Article
Biochemistry & Molecular Biology
Sergey E. Kruchinin, Ekaterina E. Kislinskaya, Gennady N. Chuev, Marina V. Fedotova
Summary: In this study, the hydrated state of protein BPTI was characterized using molecular dynamics and the integral equation method. The results revealed a well-defined hydration layer around the protein and provided insight into the localization of water molecules. This research contributes to our understanding of protein hydration.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Physics, Multidisciplinary
T. Dokoza, D. Pluemacher, M. Smuda, C. Jegust, M. Oberlack
Summary: In this paper, the one-dimensional two-phase Stefan problem is studied analytically using the unified transform method, leading to a system of non-linear Volterra-integral equations describing heat distribution. The position of the phase change can be solved numerically, followed by generating temperature distribution from their integral representation.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2021)
Article
Chemistry, Physical
Anze Hubman, Tomaz Urbic
Summary: The thermodynamic and structural properties of 2D hexagonal soft-sites fluid were investigated using integral equation theory and benchmarked against extensive Monte Carlo simulations. Satisfactory qualitative agreement was found between theory and simulations.
MOLECULAR SIMULATION
(2022)
Article
Chemistry, Physical
Takashi Yoshidome
Summary: In this study, the rotation of Bacillus PS3 F1-ATPase was investigated from the perspective of solvent entropy. It was found that the change in solvent entropy upon 44 degrees rotation of the gamma subunit is approximately zero, indicating the presence of solvent entropy compensation in F1-ATPase. The system energy and conformational entropy also remain unchanged during the rotation. Based on these findings, a rotation mechanism was proposed, which explains the 100% free-energy transduction efficiency of Bacillus PS3 F1-ATPase.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Computer Science, Software Engineering
Pham Ngoc Kien, Sang-Mook Lee
Summary: We present a C++ package called 1D Controlled Source Electromagnetic Method using Quadrature With Extrapolation (1DCSEMQWE) for computing the electromagnetic field of a one-dimensional model in geophysics. This package supports both electric and magnetic dipole sources, and allows transmitters and receivers to be placed anywhere in the layered model. By formulating the electromagnetic field in the frequency domain without positive exponential terms, higher accuracy is achieved. We introduce a new computation tool using quadrature with extrapolation for integral evaluation, effectively addressing numerical errors and providing users with control over the precision of the computed electromagnetic field.
Article
Chemistry, Physical
Sergey E. Kruchinin, Gennady N. Chuev, Marina Fedotova
Summary: A clear understanding of protein-ligand binding requires knowledge of hydration and the role of solvent. In this study, the hydration states of PTP1B in the unbound and bound states were investigated, and changes in hydration upon complex formation with 2HB1 and 2QBP inhibitors were observed. The results showed significant dehydration of the ligands and minimal changes in PTP1B hydration upon complex formation.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Daniel J. Fowles, David S. Palmer
Summary: Simultaneous calculation of entropies, enthalpies, and free energies has long been a challenge in computational chemistry. Recently, a new method called pyRISM-CNN was proposed, which combines the 1D-RISM solver with a deep learning-based free energy functional to predict solvation free energy. This method shows significant improvement in prediction accuracy compared to the standard 1D-RISM theory.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Mathematics
Ioannis K. Argyros, Samundra Regmi, Stepan Shakhno, Halyna Yarmola
Summary: This article updates the convergence developments of Newton's method for solving nonlinear equations. It introduces a finer theory to replace the Kantorovich theory, requiring weaker conditions. The article also proves the convergence order is two under these conditions, and the new convergence ratio is at least as small. Numerical experiments are conducted to complement the study.
Article
Chemistry, Physical
Sergej Friesen, Marina Fedotova, Sergey E. Kruchinin, Marija Bester-Rogac, Crtomir Podlipnik, Richard Buchner
Summary: The hydration and Cl- ion binding of the neurotransmitter acetylcholine (ACh(+)) and its synthetic analogue, carbamoylcholine (CCh(+)), have been studied. Weak but not negligible chloro ion binding was observed, with only about 1/3 of water molecules being affected by the cation. Increasing concentration and temperature significantly dehydrate ACh(+) and CCh(+).
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Polymer Science
Changhao Li, Jianfeng Li, Yuliang Yang
Summary: This work derives a more accurate reaction-diffusion equation for an A/B binary system by summing over microscopic trajectories and introduces the DRD diagram method. It is found that there are coupling terms between diffusion and reaction when there is intermolecular interaction, manifesting on the mesoscopic scale. This method can also be applied to describe chemical reactions in polymeric systems.
Article
Mathematics, Applied
Jian Mi, Jin Huang
Summary: This paper presents a method for solving the two-dimensional nonlinear Volterra-Fredholm integral equation using Lagrange interpolation and Legendre-Gauss quadrature formula. The method has the advantage of requiring few collocation points, resulting in small errors, and eliminates the need for integral calculation. It provides proofs for the existence and uniqueness of the original equation under certain conditions, as well as for the solutions of the discrete equations using compact operators theory. Furthermore, the convergence analysis and error estimates are derived, and numerical examples are provided to demonstrate its efficiency and accuracy.
JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS
(2023)
Article
Mathematics, Applied
Nadaniela Egidi, Josephin Giacomini, Pierluigi Maponi, Michael Youssef
Summary: This paper discusses the numerical differentiation of a function tabulated at equidistant points. The proposed method utilizes the Fast Fourier Transform (FFT) and the singular value expansion of a Volterra integral operator to reformulate the derivative operator. The convergence analysis of the proposed method is provided, and a numerical experiment is conducted to compare its performance with that of the Neville algorithm implemented in the NAG library.
APPLIED MATHEMATICS AND COMPUTATION
(2023)
Article
Chemistry, Physical
Sergey E. Kruchinin, Marina Fedotova
Summary: Neurotransmitters play a crucial role in neural communication, regulating various functions and their interactions with inorganic ions and other neurotransmitters in water environments. The study revealed that in concentrated solutions, NT-inorganic counterion contact pairs are the predominant associate type, shedding light on the behavior of NTs in biological media. The findings contribute to understanding the link between ion binding of NTs and their biological activity.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Mathematics, Applied
Leandro Farina, Guillaume Lang, P. A. Martin
Summary: This paper mainly focuses on a seemingly simple integral equation that arises in classical and quantum physics. Although the solution to this equation is unknown, numerical methods can be used to compute it. The paper reviews the literature on the applications of this equation and investigates methods for constructing approximate solutions.
Article
Biochemistry & Molecular Biology
Nicolas Tielker, Stefan Guessregen, Stefan M. Kast
Summary: The study successfully predicted Gibbs energies of species in solution within SAMPL6.1 and SAMPL6.2 challenges using the EC-RISM model combined with quantum-mechanical calculations and three-dimensional RISM theory. While the pK(a) predictions were very favorable, the log P model performance fell behind expectations, resulting in reasonable log D-7.4 predictions.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Chemistry, Physical
Gennady N. Chuev, Marina V. Fedotova, Marat Valiev
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Chemistry, Physical
Marina Fedotova, Sergey E. Kruchinin, Gennady N. Chuev
JOURNAL OF MOLECULAR LIQUIDS
(2020)
Article
Chemistry, Physical
Marina Fedotova, Sergey E. Kruchinin, Gennady N. Chuev
JOURNAL OF MOLECULAR LIQUIDS
(2020)
Article
Mechanics
Gennady N. Chuev, Marina Fedotova, Marat Valiev
Summary: Site density functional theory provides a rigorous framework for the statistical mechanics analysis of inhomogeneous molecular liquids, with the use of dual space methodology to improve accuracy in calculations. This approach allows for the decoupling of analysis of intra- and inter-molecular interactions, demonstrating the transformation of the molecular liquid system behavior at the inter-molecular level to resemble that of an effective simple fluid mixture.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Article
Chemistry, Physical
Gennady N. Chuev, Marina V. Fedotova, Marat Valiev
Summary: The renormalized formulation of SDFT, RSDFT, efficiently reconciles the co-existence of intra- and inter-molecular interaction regimes in molecular liquid systems. Critical assessment of RSDFT for hydrated ion systems shows significant improvement over traditional models and may be useful in coarse grained simulations.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Correction
Mechanics
Gennady N. Chuev, Marina Fedotova, Marat Valiev
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Article
Chemistry, Physical
Sergey E. Kruchinin, Marina Fedotova
Summary: Neurotransmitters play a crucial role in neural communication, regulating various functions and their interactions with inorganic ions and other neurotransmitters in water environments. The study revealed that in concentrated solutions, NT-inorganic counterion contact pairs are the predominant associate type, shedding light on the behavior of NTs in biological media. The findings contribute to understanding the link between ion binding of NTs and their biological activity.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemistry & Molecular Biology
Nitesh Kumawat, Andrejs Tucs, Soumen Bera, Gennady N. Chuev, Marat Valiev, Marina V. Fedotova, Sergey E. Kruchinin, Koji Tsuda, Adnan Sljoka, Amit Chakraborty
Summary: The binding strength between SARS-CoV-2 spike protein and hACE2 is enhanced by water-mediated interactions, facilitating the formation of the CoV-2/hACE2 complex. Additionally, significant conformational changes in RBD and altered intermolecular interactions in SARS-CoV-2 have been observed, impacting the infectivity of the virus.
Article
Computer Science, Interdisciplinary Applications
Marat Valiev, Gennady N. Chuev, Marina Fedotova
Summary: Classical density functional theory provides a theoretical framework for analyzing many-body systems, and its application has been successful in simulating simple liquids. This article presents a python-based CDFT code that includes both conventional Reference Interaction Site Model (RISM) and recently developed renormalized site density theory (RSDFT) approach. The code focuses on the problem of ion solvation and allows for comparative analysis across different interaction parameters.
COMPUTER PHYSICS COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Sergey E. Kruchinin, Ekaterina E. Kislinskaya, Gennady N. Chuev, Marina V. Fedotova
Summary: In this study, the hydrated state of protein BPTI was characterized using molecular dynamics and the integral equation method. The results revealed a well-defined hydration layer around the protein and provided insight into the localization of water molecules. This research contributes to our understanding of protein hydration.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Sergej Friesen, Marina V. Fedotova, Sergey E. Kruchinin, Richard Buchner
Summary: Room-temperature aqueous solutions of GABA and AABA were studied using DRS and statistical mechanics calculations. The results showed that only about half of the water molecules in direct contact with the solute are affected in their dynamics. GABA moderately retards -10 H2O molecules, while AABA moderately retards -6 H2O molecules and freezes -6 H2O molecules.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Sergey E. Kruchinin, Gennady N. Chuev, Marina Fedotova
Summary: A clear understanding of protein-ligand binding requires knowledge of hydration and the role of solvent. In this study, the hydration states of PTP1B in the unbound and bound states were investigated, and changes in hydration upon complex formation with 2HB1 and 2QBP inhibitors were observed. The results showed significant dehydration of the ligands and minimal changes in PTP1B hydration upon complex formation.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Sergej Friesen, Marina Fedotova, Sergey E. Kruchinin, Marija Bester-Rogac, Crtomir Podlipnik, Richard Buchner
Summary: The hydration and Cl- ion binding of the neurotransmitter acetylcholine (ACh(+)) and its synthetic analogue, carbamoylcholine (CCh(+)), have been studied. Weak but not negligible chloro ion binding was observed, with only about 1/3 of water molecules being affected by the cation. Increasing concentration and temperature significantly dehydrate ACh(+) and CCh(+).
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Sergej Friesen, Marina V. Fedotova, Sergey E. Kruchinin, Richard Buchner
Summary: The study found that the hydration of sodium L-glutamate is fragile, with most water molecules forming hydrates with carboxylate groups. Additionally, the dynamics of L-glutamate are mainly influenced by the rotational diffusion of individual anions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Saadia Shaukat, Marina V. Fedotova, Sergey E. Kruchinin, Marija Bester-Rogac, Crtomir Podlipnik, Richard Buchner
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2019)
Article
Chemistry, Physical
Rajalaxmi Sahoo, C. Reshma, D. S. Shankar Rao, C. V. Yelamaggad, S. Krishna Prasad
Summary: This study investigates the influence of the flexible spacer parity of a guest photoactive liquid crystalline dimer on the photonic bandgap features of the cholesteric and twist grain boundary smectic C phases of the host molecule. The results show that the parity of the photoactive dimer affects the width of the photonic bandgap and the blue-shift of the cholesteric phase. Additionally, the parity of the dimer also affects the layer spacing and two-dimensional periodicity of the liquid crystalline phases.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Physical
Sara Rozas, Alberto Gutierrez, Mert Atilhan, Alfredo Bol, Santiago Aparicio
Summary: This study presents a multiscale theoretical investigation on the use of bifunctional hydrophobic Deep Eutectic Solvent for carbon capture using tetrapropylammonium chloride, acetic acid, and ethanolamine. The characterization includes nanoscale analysis of CO2 absorption mechanisms and changes in liquid phase properties during gas capture.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Physical
Tabouli Eric Da-yang, Alhadji Malloum, Jean Jules Fifen, Mama Nsangou, Jeanet Conradie
Summary: In this study, the potential energy of different glycine tautomers and their interaction with Cu2+ cations was investigated. The results showed that the solvation medium and the presence of Cu2+ cations influenced the stability of glycine tautomers.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Physical
Xiaoliang Gou, Nan Ye, Qingqing Han, Junjie Cui, Long Yi Jin
Summary: In this study, amphiphilic rod-coil molecules with rigid DSA parts and flexible oligoether chains were designed and their assembly capacities were investigated. The morphology of the molecular aggregates was influenced by the pH of the solution and UV light, and the aggregates showed adsorption capacity for nitroaromatic compounds.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Physical
Shuang Liu, Liyan Shan, Cong Qi, Wenhui Zhang, Guannan Li, Bei Wang, Wei Wei
Summary: Optimizing the design of styrene-butadiene-styrene copolymer (SBS) is crucial for producing cost-effective SBS modifiers and improving road quality. This study examined the influence of SBS content and molecular structure on viscosity and compatibility. The results showed that the viscosity contribution of SBS is determined by its molecular structure and phase morphology.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Physical
Artem A. Petrov, Ekaterina A. Titova, Aydar A. Akhmadiyarov, Ilnaz T. Rakipov, Boris N. Solomonov
Summary: This work focuses on the thermochemistry of solvation of azeotropes. The enthalpies of dissolution of azeotropes in different mediums were determined, and the impact of the structure of the azeotropes on their properties in solution was discussed. A correlation between enthalpies of solvation and molar refraction was used to determine the vaporization enthalpies of azeotropes for the first time. The results were found to be consistent with literature data, obtained using direct and calculated methods. These findings contribute to the analysis of the structure-property relationships of azeotropes.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Physical
L. V. Kamaeva, E. N. Tsiok, N. M. Chtchelkatchev
Summary: Understanding the correlations between liquids and solids allows us to predict the thermodynamic parameter range favorable for the formation of intriguing solid phases by studying liquids. In this study, we experimentally and theoretically investigated an Al-Cu-Co system within different composition ranges, and identified high-temperature solid phases. Our findings demonstrated the correlation between the boundaries of different solid phases and undercooling and viscosity in the concentration area.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Physical
R. Aneesh Kumar, S. Jamelah Al-Otaibi, Y. Sheena Mary, Y. Shyma Mary, Nivedita Acharjee, Renjith Thomas, Renjith Raveendran Pillai, T. L. Leena
Summary: In this study, the interactions between doped and pristine coronenes and adenine nucleobases were investigated using Density Functional Theory. The optimal configurations, adsorption energies, charge transfer, and electrical properties of each complex were calculated. It was found that doped coronene had stronger adsorption strength and charge transfer compared to pristine coronene. The stability of the complexes was attributed to non-covalent interactions in the interactive region. The change in electrical conductivity of coronenes after adsorption suggested their sensitivity towards DNA bases. The predicted energy gap and prolonged recovery time for adenine-coronene configurations indicated the potential application of pristine/doped coronene in DNA detection.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Physical
Gang Zhou, Yongwei Liu, Biao Sun, Zengxin Liu, Cuicui Xu, Rulin Liu, Qi Zhang, Yongmei Wang
Summary: The CFD-DEM method was used to simulate the dust deposition pattern in the bronchus of anchor digging drivers, revealing the highest dust concentration in the vortex region of the working face. The study also found a positive correlation between dust particle diameter and bronchial deposition rate, and a negative correlation with alveolar deposition rate.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Physical
Yan Zhang, Yafei Luo, Lingkai Tang, Mingyan E, Jianping Hu
Summary: This study investigates the effects of different transition metal decorations on B12N12 nanocages on the adsorption properties of nitrosourea drugs using computational methods. The results reveal the presence of weak non-covalent interactions between metals and nanocages, and the interaction between drugs and nanocages plays a significant role in drug adsorption. Compared to free drugs, the adsorption of drugs on nanocages can facilitate electron transfer, reduce energy gaps and chemical hardness, indicating activity at the target site.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Physical
C. I. Alcolado, J. Poblete, L. Garcia-Rio, E. Jimenez, F. J. Poblete
Summary: In this study, the selective oxidation of aromatic aldehydes was investigated using Ru(VI) as a catalyst and hexacyanoferrate (III) as a cooxidant in an alkaline medium. The reaction mechanism involves complex reaction orders for the oxidant and the aromatic aldehyde, while the reaction order for Ru(VI) is one. The proposed mechanism includes two catalytic cycles and the formation and decomposition of complexes. Quantitative structure-activity relationship analysis showed that deactivating groups in the para-position enhance the process.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Physical
Inez A. Barbieri, Marcos L. S. Oliveira, Franciele S. Bruckmann, Theodoro R. Salles, Leonardo Zancanaro, Luis F. O. Silva, Guilherme L. Dotto, Eder C. Lima, Mu. Naushad, Cristiano R. Bohn Rhoden
Summary: This study evaluated the adsorption of zolpidem on magnetic graphene oxide and synthesized magnetic graphene oxide adsorbents for zolpidem removal. The best magnetic nanoadsorbent was found to have a removal percentage of 87.07% at specific pH and temperature conditions. The results suggest that the removal of zolpidem is related to the surface chemistry of the adsorbent rather than the surface area of graphene oxide. The adsorbent showed excellent adsorption efficiency and magnetic behavior, making it a promising material for removing zolpidem from aqueous solutions.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Physical
Hongyan Huang, Chunquan Li, Siyuan Huang, Yuling Shang
Summary: This study examines the sensitivity of the thermal conductivity of water-based alumina nanofluids to changes in concentration, sphericity, and temperature. The results show that volume fraction and temperature have a significant impact on the thermal conductivity, while sphericity also needs to be considered. A support vector machine regression model was created to analyze the sensitivity of the thermal conductivity to different parameters. The findings indicate that temperature, sphericity, and volume fraction are the most sensitive variables.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Correction
Chemistry, Physical
V. M. Pergamenshchik, T. Bryk, A. Trokhymchuk
JOURNAL OF MOLECULAR LIQUIDS
(2024)
Article
Chemistry, Physical
Valentyn Rudenko, Anatolii Tolochko, Svitlana Bugaychuk, Dmytro Zhulai, Gertruda Klimusheva, Galina Yaremchuk, Tatyana Mirnaya, Yuriy Garbovskiy
Summary: This paper reports on the synthesis, structural characterization, spectral and nonlinear-optical properties of glass nanocomposites made of glass forming ionic liquid crystals and nanoparticles. The study reveals that by exciting the nanocomposites within their absorption band, a control over effective optical nonlinearities can be achieved, allowing the modification of the magnitude and sign of the effective nonlinear absorption coefficient. The proposed strategy using metal-alkanoates based glass-forming ionic liquid crystals and nanoparticles shows great potential for the development of nanophotonics and plasmonics technologies.
JOURNAL OF MOLECULAR LIQUIDS
(2024)
