It is becoming ever more apparent that stochastic fluctuations are often crucial ingredients in biological systems. In this talk, I will present an illuminating case study, namely stochastic lattice models for predator-prey interaction and competition. The deterministic Lotka-Volterra model, which can be found in many textbooks on nonlinear kinetics, population dynamics, ecology, etc. yields stable population cycles fixed by the initial conditions. More recently, this model has been critized for of being biologically unrealistic and mathematically unstable. Indeed, introducing spatial degrees of freedom and allowing for stochastic fluctuations generically invalidates the classical mean-field picture. Moreover, local density constraints, modeling limited resources, can lead to predator extinction. The universal properties near this extinction threshold are governed by the scaling exponents of directed percolation. In the active state, where predators and prey coexist, one observes complex and correlated spatio-temporal patterns of competing and merging activity fronts. Finite systems are characterized by irregular and remarkably persistent population oscillations, whose features are determined by the intrinsic interaction rates rather than initial conditions.

References:

• M. Mobilia, I.T. Georgiev, and U.C.T., Phys. Rev. E 73 (2006) 040903(R), q-bio.PE/0508043; J. Stat. Phys. 128 (2007) 447, q-bio.PE/0512039;
• M.J. Washenberger, M. Mobilia, and U.C.T., J. Phys. Condens. Matter 19 (2007), 065139, cond-mat/0606809.

Borexino, a 1400 ton scintillator experiment installed in the Gran Sasso Underground Laboratory in Italy by a 100- member International Collaboration (including VT) has directly observed neutrinos from the decay of ⁷Be in the sun. This is the first real-time spectroscopic observation of neutrinos below 1 MeV and represents a tour de force in the quest to probe in great detail how the sun generates energy. I will describe the foundations of Borexino, how it was built over the last 20 years, how extraordinarily high barriers of background were overcome by its remarkable detector design, how the solar signal detection works in Borexino and the significance of the first results for the interior of the sun and for neutrino phenomenology. I will close with a prognosis of things to come

White dwarfs are the most common end-products of stellar evolution. Although less extreme than neutron stars and black holes, white dwarfs have a sufficiently deep gravitational potential to become bright X-ray sources when they accrete material from their binary companions. They are also numerous and therefore include some nearby examples that can be studied in details. Here I will present results of recent X-ray observations of close binary systems with accreting white dwarfs. They provide an excellent laboratory in which to develop and test theories of accretion disks in a non-relativistic regime. Moreover, X-ray spectroscopy allows us to select systems with near-Chandrasekhar mass white dwarfs, making them candidate progenitors of Type Ia supernovae.

One of the general organizing principles that emerges from the Periodic Table is that metals are characterized by an electronic band which is partially full. Insulators, by contrast, have no unfilled levels. However, a wide class of materials such as the high-temperature copper-oxide superconductors, have partially filled levels but insulate nonetheless. Such materials known as Mott insulators cannot be understood within the standard band picture. Their physics lies in the strong interactions between electrons. I will show in this talk that from the strong interactions in Mott insulators emerges a new collective excitation which has charge 2e and is not made out of the elemental excitations. This charge 2e excitation is bosonic and is responsible for many of the anomalous properties of the normal state of the high-temperature superconductors.

The possible existence of light, sterile neutrinos (neutrinos without a weak interaction) has been an open question in particle physics since the discovery of neutrino oscillations in the late 1990's. I will explain the physics motivation for (and against) this odd particle. I will also describe the MiniBooNE experiment, which is designed to test the experimental evidence for the sterile neutrino. The MiniBooNE result, testing the sterile neutrino hypothesis, will be shown and discussed.

In the neocortex, synaptic inputs have to converge in order to elicit postsynaptic action potentials, requiring neuronal activity to propagate in the form of transiently synchronous neuronal groups. The rapid and selective synchronization between neurons across many spatial and temporal scales is considered a key mechanism in the formation of neuronal cell assemblies. Recent studies have shown that this type of synchronization arises in the form of `neuronal avalanches' in which the size distribution of synchronized groups follows a power law with an exponent of -1.5 indicative of a critical network state. Propagation of such avalanches can be interpreted as a branching process on a network. We derive and test a robust algorithm for reconstructing such network from the observed avalanche dynamics and apply it to spontaneous activity in cortical organotypic cultures or acute slices. As controls, we use different network randomizations schemes: (i) Erdos-Renyi; (ii) degree sequence preserving; (iii) weight randomization. The reconstructed functional networks reveal small-world topology characterized by a large clustering coefficient and a small network diameter. The motif analysis reveals a feed-forward structure of these networks, in which the dominant network motifs have reciprocally (bi-directionally) coupled neuronal groups that provide and receive common inputs from other groups. We also report novel functional network architecture of neuronal avalanches. The architecture is organized in such way that the small-world property is preserved upon removing the weakest links in the network. We explain how such architecture can arise and discuss its functional role.

A framework is presented for understanding the common character of proteins. It is shown that the notion of a tube of non-zero thickness allows one to bridge the conventional compact polymer phase with a novel phase employed by Nature to house biomolecular structures. We build on the idea that a non-singular continuum description of a tube of arbitrary thickness entails discarding pairwise interactions and using appropriately chosen many body interactions. We suggest that the structures of folded proteins are selected based on geometrical considerations and are poised at the edge of compaction, thus accounting for their versatility and flexibility. We present an explanation for why helices and sheets are the building blocks of protein structures.

The work was done in collaboration with Amos Maritan along with Marek Cieplak, Alessandro Flammini, Oscar Gonzalez, Trinh Hoang, John Maddocks, Davide Marenduzzo, Cristian Micheletti, George Rose, Flavio Seno, Andrzej Stasiak, and Antonio Trovato.

As a simple polyanion, RNA contains only four different nitrogenous base side chains whose sequence facilitates RNA's multitude of structural, genetic, and catalytic functions. Our research focuses on understanding the various natural "tools" RNA employs to expand its structure/function capabilities within the cell. A vast number of modified bases exist within cellular RNAs beyond the common A, G, C, and U. These bases are introduced into cellular RNAs post-transcriptionally by modifying enzymes that are very often conserved among archea, bacteria, and eukaryotes (Ferré-D' Amaré, 2003). This suggests an ancient role for modified bases in RNA, and evidence for their persistence throughout evolution underscores their importance. Despite widespread modification of RNAs throughout the cell and throughout phylogeny, structural studies of modified RNAs have been limited and attempted explanations regarding their biological purposes speculative. Using biophysical methods such as fluorescence, thermal denaturation monitored by UV absorbance, and NMR spectroscopy, we have characterized the structural and dynamic effects of a post-transcriptionally modified pseudouridine base that acts to fine-tune and differentiate the function of a spliceosomal RNA. We are currently continuing our investigations on the peptidyl transferase center from human large ribosomal subunit RNA, in which pseudouridines are clustered, determining the structural and dynamic role of modified bases on ribosome catalysis. We will be enlisting the assistance of some new physical techniques for our laboratory, namely, small angle x-ray scattering (SAXS) measurements.

References: Ferré-D' Amaré, A. (2003) Curr. Opin. Struc. Biol. 13: 49-55.

When we look out on a clear night, the universe seems infinite. Yet this infinity might be an illusion. During the first half of the presentation, computer games will introduce the concept of a "multiconnected universe". Interactive 3D graphics will then take the viewer on a tour of several possible shapes for space. Finally, we'll see how recent satellite data provide tantalizing clues to the true shape of our universe. The only prerequisites for this talk are curiosity and imagination. For middle school and high school students, people interested in astronomy, and all members of the Virginia Tech community.

The search for the 1st and the 3rd generation Neutrino mixing is on (Theta-13). Unlike the mixing between 1st-&-2nd, and 2nd-&-3rd, Theta-13 is small; indeed, could be much smaller than other mixing. It is the first question to be answered before searching for the CP-violation and the Mass-Hierarchy in the Lepton sector. Increasingly precise, and complementary, measurements will be needed to gain an understanding of the Neutrino Mass-Matrix.

Colloids consist of micrometer-size particles in a fluid that interact by central potentials (hard sphere or electrostatic). At large packing fractions they form phases similar to those formed by atoms in condensed matter: liquids, crystals and glasses. Since the colloidal particles are large and slow, they can be tracked in time and in three-dimensional space by confocal microscopy. Colloidal systems, therefore, are highly efficient "analog computers" for the study of the dynamics of complex multiparticle phenomena in condensed matter. A number of examples are presented: crystal nucleation, coherency dislocations in epitaxial growth, indentation of single crystals, and plastic shear of glasses.

Prof. Spaepen did his undergraduate work at the University of Leuven and earned his doctorate (in applied physics) at Harvard University. He joined the Harvard faculty in 1977 and since then has rarely escaped.

Stem cells have been at the center of much scientific excitement and controversy for the last decade. How exactly pluripotent embryonic stem cells specialize to particular cell fates, like the ones that make the skin or neurons or blood cells, is a great mystery. At the heart of it is the ability of the cellular machinery to generate such “epigenetic” states, namely the possibility of having many different kinds of cells, despite having the exact same genetic material. Some of the "epigenetic" effects involve modifying the state of DNA is packaging. Why certain parts of our genomes are packed differently in different cells is only partially understood. We will study this same question in a much simpler system: baker's yeast.
As I will discuss, understanding multiple states of the cell has much in common with the physics of phase transitions. Armed with the approach borrowed from physics, one can make several qualitative predictions that could be experimentally verified.

With a brief review of the historical development in high energy physics, we appreciate the extraordinary achievements thus far, formulated as the "Standard Model", in understanding Nature at the highest energy scales (or the shortest distances) currently experimentally accessible. Yet, theoretical arguments and indirect experimental observations indicate the existence of new physics at the TeV scale, the "terascale". The precise form of the new physics is unknown, but may have far-reaching implications in cosmology, astroparticle physics, and nuclear physics. In 2008, the CERN Large Hadron Collider (LHC) will be in mission to explore the physics at this energy prontier. Exciting new discovery is highly anticipated. Future possible facilities like the International Linear Collider (ILC) will further help to reveal the true nature of the elementary particles. The "terascale" physics will dominate in the next two decades to come.

Founded over a century ago, statistical mechanics for systems in thermal equilibrium has been so successful that, nowadays, it forms part of our physics core curriculum. On the other hand, most of "real life" phenomena occur under non-equilibrium conditions. Unfortunately, statistical mechanics for such systems is far from being well established. The goal of understanding how complex macroscopic behavior emerge from simple microscopic rules (of evolution, say) remains elusive. As an example of the difficulties we face, imagine trying to predict the existence of a tree from a collection of H,C,O, N,... atoms, evolving according to the rules of E&M and QM.

Over the last three decades, an increasing number of condensed matter theorists are devoting their efforts to this frontier. After a brief summary of the crucial differences between equilibrium and non-equilibrium statistical mechanics, I will give a bird's-eye view of some key issues, ranging from the "fundamental" to (a small set of) the "applied." The methods used also span a wide spectrum, from "easy" computer simulations to sophisticated field theoretic techniques. These will be illustrated in the context of an overview of the projects on which Beate Schmittmann and I are working.

The question, whether there are new phases of matter at energy densities exceeding those of nuclear matter and what their properties might be, has challenged subatomic physicists for decades. With the advent of Quantum Chromodynamics as the fundamental theory of the strong interactions and the Relativistic Heavy Ion Collider as a facility enabling the production and experimental study of such matter, we are finally able to explore this question both, experimentally and theoretically. In my lecture, I will first review some basic concepts of the theory of strongly interacting matter relevant to this question and then discuss some salient results of the experimental program at the Relativistic Heavy Ion Collider (RHIC). In particular, I will explain why the matter observed in the RHIC experiments has been called a ``perfect liquid.'' I will then describe some recent ideas about the origin of the nearly inviscid nature of a plasma composed of quarks and gluons and discuss possible connections between its low viscosity and other defining properties observed in the RHIC experiments. I will also briefly touch on possible connections to string theory.

I present a study on the effect of non-evaporating primordial black holes (PBH) on the ionization and thermal history of the universe. X-rays emitted by gas accretion onto PBHs modify the cosmic recombination history producing measurable effects on the spectrum and anisotropies of the Cosmic Microwave Background (CMB).

We present experiments on the dynamics of the Belousov-Zhabotinsky (BZ) chemical reaction in vortex flows that exhibit chaotic mixing. The BZ reaction is well-known as an oscillatory reaction that can display chaotic time-dependence. In the absence of any fluid flow, the BZ system produces target and spiral patterns, similar to those found in a wide variety of reaction-diffusion systems in physics, biology and chemistry. We explore how these patterns are altered in the presence of a chain or array of oscillating and drifting vortices. Experiments show that the patterns that form mimick those associated with chaotic mixing in these flows. Furthermore, we find that if long-range chaotic mixing is superdiffusive with Levy flight trajectories, large-scale synchronization of the oscillating pattern is observed. Other experiments show that fronts propagating in an oscillating vortex flow mode-lock to the frequency of the oscillation. Cellular flows are also found to "freeze" the motion of an interface in the presence of an imposed "wind."

I will report on the discovery of new short-lived particles in the Belle experiment. These new resonances apparently do not fit the conventional mold of quark-antiquark or three-quark combinations, and therefore may provide new insight into the nature of quantum chromodynamics.

Spin-orbit coupling makes the spin degree of freedom respond to its orbital environment. Thus it gives us a "control knob" with which we can steer the purely quantum-mechanical spin degree of freedom. Often spin-orbit coupling can be interpreted as an effective magnetic field. Similar to an external magnetic field, it results in an oscillatory motion of the spins which is the well-known spin precession.

In my talk I will discuss some examples for the rich and fascinating physics that emerges from the interplay between the precessional spin dynamics and the orbital dynamics of electrons in solids. Holes in semiconductors are often characterized by an effective spin 3/2. While the precession of spin-1/2 electrons preserves the magnitude of a spin polarization, the precession of spin-3/2 holes can give rise to an alternating spin polarization. Spin precession is known to be an important cause of spin relaxation, i.e., the slow disappearance of a nonequilibrium spin polarization imposed on an electron system. Yet I will show that we can have several qualitatively different regimes of spin polarization decay depending on the interplay of spin precession and momentum scattering. Finally, I want to discuss how an external electric field combined with spin precession due to spin-orbit coupling can generate both a spin density and a spin current.

We have studied the environments of low-redshift quasars using data of ~7000 quasars from the Sloan Digital Sky Survey. We investigate correlations between the quasar environments and the intrinsic quasar properties: redshift, and the luminosities of the quasars at radio, visual, and X-ray wavelengths.

Growing materials with identical structures but different polarities on one another can result in a polar catastrophe that forces the interface to reconstruct, either electronically or through atomic rearrangement. An introduction to the polar catastrophe will be presented, eventually focusing on a specific example: ultra thin films of polar LaAlO3 on non-polar SrTiO3. It will be shown that local modifications of the surface can induce a metal- insulator transition at the interface, and, remarkably, the transition can be reversed.

The MIPP Experiment measures differential particle production cross sections of beams of charged pions, kaons, protons, and anti-protons with momenta of 5 to 90 GeV/c on nuclear and cryogenic targets spanning the periodic table from hydrogen to uranium. MIPP also used 120 GeV/c proton beam incident on the NuMI neutrino production target and several nuclei. The MIPP detector measures all charged particles created in the reactions using a time projection chamber (TPC), tracking chambers, and particle identification from dE/dx in the TPC, time-of-flight (TOF), a multi-cell threshold Cherenkov detector, and a ring imaging Cherenkov detector (RICH).

MIPP physics goals include topics in particle physics (non-perturbative QCD hadron dynamics, particle fragmentation scaling laws, light meson and baryon spectroscopy, charged kaon mass measurement), nuclear physics (y-scaling, strangeness production and flavor propagation in nuclei), and service measurements (neutrino flux for MINOS and atmospheric neutrino experiments, input for hadronic shower simulators and calorimetry design, and proton radiography).

We will present the experimental setup, the data reconstruction, first results from data taken in 2005 and 2006, and the status of an upgrade and future run of the experiment.

Inflationary cosmology - exponential expansion of the universe at early times - provides a simple, observationally tested scenario for understanding the observed flatness and homogeneity of the universe and the seeds of structure formation. Within this broad framework, there are diverse mechanisms for theoretically modeling inflation and structure, many of which make distinctive predictions for observations of the Cosmic Microwave Background Radiation (CMBR). The mechanism behind inflation is sensitive to very high-energy physics, and requires input from a more complete theory of gravity (such as string theory) going beyond Einstein's General Relativity. After introducing the phenomenon of early universe inflation, I will describe two effects of interest - gravitational radiation, and nonlinear effects in the CMBR - and their role in the challenging problem of trying to connect string theory to observations.