Semaphorins and their receptors: Novel features of neural guidance molecules

Semaphorins were originally identified as axon guidance cues involved in the development of the nervous system. In recent years, it is emerging that they also participate in various biological systems, including physiological and pathological processes. In this review, we primarily focus on our cumulative findings for the role of semaphorins and their receptors in the regulation of the immune system, while also summarizing recent progress in the context of cardiovascular system.     

Simulation of laser–plasma interactions and fast-electron transport in inhomogeneous plasma

A new framework is introduced for kinetic simulation of laser–plasma interactions in an inhomogeneous plasma motivated by the goal of performing integrated kinetic simulations of fast-ignition laser fusion. The algorithm addresses the propagation and absorption of an intense electromagnetic wave in an ionized plasma leading to the generation and transport of an energetic electron component. The energetic electrons propagate farther into the plasma to much higher densities where Coulomb collisions become important. The high-density plasma supports an energetic electron current, return currents, self-consistent electric fields associated with maintaining quasi-neutrality, and self-consistent magnetic fields due to the currents. Collisions of the electrons and ions are calculated accurately to track the energetic electrons and model their interactions with the background plasma. Up to a density well above critical density, where the laser electromagnetic field is evanescent, Maxwell’s equations are solved with a conventional particle-based, finite-difference scheme. In the higher-density plasma, Maxwell’s equations are solved using an Ohm’s law neglecting the inertia of the background electrons with the option of omitting the displacement current in Ampere’s law. Particle equations of motion with binary collisions are solved for all electrons and ions throughout the system using weighted particles to resolve the density gradient efficiently. The algorithm is analyzed and demonstrated in simulation examples. The simulation scheme introduced here achieves significantly improved efficiencies.     

Dendritic Macromolecules as Inhibitors to Protein-Protein Binding

Summary: Our initial studies into protein binding using a series of dendrimers as size selective inhibitors have been described. Two different proteins, cytochromo-c and chymotrypsin have been selected for these binding experiments.     

Point Interactions in One Dimension and Holonomic Quantum Fields

We introduce and study a family of quantum fields, associated to δ-interactions in one dimension. These fields are analogous to holonomic quantum fields of Sato et al. in Holonomic quantum fields I–V (Publ. RIMS, Kyoto University, 14: 223–267, 1978; 15: 201–278, 1979; 15: 577–629, 1979; 15: 871-972, 1979; 16: 531–584, 1979). Corresponding field operators belong to an infinite-dimensional representation of the group in the Fock space of ordinary harmonic oscillator. We compute form factors of such fields and their correlation functions, which are related to the determinants of Schroedinger operators with a finite number of point interactions. It is also shown that these determinants coincide with tau functions, obtained through the trivialization of the det^*-bundle over a Grassmannian associated to a family of Schroedinger operators.     

Study of spectator tagging in the reaction np → ppπwith a deuteron beam

The reaction has been studied in a kinematically complete experiment at a single beam momentum GeV/c (T = 759MeV). All four ejectiles have been detected in the large-acceptance time-of-flight spectrometer COSY-TOF. We analyzed the data along the lines of the spectator model as a means to isolate the quasi-free reaction. The spectator proton was identified by its momentum and flight direction thus yielding access to the associated Fermi motion of the bound neutron. A comparison is carried out with Monte Carlo simulations based on two different parameterizations of the deuteron wave function. Up to a Fermi momentum of roughly 150MeV/c no significant deviations between experimental and simulated data of various observables were found from which we conclude that the deuteron can indeed be taken as a valid substitute for the neutron.     

Effect of side by side interactions on the thermodynamic properties of adsorbed CO molecules on the Ni(111) surface: a cluster model study

The effect of electrostatic interactions on vibrational frequencies and thermodynamic properties of CO adsorbate on the Ni(111) surface is calculated by taking the first and second nearest-neighbour interactions into account. In order to obtain reasonable results, the cluster model of various surface adsorption sites with CO adsorbate is partially optimized, using Density Functional Theory and also the MP2 method for the hcp site. Comparison between DFT and MP2 results shows that DFT results are more reliable for this system. The stretching and bending frequencies of CO adsorbate are calculated using both Partial Hessian Analysis and Cluster–Adsorbate Coupling methods. Stretching and bending frequencies are both shifted by the side by side interactions. The coupling of surface phonons and adsorbate vibrations reduces the side effects. The largest side effects on the vibrational internal energy, isochoric heat capacity, entropy and total Helmholtz free energy of adsorbed CO molecule calculated using the CAC method are found for 0.5 ML coverage. The results of the CAC method are better, but the PHA method can be used as a simple upper bound estimation. The adsorptive phase acts as an intelligent material in such a way that it changes its configuration in order to reduce the side effects.     

Depletion interactions between colloidal particles in polymer solutions: density functional approach

A density functional theory for colloid–polymer mixtures based on the weighted-density approximation has been developed to investigate the depletion effects acting between two colloids immersed in a bath of polymers and the depletion effects for a colloid near a planar hard wall. The theoretical results for the polymer-induced depletion interactions and the local polymer density distributions are in good agreement with the computer simulations. The calculation shows that the depletion interaction for a colloid near a planar hard wall is much stronger than that between two colloids in a polymer solution because of the strong confinement effect. The behaviour of the depletion interactions has been analysed as a function of the polymer density, the polymer chain length, and the colloid/polymer size ratio. Strong depletion effects appear in short-chain systems and with large colloid/polymer size ratios.     

Raman Investigation of Alkali-Doped (Ch)x films

Abstract

Resonance Raman spectra induced by (CH)_x films chemically or electrochemically doped with alkali metals are reported. At low doping levels, Raman bands characteristic of the trans isomer are observed. The Raman spectra can be well fitted using the theory developped by Mulazzi based on a bimo-dal distribution of long and short trans segments respectively. At the same time, typical results obtained for a cis-rich (CH)_x sample, as well as its behavior during a thermal isomerization, are recalled in the frame of the Mulazzi model. When the polymer is highly doped with Li (or Na) atoms, new features at ? 1600 cm^?1 and 1270 cm^?1 appear and could be an indication that n-doped films are less disordered than p-doped systems.     

Fluorescence Correlation Spectroscopy (FCS): A Promising Tool for Biological Research

Abstract

Fluorescence correlation spectroscopy (FCS) is an important biophysical technique. FCS is currently being used in many areas of biology to solve several scientific problems. Its properties such as detection at the single molecular level, higher sensitivity, and use of lower sample volume make FCS a promising molecular diagnostic tool. The promising applications of FCS extend from DNA kinetics/dynamics studies to the comprehensive understanding of receptor–ligand interactions. In this article, we review various promising biological applications of FCS.     

High pressure stability of protein complexes studied by static and dynamic light scattering

The high pressure dissociation of hemocyanin prepared from the lobster Homarus americanus and casein micelles from cow milk were observed by in situ light scattering. The hemocyanin dodecamer dissociated via a hexamer into monomers in a two-step three-species reaction. The influence of ligands and the effector l-lactate on the dissociation behavior was investigated. While no effect by carbon monoxide after exchanging the ligand oxygen was observed, the addition of the effector l-lactate led to a decrease in the pressure stability. Due to a trimer intermediate which was found to be stabilized by l-lactate, the dissociation reaction in the presence of the effector was analyzed by a three-step four-species reaction. In the case of casein micelles, a two-step dissociation mechanism was found. The stabilizing interactions of casein micelles were identified and separated.