Classical ultrarelativistic bremsstrahlung in extra dimensions

The emitted energy and the cross-section of classical scalar bremsstrahlung in massive particle collisions in D=4+d dimensional Minkowski space M_D as well as in the brane world M_4 \times T^d is computed to leading ultra-relativistic order. The particles are taken to interact in the first case via the exchange of a bulk massless scalar field \Phi and in the second with an additional massless scalar \phi confined together with the particles on the brane. Energy is emitted as \Phi radiation in the bulk and/or \phi radiation on the brane. In contrast to the quantum Born approximation, the classical result is unambiguous and valid in a kinematical region which is also specified. For D=4 the results are in agreement with corresponding expressions in classical electrodynamics.Comment: Preprint number adde

Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding

Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in each step the ribosome moves forward by one codon and, simultaneously, elongates the protein by one amino acid. We present a theoretical model that captures most of the main steps in the mechano-chemical cycle of a ribosome. The stochastic movement of the ribosome consists of an alternating sequence of pause and translocation; the sum of the durations of a pause and the following translocation is the time of dwell of the ribosome at the corresponding codon. We derive the analytical expression for the distribution of the dwell times of a ribosome in our model. Whereever experimental data are available, our theoretical predictions are consistent with those results. We suggest appropriate experiments to test the new predictions of our model, particularly, the effects of the quality control mechanism of the ribosome and that of their crowding on the mRNA track.Comment: This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is available online at DOI:10.1088/1478-3975/8/2/02600

Cyclotron resonance of extremely conductive 2D holes in high Ge content strained heterostructures

Cyclotron resonance has been observed in steady and pulsed magnetic fields from high conductivity holes in Ge quantum wells. The resonance positions, splittings and linewidths are compared to calculations of the hole Landau levels

Coarsening in a Driven Ising Chain with Conserved Dynamics

We study the low-temperature coarsening of an Ising chain subject to spin-exchange dynamics and a small driving force. This dynamical system reduces to a domain diffusion process, in which entire domains undergo nearest-neighbor hopping, except for the shortest domains -- dimers -- which undergo long-range hopping. This system is characterized by two independent length scales: the average domain length L(t)~t^{1/2} and the average dimer hopping distance l(t)~ t^{1/4}. As a consequence of these two scales, the density C_k(t) of domains of length k does not obey scaling. This breakdown of scaling also leads to the density of short domains decaying as t^{-5/4}, instead of the t^{-3/2} decay that would arise from pure domain diffusion.Comment: 7 pages, 9 figures, revtex 2-column forma

Equation of State for Macromolecules of Variable Flexibility in Good Solvents: A Comparison of Techniques for Monte Carlo Simulations of Lattice Models

The osmotic equation of state for the athermal bond fluctuation model on the simple cubic lattice is obtained from extensive Monte Carlo simulations. For short macromolecules (chain length N=20) we study the influence of various choices for the chain stiffness on the equation of state. Three techniques are applied and compared in order to critically assess their efficiency and accuracy: the repulsive wall method, the thermodynamic integration method (which rests on the feasibility of simulations in the grand canonical ensemble), and the recently advocated sedimentation equilibrium method, which records the density profile in an external (e.g. gravitation-like) field and infers, via a local density approximation, the equation of state from the hydrostatic equilibrium condition. We confirm the conclusion that the latter technique is far more efficient than the repulsive wall method, but we find that the thermodynamic integration method is similarly efficient as the sedimentation equilibrium method. For very stiff chains the onset of nematic order enforces the formation of isotropic-nematic interface in the sedimentation equilibrium method leading to strong rounding effects and deviations from the true equation of state in the transition regime.Comment: 32 pages, 18 figures, submitted to Phys.Rev.E; one paragraph added to conclusions sectio

Analytical hierarchy process as a tool supporting a decision-making for assessment of the risk of transboundary infectious animal disease introduction to the Russian Federation and previously disease-free territories

The livestock industry is increasingly taking its place in the economy of the Russian Federation. Its export potential is actively growing. Already, up to 10% of agricultural products are exported to foreign markets. The demand for food steadily increases during crises, which in turn increases the role of the veterinary service, whose tasks include protecting the country’s territory from the introduction of infectious diseases of animals from foreign countries; implementation of measures to prevent and eliminate infectious and other diseases in agricultural, domestic, zoo and other animals, fur-bearing animals, birds, fish and bees, as well as the implementation of plans of the regional veterinary service in the field of animal husbandry. The article assesses the validity of the possibilities and use of modern methods of analyzing and predicting the spread of animal morbidity, identifying cause-and-effect relationships and the extent of the spread of particularly dangerous animal diseases. The authors propose to consider the possibility of using the mathematical method of hierarchy analysis as a scientifically sound decisionmaking support tool when assessing the risk of introducing trans-border infectious animal diseases into previously prosperous territories of the Russian Federation. This approach can be used in the process of choosing the most appropriate alternative from several risk assessment options. The Hierarchy Analysis Method (MAI) is a mathematical tool for a qualitative systematic approach to solving decision-making problems. This method was developed by the American scientist Thomas Lewis Saati in 1970, since then it has been actively developing and widely used in practice. The hierarchy analysis method can be used not only to compare objects, but also to solve more complex management and forecasting tasks

Persistence in Cluster--Cluster Aggregation

Persistence is considered in diffusion--limited cluster--cluster aggregation, in one dimension and when the diffusion coefficient of a cluster depends on its size $s$ as $D(s) \sim s^\gamma$. The empty and filled site persistences are defined as the probabilities, that a site has been either empty or covered by a cluster all the time whereas the cluster persistence gives the probability of a cluster to remain intact. The filled site one is nonuniversal. The empty site and cluster persistences are found to be universal, as supported by analytical arguments and simulations. The empty site case decays algebraically with the exponent $\theta_E = 2/(2 - \gamma)$. The cluster persistence is related to the small $s$ behavior of the cluster size distribution and behaves also algebraically for $0 \le \gamma < 2$ while for $\gamma < 0$ the behavior is stretched exponential. In the scaling limit $t \to \infty$ and $K(t) \to \infty$ with $t/K(t)$ fixed the distribution of intervals of size $k$ between persistent regions scales as $n(k;t) = K^{-2} f(k/K)$, where $K(t) \sim t^\theta$ is the average interval size and $f(y) = e^{-y}$. For finite $t$ the scaling is poor for $k \ll t^z$, due to the insufficient separation of the two length scales: the distances between clusters, $t^z$, and that between persistent regions, $t^\theta$. For the size distribution of persistent regions the time and size dependences separate, the latter being independent of the diffusion exponent $\gamma$ but depending on the initial cluster size distribution.Comment: 14 pages, 12 figures, RevTeX, submitted to Phys. Rev.

A convolute diversity of the Auriculariales (Agaricomycetes, Basidiomycota) with sphaeropedunculate basidia

Morphological and DNA data show that effused representatives of the Auriculariales (Basidiomycota) with sphaeropedunculate basidia belong to eleven genera of which seven are dealt with in this study. Among them, Myxarium is the largest genus containing 21 accepted species of which nine are reintroduced below and five are described as new. Protodontia is limited to three species only, P. subgelatinosa (the generic type) and two newly described species from Africa. Protoacia is a new monotypic genus for P. delicata, sp. nov., widely distributed on coniferous hosts in Eurasia. Myxariellum is erected for two new species with smooth hymenophore from northwestern North America while Gelacantha is introduced for G. pura, a new species with hydnoid hymenophore from Caucasus. Our data do not confirm the present synonymy of Sebacina sphaerospora with Tremella glaira, and these species are placed in two separate genera - Hydrophana, gen. nov., and Ofella, gen. nov., respectively. A key to European Myxarium and similar-looking species is included.Peer reviewe

Anomalous self-diffusion in the ferromagnetic Ising chain with Kawasaki dynamics

We investigate the motion of a tagged spin in a ferromagnetic Ising chain evolving under Kawasaki dynamics. At equilibrium, the displacement is Gaussian, with a variance growing as $A t^{1/2}$. The temperature dependence of the prefactor $A$ is derived exactly. At low temperature, where the static correlation length $\xi$ is large, the mean square displacement grows as $(t/\xi^2)^{2/3}$ in the coarsening regime, i.e., as a finite fraction of the mean square domain length. The case of totally asymmetric dynamics, where $(+)$ (resp. $(-)$) spins move only to the right (resp. to the left), is also considered. In the steady state, the displacement variance grows as $B t^{2/3}$. The temperature dependence of the prefactor $B$ is derived exactly, using the Kardar-Parisi-Zhang theory. At low temperature, the displacement variance grows as $t/\xi^2$ in the coarsening regime, again proportionally to the mean square domain length.Comment: 22 pages, 8 figures. A few minor changes and update

Integrating protein-protein interactions and text mining for protein function prediction

<p>Abstract</p> <p>Background</p> <p>Functional annotation of proteins remains a challenging task. Currently the scientific literature serves as the main source for yet uncurated functional annotations, but curation work is slow and expensive. Automatic techniques that support this work are still lacking reliability. We developed a method to identify conserved protein interaction graphs and to predict missing protein functions from orthologs in these graphs. To enhance the precision of the results, we furthermore implemented a procedure that validates all predictions based on findings reported in the literature.</p> <p>Results</p> <p>Using this procedure, more than 80% of the GO annotations for proteins with highly conserved orthologs that are available in UniProtKb/Swiss-Prot could be verified automatically. For a subset of proteins we predicted new GO annotations that were not available in UniProtKb/Swiss-Prot. All predictions were correct (100% precision) according to the verifications from a trained curator.</p> <p>Conclusion</p> <p>Our method of integrating CCSs and literature mining is thus a highly reliable approach to predict GO annotations for weakly characterized proteins with orthologs.</p