3,206 research outputs found
Glass transition in biomolecules and the liquid-liquid critical point of water
Using molecular dynamics simulations, we investigate the relation between the
dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and
thermodynamic properties of hydration water. We find that the dynamic
transition of the macromolecules, sometimes called a ``protein glass
transition'', occurs at the temperature of dynamic crossover in the diffusivity
of hydration water, and also coincides with the maxima of the isobaric specific
heat and the temperature derivative of the orientational order parameter.
We relate these findings to the hypothesis of a liquid-liquid critical point in
water. Our simulations are consistent with the possibility that the protein
glass transition results from crossing the Widom line, which is defined as the
locus of correlation length maxima emanating from the hypothesized second
critical point of water.Comment: 10 Pages, 12 figure
Trans-phonon effects in ultrafast nano-devices
We report a novel phenomenon in carbon nanotube (CNT) based devices, the
transphonon effects, which resemble the transonic effects in aerodynamics. It
is caused by dissipative resonance of nanotube phonons similar to the radial
breathing mode, and subsequent drastic surge of the dragging force on the
sliding tube, and multiple phonon barriers are encountered as the intertube
sliding velocity reaches critical values. It is found that the transphonon
effects can be tuned by applying geometric constraints or varying chirality
combinations of the nanotubes
Feasibility of single-order parameter description of equilibrium viscous liquid dynamics
Molecular dynamics results for the dynamic Prigogine-Defay ratio are
presented for two glass-forming liquids, thus evaluating the experimentally
relevant quantity for testing whether metastable-equilibrium liquid dynamics to
a good approximation are described by a single parameter. For the Kob-Andersen
binary Lennard-Jones mixture as well as for an asymmetric dumbbell model liquid
a single-parameter description works quite well. This is confirmed by
time-domain results where it is found that energy and pressure fluctuations are
strongly correlated on the alpha-time scale in the NVT ensemble; in the NpT
ensemble energy and volume fluctuations similarly correlate strongly.Comment: Phys. Rev. E, in pres
Influence of conformational fluctuations on enzymatic activity: modelling the functional motion of beta-secretase
Considerable insight into the functional activity of proteins and enzymes can
be obtained by studying the low-energy conformational distortions that the
biopolymer can sustain. We carry out the characterization of these large scale
structural changes for a protein of considerable pharmaceutical interest, the
human -secretase. Starting from the crystallographic structure of the
protein, we use the recently introduced beta-Gaussian model to identify, with
negligible computational expenditure, the most significant distortion occurring
in thermal equilibrium and the associated time scales. The application of this
strategy allows to gain considerable insight into the putative functional
movements and, furthermore, helps to identify a handful of key regions in the
protein which have an important mechanical influence on the enzymatic activity
despite being spatially distant from the active site. The results obtained
within the Gaussian model are validated through an extensive comparison against
an all-atom Molecular Dynamics simulation.Comment: To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo
Workshop
Molecular dynamics simulation of nanocolloidal amorphous silica particles: Part II
Explicit molecular dynamics simulations were applied to a pair of amorphous
silica nanoparticles of diameter 3.2 nm immersed in a background electrolyte.
Mean forces acting between the pair of silica nanoparticles were extracted at
four different background electrolyte concentrations. Dependence of the
inter-particle potential of mean force on the separation and the silicon to
sodium ratio, as well as on the background electrolyte concentration, are
demonstrated. The pH was indirectly accounted for via the ratio of silicon to
sodium used in the simulations. The nature of the interaction of the
counter-ions with charged silica surface sites (deprotonated silanols) was also
investigated. The effect of the sodium double layer on the water ordering was
investigated for three Si:Na+ ratios. The number of water molecules trapped
inside the nanoparticles was investigated as the Si:Na+ ratio was varied.
Differences in this number between the two nanoparticles in the simulations are
attributed to differences in the calculated electric dipole moment. The
implications of the form of the potentials for aggregation are also discussed.Comment: v1. 33 pages, 7 figures (screen-quality PDF), submitted to J. Chem.
Phys v2. 15 pages, 4 tables, 6 figures. Content, author list and title
changed; single space
Conformational and Structural Relaxations of Poly(ethylene oxide) and Poly(propylene oxide) Melts: Molecular Dynamics Study of Spatial Heterogeneity, Cooperativity, and Correlated Forward-Backward Motion
Performing molecular dynamics simulations for all-atom models, we
characterize the conformational and structural relaxations of poly(ethylene
oxide) and poly(propylene oxide) melts. The temperature dependence of these
relaxation processes deviates from an Arrhenius law for both polymers. We
demonstrate that mode-coupling theory captures some aspects of the glassy
slowdown, but it does not enable a complete explanation of the dynamical
behavior. When the temperature is decreased, spatially heterogeneous and
cooperative translational dynamics are found to become more important for the
structural relaxation. Moreover, the transitions between the conformational
states cease to obey Poisson statistics. In particular, we show that, at
sufficiently low temperatures, correlated forward-backward motion is an
important aspect of the conformational relaxation, leading to strongly
nonexponential distributions for the waiting times of the dihedrals in the
various conformational statesComment: 13 pages, 13 figure
The AMANDA Neutrino Telescope and the Indirect Search for Dark Matter
With an effective telescope area of order 10^4 m^2, a threshold of ~50 GeV
and a pointing accuracy of 2.5 degrees, the AMANDA detector represents the
first of a new generation of high energy neutrino telescopes, reaching a scale
envisaged over 25 years ago. We describe its performance, focussing on the
capability to detect halo dark matter particles via their annihilation into
neutrinos.Comment: Latex2.09, 16 pages, uses epsf.sty to place 15 postscript figures.
Talk presented at the 3rd International Symposium on Sources and Detection of
Dark Matter in the Universe (DM98), Santa Monica, California, Feb. 199
A Hydrophobic Gate in an Ion Channel: The Closed State of the Nicotinic Acetylcholine Receptor
The nicotinic acetylcholine receptor (nAChR) is the prototypic member of the
`Cys-loop' superfamily of ligand-gated ion channels which mediate synaptic
neurotransmission, and whose other members include receptors for glycine,
gamma-aminobutyric acid, and serotonin. Cryo-electron microscopy has yielded a
three dimensional structure of the nAChR in its closed state. However, the
exact nature and location of the channel gate remains uncertain. Although the
transmembrane pore is constricted close to its center, it is not completely
occluded. Rather, the pore has a central hydrophobic zone of radius about 3 A.
Model calculations suggest that such a constriction may form a hydrophobic
gate, preventing movement of ions through a channel. We present a detailed and
quantitative simulation study of the hydrophobic gating model of the nicotinic
receptor, in order to fully evaluate this hypothesis. We demonstrate that the
hydrophobic constriction of the nAChR pore indeed forms a closed gate.
Potential of mean force (PMF) calculations reveal that the constriction
presents a barrier of height ca. 10 kT to the permeation of sodium ions,
placing an upper bound on the closed channel conductance of 0.3 pS. Thus, a 3 A
radius hydrophobic pore can form a functional barrier to the permeation of a 1
A radius Na+ ion. Using a united atom force field for the protein instead of an
all atom one retains the qualitative features but results in differing
conductances, showing that the PMF is sensitive to the detailed molecular
interactions.Comment: Accepted by Physical Biology; includes a supplement and a
supplementary mpeg movie can be found at
http://sbcb.bioch.ox.ac.uk/oliver/download/Movies/watergate.mp
The AMANDA Neutrino Telescope: Principle of Operation and First Results
AMANDA is a high-energy neutrino telescope presently under construction at
the geographical South Pole. In the Antarctic summer 1995/96, an array of 80
optical modules (OMs) arranged on 4 strings (AMANDA-B4) was deployed at depths
between 1.5 and 2 km. In this paper we describe the design and performance of
the AMANDA-B4 prototype, based on data collected between February and November
1996. Monte Carlo simulations of the detector response to down-going
atmospheric muon tracks show that the global behavior of the detector is
understood. We describe the data analysis method and present first results on
atmospheric muon reconstruction and separation of neutrino candidates. The
AMANDA array was upgraded with 216 OMs on 6 new strings in 1996/97
(AMANDA-B10), and 122 additional OMs on 3 strings in 1997/98.Comment: 36 pages, 23 figures, submitted to Astroparticle Physic
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