We focus on the power spectrum of the total occupancy (i.e. the total number of particles inside the lattice at a given instant of time) of the open TASEP model in the low density phase. We perform standard Monte-Carlo simulations with sequential updates along with some analytic calculations to further investigate the findings of Adams et al. In this earlier work, unexpected oscillations in the power spectrum were found; here, we investigate them further to better understand potential boundary effects. We introduce another length scale, namely the window size l. A window is a segment of the whole lattice. Instead of calculating the power spectrum of the total occupancy for the entire system, the power spectrum is calculated inside the window. Typically a window is chosen to be a segment of the bulk far from the boundaries. The power spectrum calculated inside the window, embedded on a much larger lattice, resembles very closely to the power spectrum of entire open TASEP of length comparable to the window size. Motivated by this observation, we computed the power spectrum of the total occupancy inside a window of a periodic TASEP. The power spectrum of the periodic and the open TASEP share some generic features while differing on some others. The power spectrum of total occupancy of the periodic TASEP has two distinct sets of oscillations. We call them the large ω and the small ω oscillations. The large ω oscillations are shared by both the open and the periodic TASEP, while the small ω oscillations are salient features of the periodic TASEP alone. We argue that the small ω oscillations are artifacts of the periodic boundary condition. We present our simulation data to substantiate our claim. We provide a theoretical outlook by using a linearized discrete version of the full stochastic differential equation for the fluctuation of the density. There are two parameters in our theory, namely the diffusion constant and the noise strength. We find that the fitting parameters deviate from the naive bare value. In order to answer this puzzle we incorporate the nonlinear effect. We undertake perturbative calculation to one loop order, both in continuum and for the discrete case. Our calculations show a constant shift in the diffusion constant to one loop order.

The bio-structures found in nature are well-adapted to their environments,having gone through selective competition for over a billion years. In this talk, I present three examples of combined theoretical and experimental studies that explore the wisdom of nature.

Hosted by Beate Schmittmann.

The susceptible-infectious-recovered (SIR) model describes the evolution of three species of individuals which are subject to an infection and recovery mechanism. A susceptible S can become infectious with an infection rate β by an infectious I type provided that both are in contact. The I type may recover with a rate γ and from then on stay immune. Due to the coupling between the different individuals, the model is nonlinear and out of equilibrium. We adopt a stochastic individual-based description where individuals are represented by nodes of a graph and contact is defined by the links of the graph. Mapping the underlying master equation onto a quantum formulation in terms of spin operators, the hierarchy of evolution equations can be solved exactly for arbitrary initial conditions on a linear chain.

Hosted by Royce Zia.

Using exact diagonalization method with torus geometry, we numerically study quantum phases in different 2D electron systems. For the Dirac fermions in Graphene system with partially filled N=3 Landau level (LL), our results show that at half-filling, the equal-time density-density correlation function displays sharp peaks at nonzero wavevectors q*. Finite-size scaling reveals that the peak value grows with electron number and diverges in thermodynamic limit, suggesting an instability towards a unidirectional charge density wave. This symmetry-broken stripe phase is found robust against perturbation from disorder scattering, indicating experimentally observable through transport measurements. Associated with the special wavefunctions of the Dirac LL in Graphene, both stripe and bubble phases become possible candidates for the ground state of the Dirac fermions with lower filling factors in the N=3 LL. We also study the conventional 2D electron system with 5/2 fractional quantum hall effect. A model Hamiltonian with the additional three-body (3b) interaction has been investigated. The 3b interaction plays a role in breaking the particle-hole (PH) symmetry of the system and induces a phase transition of the ground state (GS) towards a Pfaffian (Pf) state or its PH conjugate (APf) state depending on the sign of the three-body interaction. The results of the low energy spectrum, the wave function overlap, and the PH parity evolution, have shown strong evidence of the existence of a first order phase transition between the Pf and the APf, with the pure Coulomb system sitting at the critical point of the transition. Modulated by an extra short-range pseudopotential, the above induced Pf or APf system can transfer to the nearby compressible phases with the stripe order or the composite-fermion-liquid (CFL) state.

In collaboration with D. N. Sheng (Department of Physics and Astronomy, California State University Northridge) and F. D. M. Haldane (Department of Physics, Princeton University)

One of the most important discoveries in physics in the past 25 years is the fractional quantum Hall effect (FQHE): a many-body strongly interacting system exhibiting the emergence of topological quasiparticles with fractional charged excitations and statistics and, perhaps, even non-Abelian quasiparticles for the FQHE in the second orbital Landau level at even-denominator filling factor 5/2. The 5/2 FQHE is currently motivating scientists partly due to its potential role in topological quantum computation and the fact that it still is quite mysterious after nearly 20 years. In this talk, I discuss the actual physical reality of the proposed topological non-Abelian Moore-Read Pfaffian description of the 5/2 FQHE. Specifically, theoretically it is found that the quasi-two-dimensional nature of the experimental FQHE systems, i.e., the finite width, produces a physical environment sufficient to stabilize the Moore-Read Pfaffian state (based on exact diagonalization using the spherical and torus geometries). Our results suggest the possibility of creating optimal experimental systems for the 5/2 FQHE state which are more likely to be described by the Pfaffian ansatz. I also mention the possibility of using FQHE bilayer systems to further shed light on the physical reality of the Pfaffian description at 5/2. Lastly the role of the three-body interaction Hamiltonian that produces the Moore-Read Pfaffian as an exact ground state and particle-hole symmetry in the FQHE at 5/2 will be discussed.

We acknowledge support from Microsoft Project Q and this work is done in collaboration with Sankar Das Sarma, Thierry Jolicoeur, and Kwon Park.

Hosted by Vito Scarola.

The wealth of information being obtained from genomic, proteomic, and glycomic research is allowing researchers to unravel the intricate genetic and epigenetic mechanisms associated with human health and disease. The intracellular delivery of nucleic acids, such as plasmid DNA, oligonucleotides, and small interfering RNA, to study these processes offers unprecedented promise for revolutionizing biological and medical research by presenting an effective and facile means of regulating gene expression. For this reason, many drug discovery programs have begun an exciting paradigm shift to develop novel polynucleotide-based therapeutics for combating numerous acquired and inherited diseases such as cancer, HIV, Alzheimer’s, and cardiovascular disease.

Nucleic acids have exceptional affinity and specificity for their intracellular targets; yet, many complex factors dictate the accuracy, reproducibility, and relevance of utilizing polynucleotides to regulate gene expression. Unlike small molecule drugs that can effectively diffuse through the vasculature and cell membranes to reach its therapeutic target, nucleic acids are very large structures that need delivery vehicles to promote cell entry and therapeutic efficacy. Thus, delivery systems are needed to compact nucleic acids into nanostructures (termed polyplexes) that can enter cells, protect nucleic acids from enzymatic damage, and provide the possibility of targeting the delivery to specific tissue types and sites within the cell. Viruses have proven to be the most efficient nucleic acid delivery vehicles. However, many issues have arisen in clinical trials, which have inspired the examination of synthetic vehicles, such as cationic liposomes and polymers to be developed for nucleic acid drug delivery. Indeed, the nature of the nucleic acid delivery vehicle has been found to play a central yet elusive role in dictating the efficiency, safety, mechanisms, and kinetics of gene regulation in a spatial and temporal manner. For this reason, the delivery vehicle is considered to be as important to treatment efficacy as the drug itself.

To this end, we have developed a new class of nontoxic, glycopolymer delivery agents we have termed poly(glycoamidoamine)s (PGAAs). These polymers contain carbohydrate residues linked to cationic amine groups within the polymer backbone. The sugar units promote low toxicity while the amines facilitate DNA binding and compaction into polyplexes. We have found that these polymers deliver polynucleotide payloads into cells in a highly effective manner without toxic side effects. We have examined these vehicles for the delivery of therapeutic DNA sequences termed oligodeoxynucleotide decoys. These short pieces of DNA can serve as antagonists to transcription factors implicated in disease. We have found that our glycopolymers promote efficient delivery of DNA decoys to isolated primary cardiomyocytes and the mouse heart, where 85% of the mouse myocardium was positive for the DNA drugs. The polyplexes formed with our PGAAs and DNA decoys were shown to block the activation of the transcription factor nuclear factor-kappaB, a major contributor to ischemia/reperfusion injury (post myocardial infarction or heart attack), and this nanoparticle-based drug was found to significantly limit myocardial infarction in vivo in our mouse model.

Hosted by Beate Schmittmann

The superfluid-insulator transition of bosons occurs due to the competition between kinetic energy and repulsive interaction between constituent bosons. In a superfluid phase, bosons move in phase with one another as a part of a single macroscopic wavefunction. In an insulating phase, on the other hand, strong interactions hinder the flow of bosons. As a result, each particle occupies its own quantum well, unaffected by its neighbors, and, thus, the system has no global phase coherence.

The coupling of bosons to additional degrees of freedom can modify the superfluid-insulator transition in a non-trivial way. In my talk, I will discuss what happens to the original superfluid-insulator phase diagram in the presence of fermions. This question is of fundamental importance and is relevant to many physical situations where the bosonic and fermionic degrees of freedom are coupled. The two examples I will consider are the superconductor-graphene systems and cold atom Bose-Fermi mixtures. In the former, the coupling of the Josephson junction array to the reservoir of fermionic excitations in graphene favors the superconducting phase. By changing the fermionic density of states in graphene, one can tune the transition from insulating to superconducting state of the array. In the case of Bose-Fermi mixtures, the experiments exhibit the opposite trend - the presence of fermions leads to the suppression of the superfluid state. I will show that this experimental fact can be explained by considering multi-band model for Bose-Fermi mixtures, where there is a competition between the fermionic screening effect and the renormalization of the boson-boson interaction due to the virtual boson transitions involving higher Bloch bands.

Hosted by Vito Scarola.

Mobile micro-robots have unique advantages, such as the ability to access small spaces, and the potential to be employed in large numbers as inexpensive agents of distributed systems for swarm robotic applications. Due to these characteristics, micro-robots are envisioned to impact a diverse range of applications, including minimally invasive diagnosis and localized treatment of diseases, environmental monitoring, and homeland security. While the potential impact of these systems is high, particularly for biomedical applications, many challenges remain in developing such microrobots. One of most significant obstacles to realization of mobile robots at micron length scales are the miniaturization of on-board actuators and power sources required for mobility. To address these problems for swimming micro-robots, we focus on interfacing live microorganisms (i.e. bacteria) with a microfabricated robot body, with the ultimate goal of using bacteria for actuation, control, and sensing. This talk will describe analytical and experimental research efforts on both propulsion and on/off motion control of bacteria-propelled synthetic micro-objects. Future directions, specifically efforts to facilitate localized delivery of the control agents to enable independent control of each micro-robot will also be discussed.

Hosted by Giti Khodaparast.

The incorporation of silica nanoparticles in ISAM (ionic self-assembled multilayer) deposition produces a film with high uniformity and optical quality. This is because the nanoparticles conform into a random close-packed (RCP) structure, and create a nanoporous 3-D network with a macroscopic refractive index that closely satisfies one of the key requirements for minimal reflectance of light from the film and substrate. A critical drawback of the nanoporous film however, is a limitation on the electrostatic interactions between the nanoparticles and the polycation that 'glues' them together. Consequently these optically superior films suffer from a lack of cohesion, as well as adhesion to the glass substrate. In this presentation we will look at novel methods we have explored in order to improve the mechanical stability of silica nanoparticle films. These methods range from utilization of unique chemistries to initiate cross-linking, to thermal nanoparticle fusion. Furthermore we briefly address the possibility of constructing broadband anti-reflection coatings by depositing alternating dielectric stacks of high and low refractive index. Finally we address the critical challenges of depositing silica nanoparticle films onto thermoplastics with high impact resistance; in this case polycarbonate. We show by utilizing deep UV irradiation that we can alter the molecular structure of polycarbonate, and populate the surface with functional species to permit uniform ISAM deposition.

In this talk, I will present two research projects that I have worked on here at Virginia Tech. The first project focuses on quorum sensing in bacteria. These are bacteria that are able to orchestrate the starting and stopping of critical cellular functions depending on the size of the bacterial colony. The complex signal transduction pathway that integrates the size of the colony into the final regulated output involves many different interactions. We present a model that incorporates mean-field and stochastic approaches for analyzing these interactions. We identify key dimensionless parameters that control the system's response and make testable predictions for future experiments.

The second project leaves the realm of bacteria and focuses on the first level of DNA compaction in eukaryotes, the nucleosome. The nucleosome is a DNA-protein structure where the DNA wraps around a core of histone proteins. Understanding how the DNA wraps and unwraps from the histones is important for studying the transcription of certain genes. Presented here is a quantitative model based on the electrostatic interactions between the highly negatively charged DNA the highly positively charged histone core of the nucleosome. Results from the model suggests a mechanism by which the wrapping can be controlled: alteration of the charge state of the histone core.

By resonant optical excitation of surface plasma waves in thin metallic substrates one can detect fluctuations in the dielectric constant near the metal surface. An important biochemical application of this effect is in characterizing binding reactions between proteins. Surface plasmon resonance (SPR) is a relatively new and sensitive tool for observing the progress of protein binding reactions in real time and without the need for labels. There are, however, some perturbing effects that can complicate the interpretation of experimental results. Various models have been proposed ¿ sometimes leading to widely varying conclusions. In this talk I will discuss the design and results of lattice Monte-Carlo simulations of some SPR experiments which enable us to test the interpretive performance of selected models and suggest how certain experimental parameters may be expected to affect measurements.

Dispersions of colloidal particles are excellent model systems of classical statistical mechanics in order to understand the principles of self-organization processes. Using an external field (e.g. electric or magnetic field) the effective interaction between the colloidal particles can be tailored and the system can be brought into non-equilibrium in a controlled way. In this talk, we shall discuss lane and band formation in oppositely driven colloidal mixtures, both in DC and AC driving fields. The experimental realization in colloids and dusty plasmas is highlighted.

Hosted by Royce Zia.