arXiv subjects

Biman Bagchi

Publications and source records attributed to Biman Bagchi.

135 records · Page 8Linked to original sources

arXiv2003

Diffusion of small light particles in a solvent of large massive molecules

We study diffusion of small light particles in a solvent which consists of large heavy particles. The intermolecular interactions are chosen to approximately mimic a water-sucrose (or water-polysaccharide) mixture. Both computer simulation and mode coupling theoretical (MCT) calculations have been performed for a solvent-to-solute size ratio five and for a large variation of the mass ratio, keeping the mass of the solute fixed. Even in the limit of large mass ratio the solute motion is found to remain surprisingly coupled to the solvent dynamics. Interestingly, at intermediate values of the mass ratio, the self-intermediate scattering function of the solute, F_{s}(k,t) (where k is the wavenumber and t the time), develops a stretching at long time which could be fitted to a stretched exponential function with a k-dependent exponent, β. For very large mass ratio, we find the existence of two stretched exponentials separated by a power law type plateau. The analysis of the trajectory shows the coexistence of both hopping and continuous motions for both the solute and the solvent particles. It is found that for mass ratio five, the MCT calculations of the self-diffusion underestimates the simulated value by about 20 %, which appears to be reasonable because the conventional form of MCT does not include the hopping mode. However, for larger mass ratio, MCT appears to breakdown more severely. The breakdown of the MCT for large mass ratio can be connected to a similar breakdown near the glass transition.

cond-mat.soft↗

arXiv2002

Evidence for Bound and Free Water Species in the Hydration Shell of an Aqueous Micelle

Our atomistic molecular dynamics simulations reveal the existence of bound and free water molecules in the hydration layer of an aqueous micelle. The bound water molecules can be either singly or doubly hydrogen bonded to the polar head group on the surface of the micelle. The ratio of bound to free water is found to be approximately equal to 9:1 at 300 K.

physics.bio-ph↗

arXiv2002

Origin of the Sub-diffusive Behavior and Crossover From a Sub-diffusive to a Super-diffusive Dynamics Near a Biological Surface

Diffusion of a tagged particle near a constraining biological surface is examined numerically by modeling the surface-water interaction by an effective potential. The effective potential is assumed to be given by an asymmetric double well constrained by a repulsive surface towards $r=0$ and unbound at large distances. The time and space dependent probability distribution $P(r,t)$ of the underlying Smoluchowski equation is solved by using Crank-Nicholson method. The mean square displacement shows a transition from sub-diffusive (exponent $α\sim$ 0.43) to a super-diffusive (exponent $α\sim$ 1.75) behavior with time and ultimately to a diffusive dynamics. The decay of self intermediate scattering function ($F_{s}(k,t)$) is non-exponential in general and shows a power law behavior at the intermediate time. Such features have been observed in several recent computer simulation studies on dynamics of water in protein and micellar hydration shell. The present analysis provides a simple microscopic explanation for the transition from the sub-diffusivity and super-diffusivity. {\em The super-diffusive behavior is due to escape from the well near the surface and the sub-diffusive behavior is due to return of quasi-free molecules to form the bound state again, after the initial escape}

cond-mat.soft↗

arXiv2002

Diffusion and viscosity in a supercooled polydisperse system

We have carried out extensive molecular dynamics simulations of a supercooled polydisperse Lennard-Jones liquid with large variations in temperature at a fixed pressure. The particles in the system are considered to be polydisperse both in size and mass. The temperature dependence of the dynamical properties such as the viscosity ($η$) and the self-diffusion coefficients ($D_i$) of different size particles is studied. Both viscosity and diffusion coefficients show super-Arrhenius temperature dependence and fit well to the well-known Vogel-Fulcher-Tammann (VFT) equation. Within the temperature range investigated, the value of the Angell's fragility parameter (D $\approx 1.4$) classifies the present system into a strongly fragile liquid. The critical temperature for diffusion ($T_o^{D_i}$) increases with the size of the particles. The critical temperature for viscosity ($T_o^η$) is larger than that for the diffusion and a sizeable deviations appear for the smaller size particles implying a decoupling of translational diffusion from viscosity in deeply supercooled liquid. Indeed, the diffusion shows markedly non-Stokesian behavior at low temperatures where a highly nonlinear dependence on size is observed. An inspection of the trajectories of the particles shows that at low temperatures the motions of both the smallest and largest size particles are discontinuous (jump-type). However, the crossover from continuous Brownian to large length hopping motion takes place at shorter time scales for the smaller size particles.

cond-mat.soft↗

arXiv2002

Contact Pair Dynamics During Folding of a Model Globular Protein, Hp-36

The dynamics of contact pair formation between various hydrophobic residues during folding of a model protein Hp-36 is investigated by Brownian dynamics simulation. Hydropathy scale and non-local helix propensity of amino acids are used to model the complex interaction potential. The resulting structure of the model protein mimics the native state of the real protein with a $RMSD$ of 4.5 Å. A contact pair distance time correlation function (CPCF), $C_{P}^{ij}(t)$, is introduced which shows multistage decay, including a {\it slow late stage dynamics} for a few specific pairs. {\it These pairs determine the long time folding rate}. Dynamics can be correlated with the landscape, relative contact order and topological contact.

cond-mat.soft↗

arXiv2002

Pair dynamics in a glass forming binary mixture: Simulations and theory

We have carried out molecular dynamics simulations to understand the dynamics of a tagged pair of atoms in a strongly non-ideal glass-forming binary Lennard-Jones mixture (commonly known as Kob-Andersen model). The generalized time-dependent pair distribution function is calculated separately for the three pairs (AA, BB and AB). The three pairs are found to behave differently. The relative diffusion constants are found to vary in the order $D_R^{BB} > D_R^{AB} > D_R^{AA}$, with $D_R^{BB} \simeq 2D_R^{AA}$, showing the importance of the hopping process (B hops much more than A). We introduce a non-Gaussian parameter ($α_2^P (t)$) to monitor the relative motion of a pair of atoms, and evaluate it for all the three pairs, with initial separations chosen to be at the first peak of the corresponding partial radial distribution functions. At intermediate times, significant deviation from the Gaussian behavior of the pair distribution functions is observed, with different degree for the three pairs. A simple mean-field (MF) model, proposed originally by Haan [Phys. Rev. A ${\bf 20}$, 2516 (1979)] for one component liquid, is applied to the case of binary mixture, and compared with the simulation results. While the MF model successfully describe the dynamics of the AA and AB pair, the agreement for the BB pair is less satisfactory. This is attributed to the large scale anharmonic motions of the B particles in a weak effective potential. Dynamics of next nearest neighbor pairs are also investigated.

physics.chem-ph↗

arXiv2002

Hydrogen Bond Dynamics Near A Micellar Surface: Origin of the Universal Slow Relaxation at Complex Aqueous Interfaces

The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a water molecule is found to be much longer than that between any two water molecules, and is likely to be a general feature of hydrophilic surfaces of organized assemblies. Analyses of individual water trajectories suggest that water molecules can remain bound to the micellar surface for more than a hundred picosecond. The activation energy for such a transition from the bound to a free state for the water molecules is estimated to be about 3.5kcal/mole.

cond-mat.soft↗

arXiv2001

Energy Transfer Efficiency Distributions in Polymers in Solution During Folding and Unfolding

Distribution of fluorescence resonance energy transfer (FRET) efficiency between the two ends of a Lennard-Jones polymer chain both at equilibrium and during folding and unfolding has been calculated, for the first time, by Brownian dynamics simulations. The distribution of FRET efficiency becomes {\bf bimodal} during folding of the extended state subsequent to a temperature quench, with the width of the distribution for the extended state broader than that for the folded state. The reverse process of unfolding subsequent to a upward temperature jump shows different characteristics. The distributions show significant viscosity dependence which can be tested against experiments.

cond-mat.stat-mech↗

arXiv2000

Re-entrant behavior of relaxation time with viscosity at varying composition in binary mixtures

In order to understand the long known anomalies in the composition dependence of diffusion and viscosity of binary mixtures, we introduce here two new models and carry out extensive molecular dynamic simulations. In these models, the two molecular species (A and B) have the same diameter and mass. In model I the inter-species interaction is more attractive than that between the pure components, while the reverse is true for model II. Simulations and also mode coupling theory calculations reveal that the models can capture a wide variety of behavior observed in experiments, most interesting among them are the non-monotonic variation of diffusion and viscosity with the composition and the re-entrant viscosity dependence of the relaxation time.

cond-mat.stat-mech↗