Molecular dynamic simulations of systems undergoing shear

Non-equilibrium molecular dynamics have been used to simulate, at a molecular level, fluids undergoing planar Couette flow. The results give a microscopic picture of the processes involved in viscoelasticity, shear dilatancy, shear birefringence, normal stress effects and shear thinning behavior. The calculations prove that shear dilatant fluids are not necessarily shear thickening. The results also suggest that the constitutive relations governing non-Newtonian behavior are non-analytic functions of strain rate.The calculations have led directly to the development of non-linear irreversible thermodynamics. This generalization of thermodynamics provides a macroscopic understanding of such processes as shear induced phase changes and the relation of shear dilatancy to shear induced energy changes.     

Molecular dynamic simulations of eicosanoic acid and 18-methyleicosanoic acid langmuir monolayers

The conformational and dynamical properties of Langmuir monolayers of 18-methyleicosanoic acid (18-MEA) and the parent material, eicosanoic acid (EA), are compared using molecular dynamics simulations. The effects on various properties, including film thickness, tilt angle, and order parameter, of the methyl group at the 18 position in 18-MEA were investigated as a function of film-packing density. NVT simulations were run as a function of decreasing areal-packing density similar to experimental Langmuir-Blodgett film compressions and expansions. We find that the order parameters and film thickness for 18-MEA monolayers were markedly different from those of EA. The order parameters for methylene groups for both 18-MEA and EA are greater in the middle region of the chain than at the ends in high-density films. This trend becomes reversed in lower density films. Significantly, our simulations show that the order parameters for methylene groups near the CH3 and carboxyl termini in 18-MEA are comparatively independent of film density in contrast with those of EA. Our findings show that the presence of the methyl group at the 18-position in 18-MEA induces unique intermolecular structural correlations compared to EA.     

Molecular dynamic simulations of carbon nanotubes in CO2 atmosphere

This work investigates by means of molecular dynamics the filling of carbon nanotubes by carbon dioxide molecules. Nanotubes of various sizes are simulated and the resulting CO₂ density calculated. The effects of various CO₂ models are also investigated. The results show that the carbon dioxide molecules have a natural tendency to fill the nanotubes and the final CO₂ concentration inside the nanotube can be approximately 100 times (depending on diameter and CO₂ model) higher than that of the external atmosphere.     

Molecular dynamic simulations of self-assembled alkylthiolate monolayers on an Au(III) surface

Molecular dynamics simulations incorporating explicit gold atoms in the simulations have been carried out for alkanethiol self-assembled monolayers chemisorbed on the Au(III) surface. The structural properties of the monolayer are evaluated for two force fields: one in which the Au--S--C bond is fixed (FF I), and the other in which it is flexible (FF II). The influence of these force fields on the structural properties of HS(CH2)14CH3 on the structured Au surface is compared at different temperatures. FF I yields greater tilt angles and a smaller film thickness when compared with FF II. Both of the force fields predict that the tilt angles do not follow a monotonic decrease with temperature but show minima around 200 K. Simulations carried out at different chain lengths at 300 K reveal that FF II predicts a greater film thickness than FF I; however, the difference is within 1 A.     

Guest-specific diffusion anisotropy in nanoporous materials: Molecular dynamics and dynamic Monte Carlo simulations

For anisotropic nanoporous materials, guest diffusion is often reflected by a diffusion tensor rather than a scalar diffusion coefficient. Moreover, the resulting diffusion anisotropy may notably differ for different guest molecules. As a particular class of such systems, we consider an array of two types of channels, mutually intersecting each other, where the rates of diffusion in the different directions depend on the nature of the guest molecules. The simultaneous adsorption of two types of guest molecules is considered, as in technical applications of porous materials such as catalysis. A case study is presented in which atomistic molecular dynamics (MD) and coarse-grained dynamic Monte Carlo (DMC) simulations are compared and shown to yield qualitatively similar results for non-steady-state diffusion. The two techniques are complementary. MD simulations are able to predict the details of molecular propagation over distances of a few unit cells, whereas the evolution of sorption profiles over distances comparable with entire crystallites can be studied with DMC simulations. Consideration of these longer length and time scales is necessary for applications of such systems in chemical separations and heterogeneous catalysis.     

Multiresolution stochastic simulations of reaction-diffusion processes

Stochastic simulations of reaction-diffusion processes are used extensively for the modeling of complex systems in areas ranging from biology and social sciences to ecosystems and materials processing. These processes often exhibit disparate scales that render their simulation prohibitive even for massive computational resources. The problem is resolved by introducing a novel stochastic multiresolution method that enables the efficient simulation of reaction-diffusion processes as modeled by many-particle systems. The proposed method quantifies and efficiently handles the associated stiffness in simulating the system dynamics and its computational efficiency and accuracy are demonstrated in simulations of a model problem described by the Fisher-Kolmogorov equation. The method is general and can be applied to other many-particle models of physical processes.     

A reduced phase space approach to collision processes

An exact master equation for the occupation of different states during a collision is derived. For a wide dass of initial states including those typical of scattering experiments, the transition probability matrix is independent of the initial state. The stationary solution of the master equation is the “prior” distribution.     

Inelastic collision processes of low-energy protons in liquid water

Production probabilities of ions and excited particle species along the proton beam track in liquid water are estimated around the Bragg peak region, taking into account charge-changing processes and energetic secondary electron (δ-ray) behavior. Ionization and excitation processes are divided into two categories in this study: primary processes associated with direct proton (or hydrogen) interaction and secondary processes arising from the electrons ejected by the primary process. We show that the number of events in the secondary processes producing ions and excited particles is larger than that of the primary processes around the Bragg peak while neutralized protons (i.e., hydrogen) with low energy have a large contribution to direct ionization. Effects of charge-changing processes on ionization and excitation are also discussed.     

Molecular dynamics simulations of lipid bilayers

Computer simulation methods are becoming increasingly widespread as tools for studying the structure and dynamics of lipid bilayer membranes. The length scale and time scale accessible to atomic-level molecular dynamics simulations are rapidly increasing, providing insight into the relatively slow motions of molecular reorientation and translation and demonstrating that effects due to the finite size of the simulation cell can influence simulation results. Additionally, significant advances have been made in the complexity of membrane systems studied, including bilayers with cholesterol, small solute molecules, and lipid-protein and lipid-DNA complexes. Especially promising is the progress that continues to be made in the comparison of simulation results with experiment, both to validate the simulation algorithms and to aid in the interpretation of existing experimental data.     

Molecular dynamics simulations of polyelectrolyte adsorption

We have performed molecular dynamics simulations of polyelectrolyte adsorption at oppositely charged surfaces from dilute polyelectrolyte solutions. In our simulations, polyelectrolytes were modeled by chains of charged Lennard-Jones particles with explicit counterions. We have studied the effects of the surface charge density, surface charge distribution, solvent quality for the polymer backbone, strength of the short-range interactions between polymers and substrates on the polymer surface coverage, and the thickness of the adsorbed layer. The polymer surface coverage monotonically increases with increasing surface charge density for almost all studied systems except for the system of hydrophilic polyelectrolytes adsorbing at hydrophilic surfaces. In this case the polymer surface coverage saturates at high surface charge densities. This is due to additional monomer-monomer repulsion between adsorbed polymer chains, which becomes important in dense polymeric layers. These interactions also preclude surface overcharging by hydrophilic polyelectrolytes at high surface charge densities. The thickness of the adsorbed layer shows monotonic dependence on the surface charge density for the systems of hydrophobic polyelectrolytes for both hydrophobic and hydrophilic surfaces. Thickness is a decreasing function of the surface charge density in the case of hydrophilic surfaces while it increases with the surface charge density for hydrophobic substrates. Qualitatively different behavior is observed for the thickness of the adsorbed layer of hydrophilic polyelectrolytes at hydrophilic surfaces. In this case, thickness first decreases with increasing surface charge density, then it begins to increase.     

Molecular dynamics simulations of biotin carboxylase

Biotin carboxylase catalyzes the ATP-dependent carboxylation of biotin and is one component of the multienzyme complex acetyl-CoA carboxylase that catalyzes the first committed step in fatty acid synthesis in all organisms. Biotin carboxylase from Escherichia coli, whose crystal structures with and without ATP bound have been determined, has served as a model system for this component of the acetyl-CoA carboxylase complex. The two crystal structures revealed a large conformational change of one domain relative to the other domains when ATP is bound. Unfortunately, the crystal structure with ATP bound was obtained with an inactive site-directed mutant of the enzyme. As a consequence the structure with ATP bound lacked key structural information such as for the Mg2+ ions and contained altered conformations of key active-site residues. Therefore, nanosecond molecular dynamics studies of the wild-type biotin carboxylase were undertaken to supplant and amend the results of the crystal structures. Specifically, the protein-metal interactions of the two catalytically critical Mg2+ ions bound in the active site are presented along with a reevaluation of the conformations of active-site residues bound to ATP. In addition, the regions of the polypeptide chain that serve as hinges for the large conformational change were identified. The results of the hinge analysis complemented a covariance analysis that identified the individual structural elements of biotin carboxylase that change their conformation in response to ATP binding.     

Molecular dynamics simulations of cardiolipin bilayers

Cardiolipin is a key lipid component in the inner mitochondrial membrane, where the lipid is involved in energy production, cristae structure, and mechanisms in the apoptotic pathway. In this article we used molecular dynamics computer simulations to investigate cardiolipin and its effect on the structure of lipid bilayers. Three cardiolipin/POPC bilayers with different lipid compositions were simulated: 100, 9.2, and 0% cardiolipin. We found strong association of sodium counterions to the carbonyl groups of both lipid types, leaving in the case of 9.2% cardiolipin virtually no ions in the aqueous compartment. Although binding occurred primarily at the carbonyl position, there was a preference to bind to the carbonyl groups of cardiolipin. Ion binding and the small headgroup of cardiolipin gave a strong ordering of the hydrocarbon chains. We found significant effects in the water dipole orientation and water dipole potential which can compensate for the electrostatic repulsion that otherwise should force charged lipids apart. Several parameters relevant for the molecular structure of cardiolipin were calculated and compared with results from analyses of coarse-grained simulations and available X-ray structural data.     

Molecular dynamics simulations of halide glasses

Summary Halide glasses have been extensively studied in recent years because of their potential application as infrared transmitting fibre optic materials. They are believed to be more ionic than glasses based on silica and should therefore be more amenable to molecular dynamics simulation using simple two-body potentials. Here the main features of structural models derived using such techniques are described and compared with available structural data. Possible future applications of this approach are outlined.     

Molecular dynamics simulations of peptide-surface interactions

Proteins, which are bioactive molecules, adsorb on implants placed in the body through complex and poorly understood mechanisms and directly influence biocompatibility. Molecular dynamics modeling using empirical force fields provides one of the most direct methods of theoretically analyzing the behavior of complex molecular systems and is well-suited for the simulation of protein adsorption behavior. To accurately simulate protein adsorption behavior, a force field must correctly represent the thermodynamic driving forces that govern peptide residue-surface interactions. However, since existing force fields were developed without specific consideration of protein-surface interactions, they may not accurately represent this type of molecular behavior. To address this concern, we developed a host-guest peptide adsorption model in the form of a G(4)-X-G(4) peptide (G is glycine, X is a variable residue) to enable determination of the contributions to adsorption free energy of different X residues when adsorbed to functionalized Au-alkanethiol self-assembled monolayers (SAMs). We have previously reported experimental results using surface plasmon resonance (SPR) spectroscopy to measure the free energy of peptide adsorption for this peptide model with X = G and K (lysine) on OH and COOH functionalized SAMs. The objectives of the present research were the development and assessment of methods to calculate adsorption free energy using molecular dynamics simulations with the GROMACS force field for these same peptide adsorption systems, with an oligoethylene oxide (OEG) functionalized SAM surface also being considered. By comparing simulation results to the experimental results, the accuracy of the selected force field to represent the behavior of these molecular systems can be evaluated. From our simulations, the G(4)-G-G(4) and G(4)-K-G(4) peptides showed minimal to no adsorption to the OH SAM surfaces and the G(4)-K-G(4) showed strong adsorption to the COOH SAM surface, which is in agreement with our SPR experiments. Contrary to our experimental results, however, the simulations predicted a relatively strong adsorption of G(4)-G-G(4) peptide to the COOH SAM surface. In addition, both peptides were unexpectedly predicted to adsorb to the OEG surface. These findings demonstrate the need for GROMACS force field parameters to be rebalanced for the simulation of peptide adsorption behavior on SAM surfaces. The developed methods provide a direct means of assessing, modifying, and validating force field performance for the simulation of peptide and protein adsorption to surfaces, without which little confidence can be placed in the simulation results that are generated with these types of systems.     

Molecular docking/dynamic simulations,MEP, ADME-TOX-based analysis of xanthone derivatives as CHK1 inhibitors

Structural Chemistry - CHK1 is a promising molecular target that gained immense attention recently for the development of cancer therapeutics. In this study, a simulation-based investigation was...     

Coherent control of collision processes: Penning versus associative ionization

Coherent control theory is applied to the control of Ne*(3s,(3)P2)+Ar((1)S0) collisions and computations are shown that display extensive control over these processes. Indeed we demonstrate that it is possible to essentially turn on and off the cross sections for both the Penning and associative ionization processes. This facility arises from the interference between matter waves induced by creating a linear superposition of the degenerate M={-2,-1,0,1,2} Zeeman sublevels of the Ne*(3s,(3)P2) target atom. The computations, conducted at collision energies in the 1-8 kcal/mole range, are based on combining, within the "rotating atom approximation," empirically derived and ab initio ionization widths.