Biomedical subjects

Kamakshi Jagannathan

Publications and source records attributed to Kamakshi Jagannathan.

6 recordsLinked to original sources

PubMed2006

Dynamics of probes in model glassy matrices.

The dynamics of diatomic probe molecules in matrices composed of hard spheres are studied using molecular dynamics simulations. The matrix particles are connected to fixed attachment points by strings of length, l, which is varied from l-->infinity (fluid) to 0 ("glass"). The probe diffusion coefficient, D interpolates smoothly between these limits when l is changed. As l is decreased, D displays a transition from a power-law l dependence, which is well fit by the mode-coupling theory expression, to an Arrhenius l dependence. Single particle analysis shows that the hopping motion sets in for l much larger than a critical length, l(c), and Arrhenius behavior occurs when hopping becomes the dominant mode of transport. The system displays dynamic heterogeneity even though there is no growing dynamic correlation length of any kind.

Computer Simulation↗

PubMed2005

Dynamics of fluids near the consolute critical point: a molecular-dynamics study of the Widom-Rowlinson mixture.

Molecular-dynamics simulations are presented for the dynamic behavior of the Widom-Rowlinson mixture [B. Widom, and J. S. Rowlinson, J. Chem. Phys. 52, 1670 (1970)] at its critical point. This model consists of two components where like species do not interact and unlike species interact via a hard-core potential. Critical exponents are obtained from a finite-size scaling analysis. The self-diffusion coefficient shows no anomalous behavior near the critical point. The shear viscosity and thermal conductivity show no divergent behavior for the system sizes considered, although there is a significant critical enhancement. The mutual diffusion coefficient, D(AB), vanishes as D(AB) approximately xi(-1.26 +/- 0.08), where xi is the correlation length. This is different from the renormalization-group (D(AB) approximately xi(-1.065)) mode coupling theory (D(AB) approximately xi(-1)) predictions. The theories and simulations can be reconciled if we assume that logarithmic corrections to scaling are important.

Journal Article↗

PubMed2005

Integral equation theory for symmetric nonadditive hard sphere mixtures.

An integral equation theory is presented for the pair correlation functions and phase behavior of symmetric nonadditive hard sphere mixtures with hard sphere diameters given by sigma(A)(A)() = sigma(BB) = lambdad and sigma(AB) = d. This mixture exhibits a fluid-fluid phase separation into an A-rich phase and a B-rich phase at high densities. The theory incorporates, into the closure approximation, all terms that can be calculated exactly in the density expansion of the direct correlation functions. We find that the closure approximation developed in this work is accurate for the structure and phase behavior over the entire range of lambda, when compared to computer simulations, and is significantly more accurate than the previous theories.

Journal Article↗

PubMed2004

Molecular dynamics simulations of a fluid near its critical point.

We present computer simulations for the static and dynamic behavior of a fluid near its consolute critical point. We study the Widom-Rowlinson mixture, which is a two component fluid where like species do not interact and unlike species interact via a hard core repulsion. At high enough densities this fluid exhibits a second order demixing transition that is in the Ising universality class. We find that the mutual diffusion coefficient DAB vanishes as DAB approximately xi(-1.26 +/- 0.08), where xi is the correlation length. This is different from renormalization-group and mode coupling theory predictions for model H, which are DAB approximately xi(-1.065) and DAB approximately xi(-1), respectively.

Journal Article↗

PubMed2004

Diffusion of hard sphere fluids in disordered media: a molecular dynamics simulation study.

Molecular dynamic simulations are reported for the static and dynamic properties of hard sphere fluids in matrices (or media) composed of quenched hard spheres. The effect of fluid and matrix density, matrix structure, and fluid to matrix sphere size ratio on the static and dynamic properties is studied using discontinuous molecular dynamics. The matrix density has a stronger effect on the self-diffusion coefficient than the fluid density, especially at high matrix densities where the geometric constraints due to the quenched spheres are significant. When the ratio of the size of the fluid spheres to that of the matrix spheres is equal to or greater than one, the diffusion increases as the fluid density is increased, at constant total volume fraction. This trend is however reversed if the ratio is smaller than one. Different methods of generating the matrix have a very strong effect on the dynamic properties even though the static correlations are similar. An analysis of the single-chain structure factor of the particle trajectories shows a change in the particle diffusive behavior at different time scales, suggestive of a hopping mechanism, although normal diffusion is recovered at long times. At high matrix densities, there is considerable heterogeneity in the diffusion of the fluid particles. The simulations demonstrate that the correlations in the matrix play a significant role on the diffusion of fluid spheres. For example, the diffusion constant in matrices constructed by different methods can be an order of magnitude different even though the pair correlation functions are almost identical.

Journal Article↗

PubMed2002

A Monte Carlo study of the self-assembly of bacteriorhodopsin.

Bacteriorhodopsin (BR) and specific lipid molecules self-assemble into a quasi two-dimensional lattice structure known as the purple membrane (PM). In the PM, BR molecules exist in a trimeric form with lipid molecules present in the space enclosed by each trimeric unit and in the inter-trimer space. These trimeric units, which have a roughly circular cross-section, are arranged in hexagonal patterns with long-ranged crystalline order. In this work, we investigate the self-assembly of BR in the PM via Monte Carlo simulations of a two-dimensional model of the membrane and proteins. The protein molecules are modeled as 120 degrees sectors of a circle and the lipid molecules enter into the model through effective protein-protein interactions. The sectors cannot overlap with each other, and in addition to this excluded volume interaction there are site-site attractive interactions between specific points of the proteins to mimic interactions between helices on the proteins and lipid-induced interactions. At low values of the attractive well depth, the proteins are found in the monomeric form at all concentrations. At moderate and high values of the attractive well depth, trimers are formed as the concentration increases, and with a further increase in concentration the trimers organize into a hexagonal lattice. The interactions between the proteins and those induced by the intra-trimer lipids play an equally important role in the formation of trimers and the lattice. The lipids in the inter-trimer space cause the trimers to orient in a specific direction in the hexagonal crystal lattice.

Algorithms↗