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.

A Nonlinear Threshold Model Applied to Spallation Analysis

Spallation in heterogeneous media is a complex, dynamic process. Generally speaking, the spallation process is relevant to multiple scales and the diversity and coupling of physics at different scales present two fundamental difficulties for spallation modeling and simulation. More importantly, these difficulties can be greatly enhanced by the disordered heterogeneity on multi-scales. In this paper, a driven nonlinear threshold model for damage evolution in heterogeneous materials is presented and a trans-scale formulation of damage evolution is obtained. The damage evolution in spallation is analyzed with the formulation. Scaling of the formulation reveals that some dimensionless numbers govern the whole process of deformation and damage evolution. The effects of heterogeneity in terms of Weibull modulus on damage evolution in spallation process are also investigated.

Instability in threshold voltage and subthreshold behavior in Hf-In-Zn-O thin film transistors induced by bias-and light-stress

Electrical bias and light stressing followed by natural recovery of amorphous hafnium-indium-zinc-oxide (HIZO) thin film transistors with a silicon oxide/nitride dielectric stack reveals defect density changes, charge trapping and persistent photoconductivity (PPC). In the absence of light, the polarity of bias stress controls the magnitude and direction of the threshold voltage shift (Δ VT), while under light stress, VT consistently shifts negatively. In all cases, there was no significant change in field-effect mobility. Light stress gives rise to a PPC with wavelength-dependent recovery on time scale of days. We observe that the PPC becomes more pronounced at shorter wavelengths. © 2010 American Institute of Physics.

Threshold diversity and trans-scales sensitivity in a finite nonlinear evolution model of materials failure

We present a slice-sampling method and study the ensemble evolution of a large finite nonlinear system in order to model materials failure. There is a transitional region of failure probability. Its size effect is expressed by a slowly decaying scaling law. In a meso-macroscopic range (similar to 10(5)) in realistic failure, the diversity cannot be ignored. Sensitivity to mesoscopic details governs the phenomena. (C) 1997 Published by Elsevier Science B.V.

Influence of threshold stress on the estimation of the Weibull statistics

The influence of threshold stress on the estimation of the Weibull statistics is discussed in terms of the Akaike information criterion. Numerical simulations show that, if sample data are limited in number and threshold stress is not too large, the two-parameter Weibull distribution is still a preferred choice. For example, the fit of strength data of glass and ceramics to the two- and three-parameter Weibull distributions is compared.

Mixed-mode fracture mechanisms near the fatigue threshold of aisi-316 stainless-steel

Near threshold, mixed mode (I and II), fatigue crack growth occurs mainly by two mechanisms, coplanar (or shear) mode and branch (or tensile) mode. For a constant ratio of ΔK_I/ΔK_II the shear mode growth shows a self-arrest character and it would only start again when ΔK_I and ΔK_II are increased. Both shear crack growth and the early stages of tensile crack growth, are of a crystallographic nature; the fatigue crack proceeds along slip planes or grain boundaries. The appearance of the fracture surfaces suggest that the mechanism of crack extension is by developing slip band microcracks which join up to form a macrocrack. This process is thought to be assisted by the nature of the plastic deformation within the reversed plastic zone where high back stresses are set up by dislocation pile-ups against grain boundaries. The interaction of the crack tip stress field with that of the dislocation pile-ups leads to the formation of slip band microcracks and subsequent crack extension. The change from shear mode to tensile mode growth probably occurs when the maximum tensile stress and the microcrack density in the maximum tensile plane direction attain critical values.

2D Kinetics and Forced Dissociation of Selectin-ligand Bindings

Cell adhesion is crucial to many pathophysiological processes, such as inflammatory reaction and tumor metastasis. It is mediated by specific interactions between receptors and ligands, and provides the physical linkages among cells. For example, interactions between selectins and glycoconjugate ligands mediate leukocyte initially tethering to and subsequently rolling on vascular surfaces in sites of inflammation or injury, which is determined by their fast kinetic rates. To mediate cell adhesion, the interacting receptors and ligands must anchor to apposing surfaces of two cells or a cell and the substratum, i.e. , the so-called two-dimensional (2D) binding, which differs from interactions in the fluid phase, i.e. , the three-dimensional (3D) binding. How structural variations and surface environments of interacting molecules affect their 2D kinetics, and how external forces manipulate their dissociation has little been known quantitatively, and nowadays attracts more and more attentions.

Failure process analysis of cement under explosive loading with a generalized driven nonlinear threshold model

The microstructural heterogeneity and stress fluctuation play important roles in the failure process of brittle materials. In this paper, a generalized driven nonlinear threshold model with stress fluctuation is presented to study the effects of microstructural heterogeneity on continuum damage evolution. As an illustration, the failure process of cement material under explosive loading is analyzed using the model. The result agrees well with the experimental one, which proves the efficiency of the model.

Effects of temperature on the threshold of phosphorus for algal blooms

Algal blooms, worsening marine ecosystems and causing great economic loss, have been paid much attention to for a long time. Such environmental factors as light penetration, water temperature, and nutrient concentration are crucial in blooms processes. Among them, only nutrients can be controlled. Therefore, the threshold of nutrients for algal blooms is of great concern. To begin with, a dynamic eutrophication model has been constructed to simulate the algal growth and phosphorus cycling. The model encapsulates the essential biological processes of algal growth and decay, and phosphorus regeneration due to algal decay. The nutrient limitation is based upon commonly used Monod's kinetics. The effects of temperature and phosphorus limitation are particularly addressed. Then, we have endeavored to elucidate the threshold of phosphorus at different temperature for algal blooms. Based on the numerical simulation, the isoquant contours of change rate of alga as shown in the figure are obtained, which obviously demonstrate the threshold of nutrient at an arbitrary reasonable temperature. The larger the change rate is, the more rapidly the alga grows. If the phosphorus concentration at a given temperature remains larger than the threshold the algal biomass may increase monotonically, leading to the algal blooming. With the rising of temperature, the threshold is apparently reduced, which may explain why likely red tide disasters occur in a fine summer day. So, high temperature and sufficient phosphorus supply are the major factors which result in algal growth and blowout of red tide.

Crossing the Threshold: Moving e-portfolios into the mainstream

Crossing the Threshold, one of a series of advice and guidance publications, is designed to support use of the online e-Portfolio Implementation Toolkit and video case studies by those involved in wide-scale implementation of e-portfolios in their institutions. As the resources address the needs of both managers and practitioners, the publication has relevance for a wide range of readers in further and higher education and work-based learning. To assist the planning and effective management of a large-scale e-portfolio implementation, Crossing the Threshold follows the stages of an implementation journey with insights and guidance drawn from the toolkit and its supporting case studies. Links are provided throughout the publication to more detailed information in the two online resources.

Stabilizing to disruptive transition of focal adhesion response to mechanical forces

Strong mechanical forces can, obviously, disrupt cell-cell and cell-matrix adhesions, e.g., cyclic uniaxial stretch induces instability of cell adhesion, which then causes the reorientation of cells away from the stretching direction. However, recent experiments also demonstrated the existence of force dependent adhesion growth (rather than dissociation). To provide a quantitative explanation for the two seemingly contradictory phenomena, a microscopic model that includes both integrin-integrin interaction and integrin-ligand interaction is developed at molecular level by treating the focal adhesion as an adhesion cluster. The integrin clustering dynamics and integrin-ligand binding dynamics are then simulated within one unified theoretical frame with Monte Carlo simulation. We find that the focal adhesion will grow when the traction force is higher than a relative small threshold value, and the growth is dominated by the reduction of local chemical potential energy by the traction force. In contrast, the focal adhesion will rupture when the traction force exceeds a second threshold value, and the rupture is dominated by the breaking of integrin-ligand bonds. Consistent with the experiments, these results suggest a force map for various responses of cell adhesion to different scales of mechanical force. PMID: 20542514