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.

Simulation of Coal Combustion by AUSM Turbulence-Chemistry Char Combustion Model and a Full Two-Fluid Model

An algebraic unified second-order moment (AUSM) turbulence-chemistry model of char combustion is introduced in this paper, to calculate the effect of particle temperature fluctuation on char combustion. The AUSM model is used to simulate gas-particle flows, in coal combustion in a pulverized coal combustor, together with a full two-fluid model for reacting gas-particle flows and coal combustion, including the sub-models as the k-epsilon-k(p) two-phase turbulence niodel, the EBU-Arrhenius volatile and CO combustion model, and the six-flux radiation model. A new method for calculating particle mass flow rate is also used in this model to correct particle outflow rate and mass flow rate for inside sections, which can obey the principle of mass conservation for the particle phase and can also speed up the iterating convergence of the computation procedure effectively. The simulation results indicate that, the AUSM char combustion model is more preferable to the old char combustion model, since the later totally eliminate the influence of particle temperature fluctuation on char combustion rate.

Numerical Simulation and Experimental Investigation about Internal and External Flows

In this paper, TASCflow3D is used to solve inner and outer 3D viscous incompressible turbulent flow (R-e = 5.6 X 10(6)) around axisymmetric body with duct. The governing equation is a RANS equation with standard k-epsilon turbulence model. The discrete method used is a finite volume method based on the finite element approach. In this method, the description of geometry is very flexible and at the same time important conservative properties are retained. The multi-block and algebraic multi-grid techniques are used for the convergence acceleration. Agreement between experimental results and calculation is good. It indicates that this novel approach can be used to simulate complex flow such as the interaction between rotor and stator or propulsion systems containing tip clearance and cavitation.

Statistical Simulation of Rarefied Gas Flows in Micro-Channels

Rarefied gas flows through micro-channels are simulated using particle approaches, named as the information preservation (IP) method and the direct simulation Monte Carlo (DSMC) method. In simulating the low speed flows in long micro-channels the DSMC method encounters the problem of large sample size demand and the difficulty of regulating boundary conditions at the inlet and outlet. Some important computational issues in the calculation of long micro-channel flows by using the IP method, such as the use the conservative form of the mass conservation equation to guarantee the adjustment of the inlet and outlet boundary conditions and the super-relaxation scheme to accelerate the convergence process, are addressed. Stream-wise pressure distributions and mass fluxes through micro-channels given by the IP method agree well with experimental data measured in long micro-channels by Pong et al. (with a height to length ratio of 1.2:3000), Shih et al. (l.2:4800), Arkilic et al. and Arkilic (l.3:7500), respectively. The famous Knudsen minimum of normalized mass flux is observed in IP and DSMC calculations of a short micro-channel over the entire flow regime from continuum to free molecular, whereas the slip Navier-Stokes solution fails to predict it.

Numerical Simulation Of Horizontal Migration Of Proppant

The horizontal migration of proppant was numerically investigated with a two-fluid model, in which the interaction between fracturing fluid and proppant, along with that among proppants was taken into account through interphase forces. The migration process and the volumetric concentration of the proppant were examined under various conditions, and the. averaged volumetric concentration of the proppant was obtained. The present research might be useful in the process design of the hydraulic fracturing in the oilfields.

Oil-Water Two-Phase Flow Inside T-Junction

The oil/water two-phase flow inside T-junctions was numerically simulated with a 3-D two-fluid model, and the turbulence was described using the mixture k - epsilon model. Some experiments of oil/water flow inside a single T-junction were conducted in the laboratory. The results show that the separating performance of T-junction largely depends oil the inlet volumetric fraction and flow patterns. A reasonable agreement is reached between the numerical simulation and the experiments for both the oil fraction distribution and the separation efficiency.

Atomistic Origin Of Rate-Dependent Serrated Plastic Flow In Metallic Glasses

Nanoindentation simulations on a binary metallic glass were performed under various strain rates by using molecular dynamics. The rate-dependent serrated plastic flow was clearly observed, and the spatiotemporal behavior of its underlying irreversible atomic rearrangement was probed. Our findings clearly validate that the serration is a temporally inhomogeneous characteristic of such rearrangements and not directly dependent on the resultant shear-banding spatiality. The unique spatiotemporal distribution of shear banding during nanoindentation is highlighted in terms of the potential energy landscape (PEL) theory.

Receptivity To Free-Stream Disturbance Waves For Hypersonic Flow Over A Blunt Cone

A high-order shock-fitting finite difference scheme is studied and used to do direction numerical simulation (DNS) of hypersonic unsteady flow over a blunt cone with fast acoustic waves in the free stream, and the receptivity problem in the blunt cone hypersonic boundary layers is studied. The results show that the acoustic waves are the strongest disturbance in the blunt cone hypersonic boundary layers. The wave modes of disturbance in the blunt cone boundary layers are first, second, and third modes which are generated and propagated downstream along the wall. The results also show that as the frequency decreases, the amplitudes of wave modes of disturbance increase, but there is a critical value. When frequency is over the critial value, the amplitudes decrease. Because of the discontinuity of curvature along the blunt cone body, the maximum amplitudes as a function of frequencies are not monotone.

Effects Of Subgrid-Scale Modeling On Lagrangian Statistics In Large-Eddy Simulation

The application of large-eddy simulation (LES) to turbulent transport processes requires accurate prediction of the Lagrangian statistics of flow fields. However, in most existing SGS models, no explicit consideration is given to Lagrangian statistics. In this paper, we focus on the effects of SGS modeling on Lagrangian statistics in LES ranging from statistics determining single-particle dispersion to those of pair dispersion and multiparticle dispersion. Lagrangian statistics in homogeneous isotropic turbulence are extracted from direct numerical simulation (DNS) and the LES with a spectral eddy-viscosity model. For the case of longtime single-particle dispersion, it is shown that, compared to DNS, LES overpredicts the time scale of the Lagrangian velocity correlation but underpredicts the Lagrangian velocity fluctuation. These two effects tend to cancel one another leading to an accurate prediction of the longtime turbulent dispersion coefficient. Unlike the single-particle dispersion, LES tends to underestimate significantly the rate of relative dispersion of particle pairs and multiple-particles, when initial separation distances are less than the minimum resolved scale due to the lack of subgrid fluctuations. The overprediction of LES on the time scale of the Lagrangian velocity correlation is further confirmed by a theoretical analysis using a turbulence closure theory.

Direct Numerical Simulation Of Three-Dimensional Richtmyer-Meshkov Instability

Direct numerical simulation (DNS) is used to study flow characteristics after interaction of a planar shock with a spherical media interface in each side of which the density is different. This interfacial instability is known as the Richtmyer-Meshkov (R-M) instability. The compressible Navier-Stoke equations are discretized with group velocity control (GVC) modified fourth order accurate compact difference scheme. Three-dimensional numerical simulations are performed for R-M instability installed passing a shock through a spherical interface. Based on numerical results the characteristics of 3D R-M instability are analysed. The evaluation for distortion of the interface, the deformation of the incident shock wave and effects of refraction, reflection and diffraction are presented. The effects of the interfacial instability on produced vorticity and mixing is discussed.

A Note On The Numerical Simulations Of Flow Past A Wavy Square-Section Cylinder

The flow past a square-section cylinder with a geometric disturbance is investigated by numerical simulations. The extra terms, due to the introduction of mapping transformation simulating the effect of disturbance into the transformed Navier-Stokes equations, are correctly derived, and the incorrect ones in the previous literature are pointed out and analyzed. Furthermore, the relationship between the vorticity, especially on the cylinder surface, and the disturbance is derived and explained theoretically. The computations are performed at two Reynolds numbers of 100 and 180 and three amplitudes of waviness of 0.006, 0.025 and 0.167 with another aim to explore the effects of different Reynolds numbers and disturbance on the vortex dynamics in the wake and forces on the body. Numerical results have shown that, at the mild waviness of 0.025, the Karman vortex shedding is suppressed completely for Re = 100, while the forced vortex dislocation is appeared in the near wake at the Reynolds number of 180. The drag reduction is up to 21.6% at Re = 100 and 25.7% at Re = 180 for the high waviness of 0.167 compared with the non-wavy cylinder. The lift and the Strouhal number varied with different Reynolds numbers and the wave steepness are also obtained.

Computer simulation of influence of sedimentation on rapid coagulation

A computer simulation was performed to explore the features and effects of sedimentation on rapid coagulation. To estimate the accumulated influence of gravity on coagulation for dispersions, a sedimentation influence ratio is defined. Some factors possibly related to the influence of sedimentation were considered in the simulation and analysed by comparing the size distribution of aggregates, the change in collision number, and coagulation rates at different gravity levels (0 g, 1 g and more with g being the gravitational constant).

Proper orthogonal decomposition of oscillatory Marangoni flow in half-zone liquid bridges of low-Pr fluids

Proper orthogonal decomposition (POD) using method of snapshots was performed on three different types of oscillatory Marangoni flows in half-zone liquid bridges of low-Pr fluid (Pr = 0.01). For each oscillation type, a series of characteristic modes (eigenfunctions) have been extracted from the velocity and temperature disturbances, and the POD provided spatial structures of the eigenfunctions, their oscillation frequencies, amplitudes, and phase shifts between them. The present analyses revealed the common features of the characteristic modes for different oscillation modes: four major velocity eigenfunctions captured more than 99% of the velocity fluctuation energy form two pairs, one of which is the most energetic. Different from the velocity disturbance, one of the major temperature eigenfunctions makes the dominant contribution to the temperature fluctuation energy. On the other hand, within the most energetic velocity eigenfuction pair, the two eigenfunctions have similar spatial structures and were tightly coupled to oscillate with the same frequency, and it was determined that the spatial structures and phase shifts of the eigenfunctions produced the different oscillatory disturbances. The interaction of other major modes only enriches the secondary spatio-temporal structures of the oscillatory disturbances. Moreover, the present analyses imply that the oscillatory disturbance, which is hydrodynamic in nature, primarily originates from the interior of the liquid bridge. (C) 2007 Elsevier B.V. All rights reserved.

Numerical modeling of 3-D turbulent two-phase flow and coal combustion in a pulverized-coal combustor

In the present paper, a multifluid model of two-phase flows with pulverized-coal combustion, based on a continuum-trajectory model with reacting particle phase, is developed and employed to simulate the 3-D turbulent two-phase hows and combustion in a new type of pulverized-coal combustor with one primary-air jet placed along the wall of the combustor. The results show that: (1) this continuum-trajectory model with reacting particle phase can be used in practical engineering to qualitatively predict the flame stability, concentrations of gas species, possibilities of slag formation and soot deposition, etc.; (2) large recirculation zones can be created in the combustor, which is favorable to the ignition and flame stabilization.