arXiv subjects

Alessio D'Alessandro

Publications and source records attributed to Alessio D'Alessandro.

6 recordsLinked to original sources

arXiv2021

High rate of SARS-CoV2 nonsense spike genomes coding for prematurely truncated proteins

Replication of SARS-CoV2 virions is an error-prone process which may eventually generate a percentage of impaired protein copies with complete lack of functionality. For instance, after RNA mis-replication, a very premature stop codon (UAG, UAA, UGA) coding for a prematurely truncated (nonsense-mutated) spike protein may occur. In the natural virus replication process via cell infection, the nonsense genomes are corrected by the proofreading enzymes of the virus, strongly penalized by natural selection and condemned to a very short life by the host cell's mRNA watching mechanisms. However, for the very long spike genome of 1273 codons, a truncated non-functional spike protein may potentially still occur with a high frequency, even in presence of a low mutation rate per single nucleotide. With this paper, a hi-fidelity post-processing of SARS-CoV2 spike sequences is provided: in ex-vivo samples from patients, an impressively high rate of 26\% of prematurely-stopped (nonsense-mutated) spike genomes sequences due to insertions/deletions is found, compared with a 9.7\% obtained from in-vitro cell culture. A general warning on the possible high rate of prematurely-stopped spike protein sequences is also raised for "artificial" de novo DNA synthesis processes of SARS-CoV2 spike genomes with no associated natural proofreading/selection, possibly including vaccine preparations. Finally, a metric based on the ratio between prematurely stopped and "normal" genomes is proposed as a potential host-independent variant-watching tool, able to classify the infectivity of new spike mutations.

q-bio.GN↗

arXiv2020

Electrically small matched antennas with time-periodic and space-uniform modulation

A conceptual method to realize an impedance-matched electrically small antenna is discussed, using a transmission line modulated only in time. The time-periodic space-uniform modulation of a distributed shunt array of varcapacitors excites a mode with very small frequency but still a small (microwave) wavelength: the matching line then retains a practical size. The modulated transmission line brings the problem of impedance matching to a frequency $f_0$ much higher than the signal, where the large antenna reactance can be easily compensated with a much higher bandwidth for the same $Q$ factor: actually the bandwidth $Δf= f_0 / Q$ becomes large when $f_0$ is much larger than the signal frequency. A simple way to obtain the space uniform modulation of the transmission line is illustrated, making use of a Wheatstone-bridge arrangement of the modulated varicaps. The signal and modulating lines, running in parallel on a section of the same length, see two very different equivalent shunt capacitances, so that the modulating voltage is almost uniform while the signal voltage may change significantly across the transmission line.

physics.app-ph↗

arXiv2010

Thermal Monopole Condensation and Confinement in finite temperature Yang-Mills Theories

We investigate the connection between Color Confinement and thermal Abelian monopoles populating the deconfined phase of SU(2) Yang-Mills theory, by studying how the statistical properties of the monopole ensemble change as the confinement/deconfinement temperature is approached from above. In particular we study the distribution of monopole currents with multiple wrappings in the Euclidean time direction, corresponding to two or more particle permutations, and show that multiple wrappings increase as the deconfinement temperature is approached from above, in a way compatible with a condensation of such objects happening right at the deconfining transition. We also address the question of the thermal monopole mass, showing that different definitions give consistent results only around the transition, where the monopole mass goes down and becomes of the order of the critical temperature itself.

hep-lat↗

arXiv2008

Physical understanding of an echo-Doppler test with voice-induced vibration

The physical understanding of a method of detecting mammalian cancer via vocalization during a normal echo-Doppler test is provided. The backscattered ultrasound frequency in the case of a vocal humming resonating in the chest wall is computed: the overall effect is that the signal/noise ratio could be easily improved at no cost. Clinical results are to appear separately elsewhere.

physics.med-ph↗

arXiv2008

Magnetic monopoles in the high temperature phase of Yang-Mills theories

We investigate the properties of thermal abelian magnetic monopoles in the high temperature phase of Yang--Mills theories, following a recent proposal for their identification on lattice configurations. The study is done for SU(2) pure gauge theory, for temperatures going up to about 10 times the deconfining temperature and using the Maximal Abelian gauge to perform the abelian projection. We find that the monopole density has a well defined continuum limit. Its temperature dependence disagrees with a free particle gas prediction and is instead well described by a $T^3/(\log (T/Λ))^α$ behaviour in all the explored range, with $α\sim 2$ and $Λ\sim 100$ MeV. Also the study of spatial correlations of thermal monopoles shows the presence of non-trivial interactions among them. Finally, we discuss the gauge dependence of our results, showing that it is significant and that, even within the Maximal Abelian gauge, Gribov copy effects are important.

hep-lat↗

arXiv2007

Confining properties of QCD at finite temperature and density

A disorder parameter detecting dual superconductivty of the vacuum is used as a probe to characterize the confining properties of the phase diagram of two color QCD at finite temperature and density. We obtain evidence for the disappearing of dual superconductivity (deconfinement) induced by a finite density of baryonic matter, as well as for a coincidence of this phenomenon with the restoration of chiral symmetry both at zero and finite density. The saturation transition induced by Pauli blocking is studied as well, and a general warning is given about the possible effects that this unphysical transition could have on the study of the QCD phase diagram at strong values of the gauge coupling.

hep-lat↗