588 research outputs found
Ab initio simulations of Cu binding sites in the N-terminal region of PrP
The prion protein (PrP) binds Cu2+ ions in the octarepeat domain of the
N-terminal tail up to full occupancy at pH=7.4. Recent experiments show that
the HGGG octarepeat subdomain is responsible for holding the metal bound in a
square planar coordination. By using first principle ab initio molecular
dynamics simulations of the Car-Parrinello type, the Cu coordination mode to
the binding sites of the PrP octarepeat region is investigated. Simulations are
carried out for a number of structured binding sites. Results for the complexes
Cu(HGGGW)+(wat), Cu(HGGG) and the 2[Cu(HGGG)] dimer are presented. While the
presence of a Trp residue and a H2O molecule does not seem to affect the nature
of the Cu coordination, high stability of the bond between Cu and the amide
Nitrogens of deprotonated Gly's is confirmed in the case of the Cu(HGGG)
system. For the more interesting 2[Cu(HGGG)] dimer a dynamically entangled
arrangement of the two monomers, with intertwined N-Cu bonds, emerges. This
observation is consistent with the highly packed structure seen in experiments
at full Cu occupancy.Comment: 4 pages, conference proceedin
A simple atomistic model for the simulation of the gel phase of lipid bilayers
In this paper we present the results of a large-scale numerical investigation
of structural properties of a model of cell membrane, simulated as a bilayer of
flexible molecules in vacuum. The study was performed by carrying out extensive
Molecular Dynamics simulations, in the (NVE) micro-canonical ensemble, of two
systems of different sizes (2x32 and 2x256 molecules), over a fairly large set
of temperatures and densities, using parallel platforms and more standard
serial computers. Depending on the dimension of the system, the dynamics was
followed for physical times that go from few hundred of picoseconds for the
largest system to 5--10 nanoseconds for the smallest one. We find that the
bilayer remains stable even in the absence of water and neglecting Coulomb
interactions in the whole range of temperatures and densities we have
investigated. The extension of the region of physical parameters that we have
explored has allowed us to study significant points in the phase diagram of the
bilayer and to expose marked structural changes as density and temperature are
varied, which are interpreted as the system passing from a crystal to a gel
phase.Comment: 41 pages, 13 figure
Optical response of a misaligned and suspended Fabry-Perot cavity
The response to a probe laser beam of a suspended, misaligned and detuned
optical cavity is examined. A five degree of freedom model of the fluctuations
of the longitudinal and transverse mirror coordinates is presented. Classical
and quantum mechanical effects of radiation pressure are studied with the help
of the optical stiffness coefficients and the signals provided by an FM
sideband technique and a quadrant detector, for generic values of the product
of the fluctuation frequency times the cavity round trip. A
simplified version is presented for the case of small misalignments. Mechanical
stability, mirror position entanglement and ponderomotive squeezing are
accommodated in this model. Numerical plots refer to cavities under test at the
so-called Pisa LF facility.Comment: 14 pages (4 figures) submitted to Phys. Rev.
The role of Zn ions in the interaction between SARS-CoV-2 orf7a protein and BST2/tetherin
In this paper, we provide evidence that Zn2+ ions play a role in the SARS-CoV-2 virus strategy to escape the immune response mediated by the BST2-tetherin host protein. This conclusion is based on sequence analysis and molecular dynamics simulations as well as X-ray absorption experiments [1]
The role of Zn ions in the interaction between SARS-CoV-2 orf7a protein and BST2/tetherin
In this paper, we provide evidence that Zn2+ ions play a role in the SARS-CoV-2 virus strategy to escape the immune response mediated by the BST2-tetherin host protein. This conclusion is based on sequence analysis and molecular dynamics simulations as well as X-ray absorption experiments
Displacement power spectrum measurement of a macroscopic optomechanical system at thermal equilibrium
The mirror relative motion of a suspended Fabry-Perot cavity is studied in
the frequency range 3-10 Hz. The experimental measurements presented in this
paper, have been performed at the Low Frequency Facility, a high finesse
optical cavity 1 cm long suspended to a mechanical seismic isolation system
identical to that one used in the VIRGO experiment. The measured relative
displacement power spectrum is compatible with a system at thermal equilibrium
within its environmental. In the frequency region above 3 Hz, where seismic
noise contamination is negligible, the measurement distribution is stationary
and Gaussian, as expected for a system at thermal equilibrium. Through a simple
mechanical model it is shown that: applying the fluctuation dissipation theorem
the measured power spectrum is reproduced below 90 Hz and noise induced by
external sources are below the measurement.Comment: 11 pages, 9 figures, 2 tables, to be submitte
Inertial control of the mirror suspensions of the VIRGO interferometer for gravitational wave detection
In order to achieve full detection sensitivity at low frequencies, the
mirrors of interferometric gravitational wave detectors must be isolated from
seismic noise. The VIRGO vibration isolator, called 'superattenuator', is fully
effective at frequencies above 4 Hz. Nevertheless, the residual motion of the
mirror at the mechanical resonant frequencies of the system are too large for
the interferometer locking system and must be damped. A multidimensional
feedback system, using inertial sensors and digital processing, has been
designed for this purpose. An experimental procedure for determining the
feedback control of the system has been defined. In this paper a full
description of the system is given and experimental results are presented.Comment: 17 pages, 11 figures, accepted for publication on Review of
Scientific Instrument
The variable finesse locking technique
Virgo is a power recycled Michelson interferometer, with 3 km long Fabry-Perot cavities in the arms. The locking of the interferometer has been obtained with an original lock acquisition technique. The main idea is to lock the instrument away from its working point. Lock is obtained by misaligning the power recycling mirror and detuning the Michelson from the dark fringe. In this way, a good fraction of light escapes through the antisymmetric port and the power build-up inside the recycling cavity is extremely low. The benefit is that all the degrees of freedom are controlled when they are almost decoupled, and the linewidth of the recycling cavity is large. The interferometer is then adiabatically brought on to the dark fringe. This technique is referred to as variable finesse, since the recycling cavity is considered as a variable finesse Fabry-Perot. This technique has been widely tested and allows us to reach the dark fringe in few minutes, in an essentially deterministic way
A Cross-correlation method to search for gravitational wave bursts with AURIGA and Virgo
We present a method to search for transient GWs using a network of detectors
with different spectral and directional sensitivities: the interferometer Virgo
and the bar detector AURIGA. The data analysis method is based on the
measurements of the correlated energy in the network by means of a weighted
cross-correlation. To limit the computational load, this coherent analysis step
is performed around time-frequency coincident triggers selected by an excess
power event trigger generator tuned at low thresholds. The final selection of
GW candidates is performed by a combined cut on the correlated energy and on
the significance as measured by the event trigger generator. The method has
been tested on one day of data of AURIGA and Virgo during September 2005. The
outcomes are compared to the results of a stand-alone time-frequency
coincidence search. We discuss the advantages and the limits of this approach,
in view of a possible future joint search between AURIGA and one
interferometric detector.Comment: 11 pages, 6 figures, submitted to CQG special issue for Amaldi 7
Proceeding
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