Goundla Srinivas

Coarse grain models and the computer simulation of soft materials

This article presents a topical review of coarse grain simulation techniques. First, we motivate these techniques with illustrative examples from biology and materials science. Next, approaches in the literature for increasing the efficiency of atomistic simulations are mentioned. Considerations related to a specific coarse grain modelling approach are discussed at length, and the consequences arising from the loss of detail are given. Finally, a large number of results are presented to give the reader a feeling for the types of problem which can be addressed.

A coarse grain model for n-alkanes parameterized from surface tension data

Molecular dynamics simulations are carried out in a systematic manner to develop a coarse grain model for multiple-of-three carbon n-alkanes. The procedure involves optimizing harmonic bond and bend parameters, and Lennard-Jones nonbonded parameters, to match observables taken from fully atomistic simulations and from experiment. The experimental values used consist of surface tension and bulk density data. Scaling relations are introduced to allow for the representation of the remaining n-alkanes. As n increases these relations converge to the multiple-of-three carbon values. The model is assessed by comparing it to both fully atomistic simulation and experimental data which was not used in the fitting procedure.

Nonideality in the composition dependence of viscosity in binary mixtures

In this work we introduce two models to understand the anomalous composition dependence of viscosity of binary mixtures. Both models consist of a mixture of two molecular species (A and B) with the same diameter and mass but varying solute–solvent Lennard-Jones interaction. In model I, the two different species are strongly attractive while in model II, the attraction is weaker than that between the pure components. We have carried out extensive computer simulations of the two models. In addition, we study mode coupling theory for the viscosity of binary mixtures. Both the molecular dynamics simulations and the microscopic theory show the emergence of strong nonideality even in such simple systems. Model I shows a positive departure from ideality while model II shows the reverse behavior. The reason can be traced to the enhanced mean square stress fluctuations (MSSF) in the model I but decreased MSSF in the model II. The models show deviations (from ideality) very similar to the ones observed in experiments.

A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils.

Understanding biomass structure and dynamics on a range of time and length scales is important for the development of cellulosic biofuels. Here, to enable length and time scale extension, we develop a coarse grain (CG) model for molecular dynamics (MD) simulations of cellulose. For this purpose, we use distribution functions from fully atomistic MD simulations as target observables. A single bead per monomer level coarse graining is found to be sufficient to successfully reproduce structural features of crystalline cellulose. Without the use of constraints the CG crystalline fibril is found to remain stable over the maximum simulation length explored in this study (>1 μs). We also extend the CG representation to model fully amorphous cellulose fibrils. This is done by using an atomistic MD simulation of fully solvated individual cellulose chains as a target for developing the corresponding fully amorphous CG force field. Fibril structures with different degrees of crystallinity are obtained using force fields derived using a parameter coupling the crystalline and amorphous potentials. The method provides an accurate and constraint-free approach to derive CG models for cellulose with a wide range of crystallinity, suitable for incorporation into large-scale models of lignocellulosic biomass.

Coarse-grain molecular dynamics simulations of diblock copolymer surfactants interacting with a lipid bilayer

The interaction of surfactant diblock poly(ethylene oxide)–poly(ethylethylene) copolymers (PEO–PEE) with a lipid bilayer of dimyristoylphosphatidylcholine has been studied by means of coarse-grain molecular dynamics simulations. The effect of the surfactants on the lipid bilayer was studied over a wide range of diblock copolymer concentrations. The simulations show that the hydrophilic PEO chains adopt different structures at low and high concentrations. In particular, the computed density profiles reveal that the PEO chains extend over a longer range from the bilayer surface, with increasing copolymer concentration. The simulated density profiles are in agreement with the scaling law predictions.

Nonexponentiality of time dependent survival probability and the fractional viscosity dependence of the rate in diffusion controlled reactions in a polymer chain

The simulation data presented in Fig. 8 for

The Enskog theory for transport coefficients of simple fluids with continuous potentials

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Time-dependent survival probability in diffusion-controlled reactions in a polymer chain: Beyond the Wilemski–Fixman theory

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Detection of collapsed and ordered polymer structures by fluorescence resonance energy transfer in stiff homopolymers: Bimodality in the reaction efficiency distribution

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Computational approaches to nanobiotechnology: probing the interaction of synthetic molecules with phospholipid bilayers via a coarse grain model

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