Biomedical subjects

Niharendu Choudhury

Publications and source records attributed to Niharendu Choudhury.

5 recordsLinked to original sources

PubMed2006

A molecular dynamics simulation study of buckyballs in water: atomistic versus coarse-grained models of C60.

A simple coarse-grained water-C(60) model potential is proposed to study the solvation behavior of C(60) in water. Extensive molecular dynamics simulations are performed to compare the hydration behavior of the coarse-grained C(60) with that of its atomistic counterpart. In the coarse-grained description, we model the C(60) as a spherical solute and its interaction with water is represented by a simple two-body central potential as obtained from a coarse graining of the interactions of a water molecule with all the atoms of the C(60). On the other hand, the atomistic model takes into account a discrete nature of all the atoms of C(60) explicitly. Molecular dynamics simulations are carried out in an isothermal-isobaric ensemble at normal temperature and pressure. Various spatial and orientational correlations of the water around the two model C(60)s are compared. The coarse-grained model is shown to reproduce the hydration behavior of the C(60) quite well. The simplicity and the computational economy of the coarse-grained model will allow for simulations of self-assembly processes of a much larger system over a longer period of time.

Journal Article↗

PubMed2006

Enthalpy-entropy contributions to the potential of mean force of nanoscopic hydrophobic solutes.

Entropic and enthalpic contributions to the hydrophobic interaction between nanoscopic hydrophobic solutes, modeled as graphene plates in water, have been calculated using molecular dynamics simulations in the isothermal-isobaric (NPT) ensemble with free energy perturbation methodology. We find the stabilizing contribution to the free energy of association (contact pair formation) to be the favorable entropic part, the enthalpic contribution being highly unfavorable. The desolvation barrier is dominated by the unfavorable enthalpic contribution, despite a fairly large favorable entropic compensation. The enthalpic contributions, incorporating the Lennard-Jones solute-solvent terms, largely determine the stability of the solvent separated configuration. We decompose the enthalpy into a direct solute-solute term, the solute-solvent interactions, and the remainder that contains pressure-volume work as well as contributions due to solvent reorganization. The enthalpic contribution due to changes in water-water interactions arising from solvent reorganization around the solute molecules is shown to have major contribution in the solvent induced enthalpy change.

Algorithms↗

PubMed2005

Dynamics of water trapped between hydrophobic solutes.

We describe the model dynamical behavior of the solvent between two nanoscopic hydrophobic solutes. The dynamics of the vicinal water in various sized traps is found to be significantly different from bulk behavior. We consider the dynamics at normal temperature and pressure at three intersolute distances corresponding to the three solvent separated minima in the free energy profile between the solutes with attractions. These three states correspond to one, two, and three intervening layers of water molecules. Results are obtained from a molecular dynamics simulation at constant temperature and pressure (NPT) ensemble. Translational diffusion of water molecules trapped between the two solutes has been analyzed from the velocity correlation function as well as from the mean square displacement of the water molecules. The rotational behavior has been analyzed through the reorientational dynamics of the dipole moment vector of the water molecule by calculating both first and second rank dipole-dipole correlation functions. Both the translational and reorientational mobilities of water are found to be much slower at the smaller separation and increases as the separation between solutes becomes larger. The occupation time distribution functions calculated from the trajectories also show that the relaxation is much slower for the smallest intersolute separation as compared to other wider separations. The sublinear trend in mean square displacement and the stretched exponential decay of the relaxation of dipolar correlation and occupation distribution function indicate that the dynamical behavior of water in the confined region between two large hydrophobic solutes departs from usual Brownian behavior. This behavior is reminiscent of the behavior of water in the vicinity of protein surface clefts or trapped between two domains of a protein.

Hydrophobic and Hydrophilic Interactions↗

PubMed2005

On the mechanism of hydrophobic association of nanoscopic solutes.

The hydration behavior of two planar nanoscopic hydrophobic solutes in liquid water at normal temperature and pressure is investigated by calculating the potential of mean force between them at constant pressure as a function of the solute-solvent interaction potential. The importance of the effect of weak attractive interactions between the solute atoms and the solvent on the hydration behavior is clearly demonstrated. We focus on the underlying mechanism behind the contrasting results obtained in various recent experimental and computational studies on water near hydrophobic solutes. The length scale where crossover from a solvent separated state to the contact pair state occurs is shown to depend on the solute sizes as well as on details of the solute-solvent interaction. We find the mechanism for attractive mean forces between the plates is very different depending on the nature of the solute-solvent interaction which has implications for the mechanism of the hydrophobic effect for biomolecules.

Hydrophobic and Hydrophilic Interactions↗

PubMed2002

Bridge function and other structural properties of core-softened model fluids from molecular dynamics simulations.

Molecular dynamics (MD) simulations in three dimensions have been performed for a fluid with particles interacting with a continuous version of the Stell-Hemmer core-softened potential that in two dimensions has been known to reproduce most of the static and dynamic anomalies of liquid water. The pair distribution function obtained from the MD simulation is extrapolated with the help of integral equation theory with a suitable closure relation and the bridge function is extracted. A strong dependence of the bridge function on the system size, i.e., the total number of particles (N) used in the simulation box is observed, which leads to spurious values of the structure factor at long wavelengths. A simple self-consistent correction scheme for the finite size effect has been adopted to correct the bridge function and this scheme produces the correct bridge function even for a small system size. The effects of temperature, number density, and potential parameters on the pair distribution functions and extracted bridge functions are extensively studied.

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