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At least 1,675 records · Page 93

Molecular mechanism of gas adsorption into ionic liquids: A molecular dynamics study

Room temperature ionic liquids (RTILs) have been shown to be versatile and tunable solvents that can be used in many chemical applications. In this study, we developed a dynamical, molecular-scale picture of the gas dissolution and interfacial processes in RTILs using molecular simulations. These simulations can provide the free energies associated with transporting a gas solute across various RTIL interfaces and physical insights into the interfacial properties and transport molecular mechanism of gas sorption processes. For CO2 sorption, the features in the potential of mean force (PMF) of CO2 using both polarizable and non-polarizable force fields are similar qualitatively. However, we observed some quantitative differences, and we describe the causes of these differences in this paper. We also show the significant impact of ionic-liquid chemical structures on the gas sorption process, and we discuss their influence on the H2O transport mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

L2 Milestone: Simulations as Data. Quantum Molecular Dynamics Contribution

Milestone description: Direct Numerical Simulations and Quantum Molecular Dynamics simulations have been used as one would use physical experiments for cases where the physical data are not available. The goal of this milestone is to assess these simulations in the manner that they are being used and the priority of the specific configurations being planned.

Condensed Matter Physics, Superconductivity & Supe↗

Adaptive coupling of a deep neural network potential to a classical force field

An adaptive modeling method (AMM) that couples a deep neural network potential and a classical force field is introduced to address the accuracy-efficiency dilemma faced by the molecular simulation community. The AMM simulated system is decomposed into three types of regions. The first type captures the important phenomena in the system and requires high accuracy, for which we use the Deep Potential Molecular Dynamics (DeePMD) model in this work. The DeePMD model is trained to accurately reproduce the statistical properties of the ab initio molecular dynamics. The second type does not require high accuracy, and a classical force field is used to describe it in an efficient way. The third type is used for a smooth transition between the first and the second types of regions. By using a force interpolation scheme and imposing a thermodynamics force in the transition region, we make the DeePMD region embedded in the AMM simulated system as if it were embedded in a system that is fully described by the accurate potential. A representative example of the liquid water system is used to show the feasibility and promise of this method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High-Performance Computation of Distributed-Memory Parallel 3D Voronoi and Delaunay Tessellation

Computing a Voronoi or Delaunay tessellation from a set of points is a core part of the analysis of many simulated and measured datasets: N-body simulations, molecular dynamics codes, and LIDAR point clouds are just a few examples. Such computational geometry methods are common in data analysis and visualization; but as the scale of simulations and observations surpasses billions of particles, the existing serial and shared-memory algorithms no longer suffice. A distributed-memory scalable parallel algorithm is the only feasible approach. The primary contribution of this paper is a new parallel Delaunay and Voronoi tessellation algorithm that automatically determines which neighbor points need to be exchanged among the subdomains of a spatial decomposition. Other contributions include periodic and wall boundary conditions, comparison of our method using two popular serial libraries, and application to numerous science datasets.

97 MATHEMATICS AND COMPUTING↗

Dependence of the rate of LiF ion pairing on the description of molecular interaction

We present an analysis of the dynamics of ion-pairing of Lithium Fluoride (LiF) in aqueous solvent using both detailed molecular simulation as well as reduced models within a Gener- alized Langevin Equation (GLE) framework. We explored the sensitivity of the ion-pairing phenomena to the details of descriptions of molecular interaction, comparing two empirical potentials to explicit quantum based density functional theory. We find quantitative differences in the potentials of mean force for ion-pairing as well as time dependent frictions that lead to variations in the rate constant and reactive flux correlation functions. These details reflect differences in solvent response to ion-pairing between different representations of molecular interaction and influence anharmonicity of the dynamic response. We find that the short time anharmonic response is recovered with a GLE parameterization. Recovery of the details of long time response may require extensions to the reduced model. We show that the utility of using a reduced model leads to a straight forward application of variational transition state the- ory concepts to the condensed phase system. The significance of this is reflected in the analysis of committor distributions and the variation of planar hypersurfaces, leading to an improved understanding of factors that determine the rate of LiF ion-pairing. CJM and GKS are supported by the U.S. Department of Energy‘s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest Na- tional Laboratory (PNNL) is operated for the Department of Energy by Battelle. MDB is grateful for the support of Laboratory Directed Research and Development funding under the auspices of PNNL’s Laboratory Initiative Materials Synthesis and Simulation across Scales (MS3). Additional computing resources were generously allocated by PNNL’s Institutional Computing program. EP acknowledges support from PNNL’s Alternate Sponsored Fellowship program and IMPRS Dres- den.Support to P.J. from the Czech Science Foundation (grant P208/12/G016) and the Academy of Sciences (Praemium Academie award) is gratefully acknowledged.

Pluharova, Eva↗

Editorial: Advances in computational molecular biophysics

This special issue of BBA is dedicated to Dr. Jeremy C. Smith on the occasion of his 60th birthday and his more than three decades as a practitioner of computational molecular biophysics. The special issue showcases cutting-edge work in computational molecular biophysics. The senior authors of the manuscripts in this issue are Dr. Smith’s previous or present collaborators. Their articles reflect Dr. Smith’s distinguished career integrating experimental and molecular simulation approaches into a unified description of the function, structure, and dynamics of biomolecules. Each of the articles presented here illustrates one aspect of the broad nature of computational molecular biophysics.

59 BASIC BIOLOGICAL SCIENCES↗

Cooperative Interactions between Different Classes of Disordered Proteins Play a Functional Role in the Nuclear Pore Complex of Baker’s Yeast

Nucleocytoplasmic transport is highly selective, efficient, and is regulated by a poorly understood mechanism involving hundreds of disordered FG nucleoporin proteins (FG nups) lining the inside wall of the nuclear pore complex (NPC). Previous research has concluded that FG nups in Baker’s yeast (S. cerevisiae) are present in a bimodal distribution, with the “Forest Model” classifying FG nups as either di-block polymer like “trees” or single-block polymer like “shrubs”. Using a combination of coarse-grained modeling and polymer brush modeling, the function of the di-block FG nups has previously been hypothesized in the Di-block Copolymer Brush Gate (DCBG) model to form a higher-order polymer brush architecture which can open and close to regulate transport across the NPC. In this manuscript we work to extend the original DCBG model by first performing coarse grained simulations of the single-block FG nups which confirm that they have a single block polymer structure rather than the di-block structure of tree nups. Our molecular simulations also demonstrate that these single-block FG nups are likely cohesive, compact, collapsed coil polymers, implying that these FG nups are generally localized to their grafting location within the NPC. We find that adding a layer of single-block FG nups to the DCBG model increases the range of cargo sizes which are able to translocate the pore through a cooperative effect involving single-block and di-block FG nups. This effect can explain the puzzling connection between single-block FG nup deletion mutants in S. cerevisiae and the resulting failure of certain large cargo transport through the NPC. Facilitation of large cargo transport via single-block and di-block FG nup cooperativity in the nuclear pore could provide a model mechanism for designing future biomimetic pores of greater applicability.

Science & Technology - Other Topics↗

Novel insights into the apoptosis mechanism of DNA topoisomerase I inhibitor isoliquiritigenin on HCC tumor cell

The inhibitory effect of DNA topoisomerase (Top I) by isoliquiritigenin(ISO) were investigated and their interaction mechanism was evaluated using methods including UV–vis absorption, fluorescence, coupled with molecular simulation, and using the MTT method of inhibition rate of HCC tumor cell SNU475 proliferation assay, finally, the interaction of ISO with calf thymus DNA was investigated by melting measurements and molecular docking studies. It was found that isoliquiritigenin reversibly inhibited DNA Top I in a competitive manner with the concentrations of ISO resulting in 50% activity lost (IC{sub 50}) were estimated to be 0.178 ± 0.12 mM. Isoliquiritigenin exhibited a strong ability to quench the intrinsic fluorescence of Top I through a static quenching procedure. The positive values of enthalpy change and entropy change suggested that the binding of isoliquiritigenin to Top I was driven mainly by hydrophobic interactions. The molecular docking results revealed isoliquiritigenin actually interacted with the primary amino acid residues on the active site of Top I, and the detection results of fluorescence staining and the inhibitory effect on the growth of HCC SUN475 showed that isoliquiritigenin induced the apoptosis cells increased gradually. The interaction of ISO with DNA can cause the denaturation temperature to be increased, which indicated that the stabilization of the DNA helix was increased in the presence of ISO, which indicated that the results provide strong evidence for intercalative binding of ISO with DNA. - Highlights: • ISO reversibly inhibits TOP I activity in an A dose dependent manner. • Hydrophobic interactions play a major role in ISO–TOP I interaction. • ISO has a high affinity close to the active site pocket of TOP I. • The binding of ISO to DNA induces the stability of the structure of DNA.

60 APPLIED LIFE SCIENCES↗

Temperature-Dependent Conformations of Model Viscosity Index Improvers

Lubricants are comprised of base oils and additives where additives are chemicals that are deliberately added to the oil to enhance properties and inhibit degradation of the base oils. Viscosity index (VI) improvers are an important class of additives that reduce the decline of fluid viscosity with temperature [1], enabling optimum lubricant performance over a wider range of operating temperatures. These additives are typically high molecular weight polymers, such as, but not limited to, polyisobutylenes, olefin copolymer, and polyalkylmethacrylates, that are added in concentrations of 2-5% (w/w). Appropriate polymers, when dissolved in base oil, expand from a coiled to an uncoiled state with increasing temperature [2]. The ability of VI additives to increase their molar volume and improve the temperature-viscosity dependence of lubricants suggests there is a strong relationship between molecular structure and additive functionality [3]. In this work, we aim to quantify the changes in polymer size with temperature for four polyisobutylene (PIB) based molecular structures at the nano-scale using molecular simulation tools. As expected, the results show that the polymers adopt more conformations at higher temperatures, and there is a clear indication that the expandability of a polymer is strongly influenced by molecular structure.

lubricants, base oils, viscosity↗

Combining the mapping Hamiltonian linearized semiclassical approach with the generalized quantum master equation to simulate electronically nonadiabatic molecular dynamics

The generalized quantum master equation (GQME) provides a powerful framework for simulating electronically nonadiabatic molecular dynamics. Within this framework, the effect of the nuclear degrees of freedom on the time evolution of the electronic reduced density matrix is fully captured by a memory kernel superoperator. In this paper, we consider two different procedures for calculating the memory kernel of the GQME from projection-free inputs obtained via the combination of the mapping Hamiltonian (MH) approach and the linearized semiclassical (LSC) approximation. Here, the accuracy and feasibility of the two procedures are demonstrated on the spin-boson model. We find that although simulating the electronic dynamics by direct application of the two LSC-based procedures leads to qualitatively different results that become increasingly less accurate with increasing time, restricting their use to calculating the memory kernel leads to an accurate description of the electronic dynamics. Comparison with a previously proposed procedure for calculating the memory kernel via the Ehrenfest method reveals that MH/LSC methods produce memory kernels that are better behaved at long times and lead to more accurate electronic dynamics

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simulation studies of polypeptoids using replica exchange with dynamical scaling and dihedral biasing

Polypeptoids differ from polypeptides in that the amide bond can more frequently adopt both cis and trans conformations. The transition between the two conformations requires overcoming a large energy barrier, making it difficult for conventional molecular simulations to adequately visit the cis and trans structures. A replica-exchange method is presented that allows for easy rotations of the amide bond and also an efficient linking to a high temperature replica. The method allows for just three replicas (one at the temperature and Hamiltonian of interest, a second high temperature replica with a biased dihedral potential, and a third connecting them) to overcome the amide bond sampling problem and also enhance sampling for other coordinates. Here our results indicate that for short peptoid oligomers, the conformations can range from all cis to all trans with an average cis/trans ratio that depends on side chain and potential model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Advanced Modeling of Ions in Solutions, on Surfaces, and in Biological Environments (Final Scientific/Technical Report)

The research supported by this grant focused on modeling liquid water from basic microscopic theory and on developing advanced methodologies for molecular simulation and electronic structure calculation of large and disordered systems. Water is arguably the most important molecule on earth: without it there would be no life, as we know it. Water does not behave as a simple liquid. Understanding its unique and anomalous properties at the molecular level has been the focus of intense study during the entire last century and still is a major goal of research today. To address the problem we adopted a multipronged approach that included methodological and algorithmic developments as well as simulations of important model systems. We made progress on several key issues. (i) We implemented accurate electronic structure schemes for modeling water from quantum mechanical theory that make accessible in simulations processes driven by formation and breaking of chemical bonds. We studied in this way neat bulk water and simple solvated ions. We could understand, in particular, why hydronium, i.e. the positive water ion, diffuses faster than its negative counterpart, the hydroxyl, solving a 200-year-old ionic mystery of water, as reported in a news article featuring our study on Chemistry World, the magazine of the Royal Society of Chemistry (U.K.). (ii) Using advanced statistical mechanical techniques we studied water in the deeply undercooled regime, which may hold the clue to understanding many of the water anomalies. These conditions are currently only accessible to simulations based on empirical force fields. We found that deeply undercooled water, as described by the popular force field ST2, possesses a secondary critical point, below which it would spontaneously separate into two liquids, one of low-density (LDL) and one of high-density (HDL), much in the same way in which water and oil phase-separate at room temperature. The secondary critical point is supported indirectly by many experiments, but rapid ice nucleation has so far hindered direct observation. In related studies we gained new insight on the connection of the two metastable liquids with the two corresponding amorphous ice phases, LDA and HDA, which are observed experimentally. (iii) We developed and implemented several new algorithms for computing the electronic structure of large systems and to accelerate the calculation of electron exchange energies. We applied these methodologies to model nanomaterials, such as nanoribbons and nanoflakes, and to study water absorption and splitting on nanomaterials. (iv) We developed new local order descriptors. (v) In the last year of the project we developed a methodology based on deep neural networks to construct model interatomic potentials that can accurately reproduce ab-initio quantum mechanical simulations at the computational cost of empirical force fields. These potentials will make possible to access the size and time scales that are currently only accessible with empirical force fields without loosing the predictive power of ab-initio simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Pore-Scale Process Coupling and Effective Surface Reaction Rates in Heterogeneous Subsurface Materials

This manuscript provides a review of pore-scale researches in literature including experimental and numerical approaches, and scale-dependent behavior of geochemical and biogeochemical reaction rates in heterogeneous porous media. A mathematical equation that can be used to predict the scale-dependent behavior of geochemical reaction rates in heterogeneous porous media has been derived. The derived effective rate expression explicitly links the effective reaction rate constant to the intrinsic rate constant, and to the pore-scale variations in reactant concentrations in porous media. Molecular simulations to calculate the intrinsic rate constants were provided. A few examples of pore-scale simulations were used to demonstrate the application of the equation to calculate effective rate constants in heterogeneous materials. The results indicate that the deviation of effective rate constant from the intrinsic rate in heterogeneous porous media is caused by the pore-scale distributions of reactants and their correlation, which are affected by the pore-scale coupling of reactions and transport.

Environmental Molecular Sciences Laboratory↗

Proline puckering parameters for collagen structure simulations

Collagen is made of triple helices rich in proline residues, and hence is influenced by the conformational motions of prolines. Because the backbone motions of prolines are restricted by the helical structures, the only side chain motion—proline puckering—becomes an influential factor that may affect the stability of collagen structures. In molecular simulations, a proper proline puckering population is desired so to yield valid results of the collagen properties. Here we design the proline puckering parameters in order to yield suitable proline puckering populations as demonstrated in the experimental results. We test these parameters in collagen and the proline dipeptide simulations. Compared with the results of the PDB and the quantum calculations, we propose the proline puckering parameters for the selected collagen model simulations.

36 MATERIALS SCIENCE↗

2D Surface Structures in Small Zeolite MFI Crystals

Utilization of new hierarchical zeolites comprised of small crystallites (<50 nm) provides enhanced processing rates in separation and catalytic applications. Yet, molecular permeation through surface pores in small zeolite crystals has been shown to control the overall rate, resulting in apparent site-to-site intracrystalline kinetics that vary by as much as three orders of magnitude. Here, the external surface of small zeolite MFI crystals was characterized by combining experimental kinetics and molecular simulation to evaluate the hypothesis of a two-dimensional distribution of surface pores that are either open or closed (i.e., fraction, popen). The movement of benzene through the MFI lattice and surface was evaluated with a discrete space kinetic Monte Carlo algorithm with varying particle sizes (1.0 nm ≤ R ≤ 640 nm) and fraction of surface pore openings (10 –4 < p open < 10 0 ). Introduction of randomly distributed surface pore blockages was shown to increase the molecular path length for adsorbates exiting the particle while maintaining a constant apparent activation energy, consistent with additional molecular motion near the internal surface. Comparison of the dimensionless surface barrier (λ = τ Surface /τ Bulk ) obtained by simulation to experimental measurements (zero length chromatography) for silicalite-1 particles (62 nm to 3 μm, 50–110 °C) reveals that the vast majority (>99.9%) of surface pores must be blocked (p open < 10 –3 ) to justify the observed surface permeation rate of hydrocarbon adsorbates.

36 MATERIALS SCIENCE↗

A non-additive repulsive contribution in an equation of state: The development for homonuclear square well chains equation of state validated against Monte Carlo simulation

This work consists of the adaptation of a non-additive hard sphere theory inspired by Malakhov and Volkov [Polym. Sci., Ser. A 49(6), 745–756 (2007)] to a square-well chain. Using the thermodynamic perturbation theory, an additional term is proposed that describes the effect of perturbing the chain of square well spheres by a non-additive parameter. In order to validate this development, NPT Monte Carlo simulations of thermodynamic and structural properties of the non-additive square well for a pure chain and a binary mixture of chains are performed. Good agreements are observed between the compressibility factors originating from the theory and those from molecular simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Scattering evidence of positional charge correlations in polyelectrolyte complexes

Polyelectrolyte complexation plays an important role in materials science and biology. The internal structure of the resultant polyelectrolyte complex (PEC) phase dictates properties such as physical state, response to external stimuli, and dynamics. Small-angle scattering experiments with X-rays and neutrons have revealed structural similarities between PECs and semidilute solutions of neutral polymers, where the total scattering function exhibits an Ornstein–Zernike form. In spite of consensus among different theoretical predictions, the existence of positional correlations between polyanion and polycation charges has not been confirmed experimentally. Here, we present small-angle neutron scattering profiles where the polycation scattering length density is matched to that of the solvent to extract positional correlations among anionic monomers. The polyanion scattering functions exhibit a peak at the inverse polymer screening radius of Coulomb interactions, q* ≈ 0.2 Å –1 . This peak, attributed to Coulomb repulsions between the fragments of polyanions and their attractions to polycations, is even more pronounced in the calculated charge scattering function that quantifies positional correlations of all polymer charges within the PEC. Screening of electrostatic interactions by adding salt leads to the gradual disappearance of this correlation peak, and the scattering functions regain an Ornstein–Zernike form. Experimental scattering results are consistent with those calculated from the random phase approximation, a scaling analysis, and molecular simulations.

74 ATOMIC AND MOLECULAR PHYSICS↗

On the numerical treatment of dissipative particle dynamics and related systems

We review and compare numerical methods that simultaneously control temperature while preserving the momentum, a family of particle simulation methods commonly used for the modelling of complex fluids and polymers. The class of methods considered includes dissipative particle dynamics (DPD) as well as extended stochastic-dynamics models incorporating a generalized pairwise thermostat scheme in which stochastic forces are eliminated and the coefficient of dissipation is treated as an additional auxiliary variable subject to a feedback (kinetic energy) control mechanism. In the latter case, we consider the addition of a coupling of the auxiliary variable, as in the Nosé–Hoover–Langevin (NHL) method, with stochastic dynamics to ensure ergodicity, and find that the convergence of ensemble averages is substantially improved. To this end, splitting methods are developed and studied in terms of their thermodynamic accuracy, two-point correlation functions, and convergence. In terms of computational efficiency as measured by the ratio of thermodynamic accuracy to CPU time, we report significant advantages in simulation for the pairwise NHL method compared to popular alternative schemes (up to an 80% improvement), without degradation of convergence rate. The momentum-conserving thermostat technique described here provides a consistent hydrodynamic model in the low-friction regime, but it will also be of use in both equilibrium and nonequilibrium molecular simulation applications owing to its efficiency and simple numerical implementation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗