A microscopic description of acid-base equilibrium

Acid-base reactions are ubiquitous in nature. Understanding their mechanisms is crucial in many fields, from biochemistry to industrial catalysis. Unfortunately, experiments only give limited information without much insight into the molecular behaviour. Atomistic simulations could complement experiments and shed precious light on microscopic mechanisms. The large free energy barriers connected to proton dissociation however make the use of enhanced sampling methods mandatory. Here we perform an ab initio molecular dynamics (MD) simulation and enhance sampling with the help of methadynamics. This has been made possible by the introduction of novel descriptors or collective variables (CVs) that are based on a conceptually new outlook on acid-base equilibria. We test successfully our approach on three different aqueous solutions of acetic acid, ammonia, and bicarbonate. These are representative of acid, basic, and amphoteric behaviour

Tautomeric equilibrium in condensed phases

We present an ab initio molecular dynamics (MD) investigation of the tautomeric equilibrium for aqueous solutions of glycine and acetone at realistic experimental conditions. Metadynamics is used to accelerate proton migration among tautomeric centers. Due to the formation of complex water-ion structures involved the proton dynamics in the aqueous environment, standard enhanced sampling approaches may face severe limitations in providing a general description of the phenomenon. Recently, we developed a set of Collective Variables (CVs) designed to study protons transfer reactions in complex condensed systems [Grifoni et al. PNAS, 2019, 116(10), 4054-4057]. In this work we applied this approach to study proton dissociation dynamics leading to tautomeric interconversion of biologically and chemically relevant prototypical systems, namely glycine and acetone in water. Although relatively simple from a chemical point of view, the results show that even for these small systems complex reaction pathways and non-trivial conversion dynamics are observed. The generality of our method allows obtaining these results without providing any prior information on the dissociation dynamics but only the atomic species that can exchange protons in the process. Our results agree with literature estimates and demonstrate the general applicability of this method in the study of tautomeric reactions

Native Mitral Valve Endocarditis Caused by Neisseria elongata subsp. nitroreducens in a Patient with Marfan Syndrome: First Case in Italy and Review of the Literature

Neisseria elongata (NE) is an aerobic Gram-negative organism that constitutes part of the commensal human normal oropharyngeal flora. Although previously considered not to be pathogenic, it has been recognized as an occasional cause of significant infections in humans. We report here the first case in Italy of infective endocarditis of a native prolapsing mitral valve in a patient with Marfan syndrome, caused by NE subspecies nitroreducens which has been rarely isolated from clinical specimens. The culprit organism has been confirmed by mass spectrometry directly from the positive blood culture, as previously reported. The amplified gene has been deposited in GenBank under accession number KT591873. In spite of the reported aggressive nature of NE, clinical remission was promptly obtained, there being no requirement for surgery

Limites fondamentales des réseaux avec caches partagés

In the context of communication networks, the emergence of predictable content has brought to the fore the use of caching as a fundamental ingredient for handling the exponential growth in data volumes. This thesis aims at providing the fundamental limits of shared-cache networks where the communication to users is aided by a small set of caches. Our shared-cache model, not only captures heterogeneous wireless cellular networks, but it can also represent a model for users requesting multiple files simultaneously, and it can be used as a simple yet effective way to deal with the so-called subpacketization bottleneck of coded caching. Furthermore, we will also see how our techniques developed for caching networks can find application in the context of heterogeneous coded distributed computing.Dans le contexte des réseaux de diffusion de contenu, les avantages puissants de la combinaison du cache et de la multidiffusion codée ont été démontrés pour les réseaux où chaque utilisateur est équipé de son propre cache isolé. Cette thèse vise à fournir les principes fondamentaux des réseaux à cache partagé où la communication avec les utilisateurs est assistée par un petit ensemble de caches, chacun d'entre eux servant un nombre arbitraire d'utilisateurs. Notre modèle de cache partagé, non seulement capture les réseaux cellulaires sans fil hétérogènes où les petites stations de base assistées par cache coexistent avec une macro station de base, mais il peut également représenter un modèle pour les réseaux où les utilisateurs demandent plusieurs fichiers. Nous verrons également comment ce problème des demandes de fichiers multiples se pose dans le contexte de calcul distribué codé, où nous appliquerons les mêmes idées et techniques que celles utilisées pour les réseaux avec cache. De plus, il est bien connu que la limitation du nombre de caches à une valeur beaucoup plus petite que le nombre d'utilisateurs peut être inévitable dans des scénarios pratiques où la taille des fichiers est finie et limitée. C'est pourquoi nous pensons que l'étude des réseaux de caches partagés est d'une importance critique pour le développement des techniques de mise en cache codée