Stochastic Cluster Series expansion for quantum spin systems

In this paper we develop a cluster-variant of the Stochastic Series expansion method (SCSE). For certain systems with longer-range interactions the SCSE is considerably more efficient than the standard implementation of the Stochastic Series Expansion (SSE), at low temperatures. As an application of this method we calculated the T=0-conductance for a linear chain with a (diagonal) next nearest neighbor interaction.Comment: 5 pages, 7 figure

Impending anterior ischemic optic neuropathy with elements of retinal vein occlusion in a patient on interferon for polycythemia vera.

We describe the course and likely pathophysiology of impending anterior ischemic optic neuropathy (AION) and retinal vein occlusion in a 56-year-old man with polycythemia vera managed with interferon alpha for 2 years. Our patient presented with decreased vision, scintillating scotomata, and floaters. Fundus examination findings and results of a fluorescein angiogram led to the diagnosis of impending AION and retinal vein occlusion. Considering that both polycythemia vera and interferon have possible influences on vascular occlusion and optic disc edema, we stopped interferon treatment and immediately attempted to treat the polycythemia vera empirically with pentoxifylline and any interferon-associated inflammation with prednisone. Our patient experienced complete resolution of fundus abnormalities and return of normal vision within 3 weeks, which may be attributed to our successful treatment of both etiologies. Thus, further study is warranted to elucidate the treatment of both polycythemia vera and interferon-induced impending AION

Hole Pairs in the Two-Dimensional Hubbard Model

The interactions between holes in the Hubbard model, in the low density, intermediate to strong coupling limit, are investigated. Dressed spin polarons in neighboring sites have an increased kinetic energy and an enhanced hopping rate. Both effects are of the order of the hopping integral and lead to an effective attraction at intermediate couplings. Our results are derived by systematically improving mean field calculations. The method can also be used to derive known properties of isolated spin polarons.Comment: 4 page

Modelling the Self-Assembly of Virus Capsids

We use computer simulations to study a model, first proposed by Wales [1], for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of thermodynamic and geometric factors can be qualitatively related to the potential energy landscape structure of the assembling system. Even though the model is strongly coarse-grained, it exhibits a number of features also observed in experiments, such as sigmoidal assembly dynamics, hysteresis in capsid formation and numerous kinetic traps. We also investigate the effect of macromolecular crowding on the assembly dynamics. Crowding agents generally reduce capsid yields at optimal conditions for non-crowded assembly, but may increase yields for parameter regimes away from the optimum. Finally, we generalize the model to a larger triangulation number T = 3, and observe more complex assembly dynamics than that seen for the original T = 1 model.Comment: 16 pages, 11 figure

Evolutionary Dynamics in a Simple Model of Self-Assembly

We investigate the evolutionary dynamics of an idealised model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the self-assembly process. The relationship between the model's rule set and its resulting self-assembled structure can be viewed as a genotype-phenotype map and incorporated into a genetic algorithm. The rule sets evolve under selection for specified target structures. The corresponding, complex fitness landscape generates rich evolutionary dynamics as a function of parameters such as the population size, search space size, mutation rate, and method of recombination. Furthermore, these systems are simple enough that in some cases the associated model genome space can be completely characterised, shedding light on how the evolutionary dynamics depends on the detailed structure of the fitness landscape. Finally, we apply the model to study the emergence of the preference for dihedral over cyclic symmetry observed for homomeric protein tetramers

Hydrodynamic and Brownian Fluctuations in Sedimenting Suspensions

We use a mesoscopic computer simulation method to study the interplay between hydrodynamic and Brownian fluctuations during steady-state sedimentation of hard sphere particles for Peclet numbers (Pe) ranging from 0.1 to 15. Even when the hydrodynamic interactions are an order of magnitude weaker than Brownian forces, they still induce backflow effects that dominate the reduction of the average sedimentation velocity with increasing particle packing fraction. Velocity fluctuations, on the other hand, begin to show nonequilibrium hydrodynamic character for Pe > 1Comment: 4 pages 4 figures, RevTex, to appear in Phys. Rev. Lett. New version with some minor correction

Diffuse MeV Gamma-rays and Galactic 511 keV Line from Decaying WIMP Dark Matter

The origin of both the diffuse high-latitude MeV gamma-ray emission and the 511 keV line flux from the Galactic bulge are uncertain. Previous studies have invoked dark matter physics to independently explain these observations, though as yet none has been able to explain both of these emissions within the well-motivated framework of Weakly-Interacting Massive Particles (WIMPs). Here we use an unstable WIMP dark matter model to show that it is in fact possible to simultaneously reconcile both of these observations, and in the process show a remarkable coincidence: decaying dark matter with MeV mass splittings can explain both observations if positrons and photons are produced with similar branching fractions. We illustrate this idea with an unstable branon, which is a standard WIMP dark matter candidate appearing in brane world models with large extra dimensions. We show that because branons decay via three-body final states, they are additionally unconstrained by searches for Galactic MeV gamma-ray lines. As a result, such unstable long-lifetime dark matter particles provide novel and distinct signatures that can be tested by future observations of MeV gamma-rays.Comment: 19 pages, 4 figure

Force-induced rupture of a DNA duplex

The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed force sensors and nanotechnological devices. We argue that rupture must be understood as an activated process, where the duplex state is metastable and the strands will separate in a finite time that depends on the duplex length and the force applied. Thus, the critical shearing force required to rupture a duplex within a given experiment depends strongly on the time scale of observation. We use simple models of DNA to demonstrate that this approach naturally captures the experimentally observed dependence of the critical force on duplex length for a given observation time. In particular, the critical force is zero for the shortest duplexes, before rising sharply and then plateauing in the long length limit. The prevailing approach, based on identifying when the presence of each additional base pair within the duplex is thermodynamically unfavorable rather than allowing for metastability, does not predict a time-scale-dependent critical force and does not naturally incorporate a critical force of zero for the shortest duplexes. Additionally, motivated by a recently proposed force sensor, we investigate application of stress to a duplex in a mixed mode that interpolates between shearing and unzipping. As with pure shearing, the critical force depends on the time scale of observation; at a fixed time scale and duplex length, the critical force exhibits a sigmoidal dependence on the fraction of the duplex that is subject to shearing.Comment: 10 pages, 6 figure

Coarse-grained modelling of supercoiled RNA

We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. For negative supercoiling, we predict denaturation bubble formation in plectoneme end-loops, suggesting preferential plectoneme localisation in weak base sequences. OxRNA exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations.Comment: 8 pages + 5 pages Supplementary Materia