In an experiment using a whole-culture method, every cell in a culture is forced equally. Can such a method synchronize a heterogeneous population of eukaryotic cells? Leading experts in cell cycle research debate this question. A physics theory would be helpful in shedding light on this issue, but there are no simple models on coordinated dynamics of cell cycle and cell growth. In a typical systems-biology model accounting for coupling between cell growth and cell cycle, there are hundreds of parameters and several dozen variables. Such a model would not be effective in unveiling new mechanisms of synchronization in a large population of interacting cells. In this talk we will discuss a strategy to tackle complexity in realistic mathematical models of biochemical networks, to obtain analytically treatable models that can be used for statistical characterization of a cell population. In particular, using bifurcation analysis of detailed models, we obtain a phenomenological model that allows us to reveal the conditions for synchronization in forced budding and fission yeast cell populations.

Hosted by Beate Schmittmann.

A great deal of interest in soft matter and its applications as advanced materials arises from the phenomenon of spatio-temporal pattern formation and self-assembly. Despite its potential, spontaneous self-assembly usually leads to defected structures, fact that limits their applicability. I will first discuss general properties and mechanisms of ordered pattern evolution in such nonequilibrium systems, including dynamics of topological defects and domain coarsening in some potential and nonpotential model systems. Our recent theoretical research on mesophase dynamics of block copolymers will be then introduced. Particular attention will be paid to one of the major challenges for widespread applications of nanostructured materials: the achieving of long range order. Our efforts on understanding structure, dynamics, and response of nanoscale phases will be also discussed.

Hosted by Royce Zia.

This seminar will present new approach being developed at UVa for incorporating scattering effects from molecular adducts on the channels of field effect devices. These hybrid transport devices offer an alternative to the two-terminal paradigm of molecular electronics, and offer the possibility of incorporating mesoscopic, quantum scattering effects into the transport characteristics of robust, industrially viable devices. My research group is working on two particular implementations of this approach, using silicon and also carbon nanotube channel devices. I will present our observations of random telegraph signal (RTS) and Fano interference in these devices and speculate about the tunability of these effects and the direction(s) this research will take.

Hosted by Giti Khodaparast.

An infinite class of self-dual spin 1/2 systems and binary error corrected codes (ECC) will be discussed. (One system of this class - Baxter-Wu triangular model - is known to be solvable.) Conjectures about distribution of zeros of partition functions of finite volume systems of this class, and of ECC, will be formulated. Numerical and rigorous results supporting the conjectures will be presented.

Each year more than 7 million people die as a result of coronary heart disease making it the leading cause of death in the industrialized world. The immediate cause of death in most of these cases is ventricular fibrillation, or sudden cardiac death. Ventricular fibrillation results from sustained chaotic electrical activity within the cardiac muscle. The Virtual Heart is a computational model including detailed anatomical form and physiological function created to study abnormal heart rhythms. Using insights gained from this model, Dr. Eason will discuss the normal electrical function of the heart and discuss some of the causes of cardiac arrhythmias. He will also review simulations of a defibrillation shock – the only effective treatment for a life-threatening episode of ventricular fibrillation. Finally, Dr. Eason will discuss current research in the Virtual Heart Lab seeking to explain how acute stress increases the likelihood of sudden cardiac death and how his lab is working to improve the effectiveness of portable and implantable defibrillators.

Hosted by Beate Schmittmann.

Recent years have seen a surge of interest in complex networks, which can describe systems as diverse as traffic on the world-wide web, metabolic interactions in cells, and the spread of epidemics among populations. From a statistical physics perspective, these networks provide an intriguing avenue for tackling one of the long-standing questions in the field: how the collective behavior of interacting objects is influenced by the topology of those interactions. We introduce a family of hierarchical lattices which exhibit a variety of structural features seen in real-world complex networks: scale-free degree distributions, small-world behavior, and a modular organization characterized by fractal scaling laws - recently discovered in the WWW, protein interaction, and metabolic networks, among others. When we examine cooperative behavior on the networks, their structural variety translates into highly unusual phase transitions and critical phenomena, even in a simple system like the ferromagnetic Ising model. We look at two specific networks, representative of the broader family, and obtain the exact thermodynamic behavior of the Ising model on these networks through a renormalization-group (RG) approach. In the first case we consider a scale-free network with a varying probability p of long-range bonds, and calculate the RG flows of the quenched bond probability distribution. For p < 0.494, where the network is non-small-world, we find power-law critical behavior, with critical exponents continuously varying with p. For p ≥ 0.494, coinciding with the onset of small-world scaling, there is a very interesting phase transition: a Berezinskii-Kosterlitz-Thouless (BKT) singularity between a long-range-ordered phase at low temperatures and algebraic order at high temperatures, with zero magnetization but power-law decay of correlations. This is one of the few examples of such a singularity where there is no apparent mapping of the system onto an XY magnet. In the second case the network is composed of tightly-knit communities nested hierarchically with fractal scaling, and we vary the ratio K/J of inter- to intra-community couplings. At high temperatures or small K/J we have a disordered phase with a Griffiths singularity in the free energy, due to the presence of rare large clusters. As the temperature is lowered, true long-range order is not seen, but there is a transition to algebraic order. The existence of slowly decaying pair correlations is unexpected in a fat-tailed scale-free network, where correlations longer than nearest-neighbor are typically suppressed. The observed thermodynamic phenomena - such as Griffiths singularities, BKT transitions, and algebraic order - are not unique to these two examples. Using RG analysis and duality arguments, we can show that these unusual behaviors characterize a much larger class of hierarchical lattice complex networks.

M. Hinczewski and A.N. Berker, Phys. Rev. E 73, 066126 (2006); cond-mat/0512073. M. Hinczewski, Phys. Rev. E 75, 061104 (2007); cond-mat/0701349.

Hosted by Royce Zia.

We focus on the distribution of the total particle current in a simple symmetric exclusion process on a one dimensional lattice with periodic boundary conditions (hard-core particles performing unbiased random walks). Another quantity of interest is the activity defined as the total number of particle hops (irrespective of their direction) that have taken place over a large time interval. From the probability distribution function of these two quantities in the long time limit, we build the related large deviation functions. These are dynamical analogs of, e.g., the intensive free energy that appears in standard equilibrium thermodynamics. We show that there exist regimes in which fluctuations of the current or of the activity display a universal scaling form, governed by the same scaling function, valid beyond the particular case of the symmetric exclusion process.

Work in collaboration with C. Appert-Rolland, B. Derrida, V. Lecomte.

Hosted by Michel Pleimling and Uwe Täuber.

The translation process in bacteria has been under intensive study. During translation, ribosomes, a type of macromolecules, read the genetic code in the form of codons on a messenger RNA template (mRNA) and assemble amino acids to a polypeptide chain which folds into a functioning protein product. A key question concerns the quantitative effect of different elongation rates, associated with different codons, on the overall translation efficiency. Starting with a simple particle transport model, the totally asymmetric simple exclusion process (TASEP), we incorporate the essential components of the translation process: Ribosomes, cognate tRNA concentrations, and messenger RNA (mRNA) templates correspond to particles, hopping rates, and the underlying lattice, respectively. Using simulations and mean-field approximations to obtain the stationary currents (the protein production rates) associated with different mRNA sequences, we are especially interested in the effect of slow codons, i.e., codons which are associated with rare tRNAs and are therefore translated very slowly. As the first step, we look at a "designed sequence" with one and two slow codons and quantify the marked impact of their spatial distribution to the currents. Extending the results to several mRNA sequences taken from real genes, we argue that an effective translation rate including the information from the vicinity of each codon needs to be taken into consideration when seeking an efficient strategy to optimize the protein production.

Hosted by Beate Schmittmann.

Self-organized spatio-temporal pattern formation arises in various semiconductor nanostructures [1]. Our focus is on control of those patterns by time-delayed feedback methods [2]. On one hand, deterministic chaos can be suppressed, and unstable fixed points and periodic states can be stabilized. On the other hand, purely noise-induced patterns can be considered, and their temporal coherence and time-scales can be controlled. Our findings are applied to various nanosystems: (i) double-barrier resonant-tunneling diode, (ii) semiconductor superlattices, and (iii) semiconductor lasers.

[1] E. Schöll, Nonlinear spatio-temporal dynamics and chaos in semiconductors (Cambridge University Press, Cambridge, 2001). [2] E. Schöll and H.G. Schuster (Eds.): Handbook of Chaos Control (Wiley-VCH, Weinheim, 2008), second completely revised and enlarged edition.

Hosted by Beate Schmittmann.

A dual to the Aharonov-Bohm effect exists, whereby an electric field generates a quantum phase along the path of a magnetic moment or spin. The dual quantum phase is referred to as the Aharonov-Casher phase. Through the Aharonov-Casher phase, spin-orbit interaction is predicted to produce a new collective state of matter which can be regarded as a spin dual to the fractional quantum Hall state. The fractional quantum Hall state is induced by an applied magnetic field under Coulombic electron-electron interactions in systems where kinetic energy is quenched. The new spin dual state in turn is predicted under applied electric fields when the ratio of effective spin-spin interactions to kinetic energy is high. We present experimental and materials conditions of spin-orbit interaction, spin-spin interactions and electric fields under which the new state may be observed.

Bi-dimensional SU(N) gauge theory is a simple but not trivial model which has many connections with other different theories among them string theories, statistical mechanics and random walk theories. In this seminar I am going to introduce a new large N phase transition in YM₂ which appears when the theory is defined over a surface with the topology of a sphere. The transition is the analogous of the cut off phase transition in the context of random walks theory. Exploiting the relations with fermion system and string theories I describe the properties of the different phases.

There are many qubit designs based on small superconducting circuits containing Josephson junctions. The experimental milestones achieved until now include observation of coherent superposition of states (e.g. of two charge states of a superconducting island, or of two directions of current flow in a loop), single qubit operations, coupling of two qubits, and laser operation. However, the coherence times of superconducting qubits are still relatively short (less than a microsecond). In charge qubits this is due to the 1/f charge noise originating from the environment. One strategy of dealing with resulting decoherence is to drive the qubit by a series of short pulses so that the effect of the noise is suppressed. I will discuss the application of such "dynamical decoupling" approach to a qubit affected by classical noise. Our calculations show that the coherence time can be enhanced by properly chosen pulse sequences. Furthermore, one can extract information about the noise spectral density from time-dependence of decoherence. This could be useful since the microscopic origin of noise affecting the superconducting qubits is still controversial. I will discuss the possibility that the charge fluctuations in the environment occur due to the processes of correlated tunneling of pairs of electrons from the impurities in the substrate into the superconductor. I will present a quantum-mechanical treatment of this "Andreev fluctuator" bath using non-equilibrium Keldysh technique, which allows one to easily incorporate the effect of driving the qubit by pulses into the calculation of decoherence.

Hosted by Giti Khodaparast.