Biomedical subjects

D C Rapaport

Publications and source records attributed to D C Rapaport.

7 recordsLinked to original sources

PubMed2006

Hexagonal convection patterns in atomistically simulated fluids.

Molecular dynamics simulation has been used to model pattern formation in three-dimensional Rayleigh-Bénard convection at the discrete-particle level. Two examples are considered, one in which an almost perfect array of hexagonally shaped convection rolls appears, the other a much narrower system that forms a set of linear rolls; both pattern types are familiar from experiment. The nature of the flow within the convection cells and quantitative aspects of the development of the hexagonal planform based on automated polygon subdivision are analyzed. Despite the microscopic scale of the system, relatively large simulations with several million particles and integration time steps are involved.

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PubMed2004

Self-assembly of polyhedral shells: a molecular dynamics study.

The use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures, in which icosahedral symmetry is a conspicuous feature, is a phenomenon whose dynamics remain unexplored; studying the growth process by means of computer simulation provides access to the mechanisms underlying assembly. In order to capture the more universal aspects of self-assembly, namely the manner in which component shapes influence structure and assembly pathway, in this exploratory study low-resolution approximations are used to represent the basic protein building blocks. Alternative approaches involving both irreversible and reversible assembly are discussed, models based on both schemes are introduced, and examples of the resulting behavior described.

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PubMed2003

Dynamics of polymer chain collapse into compact states.

Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional interactions. Different native-state packing arrangements and chain lengths are explored; the organization of the native state is found to affect both the ability of the chain to fold successfully and the nature of the folding pathway as the system is gradually cooled. An order parameter based on contact counts is used to provide information about the folding process, with contacts additionally classified according to criteria such as core and surface sites or local and distant site pairs. Fully detailed contact maps and their evolution are also examined.

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PubMed2002

Molecular dynamics simulation of polymer helix formation using rigid-link methods.

Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under gradual cooling are followed until each reaches a state from which no further change is possible. The interactions are chosen so that the true ground state is a helix, and a high proportion of simulation runs succeed in reaching this state; the fraction that manages to form defect-free helices is a function of both chain length and cooling rate. In order to demonstrate behavior analogous to the formation of protein tertiary structure, additional attractive interactions are introduced into the model, leading to the appearance of aligned, antiparallel helix pairs. The simulations employ a computational approach that deals directly with the internal coordinates in a recursive manner; this representation is able to maintain constant bond lengths and angles without the necessity of treating them as an algebraic constraint problem supplementary to the equations of motion.

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PubMed2002

Simulational studies of axial granular segregation in a rotating cylinder.

Discrete particle simulation methods have been used to study axial segregation in a horizontal rotating cylinder that is partially filled with a mixture of two different kinds of granular particles. Under suitable conditions segregation was found to occur, with the particles separating into a series of bands perpendicular to the axis. In certain cases the band structure exhibited time-dependent behavior, including band formation, merging and motion along the axis, all corresponding to phenomena that arise experimentally. In order to examine how the many parameters specifying the problem affect the segregation process, simulation runs were carried out using a variety of parameter settings, including combinations of friction coefficients not realizable experimentally. Both segregation and desegregation (mixing) were investigated, and cylinders with both explicit end caps and periodic ends were used to help isolate the causes of segregation.

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PubMed2001

Mechanism for granular segregation.

A process is described that produces horizontal size segregation in a vertically vibrated layer of granular material. The behavior is a consequence of two distinct phenomena that are unique to excited granular media: vibration, which causes the large particles to rise to the top of the layer, and a vibrating base with a sawtooth surface profile, which can produce stratified flows in opposite directions at different heights within the layer. The result of combining these effects is that large and small particles are horizontally driven in opposite directions. The observations reported here are based on computer simulations of granular models in two and three dimensions.

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PubMed2001

Stratified horizontal flow in vertically vibrated granular layers.

A layer of granular material on a vertically vibrating sawtooth-shaped base exhibits horizontal flow whose speed and direction depend on the parameters specifying the system in a complex manner. Discrete-particle simulations reveal that the induced flow rate varies with height within the granular layer and oppositely directed flows can occur at different levels. The behavior of the overall flow is readily understood once this feature is taken into account.

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