Material Dependence of the Wire-Particle Casimir Interaction

We study the Casimir interaction between a metallic cylindrical wire and a metallic spherical particle by employing the scattering formalism. At large separations, we derive the asymptotic form of the interaction. In addition, we find the interaction between a metallic wire and an isotropic atom, both in the non-retarded and retarded limits. We identify the conditions under which the asymptotic Casimir interaction does not depend on the material properties of the metallic wire and the particle. Moreover, we compute the exact Casimir interaction between the particle and the wire numerically. We show that there is a complete agreement between the numerics and the asymptotic energies at large separations. For short separations, our numerical results show good agreement with the proximity force approximation

Apex Exponents for Polymer--Probe Interactions

We consider self-avoiding polymers attached to the tip of an impenetrable probe. The scaling exponents $\gamma_1$ and $\gamma_2$, characterizing the number of configurations for the attachment of the polymer by one end, or at its midpoint, vary continuously with the tip's angle. These apex exponents are calculated analytically by $\epsilon$-expansion, and numerically by simulations in three dimensions. We find that when the polymer can move through the attachment point, it typically slides to one end; the apex exponents quantify the entropic barrier to threading the eye of the probe

Universality versus material dependence of fluctuation forces between metallic wires

We calculate the Casimir interaction between two parallel wires and between a wire and a metall plate. The dielectric properties of the objects are described by the plasma, Drude and perfect metal models. We find that at asymptotically large separation interactions involving plasma wires and/or plates are independent of the material properties, but depend on the dc conductivity $\sigma$ for Drude wires. Counterintuitively, at intermediate separations the interaction involving Drude wires can become independent of $\sigma$. At smaller separations, we compute the interaction numerically and observe an approach to the proximity approximation

Collective charge fluctuations and Casimir interactions for quasi one-dimensional metals

We investigate the Casimir interaction between two parallel metallic cylinders and between a metallic cylinder and plate. The material properties of the metallic objects are implemented by the plasma, Drude and perfect metal model dielectric functions. We calculate the Casimir interaction numerically at all separation distances and analytically at large separations. The large-distance asymptotic interaction between one plasma cylinder parallel to another plasma cylinder or plate does not depend on the material properties, but for a Drude cylinder it depends on the dc conductivity $\sigma$. At intermediate separations, for plasma cylinders the asymptotic interaction depends on the plasma wave length $\lambda_{\rm p}$ while for Drude cylinders the Casimir interaction can become independent of the material properties. We confirm the analytical results by the numerics and show that at short separations, the numerical results approach the proximity force approximation

Elastic Lattice Polymers

We study a model of "elastic" lattice polymer in which a fixed number of monomers $m$ is hosted by a self-avoiding walk with fluctuating length $l$. We show that the stored length density $\rho_m = 1 - /m$ scales asymptotically for large $m$ as $\rho_m=\rho_\infty(1-\theta/m + ...)$, where $\theta$ is the polymer entropic exponent, so that $\theta$ can be determined from the analysis of $\rho_m$. We perform simulations for elastic lattice polymer loops with various sizes and knots, in which we measure $\rho_m$. The resulting estimates support the hypothesis that the exponent $\theta$ is determined only by the number of prime knots and not by their type. However, if knots are present, we observe strong corrections to scaling, which help to understand how an entropic competition between knots is affected by the finite length of the chain.Comment: 10 page

What drives the translocation of stiff chains?

We study the dynamics of the passage of a stiff chain through a pore into a cell containing particles that bind reversibly to it. Using Brownian Molecular Dynamics simulations we investigate the mean-first-passage time as a function of the length of the chain inside, for different concentrations of binding particles. As a consequence of the interactions with these particles, the chain experiences a net force along its length whose calculated value from the simulations accounts for the velocity at which it enters the cell. This force can in turn be obtained from the solution of a generalized diffusion equation incorporating an effective Langmuir adsorption free energy for the chain plus binding particles. These results suggest a role of binding particles in the translocation process which is in general quite different from that of a Brownian ratchet. Furthermore, non-equilibrium effects contribute significantly to the dynamics, \emph{e.g.}, the chain often enters the cell faster than particle binding can be saturated, resulting in a force several times smaller than the equilibrium value.Comment: 7 pages, 4 figure

Completeness and properness of refinement operators in inductive logic programming

AbstractWithin Inductive Logic Programming, refinement operators compute a set of specializations or generalizations of a clause. They are applied in model inference algorithms to search in a quasi-ordered set for clauses of a logical theory that consistently describes an unknown concept. Ideally, a refinement operator is locally finite, complete, and proper. In this article we show that if an element in a quasi-ordered set 〈S, ≥〉 has an infinite or incomplete cover set, then an ideal refinement operator for 〈S, ≥〉 does not exist. We translate the nonexistence conditions to a specific kind of infinite ascending and descending chains and show that these chains exist in unrestricted sets of clauses that are ordered by θ-subsumption. Next we discuss how the restriction to a finite ordered subset can enable the construction of ideal refinement operators. Finally, we define an ideal refinement operator for restricted θ-subsumption ordered sets of clauses

Antiviral activity of Holothuria sp. a sea cucumber against herpes simplex virus type 1 (HSV-1)

BACKGROUND: Finding the new bioactive compounds with antiviral activity from the natural resources are in interest of many drug discovery scientists. Sea cucumber is among the marine organisms a traditional food item in Asia with different applications in traditional medicine. METHODS: In current study, a cold water extract of the Holothuria sp, one type Persian Gulf’s sea cucumber was evaluated for its antiviral effects against KOS strain of Herpes Simplex Virus tyoe 1 (HSV-1) in cell culture. The half maximal inhibitory concentration (IC50) values were calculated for anti-adsorption activity and intracellular antiviral activity of the crude extract separately. RESULTS: The extract exhibited antiviral activity not only against the virus adsorption to the cells, but also on virus intracellular replication.The CC50 for sea cucumber extract was 32.57 mg/ml. The IC50 values for the inhibition of the virus adsorption to the cells and virus intracellular replication were 120.2 and 189.9 μg/ml respectively. Selectivity index (SI) value for anti-adsorption activity was 189 while that value for the extract’s intracellular antiviral activity was 172. CONCLUSIONS: The results showed that Holothuria sp, water extract has remarkable antiviral effect against HSV-1 in cell culture and it is crucial to investigate the mechanism(s) of action of extract. Moreover, identification of the effective compound(s) within the extract would be necessary for future studies towards developing the new natural antiviral agent against HSV-1

Validation and assessment of variant calling pipelines for next-generation sequencing

Background: The processing and analysis of the large scale data generated by next-generation sequencing (NGS) experiments is challenging and is a burgeoning area of new methods development. Several new bioinformatics tools have been developed for calling sequence variants from NGS data. Here, we validate the variant calling of these tools and compare their relative accuracy to determine which data processing pipeline is optimal. Results: We developed a unified pipeline for processing NGS data that encompasses four modules: mapping, filtering, realignment and recalibration, and variant calling. We processed 130 subjects from an ongoing whole exome sequencing study through this pipeline. To evaluate the accuracy of each module, we conducted a series of comparisons between the single nucleotide variant (SNV) calls from the NGS data and either gold-standard Sanger sequencing on a total of 700 variants or array genotyping data on a total of 9,935 single-nucleotide polymorphisms. A head to head comparison showed that Genome Analysis Toolkit (GATK) provided more accurate calls than SAMtools (positive predictive value of 92.55% vs. 80.35%, respectively). Realignment of mapped reads and recalibration of base quality scores before SNV calling proved to be crucial to accurate variant calling. GATK HaplotypeCaller algorithm for variant calling outperformed the UnifiedGenotype algorithm. We also showed a relationship between mapping quality, read depth and allele balance, and SNV call accuracy. However, if best practices are used in data processing, then additional filtering based on these metrics provides little gains and accuracies of >99% are achievable. Conclusions: Our findings will help to determine the best approach for processing NGS data to confidently call variants for downstream analyses. To enable others to implement and replicate our results, all of our codes are freely available at http://metamoodics.org/wes

Strong Casimir force reduction through metallic surface nanostructuring

The Casimir force between bodies in vacuum can be understood as arising from their interaction with an infinite number of fluctuating electromagnetic quantum vacuum modes, resulting in a complex dependence on the shape and material of the interacting objects. Becoming dominant at small separations, the force plays a significant role in nanomechanics and object manipulation at the nanoscale, leading to a considerable interest in identifying structures where the Casimir interaction behaves significantly different from the well-known attractive force between parallel plates. Here we experimentally demonstrate that by nanostructuring one of the interacting metal surfaces at scales below the plasma wavelength, an unexpected regime in the Casimir force can be observed. Replacing a flat surface with a deep metallic lamellar grating with sub-100 nm features strongly suppresses the Casimir force and for large inter-surfaces separations reduces it beyond what would be expected by any existing theoretical prediction.Comment: 11 pages, 8 figure