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result(s) for
"Reaction kinetics"
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Markovian approaches to modeling intracellular reaction processes with molecular memory
Many cellular processes are governed by stochastic reaction events. These events do not necessarily occur in single steps of individual molecules, and, conversely, each birth or death of a macromolecule (e.g., protein) could involve several small reaction steps, creating a memory between individual events and thus leading to nonmarkovian reaction kinetics. Characterizing this kinetics is challenging. Here, we develop a systematic approach for a general reaction network with arbitrary intrinsic waiting-time distributions, which includes the stationary generalized chemical-master equation (sgCME), the stationary generalized Fokker–Planck equation, and the generalized linear-noise approximation. The first formulation converts a nonmarkovian issue into a markovian one by introducing effective transition rates (that explicitly decode the effect of molecular memory) for the reactions in an equivalent reaction network with the same substrates but without molecular memory. Nonmarkovian features of the reaction kinetics can be revealed by solving the sgCME. The latter 2 formulations can be used in the fast evaluation of fluctuations. These formulations can have broad applications, and, in particular, they may help us discover new biological knowledge underlying memory effects. When they are applied to generalized stochastic models of gene-expression regulation, we find that molecular memory is in effect equivalent to a feedback and can induce bimodality, fine-tune the expression noise, and induce switch.
Journal Article
Electrocatalysts in lithium-sulfur batteries
Lithium-sulfur (Li-S) batteries with the merits of high theoretical capacity and high energy density have gained significant attention as the next-generation energy storage devices. Unfortunately, the main pressing issues of sluggish reaction kinetics and severe shuttling of polysulfides hampered their practical application. To overcome these obstacles, various strategies adopting high-efficient electrocatalysts have been explored to enable the rapid polysulfide conversions and thereby suppressing the polysulfide shuttling. This review first summarizes the recent progress on electrocatalysts involved in hosts, interlayers, and protective layers. Then, these electrocatalysts in Li-S batteries are analyzed by listing representative works, from the viewpoints of design concepts, engineering strategies, working principles, and electrochemical performance. Finally, the remaining issues/challenges and future perspectives facing electrocatalysts are given and discussed. This review may provide new guidance for the future construction of electrocatalysts and their further utilizations in high-performance Li-S batteries.
Journal Article
Defect engineering on carbon black for accelerated Li-S chemistry
Rationally designing sulfur hosts with the functions of confining lithium polysulfides (LiPSs) and promoting sulfur reaction kinetics is critically important to the real implementation of lithium-sulfur (Li-S) batteries. Herein, the defect-rich carbon black (CB) as sulfur host was successfully constructed through a rationally regulated defect engineering. Thus-obtained defect-rich CB can act as an active electrocatalyst to enable the sulfur redox reaction kinetics, which could be regarded as effective inhibitor to alleviate the LiPS shuttle. As expected, the cathode consisting of sulfur and defect-rich CB presents a high rate capacity of 783.8 mA·h·g
−1
at 4 C and a low capacity decay of only 0.07% per cycle at 2 C over 500 cycles, showing favorable electrochemical performances. The strategy in this investigation paves a promising way to the design of active electrocatalysts for realizing commercially viable Li-S batteries.
Journal Article
Study on A New Type of High Temperature Resistant Adsorption Type Retarded Acid System
Deep carbonate reservoirs present significant hurdles for reservoir stimulation due to extreme temperatures and rapid acid-rock reactions. The dense adsorption layer has the ability to postpone the interaction between rock and hydrogen ions, which is crucial for lowering the acid rock reaction rate. Based on the surfactant and film-forming agent’s synergistic impact, the retarding agent SH-1—which has the ability to generate a dense adsorption film on the surface of rock samples—was chosen for this study. After adding synergist and corrosion inhibitor, a new type of high temperature resistant adsorption type retarding acid system ’ 0.9% SH-1 + 20% HCl + 0.1% synergist + 1.5% corrosion inhibitor ’ was developed. The retarding performance of the retarding acid system at high temperature and various parameters of acid rock reaction kinetics were studied. The results show that the new adsorption-type retarded acid system can achieve good retarding effect at high temperature and ultra-high temperature, and the retarding rate is 90 % at 180 °C. In comparison to traditional hydrochloric acid, the new adsorption-type retarded acid exhibits a lower hydrogen ion mass transfer rate and a higher acid-rock reaction activation energy. These differences can effectively lower the acid-rock reaction rate. Additionally, an examination of the etching morphology reveals that the retarded acid is more easily etched along the cracks leading to the deep core. The novel adsorption-delayed acid offers excellent retarding power, high temperature resistance, and minimal damage. Consequently, it has certain reference value for the study of acidification transformation of ultra-high temperature deep carbonate reservoirs.
Journal Article
Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme
Correlated motions of proteins are critical to function, but these features are difficult to resolve using traditional structure determination techniques. Time-resolved X-ray methods hold promise for addressing this challenge, but have relied on the exploitation of exotic protein photoactivity, and are therefore not generalizable. Temperature jumps, through thermal excitation of the solvent, have been utilized to study protein dynamics using spectroscopic techniques, but their implementation in X-ray scattering experiments has been limited. Here, we perform temperature-jump small- and wide-angle X-ray scattering measurements on a dynamic enzyme, cyclophilin A, demonstrating that these experiments are able to capture functional intramolecular protein dynamics on the microsecond timescale. We show that cyclophilin A displays rich dynamics following a temperature jump, and use the resulting time-resolved signal to assess the kinetics of conformational changes. Two relaxation processes are resolved: a fast process is related to surface loop motions, and a slower process is related to motions in the core of the protein that are critical for catalytic turnover.
Understanding how structural dynamics contribute to protein function is a longstanding challenge in structural biology. Now, time-resolved X-ray solution scattering following an infrared laser-induced temperature jump has been used to probe functional, intramolecular motions in the dynamic enzyme cyclophilin A.
Journal Article
Imaging Nucleophilic Substitution Dynamics
Anion-molecule nucleophilic substitution (SN2) reactions are known for their rich reaction dynamics, caused by a complex potential energy surface with a submerged barrier and by weak coupling of the relevant rotational-vibrational quantum states. The dynamics of the SN2 reaction of Cl⁻ + CH₃I were uncovered in detail by using crossed molecular beam imaging. As a function of the collision energy, the transition from a complex-mediated reaction mechanism to direct backward scattering of the I⁻ product was observed experimentally. Chemical dynamics calculations were performed that explain the observed energy transfer and reveal an indirect roundabout reaction mechanism involving CH₃ rotation.
Journal Article
Modeling of the Interactions Between Catalytic Surfaces and Gas-Phase
The catalytic surface interacts with the gas-phase by a variety of chemical and physical processes. Hence, optimization of design and operation conditions of catalytic reactors do not only require the understanding of the catalytic reaction sequence but also its coupling with mass and heat transport and potential homogeneous reactions. The chemical, thermal, and mass-transport interactions between the catalytic surface and the gas-phase are discussed in terms of the individual and combined interactions. The state-of-the-art modelling of reactive flows and its coupling with the catalytic surface is summarized. The interactions are illustrated by a number of examples such as reforming of hydrocarbons, catalytic combustion, exhaust-gas after-treatment, each focusing on a special aspect of catalyst–gas interactions. The potentials and limitations of the numerical simulations will be discussed including experimental techniques for model validation.
Graphical Abstract
Journal Article
Decompositional and chemical reaction kinetics study of eggshell powder waste for value-added materials
The kinetics and chemical reaction mechanisms involved in the decomposition of eggshells are studied by experimental (thermogravimetric analysis and differential thermal analysis) as well as theoretical models. X-ray diffraction pattern of calcined eggshell at 1000 °C for 4 h exhibits monophasic CaO. The optical band gap of eggshell powder is observed 4.06 eV, which is less than commercial CaCO
3
(4.32 eV). The results showed that the activation energy for decomposition calculated through different methods is in good agreement with the reported value, i.e., in the range of 207–214 kJ mol
−1
. Based on Raman spectroscopy, eggshells exhibit better crystallinity and blue shift when compared to (conventional) CaCO
3
. The present work reveals that the eggshell can be used directly as a catalyst and as resources to synthesize the value-added materials. Eggshells and their byproducts could also be used as biomaterials and host for photoluminescence instead of commercial CaCO
3
.
Journal Article
Chemical Kinetics of Serial Processes for Photogenerated Charges at Semiconductor Surface: A Classical Theoretical Calculation
The slow charge reactions at the semiconductor surface severely encumber the photocatalysis applications, which are elusive and complicated in a serial charge excitation-separation-reaction process. Both experimental and theoretical studies are essential in this area. Here, a classical numerical calculation of the charge reaction microkinetic is developed based on a simple consecutive charge separation and reaction model, a conservation law of photogenerated charges, and differential analysis. Several reaction conditions have been discussed to elucidate how a fast charge separation and reaction rate constant influence the apparent reaction kinetics. It is shown that a slower charge separation rate strongly limits the detection of higher-order reaction rates, and higher-order kinetics can be detected with all other processes faster than the reactions. This numerical calculation projects the possible limitations of kinetics study by transient techniques.
Journal Article