Signal Transduction Pathways in the Pentameric Ligand-Gated Ion Channels

The mechanisms of allosteric action within pentameric ligand-gated ion channels (pLGICs) remain to be determined. Using crystallography, site-directed mutagenesis, and two-electrode voltage clamp measurements, we identified two functionally relevant sites in the extracellular (EC) domain of the bacterial pLGIC from Gloeobacter violaceus (GLIC). One site is at the C-loop region, where the NQN mutation (D91N, E177Q, and D178N) eliminated inter-subunit salt bridges in the open-channel GLIC structure and thereby shifted the channel activation to a higher agonist concentration. The other site is below the C-loop, where binding of the anesthetic ketamine inhibited GLIC currents in a concentration dependent manner. To understand how a perturbation signal in the EC domain, either resulting from the NQN mutation or ketamine binding, is transduced to the channel gate, we have used the Perturbation-based Markovian Transmission (PMT) model to determine dynamic responses of the GLIC channel and signaling pathways upon initial perturbations in the EC domain of GLIC. Despite the existence of many possible routes for the initial perturbation signal to reach the channel gate, the PMT model in combination with Yen's algorithm revealed that perturbation signals with the highest probability flow travel either via the β1-β2 loop or through pre-TM1. The β1-β2 loop occurs in either intra- or inter-subunit pathways, while pre-TM1 occurs exclusively in inter-subunit pathways. Residues involved in both types of pathways are well supported by previous experimental data on nAChR. The direct coupling between pre-TM1 and TM2 of the adjacent subunit adds new insight into the allosteric signaling mechanism in pLGICs. © 2013 Mowrey et al

Optical Resonator Analog of a Two-Dimensional Topological Insulator

A lattice of optical ring resonators can exhibit a topological insulator phase, with the role of spin played by the direction of propagation of light within each ring. Unlike the system studied by Hafezi et al., topological protection is achieved without fine-tuning the inter-resonator couplings, which are given the same periodicity as the underlying lattice. The topological insulator phase occurs for strong couplings, when the tight-binding method is inapplicable. Using the transfer matrix method, we derive the bandstructure and phase diagram, and demonstrate the existence of robust edge states. When gain and loss are introduced, the system functions as a diode for coupled resonator modes.Comment: 10 pages, 9 figure

An investigation of nanoindentation tests on the single crystal copper thin film via an AFM and MD simulation

Nanoindentation tests performed in an atomic force microscope have been utilized to directly measure the mechanical properties of single crystal metal thin films fabricated by the vacuum vapor deposition technique. Nanoindentation tests were conducted at various indentation depths to study the effect of indentation depths on the mechanical properties of thin films. The results were interpreted by using the Oliver-Pharr method with which direct observation and measurement of the contact area are not required. The elastic modulus of the single crystal copper film at various indentation depths was determined as 67.0±6.9GPa on average which is in reasonable agreement with the results reported by others. The indentation hardness constantly increases with decreasing indentation depth, indicating a strong size effect. In addition to the experimental work, a three-dimensional nanoindentation model of molecular dynamics (MD) simulations with embedded atom method (EAM) potential is proposed to elucidate the mechanics and mechanisms of nanoindentation of thin films from the atomistic point of view. MD simulations results also show that due to the size effect the plastic deformation via amorphous transformation is more favorable than via the generation and propagation of dislocations in nanoindentation of single crystal copper thin films

Topological Bose-Mott Insulators in a One-Dimensional Optical Superlattice

We study topological properties of the Bose-Hubbard model with repulsive interactions in a one-dimensional optical superlattice. We find that the Mott insulator states of the single-component (two-component) Bose-Hubbard model under fractional fillings are topological insulators characterized by a nonzero charge (or spin) Chern number with nontrivial edge states. For ultracold atomic experiments, we show that the topological Chern number can be detected through measuring the density profiles of the bosonic atoms in a harmonic trap.Comment: 5 pages, published versio

All Maximal Independent Sets and Dynamic Dominance for Sparse Graphs

We describe algorithms, based on Avis and Fukuda's reverse search paradigm, for listing all maximal independent sets in a sparse graph in polynomial time and delay per output. For bounded degree graphs, our algorithms take constant time per set generated; for minor-closed graph families, the time is O(n) per set, and for more general sparse graph families we achieve subquadratic time per set. We also describe new data structures for maintaining a dynamic vertex set S in a sparse or minor-closed graph family, and querying the number of vertices not dominated by S; for minor-closed graph families the time per update is constant, while it is sublinear for any sparse graph family. We can also maintain a dynamic vertex set in an arbitrary m-edge graph and test the independence of the maintained set in time O(sqrt m) per update. We use the domination data structures as part of our enumeration algorithms.Comment: 10 page

On Dust Extinction of Gamma-ray Burst Host Galaxies

Although it is well recognized that gamma-ray burst (GRB) afterglows are obscured and reddened by dust in their host galaxies, the wavelength-dependence and quantity of dust extinction are still poorly known. Current studies on this mostly rely on fitting the afterglow spectral energy distributions (SEDs) with template extinction models. The inferred extinction (both quantity and wavelength-dependence) and dust-to-gas ratios are often in disagreement with that obtained from dust depletion and X-ray spectroscopy studies. We argue that this discrepancy could result from the prior assumption of a template extinction law. We propose an analytical formula to approximate the GRB host extinction law. With the template extinction laws self-contained, and the capability of revealing extinction laws differing from the conventional ones, it is shown that this is a powerful approach in modeling the afterglow SEDs to derive GRB host extinction.Comment: 9 pages, 4 figures; The Astrophysical Journal, in press (2008 Oct 1 issue

Enhancement of Quantum Tunneling for Excited States in Ferromagnetic Particles

A formula suitable for a quantitative evaluation of the tunneling effect in a ferromagnetic particle is derived with the help of the instanton method. The tunneling between n-th degenerate states of neighboring wells is dominated by a periodic pseudoparticle configuration. The low-lying level-splitting previously obtained with the LSZ method in field theory in which the tunneling is viewed as the transition of n bosons induced by the usual (vacuum) instanton is recovered. The observation made with our new result is that the tunneling effect increases at excited states. The results should be useful in analyzing results of experimental tests of macroscopic quantum coherence in ferromagnetic particles.Comment: 18 pages, LaTex, 1 figur

A comprehensive analysis of Swift/XRT data: I. Apparent spectral evolution of GRB X-ray tails

An early steep decay component following the prompt GRBs is commonly observed in {\em Swift} XRT light curves, which is regarded as the tail emission of the prompt gamma-rays. Prompted by the observed strong spectral evolution in the tails of GRBs 060218 and 060614, we present a systematic time-resolved spectral analysis for the {\em Swift} GRB tails detected between 2005 February and 2007 January. We select a sample of 44 tails that are bright enough to perform time-resolved spectral analyses. Among them 11 tails are smooth and without superimposing significant flares, and their spectra have no significant temporal evolution. We suggest that these tails are dominated by the curvature effect of the prompt gamma-rays due to delay of propagation of photons from large angles with respect to the line of sight . More interestingly, 33 tails show clear hard-to-soft spectral evolution, with 16 of them being smooth tails directly following the prompt GRBs,while the others being superimposed with large flares. We focus on the 16 clean, smooth tails and consider three toy models to interpret the spectral evolution. The curvature effect of a structured jet and a model invoking superposition of the curvature effect tail and a putative underlying soft emission component cannot explain all the data. The third model, which invokes an evolving exponential spectrum, seems to reproduce both the lightcurve and the spectral evolution of all the bursts, including GRBs 060218 and 060614. More detailed physical models are called for to understand the apparent evolution effect.Comment: 13 pages in emulateapj style,6 figures, 1 table, expanded version, matched to published version, ApJ, 2007, in press. This is the first paper of a series. Paper II see arXiv:0705.1373 (ApJ,2007, in press

SDE SIS epidemic model with demographic stochasticity and varying population size

In this paper we look at the two dimensional stochastic differential equation (SDE) susceptible-infected-susceptible (SIS) epidemic model with demographic stochasticity where births and deaths are regarded as stochastic processes with per capita disease contact rate depending on the population size. First we look at the SDE model for the total population size and show that there exists a unique non-negative solution. Then we look at the two dimensional SDE SIS model and show that there exists a unique non-negative solution which is bounded above given the total population size. Furthermore we show that the number of infecteds and the number of susceptibles become extinct in finite time almost surely. Lastly, we support our analytical results with numerical simulations using theoretical and realistic disease parameter values