211 research outputs found
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
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
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
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
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
Assessment of distraction callus in rabbits by monitoring of the electrical impedance of bone
Generation of human iPSCs from cells of fibroblastic and epithelial origin by means of the oriP/EBNA-1 episomal reprogramming system
The Antiviral Spectra of TRIM5α Orthologues and Human TRIM Family Proteins against Lentiviral Production
Rhesus monkey TRIM5α (TRIM5αrh) recognizes the incoming HIV-1 core through its C-terminal B30.2(PRYSPRY) domain and promotes its premature disassembly or degradation before reverse transcription. Previously, we have shown that TRIM5αrh blocks HIV-1 production through the N-terminal RBCC domain by the recognition of Gag polyproteins. Although all TRIM family proteins have RBCC domains, it remains elusive whether they possess similar late-restriction activities.We examined the antiviral spectra of TRIM5α orthologues and human TRIM family members which have a genetic locus proximal to human TRIM5α (TRIM5αhu), against primate lentiviral production. When HIV-1 virus-like particles (VLPs) were generated in the presence of TRIM5α proteins, rhesus, African green and cynomolgus monkey TRIM5α (TRIM5αag and TRIM5αcy), but not TRIM5αhu, were efficiently incorporated into VLPs, suggesting an interaction between HIV-1 Gag and TRIM5α proteins. TRIM5αrh potently restricted the viral production of HIV-1 groups M and O and HIV-2, but not simian lentiviruses including SIV(MAC)1A11, SIV(AGM)Tan-1 or SIV(AGM)SAB-1. TRIM5αhu did not show notable late restriction activities against these lentiviruses. TRIM5αag and TRIM5αcy showed intermediate restriction phenotypes against HIV-1 and HIV-2, but showed no restriction activity against SIV production. A series of chimeric TRIM5α constructs indicated that the N-terminal region of TRIM5αag and TRIM5αcy are essential for the late restriction activity, while the C-terminal region of TRIM5αcy negatively regulates the late restriction activity against HIV-1. When select human TRIM family proteins were examined, TRIM21 and 22 were efficiently incorporated into HIV-1 VLPs, while only TRIM22 reduced HIV-1 titers up to 5-fold. The antiviral activities and encapsidation efficiencies did not correlate with their relative expression levels in the producer cells.Our results demonstrated the variations in the late restriction activities among closely related TRIM5α orthologues and a subset of human TRIM family proteins, providing further insights into the late restriction activities of TRIM proteins
Long-Term Infection and Vertical Transmission of a Gammaretrovirus in a Foreign Host Species
Increasing evidence has indicated natural transspecies transmission of gammaretroviruses; however, viral-host interactions after initial xeno-exposure remain poorly understood. Potential association of xenotropic murine leukemia virus-related virus (XMRV) in patients with prostate cancer and chronic fatigue syndrome has attracted broad interests in this topic. Although recent studies have indicated that XMRV is unlikely a human pathogen, further understanding of XMRV xenoinfection would allow in vivo modeling of the initial steps of gammaretroviral interspecies transmission, evolution and dissemination in a new host population. In this study, we monitored the long-term consequences of XMRV infection and its possible vertical transmission in a permissive foreign host, wild-derived Mus pahari mice. One year post-infection, XMRV-infected mice showed no notable pathological changes, while proviral DNA was detected in three out of eight mice. XMRV-infected mice remained seropositive throughout the study although the levels of gp70 Env- and p30 capsid-specific antibodies gradually decreased. When vertical XMRV transmission was assessed, no viremia, humoral immune responses nor endogenization were observed in nine offspring from infected mothers, yet one offspring was found PCR-positive for XMRV-specific sequences. Amplified viral sequences from the offspring showed several mutations, including one amino acid deletion in the receptor binding domain of Env SU. Our results therefore demonstrate long-term asymptomatic infection, low incidence of vertical transmission and limited evolution of XMRV upon transspecies infection of a permissive new host, Mus pahari
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