Structure and thermodynamics of a mixture of patchy and spherical colloids: a multi-body association theory with complete reference fluid information

A mixture of solvent particles with short-range, directional interactions and solute particles with short-range, isotropic interactions that can bond multiple times is of fundamental interest in understanding liquids and colloidal mixtures. Because of multi-body correlations predicting the structure and thermodynamics of such systems remains a challenge. Earlier Marshall and Chapman developed a theory wherein association effects due to interactions multiply the partition function for clustering of particles in a reference hard-sphere system. The multi-body effects are incorporated in the clustering process, which in their work was obtained in the absence of the bulk medium. The bulk solvent effects were then modeled approximately within a second order perturbation approach. However, their approach is inadequate at high densities and for large association strengths. Based on the idea that the clustering of solvent in a defined coordination volume around the solute is related to occupancy statistics in that defined coordination volume, we develop an approach to incorporate the complete information about hard-sphere clustering in a bulk solvent at the density of interest. The occupancy probabilities are obtained from enhanced sampling simulations but we also develop a concise parametric form to model these probabilities using the quasichemical theory of solutions. We show that incorporating the complete reference information results in an approach that can predict the bonding state and thermodynamics of the colloidal solute for a wide range of system conditions.Comment: arXiv admin note: text overlap with arXiv:1601.0438

A modified proximity approach in the fusion of heavy-ions

By using a suitable set of the surface energy coefficient, nuclear radius, and universal function, the original proximity potential 1977 is modified. The overestimate of the data by 4 % reported in the literature is significantly reduced. Our modified proximity potential reproduces the experimental data nicely compared to its older versions.Comment: 9 pages, 5 figures, Chin. Phys. lett.(2010) in pres

Contributions to the mixed-alkali effect in molecular dynamics simulations of alkali silicate glasses

The mixed-alkali effect on the cation dynamics in silicate glasses is analyzed via molecular dynamics simulations. Observations suggest a description of the dynamics in terms of stable sites mostly specific to one ionic species. As main contributions to the mixed--alkali slowdown longer residence times and an increased probability of correlated backjumps are identified. The slowdown is related to the limited accessibility of foreign sites. The mismatch experienced in a foreign site is stronger and more retarding for the larger ions, the smaller ions can be temporarily accommodated. Also correlations between unlike as well as like cations are demonstrated that support cooperative behavior.Comment: 10 pages, 12 figures, 1 table, revtex4, submitted to Phys. Rev.

NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures

Software packages NUFARM and NUCGEN, are described, which can be used to understand sequence directed structural variations in nucleic acids, by analysis and generation of non-uniform structures. A set of local inter basepair parameters (viz, tilt, roll, twist, shift, slide and rise) have been defined, which use geometry and coordinates of two successive basepairs only and can be used to generate polymeric structures with varying geometries for each of the 16 possible dinucleotide steps. Intra basepair parameters, propeller, buckle, opening and the C6...C8 distance can also be varied, if required, while the sugar phosphate backbone atoms are fixed in some standard conformation in each of the nucleotides. NUPARM can be used to analyse both DNA and RNA structures, with single as well as double stranded helices. The NUCGEN software generates double helical models with the backbone fixed in B-form DNA, but with appropriate modifications in the input data, it can also generate A-form DNA and RNA duplex structures

Voltage modulated electro-luminescence spectroscopy and negative capacitance - the role of sub-bandgap states in light emitting devices

Voltage modulated electroluminescence spectra and low frequency ({\leq} 100 kHz) impedance characteristics of electroluminescent diodes are studied. Voltage modulated light emission tracks the onset of observed negative capacitance at a forward bias level for each modulation frequency. Active participation of sub-bandgap defect states in minority carrier recombination dynamics is sought to explain the results. Negative capacitance is understood as a necessary dielectric response to compensate any irreversible transient changes in the minority carrier reservoir due to radiative recombinations mediated by slowly responding sub-bandgap defects. Experimentally measured variations of the in-phase component of modulated electroluminescence spectra with forward bias levels and modulation frequencies support the dynamic influence of these states in the radiative recombination process. Predominant negative sign of the in-phase component of voltage modulated electroluminescence signal further confirms the bi-molecular nature of light emission. We also discuss how these states can actually affect the net density of minority carriers available for radiative recombination. Results indicate that these sub-bandgap states can suppress external quantum efficiency of such devices under high frequency operation commonly used in optical communication.Comment: 21 pages, 4 sets of figure

Dataplane Specialization for High-performance OpenFlow Software Switching

OpenFlow is an amazingly expressive dataplane program- ming language, but this expressiveness comes at a severe performance price as switches must do excessive packet clas- sification in the fast path. The prevalent OpenFlow software switch architecture is therefore built on flow caching, but this imposes intricate limitations on the workloads that can be supported efficiently and may even open the door to mali- cious cache overflow attacks. In this paper we argue that in- stead of enforcing the same universal flow cache semantics to all OpenFlow applications and optimize for the common case, a switch should rather automatically specialize its dat- aplane piecemeal with respect to the configured workload. We introduce ES WITCH , a novel switch architecture that uses on-the-fly template-based code generation to compile any OpenFlow pipeline into efficient machine code, which can then be readily used as fast path. We present a proof- of-concept prototype and we demonstrate on illustrative use cases that ES WITCH yields a simpler architecture, superior packet processing speed, improved latency and CPU scala- bility, and predictable performance. Our prototype can eas- ily scale beyond 100 Gbps on a single Intel blade even with complex OpenFlow pipelines

Inference of gene regulatory networks and compound mode of action from time course gene expression profiles.

MOTIVATION: Time series expression experiments are an increasingly popular method for studying a wide range of biological systems. Here we developed an algorithm that can infer the local network of gene-gene interactions surrounding a gene of interest. This is achieved by a perturbation of the gene of interest and subsequently measuring the gene expression profiles at multiple time points. We applied this algorithm to computer simulated data and to experimental data on a nine gene network in Escherichia coli. RESULTS: In this paper we show that it is possible to recover the gene regulatory network from a time series data of gene expression following a perturbation to the cell. We show this both on simulated data and on a nine gene subnetwork part of the DNA-damage response pathway (SOS pathway) in the bacteria E. coli

Sleep Quality: A Mediator in the Pathway of Stress and Cold Symptom Severity

Stress is a known contributor to immune system suppression associated with higher illness susceptibility, including acute infectious respiratory illness or the common cold. Sleep quality is an additional mechanism that may underlie the association between stress and cold symptomatology. Although the associations between stress and sleep and cold symptomatology have been examined separately, little is known about the mechanistic role of sleep in these associations. The present study fills that void by examining archival data from the Common Cold Project (Pittsburgh Cold Study 3). The results indicate sleep quality surfaced as an indirect pathway linking stress to changes in cold severity. Additionally, better sleep was associated with greater changes in cold severity above perceived stress. These findings suggest that better sleep may be associated with less severe symptomatology. Future research should address mechanisms underlying the associations between stress, sleep, and cold symptomatology

Special Theory of Relativity through the Doppler Effect

We present the special theory of relativity taking the Doppler effect as the starting point, and derive several of its main effects, such as time dilation, length contraction, addition of velocities, and the mass-energy relation, and assuming energy and momentum conservation, we discuss how to introduce the 4-momentum in a natural way. We also use the Doppler effect to explain the "twin paradox", and its version on a cylinder. As a by-product we discuss Bell's spaceship paradox, and the Lorentz transformation for arbitrary velocities in one dimension.Comment: 20 pages, 1 figur