Biomedical subjects

Rajesh K Murarka

Publications and source records attributed to Rajesh K Murarka.

3 recordsLinked to original sources

PubMed2005

Molecular view of water dynamics near model peptides.

Incoherent quasi-elastic neutron scattering (QENS) has been used to measure the dynamics of water molecules in solutions of a model protein backbone, N-acetyl-glycine-methylamide (NAGMA), as a function of concentration, for comparison with results for water dynamics in aqueous solutions of the N-acetyl-leucine-methylamide (NALMA) hydrophobic peptide at comparable concentrations. From the analysis of the elastic incoherent structure factor, we find significant fractions of elastic intensity at high and low concentrations for both solutes, which corresponds to a greater population of protons with rotational time scales outside the experimental resolution (>13 ps). The higher-concentration solutions show a component of the elastic fraction that we propose is due to water motions that are strongly coupled to the solute motions, while for low-concentration solutions an additional component is activated due to dynamic coupling between inner and outer hydration layers. An important difference between the solute types at the highest concentration studied is found from stretched exponential fits to their experimental intermediate scattering functions, showing more pronounced anomalous diffusion signatures for NALMA, including a smaller stretched exponent beta and a longer structural relaxation time tau than those found for NAGMA. The more normal water diffusion exhibited near the hydrophilic NAGMA provides experimental support for an explanation of the origin of the anomalous diffusion behavior of NALMA as arising from frustrated interactions between water molecules when a chemical interface is formed upon addition of a hydrophobic side chain, inducing spatial heterogeneity in the hydration dynamics in the two types of regions of the NALMA peptide. We place our QENS measurements on model biological solutes in the context of other spectroscopic techniques and provide both confirming as well as complementary dynamic information that attempts to give a unifying molecular view of hydration dynamics signatures near peptides and proteins.

Diffusion↗

PubMed2003

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 in both size and mass. The temperature dependence of dynamical properties such as the viscosity (eta) 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 equation. Within the temperature range investigated, the value of Angell's fragility parameter (D approximately 1.4) classifies the present system as a very fragile liquid. The critical temperature for diffusion (T(D(i))(o)) increases with the size of the particles. The critical temperature for viscosity (T(eta)(o)) is larger than that for diffusion, and sizable deviations appear for the smaller size particles, implying a decoupling of translational diffusion from viscosity in deeply supercooled liquids. 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.

Journal Article↗

PubMed2003

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 nonideal glass-forming binary Lennard-Jones mixture. Here atom B is smaller than atom A (sigma(BB)=0.88sigma(AA), where sigma(AA) is the molecular diameter of the A particles) and the AB interaction is stronger than that given by Lorentz-Berthelot mixing rule (epsilon(AB)=1.5epsilon(AA), where epsilon(AA) is the interaction energy strength between the A particles). 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(BB)(R)>D(AB)(R)>D(AA)(R), with D(BB)(R) approximately 2D(AA)(R), showing the importance of the hopping process (B hops much more than A). We introduce a non-Gaussian parameter [alpha(P)(2)(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 degrees for the three pairs. A simple mean-field (MF) model, proposed originally by Haan [Phys. Rev. A 20, 2516 (1979)] for one-component liquid, is applied to the case of a binary mixture and compared with the simulation results. While the MF model successfully describes the dynamics of the AA and AB pairs, 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 the next nearest neighbor pairs is also investigated.

Journal Article↗