Combined depletion and electrostatic forces in polymer-induced membrane adhesion: a theoretical model

We develop a semi-quantitative analytical theory to describe adhesion between two identical planar charged surfaces embedded in a polymer-containing electrolyte solution. Polymer chains are uncharged and differ from the solvent by their lower dielectric permittivity. The solution mimics physiological fluids: It contains 0.1 M of monovalent ions and a small number of divalent cations that form tight bonds with the headgroups of charged lipids. The components have heterogeneous spatial distributions. The model was derived self-consistently by combining: (a) a Poisson-Boltzmann like equation for the charge densities, (b) a continuum mean-field theory for the polymer profile, (c) a solvation energy forcing the ions toward the polymer-poor regions, and (d) surface interactions of polymers and electrolytes. We validated the theory via extensive coarse-grained Molecular Dynamics (MD) simulations. The results confirm our analytical model and reveal interesting details not detected by the theory. At high surface charges, polymer chains are mainly excluded from the gap region, while the concentration of ions increases. The model shows a strong coupling between osmotic forces, surface potential and salting-out effects of the slightly polar polymer chains. It highlights some of the key differences in the behaviour of monomeric and polymeric mixed solvents and their responses to Coulomb interactions. Our main findings are: (a) the onset of long-ranged ion-induced polymer depletion force that increases with surface charge density and (b) a polymer-modified repulsive Coulomb force that increases with surface charge density. Overall, the system exhibits homeostatic behaviour, resulting in robustness against variations in the amount of charges. Applications and extensions of the model are briefly discussed.     

燃烧反应动力学研究进展

化学反应动力学是燃烧过程分析的重要工具。燃烧微观反应过程、复杂反应机理、燃烧实验测量和湍流燃烧数值模拟等方面的研究工作已经取得了长足进步。本文主要介绍燃烧反应动力学研究方法,包括电子结构方法、燃烧反应热力学和速率常数的计算方法、燃烧详细机理构建和简化、反应力场分子模拟以及燃烧中间体测量、燃料点火延迟和光谱诊断等方面的研究现状。燃烧反应动力学具有很强的应用背景,燃烧过程化学物种的反应速率计算是湍流燃烧数值模拟的一个中心任务。由于燃烧反应网络的高度复杂性,我们对燃烧机理的认识还远不清楚。化学反应和湍流相互作用研究的深入、燃烧反应动力学和计算流体力学的协同发展,将对新燃料设计、燃烧数值模拟、发动机内流道流场结构的准确描述产生深远影响。     

Stability of ion triplets in ionic liquid/lithium salt solutions: Insights from implicit and explicit solvent models and molecular dynamics simulations

Binding energies of ion triplets formed in ionic liquids by Li⁺ with two anions have been studied using quantum‐chemical calculations with implicit and explicit solvent supplemented by molecular dynamics (MD) simulations. Explicit solvent approach confirms variation of solute‐ionic liquid interactions at distances up to 2 nm, resulting from structure of solvation shells induced by electric field of the solute. Binding energies computed in explicit solvent and from the polarizable continuum model approach differ largely, even in sign, but relative values generally agree between these two models. Stabilities of ion triplets obtained in quantum‐chemical calculations for some systems disagree with MD results; the discrepancy is attributed to the difference between static optimized geometries used in quantum chemical modeling and dynamic structures of triplets in MD simulations. © 2015 Wiley Periodicals, Inc.     

Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment

The amlyoid-β peptide (Aβ) is closely linked to the development of Alzheimer''s disease. Molecular dynamics (MD) simulations have become an indispensable tool for studying the behavior of this peptide at the atomistic level. General key aspects of MD simulations are the force field used for modeling the peptide and its environment, which is important for accurate modeling of the system of interest, and the length of the simulations, which determines whether or not equilibrium is reached. In this study we address these points by analyzing 30-μs MD simulations acquired for Aβ40 using seven different force fields. We assess the convergence of these simulations based on the convergence of various structural properties and of NMR and fluorescence spectroscopic observables. Moreover, we calculate Markov state models for the different MD simulations, which provide an unprecedented view of the thermodynamics and kinetics of the amyloid-β peptide. This further allows us to provide answers for pertinent questions, like: which force fields are suitable for modeling Aβ? (a99SB-UCB and a99SB-ILDN/TIP4P-D); what does Aβ peptide really look like? (mostly extended and disordered) and; how long does it take MD simulations of Aβ to attain equilibrium? (at least 20–30 μs). We believe the analyses presented in this study will provide a useful reference guide for important questions relating to the structure and dynamics of Aβ in particular, and by extension other similar disordered proteins.

The convergence of MD simulations is tested using varying measures for the intrinsically disordered amyloid-β peptide (Aβ). Markov state models show that 20–30 μs of MD is needed to reliably reproduce the thermodynamics and kinetics of Aβ.     

Impact of the solvent on the conformational isomerism of calix[4]arenes: a study based on continuum solvation models

The influence of solvation on the conformational isomerism of calix[4]arene and p-tert-butylcalix[4]arene has been investigated by using the continuum model reported by Miertus, Scrocco, and Tomasi (MST). The quantum mechanical (QM) and semiclassical (SC) formalisms of the MST model have been considered for two different solvents (chloroform and water). The suitability of the QM-MST and SC-MST methods has been examined by comparison with previous results derived from classical molecular dynamics (MD) simulations with explicit solvent molecules. The application of the continuum model to the solute configurations generated by using in vacuo classical MD simulations provides a fast strategy to evaluate the effects of the solvent on the conformational preferences of calixarenes. These encouraging results allow us to propose the use of continuum models to solutes with complex molecular structures, which are traditionally studied by MD simulations.     

Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: The MEMPOT algorithm implemented in DelPhi

Four chemotypes of the rough lipopolysaccharides (LPS) membrane from Pseudomonas aeruginosa were investigated by a combined approach of explicit water molecular dynamics (MD) simulations and Poisson–Boltzmann continuum electrostatics with the goal to deliver the distribution of the electrostatic potential across the membrane. For the purpose of this investigation, a new tool for modeling the electrostatic potential profile along the axis normal to the membrane, MEMbrane POTential (MEMPOT), was developed and implemented in DelPhi. Applying MEMPOT on the snapshots obtained by MD simulations, two observations were made: (a) the average electrostatic potential has a complex profile but is mostly positive inside the membrane due to the presence of Ca²⁺ ions, which overcompensate for the negative potential created by lipid phosphate groups; and (b) correct modeling of the electrostatic potential profile across the membrane requires taking into account the water phase, while neglecting it (vacuum calculations) results in dramatic changes including a reversal of the sign of the potential inside the membrane. Furthermore, using DelPhi to assign different dielectric constants for different regions of the LPS membranes, it was investigated whether a single frame structure before MD simulations with appropriate dielectric constants for the lipid tails, inner, and the external leaflet regions, can deliver the same average electrostatic potential distribution as obtained from the MD‐generated ensemble of structures. Indeed, this can be attained by using smaller dielectric constant for the tail and inner leaflet regions (mostly hydrophobic) than for the external leaflet region (hydrophilic) and the optimal dielectric constant values are chemotype‐specific. © 2014 Wiley Periodicals, Inc.     

Nonlinear shear of entangled polymers from nonequilibrium molecular dynamics

This study aims to use molecular dynamics (MD) simulations of Kremer–Grest (KG) chains to inform future developments of models of entangled polymer dynamics. We perform nonequilibrium MD simulations, under shear flow, for well‐entangled KG chains. We study chains of 512 and 1000 KG beads, corresponding to 8 and 15 entanglements, respectively. We compute the linear rheological properties from equilibrium simulations of the stress autocorrelation and obtain from these data the tube model parameters. Under nonlinear shear flow, we compute the shear viscosity, the first and second normal stress differences, and chain contour length. For chains of 512 monomers, we obtain agreement with the results of Cao and Likhtman (ACS Macro. Lett. 2015, 4, 1376). We also compare our nonlinear results with the Graham, Likhtman and Milner‐McLeish (GLaMM) model. We identify some systematic disagreement that becomes larger for the longer chains. We made a comparison of the transient shear stress maximum from our simulations, two nonlinear models and experiments on a wide range of melts and solutions, including polystyrene (PS), polybutadiene, and styrene–butadiene rubber. This comparison establishes that the PS melt data show markedly different behavior to all other melts and solutions and KG simulations reproduce the PS data more closely than either the GLaMM or Xie and Schweizer models. We discuss the performance of these models against the data and simulations. Finally, by imposing a rapid reversing flow, we produce a method to extract the recoverable strain from MD simulations, valid for sufficiently entangled monodisperse polymers. We explore how the resulting data can probe the melt state just before the reversing flow. © 2019 The Authors. Journal of Polymer Science Part B: Polymer Physics published by Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1692–1704     

Atomic-scale friction on diamond: a comparison of different sliding directions on (001) and (111) surfaces using MD and AFM

Atomic force microscopy (AFM) experiments and molecular dynamics (MD) simulations were conducted to examine single-asperity friction as a function of load, surface orientation, and sliding direction on individual crystalline grains of diamond in the wearless regime. Experimental and simulation conditions were designed to correspond as closely as state-of-the-art techniques allow. Both hydrogen-terminated diamond (111)(1 x 1)-H and the dimer row-reconstructed diamond (001)(2 x 1)-H surfaces were examined. The MD simulations used H-terminated diamond tips with both flat- and curved-end geometries, and the AFM experiments used two spherical, hydrogenated amorphous carbon tips. The AFM measurements showed higher adhesion and friction forces for (001) vs (111) surfaces. However, the increased friction forces can be entirely attributed to increased contact area induced by higher adhesion. Thus, no difference in the intrinsic resistance to friction (i.e., in the interfacial shear strength) is observed. Similarly, the MD results show no significant difference in friction between the two diamond surfaces, except for the specific case of sliding at high pressures along the dimer row direction on the (001) surface. The origin of this effect is discussed. The experimentally observed dependence of friction on load fits closely with the continuum Maugis-Dugdale model for contact area, consistent with the occurrence of single-asperity interfacial friction (friction proportional to contact area with a constant shear strength). In contrast, the simulations showed a nearly linear dependence of the friction on load. This difference may arise from the limits of applicability of continuum mechanics at small scales, because the contact areas in the MD simulations are significantly smaller than the AFM experiments. Regardless of scale, both the AFM and MD results show that nanoscale tribological behavior deviates dramatically from the established macroscopic behavior of diamond, which is highly dependent on orientation.     

Molecular Dynamics of Pectin Extension

Summary: A pectin 10mer under constant pulling speed and constant force was studied using the atomistic simulations. Molecular dynamics (MD) with the Amber99 and Amber-Glycam04 forcefields were performed. The main result of the present Amber-based MD simulations is that the two plateaux of the experimental force- extension dependence for pectin can be explained by transitions between three conformational states of pectin monomer ring (first from a chair (⁴C₁) to boat conformation and second from boat to an inverted chair (¹C₄) conformation). A multi-state dynamical model of single biopolymer extension under external force was elaborated and applied to extension of polymers with three-state monomers relevant to pectin.     

QuanPol: A full spectrum and seamless QM/MM program

The quantum chemistry polarizable force field program (QuanPol) is implemented to perform combined quantum mechanical and molecular mechanical (QM/MM) calculations with induced dipole polarizable force fields and induced surface charge continuum solvation models. The QM methods include Hartree–Fock method, density functional theory method (DFT), generalized valence bond theory method, multiconfiguration self‐consistent field method, Møller–Plesset perturbation theory method, and time‐dependent DFT method. The induced dipoles of the MM atoms and the induced surface charges of the continuum solvation model are self‐consistently and variationally determined together with the QM wavefunction. The MM force field methods can be user specified, or a standard force field such as MMFF94, Chemistry at Harvard Molecular Mechanics (CHARMM), Assisted Model Building with Energy Refinement (AMBER), and Optimized Potentials for Liquid Simulations‐All Atom (OPLS‐AA). Analytic gradients for all of these methods are implemented so geometry optimization and molecular dynamics (MD) simulation can be performed. MD free energy perturbation and umbrella sampling methods are also implemented. © 2013 Wiley Periodicals, Inc.     

Binding energies of five molecular pincers calculated by explicit and implicit solvent models

Molecular pincers or tweezers are designed to hold and release the target molecule. Potential applications involve drug distribution in medicine, environment technologies, or microindustrial techniques. Typically, the binding is dominated by van der Waals forces. Modeling of such complexes can significantly enhance their design; yet obtaining accurate complexation energies by theory is difficult. In this study, density functional theory (DFT) computations combined with dielectric continuum solvent model are compared with the potential of mean force approach using umbrella sampling and the weighted histogram analysis method (WHAM) with molecular dynamics (MD) simulations. For DFT, functional and basis set effects are discussed. The computed results are compared to experimental data based on NMR spectroscopic measurements of five synthesized tweezers based on the Tröger's basis. Whereas the DFT computations correctly provided the observed trends in complex stability, they failed to produce realistic magnitudes of complexation energies. Typically, the binding was overestimated by DFT if compared to experiment. The simpler semiempirical PM6‐DH2X scheme proposed lately yielded better magnitudes of the binding energies than DFT but not the right order. The MD‐WHAM simulations provided the most realistic Gibbs binding energies, although the approximate MD force fields were not able to reproduce completely the ordering of relative stabilities of model complexes found by NMR. Yet the modeling provides interesting insight into the complex geometry and flexibility and appears as a useful tool in the tweezers' design. © 2012 Wiley Periodicals, Inc.     

De novo and inverse folding predictions of protein structure and dynamics

Summary In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and already determined) structure. A comparison of extant inverse protein-folding algorithms is presented, and methodologies for identifying sequences likely to adopt identical folding topologies, even when they lack sequence homology, are described. Extension to produce structural templates or fingerprints from idealized structures is discussed, and for eight-membered β-barrel proteins, it is shown that idealized fingerprints constructed from simple topology diagrams can correctly identify sequences having the appropriate topology. Furthermore, this inverse folding algorithm is generalized to predict elements of supersecondary structure including β-hairpins, helical hairpins and α/β/α fragments. Then, we describe a very high coordination number lattice model that can predict the 3D structure of a number of globular proteins de novo; i.e. using just the amino acid sequence. Applications to sequences designed by DeGrado and co-workers [Biophys. J., 61 (1992) A265] predict folding intermediates, native states and relative stabilities in accord with experiment. The methodology has also been applied to the four-helix bundle designed by Richardson and co-workers [Science, 249 (1990) 884] and a redesigned monomeric version of a naturally occurring four-helix dimer, rop. Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3–4 ? from native. Furthermore, the de novo algorithms can asses the stability of the folds predicted from the inverse algorithm, while the inverse folding algorithms can assess the quality of the de novo models. Thus, the synergism of the de novo and inverse folding algorthhm approaches provides a set of complementary tools that will facilitate further progress on the protein-folding problem.     

Design,synthesis, and characterization of molecularly imprinted solid phase extraction for alpha Mangostin analysis in blood sample

Low levels of α-mangostin (AM) in biological fluids require adequate sample preparation to be analyzed. Molecularly imprinted polymers can serve as sorbents in solid phase extraction, enabling concentration and extraction of α-mangostin from complex matrices, such as biological fluids. To date, there are no molecular imprinted polymers for the analysis of α-mangostin in biological fluids. In this study, AM molecular imprinted polymer (MIP) was designed using molecular modeling, molecular dynamic simulations, and prepared by bulk polymerization and suspension polymerization methods. The geometry optimization results showed that acrylamide (AAM) monomer forms the most stable complex with AM at the pre-polymerization with the most negative Gibbs free energy (ΔG) of −6.91818 Kcal/mol. Radial distribution function (RDF) in molecular dynamics simulation of AM:AAM:ethylene glycol dimethacrylate (EGDMA) with mol ratio 1:4:20 shows the complex with the best composition through the formation of four stable hydrogen bonds. Based on the experimental results, molecularly imprinted polymers in suspension exhibit better characteristics, selectivity, and adsorption capacity than in bulk. The suspension polymerization method showed a high recovery (85.88% ± 2.5), which was higher than C18 SPE cartridge (24.19% ± 1.47). Hence, it can be concluded that the MIPs from MD simulations were accessible and could be used in practice, such as in the separation and detection of AM in blood serum.     

GALAMOST: GPU‐accelerated large‐scale molecular simulation toolkit

GALAMOST [graphics processing unit (GPU)‐accelerated large‐scale molecular simulation toolkit] is a molecular simulation package designed to utilize the computational power of GPUs. Besides the common features of molecular dynamics (MD) packages, it is developed specially for the studies of self‐assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by using some lately developed simulation techniques. To accelerate the simulations, GALAMOST contains a hybrid particle‐field MD technique where particle–particle interactions are replaced by interactions of particles with density fields. Moreover, the numerical potential obtained by bottom‐up coarse‐graining methods can be implemented in simulations with GALAMOST. By combining these force fields and particle‐density coupling method in GALAMOST, the simulations for polymers can be performed with very large system sizes over long simulation time. In addition, GALAMOST encompasses two specific models, that is, a soft anisotropic particle model and a chain‐growth polymerization model, by which the hierarchical self‐assembly of soft anisotropic particles and the problems related to polymerization can be studied, respectively. The optimized algorithms implemented on the GPU, package characteristics, and benchmarks of GALAMOST are reported in detail. © 2013 Wiley Periodicals, Inc.     

Development and validation of COMPASS force field parameters for molecules with aliphatic azide chains

To establish force-field-based (molecular) modeling capability that will accurately predict condensed-phase thermophysical properties for materials containing aliphatic azide chains, potential parameters for atom types unique to such chains have been developed and added to the COMPASS force field. The development effort identified the need to define four new atom types: one for each of the three azide nitrogen atoms and one for the carbon atom bonded to the azide. Calculations performed with the expanded force field yield (gas-phase) molecular structures and vibrational frequencies for hydrazoic acid, azidomethane, and the anti and gauche forms of azidoethane in good agreement with values determined experimentally and/or through computational quantum mechanics. Liquid densities calculated via molecular dynamics (MD) simulations were also in good agreement with published values for 13 of 15 training set compounds, the exceptions being hydrazoic acid and azidomethane. Of the 13 compounds whose densities are well simulated, nine have experimentally determined heats of vaporization reported in the open literature, and in all of these cases, MD simulated values for this property are in reasonable agreement with the published values. Simulations with the force field also yielded reasonable density estimates for a series of 2-azidoethanamines that have been synthesized and tested for use as hydrazine-alternative fuels.