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.     

Diffusion Monte Carlo method with lattice regularization

We introduce an efficient lattice regularization scheme for quantum Monte Carlo calculations of realistic electronic systems. The kinetic term is discretized by a finite difference Laplacian with two mesh sizes, a and a', chosen so that the electrons can diffuse in a configuration space which is in practice indistinguishable from the continuum, and the different length scales in the system can be efficiently taken in account. The regularized Hamiltonian goes to the continuous limit for a --> 0 and allows the inclusion of nonlocal potentials in a consistent variational scheme, substantially improving the accuracy upon previous nonvariational approaches.     

Strongly correlated superconductivity and pseudogap phase near a multiband Mott insulator

Near a Mott transition, strong electron correlations may enhance Cooper pairing. This is demonstrated in the dynamical mean field theory solution of a twofold-orbital degenerate Hubbard model with an inverted on-site Hund rule exchange, favoring local spin-singlet configurations. Close to the Mott insulator (which here is a local version of a valence bond insulator) a pseudogap non-Fermi-liquid metal, a superconductor, and a normal metal appear, in striking similarity with the physics of cuprates. The strongly correlated s-wave superconducting state has a larger Drude weight than the corresponding normal state. The role of the impurity Kondo problem is underscored.     

Algorithms for packing and scheduling problems

We survey the main results presented in the authors Ph.D Thesis (Monaci 2001), discussed on January 2002 at the University of Bologna (Italy) and supervised by Paolo Toth and Silvano Martello. The thesis deals with exact and heuristic approaches for solving a class of combinatorial optimization problems, with particular emphasis on Two-Dimensional Packing problems and Scheduling problems.     

Molecular dynamics simulations of the ligand-induced chemical information transfer in the 5-HT(1A) receptor

Comparative molecular dynamics simulations of the 5-HT(1A) receptor in its empty as well as agonist- (i.e. active) and antagonist-bound (i.e. nonactive) forms have been carried out. The agonists 5-HT and (R)-8-OH-DPAT as well as the antagonist WAY100635 have been employed. The results of this study strengthen the hypothesis that the receptor portions close to the E/DRY/W motif, with prominence to the cytosolic extensions of helices 3 and 6, are particularly susceptible to undergo structural modification in response to agonist binding. Despite the differences in the structural/dynamics behavior of the two agonists when docked into the 5-HT(1A) receptor, they both exert a destabilization of the intrahelical and interhelical interactions found in the empty and antagonist-bound receptor forms between the arginine of the E/DRY sequence and both D133(3.49) and E340(6.30). For both agonists, the chemical information transfer from the extracellular to the cytosolic domains is mediated by a cluster of aromatic amino acids in helix 6, following the ligand interaction with selected amino acids in the extracellular half of the receptor, such as D116(3.32), S199(5.42), Y195(5.38), and F361(6.51). A significant reduction in the bend at P360(6.50), as compared to the empty and the antagonist-bound receptor forms, is one of the features of the agonist-bound forms that is related to the breakage of the interhelical salt bridge between the E/DRY arginine and E340(6.30). Another structural feature, shared by the agonist-bound receptor forms and not by the empty and antagonist-bound forms, is the detachment of helices 2 and 4, as marked by the movement of W161(4.50) away from helix 2, toward the membrane space.     

Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange

We present a method for determining the ensembles of native protein structures that result from the large fluctuations of low probability revealed by hydrogen-exchange experiments. The measured protection factors are used to bias Monte Carlo simulations to sample the structures of the exchange competent species. The approach is illustrated by its application to the case of alpha-lactalbumin.     

Microwave-assisted acylation of 7-amino-5-aryl-6-cyanopyrido[2,3-d]pyrimidines

A microwave-assisted method is described for monoacylating 7-amino-5-aryl-6-cyanopyrido[2,3-d]pyrimidines using excess acid chlorides in pyridine. A diacylated intermediate is effectively deacylated to the product amide by a macroporous-Tris resin. A small library of 17 amides was prepared to validate the method. The integration of commercial microwave technology into the ArQule chemistry platform is also discussed.     

Mononuclear heterocyclic rearrangement. Note I. Kinetic study of the rearrangement of the phenylhydrazone of 3-benzoyl-5-phenyl-1,2,4-oxadiazole into 2,5-diphenyl-4-benzoylamino-1,2,3-triazole

The rates of the mononuclear heterocyclic rearrangement of the phenylhydrazone of 3-benzoyl-5-phenyl-1,2,4-oxadiazole (1) into 2,5-diphenyl-4-benzoylamino-1,2,3-triazole (II) have heen measured in dioxane/water (50:50, v:v) in the range of pS⁺ 3.8–12.2 at various temperatures and the activation parameters determined. On the basis of the results obtained, we present evidence for the occurrence of two different types of reaction: the first, base-catalyzed; the second, pS⁺ -independent. In the base-catalyzed range the catalysis is of the general type.