Biomedical subjects

Arun Yethiraj

Publications and source records attributed to Arun Yethiraj.

At least 19 recordsLinked to original sources

PubMed2006

A Monte Carlo simulation study of branched polymers.

Monte Carlo simulations are presented for the static properties of highly branched polymer molecules. The molecules consist of a semiflexible backbone of hard-sphere monomers with semiflexible side chains, also composed of hard-sphere monomers, attached to either every backbone bead or every other backbone bead. The conformational properties and structure factor of this model are investigated as a function of the stiffness of the backbone and side chains. The average conformations of the side chains are similar to self-avoiding random walks. The simulations show that there is a stiffening of the backbone as degree of crowding is increased, for example, if the branch spacing is decreased or side chain length is increased. The persistence length of the backbone is relatively insensitive to the stiffness of the side chains over the range investigated. The simulations reproduce most of the qualitative features of the structure factor observed in experiment, although the magnitude of the stiffening of the backbone is smaller than in experiment.

Journal Article↗

PubMed2006

Anisotropic diffusion of elongated and aligned polymer chains in a nematic solvent.

The translational diffusion constant, D, of a polymer solute in a single-domain, nematic liquid crystal solvent (5CB) is measured in directions parallel and perpendicular to the nematic director using a fluorescence two-beam, cross-correlation technique. The solute under investigation is the stiff, conjugated polymer, MEH-PPV. The ratio D parallel/D perpendicular) of diffusion constants (parallel and perpendicular to the director) is observed to be 1.9 +/- 0.3. This is surprisingly small considering that MEH-PPV is known to be both elongated and highly aligned along the liquid crystal director of 5CB. We therefore argue that the structural order parameter of the solvent governs the anisotropy of the diffusion of the solute.

Journal Article↗

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↗

PubMed2006

Lateral diffusion and percolation in membranes.

An algorithm based on Voronoi tessellation and percolation theory is presented to study the diffusion of model membrane components (solutes) in the plasma membrane. The membrane is modeled as a two-dimensional space with integral membrane proteins as static obstacles. The Voronoi diagram consists of vertices, which are equidistant from three matrix obstacles, joined by edges. An edge between two vertices is said to be connected if solute particles can pass directly between the two regions. The percolation threshold, pc, determined using this passage criterion is pc approximately equal to 0.53. This is smaller than if the connectivity of edges were assigned randomly, in which case the percolation threshold pr=2/3, where p is the fraction of connected edges. Molecular dynamics simulations show that diffusion is determined by percolation of clusters of edges.

Algorithms↗

PubMed2006

A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL.

The gating pathways of mechanosensitive channels of large conductance (MscL) in two bacteria (Mycobacterium tuberculosis and Escherichia coli) are studied using the finite element method. The phenomenological model treats transmembrane helices as elastic rods and the lipid membrane as an elastic sheet of finite thickness; the model is inspired by the crystal structure of MscL. The interactions between various continuum components are derived from molecular-mechanics energy calculations using the CHARMM all-atom force field. Both bacterial MscLs open fully upon in-plane tension in the membrane and the variation of pore diameter with membrane tension is found to be essentially linear. The estimated gating tension is close to the experimental value. The structural variations along the gating pathway are consistent with previous analyses based on structural models with experimental constraints and biased atomistic molecular-dynamics simulations. Upon membrane bending, neither MscL opens substantially, although there is notable and nonmonotonic variation in the pore radius. This emphasizes that the gating behavior of MscL depends critically on the form of the mechanical perturbation and reinforces the idea that the crucial gating parameter is lateral tension in the membrane rather than the curvature of the membrane. Compared to popular all-atom-based techniques such as targeted or steered molecular-dynamics simulations, the finite element method-based continuum-mechanics framework offers a unique alternative to bridge detailed intermolecular interactions and biological processes occurring at large spatial scales and long timescales. It is envisioned that such a hierarchical multiscale framework will find great value in the study of a variety of biological processes involving complex mechanical deformations such as muscle contraction and mechanotransduction.

Cell Membrane↗

PubMed2006

Dynamics of chain molecules in disordered materials.

The dynamic behavior of hard chains in disordered materials composed of fixed hard spheres is studied using discontinuous molecular dynamics simulations. The matrix induces entanglements in the chain fluid, i.e., for high matrix densities the diffusion coefficient D scales with the chain length N as D is approximately N(-2). At high matrix densities the rotational relaxation time becomes very large but the translational diffusion is not affected significantly; i.e., the chains display a dynamic heterogeneity reminiscent of probe diffusion in supercooled liquids and glasses. We show that this is because some chains are trapped, and move via a hopping mechanism. There are no signatures of this dynamic heterogeneity in the matrix static structure, however, which is identical to that of a hard-sphere liquid.

Journal Article↗

PubMed2006

Orthogonal orientations for solvation of polymer molecules in smectic solvents.

We explore the solvation of single conjugated polymer molecules in a smectic liquid crystal using single molecule spectroscopy. We find evidence for two distinct orientations for solvation: the majority of polymers are narrowly orientated parallel to the nematic director, as expected, but, unexpectedly, a second population is aligned perpendicular to the director. These molecules reside in the gaps between the layers. This latter type of solvation has not been previously observed and is not expected when the density variation along the director is sinusoidal.

Journal Article↗

PubMed2005

Integral equation theory of randomly coupled multiblock copolymer melts: effect of block size on the phase behavior.

The phase behavior of randomly coupled multiblock copolymer melts is studied using the polymer reference interaction site model integral equation theory. The molecules are modeled as flexible chains with random sequences of two types of blocks, each of which consists of the same number (R) of monomer beads. In the random copolymer (R=1) limit the theory predicts macrophase separation as the temperature is decreased for all values of the monomer correlation length lambda. For R>2, however, the theory predicts a microphase separation for values of lambda less than some critical value which increases as the block size increases.

Journal Article↗

PubMed2005

Molecular-dynamics simulations for nonclassical kinetics of diffusion-controlled bimolecular reactions.

Molecular-dynamics simulations are presented for the diffusion-controlled bimolecular reaction A+B<==>C in two and three dimensions. The reactants and solvent molecules are modeled as spheres interacting via continuous potential-energy functions. The interaction potential between two reactants contains a deep well that results in a reaction. When the solvent concentration is low and the reactant dynamics is essentially ballistic, the system reaches equilibrium rapidly, and the reaction follows classical kinetics with exponential decay to the equilibrium. When the solvent concentration is high the particles enter the normal diffusion regime quickly and nonclassical behavior is observed, i.e., the reactant concentrations approach equilibrium as t(-d/2) where d is the dimensionality of space. When the reaction well depth is large, however, the reaction becomes irreversible within the simulation time. In this case the reactant concentrations decay as t(-d/4). Interestingly this behavior is also observed at intermediate times for reversible reactions.

Journal Article↗

PubMed2005

Monte Carlo simulation and self-consistent integral equation theory for polymers in quenched random media.

The conformational properties and static structure of freely jointed hard-sphere chains in matrices composed of stationary hard spheres are studied using Monte Carlo simulations and integral equation theory. The simulations show that the chain size is a nonmonotonic function of the matrix density when the matrix spheres are the same size as the monomers. When the matrix spheres are of the order of the chain size the chain size decreases monotonically with increasing matrix volume fraction. The simulations are used to test the replica-symmetric polymer reference interaction site model (RSP) integral equation theory. When the simulation results for the intramolecular correlation functions are input into the theory, the agreement between theoretical predictions and simulation results for the pair-correlation functions is quantitative only at the highest fluid volume fractions and for small matrix sphere sizes. The RSP theory is also implemented in a self-consistent fashion, i.e., the intramolecular and intermolecular correlation functions are calculated self-consistently by combining a field theory with the integral equations. The theory captures qualitative trends observed in the simulations, such as the nonmonotonic dependence of the chain size on media fraction.

Journal Article↗

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 of random copolymer melts: self-consistent treatment of intramolecular and intermolecular correlations.

A self-consistent integral equation theory is presented for the conformational properties and spinodal lines of random copolymer melts. The theory combines field-theoretic methods with the polymer reference interaction site model (PRISM) theory. The many-chain problem is replaced by a single chain where the sites interact via a bare plus a self-consistently determined medium-induced potential, and the conformational properties are obtained using a variational method. The theoretical prediction for the spinodal line is qualitatively similar to that of non-self-consistent PRISM theory. The theory predicts macroscopic phase separation for all values of the monomer correlation strength, lambda. The inverse spinodal temperature is a nonmonotonic function of lambda with a maximum at lambda(max). For large values of lambda( approximately 1), the values of spinodal temperatures are almost identical to those of non-self-consistent PRISM theory. For low values of lambda, however, the theory predicts higher values for spinodal temperatures than non-self-consistent PRISM theory. The theory predicts significant changes in the mean-square end-to-end distance as the temperature is decreased.

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↗

PubMed2005

Integral equation theory for two-dimensional polymer melts.

The polymer reference interaction site model theory is investigated for two-dimensional polymer melts composed of freely-jointed hard disk chains and tangent-disk rods. Exact results for the intramolecular pair correlation functions are input into the theory, and predictions of the theory for the intermolecular pair correlation functions are tested via comparison with simulation. The theory is not as accurate for this system as it is for three-dimensional polymer melts, and the quantitative predictions are not good except at the highest area fractions. Possible reasons for the deficiency in the theory are discussed.

Journal Article↗

PubMed2004

Self-consistent mode-coupling theory for the viscosity of rodlike polyelectrolyte solutions.

A self-consistent mode-coupling theory is presented for the viscosity of solutions of charged rodlike polymers. The static structure factor used in the theory is obtained from polymer integral equation theory; the Debye-Huckel approximation is inadequate even at low concentrations. The theory predicts a nonmonotonic dependence of the reduced excess viscosity eta(R) on concentration from the behavior of the static structure factor in polyelectrolyte solutions. The theory predicts that the peak in eta(R) occurs at concentrations slightly lower than the overlap threshold concentration, c*. The peak height increases dramatically with increasing molecular weight and decreases with increased concentrations of added salt. The position of the peak, as a function of concentration divided by c*, is independent of salt concentration or molecular weight. The predictions can be tested experimentally.

Journal Article↗

PubMed2004

The behavior of fluids near solutes: a density functional theory and computer simulation study.

The density distribution of solvent near a solute particle is studied using density functional theory and Monte Carlo simulation. The fluid atoms interact with each other via a hard sphere plus Yukawa potential, and interact with the solute via a hard sphere potential. For small solute sizes, the solvent displays liquidlike ordering near the particle. When the solute become larger, a drying transition is observed at state points near the coexistence conditions of the solvent. These predictions are similar to those of a recent theory for the hydrophobic effect by Lum, Chandler, and Weeks [J. Phys. Chem. 103, 4570 (1999)], although a comparison with simulations shows that the theory of this work is quantitatively more accurate. The connection between density functional methods and the LCW approach is also established.

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↗