arXiv subjects

D. C. Rapaport

Publications and source records attributed to D. C. Rapaport.

At least 19 recordsLinked to original sources

arXiv2018

Molecular dynamics study of T=3 capsid assembly

Molecular dynamics simulation is used to model the self-assembly of polyhedral shells containing 180 trapezoidal particles that correspond to the T=3 virus capsid. Three kinds of particle, differing only slightly in shape, are used to account for the effect of quasi-equivalence. Bond formation between particles is reversible and an explicit atomistic solvent is included. Under suitable conditions the simulations are able to produce complete shells, with the majority of unused particles remaining as monomers, and practically no other clusters. There are also no incorrectly assembled clusters. The simulations reveal details of intermediate structures along the growth pathway, information that is relevant for interpreting experiment.

q-bio.BM↗

arXiv2016

Packaging stiff polymers in small containers: A molecular dynamics study

The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of the system -- the DNA polymer and the spherical viral capsid -- has been studied by molecular dynamics simulation. The results, involving longer polymers than in earlier work, show that as polymers become more rigid there is an increasing tendency to self-organize as spools that wrap from the inside out, rather than the inverse direction seen previously. In the final state, a substantial part of the polymer is packed into one or more coaxial spools, concentrically layered with different orientations, a form of packaging achievable without twisting the polymer.

q-bio.BM↗

arXiv2014

Molecular dynamics simulation: a tool for exploration and discovery using simple models

Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome is not always a foregone conclusion. The present survey focuses on several simple model systems that exhibit surprisingly rich emergent behavior, all studied by MD simulation. The examples are taken from the disparate fields of fluid dynamics, granular matter and supramolecular self-assembly. In studies of fluids modeled at the detailed microscopic level using discrete particles, the simulations demonstrate that complex hydrodynamic phenomena in rotating and convecting fluids, the Taylor-Couette and Rayleigh-Bénard instabilities, can not only be observed within the limited length and time scales accessible to MD, but even quantitative agreement can be achieved. Simulation of highly counterintuitive segregation phenomena in granular mixtures, again using MD methods, but now augmented by forces producing damping and friction, leads to results that resemble experimentally observed axial and radial segregation in the case of a rotating cylinder, and to a novel form of horizontal segregation in a vertically vibrated layer. Finally, when modeling self-assembly processes analogous to the formation of the polyhedral shells that package spherical viruses, simulation of suitably shaped particles reveals the ability to produce complete, error-free assembly, and leads to the important general observation that reversible growth steps contribute to the high yield. While there are limitations to the MD approach, both computational and conceptual, the results offer a tantalizing hint of the kinds of phenomena that can be explored, and what might be discovered when sufficient resources are brought to bear on a problem.

cond-mat.soft↗

arXiv2012

Molecular dynamics simulation of reversibly self-assembling shells in solution using trapezoidal particles

The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the capsid of a T=1 virus. Growth occurs in the presence of an atomistic solvent and, under suitable conditions, achieves a high yield of complete shells. The simulations provide details of the structure and lifetime of the particle clusters that appear as intermediate states along the growth pathway, and the nature of the transitions between them. In certain respects the growth of size-60 shells from trapezoidal particles resembles the growth of icosahedral shells from triangular particles studied previously, with reversible bonding playing a major role in avoiding incorrect assembly, although the details differ due to particle shape and bond organization. The strong preference for maximal bonding exhibited by the triangular particle clusters is also apparent for trapezoidal particles, but this is now confined to early growth, and is less pronounced as shells approach completion along a variety of pathways.

cond-mat.soft↗

arXiv2011

Evaluating cumulative ascent: Mountain biking meets Mandelbrot

The problem of determining total distance ascended during a mountain bike trip is addressed. Altitude measurements are obtained from GPS receivers utilizing both GPS-based and barometric altitude data, with data averaging used to reduce fluctuations. The estimation process is sensitive to the degree of averaging, and is related to the well-known question of determining coastline length. Barometric-based measurements prove more reliable, due to their insensitivity to GPS altitude fluctuations.

physics.data-an↗

arXiv2011

Enhanced molecular dynamics performance with a programmable graphics processor

Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of scalable streaming-multiprocessor hardware necessitates a reformulation of the underlying algorithm. Performance measurements demonstrate the considerable benefit and cost-effectiveness of such an approach, which produces a factor of 2.5 speed improvement over previous work for the case of the soft-sphere potential.

physics.comp-ph↗

arXiv2010

Modeling capsid self-assembly: Design and analysis

A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms. The fact that different viruses adopt similar structural forms is an indication of a common underlying design, motivating the use of simplified, low-resolution models in exploring the assembly process. Several versions of a molecular dynamics approach are described. Polyhedral shells of different sizes are involved, the assembly pathways are either irreversible or reversible, and an explicit solvent is optionally included. Model design, simulation methodology and analysis techniques are discussed. The analysis focuses on the growth pathways and the nature of the intermediate states, properties that are hard to access experimentally. Among the key observations are that efficient growth proceeds by means of a cascade of highly reversible stages, and that while there are a large variety of possible partial assemblies, only a relatively small number of strongly bonded configurations are actually encountered.

cond-mat.soft↗

arXiv2009

Studies of reversible capsid shell growth

Results from molecular dynamics simulations of simple, structured particles capable of self-assembling into polyhedral shells are described. The analysis focuses on the growth histories of individual shells in the presence of an explicit solvent and the nature of the events along their growth pathways; the results provide further evidence of the importance of reversibility in the assembly process. The underlying goal of this approach is the modeling of virus capsid growth, a phenomenon at the submicroscopic scale that, despite its importance, is little understood.

cond-mat.soft↗

arXiv2009

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine

A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

physics.comp-ph↗

arXiv2008

Role of reversibility in viral capsid growth: A paradigm for self-assembly

Self-assembly at submicroscopic scales is an important but little understood phenomenon. A prominent example is virus capsid growth, whose underlying behavior can be modeled using simple particles that assemble into polyhedral shells. Molecular dynamics simulation of shell formation in the presence of an atomistic solvent provides new insight into the self-assembly mechanism, notably that growth proceeds via a cascade of strongly reversible steps and, despite the large variety of possible intermediates, only a small fraction of highly bonded forms appear on the pathway.

cond-mat.soft↗

arXiv2007

Microscale swimming: The molecular dynamics approach

The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in specifying the swimmer design and its coupling with the surrounding fluid. A series of two-dimensional swimming bodies employing a variety of propulsion mechanisms -- motivated by biological and microrobotic designs -- is investigated, including the use of moving limbs, changing body shapes and fluid jets. The swimming efficiency and the nature of the induced, time-dependent flow fields are found to differ widely among body designs and propulsion mechanisms.

cond-mat.soft↗

arXiv2007

Simulated three-component granular segregation in a rotating drum

Discrete particle simulations are used to model segregation in granular mixtures of three different particle species in a horizontal rotating drum. Axial band formation is observed, with medium-size particles tending to be located between alternating bands of big and small particles. Partial radial segregation also appears; it precedes the axial segregation and is characterized by an inner core region richer in small particles. Axial bands are seen to merge during the long simulation runs, leading to a coarsening of the band pattern; the relocation of particles involved in one such merging event is examined. Overall, the behavior is similar to experiment and represents a generalization of what occurs in the simpler two-component mixture.

cond-mat.soft↗

arXiv2007

Radial and axial segregation of granular matter in a rotating cylinder: A simulation study

The phenomena of radial and axial segregation in a horizontal rotating cylinder containing a mixture of granular particles of two different species have been modeled using discrete particle simulation. Space-time plots and detailed imagery provide a comprehensive description of what occurs in the system. As is the case experimentally, the nature of the segregation depends on the parameters defining the problem; the radial component of the segregation may be transient or long-lasting, and the axial component may or may not develop. Simulations displaying the different kinds of behavior are described and the particle dynamics associated with the axially segregated state examined. The importance of an appropriate choice of interaction for representing the effective friction force is demonstrated.

cond-mat.soft↗

arXiv2006

Hexagonal convection patterns in atomistically simulated fluids

Molecular dynamics simulation has been used to model pattern formation in three-dimensional Rayleigh--Benard 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 timesteps are involved.

cond-mat.other↗

arXiv2004

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.

cond-mat.soft↗

arXiv2003

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.

cond-mat.soft↗

arXiv2002

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.

cond-mat.soft↗

arXiv2002

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 manage 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.

cond-mat.soft↗