45915 research outputs found
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Crystallization of ion clouds in octupole traps: structural transitions, core melting, and scaling laws
No full textThe stable structures and melting properties of ion clouds in isotropic octupole traps are investigated using a combination of semianalytical and numerical models, with a particular emphasis at finite-size scaling effects. Small-size clouds are found to be hollow and arranged in shells corresponding approximately to the solutions of the Thomson problem. The shell structure is lost in clusters containing more than a few thousands of ions, the inner parts of the cloud becoming soft and amorphous. While melting is triggered in the core shells, the melting temperature follows the rule expected for three-dimensional dense particles, with a depression scaling linearly with the inverse radius
Electrically tunable Dicke effect in a double-ring resonator
No full textWe study the finite-element method analysis of the Dicke effect using numerical simulations in an all-optical system of an optical waveguide side-coupled to two interacting ring resonators in a liquid crystal environment. The system is shown to exhibit all the signatures of the Dicke effect under active and reversible control by an applied voltage
Denaturation of circular DNA: supercoil mechanism 2011
No full textThe denaturation transition which takes place in circular DNA is analyzed by extending the Poland-Scheraga (PS) model to include the winding degrees of freedom. We consider the case of a homopolymer whereby the winding number of the double-stranded helix, released by a loop denaturation, is absorbed by supercoils. We find that as in the case of linear DNA, the order of the transition is determined by the loop exponent c. However the first-order transition displayed by the PS model for c > 2 in linear DNA is replaced by a continuous transition with arbitrarily high order as c approaches 2, while the second-order transition found in the linear case in the regime 1 < c <= 2 disappears. In addition, our analysis reveals that melting under fixed linking number is a condensation transition, where the condensate is a macroscopic loop which appears above the critical temperature
Spectral singularities of complex scattering potentials and ınfinite reflection and transmission coefficients at real energies
No full textSpectral singularities are spectral points that spoil the completeness of the eigenfunctions of certain non-Hermitian Hamiltonian operators. We identify spectral singularities of complex scattering potentials with the real energies at which the reflection and transmission coefficients tend to infinity, i.e., they correspond to resonances having a zero width. We show that a waveguide modeled using such a potential operates like a resonator at the frequencies of spectral singularities. As a concrete example, we explore the spectral singularities of an imaginary PT-symmetric barrier potential and demonstrate the above resonance phenomenon for a certain electromagnetic waveguide
Identification of ligand binding sites of proteins using the Gaussian network model
No full textThe nonlocal nature of the protein-ligand binding problem is investigated via the Gaussian Network Model with which the residues lying along interaction pathways in a protein and the residues at the binding site are predicted. The predictions of the binding site residues are verified by using several benchmark systems where the topology of the unbound protein and the bound protein-ligand complex are known. Predictions are made on the unbound protein. Agreement of results with the bound complexes indicates that the information for binding resides in the unbound protein. Cliques that consist of three or more residues that are far apart along the primary structure but are in contact in the folded structure are shown to be important determinants of the binding problem. Comparison with known structures shows that the predictive capability of the method is significant
The information coded in the yeast response elements accounts for most of the topological properties of its transcriptional regulation network
No full textThe regulation of gene expression in a cell relies to a major extent on transcription factors, proteins which recognize and bind the DNA at specific binding sites (response elements) within promoter regions associated with each gene. We present an information theoretic approach to modeling transcriptional regulatory networks, in terms of a simple "sequence-matching" rule and the statistics of the occurrence of binding sequences of given specificity in random promoter regions. The crucial biological input is the distribution of the amount of information coded in these cognate response elements and the length distribution of the promoter regions. We provide an analysis of the transcriptional regulatory network of yeast Saccharomyces cerevisiae, which we extract from the available databases, with respect to the degree distributions, clustering coefficient, degree correlations, rich-club coefficient and the k-core structure. We find that these topological features are in remarkable agreement with those predicted by our model, on the basis of the amount of information coded in the interaction between the transcription factors and response elements
The present and future opportunities of the Rare Cancer network: an international consortium for advancement of oncologic care
No full textTo date, the Rare Cancer Network (RCN) has initiated more than 90 studies and 54 peer-reviewed publications were produced as a result. The Second International Symposium of the Rare Cancer Network recently took place in Istanbul, Turkey on April 17-18, 2015, and update was given on multiple currently ongoing projects, while also giving room for new proposals which will shape the direction of future studies for the group. This companion issue of the RCN Proceedings summarized the findings of this meeting, while also serving as a call for fresh projects and papers which will continue to energize the group and advance the oncologic science. A brief introduction to the principles, history, and vision of the RCN was also included. To review, the academic year of 2014-15 marked an enormous success for the international members of the RCN, with the generation of 8 fully published papers and more than 12 newly proposed topics. By the collective efforts of all RCN members, in the future, we look forward to the upcoming opportunities in continuing to advance the standard of chemo-and radiotherapeutic oncologic care for selected rare tumor topics. The studies of these rare cancers often do not allow the design and execution of prospectively enrolled trials; however, these uncommon malignancies do impact the humankind and add to its suffering globally in significant ways
Antimicrobial activities of phosphonium containing polynorbornenes
No full textIn this study, amphiphilic polyoxanorbornene with different alkyl and aromatic phosphonium side chains was synthesized. The biological activities of these polymers were determined by the minimal inhibitory concentration (MIC) against E. coli, S. aureus, M. tuberculosis and the yeast C. albicans, and cytotoxicity studies on red blood cells were performed. A series of polymers with different alkyl and aromatic substituents (methyl, ethyl, tripropyl, tert-butyl, phenyl, and tris 4-methoxyphenyl) and two types different molecular weight, 3000 g mol(-1) and 10 000 g mol(-1), were prepared. It was observed that the biological activity of the polymers with aromatic group substituents had an MIC of 16, 8, 64 and 128 mu g mL(-1) against E. coli, S. aureus, M. tuberculosis and C. albicans, respectively, while those with nonaromatic carbons had a higher MIC compared to those with aromatic carbons. The aromaticity of the repeat unit had impressive effects on hemolytic activities as well. Zeta potential measurements of E. coli incubated with active and inactive polymer concentration revealed a relationship between the MIC and membrane surface charge density. Polymers bearing aromatic groups killed the bacteria with widespread damage after the polymers, holding the threshold concentration, were added to the bacteria
Density of a random interval catch digraph family and its use for testing uniformity
No full textWe consider (arc) density of a parameterized interval catch digraph (ICD) family with random vertices residing on the real line. The ICDs are random digraphs where randomness lies in the vertices and are defined with two parameters, a centrality parameter and an expansion parameter, hence they will be referred as central similarity ICDs (CS-ICDs). We show that arc density of CS-ICDs is a U-statistic for vertices being from a wide family of distributions with support on the real line, and provide the asymptotic (normal) distribution for the (interiors of) entire ranges of centrality and expansion parameters for one dimensional uniform data. We also determine the optimal parameter values at which the rate of convergence (to normality) is fastest. We use arc density of CS-ICDs for testing uniformity of one dimensional data, and compare its performance with arc density of another ICD family and two other tests in literature (namely, Kolmogorov-Smirnov test and Neyman’s smooth test of uniformity) in terms of empirical size and power. We show that tests based on ICDs have better power performance for certain alternatives (that are symmetric around the middle of the support of the data)
Broadly tunable continuous-wave solid-state red source based on intracavity-doubled Cr (4+): forsterite laser
No full textThis work describes the development and characterization of a continuous-wave (cw) room-temperature intracavity-doubled Cr4+:forsterite laser which produces broadly tunable red radiation. Such a source is potentially important in spectroscopy, display technologies, and medical applications. In the experiments, a 2-cm-long Cr4+:forsterite crystal was placed in an astigmatically compensated x-cavity which was end-pumped by a 1064-nm Nd:YAG laser. The crystal which had a small-signal pump absorption of 68% was maintained at 20 degreesC. An intracavity Brewster-cut SF10 prism was used to tune the output of the laser. Intracavity frequency doubling was achieved by using a periodically poled lithium niobate (PPLN) crystal which had 8 different poling periods. The PPLN crystal was placed inside the resonator between a curved folding mirror and the curved output coupler. The transmission of the output coupler was 2.6% at 1260 nm. The PPLN temperature was maintained at 188 degreesC. By translating the PPLN crystal through sections with different poling periods, second harmonic generation was obtained in the wavelength region between 613 and 655 run. With an incident pump power of 6.8 W at 1064 rim, the Cr4+:forsterite laser produced 245 mW of cw output power at 1260 nm and intracavity frequency doubling yielded 45 mW at 630 nm