On practical applicability of the Jarzynski relation in statistical mechanics: a pedagogical example

We suggest and discuss a simple model of an ideal gas under the piston to gain an insight into the workings of the Jarzynski identity connecting the average exponential of the work over the non-equilibrium trajectories with the equilibrium free energy. We show that the Jarzynski identity is valid for our system due to the very rapid molecules belonging to the tail of the Maxwell distribution. For the most interesting extreme, when the system volume is large, while the piston is moving with large speed (compared to thermal velocity) for a very short time, the necessary number of independent experimental runs to obtain a reasonable approximation for the free energy from averaging the non-equilibrium work grows exponentially with the system size.Comment: 15 pages, 7 figures, submitted to JP

Topologically Driven Swelling of a Polymer Loop

Numerical studies of the average size of trivially knotted polymer loops with no excluded volume are undertaken. Topology is identified by Alexander and Vassiliev degree 2 invariants. Probability of a trivial knot, average gyration radius, and probability density distributions as functions of gyration radius are generated for loops of up to N=3000 segments. Gyration radii of trivially knotted loops are found to follow a power law similar to that of self avoiding walks consistent with earlier theoretical predictions.Comment: 6 pages, 4 figures, submitted to PNAS (USA) in Feb 200

Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants

Background: Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. Methods: Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea. Results: We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics. Conclusions: The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants

Investigation of passive flow control techniques to enhance the stall characteristics of a microlight aircraft

This report investigates the enhancement of aerodynamic stall characteristics of a Skyranger microlight aircraft by the use of passive flow control techniques, namely vortex generators and turbulators. Each flow control device is designed and scaled to application conditions. Force balance measurements and surface oil flow visualisation are carried out on a half-model of the microlight to further investigate the nature of the flow on the aircraft with and without the flow control devices. The results indicate a clear advantage to the use of turbulators compared with vortex generators. Turbulators increased the maximum lift coefficient by 2.8%, delayed the onset of stall by increasing the critical angle by 17.6% and reduced the drag penalty at both lower (pre-stall) and higher angles of attack by 8% compared to vortex generators. With vortex generators applied, the results indicated a delayed stall with an increase in the critical angle by 2% and a reduced drag penalty at higher angles of attack

Polymer translocation through a nanopore - a showcase of anomalous diffusion

The translocation dynamics of a polymer chain through a nanopore in the absence of an external driving force is analyzed by means of scaling arguments, fractional calculus, and computer simulations. The problem at hand is mapped on a one dimensional {\em anomalous} diffusion process in terms of reaction coordinate $s$ (i.e. the translocated number of segments at time $t$) and shown to be governed by an universal exponent $\alpha = 2/(2\nu+2-\gamma_1)$ whose value is nearly the same in two- and three-dimensions. The process is described by a {\em fractional} diffusion equation which is solved exactly in the interval $0 <s < N$ with appropriate boundary and initial conditions. The solution gives the probability distribution of translocation times as well as the variation with time of the statistical moments: $$, and $- < s(t)>^2$ which provide full description of the diffusion process. The comparison of the analytic results with data derived from extensive Monte Carlo (MC) simulations reveals very good agreement and proves that the diffusion dynamics of unbiased translocation through a nanopore is anomalous in its nature.Comment: 5 pages, 3 figures, accepted for publication in Phys. Rev.

Demonstration of the protective effects of fluorescent proteins in baculoviruses exposed to ultraviolet light inactivation

Autographa californica multiple nucleopolyhedrovirus (AcMNPV) recombinants, namely AcRFP produced by fusion of the red fluorescent protein (RFP) gene with the polyhedrin gene, and a recombinant (pAcUW21-23GFP) carrying the green fluorescent protein (GFP) in its viral envelope, were evaluated for their resistance to inactivation by ultraviolet light. AcRFP recombinants produced incomplete polyhedra with low infectivity for Trichoplusia ni larvae, whereas AcuW21-23GFP produced normal polyhedra with high infectivity. Electron microscopy of AcRFP CL14 showed the incorporation of very few viral particles into polyhedrin matrix protein material. The LC(50) for AcuW21-23GFP was 0.10 occlusion bodies/mm(2), whereas the LC(50) values for several AcRFP recombinants ranged from 20 to 329 occlusion bodies/mm(2). When both the RFP and GFP recombinants were exposed to ultraviolet light (UV-B 280–320 nm), the results support the conclusion that these fluorescent proteins afford some protection against its damaging effects. Abbreviation: / AcMNPV: Autographa californica multiple nucleopolyhedrovirus BV: budded virus CPE: cytopathogenic effect ECV: extracellular virus OB: occlusion body ODV: occlusion derived virus RFP: red fluorescent protein GFP: green fluorescent protein TCID(50): tissue culture infective dose at the 50 % level UV-B: ultraviolet light of 280–320 n

A classification framework for drug relapse prediction

This paper proposes a framework for relapse prediction using Artificial Neural Networkalgorithms among drug addicts at Pusat Rawatan Inabah. The data collected will be miningthrough Artificial Neural Network algorithms to generate patterns and useful knowledge andthen automatically classifying the relapse possibility. This research collaborates with PusatRawatan Inabah, which is one of the rehabilitation centers that provide a specific treatment torehabilitate the drug addicts from addiction. We expect that among the classification datamining algorithms, Artificial Intelligence Neural Network (ANN) is one of the bestalgorithms to predict relapse among drug addicts. This may help the rehabilitation center topredict relapse individually and the prediction result is hoped to prevent drug addicts fromrelapse.Keywords: classification; artificial neural network; drug addiction; Inabah rehabilitation

Model-based relative entropy stochastic search

Stochastic search algorithms are general black-box optimizers. Due to their ease of use and their generality, they have recently also gained a lot of attention in operations research, machine learning and policy search. Yet, these algorithms require a lot of evaluations of the objective, scale poorly with the problem dimension, are affected by highly noisy objective functions and may converge prematurely. To alleviate these problems, we introduce a new surrogate-based stochastic search approach. We learn simple, quadratic surrogate models of the objective function. As the quality of such a quadratic approximation is limited, we do not greedily exploit the learned models. The algorithm can be misled by an inaccurate optimum introduced by the surrogate. Instead, we use information theoretic constraints to bound the ‘distance’ between the new and old data distribution while maximizing the objective function. Additionally the new method is able to sustain the exploration of the search distribution to avoid premature convergence. We compare our method with state of art black-box optimization methods on standard uni-modal and multi-modal optimization functions, on simulated planar robot tasks and a complex robot ball throwing task. The proposed method considerably outperforms the existing approaches

Development of Parkinsonism following exposure to aripiprazole: two case reports

which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Introduction: Aripiprazole is a novel atypical neuroleptic used in the treatment of psychosis. A few recent studies have demonstrated an association between the use of aripiprazole and an exacerbation of Parkinsonism, although this relationship is poorly defined. To our knowledge, this is the first case series describing an onset of Parkinsonism in patients without prior history of Parkinson’s diseas