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Showing 1 to 11 of 11 for “"solvent models"”.
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Finite element methods for implicit solvent models
… finite element methods (FEMs) for implicit solvent models. Implicit models treat the solvent in biomolecular systems as bulk continuum and are thus computationally efficient. The Poisson-Boltzmann equation (PBE) is one important example. We design a FEM for the linear PBE by directly …
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Improving of the accuracy and efficiency of implicit solvent models in Biomolecular Modeling
… modeling is an accurate description of the solvent (water). The challenge is to make this description computationally facile that is reasonably fast, simple, robust and easy to incorporate into existing software packages. The most rigorous procedure to model the effect of aqueous solvent is …
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Stratification in Drying Particle Suspensions
… nanoparticle mixtures. I first use an explicit solvent model to investigate how the structure of the dry film depends on the evaporation rate of the solvent and the initial volume fractions of the nanoparticles. My simulation results show that the particle mixtures stratify according to their …
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Lengthening the timescale reach of molecular dynamics
… Second, a generalized Born model of implicit solvent accelerates simulation through reduced computational expense as well as increased conformational sampling due to reduced viscosity of the implicit solvent. Finally, advanced computing technologies, such as graphics processing units, …
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Molecular simulation of biomaterials and biomolecules at the solid-liquid interface
… of adsorption mechanisms. While simple models involving reduced solvent representations and polymer flexibility have found some success in limited applications, robust performance for systems of varying size and composition can generally be expected only through accurate inclusion of …
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Electronic Structure Modelling of Singlet Fission in Organic Photovoltaics
… the influence of different side-groups and solvent environments on fission in pentacene dimers. To this end, we employ DFT with both implicit and explicit solvent models, combined with large-scale calculations to achieve sufficient sampling of solvent-solute configurations.
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Investigating the effect of charge hydration asymmetry and incorporating it in continuum solvation framework
… is an accurate description of water as a solvent. The challenge is to make this description computationally facile -- reasonably fast, simple, robust and easy to incorporate into existing software packages, yet accurate. The most rigorous procedure to model the effect of aqueous solvent is …
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Computer simulation of lipids and DNA using a coarse grain methodology
… to develop simple and robust lipid and<br/>DNA models that will allow for these complex molecules to be mixed together in order to<br/>elucidate the possible interactions. The large percentage of lipids found within the nucleus<br/>makes it likely that they exist in aggregates, although the …
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Understanding the ATP hydrolysis mechanism in myosin using computer simulation techniques
… (QM/MM) reaction path simulations. To include solvent screening effects in the calculations, a new approximate method "Non-Uniform Charge Scaling" (NUCS) was developed which scales the partial atomic charges on the molecular mechanical atoms so as to optimally reproduce electrostatic …
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Computational Modelling of Nanoscale Interactions for Nanophotonics and Biosensing
… section, we develop a model to investigate solvent effects on the polarizability of Ångstrom-sized amino acids. Molecular polarizability serves as a molecular fingerprint that is encoded in the biosensor signals. Our model builds on existing methods in density functional theory to calculate …
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Towards more robust and efficient methods for the calculation of Protein-Ligand binding affinities
… considers the explicit driving force from the solvent, in which several individual water molecules in the binding pocket play an active role in the binding process. We demonstrate that protein may adopt active site geometries that will destabilize the water molecules in the binding pocket …