Biomedical subjects

Cameron F Abrams

Publications and source records attributed to Cameron F Abrams.

6 recordsLinked to original sources

PubMed2007

Simulations of chemotaxis and random motility in 2D random porous domains.

We discuss a generic computational model of eukariotic chemotaxis in 2D random porous domains. The model couples the fully time-dependent finite-difference solution of a reaction-diffusion equation for the concentration field of a chemoattractant to biased random walks representing individual chemotactic cells. We focus in particular on the influence of consumption of chemoattractant by the boundaries of obstacles with irregular shapes which are distributed randomly in the domain on the chemotactic response of the cells. Cells are stimulated to traverse a field of obstacles by a line source of chemoattractant. We find that the reactivity of the obstacle boundaries with respect to the chemoattractant strongly determines the transit time of cells through two primary mechanisms. The channeling effect arises because cells are effectively repelled from surfaces which consume chemoattractant, and opposing surfaces therefore act to keep cells in the middle of channels. This reduces traversal times relative to the case with unreactive boundaries, provided that the appropriate Péclet number relating the strength of reactivity to diffusion in governing chemoattractant transport is neither too low nor too high. The dead-zone effect arises due to a realistic threshold on the chemotactic response, which at steady state results in portions of the domain having no detectable gradient. Of these two, the channeling effect is responsible for 90% of the sensitivity of transit times to boundary reactivity. Based on these results, we speculate that it may be possible to tune the rates of cellular penetration into porous domains by engineering the reactivity of the internal surfaces to cytokines.

Chemotactic Factors↗

PubMed2005

Concurrent dual-resolution Monte Carlo simulation of liquid methane.

We conduct molecular simulations of liquid methane in a system where molecular resolution fluctuates between atomically explicit and spherically symmetric united atoms. An appropriate dual-resolution canonical ensemble is constructed using (a) effective united atom pair potentials and (b) resolution-control potentials that confine explicit and united atoms chiefly to different slabs in the simulation domain. A Monte Carlo simulation is developed to sample this ensemble. We show that compatibility of the united-atom potentials with the explicit potentials in a concurrent simulation can be tuned by adjusting the width of the interface between the two resolution regions and by direct modification of the united-atom pair potentials. Our results lay the groundwork for treatment of larger atomically specific molecules with similar concurrent multiresolution techniques.

Journal Article↗

PubMed2005

Chemotaxis and random motility in unsteady chemoattractant fields: a computational study.

We discuss a generic computational model which captures the effects of transient chemoattractant concentration on the chemotactic motility of individual cells. The model solves the appropriate unsteady chemoattractant transport equation using finite differences, while simultaneously executing biased random walks representing individual cells. The simulations were implemented for a 2D homogeneous domain, and two case studies were considered. In the first case study, we consider a single-point source at the origin of the domain which produces chemoattractant, while other cells execute biased random walks toward this point source. We observe that for continuous chemoattractant production, chemoattractant diffusivity has no effect on cell motility, as measured by the mean of time to reach the source. However, in the case of pulsed random production with a specific average duty cycle, the mean time-to-contact is generally minimal with respect to chemoattractant diffusivity over a moderate range of diffusivities. In the second case study, two mobile cells which simultaneously secrete chemoattractant are initially placed a certain distance apart and are then allowed to execute biased random walks. Our model shows that a pulsed random protocol for chemoattractant production facilitates the two cells "finding" one another compared to continuous production. From this case study we also learn that there exists a range of moderate chemoattractant diffusivities for which the mean time-to-contact is minimal when cells both produce/detect chemoattractant and chemotactically migrate. Using these case studies, we discuss how transience in chemoattractant concentration becomes important in characterizing the effectiveness of chemotaxis.

Algorithms↗

PubMed2004

Kinetics of a polysoap collapse.

We study the dynamics of collapse of a polysoap by means of large-scale molecular dynamics simulation and scaling arguments. A polysoap consists of a hydrophilic backbone and hydrophobic side chains attached at regular intervals along the backbone. In selective solvent conditions, the hydrophobic components aggregate, forcing the hydrophilic backbone to form loops anchored at the surface of the core, ultimately forming a micelle. The kinetics of polysoap collapse includes two major mechanisms: (1) early aggregation of the hydrophobic side chains controlled by first-order kinetics whose rate constant is given by a contact probability and (2) coalescence into larger clusters which requires activation to overcome energy barriers due to excluded volume repulsions between intermediate micelle coronas. In the late stage, the energy barrier is increasing as p(3/2), with p the number of aggregated side chains in an intermediate micelle. The corresponding late-stage rate constant decays exponentially as approximately exp(-p(3/2)).

Computer Simulation↗

PubMed2003

Arrested swelling of highly entangled polymer globules.

Upon aging, a collapsed long chain evolves from a crumpled state to a self-entangled globule which can be thought of as a large knot. Swelling of an equilibrium globule in good solvent is a two-step process: (i) fast swelling into an arrested stretched structure with conserved entanglement topology followed by (ii) slow disentanglement. Using computer simulation, we found both mass-mass (m-m) and entanglement-entanglement (e-e) power law correlations inside the swollen globule. The m-m correlations are characterized by a set of two exponents in agreement with a Flory-type argument. The e-e correlations are also characterized by two exponents, both of them larger (by approximately 0.3) than the related m-m exponents. We interpret this difference as evidence of distance-dependent repulsion E=-0.3ln((rho)k(B)T between entanglements sliding along the polymer chain.

Models, Chemical↗

PubMed2003

Dual-resolution coarse-grained simulation of the bisphenol-A-polycarbonate/nickel interface.

We present a dual-resolution coarse-graining scheme for efficient molecular dynamics simulations of bisphenol-A-polycarbonate (BP-A-PC) liquids in contact with a (111) nickel surface. The essential feature of this model is the strong adsorption of phenoxy chain ends, and the absence of adsorption by other parts of the chains. Details of how phenoxy chain ends interact with the nickel surface were extracted from Car-Parrinello molecular dynamics calculations of adsorption of phenol on nickel. These calculations show that phenol adsorption on nickel is short ranged (<3 A) and strongly dependent on the C1-C4 orientation of the ring. The structure of BP-A-PC prevents internal phenylene groups from interacting with the surface, due to steric hindrances from the noninteracting isopropylidenes. These dependencies are incorporated in the coarse-grained model of the BP-A-PC chain by resolving chain-terminating carbonate groups with atomistic detail, while the rest of the chain is represented by coarsened "beads." This allows specification of the C1-C4 orientation of the terminal phenoxy groups, while overall allowing for system equilibration with reasonable computer time. We simulate liquids of up to 240 chains of ten chemical repeat units, confined in a slit pore formed by two frozen (111) planes of atoms with the lattice spacing of nickel. We find that the strong adsorption of chain ends has a large effect on the liquid structure through a distance of more than two bulk radii of gyration from the surface. These effects are explained by a competition among single- and double-end adsorption, and dense packing. The structure of the interface less than 10 A from the wall is greatly sensitive to the orientational dependence of the phenoxy adsorption.

Journal Article↗