235 research outputs found
A simplified picture for Pi electrons in conjugated polymers : from PPP Hamiltonian to an effective molecular crystal approach
An excitonic method proper to study conjugated oligomers and polymers is
described and its applicability tested on the ground state and first excited
states of trans-polyacetylene, taken as a model. From the Pariser-Parr-Pople
Hamiltonian, we derive an effective Hamiltonian based on a local description of
the polymer in term of monomers; the relevant electronic configurations are
build on a small number of pertinent local excitations. The intuitive and
simple microscopic physical picture given by our model supplement recent
results, such as the Rice and Garstein ones. Depending of the parameters, the
linear absorption appears dominated by an intense excitonic peak.Comment: 41 Pages, 6 postscript figure
Thermodynamic and structural aspects of the potential energy surface of simulated water
Relations between the thermodynamics and dynamics of supercooled liquids
approaching a glass transition have been proposed over many years. The
potential energy surface of model liquids has been increasingly studied since
it provides a connection between the configurational component of the partition
function on one hand, and the system dynamics on the other. This connection is
most obvious at low temperatures, where the motion of the system can be
partitioned into vibrations within a basin of attraction and infrequent
inter-basin transitions. In this work, we present a description of the
potential energy surface properties of supercooled liquid water. The dynamics
of this model has been studied in great details in the last years.
Specifically, we locate the minima sampled by the liquid by ``quenches'' from
equilibrium configurations generated via molecular dynamics simulations. We
calculate the temperature and density dependence of the basin energy,
degeneracy, and shape. The temperature dependence of the energy of the minima
is qualitatively similar to simple liquids, but has anomalous density
dependence. The unusual density dependence is also reflected in the
configurational entropy, the thermodynamic measure of degeneracy. Finally, we
study the structure of simulated water at the minima, which provides insight on
the progressive tetrahedral ordering of the liquid on cooling
Transitions between Inherent Structures in Water
The energy landscape approach has been useful to help understand the dynamic
properties of supercooled liquids and the connection between these properties
and thermodynamics. The analysis in numerical models of the inherent structure
(IS) trajectories -- the set of local minima visited by the liquid -- offers
the possibility of filtering out the vibrational component of the motion of the
system on the potential energy surface and thereby resolving the slow
structural component more efficiently. Here we report an analysis of an IS
trajectory for a widely-studied water model, focusing on the changes in
hydrogen bond connectivity that give rise to many IS separated by relatively
small energy barriers. We find that while the system \emph{travels} through
these IS, the structure of the bond network continuously modifies, exchanging
linear bonds for bifurcated bonds and usually reversing the exchange to return
to nearly the same initial configuration. For the 216 molecule system we
investigate, the time scale of these transitions is as small as the simulation
time scale ( fs). Hence for water, the transitions between each of
these IS is relatively small and eventual relaxation of the system occurs only
by many of these transitions. We find that during IS changes, the molecules
with the greatest displacements move in small ``clusters'' of 1-10 molecules
with displacements of nm, not unlike simpler liquids.
However, for water these clusters appear to be somewhat more branched than the
linear ``string-like'' clusters formed in a supercooled Lennar d-Jones system
found by Glotzer and her collaborators.Comment: accepted in PR
The potential energy landscape of a model glass former: thermodynamics, anharmonicities, and finite size effects
It is possible to formulate the thermodynamics of a glass forming system in
terms of the properties of inherent structures, which correspond to the minima
of the potential energy and build up the potential energy landscape in the
high-dimensional configuration space. In this work we quantitatively apply this
general approach to a simulated model glass-forming system. We systematically
vary the system size between N=20 and N=160. This analysis enables us to
determine for which temperature range the properties of the glass former are
governed by the regions of the configuration space, close to the inherent
structures. Furthermore, we obtain detailed information about the nature of
anharmonic contributions. Moreover, we can explain the presence of finite size
effects in terms of specific properties of the energy landscape. Finally,
determination of the total number of inherent structures for very small systems
enables us to estimate the Kauzmann temperature
Water Dynamics at Protein Interfaces: Ultrafast Optical Kerr Effect Study
The behavior of water molecules surrounding a protein can have an important bearing on its structure and function. Consequently, a great deal of attention has been focused on changes in the relaxation dynamics of water when it is located at the protein surface. Here we use the ultrafast optical Kerr effect to study the H-bond structure and dynamics of aqueous solutions of proteins. Measurements are made for three proteins as a function of concentration. We find that the water dynamics in the first solvation layer of the proteins are slowed by up to a factor of 8 in comparison to those in bulk water. The most marked slowdown was observed for the most hydrophilic protein studied, bovine serum albumin, whereas the most hydrophobic protein, trypsin, had a slightly smaller effect. The terahertz Raman spectra of these protein solutions resemble those of pure water up to 5 wt % of protein, above which a new feature appears at 80 cm–1, which is assigned to a bending of the protein amide chain
Inherent Structure Entropy of Supercooled Liquids
We present a quantitative description of the thermodynamics in a supercooled
binary Lennard Jones liquid via the evaluation of the degeneracy of the
inherent structures, i.e. of the number of potential energy basins in
configuration space. We find that for supercooled states, the contribution of
the inherent structures to the free energy of the liquid almost completely
decouples from the vibrational contribution. An important byproduct of the
presented analysis is the determination of the Kauzmann temperature for the
studied system. The resulting quantitative picture of the thermodynamics of the
inherent structures offers new suggestions for the description of equilibrium
and out-of-equilibrium slow-dynamics in liquids below the Mode-Coupling
temperature.Comment: 11 pages of Latex, 3 figure
LeukoCatch, a quick and efficient tool for the preparation of leukocyte extracts from blood
<p>Abstract</p> <p>Background</p> <p>Whole-protein extracts from peripheral blood leukocytes are ideal for basic and clinical research. However, lack of a simple preparation technique has limited the use of such extracts. The aim of this study is to develop a simple and easy system that can selectively obtain leukocyte extracts without hemoglobin.</p> <p>Methods</p> <p>A filter that captures the leukocytes but not RBCs was set at the bottom of a 10-mL medical syringe by sandwiching it between plastic stoppers. The capturing efficiency of leukocytes with this tool, called LeukoCatch, was examined using human macrophage cells (MONO-MAC-6). The abilities of LeukoCatch system to capture the leukocyte proteins and to remove the hemoglobin from RBCs were tested by western blot analysis using human blood samples.</p> <p>Results</p> <p>This study presents the development of LeukoCatch, a novel tool that allows the preparation of leukocyte extracts from blood samples within 3 min without centrifugation. Tissue-cultured human macrophage cells were tested to determine the optimal filter numbers and pass-through frequencies of LeukoCatch, which was then applied to 2-mL blood samples. Samples were passed 2~5 times through a LeukoCatch equipped with 5 filters, washed twice with phosphate-buffered saline for red cell removal, and leukocyte proteins were extracted with 0.5 mL of elution buffer. Western blot analysis of the purified extract indicated that more than 90% of hemoglobin was removed by the LeukoCatch and that the protein recovery rate of leukocytes was at least 4 times better than that of the conventional centrifugation method.</p> <p>Conclusion</p> <p>We conclude that LeukoCatch is useful not only for diagnosis at the bedside but also for basic research using blood samples or tissue culture cells.</p
Mean-atom-trajectory model for the velocity autocorrelation function of monatomic liquids
We present a model for the motion of an average atom in a liquid or
supercooled liquid state and apply it to calculations of the velocity
autocorrelation function and diffusion coefficient . The model
trajectory consists of oscillations at a distribution of frequencies
characteristic of the normal modes of a single potential valley, interspersed
with position- and velocity-conserving transits to similar adjacent valleys.
The resulting predictions for and agree remarkably well with MD
simulations of Na at up to almost three times its melting temperature. Two
independent processes in the model relax velocity autocorrelations: (a)
dephasing due to the presence of many frequency components, which operates at
all temperatures but which produces no diffusion, and (b) the transit process,
which increases with increasing temperature and which produces diffusion.
Because the model provides a single-atom trajectory in real space and time,
including transits, it may be used to calculate all single-atom correlation
functions.Comment: LaTeX, 8 figs. This is an updated version of cond-mat/0002057 and
cond-mat/0002058 combined Minor changes made to coincide with published
versio
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