Lack of self-averaging in neutral evolution of proteins

We simulate neutral evolution of proteins imposing conservation of the thermodynamic stability of the native state in the framework of an effective model of folding thermodynamics. This procedure generates evolutionary trajectories in sequence space which share two universal features for all of the examined proteins. First, the number of neutral mutations fluctuates broadly from one sequence to another, leading to a non-Poissonian substitution process. Second, the number of neutral mutations displays strong correlations along the trajectory, thus causing the breakdown of self-averaging of the resulting evolutionary substitution process.     

Restrictions and expansions of holomorphic representations

We compute tensor products of representations of the holomorphic discrete series of a Lie group G, or restrictions to some subgroup G′. A detailed study is done for the case of the conformal group O(4, 2).     

Principio di entropia e restrizioni termodinamiche per fluidi con memoria

Riassunto In questo lavoro si affrontano i problemi relativi alle restrizioni termodinamiche, imposte dal principio di entropia nella formulazione di Müller [1], per fluidi con memoria, mediante il metodo dei moltiplicatori di Lagrange.

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Summary In this work Author deals with the problems pertinent to the thermodynamic restrictions, which are due to principle of entropy in the formulation of Müller [1], for fluids with a memory, through the Lagrange multipliers.

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Lavoro eseguito nell'ambito del G.N.F.M. del C.N.R.     

Reciprocal and variational theorems for nonlocal theory of viscoelastic materials

Summary We study some variational and reciprocal problems for viscoelastic materials with nonlocal constitutive equations and in particular with dissipative boundary conditions.

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Riassunto Si determinano alcuni teoremi variazionali e di reciprocitá per materiali viscoelastici con una dipendenza anche spaziale e con condizioni al contorno dissippative.

     

Research on heterocyclic compounds. XIII. Synthesis of 4,5-dihydro-5-oxo-3-isoxazoleacetic acid and related compounds

Some new 4,5-dihydro-5-oxoisoxazole derivatives were synthesized as part of a study to prepare potential antiinflammatory agents. The reaction of the diethyl ester of 3-oxopentanedioic acid with hydroxylamine afforded the 3-hydroxyimino derivative, which was then cyclized to the title compound. This reacted with diazomethane to give a couple of isomeric methyl derivatives, namely methyl 2,5-dihydro-2-methyl-5-oxo-3-isoxazoleacetate and methyl 5-methoxy-3-isoxazoleacetate. Reaction of these compounds with ammonia gave the corresponding acetamides. All compounds were characterized by elemental analysis, uv, ir, and ¹H-nmr spectra.     

Chemical modification of chitosan under high-intensity ultrasound

Chitosan (CTS), a biocompatible, biodegradable, non-toxic polymer, dissolves in water only if pH is lowered under 6.5, when a substantial fraction of the amino groups is protonated. Its range of application has been much extended by partially depolymerising it or converting it to water-soluble derivatives. Working under high-intensity ultrasound at 17.8-18.5 kHz, using either a simple horn or a cup horn, we achieved a controlled depolymerization of CTS, also prepared in high yields several derivatives that can be useful intermediates for further chemical modification, as well as several water-soluble derivatives that lend themselves to a host of industrial applications. Compared to conventional methods, all these reactions went to completion in considerably shorter times at lower temperatures.     

Probing fragment complementation by rigid-body docking: in silico reconstitution of calbindin D9k

Fragment complementation is gaining an increasing impact as a nonperturbing method to probe noncovalent interactions within protein supersecondary structures. In this study, the fast Fourier transform rigid-body docking algorithm ZDOCK has been employed for in silico reconstitution of the calcium binding protein calbindin D9k, from its two EF-hands subdomains, namely, EF1 (residues 1-43) and EF2 (residues 44-75). The EF1 fragment has been used both in its wild type and in nine mutant forms, in line with in vitro experiments. Consistent with in vitro data, ZDOCK reconstituted the proper fold of wild-type and mutated calbindin, locating the nativelike structures (i.e., holding a root-mean-square deviation < 1 A with respect to the X-ray structure) among the first 10 top-scored solutions out of 4000. Moreover, the three independent in silico reconstitutions of wild-type calbindin ranked a nativelike structure at the top of the output list, that is, the best scored one. The algorithm has been also successfully challenged in reconstituting the EF2 homodimer from two identical copies of the monomer. Furthermore, quantitative models consisting of linear correlations between thermodynamic data and ZDOCK scores were built, providing a tested tool for very fast in silico predictions of the free energy of association of protein-protein complexes solved at the atomic level and known to not undergo significant conformational changes upon binding.     

Topological defects and bulk melting of hexagonal ice

We use classical molecular dynamics combined with the recently developed metadynamics method [Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 20] to study the process of bulk melting in hexagonal ice. Our simulations show that bulk melting is mediated by the formation of topological defects which preserve the coordination of the tetrahedral network. Such defects cluster to form a defective region involving about 50 molecules with a surprisingly long lifetime. The subsequent formation of coordination defects triggers the transition to the liquid state.     

Gibbs sampling for time-delay-and amplitude estimation in underwater acoustics

Multipath arrivals at a receiving sensor are frequently encountered in many signal-processing areas, including sonar, radar, and communication problems. In underwater acoustics, numerous approaches to source localization, geoacoustic inversion, and tomography rely on accurate multipath arrival extraction. A novel method for estimation of time delays and amplitudes of arrivals with maximum a posteriori (MAP) estimation is presented here. MAP estimation is optimal if appropriate statistical models are selected for the data; implementation, requiring maximization of a multidimensional function, is computationally demanding. Gibbs sampling is proposed as an efficient means for estimating necessary posterior probability distributions, bypassing analytical calculations. The Gibbs sampler includes as unknowns time delays, amplitudes, noise variance, and number of arrivals. Through Monte Carlo simulations, the method is shown to have a performance very close to that of analytical MAP estimation. The method is also shown to be superior to expectation-maximization, which is often applied to time-delay estimation. The Gibbs sampling approach is demonstrated to be more informative than other time-delay estimation methods, providing complete posterior distributions compared to just point estimates; the distributions capture the uncertainty in the problem, presenting likely values of the unknowns that are different from simple point estimates.