686 research outputs found
Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory
No full textThe statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an essential part of a multiscale modeling framework, covering a vast region of molecular simulation techniques. The successful application ranges from the small molecule solvation energy to the bulk phase behavior of polymers, macromolecules, etc. The 3D-RISM-KH successfully predicts and explains the molecular mechanisms of self-assembly and aggregation of proteins and peptides related to neurodegeneration, protein-ligand binding, and structure-function related solvation properties. Upon coupling the 3D-RISM-KH theory with a novel multiple time-step molecular dynamic (MD) of the solute biomolecule stabilized by the optimized isokinetic Nosé–Hoover chain thermostat driven by effective solvation forces obtained from 3D-RISM-KH and extrapolated forward by generalized solvation force extrapolation (GSFE), gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties were obtained in this new quasidynamics protocol. The multiscale OIN/GSFE/3D-RISM-KH algorithm was implemented in the Amber package and well documented for fully flexible model of alanine dipeptide, miniprotein 1L2Y, and protein G in aqueous solution, with a solvent sampling rate ~150 times faster than a standard MD simulation in explicit water. Further acceleration in computation can be achieved by modifying the extent of solvation layers considered in the calculation, as well as by modifying existing closure relations. This enhanced simulation technique has proven applications in protein-ligand binding energy calculations, ligand/solvent binding site prediction, molecular solvation energy calculations, etc. Applications of the RISM-KH theory in molecular simulation are discussed in this work
Benchmarking Free Energy Calculations in Liquid Aliphatic Ketone Solvents Using the 3D-RISM-KH Molecular Solvation Theory
No full textThe three-dimensional reference interaction site model of the molecular solvation theory with the Kovalenko–Hirata closure is used to calculate the free energy of solvation of organic solutes in liquid aliphatic ketones. The ketone solvent sites were modeled using a modified united-atom force field. The successful application of these solvation models in calculating ketone–water partition coefficients of a large number of solutes supports the validation and benchmarking reported here
Microscopic Theory of Liquid Interfaces in Molecular Systems
No full textA statistical-mechanical theory of inhomogeneous polyatomic fluids is proposed. It enables microscopic description of liquid interfaces in molecular systems with both non-polar and polar species. The method introduces a site-site generalization of the Lovett-Mow-Buff-Wertheim integro-differential equation for the one-particle density distributions to polyatomic fluids. It uses the inhomogeneous site-site direct correlation functions of molecular fluid consistently constructed by nonlinear interpolation between the homogeneous ones. The site-site correlations of the coexisting bulk phases are obtained from the reference interaction site model (RISM) integral equation with the closure approximation proposed by Kovalenko and Hirata. The theory is applied to the planar liquid-vapor as well as liquid-liquid interfaces of n-hexane and methanol in ambient conditions.Peer reviewed: YesNRC publication: Ye
Understanding the Liquid States of Cyclic Hydrocarbons Containing N, O, and S Atoms via the 3D-RISM-KH Molecular Solvation Theory
No full textThe 3D-reference interaction site model (3D-RISM) molecular solvation theory in combination with the Kovalenko–Hirata (KH) closure is extended to seven heterocyclic liquids to understand their liquid states and to test the performance of the theory in solvation free energy (SFE) calculations of solutes in select solvents. The computed solvent site distribution profiles were compared with the all-atom molecular dynamics (MD) simulations, showing comparable performances. The computational results were compared against the structural parameters for liquids, whenever available, as well as against the experimental SFEs. The liquids are found to have local ordered structures held together via weak interactions in both the RISM and MD simulations. The 3D-RISM-KH computed SFEs are in good agreement with the benchmark values for the tetrahydrothiophene-S,S-dioxide, and showed comparatively larger deviations in the case of the SFEs in the tetrahydrofuran continuum
Limonius (Pheletes) californicus
No full textWithin the framework of this work, the type material (two syntypes) of Cardiophorus californicus Mannerheim, 1843 was studied in detail; it was photographed. The author of the original description did not identify the holotype, which, in accordance with the provisions of the International Code of Zoological Nomenclature, entails the need to distinguish the lectotype and paralectotype for the subsequent supposed redescription of the species
On the class of limit distributions for thinning currents of homogeneous events
No full textThe abstracts (in two languages) can be found in the pdf file of the article.
Original author name(s) and title in Russian and Lithuanian:
И. Н. Коваленко, О классе предельных распределений для редеющих потоков однородных событий
I. N. Kovalenko, Apie homogeninių įvykių retėjančių srautų ribinių pasiskirstymų klas
Predicting 1,9-Decadiene−Water Partition Coefficients Using the 3D-RISM-KH Molecular Solvation Theory
No full textThe Three-Dimensional Reference Interaction Site Model (3D-RISM) with Kovalenko−Hirata (KH) closure is applied to calculate the 1,9-Decadiene/Water partition coefficients for a diverse class of compounds. The liquid state of 1,9-Decadiene is represented with the united atom TraPPE force field parameters. The 3D-RISM-KH computed partition functions are in good agreement with the experimental results. Our computational scheme can be used for a quantitative structure partitioning prediction for decadiene-water system, which has been used in membrane-mimicking of the egg-lecithin/water permeability experiments
On the class of limiting distributions for a sequence of series of sums of independent renewals
No full textThe abstracts (in two languages) can be found in the pdf file of the article.
Original author name(s) and title in Russian and Lithuanian:
И. И. Коваленко, О классе предельных распределений для последовательности серий сумм независимых процессов восстановления
I. N. Kovalenko, Apie nepriklausomų atstatymo procesų serijų sekos sumų ribinių pasiskirstymų klas
On some research guidelines initiated by articles of Academician I.N. Kovalenko
No full textНаведено огляд деяких напрямків досліджень, які були ініційовані І.М. Коваленком та знайшли відображення у сумісних роботах з автором даної статті. До них відносяться: метод «штучних» моментів регенерації, асимптотична нечутливість, метод Монте-Карло та методи зменшення дисперсії оцінок, принцип монотонних відмов.A review of some research guidelines which were initiated by I.N. Kovalenko and used in joint articles with the author is given. These are: method of «artificial» regeneration moments, asymptotic insensitivity, Monte Carlo method and variance reduction methods, principle of monotone failures
Performance of 3D-RISM-KH in Predicting Hydration Free Energy: Effect of Solute Parameters
No full textThe three-dimensional
reference interaction site model molecular
solvation theory with the Kovalenko–Hirata closure relation
has been shown to produce excellent solvation characteristics for
a large class of (bio)chemical systems in solution. Correct calculation
of hydration free energy is central to successful application of any
solvation model. In order to find out the best possible force-field
parameters to be used for hydration free energy calculation with the
aforementioned theory, we have developed an extended database containing
a large number of experimental solvation free energies available in
the current literature and used a plethora of theoretical models for
assessment. The general Amber force field was found to perform satisfactorily,
whereas special care should be taken in solute charge assignment with
the universal force field
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