On the origin of the Boson peak in globular proteins

We study the Boson Peak phenomenology experimentally observed in globular proteins by means of elastic network models. These models are suitable for an analytic treatment in the framework of Euclidean Random Matrix theory, whose predictions can be numerically tested on real proteins structures. We find that the emergence of the Boson Peak is strictly related to an intrinsic mechanical instability of the protein, in close similarity to what is thought to happen in glasses. The biological implications of this conclusion are also discussed by focusing on a representative case study.Comment: Proceedings of the X International Workshop on Disordered Systems, Molveno (2006

Multiple-scattering effects on incoherent neutron scattering in glasses and viscous liquids

Incoherent neutron scattering experiments are simulated for simple dynamic models: a glass (with a smooth distribution of harmonic vibrations) and a viscous liquid (described by schematic mode-coupling equations). In most situations multiple scattering has little influence upon spectral distributions, but it completely distorts the wavenumber-dependent amplitudes. This explains an anomaly observed in recent experiments

Metastable Dynamics above the Glass Transition

The element of metastability is incorporated in the fluctuating nonlinear hydrodynamic description of the mode coupling theory (MCT) of the liquid-glass transition. This is achieved through the introduction of the defect density variable $n$ into the set of slow variables with the mass density $\rho$ and the momentum density ${\bf g}$. As a first approximation, we consider the case where motions associated with $n$ are much slower than those associated with $\rho$. Self-consistently, assuming one is near a critical surface in the MCT sense, we find that the observed slowing down of the dynamics corresponds to a certain limit of a very shallow metastable well and a weak coupling between $\rho$ and $n$. The metastability parameters as well as the exponents describing the observed sequence of time relaxations are given as smooth functions of the temperature without any evidence for a special temperature. We then investigate the case where the defect dynamics is included. We find that the slowing down of the dynamics corresponds to the system arranging itself such that the kinetic coefficient $\gamma_v$ governing the diffusion of the defects approaches from above a small temperature-dependent value $\gamma^c_v$.Comment: 38 pages, 14 figures (6 figs. are included as a uuencoded tar- compressed file. The rest is available upon request.), RevTEX3.0+eps

Evidence of coexistence of change of caged dynamics at Tg and the dynamic transition at Td in solvated proteins

Mossbauer spectroscopy and neutron scattering measurements on proteins embedded in solvents including water and aqueous mixtures have emphasized the observation of the distinctive temperature dependence of the atomic mean square displacements, , commonly referred to as the dynamic transition at some temperature Td. At low temperatures, increases slowly, but it assume stronger temperature dependence after crossing Td, which depends on the time/frequency resolution of the spectrometer. Various authors have made connection of the dynamics of solvated proteins including the dynamic transition to that of glass-forming substances. Notwithstanding, no connection is made to the similar change of temperature dependence of obtained by quasielastic neutron scattering when crossing the glass transition temperature Tg, generally observed in inorganic, organic and polymeric glass-formers. Evidences are presented to show that such change of the temperature dependence of from neutron scattering at Tg is present in hydrated or solvated proteins, as well as in the solvents used unsurprisingly since the latter is just another organic glass-formers. The obtained by neutron scattering at not so low temperatures has contributions from the dissipation of molecules while caged by the anharmonic intermolecular potential at times before dissolution of cages by the onset of the Johari-Goldstein beta-relaxation. The universal change of at Tg of glass-formers had been rationalized by sensitivity to change in volume and entropy of the beta-relaxation, which is passed onto the dissipation of the caged molecules and its contribution to . The same rationalization applies to hydrated and solvated proteins for the observed change of at Tg.Comment: 28 pages, 10 figures, 1 Tabl

Metastable Dynamics of the Hard-Sphere System

The reformulation of the mode-coupling theory (MCT) of the liquid-glass transition which incorporates the element of metastability is applied to the hard-sphere system. It is shown that the glass transition in this system is not a sharp one at the special value of the density or the packing fraction, which is in contrast to the prediction by the conventional MCT. Instead we find that the slowing down of the dynamics occurs over a range of values of the packing fraction. Consequently, the exponents governing the sequence of time relaxations in the intermediate time regime are given as functions of packing fraction with one additional parameter which describes the overall scale of the metastable potential energy for defects in the hard-sphere system. Implications of the present model on the recent experiments on colloidal systems are also discussed.Comment: 21 pages, 5 figures (available upon request), RevTEX3.0, JFI Preprint

Fast mode decomposition in few-mode fibers

Retrieval of the optical phase information from measurement of intensity is of a high interest because this would facilitate simple and cost-efficient techniques and devices. In scientific and industrial applications that exploit multi-mode fibers, a prior knowledge of spatial mode structure of the fiber, in principle, makes it possible to recover phases using measured intensity distribution. However, current mode decomposition algorithms based on the analysis of the intensity distribution at the output of a few-mode fiber, such as optimization methods or neural networks, still have high computational costs and high latency that is a serious impediment for applications, such as telecommunications. Speed of signal processing is one of the key challenges in this approach. We present a high-performance mode decomposition algorithm with a processing time of tens of microseconds. The proposed mathematical algorithm that does not use any machine learning techniques, is several orders of magnitude faster than the state-of-the-art deep-learning-based methods. We anticipate that our results can stimulate further research on algorithms beyond popular machine learning methods and they can lead to the development of low-cost phase retrieval receivers for various applications of few-mode fibers ranging from imaging to telecommunications

Description of a strain from an atypical population of Aspergillus parasiticus that produces aflatoxins B only, and the impact of temperature on fungal growth and mycotoxin production

In this study, an atypical strain of Aspergillus parasiticus is described. This strain, reported from Portuguese almonds, was named Aspergillus parasiticus B strain. The strain is herein characterised at the morphological and physiological levels, and compared with the typical A. parasiticus strain and other similar species in section Flavi. Previously published morphological and molecular data support that the B strain is very closely related to the A. parasiticus type strain. However, while A. parasiticus typically produces aflatoxins B and G, B strain produces aflatoxins B only. Furthermore, this atypical strain showed to differ from the typical strain in the fact that higher growth (colony diameter) and strain. This strain can become a major food safety concern in colder regions where the typical A. parasiticus strains are not well adapted.NORTE-07-0124-FEDER-000028PEst-OE/EQB/LA0023/2013PEst-OE/AGR/UI0690/201