Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

LEVEL SET输运方程的求解方法及其对气-液两相流运动界面数值模拟的影响

用数值模拟方法来研究气-液两相流动与传热现象是当今多相流领域的一个热门课题.由于两相流固有的复杂性,气-液两相流界面迁移现象的数值模拟一直是两相流研究中的一大难点.本文介绍了捕捉气-液两相流相界面运动的水平集方法(Level Set)及其研究进展,介绍了求解Level Set输运方程的3种方法,即一般差分格式、Superbee-TVD格式和Runge-Kutta法-5阶WENO组合格式.结合主流场的求解,分别用这3种方法对4种典型相界面在5种流场中的迁移特性进行了模拟计算,并对计算结果进行了比较和分析.结果表明,Runge-Kutta法-5阶WENO组合格式求解Level Set输运方程的效果最好,在以后的计算中将主要采用这种组合格式来进行气-液相界面输运方程的求解.

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...

Measuring Receptor/Ligand Interaction at the Single-Bond Level: Experimental and Interpretative Issues

There is increased interest in measuring kinetic rates, lifetimes, and rupture forces of single receptor/ligand bonds. Valuable insights have been obtained from previous experiments attempting such measurements. However, it remains difficult to know with sufficient certainty that single bonds were indeed measured. Using exemplifying data, evidence supporting single-bond observation is examined and caveats in the experimental design and data interpretation are identified. Critical issues preventing definitive proof and disproof of single-bond observation include complex binding schemes, multimeric interactions, clustering, and heterogeneous surfaces. It is concluded that no single criterion is sufficient to ensure that single bonds are actually observed. However, a cumulative body of evidence may provide reasonable confidence. 0 2002 Biomedical Engineering Society.

Experimental study on pore pressure in rock-soil slope during reservoir water level fluctuation

A test system was developed for measuring the pore pressure in porous media, and a new model was devised for the pore pressure testing in both saturated and unsaturated rock-soil. Laboratory experiments were carried out to determine the pore pressure during water level fluctuation. The variations of transient pore pressure vs. time at different locations of the simulated rock-soil system were acquired and processed, and meanwhile the deformation and failure of the model are observed. The experiment results show that whether the porous media are saturated or not, the transient pore pressure is mainly dependent on the water level fluctuation, and coupled with the variation of the stress field.

Mechanism Analysis of Landslide of a Layered Slope Induced by Drawdown of Water Level

The frequent drawdown of water level of Yangtze River will greatly influence the stability of the widely existing slopes in the Three Gorges reservoir zone, especially those layered ones. Apart from the fluctuating speed of water level, the different geological materials will also play important roles in the failure of slopes. Thus, it must be first to study the mechanism of such a landslide caused by drawdown of water level.A new experimental setup is designed to study the performance of a layered slope under the drawdown of water level. The pattern of landslide of a layered slope induced by drawdown of water level has been explored by means of simulating experiments. The influence of fluctuating speed of water level on the stability of the layered slope is probed,especially the whole process of deformation and development of landslide of the slope versus time. The experimental results show that the slope is stable during the water level rising, and the sliding body occurs in the upper layer of the slope under a certain drawdown speed of water level. In the process of slope failure, some new small sliding body will develop on the main sliding body, and the result is that they speed up the disassembly of the whole slope.Based on the simulating experiment on landslide of a layered slope induced by drawdown of water level, the stress and displacement field of the slope are calculated.The seepage velocity, the pore water pressure, and the gradient of pore water head are also calculated for the whole process of drawdown of water level. The computing results are in good agreement with the experimental results. Accordingly, the mechanism of deformation and landslide of the layered slope induced by drawdown of water level is analyzed. It may provide basis for treating this kind of layered slopes in practical engineering.

Influence of low-gravity level on crystal-growth in floating-zone

The influence of low gravity level on crystal growth in the floating zone, which involves thermocapillary convection, phase change convection, thermal and solutal diffusion, is investigated numerically by a finite element method for the silicon crystal growth process. The velocity, temperature, concentration fields and phase change interfaces depending on heating temperature and growth rates are analyzed. The influence of low gravity level on the concentration is studied especially. The results show that the non-uniformities of concentration are about 10(-3) for growth rate nu(p) = 5.12 x 10(-8) m/s, 10(-2) for nu(p) = 5.12 x 10(-7) m/s and relatively larger for larger growth rate in the gravity level g = 0-9.8 m/s2. The thermocapillary effect is strong in comparison with the Bridgman system, and the level of low gravity is relatively insensitive for lower growth rates.

High-Strength Composite Fibers: Realizing True Potential of Carbon Nanotubes in Polymer Matrix through Continuous Reticulate Architecture and Molecular Level Couplings

Carbon nanotubes have unprecedented mechanical properties as defect-free nanoscale building blocks, but their potential has not been fully realized in composite materials due to weakness at the interfaces. Here we demonstrate that through load-transfer-favored three-dimensional architecture and molecular level couplings with polymer chains, true potential of CNTs can be realized in composites as Initially envisioned. Composite fibers with reticulate nanotube architectures show order of magnitude improvement in strength compared to randomly dispersed short CNT reinforced composites reported before. The molecular level couplings between nanotubes and polymer chains results in drastic differences in the properties of thermoset and thermoplastic composite fibers, which indicate that conventional macroscopic composite theory falls to explain the overall hybrid behavior at nanoscale.

Two mechanisms for population inversion via two-colour coherent excitation in three-level systems

We analyse the physical origin of population inversion via continuous wave two-colour coherent excitation in three-level systems by dressing the inverted transition. Two different mechanisms are identified as being responsible for the population inversion. For V-configured systems and cascade (E) configured systems with inversion on the lower transition, the responsible mechanism is the selective trapping of dressed states, and the population inversion approaches the ideal value of 1. For Lambda-configured systems and Xi-configured systems with inversion on the upper transition, population inversion is based on the selective excitation of dressed states, with the population inversion tending towards 0.5. As the essential difference between these two mechanisms, the selective trapping of dressed states occurs in systems with strong decay into dressed states while the selective excitation appears in systems with strong decay out of dressed states.

Near dipole-dipole effects on the propagation of few-cycle pulse in a dense two-level medium

The propagation behaviors, which include the carrier-envelope phase, the area evolution and the solitary pulse number of few-cycle pulses in a dense two-level medium, are investigated based on full-wave Maxwell-Bloch equations by taking Lorentz local field correction (LFC) into account. Several novel features are found: the difference of the carrier-envelope phase between the cases with and without LFC can go up to pi at some location; although the area of ultrashort solitary pulses is lager than 2 pi, the area of the effective Rabi frequency, which equals to that the Rabi frequency pluses the product of the strength of the near dipole-dipole (NDD) interaction and the polarization, is consistent with the standard area theorem and keeps 2 pi; the large area pulse penetrating into the medium produces several solitary pulses as usual, but the number of solitary pulses changes at certain condition. (C) 2005 Optical Society of America.

Influence of atomic densities on propagation property for ultrashort pulses in a two-level medium

The influence of atomic densities on the propagation property for ultrashort pulses in a two-level atom (TLA) medium is investigated. With higher atomic densities, the self-induced transparency (SIT) cannot be recovered even for 2π ultrashort pulses. New features such as pulse splitting, red-shift and blue-shift of the corresponding spectra arise, and the component of central frequency gradually disappears.

Spectral effects for an ultrashort pulse train propagating in a two-level atom medium

We investigate the spectra of a femtosecond pulse train propagating in a resonant two-level atom (TLA) medium. it is found that higher spectral components can be produced even for a 2 pi femtosecond pulse train. Furthermore, the spectral effects depend crucially on both the relative shift phi and the delay time tau between the successive pulses of the femtosecond pulse train.

Effect of time-dependent ionization on the propagation of a few-cycle laser pulse in a two-level medium

We investigate the influence of ionization on the propagation and spectral effects of a few-cycle ultrashort laser pulse in a two-level medium. It is found that when the fractional ionization is weak, the production of higher spectral components makes no difference. However, when the two states are essentially depleted before the peak of the laser pulse, the impact of ionization on the higher spectral components is very significant.