Modeling of drug molecule orientation within a receptor cavity in the BiS algorithm framework

The BiS algorithm is suggested for modeling the drug molecule orientation within a receptor cavity. It is based on the assumption of complementarity of the field created by biologically active compounds and the field of the responsive receptor. The comparison of predicted orientations of various biologically active compounds on the relevant receptors with the data of X-ray structural studies (Protein Data Bank) reveals that the results obtained with this approach surpasses those reported in the literature. The suggested technique made it possible to elucidate the details of the action mechanism of DNA antimetabolites, dihydrofolate reductase inhibitors. The dependence of the activity on the structural parameters of “ligand-receptor” complexes is determined.     

Classical Coulomb fluids in a confined geometry

It has already been argued that a classical (three-dimensional) Coulomb fluid confined between two parallel walls exhibits ideal gas features when the distance between the walls becomes small; this is confirmed in the present paper. Two-dimensional models of Coulomb fluids (with a logarithmic interaction), confined in a strip, are also studied. These models do not become ideal gases in the narrow strip limit. The correlation functions are also studied. There is a special temperature at which exact results are obtained. At that temperature, the two-dimensional, two-component plasma (two-dimensional Coulomb gas), which is a conductor when unconfined, becomes a dielectric as soon as it is confined in a strip of noninfinite width. This can be understood as a displacement of the Kosterlitz-Thouless transition by the confinement.     

Crossover from BCS-superconductivity to Bose-condensation

Starting from a model of free Fermions in two dimensions with an arbitrary strong effective interaction, we derive a Ginzburg-Landau theory describing the crossover from BCS-superconductivity to Bose-condensation. We find a smooth crossover from the standard BCS-limit to a Gross-Pitaevski type equation for the order parameter in a Bose superfluid. The mean field transition temperature exhibits a maximum at a coupling strength, where the behaviour crosses over from BCS to Bose like with corresponding values of 2 Δ₀/T_c ≈ 5 which are characteristic for high T_c superconductors.     

A C + + computational environment for biomolecular sequence management

The wide production of biomolecular data of the last 30 years, mainly due to the rapid evolving of technologies as well as to the accomplishment of the Genome Projects, led to the necessity of appropriate computational approaches for data storage, manipulation and analyses, giving place to a fast evolving area of Biology: Computational Biology or Bioinformatics.We propose here a new method for the storage of the sequences and their analyses using the C + + programming language, checking the effectiveness of an object oriented approach for new models, suitable to manage data representation and analyses, to improve the efficiency of computational methodologies to solve problems of general interest in bioinformatics. We developed a framework with the aim to decrease the computational costs for the storage and some basic manipulations of nucleic acid sequences. The remarkable reduction of memory requirements with no loss of efficiency makes this approach a first well promising step in order to get a more efficient environment for the manipulation and the management of nucleic acid data sets, in a field of research with hard challenges for Computer and Life Sciences.Mathematics Subject Classification: 68U99G. Toraldo, via Universita’ 100, 80055 Portici, Napoli, Italy     

Analysis of plane and axisymmetric flows of incompressible fluids with the stream tube method: Numerical simulation by trust-region optimization algorithm

New concepts for the study of incompressible plane or axisymmetric flows are analysed by the stream tube method. Flows without eddies and pure vortex flows are considered in a transformed domain where the mapped streamlines are rectilinear or circular. The transformation between the physical domain and the computational domain is an unknown of the problem. In order to solve the non-linear set of relevant equations, we present a new algorithm based on a trust region technique which is effective for non-convex optimization problems. Experimental results show that the new algorithm is more robust compared to the Newton-Raphson method.     

On the tribological characteristics of dynamically loaded journal bearing with micropolar fluids

The addition of the additives to the lubricant oil to enhance the characteristics of the lubricant will influence the performance of the bearings. Based on the theory of micropolar fluids, the tribological characteristics of a dynamically-loaded journal bearing are numerically studied. Comparisons are made between the Newtonian fluids and the micropolar fluids. It is shown that for a dynamically-loaded journal bearing, the micropolar fluids yield an increase not only in the friction force, but also in the friction coefficient. In addition, the oil film pressure and the oil film thickness are obviously higher than that of Newtonian fluids.     

Production of superfine fibers by the electrospinning method

Weakly conducting fluid flows in an electric field in the presence of phase interfaces are investigated theoretically and experimentally. The object of the investigation is an axisymmetric jet. The analysis is carried out within the framework of electrohydrodynamics (EHD) with allowance for surface charge transfer on mobile interfaces. The jet shape is calculated at large distances from the outflow point. The theoretical and experimental data are compared for Newtonian and polymeric fluids.     

Polarization Sensitive Spectral Interferometric Optical Coherence Tomography for Biological Samples

A spectral interferometric optical coherence tomography (OCT) system which has polarization sensitivity is developed. This system reduces the mechanical scanning dimension by employing the principle of spectral interferometry, and measures a two dimensional cross-sectional image of biological tissue with one dimensional mechanical scanning. Sixteen OCT images with different polarization conditions are measured, and two dimensional distributions of each element of the Müller matrix of a sample to be measured are calculated.     

Analysis and finite element simulations of a second‐order fluid model in a bounded domain

This article is concerned with the equations governing the steady motion of a viscoelastic incompressible second‐order fluid in a bounded domain. A new proof of existence and uniqueness of strong solutions is given. In addition, using appropriate finite element methods to approximate a coupled equivalent problem, sharp error estimates are obtained using a fixed point argument. The method is applied to the two‐dimensional lid‐driven cavity problem, at low Reynolds number and in a certain range of values of the viscoelastic parameters, to analyze the combined effects of inertia and viscoelasticity on the flow. © 2007 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2007