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No description available.

1 / Bin Meng

Fully atomistic molecular dynamics (MD) simulations were used to predict the properties of EPON 862 cross-linked with curing agent DETDA, a potentially useful epoxy resin for future applications of nanocomposites. The properties of interest were density (at nearambient pressure and temperature), glass transition temperature, bulk modulus, and shear modulus. The EPON molecular topology, degree of curing, and MD force-field were investigated as variables. The range of molecular weights explored was limited to the oligomer region, due to practical restrictions on model size. For high degrees of curing (greater than 90%), the density was found to be insensitive to the EPON molecular topology and precise value of degree of curing. Of the two force-fields that were investigated, cff91 and COMPASS, COMPASS clearly gave more accurate values for the density and moduli as compared to experiment. In fact, the density predicted by COMPASS was in excellent agreement with reported experimental values. However, the bulk and shear moduli predicted by simulation were about two times higher than the corresponding experimental values.

In contrast to traditional conjugated polymer, the non-conjugated polycyanate network represents an interesting example to work with. Close packings among the phenylene and s-triazine rings in polycyanate may introduce £k-£k interaction and thereby, induce light emission. There is an important relationship between molecular packing and photo-luminescence properties. To clarify it, we also add aromatic fluorophore to hopefully alter the packing situation and from the response, further evaluation can be made. Detailed molecular packing in the network polycyanate can be evaluated by the molecular simulation technique. The simulation results for the pure polycyanate show that the most-likely inter-ring distance is 3 ~ 5

One of the important early applications of Quantum Mechanics was to explain the Van-der-Waal’s 1/R6 potential that is observed experimentally between two neutral species, such as noble gas atoms, in terms of correlated uncertainty between interacting dipoles, an effect that does not occur in the classical limit [London-Eisenschitz,1930]. When many-body correlations and higher-multipole interactions are taken into account they yield additional many-body and higher-multipole dispersion terms. Dispersion energies are closely related to electrostatic interactions and polarisation [Hirschfelder-Curtiss-Bird,1954]. Hydrogen bonding, the dominant force in water, is an example of an electrostatic effect, which is also strongly modified by polarisation effects. The behaviour of ions is also strongly influenced by polarisation. Where hydrogen bonding is disrupted, dispersion tends to act as a more constant cohesive force. It is the only attractive force that exists between hydrophobes, for example. Thus all three are important for understanding the detailed behaviour of water, and effects that happen in water, such as the solvation of ions, hydrophobic de-wetting, and thus biological nano-structures. Current molecular simulation methods rarely go beyond pair-wise potentials, and so lose the rich detail of many-body polarisation and dispersion that would permit a force field to be transferable between different environments. Empirical force-fields fitted in the gas phase, which is dominated by two-body interactions, generally do not perform well in the condensed (many-body) phases. The leading omitted dispersion term is the Axilrod-Teller-Muto 3-body potential, which does not feature in standard biophysical force-fields. Polarization is also usually ommitted, but it is sometimes included in next-generation force-fields following seminal work by Cochran [1971]. In practice, many-body forces are approximated using two-body potentials fitted to reflect bulk behaviour, but these are not transferable because they do not reproduce detailed behaviour well, resulting in spurious results near inhomogeneities, such as solvated hydrophobes and ions, surfaces and interfaces. The Quantum Drude Oscillator model (QDO) unifies many-body, multipole polarisation and dispersion, intrinsically treating them on an equal footing, potentially leading to simpler, more accurate, and more transferable force fields when it is applied in molecular simulations. The Drude Oscillator is simply a model atom wherein a single pseudoelectron is bound harmonically to a single pseudonucleus, that interacts via damped coulomb interactions [Drude,1900]. Path Integral [Feynman-Hibbs,1965] Molecular Dynamics (PIMD) can, in principle, provide an exact treatment for moving molecules at finite temperature on the Born- Oppenheimer surface due to their pseudo-electrons. PIMD can be applied to large systems, as it scales like N log(N), with multiplicative prefactor P that can be effectively parallelized away on modern supercomputers. There are other ways to treat dispersion, but all are computationally intensive and cannot be applied to large systems. These include, for example, Density Functional Theory provides an existence proof that a functional exists to include dispersion, but we dont know the functional. We outline the existing methods, and then present new density matrices to improve the discretisation of the path integral. Diffusion Monte Carlo (DMC), first proposed by Fermi, allows the fast computation of high-accuracy energies for static nuclear configurations, making it a useful method for model development, such as fitting repulsion potentials, but there is no straightforward way to generate forces. We derived new methods and trial wavefunctions for DMC, allowing the computation of energies for much larger systems to high accuracy. A Quantum Drude model of Xenon, fit in the gas-phase, was simulated in the condensed-phase using both DMC and PIMD. The new DMC methods allowed for calculation of the bulk modulus and lattice constant of FCC-solid Xenon. Both were in excellent agreement with experiment even though this model was fitted in the gasphase, demonstrating the power of Quantum Drudes to build transferable models by capturing many-body effects. We also used the Xenon model to test the new PIMD methods. Finally, we present the outline of a new QDO model of water, including QDO parameters fitted to the polarisabilities and dispersion coefficients of water.

In this thesis, we use nonequilibrium molecular dynamics (NEMD) methods to investigate the structural and dynamic properties of highly confined atomic and polymeric fluids undergoing planar Poiseuille flow. We derive 'method of planes' expressions for pressure tensor and heat flux vector for confined inhomogeneous atomic fluids under the influence of three-body forces. Our derivation is validated against NEMD simulations of a confined atomic fluid acted upon by a two-body Barker-Fisher-Watts force coupled with the Axilrod-Teller three-body force. Our method of planes calculations are in excellent agreement with the equivalent mesoscopic route of integrating the momentum and energy continuity equations directly from the simulation data. Our calculations reveal that three-body forces have an important consequence for the isotropic pressure, but have negligible in�uence on the shear stress and heat flux vector for a confined simple fluid. We use the non-local linear hydrodynamic constitutive model, proposed by Evans and Morriss [1] for computing a viscosity kernel, a function of compact support, for inhomogeneous nonequilibrium fluids. Our results show that the viscosity kernel, �(y), has a peak at y = 0, and gets smaller and decays to zero as y increases. Physically, it means that the strain rate at the location where we want to know the stress contributes most to the stress, and the contribution of the strain rate becomes less significant as the relative distance y increases. We demonstrate that there is a limitation in the model when it is applied to our confined fluids due to the effect of domain restriction on inverse convolution. We study the nanorheology of simple polymeric fluids. Our NEMD simulation results show that sufficiently far from the walls, the radius of gyration for molecules under shear in the middle of the channel follows the power law, Rg / N�, where N is the number of bonds and the exponent has a value � = 0:60�0:04, which is larger than the melt value of 0:5 for a homogeneous equilibrium �uid. Under the conditions simulated, we find that viscous forces dominate the flow, resulting in the onset of plug-like flow velocity pro�les with some wall slippage. An examination of the streaming angular velocity displays a strong correlation with the radius of gyration, being maximum in those regions where Rg is minimum and vice-versa. The angular velocity is shown to be proportional to half the strain rate su�ciently far from the walls, consistent with the behaviour for homogeneous fluids in the linear regime. Finally, we make some concluding remarks and suggestions for future work in the final chapter.

Yes / Investigation of the non-covalent interaction of biomolecules with aqueous graphene interfaces is a rapidly expanding area. However, reliable exploitation of these interfaces in many applications requires that the links between the sequence and binding of the adsorbed peptide structures be clearly established. Molecular dynamics (MD) simulations can play a key role in elucidating the conformational ensemble of peptides adsorbed at graphene interfaces, helping to elucidate these rules in partnership with experimental characterisation. We apply our recently-developed polarisable force-field for biomolecule–graphene interfaces, GRAPPA, in partnership with advanced simulation approaches, to probe the adsorption behaviour of peptides at aqueous graphene. First we determine the free energy of adsorption of all twenty naturally occurring amino acids (AAs) via metadynamics simulations, providing a benchmark for interpreting peptide–graphene adsorption studies. From these free energies, we find that strong-binding amino acids have flat and/or compact side chain groups, and we relate this behaviour to the interfacial solvent structuring. Second, we apply replica exchange with solute tempering simulations to efficiently and widely sample the conformational ensemble of two experimentally-characterised peptide sequences, P1 and its alanine mutant P1A3, in solution and adsorbed on graphene. For P1 we find a significant minority of the conformational ensemble possesses a helical structure, both in solution and when adsorbed, while P1A3 features mostly extended, random-coil conformations. In solution this helical P1 configuration is stabilised through favourable intra-peptide interactions, while the adsorbed structure is stabilised via interaction of four strongly-binding residues, identified from our metadynamics simulations, with the aqueous graphene interface. Our findings rationalise the performance of the P1 sequence as a known graphene binder. / veski

Yes / We report results of atomistic molecular dynamics simulations of an industrially-relevant, exemplar triacylglycerol (TAG), namely tristearin (TS), under aqueous conditions, at different temperatures and in the presence of an anionic surfactant, sodium dodecylbenzene sulphonate (SDBS). We predict the TS bilayers to be stable and in a gel phase at temperatures of 350 K and below. At 370 K the lipid bilayer was able to melt, but does not feature a stable liquid–crystalline phase bilayer at this elevated temperature. We also predict the structural characteristics of TS bilayers in the presence of SDBS molecules under aqueous conditions, where surfactant molecules are found to spontaneously insert into the TS bilayers. We model TS bilayers containing different amounts of SDBS, with the presence of SDBS imparting only a moderate effect on the structure of the system. Our study represents the first step in applying atomistic molecular dynamics simulations to the investigation of TAG-aqueous interfaces. Our results suggest that the CHARMM36 force-field appears suitable for the simulation of such systems, although the phase behaviour of the system may be shifted to lower temperatures than is the case for the actual system. Our findings provide a foundation for further simulation studies of the TS-aqueous interface. / veski