Langevin Trajectories between Fixed Concentrations

We consider the trajectories of particles diffusing between two infinite baths of fixed concentrations connected by a channel, e.g. a protein channel of a biological membrane. The steady state influx and efflux of Langevin trajectories at the boundaries of a finite volume containing the channel and parts of the two baths is replicated by termination of outgoing trajectories and injection according to a residual phase space density. We present a simulation scheme that maintains averaged fixed concentrations without creating spurious boundary layers, consistent with the assumed physics

Growth factor restriction impedes progression of wound healing following cataract surgery: identification of VEGF as a putative therapeutic target

Secondary visual loss occurs in millions of patients due to a wound-healing response, known as posterior capsule opacification (PCO), following cataract surgery. An intraocular lens (IOL) is implanted into residual lens tissue, known as the capsular bag, following cataract removal. Standard IOLs allow the anterior and posterior capsules to become physically connected. This places pressure on the IOL and improves contact with the underlying posterior capsule. New open bag IOL designs separate the anterior capsule and posterior capsules and further reduce PCO incidence. It is hypothesised that this results from reduced cytokine availability due to greater irrigation of the bag. We therefore explored the role of growth factor restriction on PCO using human lens cell and tissue culture models. We demonstrate that cytokine dilution, by increasing medium volume, significantly reduced cell coverage in both closed and open capsular bag models. This coincided with reduced cell density and myofibroblast formation. A screen of 27 cytokines identified nine candidates whose expression profile correlated with growth. In particular, VEGF was found to regulate cell survival, growth and myofibroblast formation. VEGF provides a therapeutic target to further manage PCO development and will yield best results when used in conjunction with open bag IOL designs

Nanoindentation Of Si Nanostructures: Buckling And Friction At Nanoscales

A nanoindentation system was employed to characterize mechanical properties of silicon nanolines (SiNLs), which were fabricated by an anisotropic wet etching (AWE) process. The SiNLs had the linewidth ranging from 24 nm to 90 nm, having smooth and vertical sidewalls and the aspect ratio (height/linewidth) from 7 to 18. During indentation, a buckling instability was observed at a critical load, followed by a displacement burst without a load increase, then a full recovery of displacement upon unloading. This phenomenon was explained by two bucking modes. It was also found that the difference in friction at the contact between the indenter and SiNLs directly affected buckling response of these nanolines. The friction coefficient was estimated to be in a range of 0.02 to 0.05. For experiments with large indentation displacements, irrecoverable indentation displacements were observed due to fracture of Si nanolines, with the strain to failure estimated to be from 3.8% to 9.7%. These observations indicated that the buckling behavior of SiNLs depended on the combined effects of load, line geometry, and the friction at contact. This study demonstrated a valuable approach to fabrication of well-defined Si nanoline structures and the application of the nanoindentation method for investigation of their mechanical properties at the nanoscale.Microelectronics Research Cente

Luminosity Functions of Elliptical Galaxies at z < 1.2

The luminosity functions of E/S0 galaxies are constructed in 3 different redshift bins (0.2 < z < 0.55, 0.55 < z < 0.8, 0.8 < z < 1.2), using the data from the Hubble Space Telescope Medium Deep Survey (HST MDS) and other HST surveys. These independent luminosity functions show the brightening in the luminosity of E/S0s by about 0.5~1.0 magnitude at z~1, and no sign of significant number evolution. This is the first direct measurement of the luminosity evolution of E/S0 galaxies, and our results support the hypothesis of a high redshift of formation (z > 1) for elliptical galaxies, together with weak evolution of the major merger rate at z < 1.Comment: To be published in ApJ Letters, 4 pages, AAS Latex, 4 figures, and 2 table

Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach

Polymorphism discovery is a routine application of next-generation sequencing technology where multiple samples are sent to a service provider for library preparation, subsequent sequencing, and bioinformatic analyses. The decreasing cost and advances in multiplexing approaches have made it possible to analyze hundreds of samples at a reasonable cost. However, because of the manual steps involved in the initial processing of samples and handling of sequencing equipment, cross-contamination remains a significant challenge. It is especially problematic in cases where polymorphism frequencies do not adhere to diploid expectation, for example, heterogeneous tumor samples, organellar genomes, as well as during bacterial and viral sequencing. In these instances, low levels of contamination may be readily mistaken for polymorphisms, leading to false results. Here we describe practical steps designed to reliably detect contamination and uncover its origin, and also provide new, Galaxy-based, readily accessible computational tools and workflows for quality control. All results described in this report can be reproduced interactively on the web as described at http://usegalaxy.org/contamination

Irreducible characters of GSp(4, q) and dimensions of spaces of fixed vectors

In this paper, we compute the conjugacy classes and the list of irreducible characters of GSp(4,q), where q is odd. We also determine precisely which irreducible characters are non-cuspidal and which are generic. These characters are then used to compute dimensions of certain subspaces of fixed vectors of smooth admissible non-supercuspidal representations of GSp(4,F), where F is a non-archimedean local field of characteristic zero with residue field of order q.Comment: 48 pages, 21 tables. Corrected an error in Table 16 for type V* representations (theta_11 and theta_12 were switched

Orientation of Fluorescent Lipid Analog BODIPY-PC to Probe Lipid Membrane Properties: Insights from Molecular Dynamics Simulations

Single-molecule fluorescence measurements have been used to characterize membrane properties, and recently showed a linear evolution of the fluorescent lipid analog BODIPY-PC towards small tilt angles in Langmuir-Blodgett monolayers as the lateral surface pressure is increased. In this work, we have performed comparative molecular dynamics (MD) simulations of BODIPY-PC in DPPC (dipalmitoylphosphatidylcholine) monolayers and bilayers at three surface pressures (3, 10, and 40 mN/m) to explore 1) the microscopic correspondence between monolayer and bilayer structures, 2) the fluorophore’s position within the membrane, and 3) the microscopic driving forces governing the fluorophore’s tilting. The MD simulations reveal very close agreement between the monolayer and bilayer systems in terms of the fluorophore’s orientation and lipid chain order, suggesting that monolayer experiments can be used to approximate bilayer systems. The simulations capture the trend of reduced tilt angle of the fluorophore with increasing surface pressure as seen in the experimental results, and provide detailed insights into fluorophore location and orientation, not obtainable in the experiments. The simulations also reveal that the enthalpic contribution is dominant at 40 mN/m resulting in smaller tilt angles of the fluorophore, and the entropy contribution is dominant at lower pressures resulting in larger tilt angles

Coalescence and T-junction formation of carbon nanotubes: Action-derived molecular dynamics simulations

The mechanisms of coalescence and T-junction formation of carbon nanotubes are analyzed using action-derived molecular dynamics. The control of kinetic energy in addition to the total energy leads to the determination of the minimum-energy atomistic pathway for each of these processes. Particularly, we find that the unit merging process of two carbon nanotubes consists of four sequential generalized Stone-Wales transformations occurring in four hexagon-heptagon pairs around the jointed part. In addition, we show that a single carbon atom may play the role of an autocatalyst, which significantly reduces the global activation energy barrier of the merging process. For T junction formation, two different models are chosen for simulation. One contains defects near the point of junction formation, while the other consists of two perfect nanotubes plus two additional carbon atoms. Our results indicate that the coalescence and junction formation of nanotubes may occur more easily than theoretically predicted in the presence of additional carbon atoms at moderate temperatures.open9

Optical Cherenkov radiation by cascaded nonlinear interaction: an efficient source of few-cycle energetic near- to mid-IR pulses

When ultrafast noncritical cascaded second-harmonic generation of energetic femtosecond pulses occur in a bulk lithium niobate crystal optical Cherenkov waves are formed in the near- to mid-IR. Numerical simulations show that the few-cycle solitons radiate Cherenkov (dispersive) waves in the \lambda=2.2-4.5\mic range when pumping at \lambda_1=1.2-1.8\mic. The exact phase-matching point depends on the soliton wavelength, and we show that a simple longpass filter can separate the Cherenkov waves from the solitons. The Cherenkov waves are born few-cycle with an excellent Gaussian pulse shape, and the conversion efficiency is up to 25%. Thus, optical Cherenkov waves formed with cascaded nonlinearities could become an efficient source of energetic near- to mid-IR few-cycle pulses.Comment: Extended version of Nonlinear Optics 2011 contribution http://www.opticsinfobase.org/abstract.cfm?URI=NLO-2011-NTuA7. Submitted for Optics Express special issue for NLO conferenc