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https://www.readbyqxmd.com/read/28537287/reaction-mechanism-and-product-branching-ratios-of-the-ch-c3h4-reactions-a-theoretical-study
#1
Joao Marcelo Ribeiro, Alexander M Mebel
Two ground-state CH radical reactions with the C3H4 isomers allene and methylacetylene occurring along the C4H5 potential energy surface (PES) were studied to probe the reaction mechanisms and final product distributions. The calculations were performed using a CCSD(T)-F12//B2PLYPD3 PES in combination with the 1-D chemical master equation. The reaction between the CH radical and allene was found to lead to exclusive "funneling" of the energized C4H5 intermediates into linear C4H5 configurations before reaching the exit channels, regardless of the specific nature of the initial bimolecular reactive encounter...
May 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28534618/microsecond-timescale-proton-rotating-frame-relaxation-under-magic-angle-spinning
#2
Petra Rovó, Rasmus Linser
This paper deals with the theoretical foundation of proton magic-angle-spinning rotating-frame relaxation (R1ρ) and establishes the range of validity and accuracy of the presented approach to describe low-amplitude microsecond timescale motion in the solid state. Beside heteronuclear dipolar and chemical shift anisotropy interactions, a major source of relaxation for protons is the homonuclear dipolar interaction. For this latter relaxation process no general analytical equation has been published until now which would describe the R1ρ relaxation at any spinning-speed, spin-lock field, or tilt-angle...
May 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28483564/the-influence-of-nuclear-compartmentalisation-on-stochastic-dynamics-of-self-repressing-gene-expression
#3
Marc Sturrock, Shiyu Li, Vahid Shahrezaei
Gene expression is an inherently noisy process. This noise is generally thought to be deleterious as precise internal regulation of biochemical reactions is essential for cell growth and survival. Self-repression of gene expression, which is the simplest form of a negative feedback loop, is commonly believed to be employed by cellular systems to decrease the stochastic fluctuations in gene expression. When there is some delay in autoregulation, it is also believed that this system can generate oscillations...
May 5, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28463205/aggregation-for-computing-multi-modal-stationary-distributions-in-1-d-gene-regulatory-networks
#4
Neslihan Avcu, Nihal Pekergin, Ferhan Pekergin, Cuneyt Guzelis
This paper proposes aggregation-based, three-stage algorithms to overcome the numerical problems encountered in computing stationary distributions and mean first passage times for multi-modal birth-death processes of large state space sizes. The considered birth-death processes which are defined by Chemical Master Equations are used in modeling stochastic behavior of gene regulatory networks. Computing stationary probabilities for a multi-modal distribution from Chemical Master Equations is subject to have numerical problems due to the probability values running out of the representation range of the standard programming languages with the increasing size of the state space...
April 27, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28451881/theoretical-study-of-the-h-hcn-%C3%A2-h-hcn-process
#5
Eberth Correa, Washington Barbosa da Silva, Patricia R P Barreto, Alessandra F Albernaz
We present a theoretical study on the detailed mechanism and kinetics of the H + HCN → H + HNC process. The potential energy surface was calculated at the complete basis set quantum chemical method, CBS-QB3. The vibrational frequencies and geometries for four isomers (H 2CN, cis-HCNH, trans-HCNH, CNH 2), and seven saddle points (TSn where n = 1 - 7) are very important and must be considered during the process of formation of the HNC in the reaction were calculated at the B3LYP/6-311G(2d,d,p) level, within CBS-QB3 method...
May 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28435938/obtaining-effective-rate-coefficients-to-describe-the-decomposition-kinetics-of-the-corannulene-oxyradical-at-high-temperatures
#6
Hongmiao Wang, Xiaoqing You, Mark A Blitz, Michael J Pilling, Struan H Robertson
Unimolecular reactions play an important role in combustion kinetics. An important task of reaction kinetic analysis is to obtain the phenomenological rate coefficients for unimolecular reactions based on the master equation approach. In most cases, the eigenvalues of the transition matrix describing collisional internal energy relaxation are of much larger magnitude than and well separated from the chemically significant eigenvalues, so that phenomenological rate coefficients may be unequivocally derived for incorporation in combustion mechanisms...
April 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28388111/stochastic-simulation-of-reaction-diffusion-systems-a-fluctuating-hydrodynamics-approach
#7
Changho Kim, Andy Nonaka, John B Bell, Alejandro L Garcia, Aleksandar Donev
We develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuatinghydrodynamics (FHD). For hydrodynamicsystems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our SPDEs are spatially discretized and reactions are modeled as a source term having Poissonfluctuations. However, unlike the RDME, which becomes prohibitively expensive for an increasing number of molecules, our FHD-based description naturally extends from the regime where fluctuations are strong, i...
March 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28383887/kinetics-of-thermal-unimolecular-decomposition-of-acetic-anhydride-an-integrated-deterministic-and-stochastic-model
#8
Tam V-T Mai, Minh V Duong, Hieu T Nguyen, Kuang C Lin, Lam K Huynh
An integrated deterministic and stochastic model within the master equation/Rice-Ramsperger-Kassel-Marcus (ME/RRKM) framework was first used to characterize temperature- and pressure-dependent behaviors of thermal decomposition of acetic anhydride in a wide range of conditions (i.e., 300-1500 K and 0.001-100 atm). Particularly, using potential energy surface and molecular properties obtained from high-level electronic structure calculations at CCSD(T)/CBS, macroscopic thermodynamic properties and rate coefficients of the title reaction were derived with corrections for hindered internal rotation and tunneling treatments...
April 14, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28341132/stochastic-modeling-and-numerical-simulation-of-gene-regulatory-networks-with-protein-bursting
#9
Manuel Pájaro, Antonio A Alonso, Irene Otero-Muras, Carlos 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
#10
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
#11
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
#12
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...
May 5, 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
#13
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
#14
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/nucleotide-selectivity-at-a-preinsertion-checkpoint-of-t7-rna-polymerase-transcription-elongation
#15
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 preinsertion site where a critical tyrosine residue locates nearby to assist the nucleotide selection...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28166778/markov-state-models-of-gene-regulatory-networks
#16
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
#17
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
#18
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
#19
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
#20
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
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