Global potential energy surface and product pair-correlated distributions for the F(2P) + SiH4 reaction. Comparison with experiments.

In this paper we study the gas-phase hydrogen abstraction reaction between fluorine atoms and silane in a three-step process: potential energy surface, kinetics and dynamics. Firstly, we developed for the...

Mathematical Modelling in Analytical Chromatography: Problems and Solutions

Based on an analysis of the results of original research performed in the Laboratory of Sorption Methods of the Vernadsky Institute of Geochemistry and Analytical Chemistry of the Russian Academy of Sciences within the project “Mathematical Chromatograph,” the review covers the aim and strategy of the imitation modeling of high-performance chromatography; associated problems of the theory of intermolecular interactions; classifications of polar stationary phases by their selectivity; descriptions of the kinetics and dynamics of sorption processes, choice of the composition of multicomponent mobile phases in HPLC and ion chromatography using the method of the dynamic map of a chromatographic system; and the development of alternating gradient modes using a mathematical experiment.

BioSANS: A Software Package for Symbolic and Numeric Biological Simulation

Modeling biochemical systems can provide insights into behaviors that are difficult to observe or understand. It requires software, programming, and understanding of the system to build a model and study it. Softwares exist for such systems biology modeling, but most support only certain types of modeling tasks. Desirable features including ease in preparing input, symbolic or analytical computation, parameter estimation, graphical user interface, and systems biology markup language (SBML) support are not seen concurrently in one software package. In this study, we developed a python-based software that supports these features, with both deterministic and stochastic propagations. The software can be used by graphical user interface, command line, or as a python import. We also developed a semi-programmable and intuitively easy topology input method for the biochemical reactions. We tested the software with semantic and stochastic SBML test cases. Tests on symbolic solution and parameter estimation were also included. The software we developed is reliable, well performing, convenient to use, and compliant with most of the SBML tests. So far it is the only systems biology software that supports symbolic, deterministic, and stochastic modeling in one package that also features parameter estimation and SBML support. This work offers a comprehensive set of tools and allows for better availability and accessibility for studying kinetics and dynamics in biochemical systems.

Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics

The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.

Quasi-Classical Trajectory Study of the CN + NH3 Reaction Based on a Global Potential Energy Surface

Based on a combination of valence-bond and molecular mechanics functions which were fitted to high-level ab initio calculations, we constructed an analytical full-dimensional potential energy surface, named PES-2020, for the hydrogen abstraction title reaction for the first time. This surface is symmetrical with respect to the permutation of the three hydrogens in ammonia, it presents numerical gradients and it improves the description presented by previous theoretical studies. In order to analyze its quality and accuracy, stringent tests were performed, exhaustive kinetics and dynamics studies were carried out using quasi-classical trajectory calculations, and the results were compared with the available experimental evidence. Firstly, the properties (geometry, vibrational frequency and energy) of all stationary points were found to reasonably reproduce the ab initio information used as input; due to the complicated topology with deep wells in the entrance and exit channels and a “submerged” transition state, the description of the intermediate complexes was poorer, although it was adequate to reasonably simulate the kinetics and dynamics of the title reaction. Secondly, in the kinetics study, the rate constants simulated the experimental data in the wide temperature range of 25–700 K, improving the description presented by previous theoretical studies. In addition, while previous studies failed in the description of the kinetic isotope effects, our results reproduced the experimental information. Finally, in the dynamics study, we analyzed the role of the vibrational and rotational excitation of the CN(v,j) reactant and product angular scattering distribution. We found that vibrational excitation by one quantum slightly increased reactivity, thus reproducing the only experimental measurement, while rotational excitation strongly decreased reactivity. The scattering distribution presented a forward-backward shape, associated with the presence of deep wells along the reaction path. These last two findings await experimental confirmation.

Real-time NMR spectroscopy in the study of biomolecular kinetics and dynamics

The review describes the application of NMR spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular irreversible folding experiments pose large requirements on (i) the signal-to-noise due to the time limitations and (ii) on synchronizing the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases including dynamic nuclear polarization, hyperpolarization and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure- and temperature-jump, light induction and rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.

MATHEMATICAL MODELING OF CONCRETE STRUCTURE CORROSION IN BIOLOGICALLY AGGRESSIVE ENVIRONMENTS

In the aquatic environment, biocorrosion is an important factor affecting the reliability and durability of concrete structures. The destruction of cement concretes during biological corrosion is determined by the processes of mass transfer. The article presents the development of a calculated mathematical model of liquid corrosion in cement concrete, taking into account the biogenic factor. For the first time, a model of mass transfer in an unbounded two-layer plate is considered in the form of differential equations of parabolic type in partial derivatives with boundary conditions of the second kind at the interface between concrete and liquid and of the fourth kind at the interface between concrete and biofilm. The results of a numerical experiment are presented to study the influence of the coefficients of mass conductivity and mass transfer on the kinetics and dynamics of the process.

Trichloroethylene adsorption extraction under kinetic conditions by carbon materials in the processes of water treatment of food production

The high level of environmental pollution currently represent a great danger to ecosystems and human health, since a significant part of the generated industrial wastewater is discharged into reservoirs either insufficiently treated or without treatment. In order to reduce the organic substances concentration in the discharged effluents, the use of carbon sorbents is promising. The sorption process requires a comprehensive study, including the process statics, kinetics and dynamics which allows us to establish the features and extraction mechanism. In this paper a model of the studied sorbents granules structure is determined, the mass transfer mechanism in the adaptive control systems is a trichloroethylene (trilene) aqua solution is established, the external mass transfer coefficients which is necessary for engineering calculations are determined. The research results scientific significance lies in the development of the organic substances adsorption theory on the example of trilen by carbon sorbents that differ in the surface structure and properties. The practical significance lies in obtaining kinetic data which is necessary for calculating the wastewater treatment process technological parameters.