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.

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.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by "GAMESS", and the rest atoms are treated as MM part calculated by "TINKER". The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(100) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the in-tidazole rings are attached to the substrate more tightly than other bases in this peptide.

Generation of periodic ultrashort electron bunches and strongly asymmetric ion Coulomb explosion in nanometer foils interacting with ultra-intense laser pulse

The interaction of a linearly polarized intense laser pulse with an ultrathin nanometer plasma layer is investigated to understand the physics of the ion acceleration. It is shown by the computer simulation that the plasma response to the laser pulse comprises two steps. First, due to the vxB effect, electrons in the plasma layer are extracted and periodic ultrashort relativistic electron bunches are generated every half of a laser period. Second, strongly asymmetric Coulomb explosion of ions in the foil occurs due to the strong electrostatic charge separation, once the foil is burnt through. Followed by the laser accelerated electron bunch, the ion expansion in the forward direction occurs along the laser beam that is much stronger as compared to the backward direction. (c) 2008 American Institute of Physics.

Influence of target thickness on the generation of high-density ion bunches by ultrashort circularly polarized laser pulses

Ion acceleration by ultrashort circularly polarized laser pulse in a solid-density target is investigated using two-dimensional particle-in-cell simulation. The ions are accelerated and compressed by the continuously extending space-charge field created by the evacuation and compression of the target electrons by the laser light pressure. For a sufficiently thin target, the accelerated and compressed ions can reach and exit from the rear surface as a high-density high-energy ion bunch. The peak ion energy depends on the target thickness and reaches maximum when the compressed ion layer can just reach the rear target surface. The compressed ion layer exhibits lateral striation which can be suppressed by using a sharp-rising laser pulse. (c) 2008 American Institute of Physics.

Steady state ion acceleration by a circularly polarized laser pulse

The steady state ion acceleration at the front of a cold solid target by a circularly polarized flat-top laser pulse is studied with one-dimensional particle-in-cell (PIC) simulation. A model that ions are reflected by a steady laser-driven piston is used by comparing with the electrostatic shock acceleration. A stable profile with a double-flat-top structure in phase space forms after ions enter the undisturbed region of the target with a constant velocity. (C) 2007 Elsevier B.V. All rights reserved.

Multistaged acceleration of ions by circularly polarized laser pulse: Monoenergetic ion beam generation

A multiple-staged ion acceleration mechanism in the interaction of a circularly polarized laser pulse with a solid target is studied by one-dimensional particle-in-cell simulation. The ions are accelerated from rest to several MeV monoenergetically at the front surface of the target. After all the plasma ions are accelerated, the acceleration process is repeated on the resulting monoenergetic ions. Under suitable conditions multiple repetitions can be realized and a high-energy quasi-monoenergetic ion beam can be obtained.

Effect of plasma temperature on electrostatic shock generation and ion acceleration by laser

The effect of plasma temperature on electrostatic shock generated by a circularly polarized laser pulse in overdense plasma is studied by particle-in-cell simulation. Ion reflection and transmission in the collisionless electrostatic shock (CES) are investigated analytically. As the initial ion temperature is varied, a distinct transition from the laser-driven piston scenario with all ions being reflected to the CES scenario with partial ion reflection is found. The results show that at low but finite temperatures the ions are much more accelerated than if they were cold.

Ridge optical waveguide in an Er3+/Yb3+ co-doped phosphate glass produced by He+ ion implantation combined with Ar+ ion beam etching

This paper reports on the fabrication and characterization of a ridge optical waveguide in an Er3+/Yb3+ co-doped phosphate glass. The He+ ion implantation (at energy of 2.8 MeV) is first applied onto the sample to produce a planar waveguide substrate, and then Ar+ ion beam etching (at energy of 500 eV) is carried out to construct rib stripes on the sample surface that has been deposited by a specially designed photoresist mask. According to a reconstructed refractive index profile of the waveguide cross section, the modal distribution of the waveguide is simulated by applying a computer code based on the beam propagation method, which shows reasonable agreement with the experimentally observed waveguide mode by using the end-face coupling method. Simulation of the incident He ions at 2.8 MeV penetrating into the Er3+/Yb3+ co-doped phosphate glass substrate is also performed to provide helpful information on waveguide formation.

Structural and up-conversion luminescence properties in Tm (3+)/Yb3+-codoped heavy metal oxide-halide glasses

Tm3+/Yb3+-codoped heavy metal oxide-halide glasses have been synthesized by conventional melting and quenching method. Structural properties were obtained based on the Raman spectra, indicating that halide ion has an important influence on the phonon density and maximum phonon energy of host glasses. Intense blue and weak red emissions centered at 477 and 650 nm, corresponding to the transitions (1)G(4) -> H-3(6) and (1)G(4) -> H-3(4), respectively, were observed at room temperature. The possible up-conversion mechanisms are discussed and estimated. With increasing halide content, the up-conversion luminescence intensity and blue luminescence lifetimes of Tm3+ ion increase notably. Our results show that with the substitution of halide ion for oxygen ion, the decrease of phonon density and maximum phonon energy of host glasses both contribute to the enhanced up-conversion emissions. (c) 2005 Elsevier B.V. All rights reserved.

Luminescence behavior of Yb(3+)heavy-doped yttrium lanthanum oxide transparent ceramics

Yb3+ heavy-doped yttrium lanthanum oxide transparent ceramics were fabricated and their spectroscopic properties were investigated. The absorption bands of (YbxY0.9-xLa0.1)(2)O-3 (x = 0.05-0.15) ceramics are broad at wavelength of 900-1000 nm. The absorption cross-sections centered at 974 nm and the emission cross-sections at 1031 nm of Yb3+ ion are 0.89-1.12 x 10(-20) cm(2) and 1.05 x 10(-20) cm(2) respectively. The up-conversion luminescence intensity of Yb3+-doped yttrium lanthanum oxide ceramics increased firstly, then decreased with the increase of Yb3+ ion content. (C) 2008 Elsevier B.V. All rights reserved.

Mobilization potential of heavy metals: A comparison between river and lake sediments

Toxic metals introduced into aquatic environments by human activities accumulation in sediments. A common notion is that the association of metals with acid volatile sulfides (AVS) affords a mechanism for partitioning metals from water to solid phase, thereby reducing biological availability. However, variation in environmental conditions can mobilize the sediment-bound metal and result in adverse environmental impacts. The AVS levels and the effect of AVS on the fate of Cu, Cd, Zn, Ni in sediments in the the Changjiang River, a suboxic river with sandy bottom sediment and the Donghu Lake, a anoxic lake with muddy sediment in China, were compared through aeration, static adsorption and release experiments in laboratory. Sips isotherm equation, kinetic equation and grade ion exchange theory were used to describe the heavy metal adsorb and release process. The results showed that AVS level in the lake sediment are higher than that of the river. Heavy metals in the overlying water can transfer to sediments incessantly as long as the sediment remains undisturbed. The metal release process is mainly related to AVS oxidation in lake sediment while also related to Org-C and Fe-Mn oxyhydroxide oxidation in river sediment. The effect of sulfides on Zn and Ni is high, followed by Cd, and Cu is easy bound to Org-C. AVS plays a major role in controlling metals activity in lake sediment and its presence increase the adsorption capacity both of the lake and river sediments.

Spin states in semiconductor quantum dot with a single magnetic ion

We investigate theoretically CdTe quantum dots containing a single Mn2+ impurity, including the sp-d exchange interaction between carriers and the magnetic ion and the short-range exchange interaction between electron and hole. We find anticrossing behaviors in the energy spectrum of the electron-hole (e-h) pair that arise from the interplay between exchange interactions and the magnetic field. In addition to the s-d exchange interaction, we find that other mechanisms inducing the anticrossings become important in the strong heavy hole-light hole (hh-lh) mixing regime. The transition strengths between the states with spin projection of Mn2+ ion S-z not equal -5/2 (S-z = -5/2) decrease (increase) with increasing magnetic fields due to the alignment of the Mn2+ spin. The spin splitting of the e-h pair states depends sensitively on the external magnetic and electric field, which reveals useful information about the spin orientation and position of the magnetic ion. Meanwhile, the manipulation of the position of the magnetic ion offers us a way to control the spin splitting of the carriers. (C) 2008 Elsevier B.V. All rights reserved.

The micro-magnetic structures of Mn+ ion-implanted GaSb

The micro-magnetic structures of Mn+ ion-implanted GaSb are studied using a magnetic force microscope (MFM). MFM images reveal that there are many magnetic domains with different magnetization directions in our samples. The magnetic domain structures and the magnetization direction of typical MFM patterns are analyzed by numeric simulation.

Mechanism of induced reaction during XPS depth profile measurements of CeO2/Si films grown by ion beam epitaxy

In a search for the mechanism of the induced reduction reaction that occurred in X-ray photoelectron Spectroscopy (XPS) depth profiles measured experimentally on CeO2/Si epilayers grown by ion beam epitaxy (IBE), several possibilities have been checked. The first possibility, that the X-ray induces the reaction, has been ruled out by experimentation. Other possible models for the incident-ion induced reaction, one based on short-range interaction (direct collision) and the other based on long-range potential accompanied with the incident-ions, have been tested by simulation on computer. The results proved that the main mechanism is the former, not the latter. (C) 1998 Elsevier Science Ltd. All rights reserved.