Molecular dynamics of folding of secondary structures in Go-type models of proteins

We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and a soft repulsion for the non-native contacts. The interactions are chosen to make the target secondary structure be the native state of the system. We provide a thorough equilibrium and kinetic characterization of the sequences through the molecular dynamics simulations with the Langevin noise. Models with the steric constraints are found to be better folders and to be more stable, especially in the case of the $\beta$-structures. Phononic spectra for vibrations around the native states have low frequency gaps that correlate with the thermodynamic stability. Folding of the secondary structures proceeds through a well defined sequence of events. For instance, $\alpha$-helices fold from the ends first. The closer to the native state, the faster establishment of the contacts. Increasing the system size deteriorates the folding characteristics. We study the folding times as a function of viscous friction and find a regime of moderate friction with the linear dependence. We also consider folding when one end of a structure is pinned which imitates instantaneous conditions when a protein is being synthesized. We find that, under such circumstances, folding of helices is faster and of the $\beta$-sequences slower.Comment: REVTeX, 14 pages, EPS figures included, JCP in pres

Elastic behavior in Contact Dynamics of rigid particles

The systematic errors due to the practical implementation of the Contact Dynamics method for simulation of dense granular media are examined. It is shown that, using the usual iterative solver to simulate a chain of rigid particles, effective elasticity and sound propagation with a finite velocity occur. The characteristics of these phenomena are investigated analytically and numerically in order to assess the limits of applicability of this simulation method and to compare it with soft particle molecular dynamics.Comment: submitted to PRE, 7 pages, 6 figure

Methodology for evaluating LCC

Evaluating the life cycle costs (LCC) of food waste is a challenging task and few examples of previous LCC exist. This REFRESH report reviewed existing measures and methods for the evaluation of LCC of food waste. It conducted a comprehensive literature review to identify major methodological challenges related to cost modelling and externalities. The report contributes to the development of recommendations for a standardized system approach

Sub 20 nm Short Channel Carbon Nanotube Transistors

Carbon nanotube field-effect transistors with sub 20 nm long channels and on/off current ratios of > 1000000 are demonstrated. Individual single-walled carbon nanotubes with diameters ranging from 0.7 nm to 1.1 nm grown from structured catalytic islands using chemical vapor deposition at 700 degree Celsius form the channels. Electron beam lithography and a combination of HSQ, calix[6]arene and PMMA e-beam resists were used to structure the short channels and source and drain regions. The nanotube transistors display on-currents in excess of 15 microA for drain-source biases of only 0.4 Volt.Comment: Nano Letters in pres

On the Nature of Intrinsic Absorption in Reddened Seyfert 1 Galaxies

We discuss the origin of the ``dusty lukewarm absorber'', which we previously identified in the reddened Seyfert 1 galaxies NGC 3227 and Akn 564. This absorber is characterized by saturated UV absorption lines (C IV, N V) near the systemic velocity of the host galaxy, and is likely responsible for reddening both the continuum and the emission lines (including those from the narrow-line region) from these Seyferts. From a large sample of Seyfert 1 galaxies, we find that continuum reddening (as measured by UV color) tends to increase with inclination of the host galaxy. Furthermore, reddened, inclined Seyfert galaxies observed at moderate to high spectral resolution all show evidence for dusty lukewarm absorbers. We suggest that these absorbers lie in the plane of the host galaxy at distances > 100 pc from the nucleus, and are physically distinct from the majority of intrinsic absorbers that are outflowing from the nucleus.Comment: 14 pages, including 2 figures, accepted for publication in the Astrophysical Journal (Letters

On the measurement of the proton-air cross section using longitudinal shower profiles

In this paper, we will discuss the prospects of deducing the proton-air cross section from fluorescence telescope measurements of extensive air showers. As it is not possible to observe the point of first interaction $X_{\rm 1}$ directly, other observables closely linked to $X_{\rm 1}$ must be inferred from the longitudinal profiles. This introduces a dependence on the models used to describe the shower development. The most straightforward candidate for a good correlation to $X_{\rm 1}$ is the depth of shower maximum $X_{\rm max}$. We will discuss the sensitivity of an $X_{\rm max}$-based analysis on $\sigma_{\rm p-air}$ and quantify the systematic uncertainties arising from the model dependence, parameters of the reconstruction method itself and a possible non-proton contamination of the selected shower sample.Comment: 4 pages, Proceedings for ISVHECRI Weihei 200

567 ANTI-INFLAMMATORY ACTIVITY OF AN ETHANOLIC CAESALPINIA SAPPAN EXTRACT IN HUMAN CHONDROCYTES IN VITRO

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