Mechano-Chemical Coupling at Molecular Level: Forced Dissociation of Selectin/Ligand Binding

Mechano-chemical coupling is a common phenomenon that exists in various biological processes at different physiological levels. Bone tissue remodeling strongly depends on the local mechanical load. Leukocytes are sheared to form the transient aggregates with platelets or other leukocytes in the circulation. Flow pattern affects the signal transduction pathways in endothelial cells. Receptor/ligand interactions are important to cell adhesion since they supply the physical linkages...

Perturbational Finite Volume Method For The Solution of 2-D Navier-Stokes Equations on Unstructured and Structured Colocated Meshes

Based on the first-order upwind and second-order central type of finite volume( UFV and CFV) scheme, upwind and central type of perturbation finite volume ( UPFV and CPFV) schemes of the Navier-Stokes equations were developed. In PFV method, the mass fluxes of across the cell faces of the control volume (CV) were expanded into power series of the grid spacing and the coefficients of the power series were determined by means of the conservation equation itself. The UPFV and CPFV scheme respectively uses the same nodes and expressions as those of the normal first-order upwind and second-order central scheme, which is apt to programming. The results of numerical experiments about the flow in a lid-driven cavity and the problem of transport of a scalar quantity in a known velocity field show that compared to the first-order UFV and second-order CFV schemes, upwind PFV scheme is higher accuracy and resolution, especially better robustness. The numerical computation to flow in a lid-driven cavity shows that the under-relaxation factor can be arbitrarily selected ranging from 0.3 to 0. 8 and convergence perform excellent with Reynolds number variation from 102 to 104.

Simulation of Free-Surface Flow in a Tank Using the Navier-Stokes Model and Unstructured Finite Volume Method

Modelling free-surface flow has very important applications in many engineering areas such as oil transportation and offshore structures. Current research focuses on the modelling of free surface flow in a tank by solving the Navier-Stokes equation. An unstructured finite volume method is used to discretize the governing equations. The free surface is tracked by dynamically adapting the mesh and making it always surface conforming. A mesh-smoothing scheme based on the spring analogy is also implemented to ensure mesh quality throughout the computaiton. Studies are performed on the sloshing response of a liquid in an elastic container subjected to various excitation frequencies. Further investigations are also carried out on the critical frequency that leads to large deformation of the tank walls. Another numerical simulation involves the free-surface flow past as submerged obstacle placed in the tank to show the flow separation and vortices. All these cases demonstrate the capability of this numerical method in modelling complicated practical problems.

Effect of liquid bridge volume on the instability in small-Prandtl-number half zones

A perturbation method is used to examine the linear instability of thermocapillary convection in a liquid bridge of floating half-zone filled with a small Prandtl number fluid. The influence of liquid bridge volume on critical Marangoni number and flow features is analyzed. The neutral modes show that the instability is mainly caused by the bulk flow that is driven by the nonuniform thermocapillary forces acting on the free surface. The hydrodynamic instability is dominant in the case of small Prandtl number fluid and the first instability mode is a stationary bifurcation. The azimuthal wave number for the most dangerous mode depends on the liquid bridge volume, and is not always two as in the case of a cylindrical liquid bridge with aspect ratio near 0.6. Its value may be equal to unity when the liquid bridge is relatively slender.

Forced Dissociation of Selectin-ligand Complexes Using Steered Molecular Dynamics Simulation

Selectin-ligand interactions are crucial to such biological processes as inflammatory cascade or tumor metastasis. How transient formation and dissociation of selectin-ligand bonds in blood flow are coupled to molecular conformation at atomic level, however, has not been well understood. In this study, steered molecular dynamics (SMD) simulations were used to elucidate the intramolecular and intermolecular conformational evolutions involved in forced dissociation of three selectin-ligand systems: the construct consisting of P-selectin lectin (Lec) and epidermal growth factor (EGF)-like domains (P-LE) interacting with synthesized sulfoglycopeptide or SGP-3, P-LE with sialyl Lewis X (sLeX), and E-LE with sLeX. SMD simulations were based on newly built-up force field parameters including carbohydrate units and sulfated tyrosine(s) using an analogy approach. The simulations demonstrated that the complex dissociation was coupled to the molecular extension. While the intramolecular unraveling in P-LESGP-3 system mainly resulted from the destroy of the two anti-parallel sheets of EGF domain and the breakage of hydrogen-bond cluster at the Lec-EGF interface, the intermolecular dissociation was mainly determined by separation of fucose (FUC) from Ca2+ ion in all three systems. Conformational changes during forced dissociations depended on pulling velocities and forces, as well as on how the force was applied. This work provides an insight into better understanding of conformational changes and adhesive functionality of selectin-ligand interactions under external forces.

Influence of Forced Convection on Columnar Microstructure During Directional Solidification of Al-Ni Alloys

This paper presents a summary of cellular and dendritic morphologies resulting from the upward directional solidification of Al - Ni alloys in a cylindrical crucible. We analysed the coupling of solid-liquid interface morphology with natural and forced convection. The influence of natural convection was first analyzed as a function of growth parameters (solute concentration, growth rate and thermal gradient). In a second step, the influence of axial vibrations on solidification microstructure was investigated by varying vibration parameters (amplitude and frequency). Experimental results were compared to preliminary numerical simulations and a good agreement is found for natural convection. In this study, the critical role of the mushy zone in the interaction between fluid flow and solidification microstructure is pointed out.

Constant volume combustion of aluminum and cornstarch dust in microgravity

The subject of the present work is to report an experimental comparative study of the effect of dispersion-induced turbulence on dust combustion in constant volume vessel, carried out both in normal gravity and in microgravity environment. Dispersion system with small scale of turbulence, creating uniform homogeneous mixture, was used in experiments. To improve reproducibility of the explosion data an ignitor of small energy, with local soft ignition was developed. Both factors contributed to acquisition of more reproducible experimental data. In experiments under microgravity conditions a dust suspension during combustion remains constant. This makes possible to study dust explosion under stationary dust suspension without influence of turbulence.

Influence of liquid bridge volume on instability of floating half zone convection

Thermocapillary instabilities on floating half zone convection in microgravity environment were investigated by linear instability analysis method. The critical Marangoni numbers were obtained and compared with the experimental ones. The influences of the liquid bridge volume and the aspect ratio on the critical Marangoni number were analyzed. It is found that the liquid bridge volume and the aspect ratio have great influence on the critical Marangoni number. There was a gap region where the oscillatory convection will not be observed in present analyses and in experiments in the curve of the critical Marangoni number vs the liquid bridge volume for the case of large Prandtl number and small aspect ratio.

Influence of liquid bridge volume on the onset of oscillation in floating-zone convection III. Three-dimensional model

An unsteady and three-dimensional model of the floating-half-zone convection on the ground is studied by the direct numerical simulation for the medium of 10 cSt silicon oil, and the influence of the liquid bridge volume on the critical applied temperature difference is especially discussed. The marginal curves for the onset of oscillation are separated into two branches related, respectively, to the slender liquid bridge and the fat liquid bridge. The oscillatory features of the floating-half-zone convection are also discussed.

Forced extension of P-selectin construct using steered molecular dynamics

P-selectin, a 70-nm-long cellular adhesive molecule, possesses elastic and extensible properties when neutrophils roll over the activated endotheliam of blood vessel in inflammatory reaction. Transient formation and dissociation of P-selectin/ligand bond on applied force of blood flow induces the extension of P-selectin and relevant ligands. Steered molecular dynamics simulations were performed to stretch a single P-selectin construct consisting of a lectin (Lec) domain and an epithelial growth factor (EGF)-like domain, where P-selectin construct was forced to extend in water with pulling velocities of 0.005-0.05 nm/ps and with constant forces of 1000-2500 pN respectively. Resulting force-extension profiles exhibited a dual-peak pattern on various velocities, while both plateaus and shoulders appeared in the extension-time profiles on various forces. The force or extension profiles along stretching pathways were correlated to the conformational changes, suggesting that the structural collapses of P-selectin Lec/EGF domains were mainly attributed to the burst of hydrogen bonds within the major beta sheet of EGF domain and the disruptions of two hydrophobic cores of Lee domain. This work furthers the understanding of forced dissociation of P-selectin/ligand bond.

Influence of Liquid Bridge Volume on the Floating Zone Convection

The liquid bridge volume is a critical geometrical parameter in addition to the aspect ratio for onset of oscillation in the floating zone convection. The oscillatory features are generally divided into two characteristic regions: slender liquid bridge region and fat liquid bridge region. The oscillatory modes in two regions are discussed in the present paper.

Microgravity Smoldering Combustion Of Flexible Polyurethane Foam With Central Ignition

Smoldering constitutes a significant fire risk both in normal gravity and in microgravity. This space experiment has been conducted aboard the China Recoverable Satellite SJ-8 to investigate smoldering characteristics of flexible polyurethane foam with central ignition in a forced flow of oxidizer. This configuration resulted in a combination of opposed and forward flow smolder. The microgravity experiment is rather unique in that it was performed at constant pressure, and with a relatively high ambient oxygen concentration (35% by volume). The smoldering characteristics are inferred from measurements of temperature histories at several locations along the foam sample. Particularly important is the discovery that there is a transition from smoldering to flaming near the sample end in the opposed smoldering. This transition seems to be caused by strong acceleration of the smoldering reaction. The observed transition serves to initiate a vigorous forward-propagating oxidation reaction in the char left behind by the smoldering reaction. The secondary char oxidation reaction propagates through the sample and consumes most of the remaining char. In forward flow smoldering, the oxidizer depletion by the upstream opposed smolder prevents an exothermic oxidation reaction from being established in the foam until this preceding reaction is completed. Once fresh oxidizer flows in the sample, the existing conditions are sufficient for a self-sustained forward smoldering reaction to take place.

Comparison Of Shear Banding In Bmgs Due To Thermal-Softening And Free Volume Creation

This paper reports a comparative study of shear banding in BMGs resulting from thermal softening and free volume creation. Firstly, the effects of thermal softening and free volume creation on shear instability are discussed. It is known that thermal softening governs thermal shear banding, hence it is essentially energy related. However, compound free volume creation is the key factor to the other instability, though void-induced softening seems to be the counterpart of thermal softening. So, the driving force for shear instability owing to free volume creation is very different from the thermally assisted one. In particular, long wave perturbations are always unstable owing to compound free volume creation. Therefore, the shear instability resulting from coupled compound free volume creation and thermal softening may start more like that due to free volume creation. Also, the compound free volume creation implies a specific and intrinsic characteristic growth time of shear instability. Finally, the mature shear band width is governed by the corresponding diffusions (thermal or void diffusion) within the band. As a rough guide, the dimensionless numbers: Thermal softening related number B, Deborah number (denoting the relation of instability growth rate owing to compound free volume and loading time) and Lewis number (denoting the competition of different diffusions) show us their relative importance of thermal softening and free volume creation in shear banding. All these results are of particular significance in understanding the mechanism of shear banding in bulk metallic glasses (BMGs).

A Multimoment Finite-Volume Shallow-Water Model On The Yin-Yang Overset Spherical Grid

A numerical model for shallow-water equations has been built and tested on the Yin-Yang overset spherical grid. A high-order multimoment finite-volume method is used for the spatial discretization in which two kinds of so-called moments of the physical field [i.e., the volume integrated average ( VIA) and the point value (PV)] are treated as the model variables and updated separately in time. In the present model, the PV is computed by the semi-implicit semi-Lagrangian formulation, whereas the VIA is predicted in time via a flux-based finite-volume method and is numerically conserved on each component grid. The concept of including an extra moment (i.e., the volume-integrated value) to enforce the numerical conservativeness provides a general methodology and applies to the existing semi-implicit semi-Lagrangian formulations. Based on both VIA and PV, the high-order interpolation reconstruction can only be done over a single grid cell, which then minimizes the overlapping zone between the Yin and Yang components and effectively reduces the numerical errors introduced in the interpolation required to communicate the data between the two components. The present model completely gets around the singularity and grid convergence in the polar regions of the conventional longitude-latitude grid. Being an issue demanding further investigation, the high-order interpolation across the overlapping region of the Yin-Yang grid in the current model does not rigorously guarantee the numerical conservativeness. Nevertheless, these numerical tests show that the global conservation error in the present model is negligibly small. The model has competitive accuracy and efficiency.

Shallow Water Model On Cubed-Sphere By Multi-Moment Finite Volume Method

A global numerical model for shallow water flows on the cubed-sphere grid is proposed in this paper. The model is constructed by using the constrained interpolation profile/multi-moment finite volume method (CIP/MM FVM). Two kinds of moments, i.e. the point value (PV) and the volume-integrated average (VIA) are defined and independently updated in the present model by different numerical formulations. The Lax-Friedrichs upwind splitting is used to update the PV moment in terms of a derivative Riemann problem, and a finite volume formulation derived by integrating the governing equations over each mesh element is used to predict the VIA moment. The cubed-sphere grid is applied to get around the polar singularity and to obtain uniform grid spacing for a spherical geometry. Highly localized reconstruction in CIP/MM FVM is well suited for the cubed-sphere grid, especially in dealing with the discontinuity in the coordinates between different patches. The mass conservation is completely achieved over the whole globe. The numerical model has been verified by Williamson's standard test set for shallow water equation model on sphere. The results reveal that the present model is competitive to most existing ones. (C) 2008 Elsevier Inc. All rights reserved.