arXiv subjects

Stephen Pankavich

Publications and source records attributed to Stephen Pankavich.

52 records · Page 3Linked to original sources

arXiv2013

Hierarchical Multiscale Modeling of Macromolecules and their Assemblies

Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character of such systems often makes traditional molecular dynamics simulation impractical, a multiscale approach has been presented that allows for long-time simulation with atomic detail based on the co-evolution of slowly-varying order parameters (OPs) with the quasi-equilibrium probability density of atomic configurations. However, this approach breaks down when the structural change is extreme, or when nearest-neighbor connectivity of atoms is not maintained. In the current study, a self-consistent approach is presented wherein OPs and a reference structure co-evolve slowly to yield long-time simulation for dynamical soft-matter phenomena such as structural transitions and self assembly. The development begins with the Liouville equation for N classical atoms and an ansatz on the form of the associated N-atom probability density. Multiscale techniques are used to derive Langevin equations for the coupled OP configurational dynamics. The net result is a set of equations for the coupled stochastic dynamics of the OPs and centers of mass of the subsystems that constitute a soft material body. The theory is based on an all-atom methodology and an interatomic force field, and therefore enables calibration-free simulations of soft matter, such as macromolecular assemblies.

cond-mat.soft↗

arXiv2012

Multiscale Theory of Finite Size Bose Systems: Implications for Collective and Single-Particle Excitations

Boson droplets (i.e., dense assemblies of bosons at low temperature) are shown to mask a significant amount of single-particle behavior and to manifest collective, droplet-wide excitations. To investigate the balance between single-particle and collective behavior, solutions to the wave equation for a finite size Bose system are constructed in the limit where the ratio \varepsilon of the average nearest-neighbor boson distance to the size of the droplet or the wavelength of density disturbances is small. In this limit, the lowest order wave function varies smoothly across the system, i.e., is devoid of structure on the scale of the average nearest-neighbor distance. The amplitude of short range structure in the wave function is shown to vanish as a power of \varepsilon when the interatomic forces are relatively weak. However, there is residual short range structure that increases with the strength of interatomic forces. While the multiscale approach is applied to boson droplets, the methodology is applicable to any finite size bose system and is shown to be more direct than field theoretic methods. Conclusions for Helium-4 nanodroplets are drawn.

math-ph↗

arXiv2011

Time Decay for solutions to One-Dimensional Two-Component Plasma Equations

We represent three generations of students: Bob Glassey, Walter's student finishing at Brown in 1972, Jack Schaeffer, Bob's student finishing at Indiana University in 1983, and Steve Pankavich, Jack's student finishing at Carnegie Mellon in 2005. We have all thrived professionally from our association with Walter and are delighted to dedicate this note to him on the occasion of his 70th birthday. The problem we study concerns the asymptotic behavior of solutions to Vlasov equations, an area to which Walter has contributed greatly.

math.AP↗

arXiv2011

Multiscaling for Systems with a Broad Continuum of Characteristic Lengths and Times: Structural Transitions in Nanocomposites

The multiscale approach to N-body systems is generalized to address the broad continuum of long time and length scales associated with collective behaviors. A technique is developed based on the concept of an uncountable set of time variables and of order parameters (OPs) specifying major features of the system. We adopt this perspective as a natural extension of the commonly used discrete set of timescales and OPs which is practical when only a few, widely-separated scales exist. The existence of a gap in the spectrum of timescales for such a system (under quasiequilibrium conditions) is used to introduce a continuous scaling and perform a multiscale analysis of the Liouville equation. A functional-differential Smoluchowski equation is derived for the stochastic dynamics of the continuum of Fourier component order parameters. A continuum of spatially non-local Langevin equations for the OPs is also derived. The theory is demonstrated via the analysis of structural transitions in a composite material, as occurs for viral capsids and molecular circuits.

physics.bio-ph↗

arXiv2010

Self-Assembly of Nanocomponents into Composite Structures: Derivation and Simulation of Langevin Equations

The kinetics of the self-assembly of nanocomponents into a virus, nanocapsule, or other composite structure is analyzed via a multiscale approach. The objective is to achieve predictability and to preserve key atomic-scale features that underlie the formation and stability of the composite structures. We start with an all-atom description, the Liouville equation, and the order parameters characterizing nanoscale features of the system. An equation of Smoluchowski type for the stochastic dynamics of the order parameters is derived from the Liouville equation via a multiscale perturbation technique. The self-assembly of composite structures from nanocomponents with internal atomic structure is analyzed and growth rates are derived. Applications include the assembly of a viral capsid from capsomers, a ribosome from its major subunits, and composite materials from fibers and nanoparticles. Our approach overcomes errors in other coarse-graining methods which neglect the influence of the nanoscale configuration on the atomistic fluctuations. We account for the effect of order parameters on the statistics of the atomistic fluctuations which contribute to the entropic and average forces driving order parameter evolution. This approach enables an efficient algorithm for computer simulation of self-assembly, whereas other methods severely limit the timestep due to the separation of diffusional and complexing characteristic times. Given that our approach does not require recalibration with each new application, it provides a way to estimate assembly rates and thereby facilitate the discovery of self-assembly pathways and kinetic dead-end structures.

physics.chem-ph↗

arXiv2010

Decay in Time for a One-Dimensional Two-Component Plasma

The motion of a collisionless plasma is described by the Vlasov-Poisson system, or in the presence of large velocities, the relativistic Vlasov-Poisson system. Both systems are considered in one space and one momentum dimension, with two species of oppositely charged particles. A new identity is derived for both systems and is used to study the behavior of solutions for large times.

math.AP↗

arXiv2010

Local Existence for the One-dimensional Vlasov-Poisson System with Infinite Mass

A collisionless plasma is modeled by the Vlasov-Poisson system in one dimension. We consider the situation in which mobile negative ions balance a fixed background of positive charge, which is independent of space and time, as x tends to positive or negative infinity. Thus, the total positive charge and the total negative charge are both infinite. Smooth solutions with appropriate asymptotic behavior are shown to exist locally in time, and criteria for the continuation of these solutions are established.

math.AP↗

arXiv2010

Explicit Solutions of the One-dimensional Vlasov-Poisson System with Infinite Mass and Energy

A collisionless plasma is modeled by the Vlasov-Poisson system in one-dimension. A fixed background of positive charge, dependent only upon velocity, is assumed and the situation in which the mobile negative ions balance the positive charge as x tends to positive or negative infinity. Thus, the total positive charge and the total negative charge are infinite. In this paper, the charge density of the system is shown to be compactly supported. More importantly, both the electric field and the number density are determined explicitly for large values of x.

math.AP↗

arXiv2010

Multiscaling for Classical Nanosystems: Derivation of Smoluchowski and Fokker-Planck Equations

Using multiscale analysis and methods of statistical physics, we show that a solution to the N-atom Liouville Equation can be decomposed via an expansion in terms of a smallness parameter epsilon, wherein the long scale time behavior depends upon a reduced probability density that is a function of slow-evolving order parameters. This reduced probability density is shown to satisfy the Smoluchowski equation up to order epsilon squared for a given range of initial conditions. Furthermore, under the additional assumption that the nanoparticle momentum evolves on a slow time scale, we show that this reduced probability density satisfies a Fokker-Planck equation up to the same order in epsilon. This approach applies to a broad range of problems in the nanosciences.

cond-mat.mes-hall↗

arXiv2010

Stochastic Dynamics of Bionanosystems: Multiscale Analysis and Specialized Ensembles

An approach for simulating bionanosystems, such as viruses and ribosomes, is presented. This calibration-free approach is based on an all-atom description for bionanosystems, a universal interatomic force field, and a multiscale perspective. The supramillion-atom nature of these bionanosystems prohibits the use of a direct molecular dynamics approach for phenomena like viral structural transitions or self-assembly that develop over milliseconds or longer. A key element of these multiscale systems is the cross-talk between, and consequent strong coupling of, processes over many scales in space and time. We elucidate the role of interscale cross-talk and overcome bionanosystem simulation difficulties with automated construction of order parameters (OPs) describing supra-nanometer scale structural features, construction of OP dependent ensembles describing the statistical properties of atomistic variables that ultimately contribute to the entropies driving the dynamics of the OPs, and the derivation of a rigorous equation for the stochastic dynamics of the OPs. Since the atomic scale features of the system are treated statistically, several ensembles are constructed that reflect various experimental conditions. The theory provides a basis for a practical, quantitative bionanosystem modeling approach that preserves the cross-talk between the atomic and nanoscale features. A method for integrating information from nanotechnical experimental data in the derivation of equations of stochastic OP dynamics is also introduced.

cond-mat.stat-mech↗

arXiv2010

Global Existence for the Vlasov-Poisson System with Steady Spatial Asymptotics

A collisionless plasma is modeled by the Vlasov-Poisson system in three space dimensions. A fixed background of positive charge - dependant upon only velocity - is assumed. The situation in which mobile negative ions balance the positive charge as x tends to infinity is considered. Thus, the total positive charge and the total negative charge are both infinite. Smooth solutions with appropriate asymptotic behavior for large x, which were previously shown to exist locally in time, are continued globally. This is done by showing that the charge density decays at least as fast as x^{-6}. This article also establishes spatial decay estimates for the electrostatic field and its derivatives.

math.AP↗

arXiv2010

Global Existence and Increased Spatial Decay for the Radial Vlasov-Poisson System with Steady Spatial Asymptotics

A collisionless plasma is modeled by the Vlasov-Poisson system in three space dimensions. A fixed background of positive charge, which is independent of time and space, is assumed. The situation in which mobile negative ions balance the positive charge as x tends to infinity is considered. Hence the total positive charge, total negative charge, and total energy are all infinite. Smooth solutions with appropriate asymptotic behavior for large x, which were previously shown to exist locally in time, are continued globally for spherically symmetric data. This is done by showing that the charge density decays at least as fast as x^{-4}. Finally, an increased decay rate of x^{-6} is shown in the general case without the assumption of spherical symmetry.

math.AP↗

arXiv2010

Liquid-Crystal Transitions: A First Principles Multiscale Approach

A rigorous theory of liquid-crystal transitions is developed starting from the Liouville equation. The starting point is an all-atom description and a set of order parameter field variables that are shown to evolve slowly via Newton's equations. The separation of timescales between that of atomic collisions and the order parameter fields enables the derivation of rigorous equations for stochastic order parameter field dynamics. When the fields provide a measure of the spatial profile of the probability of molecular position, orientation, and internal structure, a theory of liquid-crystal transitions emerges. The theory uses the all-atom/continuum approach developed earlier to obtain a functional generalization of the Smoluchowski equation wherein key atomic details are embedded. The equivalent non-local Langevin equations are derived and computational aspects are discussed. The theory enables simulations that are much less computationally intensive than molecular dynamics and thus does not require oversimplification of the system's constituent components. The equations obtained do not include factors that require calibration and can thus be applicable to various phase transitions which overcomes the limitations of phenomenological field models. The relation of the theory to phenomenological descriptions of Nematic and Smectic phase transitions, and the possible existence of other types of transitions involving intermolecular structural parameters are discussed.

cond-mat.soft↗

arXiv2010

A Particle Method for a Collisionless Plasma with Infinite Mass

The one-dimensional Vlasov-Poisson system is considered and a particle method is developed to approximate solutions without compact support which tend to a fixed background of charge as $| x | \to \infty$. Such a system of equations can be used to model kinetic phenomena occurring in plasma physics, such as the solar wind. The particle method is constructed, implemented, and used to determine information regarding the time asymptotics of the electrostatic field.

math.NA↗

arXiv2009

Large Time Behavior of the Relativistic Vlasov Maxwell System in Low Space Dimension

When particle speeds are large the motion of a collisionless plasma is modeled by the relativistic Vlasov Maxwell system. Large time behavior of solutions which depend on one position variable and two momentum variables is considered. In the case of a single species of charge it is shown that there are solutions for which the charge density does not decay in time. This is in marked contrast to results for the non-relativistic Vlasov Poisson system in one space dimension. The case when two oppositely charged species are present and the net total charge is zero is also considered. In this case, it is shown that the support in the first component of momentum can grow at most like t to the three-fourths power.

math.AP↗

arXiv2009

On long-time behavior of monocharged and neutral plasma in one and one-half dimensions

The motion of a collisionless plasma - a high-temperature, low-density, ionized gas - is described by the Vlasov-Maxwell system. In the presence of large velocities, relativistic corrections are meaningful, and when symmetry of the particle densities is assumed this formally becomes the relativistic Vlasov-Poisson system. These equations are considered in one space dimension and two momentum dimensions in both the monocharged (i.e., single species of ion) and neutral cases. The behavior of solutions to these systems is studied for large times, yielding estimates on the growth of particle momenta and a lower bound, uniform-in-time, on norms of the charge density. We also present similar results in the same dimensional settings for the classical Vlasov-Poisson system, which excludes relativistic effects.

math.AP↗