization, which may influence the relative activation energies...
August 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28764339/an-adaptive-solution-to-the-chemical-master-equation-using-tensors
#15
Huy D Vo, Roger B Sidje
Solving the chemical master equation directly is difficult due to the curse of dimensionality. We tackle that challenge by a numerical scheme based on the quantized tensor train (QTT) format, which enables us to represent the solution in a compressed form that scales linearly with the dimension. We recast the finite state projection in this QTT framework and allow it to expand adaptively based on proven error criteria. The end result is a QTT-formatted matrix exponential that we evaluate through a combination of the inexact uniformization technique and the alternating minimal energy algorithm...
July 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28692269/unimolecular-decay-of-the-dimethyl-substituted-criegee-intermediate-in-alkene-ozonolysis-decay-time-scales-and-the-importance-of-tunneling
#16
Greg T Drozd, Theo Kurtén, Neil M Donahue, Marsha I Lester
We used the steady-state master equation to model unimolecular decay of the Criegee intermediate formed from ozonolysis of 2,3-dimethyl-2-butene (tetramethylethylene, TME). Our results show the relative importance and time scales for both the prompt and thermal unimolecular decay of the dimethyl-substituted Criegee intermediate, (CH3)2COO. Calculated reactive fluxes show the importance of quantum mechanical tunneling for both prompt and thermal decay to OH radical products. We constrained the initial energy distribution of chemically activated (CH3)2COO formed in TME ozonolysis by combining microcanonical rates k(E) measured experimentally under collision-free conditions and modeled using semiclassical transition-state theory (SCTST) with pressure-dependent yields of stabilized Criegee intermediates measured with scavengers in flow-tube experiments...
August 2, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28676416/noise-slows-the-rate-of-michaelis-menten-reactions
#17
J David Van Dyken
Microscopic randomness and the small volumes of living cells combine to generate random fluctuations in molecule concentrations called "noise". Here I investigate the effect of noise on biochemical reactions obeying Michaelis-Menten kinetics, concluding that substrate noise causes these reactions to slow. I derive a general expression for the time evolution of the joint probability density of chemical species in arbitrarily connected networks of non-linear chemical reactions in small volumes. This equation is a generalization of the chemical master equation (CME), a common tool for investigating stochastic chemical kinetics, extended to reaction networks occurring in small volumes, such as living cells...
July 1, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28668036/quantifying-uncertainty-in-the-chemical-master-equation
#18
Basil S Bayati
We describe a novel approach to quantifying the uncertainty inherent in the chemical kinetic master equation with stochastic coefficients. A stochastic collocation method is coupled to an analytical expansion of the master equation to analyze the effects of both extrinsic and intrinsic noise. The method consists of an analytical moment-closure method resulting in a large set of differential equations with stochastic coefficients that are in turn solved via a Smolyak sparse grid collocation method. We discuss the error of the method relative to the dimension of the model and clarify which methods are most suitable for the problem...
June 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28667253/inhibitors-alter-the-stochasticity-of-regulatory-proteins-to-force-cells-to-switch-to-the-other-state-in-the-bistable-system
#19
Wun-Sin Jhang, Shih-Chiang Lo, Chen-Chao Yeh, Che-Chi Shu
The cellular behaviors under the control of genetic circuits are subject to stochastic fluctuations, or noise. The stochasticity in gene regulation, far from a nuisance, has been gradually appreciated for its unusual function in cellular activities. In this work, with Chemical Master Equation (CME), we discovered that the addition of inhibitors altered the stochasticity of regulatory proteins. For a bistable system of a mutually inhibitory network, such a change of noise led to the migration of cells in the bimodal distribution...
June 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28618775/thermal-decomposition-of-2-3-3-3-and-trans-1-3-3-3-tetrafluoropropenes
#20
Akira Matsugi, Kazuo Takahashi
The thermal decomposition reactions of 2,3,3,3- and trans-1,3,3,3-tetrafluoropropenes (TFPs) have been studied both experimentally and computationally to elucidate their kinetics and mechanism. The experiments were performed by observing the temporal profiles of HF produced in the decomposition of the tetrafluoropropenes behind shock waves at temperatures of 1540-1952 K (for 2,3,3,3-TFP) or 1525-1823 K (for trans-1,3,3,3-TFP) and pressure of 100-200 kPa in Ar bath. The reaction pathways responsible for the profiles were explored based on quantum chemical calculations...
June 27, 2017: Journal of Physical Chemistry. A
keyword
keyword
23903
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"