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Andriy Kovalenko - One of the best experts on this subject based on the ideXlab platform.
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Solvent Composition Effects on the Structural Properties of the Aβ42 Monomer from the 3D-RISM-KH Molecular Theory of Solvation
2019Co-Authors: Nikolay Blinov, David S. Wishart, Andriy KovalenkoAbstract:Structural characterization of amyloid (A)β peptides implicated in Alzheimer’s disease is a challenging problem due to their intrinsically disordered nature and their high propensity for aggregation. Only limited information is currently available from experiments on conformational properties and aggregation pathways of the peptides in cellular environments. In silico modeling complements experimental information, providing atomistic insight into structure and dynamics of different Aβ species. All-atom explicit solvent Molecular dynamics (MD) simulations with a properly selected force field can deliver reliable structural and dynamic information. In the case of intrinsically disordered Aβ peptides, enhanced sampling simulations beyond the nanosecond time scale are required to obtain statistically meaningful results even for simple solvent conditions. To overcome the challenges of conformational sampling in crowded cellular environments, alternative approaches have to be used, including postprocessing of MD data. In this study, we employ the statistical–mechanical, three-dimensional reference interaction site model with the Kovalenko–Hirata closure integral equation Molecular Theory of solvation to describe solvent composition effects on the conformational equilibrium in a structural ensemble of the Aβ42 (covering residues 1–42) monomer based on a statistical reweighting technique. The methodology enables a computationally efficient prediction on how different factors in the cellular environment, such as solvent composition, nonpolar solvation, and macroMolecular crowding, affect the structural properties of the monomer. Similarities have been identified between changes in the structural ensemble caused by nonpolar solvation and crowded environments modeled by ionic solution with large negative ions. In particular, both solvent conditions reduce the random coil content and enhance the helical structure content of the monomer. In contrast to the previous studies, which reported increased α-helical content of peptides in crowded environments, this work attributes these structural features to the difference in solvent exposure of hydrophilic residues of the monomer for different secondary structure elements, rather than to (entropic) excluded volume effects
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octanol water partition coefficient from 3d rism kh Molecular Theory of solvation with partial molar volume correction
Journal of Physical Chemistry B, 2015Co-Authors: Wenjuan Huang, Nikolay Blinov, Andriy KovalenkoAbstract:The octanol–water partition coefficient is an important physical–chemical characteristic widely used to describe hydrophobic/hydrophilic properties of chemical compounds. The partition coefficient is related to the transfer free energy of a compound from water to octanol. Here, we introduce a new protocol for prediction of the partition coefficient based on the statistical-mechanical, 3D-RISM-KH Molecular Theory of solvation. It was shown recently that with the compound–solvent correlation functions obtained from the 3D-RISM-KH Molecular Theory of solvation, the free energy functional supplemented with the correction linearly related to the partial molar volume obtained from the Kirkwood–Buff/3D-RISM Theory, also called the “universal correction” (UC), provides accurate prediction of the hydration free energy of small compounds, compared to explicit solvent Molecular dynamics [Palmer, D. S.; J. Phys.: Condens. Matter 2010, 22, 492101]. Here we report that with the UC reparametrized accordingly this Theory...
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Role of Water in Ligand Binding to Maltose-Binding Protein: Insight from a New Docking Protocol Based on the 3D-RISM-KH Molecular Theory of Solvation
Journal of chemical information and modeling, 2015Co-Authors: Wenjuan Huang, Nikolay Blinov, David S. Wishart, Andriy KovalenkoAbstract:Maltose-binding protein is a periplasmic binding protein responsible for transport of maltooligosaccarides through the periplasmic space of Gram-negative bacteria, as a part of the ABC transport system. The Molecular mechanisms of the initial ligand binding and induced large scale motion of the protein's domains still remain elusive. In this study, we use a new docking protocol that combines a recently proposed explicit water placement algorithm based on the 3D-RISM-KH Molecular Theory of solvation and conventional docking software (AutoDock Vina) to explain the mechanisms of maltotriose binding to the apo-open state of a maltose-binding protein. We confirm the predictions of previous NMR spectroscopic experiments on binding modes of the ligand. We provide the Molecular details on the binding mode that was not previously observed in the X-ray experiments. We show that this mode, which is defined by the fine balance between the protein-ligand direct interactions and solvation effects, can trigger the protein's domain motion resulting in the holo-closed structure of the maltose-binding protein with the maltotriose ligand in excellent agreement with the experimental data. We also discuss the role of water in blocking unfavorable binding sites and water-mediated interactions contributing to the stability of observable binding modes of maltotriose.
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supraMolecular interactions in secondary plant cell walls effect of lignin chemical composition revealed with the Molecular Theory of solvation
Journal of Physical Chemistry Letters, 2015Co-Authors: Rodrigo L Silveira, Stanislav R Stoyanov, Sergey Gusarov, Munir S Skaf, Andriy KovalenkoAbstract:Plant biomass recalcitrance, a major obstacle to achieving sustainable production of second generation biofuels, arises mainly from the amorphous cell-wall matrix containing lignin and hemicellulose assembled into a complex supraMolecular network that coats the cellulose fibrils. We employed the statistical-mechanical, 3D reference interaction site model with the Kovalenko–Hirata closure approximation (or 3D-RISM-KH Molecular Theory of solvation) to reveal the supraMolecular interactions in this network and provide Molecular-level insight into the effective lignin–lignin and lignin–hemicellulose thermodynamic interactions. We found that such interactions are hydrophobic and entropy-driven, and arise from the expelling of water from the mutual interaction surfaces. The Molecular origin of these interactions is carbohydrate−π and π–π stacking forces, whose strengths are dependent on the lignin chemical composition. Methoxy substituents in the phenyl groups of lignin promote substantial entropic stabilizatio...
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plant biomass recalcitrance effect of hemicellulose composition on nanoscale forces that control cell wall strength
Journal of the American Chemical Society, 2013Co-Authors: Rodrigo L Silveira, Stanislav R Stoyanov, Sergey Gusarov, Munir S Skaf, Andriy KovalenkoAbstract:Efficient conversion of lignocellulosic biomass to second-generation biofuels and valuable chemicals requires decomposition of resilient plant cell wall structure. Cell wall recalcitrance varies among plant species and even phenotypes, depending on the chemical composition of the noncellulosic matrix. Changing the amount and composition of branches attached to the hemicellulose backbone can significantly alter the cell wall strength and microstructure. We address the effect of hemicellulose composition on primary cell wall assembly forces by using the 3D-RISM-KH Molecular Theory of solvation, which provides statistical–mechanical sampling and Molecular picture of hemicellulose arrangement around cellulose. We show that hemicellulose branches of arabinose, glucuronic acid, and especially glucuronate strengthen the primary cell wall by strongly coordinating to hydrogen bond donor sites on the cellulose surface. We reveal Molecular forces maintaining the cell wall structure and provide directions for genetic...
M A Osipov - One of the best experts on this subject based on the ideXlab platform.
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Molecular Theory of high frequency dielectric susceptibility of nematic nanocomposites
Crystals, 2020Co-Authors: M A Osipov, A S Merekalov, A A EzhovAbstract:A Molecular-statistical Theory of the high frequency dielectric susceptibility of the nematic nanocomposites has been developed and approximate analytical expressions for the susceptibility have been obtained in terms of the effective polarizability of a nanoparticle in the nematic host, volume fraction of the nanoparticles and the susceptibility of the pure nematic phase. A simple expression for the split of the plasmon resonance of the nanoparticles in the nematic host has been obtained and it has been shown that in the resonance frequency range the high frequency dielectric anisotropy of the nanocomposite may be significantly larger than that of the pure nematic host. As a result, all dielectric and optical properties of the nanocomposite related to the anisotropy are significantly enhanced which may be important for emerging applications. The components of the dielectric susceptibility have been calculated numerically for particular nematic nanocomposites with gold and silver nanoparicles as functions of the nanoparticle volume fraction and frequency. The splitting of the plasmon resonance has been observed together with the significant dependence on the nanoparticle volume fraction and the parameters of the nematic host phase.
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Molecular Theory of the tilting transition and computer simulations of the tilted lamellar phase of rod coil diblock copolymers
Journal of Chemical Physics, 2020Co-Authors: M A Osipov, M V Gorkunov, Anatoly V Berezkin, Alexander A Antonov, Yaroslav V KudryavtsevAbstract:Symmetric rod-coil diblock copolymers have been simulated using the method of dissipative particle dynamics in the broad range of the Flory-Huggins parameter. It has been found that the tilted lamellar phase appears to be the most stable one at strong segregation. The rod-coil copolymer tilt angle and orientational order parameters have been determined as functions of the segregation strength. The density functional Theory of rod-coil diblock copolymers has been generalized to the case of the tilted lamellar phase and used to study the stability of the orthogonal lamellar phase with respect to tilt. The orthogonal phase indeed appears to be unstable in the broad region of the parameter space in the case of relatively strong segregation. It has also been shown that the transition into the tilted lamellar phase is determined by a strong coupling between two independent tilt order parameters.
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ordering of anisotropic nanoparticles in diblock copolymer lamellae simulations with dissipative particle dynamics and a Molecular Theory
Journal of Chemical Physics, 2017Co-Authors: Anatoly V Berezkin, M V Gorkunov, Yaroslav V Kudryavtsev, M A OsipovAbstract:Local distribution and orientation of anisotropic nanoparticles in microphase-separated symmetric diblock copolymers has been simulated using dissipative particle dynamics and analyzed with a Molecular Theory. It has been demonstrated that nanoparticles are characterized by a non-trivial orientational ordering in the lamellar phase due to their anisotropic interactions with isotropic monomer units. In the simulations, the maximum concentration and degree of ordering are attained for non-selective nanorods near the domain boundary. In this case, the nanorods have a certain tendency to align parallel to the interface in the boundary region and perpendicular to it inside the domains. Similar orientation ordering of nanoparticles located at the lamellar interface is predicted by the Molecular Theory which takes into account that the nanoparticles interact with monomer units via both isotropic and anisotropic potentials. Computer simulations enable one to study the effects of the nanorod concentration, length, stiffness, and selectivity of their interactions with the copolymer components on the phase stability and orientational order of nanoparticles. If the volume fraction of the nanorods is lower than 0.1, they have no effect on the copolymer transition from the disordered state into a lamellar microstructure. Increasing nanorod concentration or nanorod length results in clustering of the nanorods and eventually leads to a macrophase separation, whereas the copolymer preserves its lamellar morphology. Segregated nanorods of length close to the width of the diblock copolymer domains are stacked side by side into smectic layers that fill the domain space. Thus, spontaneous organization and orientation of nanorods leads to a spatial modulation of anisotropic composite properties which may be important for various applications.
Chaimongkol Saengow - One of the best experts on this subject based on the ideXlab platform.
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pattern method for higher harmonics of first normal stress difference from Molecular orientation in oscillatory shear flow
Physics of Fluids, 2020Co-Authors: Layal M Jbara, Chaimongkol Saengow, Jeffrey A GiacominAbstract:This study examines the simplest relevant Molecular model of a polymeric liquid in large-amplitude oscillatory shear (LAOS) flow: rigid dumbbells suspended in a Newtonian solvent. For such suspensions, the viscoelastic response of the polymeric liquid depends exclusively on the dynamics of dumbbell orientation. Previously, the explicit analytical expressions of the zeroth, second, and fourth harmonics of the alternating first normal stress difference response in LAOS have been derived. In this paper, we correct and extend these expressions by seeking an understanding of the next higher harmonic. Specifically, this paper continues a series of studies that shed light on Molecular Theory as a useful approach in investigating the response of polymeric liquids to oscillatory shear. Following the general method of Bird and Armstrong [“Time-dependent flows of dilute solutions of rodlike macromolecules,” J. Chem. Phys. 56, 3680 (1972)], we derive the expression of the first normal stress coefficient up to and including the sixth harmonic. Our analysis relies on the extension of the orientation distribution function to the sixth power of the shear rate. Our expression is the only one to have been derived from a Molecular Theory for a sixth harmonic and thus provides the first glimpse of the Molecular origins of a first normal stress difference higher than the fourth.
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pattern method for higher harmonics of first normal stress difference from Molecular orientation in oscillatory shear flow
Physics of Fluids, 2020Co-Authors: Layal M Jbara, Chaimongkol Saengow, Jeffrey A GiacominAbstract:This study examines the simplest relevant Molecular model of a polymeric liquid in large-amplitude oscillatory shear (LAOS) flow: rigid dumbbells suspended in a Newtonian solvent. For such suspensions, the viscoelastic response of the polymeric liquid depends exclusively on the dynamics of dumbbell orientation. Previously, the explicit analytical expressions of the zeroth, second, and fourth harmonics of the alternating first normal stress difference response in LAOS have been derived. In this paper, we correct and extend these expressions by seeking an understanding of the next higher harmonic. Specifically, this paper continues a series of studies that shed light on Molecular Theory as a useful approach in investigating the response of polymeric liquids to oscillatory shear. Following the general method of Bird and Armstrong [“Time-dependent flows of dilute solutions of rodlike macromolecules,” J. Chem. Phys. 56, 3680 (1972)], we derive the expression of the first normal stress coefficient up to and including the sixth harmonic. Our analysis relies on the extension of the orientation distribution function to the sixth power of the shear rate. Our expression is the only one to have been derived from a Molecular Theory for a sixth harmonic and thus provides the first glimpse of the Molecular origins of a first normal stress difference higher than the fourth.This study examines the simplest relevant Molecular model of a polymeric liquid in large-amplitude oscillatory shear (LAOS) flow: rigid dumbbells suspended in a Newtonian solvent. For such suspensions, the viscoelastic response of the polymeric liquid depends exclusively on the dynamics of dumbbell orientation. Previously, the explicit analytical expressions of the zeroth, second, and fourth harmonics of the alternating first normal stress difference response in LAOS have been derived. In this paper, we correct and extend these expressions by seeking an understanding of the next higher harmonic. Specifically, this paper continues a series of studies that shed light on Molecular Theory as a useful approach in investigating the response of polymeric liquids to oscillatory shear. Following the general method of Bird and Armstrong [“Time-dependent flows of dilute solutions of rodlike macromolecules,” J. Chem. Phys. 56, 3680 (1972)], we derive the expression of the first normal stress coefficient up to and inc...
Wei Wang - One of the best experts on this subject based on the ideXlab platform.
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the oseen frank limit of onsager s Molecular Theory for liquid crystals
Archive for Rational Mechanics and Analysis, 2018Co-Authors: Yuning Liu, Wei WangAbstract:We study the relationship between Onsager’s Molecular Theory, which involves the effects of nonlocal Molecular interactions and the Oseen–Frank Theory for nematic liquid crystals. Under the Molecular setting, we prove the existence of global minimizers for the generalized Onsager’s free energy, subject to a nonlocal boundary condition which prescribes the second moment of the number density function near the boundary. Moreover, when the re-scaled interaction distance tends to zero, the global minimizers will converge to a uniaxial distribution predicted by a minimizing harmonic map. This is achieved through the investigations of the compactness property and the boundary behaviors of the corresponding second moments. A similar result is established for critical points of the free energy that fulfill a natural energy bound.
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the oseen frank limit of onsager s Molecular Theory for liquid crystals
arXiv: Analysis of PDEs, 2016Co-Authors: Yuning Liu, Wei WangAbstract:We study the relationship between Onsager's Molecular Theory and the Oseen-Frank Theory for nematic liquid crystals. Under the Molecular setting, we consider the free energy that includes the effects of nonlocal Molecular interactions. By imposing the strong anchoring boundary condition on the second moment of the number density function, we prove the existence of global minimizers for the free energy. Moreover, when the re-scaled interaction distance tends to zero, the corresponding global minimizers will converge to a uniaxial distribution whose orientation is described by a minimizer of Oseen-Frank energy.
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from microscopic Theory to macroscopic Theory a systematic study on modeling for liquid crystals
Archive for Rational Mechanics and Analysis, 2015Co-Authors: Jiequn Han, Wei Wang, Yi Luo, Pingwen Zhang, Zhifei ZhangAbstract:In this paper, we propose a systematic way of liquid crystal modeling to build connections between microscopic Theory and macroscopic Theory. In the first part, we propose a new Q-tensor model based on Onsager’s Molecular Theory for liquid crystals. The Oseen–Frank Theory can be recovered from the derived Q-tensor Theory by making a uniaxial assumption, and the coefficients in the Oseen–Frank model can be examined. In addition, the smectic-A phase can be characterized by the derived macroscopic model. In the second part, we derive a new dynamic Q-tensor model from Doi’s kinetic Theory by the Bingham closure, which obeys the energy dissipation law. Moreover, the Ericksen–Leslie system can also be derived from new Q-tensor system by making an expansion near the local equilibrium.
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from microscopic Theory to macroscopic Theory a systematic study on static modeling for liquid crystals
arXiv: Analysis of PDEs, 2013Co-Authors: Jiequn Han, Wei Wang, Yi Luo, Pingwen ZhangAbstract:In this paper, we propose a systematic way of liquid crystal modeling to build connection between microscopic Theory and macroscopic Theory. A new Q-tensor Theory based on Onsager's Molecular Theory which leads to liquid crystals with certain shape has been proposed. Making uniaxial assumption, we can recover the Oseen-Frank Theory from the derived $Q$-tensor Theory, and the Oseen-Frank model coefficients can be examined. In addition, the smectic-A phase can also be characterized by the derived macroscopic model.
Howard Reiss - One of the best experts on this subject based on the ideXlab platform.
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a Molecular Theory of the homogeneous nucleation rate ii application to argon vapor
Journal of Chemical Physics, 1999Co-Authors: Bernard Senger, D Pointu, Richard K. Bowles, Pierre Schaaf, David S. Corti, Jean-claude Voegel, Howard ReissAbstract:The Molecular Theory of the homogeneous nucleation rate based on the n/v-Stillinger cluster, and developed in the preceding paper (paper I), is applied to the condensation of supersaturated argon vapor, in a preliminary calculation of the rate of nucleation for a single set of conditions (temperature=85 K, pressure=2500 Torr). Free energies are obtained by means of Monte Carlo simulation. Upper and lower bounds differing by only two orders of magnitude are obtained. Since the best current measurements of vapor phase nucleation rates are accurate to within about a single order of magnitude, this result is considered promising. The direction of future work to improve the accuracy of the predicted rate is clear, and considerable improvement should be possible. These directions are discussed in the paper. Also, the essentially non ad hoc nature of the n/v-Stillinger cluster is demonstrated by the appearance of a range of connectivity distances (in a predicted location) within which the calculated nucleation r...
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a Molecular Theory of the homogeneous nucleation rate i formulation and fundamental issues
Journal of Chemical Physics, 1999Co-Authors: Bernard Senger, Richard K. Bowles, Pierre Schaaf, David S. Corti, Jean-claude Voegel, Howard ReissAbstract:A Molecular Theory of the rate of homogeneous vapor phase nucleation is formulated. The ultimate goal is a Theory that contains no ad hoc assumptions or arbitrary parameters having magnitudes that must be assigned in an ad hoc manner. The centerpiece of the Theory is a defined cluster denoted as the n/v-Stillinger cluster, a hybrid that combines the original Stillinger cluster and the more recent n/v cluster. The Stillinger component assures that redundancy is avoided in the characterization of the cluster and the n/v component makes the Monte Carlo simulation of the free energy of the cluster relatively simple, and also allows dynamics to weight the importance of a cluster to the nucleation rate process. In the companion paper (paper II), dealing with the application of the Theory to argon vapor, it is shown that the avoidance of redundancy is of primary importance to the non ad hoc nature of the Theory. The Theory provides a standard against which subtle inconsistencies in earlier theories, both molecul...