Biomedical subjects

James M Polson

Publications and source records attributed to James M Polson.

3 recordsLinked to original sources

PubMed2006

Discontinuous molecular dynamics simulation study of polymer collapse.

Discontinuous molecular dynamics simulations were used to study the coil-globule transition of a polymer in an explicit solvent. Two different versions of the model were employed, which are differentiated by the nature of monomer-solvent, solvent-solvent, and nonbonded monomer-monomer interactions. For each case, a model parameter lambda determines the degree of hydrophobicity of the monomers by controlling the degree of energy mismatch between the monomers and solvent particles. We consider a lambda-driven coil-globule transition at constant temperature. The simulations are used to calculate average static structure factors, which are then used to determine the scaling exponents of the system in order to determine the theta-point values lambda(theta) separating the coil from the globule state. For each model we construct coil-globule phase diagrams in terms of lambda and the particle density rho. Additionally, we explore for each model the effects of varying the range of the attractive interactions on the phase boundary separating the coil and globule phases. The results are analyzed in terms of a simple Flory-type theory of the collapse transition.

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PubMed2006

Equilibrium conformational dynamics of a polymer in a solvent.

Molecular dynamics simulations were used to study the conformational dynamics of a bead-spring model polymer in an explicit solvent under good solvent conditions. The dynamics of the polymer chain were investigated using an analysis of the time autocorrelation functions of the Rouse coordinates of the polymer chain. We have investigated the variation of the correlation functions with polymer chain length N, solvent density rho, and system size. The measured initial decay rates gamma(p) of the correlation functions were compared with the predictions from a theory of polymer dynamics which uses the Oseen tensor to describe hydrodynamic interactions between monomers. Over the range of chain lengths considered (N = 30-60 monomers), the predicted scaling of gamma(p) proportional to N(-3nu) was observed at high rho, where nu is the polymer scaling exponent. The predicted gamma(p) are generally higher than the measured values. This discrepancy increases with decreasing rho, as a result in the breakdown in the conditions required for the Oseen approximation. The agreement between theory and simulation at high rho improves considerably if the theoretical expression for gamma(p) is modified to avoid sum-to-integral approximations, and if the values of (R(p)2), which are used in the theory, are taken directly from the simulation rather than being calculated using approximate scaling relations. The observed finite-size scaling of gamma(p) is not quantitatively consistent with the theoretical predictions.

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PubMed2005

Simulation study of the coil-globule transition of a polymer in solvent.

Molecular dynamics simulations are used to study the coil-globule transition for a system composed of a bead-spring polymer immersed in an explicitly modeled solvent. Two different versions of the model are used, which are differentiated by the nature of monomer-solvent, solvent-solvent, and nonbonded monomer-monomer interactions. For each case, a model parameter lambda determines the degree of hydrophobicity of the monomers by controlling the degree of energy mismatch between the monomers and solvent particles. We consider a lambda-driven coil-globule transition at constant temperature. The simulations are used to calculate average static structure factors, which are then used to determine the scaling exponents of the system in order to determine the theta-point values lambdatheta separating the coil from the globule states. For each model we construct coil-globule phase diagrams in terms of lambda and the particle density rho. The results are analyzed in terms of a simple Flory-type theory of the collapse transition. The ratio of lambdatheta for the two models converges in the high density limit exactly to the value predicted by the theory in the random mixing approximation. Generally, the predicted values of lambdatheta are in reasonable agreement with the measured values at high rho, though the accuracy improves if the average chain size is calculated using the full probability distribution associated with the polymer-solvent free energy, rather than merely using the value obtained from the minimum of the free energy.

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