Parallel computing and molecular dynamics of biological membranes

In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from CPU to individual nodes puts strong constraints on the possible programming strategies. Liquids can be very satisfactorily simulated using the "systolic" method. For more complex systems, like the biological ones at which we are ultimately interested in, the "domain decomposition" approach is best suited to beat the quadratic growth of the inter-molecular computational time with the number of elementary components of the system. The promising perspectives of using this strategy for extensive simulations of lipid bilayers are briefly reviewed.Comment: 4 pages LaTeX, 2 figures included, espcrc2.sty require

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 $\varpi \tau$ 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.

Zn-induced interactions between SARS-CoV-2 orf7a and BST2/Tetherin

We present in this work a first X-ray Absorption Spectroscopy study of the interactions of Zn with human BST2/tetherin and SARS-CoV-2 orf7a proteins as well as with some of their complexes. The analysis of the XANES region of the measured spectra shows that Zn binds to BST2, as well as to orf7a, thus resulting in the formation of BST2-orf7a complexes. This structural information confirms the the conjecture, recently put forward by some of the present Authors, according to which the accessory orf7a (and possibly also orf8) viral protein are capable of interfering with the BST2 antiviral activity. Our explanation for this behavior is that, when BST2 gets in contact with Zn bound to the orf7a Cys(15) ligand, it has the ability of displacing the metal owing to the creation of a new disulfide bridge across the two proteins. The formation of this BST2-orf7a complex destabilizes BST2 dimerization, thus impairing the antiviral activity of the latter

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

Metal ion binding in wild-type and mutated frataxin: a stability study

This work studies the stability of wild-type frataxin and some of its variants found in cancer tissues upon Co2+ binding. Although the physiologically involved metal ion in the frataxin enzymatic activity is Fe2+, as it is customarily done, Co2+ is most often used in experiments because Fe2+ is extremely unstable owing to the fast oxidation reaction Fe2+ → Fe3+. Protein stability is monitored following the conformational changes induced by Co2+ binding as measured by circular dichroism, fluorescence spectroscopy, and melting temperature measurements. The stability ranking among the wild-type frataxin and its variants obtained in this way is confirmed by a detailed comparative analysis of the XAS spectra of the metal-protein complex at the Co K-edge. In particular, a fit to the EXAFS region of the spectrum allows positively identifying the frataxin acidic ridge as the most likely location of the metal-binding sites. Furthermore, we can explain the surprising feature emerging from a detailed analysis of the XANES region of the spectrum, showing that the longer 81-210 frataxin fragment has a smaller propensity for Co2+ binding than the shorter 90-210 one. This fact is explained by the peculiar role of the N-terminal disordered tail in modulating the protein ability to interact with the metal

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

Measurement and application of electron stripping of ultrarelativistic 208Pb81+^{208}\textrm{Pb}^{81+}

New measurements of the stripping cross-section for ultrarelativistic hydrogen-like lead ions passing through aluminium and silicon have been performed at the Advanced Wakefield experiment at CERN. Agreement with existing measurements and theory has been obtained. Improvements in terms of electron beam quality and ion beam diagnostic capability, as well as further applications of such an electron beam, are discussed

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