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.     

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.     

Computational maturation of a single-domain antibody against Aβ42 aggregation

The expansion of structural databases and the increase in computing power are enabling approaches for antibody discovery based on computational design. It has already been shown that it is possible to use this approach to generate antibodies for specific epitopes on challenging targets. Here we describe an application of this procedure for antibody maturation through the computational design of mutational variants of increased potency. We illustrate this procedure in the case of a single-domain antibody targeting an epitope in the N-terminal region of Aβ42, a peptide whose aggregation is closely associated with Alzheimer''s disease. We show that this approach enables the generation of an antibody variant with over 200-fold increased potency against the primary nucleation process in Aβ42 aggregation. Our results thus demonstrate that potentiated antibody variants can be obtained by computational maturation.

A computational maturation method enables the generation of an antibody variant with over 200-fold increased potency against the primary nucleation process in Aβ42 aggregation.     

Comparison of confinement characters between porous silicon and silicon nanowires

Confinement character and its effects on photoluminescence (PL) properties are theoretically investigated and compared between porous silicon (p-Si) and silicon nanowires (Si-NWs). The method is based on the application of the tight-binding technique using the minimal sp³-basis set, including the second-nearest-neighbor interactions. The results show that the quantum confinement (QC) is not entirely controlled by the porosity, rather it is mainly affected by the average distance between pores (d). The p-Si is found to exhibit weaker confinement character than Si-NWs. The confinement energy of charge carriers decays against d exponentially for p-Si and via a power-law for Si-NWs. This latter type of QC is much stronger and is somewhat similar to the case of a single particle in a quantum box. The excellent fit to the PL data demonstrates that the experimental samples of p-Si do exhibit strong QC character and thus reveals the possibility of silicon clustering into nano-crystals and/or nanowires. Furthermore, the results show that the passivation of the surface dangling bonds by the hydrogen atoms plays an essential role in preventing the appearance of gap states and consequently enhances the optical qualities of the produced structures. The oscillator strength (OS) is found to increase exponentially with energy in Si-NWs confirming the strong confinement character of carriers. Our theoretical findings suggest the existence of Si nanocrystals (Si-NCs) of sizes 1-3 nm and/or Si-NWs of cross-sectional sizes in the 1-3 nm range inside the experimental p-Si samples. The experimentally-observed strong photoluminescence from p-Si should be in favor of an exhibition of 3D-confinement character. The favorable comparison of our theoretical results with the experimental data consolidates our above claims.     

Quantum line defects and refined BPS spectra

Letters in Mathematical Physics - In this note, we study refined BPS invariants associated with certain quantum line defects in quantum field theories of class $${{mathcal {S}}}$$. Such defects...