A proposal for a scalable universal bosonic simulator using individually trapped ions

We describe a possible architecture to implement a universal bosonic simulator (UBS) using trapped ions. Single ions are confined in individual traps, and their motional states represent the bosonic modes. Single-mode linear operators, nonlinear phase-shifts, and linear beam splitters can be realized by precisely controlling the trapping potentials. All the processes in a bosonic simulation, except the initialization and the readout, can be conducted beyond the Lamb-Dicke regime. Aspects of our proposal can also be applied to split adiabatically a pair of ions in a single trap

Endoplasmic reticulum stress enhances fibrosis through IRE1α-mediated degradation of miR-150 and XBP-1 splicing

ER stress results in activation of the unfolded protein response and has been implicated in the development of fibrotic diseases. In this study, we show that inhibition of the ER stress-induced IRE1α signaling pathway, using the inhibitor 4μ8C, blocks TGFβ-induced activation of myofibroblasts in vitro, reduces liver and skin fibrosis in vivo, and reverts the fibrotic phenotype of activated myofibroblasts isolated from patients with systemic sclerosis. By using IRE1α(-/-) fibroblasts and expression of IRE1α-mutant proteins lacking endoribonuclease activity, we confirmed that IRE1α plays an important role during myofibroblast activation. IRE1α was shown to cleave miR-150 and thereby to release the suppressive effect that miR-150 exerted on αSMA expression through c-Myb. Inhibition of IRE1α was also demonstrated to block ER expansion through an XBP-1-dependent pathway. Taken together, our results suggest that ER stress could be an important and conserved mechanism in the pathogenesis of fibrosis and that components of the ER stress pathway may be therapeutically relevant for treating patients with fibrotic diseases

Analytic structure of radiation boundary kernels for blackhole perturbations

Exact outer boundary conditions for gravitational perturbations of the Schwarzschild metric feature integral convolution between a time-domain boundary kernel and each radiative mode of the perturbation. For both axial (Regge-Wheeler) and polar (Zerilli) perturbations, we study the Laplace transform of such kernels as an analytic function of (dimensionless) Laplace frequency. We present numerical evidence indicating that each such frequency-domain boundary kernel admits a "sum-of-poles" representation. Our work has been inspired by Alpert, Greengard, and Hagstrom's analysis of nonreflecting boundary conditions for the ordinary scalar wave equation.Comment: revtex4, 14 pages, 12 figures, 3 table

Thermodynamics of aggregation of two proteins

We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is used for numerical calculations. We find that a dimer can be formed spontaneously as a thermodynamically stable state when the system is small enough. It implies the possibility that the aggregation of proteins in a cell is triggered when they are confined in a small region by, for example, being surrounded by other macromolecules.We also find that the dimer exhibits a transition between unstable state and metastable state in the infinite system.Comment: jpsj2.cls, 7 pages, 14 figures; misconfigurations of Fig.Nos. correcte

Helical Tubes in Crowded Environments

When placed in a crowded environment, a semi-flexible tube is forced to fold so as to make a more compact shape. One compact shape that often arises in nature is the tight helix, especially when the tube thickness is of comparable size to the tube length. In this paper we use an excluded volume effect to model the effects of crowding. This gives us a measure of compactness for configurations of the tube, which we use to look at structures of the semi-flexible tube that minimize the excluded volume. We focus most of our attention on the helix and which helical geometries are most compact. We found that helices of specific pitch to radius ratio 2.512 to be optimally compact. This is the same geometry that minimizes the global curvature of the curve defining the tube. We further investigate the effects of adding a bending energy or multiple tubes to begin to explore the more complete space of possible geometries a tube could form.Comment: 10 page

Measurement of adsorption of a single component from the liquid phase : modelling investigation and sensitivity analysis

In this work, we consider an alternative approach for the measurement of adsorption from the liquid phase. Consider a mixture consisting of a non-adsorbed component (B) and an adsorbed component (A) present at some low concentration. Initially, a feed of component B only flows through a column packed with an adsorbent. Then, the feed is switched to the mixture of A and B. As soon as the mixture enters the column, there will be a reduction in the outlet flow rate as component A leaves the liquid phase and passes into the adsorbed phase. There are three stages to this work. The first is to develop overall and component balances to show how the amount adsorbed of component A can be determined from the variation in the column outlet flow rate. The second is to determine the actual variation in the column outlet flow rate for both plug flow and axial-dispersed plug flow. The final stage is to consider the suitability of a gravity-fed system to deliver the feed to the column. An analysis of the results shows that the experimental arrangement should be able to accurately monitor adsorption from the liquid phase where the mass fraction of the solute is of the order of 1%: the limiting experimental factor is how constant the volumetric flow rate of the liquid feed can be maintained

Information Loss in Coarse Graining of Polymer Configurations via Contact Matrices

Contact matrices provide a coarse grained description of the configuration omega of a linear chain (polymer or random walk) on Z^n: C_{ij}(omega)=1 when the distance between the position of the i-th and j-th step are less than or equal to some distance "a" and C_{ij}(omega)=0 otherwise. We consider models in which polymers of length N have weights corresponding to simple and self-avoiding random walks, SRW and SAW, with "a" the minimal permissible distance. We prove that to leading order in N, the number of matrices equals the number of walks for SRW, but not for SAW. The coarse grained Shannon entropies for SRW agree with the fine grained ones for n <= 2, but differs for n >= 3.Comment: 18 pages, 2 figures, latex2e Main change: the introduction is rewritten in a less formal way with the main results explained in simple term

Testing outer boundary treatments for the Einstein equations

Various methods of treating outer boundaries in numerical relativity are compared using a simple test problem: a Schwarzschild black hole with an outgoing gravitational wave perturbation. Numerical solutions computed using different boundary treatments are compared to a `reference' numerical solution obtained by placing the outer boundary at a very large radius. For each boundary treatment, the full solutions including constraint violations and extracted gravitational waves are compared to those of the reference solution, thereby assessing the reflections caused by the artificial boundary. These tests use a first-order generalized harmonic formulation of the Einstein equations. Constraint-preserving boundary conditions for this system are reviewed, and an improved boundary condition on the gauge degrees of freedom is presented. Alternate boundary conditions evaluated here include freezing the incoming characteristic fields, Sommerfeld boundary conditions, and the constraint-preserving boundary conditions of Kreiss and Winicour. Rather different approaches to boundary treatments, such as sponge layers and spatial compactification, are also tested. Overall the best treatment found here combines boundary conditions that preserve the constraints, freeze the Newman-Penrose scalar Psi_0, and control gauge reflections.Comment: Modified to agree with version accepted for publication in Class. Quantum Gra

Protein design in a lattice model of hydrophobic and polar amino acids

A general strategy is described for finding which amino acid sequences have native states in a desired conformation (inverse design). The approach is used to design sequences of 48 hydrophobic and polar aminoacids on three-dimensional lattice structures. Previous studies employing a sequence-space Monte-Carlo technique resulted in the successful design of one sequence in ten attempts. The present work also entails the exploration of conformations that compete significantly with the target structure for being its ground state. The design procedure is successful in all the ten cases.Comment: RevTeX, 12 pages, 1 figur

Toxic effect of high concentration of sonochemically synthesized polyvinylpyrrolidone-coated silver nanoparticles on Citrobacter sp. A1 and Enterococcus sp. C1

Background/Purpose Currently, silver nanoparticles (AgNPs) have gained importance in various industrial applications. However, their impact upon release into the environment on microorganisms remains unclear. The aim of this study was to analyze the effect of polyvinylpyrrolidone-capped AgNPs synthesized in this laboratory on two bacterial strains isolated from the environment, Gram-negative Citrobacter sp. A1 and Gram-positive Enterococcus sp. C1. Methods Polyvinylpyrrolidone-capped AgNPs were synthesized by ultrasound-assisted chemical reduction. Characterization of the AgNPs involved UV–visible spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, transmission electron microscopy, and energy dispersive X-ray spectroscopy. Citrobacter sp. A1 and Enterococcus sp. C1 were exposed to varying concentrations of AgNPs, and cell viability was determined. Scanning electron microscopy was performed to evaluate the morphological alteration of both species upon exposure to AgNPs at 1000 mg/L. Results The synthesized AgNPs were spherical in shape, with an average particle size of 15 nm. The AgNPs had different but prominent effects on either Citrobacter sp. A1 or Enterococcus sp. C1. At an AgNP concentration of 1000 mg/L, Citrobacter sp. A1 retained viability for 6 hours, while Enterococcus sp. C1 retained viability only for 3 hours. Citrobacter sp. A1 appeared to be more resistant to AgNPs than Enterococcus sp. C1. The cell wall of both strains was found to be morphologically altered at that concentration. Conclusion Minute and spherical AgNPs significantly affected the viability of the two bacterial strains selected from the environment. Enterococcus sp. C1 was more vulnerable to AgNPs, probably due to its cell wall architecture and the absence of silver resistance-related genes