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A multispecies, collisionless plasma is modeled by the Vlasov-Poisson system. Assuming the plasma is neutral and the electric field decays with sufficient rapidity as $t \to\infty$, we show that solutions can be constructed with arbitrarily fast, polynomial rates of decay, depending upon the properties of the limiting spatial average and its derivatives. In doing so, we establish, for the first time, a countably infinite number of asymptotic profiles for the charge density, electric field, and their derivatives, each of which is necessarily realized by a sufficiently smooth solution and exceeds the established dispersive decay rates. Finally, in each case we establish a linear $L^\infty$ scattering result for every particle distribution function, namely we show that they converge as $t \to \infty$ along the transported spatial characteristics at increasingly faster rates., Comment: 35 pages

We consider the relativistic Vlasov-Maxwell system in three dimensions and study the limiting asymptotic behavior as $t \to \infty$ of solutions launched by small, compactly supported initial data. In particular, we prove that such solutions scatter to a modification of the free-streaming asymptotic profile. More specifically, we show that the spatial average of the particle distribution function converges to a smooth, compactly-supported limit and establish the precise, self-similar asymptotic behavior of the electric and magnetic fields, as well as, the macroscopic densities and their derivatives in terms of this limiting function. Upon constructing the limiting fields, a modified $L^\infty$ scattering result for the particle distribution function along the associated trajectories of free transport corrected by the limiting Lorentz force is then obtained. When the limiting charge density does not vanish, our estimates are sharp up to a logarithmic correction. However, when this quantity is identically zero in the limit, the limiting current density and fields may also vanish, which gives rise to decay rates that are faster than those attributed to the dispersive mechanisms in the system., Comment: 49 pages, 2 figures

We develop a multi-dimensional, parallelized domain decomposition strategy (DDC) for mass-transfer particle tracking (MTPT) methods. These methods are a type of Lagrangian algorithm for simulating reactive transport and are able to be parallelized by employing large numbers of CPU cores to accelerate run times. In this work, we investigate different procedures for "tiling" the domain in two and three dimensions, (2-d and 3-d), as this type of formal DDC construction is currently limited to 1-d. An optimal tiling is prescribed based on physical problem parameters and the number of available CPU cores, as each tiling provides distinct results in both accuracy and run time. We further extend the most efficient technique to 3-d for comparison, leading to an analytical discussion of the effect of dimensionality on strategies for implementing DDC schemes. Increasing computational resources (cores) within the DDC method produces a trade-off between inter-node communication and on-node work. For an optimally subdivided diffusion problem, the 2-d parallelized algorithm achieves nearly perfect linear speedup in comparison with the serial run up to around 2700 cores, reducing a 5-hour simulation to 8 seconds, and the 3-d algorithm maintains appreciable speedup up to 1700 cores., Comment: 26 pages, 21 figures, Submitted to Journal of Computational Physics (JCP)

We study the large time behavior of classical solutions to the two-dimensional Vlasov-Poisson (VP) and relativistic Vlasov-Poisson (RVP) systems launched by radially-symmetric initial data with compact support. In particular, we prove that particle positions and momenta grow unbounded as $t \to \infty$ and obtain sharp rates on the maximal values of these quantities on the support of the distribution function for each system. Furthermore, we establish nearly sharp rates of decay for the associated electric field, as well as upper and lower bounds on the decay rate of the charge density in the large time limit. We prove that, unlike (VP) in higher dimensions, smooth solutions do not scatter to their free-streaming profiles as $t \to \infty$ because nonlinear, long-range field interactions dominate the behavior of characteristics due to the exchange of energy from the potential to the kinetic term. In this way, the system may "forget" any previous configuration of particles., Comment: 27 pages

We consider the repulsive Vlasov-Poisson system in dimension $d \geq 4$. A sufficient condition on the decay rate of the associated electric field is presented that guarantees the scattering and determination of the complete asymptotic behavior of large data solutions as $t \to \infty$. More specifically, we show that under this condition the spatial average of the particle distribution function converges, and we establish the precise asymptotic profiles of the electric field and macroscopic densities. An $L^\infty$ scattering result for the particle distribution function along the associated trajectories of free transport is also proved. Finally, we construct small data solutions that display this asymptotic behavior. These solutions do not require smallness of $\|f_0\|_\infty$ or derivatives, as only a condition on integrated moments of the distribution function is imposed., Comment: 19 pages

The global-in-time existence of classical solutions to the relativistic Vlasov-Maxwell (RVM) system in three space dimensions remains elusive after nearly four decades of mathematical research. In this note, a simplified ``toy model'' is presented and studied. This toy model retains one crucial aspect of the RVM system: the phase-space evolution of the distribution function is governed by a transport equation whose forcing term satisfies a wave equation with finite speed of propagation., Comment: 13 pages, final version for publication in KRM

Active subspace analysis is a useful computational tool to identify and exploit the most important linear combinations in the space of a model's input parameters. These directions depend inherently on a quantity of interest, which can be represented as a function from input parameters to model outputs. As the dynamics of many plasma models are driven by potentially uncertain parameter values, the utilization of active subspaces to perform global sensitivity analysis represents an important tool to understand how certain physical phenomena depend upon fluctuations in the values of these parameters. In the current paper, we construct and implement new computational methods to quantify the induced uncertainty within the growth rate generated by perturbations in a collisionless plasma modeled by the one-dimensional Vlasov-Poisson system near an unstable, spatially-homogeneous equilibrium in the linear regime., Comment: 41 pages, 19 figures

Traditional probabilistic methods for the simulation of advection-diffusion equations (ADEs) often overlook the entropic contribution of the discretization, e.g., the number of particles, within associated numerical methods. Many times, the gain in accuracy of a highly discretized numerical model is outweighed by its associated computational costs or the noise within the data. We address the question of how many particles are needed in a simulation to best approximate and estimate parameters in one-dimensional advective-diffusive transport. To do so, we use the well-known Akaike Information Criterion (AIC) and a recently-developed correction called the Computational Information Criterion (COMIC) to guide the model selection process. Random-walk and mass-transfer particle tracking methods are employed to solve the model equations at various levels of discretization. Numerical results demonstrate that the COMIC provides an optimal number of particles that can describe a more efficient model in terms of parameter estimation and model prediction compared to the model selected by the AIC even when the data is sparse or noisy, the sampling volume is not uniform throughout the physical domain, or the error distribution of the data is non-IID Gaussian., Comment: 24 pages

A multispecies, collisionless plasma is modeled by the Vlasov-Poisson system. Assuming that the electric field decays with sufficient rapidity as $t \to\infty$, we show that the velocity characteristics and spatial averages of the particle distributions converge as time grows large. Using these limits we establish the precise asymptotic profile of the electric field and its derivatives, as well as, the charge and current densities. Modified spatial characteristics are then shown to converge using the limiting electric field. Finally, we establish a modified $L^\infty$ scattering result for each particle distribution function, namely we show that they converge as $t \to \infty$ along the modified spatial characteristics. When the plasma is non-neutral, the estimates of these quantities are sharp, while in the neutral case they may imply faster rates of decay., Comment: 29 pages

Traditional interpolation techniques for particle tracking include binning and convolutional formulas that use pre-determined (i.e., closed-form, parameteric) kernels. In many instances, the particles are introduced as point sources in time and space, so the cloud of particles (either in space or time) is a discrete representation of the Green's function of an underlying PDE. As such, each particle is a sample from the Green's function; therefore, each particle should be distributed according to the Green's function. In short, the kernel of a convolutional interpolation of the particle sample "cloud" should be a replica of the cloud itself. This idea gives rise to an iterative method by which the form of the kernel may be discerned in the process of interpolating the Green's function. When the Green's function is a density, this method is broadly applicable to interpolating a kernel density estimate based on random data drawn from a single distribution. We formulate and construct the algorithm and demonstrate its ability to perform kernel density estimation of skewed and/or heavy-tailed data including breakthrough curves.

We consider the classical and relativistic Vlasov-Poisson systems with spherically-symmetric initial data and prove the optimal decay rates for all suitable $L^p$ norms of the charge density and electric field, as well as, the optimal growth rates for the largest particle position and momentum on the support of the distribution function. Though a previous work \cite{Horst} established upper bounds on the decay of the supremum of the charge density and electric field, we provide a slightly different proof, attain optimal rates, and extend this result to include all other norms. Additionally, we prove sharp lower bounds on each of the aforementioned quantities and establish the time-asymptotic behavior of all spatial and momentum characteristics. Finally, we investigate the limiting behavior of the spatial average of the particle distribution as $t \to \infty$. In particular, we show that it converges uniformly to a smooth, compactly-supported function that preserves the mass, angular momentum, and energy of the system and depends only upon limiting particle momenta., Comment: 39 pages

The problem of a spatially discontinuous diffusion coefficient ($D(\boldsymbol x)$) is one that may be encountered in hydrogeologic systems due to natural geological features or as a consequence of numerical discretization of flow properties. To date, mass-transfer particle-tracking (MTPT) methods, a family of Lagrangian methods in which diffusion is jointly simulated by random walk and diffusive mass transfers, have been unable to solve this problem. This manuscript presents a new mass-transfer (MT) algorithm that enables MTPT methods to accurately solve the problem of discontinuous $D(\boldsymbol x)$. To achieve this, we derive a semi-analytical solution to the discontinuous $D(\boldsymbol x)$ problem by employing a predictor-corrector approach, and we use this semi-analytical solution as the weighting function in a reformulated MT algorithm. This semi-analytical solution is generalized for cases with multiple 1D interfaces as well as for 2D cases, including a $2 \times 2$ tiling of 4 subdomains that corresponds to a numerically-generated diffusion field. The solutions generated by this new mass-transfer algorithm closely agree with an analytical 1D solution or, in more complicated cases, trusted numerical results, demonstrating the success of our proposed approach., Comment: 26 pages, 11 figures

Recent clinical studies have shown that HIV disease pathogenesis can depend strongly on many factors at the time of transmission, including the strength of the initial viral load and the local availability of CD4+ T-cells. In this article, a new within-host model of HIV infection that incorporates the homeostatic proliferation of T-cells is formulated and analyzed. Due to the effects of this biological process, the influence of initial conditions on the proliferation of HIV infection is further elucidated. The identifiability of parameters within the model is investigated and a local stability analysis, which displays additional complexity in comparison to previous models, is conducted. The current study extends previous theoretical and computational work on the early stages of the disease and leads to interesting nonlinear dynamics, including a parameter region featuring bistability of infectious and viral clearance equilibria and the appearance of a Hopf bifurcation within biologically relevant parameter regimes., Comment: 28 pages, many figures

Geochemical systems are known to exhibit highly variable spatiotemporal behavior. This may be observed both in non-smooth concentration curves in space for a single sampling time and also in variability between samples taken from the same location at different times. However, most models that are designed to simulate these systems provide only single-solution smooth curves and fail to capture the noise and variability seen in the data. We apply a recently developed reactive particle-tracking method to a system that displays highly-complex geochemical behavior. When the method is made to most closely resemble a corresponding Eulerian method, in its unperturbed form, we see near-exact match between solutions of the two models. More importantly, we consider two approaches for perturbing the model and find that the spatially-perturbed condition is able to capture a greater degree of the variability present in the data. This method of perturbation is a task to which particle methods are uniquely suited and Eulerian models are not well-suited. Additionally, because of the nature of the algorithm, noisy spatial gradients can be highly resolved by a large number of mobile particles, and this incurs negligible computational cost, as compared to expensive chemistry calculations., Comment: 29 pages, 8 figures

Traditional random-walk particle-tracking (PT) models of advection and dispersion do not track entropy, because particle masses remain constant. Newer mass-transfer particle tracking (MTPT) models have the ability to do so because masses of all compounds may change along trajectories. Additionally, the probability mass functions (PMF) of these MTPT models may be compared to continuous solutions with probability density functions, when a consistent definition of entropy (or similarly, the dilution index) is constructed. This definition reveals that every numerical model incurs a computational entropy. Similar to Akaike's entropic penalty for larger numbers of adjustable parameters, the computational complexity of a model (e.g., number of nodes) adds to the entropy and, as such, must be penalized. The MTPT method can use a particle-collision based kernel or an SPH-derived adaptive kernel. The latter is more representative of a locally well-mixed system (i.e., one in which the dispersion tensor equally represents mixing and solute spreading), while the former better represents the separate processes of mixing versus spreading. We use computational means to demonstrate the viability of each of these methods.

Several Lagrangian methodologies have been proposed in recent years to simulate advection-dispersion of solutes in fluids as a mass exchange between numerical particles carrying the fluid. In this paper, we unify these methodologies, showing that mass transfer particle tracking (MTPT) algorithms can be framed within the context of smoothed particle hydrodynamics (SPH), provided the choice of a Gaussian smoothing kernel whose bandwidth depends on the dispersion and the time discretization. Numerical simulations are performed for a simple dispersion problem, and they are compared to an analytical solution. Based on the results, we advocate for the use of a kernel bandwidth of the size of the characteristic dispersion length $\ell=\sqrt{2D\Delta t}$, at least given a "dense enough" distribution of particles, for in this case the mass transfer operation is not just an approximation, but in fact the exact solution, of the solute's displacement by dispersion in a time step.

The Eulerian advection-dispersion-reaction equation (ADRE) suffers the well-known scale-effect of reduced apparent reaction rates between chemically dissimilar fluids at larger scales (or dimensional averaging). The dispersion tensor in the ADRE must equally and simultaneously account for both solute mixing and spreading. Recent reactive-particle-tracking (RPT) algorithms can, by separate mechanisms, simulate 1) smaller-scale mixing by inter-particle mass transfer, and 2) mass spreading by traditional random walks. To test the supposition that the RPT can accurately track these separate mechanisms, we upscale reactive transport in Hagen-Poiseuille flow between two plates. The simple upscaled 1-D RPT model with one velocity value, an upscaled Taylor macro-dispersivity, and the local molecular diffusion coefficient matches the results obtained from a detailed 2-D model with fully described velocity and diffusion. Both models use the same thermodynamic reaction rate, because the rate is not forced to absorb the loss of information upon upscaling. Analytic and semi-analytic upscaling is also performed using volume averaging and ensemble streamtube techniques. Volume averaging does not perform as well as the RPT, while ensemble streamtubes (using an effective dispersion coefficient along with macro-dispersion) perform almost exactly the same as RPT.

We study smooth, global-in-time solutions of the relativistic Vlasov-Maxwell system that possess arbitrarily large charge densities and electric fields. In particular, we construct spherically symmetric solutions that describe a thin shell of equally charged particles concentrating arbitrarily close to the origin and which give rise to charge densities and electric fields as large as one desires at some finite time. We show that these solutions exist even for arbitrarily small initial data or any desired mass. In the latter case, the time at which solutions concentrate can also be made arbitrarily large., Comment: 19 pages. arXiv admin note: text overlap with arXiv:1708.02307

A significant drawback of Lagrangian (particle-tracking) reactive transport models has been their inability to properly simulate interactions between solid and liquid chemical phases, such as dissolution and precipitation reactions. This work addresses that problem by implementing a mass-transfer algorithm between mobile and immobile sets of particles that allows aqueous species of reactant that are undergoing transport to interact with stationary solid species. This mass-transfer algorithm is demonstrated to solve the diffusion equation and thus does not introduce any spurious mixing. The algorithm is capable of simulating an arbitrarily small level of diffusion, and can be combined with diffusive random walks to simulate the desired level of diffusion in a reactive transport system., Comment: 43 pages, 15 figures

Several algorithms have been used for mass transfer between particles undergoing advective and macro-dispersive random walks. The mass transfer between particles is required for general reactions on, and among, particles. The mass transfer is shown to be diffusive, and may be simulated using implicit, explicit, or mixed methods. All algorithms investigated are accurate to $\mathcal{O}(\Delta t)$. For $N$ particles, the implicit and semi-implicit methods require inverse matrix solutions and $\mathcal{O}(N^3)$ calculations. The explicit methods use forward matrix solves and require only $\mathcal{O}(N^2)$ calculations. Practically, this means that naive implementations with more than about 5,000 particles run more reliably using explicit methods, Comment: 14 pages, 3 figures

We study smooth, global-in-time solutions of the Vlasov-Poisson system in the plasma physical case that possess arbitrarily large charge densities and electric fields. In particular, we construct two classes of solutions with this property. The first class are spherically-symmetric solutions that initially possess arbitrarily small density and field values, but attain arbitrarily large values of these quantities at some later time. Additionally, we construct a second class of spherically-symmetric solutions that possess any desired mass and attain arbitrarily large density and field values at any later prescribed time.

As South and Central American countries prepare for increased birth defects from Zika virus outbreaks and plan for mitigation strategies to minimize ongoing and future outbreaks, understanding important characteristics of Zika outbreaks and how they vary across regions is a challenging and important problem. We developed a mathematical model for the 2015 Zika virus outbreak dynamics in Colombia, El Salvador, and Suriname. We fit the model to publicly available data provided by the Pan American Health Organization, using Approximate Bayesian Computation to estimate parameter distributions and provide uncertainty quantification. An important model input is the at-risk susceptible population, which can vary with a number of factors including climate, elevation, population density, and socio-economic status. We informed this initial condition using the highest historically reported dengue incidence modified by the probable dengue reporting rates in the chosen countries. The model indicated that a country-level analysis was not appropriate for Colombia. We then estimated the basic reproduction number, or the expected number of new human infections arising from a single infected human, to range between 4 and 6 for El Salvador and Suriname with a median of 4.3 and 5.3, respectively. We estimated the reporting rate to be around 16% in El Salvador and 18% in Suriname with estimated total outbreak sizes of 73,395 and 21,647 people, respectively. The uncertainty in parameter estimates highlights a need for research and data collection that will better constrain parameter ranges., Comment: 35 pages, 16 figures

Current Lagrangian (particle-tracking) algorithms used to simulate diffusion-reaction equations must employ a certain number of particles to properly emulate the system dynamics---particularly for imperfectly-mixed systems. The number of particles is tied to the statistics of the initial concentration fields of the system at hand. Systems with shorter-range correlation and/or smaller concentration variance require more particles, potentially limiting the computational feasibility of the method. For the well-known problem of bimolecular reaction, we show that using kernel-based, rather than Dirac-delta, particles can significantly reduce the required number of particles. We derive the fixed width of a Gaussian kernel for a given reduced number of particles that analytically eliminates the error between kernel and Dirac solutions at any specified time. We also show how to solve for the fixed kernel size by minimizing the squared differences between solutions over any given time interval. Numerical results show that the width of the kernel should be kept below about 12% of the domain size, and that the analytic equations used to derive kernel width suffer significantly from the neglect of higher-order moments. The simulations with a kernel width given by least squares minimization perform better than those made to match at one specific time. A heuristic time-variable kernel size, based on the previous results, performs on a par with the least squares fixed kernel size., Comment: 28 pages, 7 figures

The Einstein-Vlasov-Fokker-Planck system describes the kinetic diffusion dynamics of self-gravitating particles within the Einstein theory of general relativity. We study the Cauchy problem for spatially homogeneous and isotropic solutions and prove the existence of both global solutions and solutions that blow-up in finite time depending on the size of certain functions of the initial data. We also derive information on the large-time behavior of global solutions and toward the singularity for solutions which blow-up in fine time. Our results entail the existence of a phase of decelerated expansion followed by a phase of accelerated expansion, in accordance with the physical expectations in cosmology., Comment: 24 pages, no figures. Version in press

Principal Component Analysis (PCA) is a highly useful topic within an introductory Linear Algebra course, especially since it can be used to incorporate a number of applied projects. This method represents an essential application and extension of the Spectral Theorem and is commonly used within a variety of fields, including statistics, neuroscience, and image compression. We present a synopsis of PCA and include a number of examples that can be used within upper-level mathematics courses to engage undergraduate students while introducing them to one of the most widely-used applications of linear algebra., Comment: 25 pages, 11 figures

Recently, a long-term model of HIV infection dynamics was developed to describe the entire time course of the disease. It consists of a large system of ODEs with many parameters, and is expensive to simulate. In the current paper, this model is analyzed by determining all infection-free steady states and studying the local stability properties of the unique biologically-relevant equilibrium. Active subspace methods are then used to perform a global sensitivity analysis and study the dependence of an infected individual's T-cell count on the parameter space. Building on these results, a global-in-time approximation of the T-cell count is created by constructing dynamic active subspaces and reduced order models are generated, thereby allowing for inexpensive computation., Comment: 26 pages, 17 figures

The motion of a collisionless plasma - a high-temperature, low-density, ionized gas - is described by the Vlasov-Maxwell (VM) system. These equations are considered in one space dimension and two momentum dimensions without the assumption of relativistic velocity corrections. The main results are bounds on the spatial and velocity supports of the particle distribution function and uniform estimates on derivatives of this function away from the critical velocity $| v_1 | = 1$. Additionally, for initial particle distributions that are even in the second velocity argument $v_2$, the global-in-time existence of solutions is shown., Comment: 13 pages

A modified, deterministic SEIR model is developed for the 2014 Ebola epidemic occurring in the West African nations of Guinea, Liberia, and Sierra Leone. The model describes the dynamical interaction of susceptible and infected populations, while accounting for the effects of hospitalization and the spread of disease through interactions with deceased, but infectious, individuals. Using data from the World Health Organization (WHO), parameters within the model are fit to recent estimates of infected and deceased cases from each nation. The model is then analyzed using these parameter values. Finally, several metrics are proposed to determine which of these nations is in greatest need of additional resources to combat the spread of infection. These include local and global sensitivity metrics of both the infected population and the basic reproduction number with respect to rates of hospitalization and proper burial., Comment: 28 pages, 9 figures

We construct a seven-component model of the in-host dynamics of the Human Immunodeficiency Virus Type-1 (i.e, HIV) that accounts for latent infection and the propensity of viral mutation. A dynamical analysis is conducted and a theorem is presented which characterizes the long time behavior of the model. Finally, we study the effects of an antiretroviral drug and treatment implications., Comment: 10 pages, 7 figures, Proceedings of AIMS Conference on Differential Equations and Dynamical Systems (2015)

A one-dimensional, collisionless plasma given by the Vlasov-Poisson system is considered and the stability properties of periodic steady state solutions known as Bernstein-Greene-Kruskal (BGK) waves are investigated. Sufficient conditions are determined under which BGK waves are linearly unstable under perturbations that share the same period as the equilibria. It is also shown that such solutions cannot support a monotonically decreasing particle distribution function., Comment: 8 pages; PACS codes 52.25.Dg, 02.30.Jr, 52.35.-g

We consider a spatially-heterogeneous generalization of a well-established model for the dynamics of the Human Immunodeficiency Virus-type 1 (HIV) within a susceptible host. The model consists of a nonlinear system of three coupled reaction-diffusion equations with parameters that may vary spatially. Upon formulating the model, we prove that it preserves the positivity of initial data and construct global-in-time solutions that are both bounded and smooth. Finally, additional results concerning the local and global asymptotic behavior of these solutions are also provided., Comment: 21 pages

We study the "one and one-half" dimensional Vlasov-Maxwell-Fokker-Planck system and obtain the first results concerning well-posedness of solutions. Specifically, we prove the global-in-time existence and uniqueness in the large of classical solutions to the Cauchy problem and a gain in regularity of the distribution function in its momentum argument., Comment: 28 pages. arXiv admin note: text overlap with arXiv:1312.3666

We present a new, short proof of the increased regularity obtained by solutions to uniformly parabolic partial differential equations. Though this setting is fairly introductory, our new method of proof, which uses a priori estimates, can be extended to prove analogous results for problems with time-dependent coefficients, transport equations, and nonlinear equations even when other tools, such as semigroup methods or the use of explicit fundamental solutions, are unavailable., Comment: 8 pages

The Vlasov-Nordstr\"{o}m-Fokker-Planck system describes the evolution of self-gravitating matter experiencing collisions with a fixed background of particles in the framework of a relativistic scalar theory of gravitation. We study the spatially-homogeneous system and prove global existence and uniqueness of solutions for the corresponding initial value problem in three momentum dimensions. Additionally, we study the long time asymptotic behavior of the system and prove that even in the absence of friction, solutions possess a non-trivial asymptotic profile. An exact formula for the long time limit of the particle density is derived in the ultra-relativistic case., Comment: 25 pages, 1 figure. Several changes from previous version. To appear in J. Diff. Eqs

We consider the self-assembly of composite structures from a group of nanocomponents, each consisting of particles within an $N$-atom system. Self-assembly pathways and rates for nanocomposites are derived via a multiscale analysis of the classical Liouville equation. From a reduced statistical framework, rigorous stochastic equations for population levels of beginning, intermediate, and final aggregates are also derived. It is shown that the definition of an assembly type is a self-consistency criterion that must strike a balance between precision and the need for population levels to be slowly varying relative to the time scale of atomic motion. The deductive multiscale approach is complemented by a qualitative notion of multicomponent association and the ensemble of exact atomic-level configurations consistent with them. In processes such as viral self-assembly from proteins and RNA or DNA, there are many possible intermediates, so that it is usually difficult to predict the most efficient assembly pathway. However, in the current study, rates of assembly of each possible intermediate can be predicted. This avoids the need, as in a phenomenological approach, for recalibration with each new application. The method accounts for the feedback across scales in space and time that is fundamental to nanosystem self-assembly. The theory has applications to bionanostructures, geomaterials, engineered composites, and nanocapsule therapeutic delivery systems., Comment: 3 figures

Motivated by the fundamental model of a collisionless plasma, the Vlasov-Maxwell (VM) system, we consider a related, nonlinear system of partial differential equations in one space and one momentum dimension. As little is known regarding the regularity properties of solutions to the non-relativistic version of the (VM) equations, we study a simplified system which also lacks relativistic velocity corrections and prove local-in-time existence and uniqueness of classical solutions to the Cauchy problem. For special choices of initial data, global-in-time existence of these solutions is also shown. Finally, we provide an estimate which, independent of the initial data, yields additional global-in-time regularity of the associated field., Comment: 23 pages

In a recent paper Calogero and Alcantara derived a Lorentz-invariant Fokker-Planck equation, which corresponds to the evolution of a particle distribution associated with relativistic Brownian Motion. We study the "one and one-half" dimensional version of this problem with nonlinear electromagnetic interactions - the relativistic Vlasov-Maxwell-Fokker-Planck system - and obtain the first results concerning well-posedness of solutions. Specifically, we prove the global-in-time existence and uniqueness of classical solutions to the Cauchy problem and a gain in regularity of the distribution function in its momentum argument., Comment: 29 pages

One way in which the human immunodeficiency virus (HIV-1) replicates within a host is by infecting activated CD4+ T-cells, which then produce additional copies of the virus. Even with the introduction of antiretroviral drug therapy, which has been very successful over the past decade, a large obstacle to the complete eradication of the virus is the presence of viral reservoirs in the form of latently infected CD4+ T-cells. We consider a model of HIV infection that describes T-cell and viral interactions, as well as, the production and activation of latently infected T-cells. Upon determining equilibrium states of the latent cell model, the local and global asymptotic behavior of solutions is examined, and the basic reproduction number of the system is computed to be strictly less than that of the corresponding three-component model, which omits the effects of latent infection. In particular, this implies that a wider variety of parameter values will lead to viral eradication as $t \to \infty$ due to the appearance of latent CD4+ T-cells. With this realization we discuss possible alternative notions for eradication and persistence of infection other than traditional tools. These results are further illustrated by a number of numerical simulations.

Mathematical modeling of biological systems is crucial to effectively and efficiently developing treatments for medical conditions that plague humanity. Often, systems of ordinary differential equations are a traditional tool used to describe the spread of disease within the body. We consider the dynamics of the Human Immunodeficiency Virus (HIV) in vivo during the initial stage of infection. In particular, we examine the well-known three-component model and prove the existence, uniqueness, and boundedness of solutions. Furthermore, we prove that solutions remain biologically meaningful, i.e., are positivity preserving, and perform a thorough, local stability analysis for the equilibrium states of the system. Finally, we incorporate random coefficients within the model and obtain numerical results to predict the probability of infection given the transmission of the virus to a new individual.

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., Comment: 38 pages, 8 figures

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., Comment: 28 pages, 5 figures

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., Comment: 7 pages

We consider semilinear evolution equations of the form $a(t)\partial_{tt}u + b(t) \partial_t u + Lu = f(x,u)$ and $b(t) \partial_t u + Lu = f(x,u),$ with possibly unbounded $a(t)$ and possibly sign-changing damping coefficient $b(t)$, and determine precise conditions for which linear instability of the steady state solutions implies nonlinear instability. More specifically, we prove that linear instability with an eigenfunction of fixed sign gives rise to nonlinear instability by either exponential growth or finite-time blow-up. We then discuss a few examples to which our main theorem is immediately applicable, including evolution equations with supercritical and exponential nonlinearities., Comment: 20 pages

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., Comment: 34 pages, 11 figures

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., Comment: 17 pages, no figures