588 research outputs found
Simulation study of pressure and temperature dependence of the negative thermal expansion in Zn(CN)(2)
12 pages, 16 figures12 pages, 16 figures12 pages, 16 figures12 pages, 16 figure
A multiply substituted G-H loop from foot-and-mouth disease virus in complex with a neutralizing antibody: A role for water molecules
The crystal structure of a 15 amino acid synthetic peptide, corresponding to the sequence of the major antigenic site A (G-H loop of VP1) from a multiple variant of foot-and-mouth disease virus (FMDV), has been determined at 2·3 resolution. The variant peptide includes four amino acid substitutions in the loop relative to the previously studied peptide representing FMDV C-S8c1 and corresponds to the loop of a natural FMDV isolate of subtype C1. The peptide was complexed with the Fab fragment of the neutralizing monoclonal antibody 4C4. The peptide adopts a compact fold with a nearly cyclic conformation and a disposition of the receptor-recognition motif Arg-Gly-Asp that is closely related to the previously determined structure for the viral loop, as part of the virion, and for unsubstituted synthetic peptide antigen bound to neutralizing antibodies. New structural findings include the observation that well-defined solvent molecules appear to play a major role in stabilizing the conformation of the peptide and its interactions with the antibody. Structural results are supported by molecular-dynamic simulations. The multiply substituted peptide developed compensatory mechanisms to bind the antibody with a conformation very similar to that of its unsubstituted counterpart. One water molecule, which for steric reasons could not occupy the same position in the unsubstituted antigen, establishes hydrogen bonds with three peptide amino acids. The constancy of the structure of an antigenic domain despite multiple amino acid substitutions has implications for vaccine design
Both cis and trans Activities of Foot-and-Mouth Disease Virus 3D Polymerase Are Essential for Viral RNA Replication
The Picornaviridae is a large family of positive-sense RNA viruses that contains numerous human and animal pathogens, including foot-and-mouth disease virus (FMDV). The picornavirus replication complex comprises a co-ordinated network of protein-protein and protein-RNA interactions involving multiple viral and host-cellular factors. Many of the proteins within the complex possess multiple roles in viral RNA replication, some of which can be provided in trans (i.e. via expression from a separate RNA molecule), whilst other are required in cis (i.e. expressed from the template RNA molecule). In vitro studies have suggested that multiple copies of the RNA-dependent RNA-polymerase (RdRp), 3D, are involved in the viral replication complex. However, it is not clear whether all these molecules are catalytically active or what other function(s) they provide. In this study, we aimed to distinguish between catalytically-active 3D molecules and those which build a replication complex. We report a novel non-enzymatic cis-acting function of 3D that is essential for viral genome replication. Using a FMDV replicon in complementation experiments, our data demonstrate that this cis-acting role of 3D is distinct from the catalytic activity, which is predominantly trans-acting. Immunofluorescence studies suggest that both cis- and trans acting 3D molecules localise to the same cellular compartment. However, our genetic and structural data suggest that 3D interacts in cis with RNA stem-loops that are essential for viral RNA replication. Together, this study identifies a previously undescribed aspect of picornavirus replication complex structure-function and an important methodology for probing such interactions further
Free-Field Realization of D-dimensional Cylindrical Gravitational Waves
We find two-dimensional free-field variables for D-dimensional general
relativity on spacetimes with D-2 commuting spacelike Killing vector fields and
non-compact spatial sections for D>4. We show that there is a canonical
transformation which maps the corresponding two-dimensional dilaton gravity
theory into a two-dimensional diffeomorphism invariant theory of the free-field
variables. We also show that the spacetime metric components can be expressed
as asymptotic series in negative powers of the dilaton, with coefficients which
can be determined in terms of the free fields.Comment: 15 pages, Late
Exchange couplings in the magnetic molecular cluster Mn12Ac
The magnetic properties of the molecular cluster Mn12Ac are due to the four
Mn3+ ions which have spins S=3/2 and the eight Mn4+ ions with spins S=2. These
spins are coupled by superexchange mechanism. We determine the four exchange
couplings assuming a Heisenberg-type interaction between the ions. We use exact
diagonalization of the spin Hamiltonian by a Lanczos algorithm and we adjust
the couplings to reproduce the magnetization curve of Mn12Ac. We also impose
the constraint of reproducing a gap of 35K between a S=10 ground state and a
first excited state with S=9. We predict that there is an excited level with
S=8 at 37K above the ground state, only slightly above the S=9 excited state
which lies at 35K and the next excited state is a S=9 multiplet at 67K above
the S=10 ground state.Comment: 15 pages, 6 figures, submitted to Phys Rev B, corrected a misTeX:
values of J1, J2 have changed, refs update
Backreaction from non-conformal quantum fields in de Sitter spacetime
We study the backreaction on the mean field geometry due to a non-conformal
quantum field in a Robertson-Walker background. In the regime of small mass and
small deviation from conformal coupling, we compute perturbatively the
expectation value of the stress tensor of the field for a variety of vacuum
states, and use it to obtain explicitly the semiclassical gravity solutions for
isotropic perturbations around de Sitter spacetime, which is found to be
stable. Our results show clearly the crucial role of the non-local terms that
appear in the effective action: they cancel the contribution from local terms
proportional to the logarithm of the scale factor which would otherwise become
dominant at late times and prevent the existence of a stable self-consistent de
Sitter solution. Finally, the opposite regime of a strongly non-conformal field
with a large mass is also considered.Comment: 31 page
Stability of de Sitter spacetime under isotropic perturbations in semiclassical gravity
A spatially flat Robertson-Walker spacetime driven by a cosmological constant
is non-conformally coupled to a massless scalar field. The equations of
semiclassical gravity are explicitly solved for this case, and a
self-consistent de Sitter solution associated with the Bunch-Davies vacuum
state is found (the effect of the quantum field is to shift slightly the
effective cosmological constant). Furthermore, it is shown that the corrected
de Sitter spacetime is stable under spatially-isotropic perturbations of the
metric and the quantum state. These results are independent of the free
renormalization parameters.Comment: 19 pages, REVTeX
Stochastic Gravity: Beyond Semiclassical Gravity
The back-reaction of a classical gravitational field interacting with quantum
matter fields is described by the semiclassical Einstein equation, which has
the expectation value of the quantum matter fields stress tensor as a source.
The semiclassical theory may be obtained from the quantum field theory of
gravity interacting with N matter fields in the large N limit. This theory
breaks down when the fields quantum fluctuations are important. Stochastic
gravity goes beyond the semiclassical limit and allows for a systematic and
self-consistent description of the metric fluctuations induced by these quantum
fluctuations. The correlation functions of the metric fluctuations obtained in
stochastic gravity reproduce the correlation functions in the quantum theory to
leading order in an 1/N expansion. Two main applications of stochastic gravity
are discussed. The first, in cosmology, to obtain the spectrum of primordial
metric perturbations induced by the inflaton fluctuations, even beyond the
linear approximation. The second, in black hole physics, to study the
fluctuations of the horizon of an evaporating black hole.Comment: 12 pages, no figures, proceedings of the XXIX Spanish Relativity
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Conformations in crystals and solutions of d(CACGTG), d(CCGCGG) and d(GGCGCC) studied by vibrational spectroscopy
Crystals of self camplementary DMA hexamers dCCACGTG>, dCCCGCGG> and d were grown bf vapour dlffuslon technlque and studled by mlcroRaman and mlcroiR spectroscop es. The ollgonucleotldes were studled ln parallel ln solutlon by vlbratlonal spectroscopy. A B->Z transltlon was detected by Raman spectroscopy cl.lrlng the crystalllzatlon procese for dCCACGTG>. Vlbratlonal spectroscopy shows that the dCGGCGCC> crystals adopt a B geametry. On the contrary the d sequence whlch ls shown to be able to undergo ln solutlon or ln fllms qulte easlly the B->Z transltlon, remalns trapped ln crystals ln a geametry whlch may correspond to an lntermedlate conformatlon often proposed ln modele of the B->Z transltlon. The crystals used ln thls study were characterlzed by X-ray dlffractlon. The unlt cell and space group have been determlned
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