Multi-scale analysis of AFM tip and surface interactions

Thoroughly understanding AFM tip-surface interactions is crucial for many experimental studies and applications. It is important to realize that despite its simple appearance, the system of tip and sample surface involves multiscale interactions. In fact, the system is governed by a combination of molecular force (like the van der Waals force), its macroscopic representations (such as surface force) and gravitational force (a macroscopic force). Hence, in the system, various length scales are operative, from sub-nanoscale (at the molecular level) to the macroscopic scale. By integrating molecular forces into continuum equations, we performed a multiscale analysis and revealed the nonlocality effect between a tip and a rough solid surface and the mechanism governing liquid surface deformation and jumping. The results have several significant implications for practical applications. For instance, nonlocality may affect the measurement accuracy of surface morphology. At the critical state of liquid surface jump, the ratio of the gap between a tip and a liquid dome (delta) over the dome height (y(o)) is approximately (n-4) (for a large tip), which depends on the power law exponent n of the molecular interaction energy. These findings demonstrate that the multiscale analysis is not only useful but also necessary in the understanding of practical phenomena involving molecular forces. (c) 2007 Elsevier Ltd. All rights reserved.

Stability and bifurcation behaviour of electrostatic torsional NEMS varactor influenced by dispersion forces

The influences of Casimir and van der Waals forces on the nano-electromechanical systems (NEMS) electrostatic torsional varactor are studied. A one degree of freedom, the torsional angle, is adopted, and the bifurcation behaviour of the NEMS torsional varactor is investigated. There are two bifurcation points, one of which is a Hopf bifurcation point and the other is an unstable saddle point. The phase portraits are also drawn, in which periodic orbits are around the Hopf bifurcation point, but the periodic orbit will break into a homoclinic orbit when meeting the unstable saddle point.

分子间相互作用对蛋白质晶体生长的影响

采用原子力显微镜对溶菌酶和刀豆蛋白A的分子间相互作用力的情况进行了研究,并用动态光散射研究了此二种分子间相互作用力有较大差异的蛋白质在晶体生长条件和非生长条件下,溶液中的聚集体的状态(大小和分散度)随浓度和温度的变化情况.实验结果表明,范德华力强的刀豆蛋白A在成核前,溶液中的聚集体不能很快转变为生长基元,导致晶体生长时间长;而范德华力弱的溶菌酶,溶液中的聚集体可以很快转变成生长基元,晶体生长时间也较短.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated. We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard-Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

Instability Analysis Of Torsional Mems/Nems Actuators Under Capillary Force

The static and dynamic instabilities of a torsional MEMS/NEMS actuator caused by capillary effects are studied, respectively. An instability number, eta, is defined, and the critical gap distance, g(cr), between the mainplate and the substrate is derived. According to the values of eta and g, the instability criteria of the actuator are presented. The dimensionless motion equation of the MEMS/NEMS torsional actuator is derived when it makes nonlinear oscillation under capillary force. The qualitative analysis of the nonlinear equation is made, and the phase portraits are presented on the phase plane. In addition, the bifurcation phenomena in the system are also analyzed. (C) 2008 Elsevier Inc. All rights reserved.

Numerical modeling of optical levitation and trapping of the "stuck" particles with a pulsed optical tweezers

We present the theoretical analysis and the numerical modeling of optical levitation and trapping of the stuck particles with a pulsed optical tweezers. In our model, a pulsed laser was used to generate a large gradient force within a short duration that overcame the adhesive interaction between the stuck particles and the surface; and then a low power continuous - wave (cw) laser was used to capture the levitated particle. We describe the gradient force generated by the pulsed optical tweezers and model the binding interaction between the stuck beads and glass surface by the dominative van der Waals force with a randomly distributed binding strength. We numerically calculate the single pulse levitation efficiency for polystyrene beads as the function of the pulse energy, the axial displacement from the surface to the pulsed laser focus and the pulse duration. The result of our numerical modeling is qualitatively consistent with the experimental result. (C) 2005 Optical Society of America.

Interaction of corticosterone and nicotine in regulation of prepulse inhibition in mice

The aim of the present Study was to investigate if different levels of circulating corticosterone (CORT) modulate the effect of nicotine on prepulse inhibition (PPI), a measure of sensorimotor gating that is disrupted in schizophrenia and other mental illnesses. Four groups of mice were investigated: sham-operated, adrenalectomized (ADX) and implanted with a cholesterol pellet, ADX and implanted with a 10 mg CORT pellet, or ADX and 50 mg, of CORT. Different CORT levels or doses of nicotine did not significantly affect startle responses. Baseline PPI was significantly reduced in mice implanted with the highest dose of CORT. In ADX mice implanted with cholesterol, nicotine treatment influenced PPI depending on the prepulse intensity. In ADX mice implanted with 50 mg of CORT, treatment with 10 mg/kg of nicotine caused a significant increase in PPI at all prepulse intensities. Binding studies showed that corticosterone treatment had significantly affected nicotinic acetylcholine receptor (nAChR) density in the mouse brain. Treatment with 50 mg CORT decreased I-125-epibatidine binding in the globus pallidus and I-125-alpha-bungarotoxin binding in the claustrum. These results suggest a possible interaction of corticosterone and nicotine at the level of the alpha4- and alpha7-type nAChR in the regulation of PPI. In situations of high circulating levels of corticosterone, nicotine may be beneficial to restore disruption of PPI. (C) 2004 Elsevier Ltd. All rights reserved.

Molecular modeling on human CCR5 receptors and complex with CD4 antigens and HIV-1 envelope glycoprotein gp120

AIM: To investigate the interaction between human CCR5 receptors (CCR5) and HIV-1 envelope glycoprotein gp120 (HIV-1 gp120) and HIV-1 receptor CD4 antigens (CD4). METHODS: The structurally con served regions (SCR) of human CCR5 was built by the SYBYL/Biopolymer module using the corresponding transmembrane (TM) domain of bacteriorhodopsin (bR) as the template. The coordinates for amino-ter minal residue sequence, and carboxyl-terminal residue sequence, extracellular and cytoplasmic loops were generated using LOOP SEARCH algorithm. Subsequently the structural model was merged into the complex with HIV-1 gp120 and CD4. RESULTS: Human CCR5 interacted with both an HIV-1 gp120 and CD4. The N-terminal residues (especially Met1 and Gln4) of human CCR5, contacted with CD4 residues, mainly 7Nith one span (56 - 59) of CD4 in electrostatic interaction and hydrogen-bonds. The binding sites of human CCR5 were buried in a hydrophobic center surrounded by a highly basic periphery. On the other hand, direct interatomic contacts were made between ? CCR5 residues and 6 gp120 amino-acid residues, which included van der Waals contacts, hydrophobic interaction, and hydrogen bonds. CONCLUSION: The interaction model should be helpful for rational design of novel anti-HIV drugs.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

抗新霉素基因对草鱼肾细胞的磷酸钙共沉淀转移

<正> 自1973年 Graham 和 Van der Eb 首次成功地应用 DNA-磷酸钙共沉淀法转化哺乳动物培养细胞以来,又提出了电脉冲法;显微注射法;磷脂载体法及细菌原生质体融合法等多种培养细胞基因转移方法。然而,目前的研究多局限于哺乳动物细胞,鱼类培养细胞方面的报道却很少。建立鱼类培养细胞基因转移的方

Effect of ion flux on recrystallization and resistance lowering in phosphorus-implanted (0001)-oriented 4H-SiC

High-dose ion implantation of phosphorus into 4H-SiC (0001) has been investigated with three different ion fluxes ranging from 1.0 to 4.0 x 10(12) P(+)cm(-2.)s(-1) and keeping the implantation dose constant at 2.0 x 10(15) P(+)cm(-2). The implantations are performed at room temperature and subsequently annealed at 1500 degrees C. Photoluminescence and Raman scattering are employed to investigate the implantation-induced damages and the residual defects after annealing. The electrical properties of the implanted layer are evaluated by Hall effect measurements on the sample with a van der Pauw configuration. Based on these results, it is revealed that the damages and defects in implanted layers can be greatly reduced by decreasing the ion flux. Considering room temperature implantation and a relatively low annealing temperature of 1500 degrees C, a reasonably low sheet resistance of 106 Omega/square is obtained at ion flux of 1.0 x 10(12) P(+)cm(-2.)s(-1) with a donor concentration of 4.4 x 10(19)cm(-3).

Changing planar thin film growth into self-assembled island formation by adjusting experimental conditions

Illustrated in this paper are two examples of altering planar growth into self-assembled island formation by adapting experimental conditions. Partial oxidation, undersaturated solution and high temperature change Frank-Van der Merwe (FM) growth of Al0.3Ga0.7As in liquid phase epitaxy (LPE) into isolated island deposition. Low growth speed, high temperature and in situ annealing in molecular beam epitaxy (MBE) cause the origination of InAs/GaAs quantum dots (QDs) to happen while the film is still below critical thickness in Stranski-Krastanow (SK) mode. Sample morphologies are characterized by scanning electron microscopy (SEM) or atomic force microscopy (AFM). It is suggested that such achievements are of value not only to fundamental researches but also to spheres of device applications as well. (c) 2004 Elsevier B.V. All rights reserved.

Electrical properties of undoped In0.53Ga0.47As grown on InP substrates by molecular beam epitaxy

A series of 1-mu m-thick undoped In0.53Ga0.47As with different substrate growth temperature (T-g) or different beam flux pressure (BFP) of As were grown on lattice-matched semi-insulating InP (001) substrates by molecular beam epitaxy (MBE). Van der Pauw Hall measurements were carried out for these In0.53Ga0.47As samples. The residual electron concentration decreased with increasing temperature from 77 to 140 K, but increased with increasing temperature from 140 to 300 K. Rapid thermal annealing (RTA) can reduce the residual electron concentration. The residual electron mobility increased with increasing temperature from 77 to 300 K. All these electrical properties are associated with As antisite defects. (c) 2006 Elsevier B.V. All rights reserved.