The Totally Asymmetric Simple Exclusion Process (TASEP) is one of the simplest and most well-understood processes. Exact solutions are available for a homogeneous system. We expand the TASEP model to an "almost homogeneous" system with a few blockages to explore the changes in the density profiles and the currents. As the protein production process resembles this TASEP model and the local translation rates are related to correponding codon concentrations, TASEP serves as a good model to simulate this process and provides us with some interesting insights in predicting the protein production rate. In the talk, some preliminary simulation results will be presented. Interpretations of the results using mean field theory will be discussed.

The understanding of critical phenomena has benefited greatly from the advent of field theoretic techniques, in particular the renormalisation group. Almost 40 years after Leo Kadanoff's introduction of ``block spins'' and more than 30 years after Michael E. Fisher and Kenneth Wilson's seminal article on critical phenomena, the renormalisation group is part of our textbook understanding of phase transitions and helped to form the very notion of universality.

Field theoretic renormalisation group is no less successful in non-equilibrium. Yet, plenty of models remain elusive to this method, due not only to the absence of a small coupling, but also because of the sheer plethora of models and universality classes. Non-perturbative techniques might provide an alternative avenue, being able to handle strong coupling regimes and a very diverse range of models.

In this talk I will briefly trace the history of the renormalisation group and its different flavours. The non perturbative renormalisation group is then introduced, initially focusing on static problems and the exactly soluble free theory. Using model A as a touchstone, various central features are assessed, exposing fundamental differences to traditional techniques, as well as key questions and advantages. I would like to discuss the non-perturbative renormalisation group as a promising path to tackle some of the more recent and hitherto unsolved questions in non-equilibrium statistical mechanics.

I will present an overview of our work motivated by the emerging fields of spintronics and quantum computation, concentrating on two different topics. (1) Several spintronics device proposals require spin-injection into a narrow-gap material such as InAs, as the large spin-orbit (SO) interaction effects allow for improved spin-control and manipulation. The circular polarization degree, related to the spin polarization of injected electrons, was measured for several structures. Spin-alignment was accomplished with the II-VI diluted magnetic semiconductor CdMnSe. Spin-injection into the InAs-based samples is dominated by band structure effects, and the finite ratio of spin-relaxation and recombination times. These conclusions are based on analysis with a detailed rate equation model. Very recent results demonstrating possible spin-injection into InAs are also discussed. (2) Understanding electron spins in quantum dots (QDs) is important for realistic implementations of quantum-computational applications. Ensemble and single-QD photoluminescence (PL) was studied in an MBE-grown sample consisting of 5 different width GaAs quantum wells (QWs) with growth interruption at the interfaces to produce interface fluctuation QDs. Optically detected resonance (ODR) was measured for ensembles and single dots. This technique monitors resonant PL changes induced by far-infrared radiation. The well-width dependence of the ensemble ODR was studied, and the importance of the combination of translational invariance and cylindrical symmetry for the internal transitions of trions in wide QWs is demonstrated. The ensemble ODR spectra for the narrowest wells, on the other hand, are interpreted in terms of internal transitions of an ensemble of excitonic complexes in weakly confining QDs.

Colloidal assemblies are ideal model systems in which to study basic equilibrium and non-equilibrium phenomena relevant to a wide range of condensed matter systems. Additionally, there are a variety of technological applications for self-organizing colloid structures, including photonic band gap materials and patterned nanostructures. Here we study the statics and dynamics of colloids interacting with external fields. When the fields are used to create a periodic substrate, we find a variety of novel crystalline states that we term "colloidal molecular crystals." These have interesting multi-step melting transitions and can be used to realize a variety of canonical statistical mechanics models physically. When the substrate is dynamic, we show that novel dynamical phases arise and lead to ratchet effects, which can be used to create new types of logic gates and new fractionation techniques. Many of these results have recently been realized experimentally for colloids interacting with periodic optical arrays.

Solar energy is an attractive alternative source of renewable energy. The current inorganic solar cells mostly based on amorphous Si have been able to provide an efficiency of 10-30% for solar energy conversion. Organic solar cells have been proposed as another alternative mostly due to the high quantum efficiency of solar power conversion seen in the natural world. The idea is to use a pigment or chromophore to absorb light and to store the energy through electron transfer similar to the photosynthetic process. In this talk I will discuss calculations aimed at understanding some of the fundamental aspects of light-induced charge transfer from density-functional calculations. Specifically, I will discuss a first-principles study on a biomimetic light harvesting organic composed of a fullerene molecule, a porphyrin molecule and a long hydrocarbon chain (carotenoid polyene). The geometry of this triad (C 132 H 68 N 6 O) was optimized at the all-electron level using the generalized gradient approximation.

We find that the molecule can possess a dipole moment of 180 D in a charge-separated state. A new approximate method for obtaining accurate energies of the charge-separated excited states from density functional calculation is discussed. The life times of the excited states are calculated from Einstein A and B coefficients and used in a classical Monte Carlo simulation to determine the rise-time for the large dipole state. We show that an applied electric field and incident solar radiation are allow for a reasonably fast transition to the charge-separated states. Other effects due to polarization and electron-phonon interactions will also be discussed.

We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single-molecule time series. It is demonstrated that the model recovers the equilibrium properties. We also study measurable dynamical quantities such as the bubble size autocorrelation function. This efficient computational approach will be useful to analyse in detail recent single-molecule experiments on clamped homopolymer breathing domains, to probe the parameter values of the underlying Poland-Scheraga model, as well as to design experimental conditions for similar setups.

Injection of gold and silver nanoparticles are advertised for years to provide relief from arthritis and other degenerative or inflammatory diseases. Magnetic nanoparticles, such as superparamagnetic iron oxide nanoparticles (SPIONs), have been used as contrast agents in magnetic resonance imaging (MRI) as they accumulate in cells at the boundary, or margins, between cancer tumors and normal tissue. More recently, optically active nanoparticles have been used as biomarkers and molecular beacons to trace the location or presence of specific biomolecules or cells. Even more significant applications of nanoparticles in biomedical research and medical practice can be developed in the near future when they can be used to detect in-vivo changes in the chemical composition of the cells and organisms. We have developed aqueous-based synthesis routes for several nanomaterials, optimizing the synthesis techniques to obtain high quality, monodispersed nanoparticles. Once functionalized, we will begin studies to demonstrate that these structures can be used to identify the presence of specific biomolecules and track their distribution within living organisms.

Optical spectroscopy is one of the dominant probes in the arsenal of techniques used to understand a variety of systems at high magnetic fields. Far infrared (FIR) spectroscopy represents a natural technique for high magnetic field studies because the energy range of FIR radiation matches the magnetic energies available in high fields magnets as well as the energy scale of many phenomena in solids, such as, cyclotron resonance (CR) energy in semiconductors. Electron CR is useful not only for determining band parameters but also for studying fundamental interactions that are associated with the CR, such as electron-phonon (e-ph) interaction and spin-flip transition. Many scientists around the world have come and used the NHMFL's IR facilities. In this talk, I will discuss several IR studies of semiconductor at the NHMFL. The examples presented in the talk will involve the interactions of electron CR with other fundamental physics phenomena, such as, polaron effects, spin-flip and spin resolved transitions, and e-e interactions with unknown origin.

We separate a Bose-Einstein condensate into an array of 2D sheets using a 1D optical lattice, and then excite quantized vibrational motion in the direction normal to the sheets – analogous to excited subbands in 2D electron systems. Collisions between atoms induce vibrational de-excitation, transferring the “large” excitation energy (h × 50 kHz) into back-to-back outgoing atoms, imaged as rings in the 2D plane. The ring diameters correspond to vibrational energy level differences, and edge-on imaging allows identification of the final vibrational states. Time dependence of these data provides a nearly complete characterization of the decay process including the energies, populations, and lifetimes of the lowest two excited vibrational levels. In contrast with electron systems where the excited state lifetimes are of order 10 ps, the lifetimes here range from 1 to 10 ms.

In the rod-shaped bacterium E. coli, the Min proteins oscillate from pole to pole every ~40 seconds. This internal spatial oscillator plays an essential role in the high accuracy of E. coli's cell division. Homologs of the Min proteins also exist in round cells (cocci) such as Neisseria gonorrhoeae. While oscillations have not been directly observed in N. gonorrhoeae cells because of their small size (~1 micron in diameter), evidence is accumulating that the Min proteins do oscillate in these cells. For example, the Min proteins are observed to oscillate in round mutants of E. coli, and the N. gonorrhoeae Min proteins oscillate when expressed in rod-shaped E. coli. Adding to the evidence for Min-protein oscillations in N. gonorrhoeae, we report that a numerical model for Min-protein oscillations in rod-shaped cells also produces oscillations in round cells. Our results moreover explain why the rings of MinE protein found in wild-type E. coli are absent in round E. coli mutants. Importantly, we find that there is a minimum radius below which oscillations do not occur. In addition, we show that Min-protein oscillations are able to select the longest axis of nearly round cells. This sensitivity of Min-protein oscillations to cell geometry suggests a role for the oscillations in selecting the plane of cell division. Finally, we compare our simulations to recent experimental observations of Min-protein oscillatory patterns in round MreB- cells and discuss other mechanisms for detection of cell geometry in bacteria.

Recent measurements of protein concentrations in yeast cell shows that cell-cycle regulatory proteins are present in 100-1000 copies per cell and their encoding mRNAs are present in very low abundance (~1 molecule per cell on average). These results imply that stochastic processes, due to random fluctuations of a few molecules per cell, may have significant effects on how individual cells progress through the division cycle. When cell-cycle controls are compromised by mutations, random fluctuations may create responses that are not seen in robust wild-type cells. Moreover, because cancer cells have accumulated multiple mutations in growth, division, and death pathways their physiology may be greatly affected by noise. To model these situations where, molecular and other sources of noise may play a significant roles in cell proliferation, requires a proper stochastic formulation of the underlying molecular regulatory system.

As a first step towards a full stochastic description of eukaryotic cell division cycle, we have developed a stochastic model of the START and FINISH in budding yeast. We have formulated a set of biochemical elementary reactions for the synthesis and degradation of B-type cyclins in budding yeast. In the model we have circumvented the two bottlenecks to exact stochastic simulation of cyclin dependent kinase control system: (1) generating bistability in an elementary reaction mechanism of mutual antagonism, and (2) finding parameter values for which a complex will exhibit bifurcations needed to model cell cycle transitions.

Many claims have been made about the importance of specific structural properties, e.g. statistics such as vertex degree distribution, for understanding the dynamics of reaction-diffusion processes on networks. This talk will explore the relevance of these statistics for the two most important questions about such processes in the context of epidemiology: who gets sick and what is the most effective control strategy? I will introduce time-dependent definitions for vulnerability and criticality in the case of an initial pulse of infection. Further, I will argue that previously proposed statistics fail adequately to capture the long time behavior of the system because they are evaluated under a non-ergodic measure. I will propose alternative measures appropriate for estimating the vulnerability and criticality of vertices.

It is studied how the Casimir effect in d-dimensional slabs with 2<d<4 and periodic boundary conditions is affected at and near the bulk critical temperature T_c,∞ by long-range pair interactions whose potential decays as b x^-(d+σ) as x→∞, with 2<σ<4 and 2<d+σ≤6. While such interactions decay sufficiently fast to leave bulk critical exponents and other universal bulk quantities unchanged, they entail important modifications of the standard scaling behavior of the excess free energy and the Casimir force, and give algebraically decaying contributions that dominate the behavior of these quantities for T≠T_c,∞ as a function of the slab's thickness. An account of recent exact results for an appropriate mean spherical model (obtained in collaboration with Danchev and Grüneberg) is given. The scaling functions of the excess free energy and the Casimir force are determined exactly, including the contributions to first order in the usual leading irrelevant scaling field g_ω and the scaling field g_σ to which the long-range interactions give rise. In the case d+σ=6, which includes that of nonretarded van-der-Waals interactions in d=3 dimensions, the power laws of the corrections to scaling ∝b of the spherical model get modified by logarithms. The origin of these anomalies is clarified.