Biomedical subjects

Martin Grant

Publications and source records attributed to Martin Grant.

9 recordsLinked to original sources

PubMed2006

Rupture of an extended object: a many-body Kramers calculation.

We show how an extended object's strain field is redistributed when the material ruptures under by thermal activation. Through analytical calculations and molecular dynamics simulations, we show that in a polymer chain the distribution is exponentially localized around the point of rupture. The length scale of localization is determined by the strain and microscopic parameters of the interaction potential. We also derive an analytic expression for the rate of bond rupture by consistently treating the collective modes of the chain and the effect of dissipation on those modes. Our theoretical estimates are of the same order of magnitude as those obtained by simulations, as compared to earlier theories which had overestimated the rate of rupture by approximately two orders of magnitude. It is also noteworthy that the correction comes about through the effective attempt frequency rather than the effective barrier height.

Journal Article↗

PubMed2006

Designable structures are easy to unfold.

We study the structural stability of models of proteins for which the selected folds are unusually stable to mutation, that is, designable. A two-dimensional hydrophobic-polar lattice model was used to determine designable folds and these folds were investigated through Langevin dynamics. We find that the phase diagram of these proteins depends on their designability. In particular, highly designable folds are found to be weaker, i.e., easier to unfold, than low designable ones. We expect this to be related to protein flexibility.

Amino Acid Sequence↗

PubMed2005

Phase separation of a binary fluid in the inertia-dominated regime.

The phase separation kinetics of a binary fluid is studied analytically through an effective one-fluid model with a random force spectrum determined self-consistently: the rate of kinetic energy injection by the random force is consistent with the droplet coalescence rate. Our detailed results for the rates of energy dissipation and kinetic energy decay are consistent with previous numerical studies. We find that simple nontrivial scaling, if any, is associated with a new universality class where the velocity length scale follows .

Journal Article↗

PubMed2005

Scaling in force spectroscopy of macromolecules.

We use molecular dynamics to determine the force needed to rupture a chain molecule being stretched at constant loading rate and temperature. When all energy bonds of the molecule are identical, we find that the force F depends on the pulling rate r and temperature T according to F approximately const- T(1/3)|ln (r/T)|(1/3). When a single weak bond is introduced, this result is modified to F approximately const - T(2/3|ln (r/T)(2/3)|. This scaling, which is model independent, can be used with experiment to quantitatively extract relevant microscopic parameters.

Animals↗

PubMed2004

Modeling elastic and plastic deformations in nonequilibrium processing using phase field crystals.

A continuum field theory approach is presented for modeling elastic and plastic deformation, free surfaces, and multiple crystal orientations in nonequilibrium processing phenomena. Many basic properties of the model are calculated analytically, and numerical simulations are presented for a number of important applications including, epitaxial growth, material hardness, grain growth, reconstructive phase transitions, and crack propagation.

Journal Article↗

PubMed2003

Seaweed to dendrite transition in directional solidification.

We simulate directional solidification using a phase-field model solved with adaptive mesh refinement. For small surface tension anisotropy directed at 45 degrees relative to the pulling direction we observe a crossover from a seaweed to a dendritic morphology as the thermal gradient is lowered, consistent with recent experimental findings. We show that the morphology of crystal structures can be unambiguously characterized through the local interface velocity distribution. We derive semiempirically an estimate for the crossover from seaweed to dendrite as a function of thermal gradient and pulling speed.

Journal Article↗

PubMed2002

Instabilities and resistance fluctuations in thin accelerated superconducting rings.

The nonequilibrium properties of a driven quasi-one-dimensional superconducting ring subjected to a constant electromotive force (emf) is studied. The emf accelerates the superconducting electrons until the critical current is reached and a dissipative phase slip occurs that lowers the current. The phase-slip phenomena is examined as a function of the strength of the emf, thermal noise, and normal state resistivity. Numerical and analytic methods are used to make detailed predictions for the magnitude of phase slips and subsequent dissipation.

Journal Article↗

PubMed2002

Modeling elasticity in crystal growth.

A new model of crystal growth is presented that describes the phenomena on atomic length and diffusive time scales. The former incorporates elastic and plastic deformation in a natural manner, and the latter enables access to time scales much larger than conventional atomic methods. The model is shown to be consistent with the predictions of Read and Shockley for grain boundary energy, and Matthews and Blakeslee for misfit dislocations in epitaxial growth.

Journal Article↗

PubMed2002

Lattice Boltzmann method for viscoelastic fluids.

A lattice Boltzmann model for viscoelastic flow simulation is proposed. Elastic effects are taken into account within the framework of a Maxwell model. To test the approach, we estimate the transverse velocity autocorrelation function for a freely evolving system, and find clear manifestations of shear at large frequencies. We then characterize boundary-driven shear waves, and the resonant enhancement of shear oscillations in a periodically driven fluid confined within a capillary. The measured shear-wave dispersion relation is compared to that obtained from the Navier-Stokes equation with a Maxwell viscoelastic term, and good agreement is obtained.

Journal Article↗