Measurement and minimisation of the Mapping Entropy of a Coarse-Grained biomolecular system

All-atom Molecular Dynamics (MD) is the standard approach to perform in silico simulations of biomolecular systems. Despite its central role in modern computational biophysics, MD cannot span the time scales where the majority of relevant biological processes take place. An alternative is represented by coarse-grained (CG) modelling [1], that is, those lower-resolution representations of the system which aim at effectively reducing the number of degrees of freedom of a biomolecule in order to reach previously inaccessible time scales. Among the several statistical mechanics-based CG'ing techniques, we focused on those that measure the difference in information content between the coarse-grained and the all-atom system. We developed a protocol [2] able to compute the Mapping Entropy, which quantifies the amount of information retained upon the process of CG'ing due only to the choice of the Mapping. Our approach can therefore provide the user with the subset of sites which are maximally informative about the original, fully atomistic system. Tests conducted over a set of well-known proteins showed that regions retained with high probability are often related to the biological function of the molecule. [1] William George Noid. Perspective: Coarse-grained models for biomolecular systems. The Journal of chemical physics, 139(9):09B201 1, 2013.[2] Marco Giulini, Roberto Menichetti, M Scott Shell, and Raffaello Potestio. An information-theory-based approach for optimal model reduction of biomolecules. Journal of chemical theory and computation, 16(11):6795–6813, 2020

General Theorems on Decoherence in the Thermodynamic Limit

We extend the results on decoherence in the thermodynamic limit [M. Frasca, Phys. Lett. A {\bf 283}, 271 (2001)] to general Hamiltonians. It is shown that N independent particles, initially properly prepared, have a set of observables behaving classically in the thermodynamic limit. This particular set of observables is then coupled to a quantum system that in this way decoheres so to have the density matrix in a mixed form. This gives a proof of the generality of this effect.Comment: 8 pages, no figures. Version accepted by Physics Letters

Thermodynamic Limit and Decoherence: Rigorous Results

Time evolution operator in quantum mechanics can be changed into a statistical operator by a Wick rotation. This strict relation between statistical mechanics and quantum evolution can reveal deep results when the thermodynamic limit is considered. These results translate in a set of theorems proving that these effects can be effectively at work producing an emerging classical world without recurring to any external entity that in some cases cannot be properly defined. In a many-body system has been recently shown that Gaussian decay of the coherence is the rule with a duration of recurrence more and more small as the number of particles increases. This effect has been observed experimentally. More generally, a theorem about coherence of bulk matter can be proved. All this takes us to the conclusion that a well definite boundary for the quantum to classical world does exist and that can be drawn by the thermodynamic limit, extending in this way the deep link between statistical mechanics and quantum evolution to a high degree.Comment: 5 pages, no figures. Contribution to proceedings of DICE 2006 (Piombino, Italy, September 11-15, 2006

Dynamical decoherence in a cavity with a large number of two-level atoms

We consider a large number of two-level atoms interacting with the mode of a cavity in the rotating-wave approximation (Tavis-Cummings model). We apply the Holstein-Primakoff transformation to study the model in the limit of the number of two-level atoms, all in their ground state, becoming very large. The unitary evolution that we obtain in this approximation is applied to a macroscopic superposition state showing that, when the coherent states forming the superposition are enough distant, then the state collapses on a single coherent state describing a classical radiation mode. This appear as a true dynamical effect that could be observed in experiments with cavities.Comment: 9 pages, no figures. This submission substitutes paper quant-ph/0212148 that was withdrawn. Version accepted for publication in Journal of Physics B: Atomic, Molecular & Optical Physic

Simultaneity as an Invariant Equivalence Relation

This paper deals with the concept of simultaneity in classical and relativistic physics as construed in terms of group-invariant equivalence relations. A full examination of Newton, Galilei and Poincar\'e invariant equivalence relations in $\R^4$ is presented, which provides alternative proofs, additions and occasionally corrections of results in the literature, including Malament's theorem and some of its variants. It is argued that the interpretation of simultaneity as an invariant equivalence relation, although interesting for its own sake, does not cut in the debate concerning the conventionality of simultaneity in special relativity.Comment: Some corrections, mostly of misprints. Keywords: special relativity, simultaneity, invariant equivalence relations, Malament's theore

A drastic complex atheromatous aorta A case report

Aortic atherosclerosis is the most common disease of the aorta. More than 50% of the plaques thicker than 4 mm are located along the descending aorta. The complex morphology of the plaque, such as ulceration or the presence of thrombi, is associated with increased embolic risk. The increasing use of transesophageal echocardiogram has enhanced the recognition of aortic atheromas. We describe a case of a male patient with complex atherosclerotic disease involving the coronary vessels and descending aortic tract with some embolic complications

dosimetry methods in boron neutron capture therapy

Dosimetry studies have been carried out at thermal and epithermal columns of LVR- 15 research reactor for investigating the spatial distribution of gamma dose, fast neutron dose and thermal neutron fluence. Two different dosimetry methods, both based on solid state detectors, have been studied and applied and the accuracy and consistency of the results have been inspected. One method is based on Fricke gel dosimeters that are dilute water solutions and have good tissue equivalence for neutrons and also for all the secondary radiations produced by neutron interactions in tissue or water phantoms. Fricke gel dosimeters give the possibility of separating the various dose contributions, i.e. the gamma dose, the fast neutron dose and the dose due to charged particles generated during thermal neutron reactions by isotopes having high cross section, like 10B. From this last dose, thermal neutron fluence can be obtained by means of the kerma factor. The second method is based on thermoluminescence dosimeters. In particular, the developed method draw advantage from the different heights of the peaks of the glow curve of such phosphors when irradiated with photons or with thermal neutrons. The results show that satisfactory results can be obtained with simple methods, in spite of the complexity of the subject. However, the more suitable dosimeters and principally their utilization and analysis modalities are different for the various neutron beams, mainly depending on the relative intensities of the three components of the neutron field, in particular are different for thermal and epithermal columns