6,116 research outputs found
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 -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, -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
-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
directly, other observables closely linked to 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 is the depth of shower maximum . We
will discuss the sensitivity of an -based analysis on 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
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