Analysis of the factors that influence the C=N stretching frequency of polyene Schiff bases. Implications for bacteriorhodopsin and rhodopsin.

In this study quantum mechanical calculations of force constants and normal mode analysis are used to elucidate the factors that influence the C=C and C=N stretching frequencies in polyenes and in protonated Schiff bases. The C=N stretching frequency is found to depend on both the C=N stretching force constant and the C=N-H bending force constant. Due to the contributions of these two modes, the C=N stretching frequency is particularly sensitive to the magnitude of the Schiff base counterion interactions and to the hydrogen bonding environment of the Schiff base nitrogen. Models for chromophore-protein interactions in the retinal binding site and for the photochemical transformations of bacteriorhodopsin and rhodopsin are evaluated in light of these results.     

Radiative Hydromagnetic Flow of Jeffrey Nanofluid by an Exponentially Stretching Sheet

Two-dimensional hydromagnetic flow of an incompressible Jeffrey nanofluid over an exponentially stretching surface is examined in the present article. Heat and mass transfer analysis is performed in the presence of thermal radiation, viscous dissipation, and Brownian motion and thermophoresis effects. Mathematical modelling of considered flow problem is developed under boundary layer and Rosseland’s approximations. The governing nonlinear partial differential equations are converted into ordinary differential equations via transformations. Solution expressions of velocity, temperature and concentration are presented in the series forms. Impacts of physical parameters on the dimensionless temperature and concentration are shown and discussed. Skin-friction coefficients are analyzed numerically. A comparison in a limiting sense is provided to validate the present series solutions.     

Radiation Effects on the Flow of Powell-Eyring Fluid Past an Unsteady Inclined Stretching Sheet with Non-Uniform Heat Source/Sink

This study investigates the unsteady flow of Powell-Eyring fluid past an inclined stretching sheet. Unsteadiness in the flow is due to the time-dependence of the stretching velocity and wall temperature. Mathematical analysis is performed in the presence of thermal radiation and non-uniform heat source/sink. The relevant boundary layer equations are reduced into self-similar forms by suitable transformations. The analytic solutions are constructed in a series form by homotopy analysis method (HAM). The convergence interval of the auxiliary parameter is obtained. Graphical results displaying the influence of interesting parameters are given. Numerical values of skin friction coefficient and local Nusselt number are computed and analyzed.     

On Comparison of Series and Numerical Solutions for Flow of Eyring-Powell Fluid with Newtonian Heating And Internal Heat Generation/Absorption

In this paper, we have investigated the combined effects of Newtonian heating and internal heat generation/absorption in the two-dimensional flow of Eyring-Powell fluid over a stretching surface. The governing non-linear analysis of partial differential equations is reduced into the ordinary differential equations using similarity transformations. The resulting problems are computed for both series and numerical solutions. Series solution is constructed using homotopy analysis method (HAM) whereas numerical solution is presented by two different techniques namely shooting method and bvp4c. A comparison of homotopy solution with numerical solution is also tabulated. Both solutions are found in an excellent agreement. Dimensionless velocity and temperature profiles are plotted and discussed for various emerging physical parameters.     

Tensotaxis--a collective movement of embryonic cells up along the gradients of mechanical tensions]

We have examined the active collective movement of ectodermal cells from early gastrula of Xenopus laevis towards the point source of stretching, using techniques of videomicroscopy and scanning electron microscopy. We define this mode of cell movement as tensotaxis. This movement begins near the source of tension 5-10 min after the beginning of stretching and is spread in a relay fashion to more distant cells. As a result, a considerable fraction of observed cells more towards the source of stretching over a considerable territory at a rate of 0.6-3 mu/min. Subsequently, these movements are replaced by cell intercalation roughly oriented in the direction transverse to that of tissue stretching. It is proposed that tensotaxis is initiated by asymmetric deformation of the embryonic tissue due to the concentration (focusing) of a stretching force and contains both passive and active components. Data are presented supporting the view that, during normal development, tensotaxis may determine the movement of embryonic cells towards the blastopore and can also participate in other morphogenetic processes.     

Preparation and properties of stretched polytene chromosomes. 2. Mechanism of stretching]

Isolated polytene chromosomes were stretched in a 0.125 M NaCl solution with constant speed, by constant force and by cyclically changing force. For each regime, the dependence of chromosome length on the time and force magnitude were recorded. From this it may be concluded that three processes are involved in chromosome stretching: viscoelastic deformation, viscous flow of DNP segments, and cristallization, i.e. intermolecular cross-linking of neighbour segments. At a high rate stretching (V greater than Vo) chromosome may be torn like at small deformation; when rate is V greater than Vo chromosome deformation is mostly viscoelastic; at rates V approximately Vo viscous flow of DNP segments if predominant. We estimate Vo approximately less than 3--6 mum/s. Electron microscopy shows that during chromosome stretching its DNP fibers are oriented along chromosome axis without detectable breaks.     

Entropic elasticity controls nanomechanics of single tropocollagen molecules

We report molecular modeling of stretching single molecules of tropocollagen, the building block of collagen fibrils and fibers that provide mechanical support in connective tissues. For small deformation, we observe a dominance of entropic elasticity. At larger deformation, we find a transition to energetic elasticity, which is characterized by first stretching and breaking of hydrogen bonds, followed by deformation of covalent bonds in the protein backbone, eventually leading to molecular fracture. Our force-displacement curves at small forces show excellent quantitative agreement with optical tweezer experiments. Our model predicts a persistence length xi(p) approximately 16 nm, confirming experimental results suggesting that tropocollagen molecules are very flexible elastic entities. We demonstrate that assembly of single tropocollagen molecules into fibrils significantly decreases their bending flexibility, leading to decreased contributions of entropic effects during deformation. The molecular simulation results are used to develop a simple continuum model capable of describing an entire deformation range of tropocollagen molecules. Our molecular model is capable of describing different regimes of elastic and permanent deformation, without relying on empirical parameters, including a transition from entropic to energetic elasticity.     

XmMol: An X11 and motif program for macromolecular visualization and modeling

XmMol is a desktop tool designed to provide both interactive molecular graphics on X11 displays and easy interface with external applications. A kernel provides an interactive wire-frame display of macromolecules. It supports depth cueing, 3D clipping, and stereo. Various representations, coloring, and labeling modes are proposed. Docking and interactive back-bone deformation tools are also supported. Communication protocols allow the user to develop new external features or to use XmMol as a visualization tool for external numerical programs.     

Specificity of endothelial cell reorientation in response to cyclic mechanical stretching

Evidence suggests that cellular responses to mechanical stimuli depend specifically on the type of stimuli imposed. For example, when subjected to fluid shear stress, endothelial cells align along the flow direction. In contrast, in response to cyclic stretching, cells align away from the stretching direction. However, a few aspects of this cell alignment response remain to be clarified: (1) Is the cell alignment due to actual cell reorientation or selective cell detachment? (2) Does the resulting cell alignment represent a response of the cells to elongation or shortening, or both? (3) Does the cell alignment depend on the stretching magnitude or rate, or both? Finally, the role of the actin cytoskeleton and microtubules in the cell alignment response remains unclear. To address these questions, we grew human aortic endothelial cells on deformable silicone membranes and subjected them to three types of cyclic stretching: simple elongation, pure uniaxial stretching and equi-biaxial stretching. Examination of the same cells before and after stretching revealed that they reoriented. Cells subjected to either simple elongation or pure uniaxial stretching reoriented specifically toward the direction of minimal substrate deformation, even though the directions for the two types of stretching differed by only about 20°. At comparable stretching durations, the extent of cell reorientation was more closely related to the stretching magnitude than the stretching rate. The actin cytoskeleton of the endothelial cell subjected to either type of stretching was reorganized into parallel arrays of actin filaments (i.e., stress fibers) aligned in the direction of the minimal substrate deformation. Furthermore, in response to equi-biaxial stretching, the actin cytoskeleton was remodeled into a “tent-like” structure oriented out of the membrane plane—again towards the direction of the minimal substrate deformation. Finally, abolishing microtubules prevented neither the formation of stress fibers nor cell reorientation. Thus, endothelial cells respond very specifically to the type of deformation imposed upon them.     

Gene expression data preprocessing

We present an interactive web tool for preprocessing microarray gene expression data. It analyses the data, suggests the most appropriate transformations and proceeds with them after user agreement. The normal preprocessing steps include scale transformations, management of missing values, replicate handling, flat pattern filtering and pattern standardization and they are required before performing any pattern analysis. The processed data set can be sent to other pattern analysis tools.     

Three-Dimensional Flow of an Oldroyd-B Nanofluid towards Stretching Surface with Heat Generation/Absorption

This article addresses the steady three-dimensional flow of an Oldroyd-B nanofluid over a bidirectional stretching surface with heat generation/absorption effects. Suitable similarity transformations are employed to reduce the governing partial differential equations into coupled nonlinear ordinary differential equations. These nonlinear ordinary differential equations are then solved analytically by using the homotpy analysis method (HAM). Graphically results are presented and discussed for various parameters, namely, Deborah numbers and , heat generation/absorption parameter Prandtl parameter , Brownian motion parameters, thermophoresis parameter and Lewis number . We have seen that the increasing values of the Brownian motion parameter and thermophoresis parameter leads to an increase in the temperature field and thermal boundary layer thickness while the opposite behavior is observed for concentration field and concentration boundary layer thickness. To see the validity of the present work, the numerical results are compared with the analytical solutions obtained by Homotopy analysis method and noted an excellent agreement for the limiting cases.     

Flow and Heat Transfer to Sisko Nanofluid over a Nonlinear Stretching Sheet

The two-dimensional boundary layer flow and heat transfer to Sisko nanofluid over a non-linearly stretching sheet is scrutinized in the concerned study. Our nanofluid model incorporates the influences of the thermophoresis and Brownian motion. The convective boundary conditions are taken into account. Implementation of suitable transformations agreeing with the boundary conditions result in reduction of the governing equations of motion, energy and concentration into non-linear ordinary differential equations. These coupled non-linear ordinary differential equations are solved analytically by using the homotopy analysis method (HAM) and numerically by the shooting technique. The effects of the thermophoresis and Brownian motion parameters on the temperature and concentration fields are analyzed and graphically presented. The secured results make it clear that the temperature distribution is an increasing function of the thermophoresis and Brownian motion parameters and concentration distribution increases with the thermophoresis parameter but decreases with the Brownian motion parameter. To see the validity of the present work, we made a comparison with the numerical results as well as previously published work with an outstanding compatibility.     

Leukotrienes and tyrosine phosphorylation mediate stretching-induced actin cytoskeletal remodeling in endothelial cells

We studied actin cytoskeletal remodeling and the role of leukotrienes and tyrosine phosphorylation in the response of endothelial cells to different types of cyclic mechanical stretching. Human aortic endothelial cells were grown on deformable silicone membranes subjected to either cyclic one-directional (strip) stretching (10%, 0.5 Hz), or biaxial stretching. After 1 min of either type of stretching, actin cytoskeletons of the stretched cells were already disrupted. After stretching for 10 and 30 min, the percentage of the stretched cells that had disrupted actin cytoskeletons were significantly increased, compared with control cells without stretching. Also, at these two time points, biaxial stretching consistently produced higher frequencies of actin cytoskeleton disruption. At 3 h, strip stretching caused the formation of stress fiber bundles, which were oriented nearly perpendicular to the stretching direction. With biaxial stretching, however, actin cytoskeletons in many stretched cells were remodeled into three-dimensional actin structures protruding outside the substrate plane, within which cyclic stretching was applied. In both stretching conditions, actin filaments were formed in the direction without substrate deformation. Moreover, substantially inhibiting either leukotriene production with nordihydroguaiaretic acid or tyrosine phosphorylation with tyrphostin A25 did not block the actin cytoskeletal remodeling. However, inhibiting both leukotriene production and tyrosine phosphorylation completely blocked the actin cytoskeletal remodeling. Thus, the study showed that the remodeling of actin cytoskeletons of the stretched endothelial cells include rapid disruption first and then re-formation. The resulting pattern of the actin cytoskeleton after remodeling depends on the type of cyclic stretching applied, but under either type of cyclic stretching, the actin filaments are formed in the direction without substrate deformation. Finally, leukotrienes and tyrosine phosphorylation are necessary for actin cytoskeletal remodeling of the endothelial cells in response to mechanical stretching.     

A quantitative study of regional and stage specific reaction of African clawed frog embryonic tissues on mechanical stress

Residual deformation of fragments of the embryonic tissues preserved after relaxation of the stretching force serve as a criterion of active redistribution of their cells caused by this stretching. We measured residual deformations of the Xenopus laevis ventral and dorsal ectoderm at the early gastrula and lateral ectoderm at the late gastrula-early neurula after stretching of varying time and force. While the samples responded to moderate (up to 40%) short-term stretching as elastic bodies (residual deformations were absent), residual deformation appeared in the early gastrula tissues after 30-60-min stretching, which were more pronounced in the ventral tissues than in the dorsal ones. On the contrary, a contractile reaction developed in the late gastrula-early neurula tissues in response to 60-min stretching, which almost relaxed residual deformation within 20 min after unloading. A conclusion was drawn that gastrulation and neurulation proceed under the conditions of relaxing and nonrelaxing mechanical tensions, respectively. Mechanical bases and morphogenetic role of the described reactions is discussed.     

Comparison of the effects of cyclic stretching and compression on endothelial cell morphological responses

Recent results demonstrate the exquisite sensitivity of cell orientation responses to the pattern of imposed deformation. Cells undergoing pure in-plane uniaxial stretching orient differently than cells that are simply elongated--likely because the latter stimulus produces simultaneous compression in the unstretched direction. It is not known, however, if cells respond differently to pure stretching than to pure compression. This study was performed to address this issue. Human aortic endothelial cells were seeded on deformable silicone membranes and subjected to various magnitudes and rates of pure stretching or compression. The cell orientation and cytoskeletal stress fiber organization responses were examined. Both stretching and compression resulted in magnitude-dependent but not rate-dependent orientation responses away from the deforming direction. Compression produced a slower temporal response than stretching. However, stress fiber reorganization responses-early disruption followed by reassembly into parallel arrays along the cells' long axes were similar between the two stimuli. Moreover, the cell orientation and stress fiber responses appeared to be uncoupled since disruption of stress fibers was not required for the cell orientation. Moreover, parallel actin stress fibers were observed at oblique angles to the deforming direction indicating that stress fibers can reassemble when undergoing deformation.     

A Quantitative Study of Regional and Stage Specific Reaction of Xenopus laevisEmbryonic Tissues on Mechanical Load

Residual deformation of fragments of the embryonic tissues preserved after relaxation of the stretching force serve as a criterion of active redistribution of their cells caused by this stretching. We measured residual deformations of the Xenopus laevis ventral and dorsal ectoderm at the early gastrula and lateral ectoderm at the late gastrula-early neurula after stretching of varying time and force. While the samples responded to moderate (up to 40%) short-term stretching as elastic bodies (residual deformations were absent), residual deformation appeared in the early gastrula tissues after 30–60-min stretching, which were more pronounced in the ventral tissues than in the dorsal ones. On the contrary, a contractile reaction developed in the late gastrula-early neurula tissues in response to 60-min stretching, which almost relaxed residual deformation within 20 min after unloading. A conclusion was drawn that gastrulation and neurulation proceed under the conditions of relaxing and nonrelaxing mechanical tensions, respectively. Mechanical bases and morphogenetic role of the described reactions is discussed.     

Effect of stretching on the action potentials of the human and rabbit ventricular myocardium

The effect of stretching from L0 to Lmax on the electrical activity was studied on human myocardial preparations from patients with heart disease and on strips of rabbit ventricular myocardium. Muscular deformation was shown to decrease the amplitude and velocity of depolarization in slow action potentials. The action potentials (AP) possessing a fast depolarization phase were not sensitive to physiological stretching. Antiarrhythmic drugs--ethmozin (2 X 10(-5) M) and ethacizin (2 X 10(-6) M)--caused a decrease in the rate of AP depolarization, thus increasing AP sensitivity to deformation. It is suggested that stretching under the action of ethmozin and ethacizin reduced cardiomyocyte excitability due to suppression of slow Ca-current.     

Aligning families of two-dimensional gels by a combined multiresolution forward-inverse transformation approach.

A new method for aligning families of two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) images arising in proteomics studies is presented. Forward piecewise bilinear transformations are used to determine an ideal gel and to obtain an initial alignment of the family of gels to this ideal gel. Both the ideal landmarks and the coefficients defining the transformations are obtained by solving a quadratic programming problem. The alignment is then improved by using inverse transformations on finer grids. Numerical results for a family of 123 gels are reported.     

Skew orientation of biological samples Anacystis nidulans cyanobacteria and their fragments in a polymer matrix.

Anacystis nidulans cyanobacteria and their fragments embedded in unstretched, uniaxial and skew (two axes of stretching forming an angle of 40 degrees) stretched poly(vinyl alcohol) films have been investigated. Polarized absorption spectra for uniaxial and skew stretching samples were measured. Both unoriented and oriented samples were photographed under fluorescence microscope. In skew samples a high degree of cell orientation was reached. Skew deformation of polymer matrix compared to one axis stretching provides better band resolution in polarized absorption spectra of Anacystis nidulans samples. The shapes of absorption components measured in respect to the first and second axis of stretching are different which gives the opportunity to investigate position of various group of chlorophyll molecules in membrane.     

Modeling the mechanics of a DNA oligomer

DNA stretching and strand separation have been studied by molecular mechanics using an oligomer which has been the subject of nanomanipulation experiments (Noy et al., Chem. Biol. 4, 519, 1997). Adiabatic mapping of conformational energy carried out as a function of stretching leads to force/extension curves in good correlation with the experimental results. Other types of deformation are also modeled and compared with the experimental results obtained on polymeric DNA. The results highlight overall similarities, but point to thermodynamic differences and also to local base sequence effects which can be expected to play an important role at the level of biologically induced structural deformations.