Microstructure and surface roughness of graphite‐like carbon films deposited on silicon substrate by molecular dynamic simulation

Molecular dynamics simulations are performed on the atomic origin of the growth process of graphite‐like carbon film on silicon substrate. The microstructure, mass density, and internal stress of as‐deposited films are investigated systematically. A strong energy dependence of microstructure and stress is revealed by varying the impact energy of the incident atoms (in the range 1–120 eV). As the impact energy is increased, the film internal stress converts from tensile stress to compressive stress, which is in agreement with the experimental results, and the bonding of C‐Si in the film is also increased for more substrate atoms are sputtered into the grown film. At the incident energy 40 eV, a densification of the deposited material is observed and the properties such as density, sp³ fraction, and compressive stress all reach their maximums. In addition, the effect of impact energy on the surface roughness is also studied. The surface morphology of the film exhibits different characteristics with different incident energy. When the energy is low (<40 eV), the surface roughness is reduced with the increasing of incident energy, and it reaches the minimum at 50 eV. Copyright © 2012 John Wiley & Sons, Ltd.     

Exploring sequential quantum adiabatic switching across supersymmetric partners for finding the eigenstates of a system

We demonstrate that one can exhaustively determine the n‐bound eigenstates of a Hamiltonian H by constructing a sequence of supersymmetric (SUSY) partner Hamiltonians and invoking a time‐dependent quantum adiabatic switching algorithm for passage from the ground state of one to the other. The ground states of the initial pair H⁽⁰⁾ and H⁽¹⁾ are constructed by solving the Riccati equation for the superpotential ?⁽⁰⁾ for H⁽⁰⁾ and adiabatically switching from the ground state Ψ of H⁽⁰⁾ to the ground state Ψ of H⁽¹⁾. The charge operator Q is then used to recover the first excited state Ψ of H⁽⁰⁾. The procedure is repeated for the ground states of SUSY pairs H^{(n + 1)} and H^{(n + 2)}, and appropriate charge operators lead to the excited states Ψ of H⁽⁰⁾ with , thereby exhausting the full eigenspectrum of H⁽⁰⁾. The workability of the proposed method is shown with several well‐known examples. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Effects of Poly(ethylene glycol) Doping on the Behavior of Pyrene, Rhodamine 6G, and Acrylodan-Labeled Bovine Serum Albumin Sequestered within Tetramethylorthosilane-Derived Sol-Gel-Processed Composites

We investigate the effects of controlled poly(ethylene glycol) (PEG) doping on the behavior of pyrene, rhodamine 6G (R6G), and acrylodan-labeled bovine serum albumin (BSA-Ac) sequestered within tetramethylorthosilicate (TMOS)-derived sol-gel-processed materials. To probe the dipolarity of the local environment within the composite we performed static fluorescence measurements on pyrene as the composites aged. We found that small levels of PEG loading effected significant enhancements in the local dipolarity surrounding the average pyrene molecule. Time-resolved fluorescence anisotropy measurements were used to follow the rotational reorientation dynamics of R6G as the composites aged. As the PEG loading increased, the R6G reorientational mobility increased. Nitrogen adsorption techniques were used to quantify the effects of PEG doping level on the surface area and final xerogel pore features. A large reduction in surface area was observed with PEG doping, but no detectable change in pore size was noted. The effects of PEG doping on a biomolecule were probed by following the time-resolved fluorescence anisotropy decay of BSA-Ac. These results showed that PEG doping resulted in increased biomolecule dynamics relative to that found for a neat, undoped TMOS-derived composites. Together these results show that PEG doping can be used to tune the sol-gel-processed composite dipolarity, alter the mobility of dopants sequestered within the composite, control analyte acessibility to the sensing chemistry, and modulate the internal dynamics within a biodopant.     

Computer simulation of electron transfer processes across the electrode|electrolyte interface: a treatment of solvent and electrode polarizability

A polarizable molecular dynamics model for adiabatic electron transfer across the electrode|electrolyte interface is presented. The electronic polarizability of the water and of the metal electrode is accounted for by a dynamical fluctuating charge algorithm, image charges, and the Ewald summation adapted for a conducting interface. The effects of the solvent electronic polarizability are studied by computing the diabatic and adiabatic free energy curves for both polarizable and non-polarizable water models. This represents the first effort to compute the adiabatic free energy curves from simulation for a fully polarizable electrochemical system.     

Structure formation and dynamics of water in strong external electric fields

We have performed molecular dynamics computer simulations of water in homogeneous external electric fields which were varied in a wide range of field strengths. The dielectric response is found to be linear up to fields E₀≈0.01 V/Å from where dielectric saturation effects become important. At fields of E₀≈3 V/Å a phase transition into an ordered, ice-like structure is observed, which is stabilized through hydrogen-bonds. With an increasing external electric field, the frequency spectrum of the water dynamics shows a remarkable red shift of the intramolecular modes and a blue shift of the librational motions, where the frequency varies quadratically with the field strength. A simple analytical model is discussed which reproduces the observed behavior.     

大肠杆菌有限生长的微量热及非线性动力学研究

The finite growth of Escherichia coli was studied by using a LKB 2277 BioActivity Mollitor. We found that the finite growth is a nonliear dynamic process. The nonlinear dynamic behaviour in the finite growth process and the nonlinear dynamic models describing the process were discovered and established. The curve of logistic map corresponding to the finite growth thermogram of Escherichia coli was obtained and the nonlinear dynamic parameters were calculated by means of a computer. Moreover, we also discussed the nonlinear dynamic characters of Escherichia colt in its finite growth process.     

Structural Studies on Host + Guest Recognition Sensory Systems

Rhodamine B-ethylenediamine--cyclodextrins (RhB--CDen) and rhodamine B--cyclodextrins (RhB--CD) can form inclusive complexes with many guest molecules, a reaction which can be used as a nucleic acid probe. In this paper, the most stable conformations of RhB--CDen and RhB--CD have been determined by fluorescence experiments and analyzed by molecular modeling simulation. The interaction between RhB--CDen and two guest molecules, 1-borneol and cyclohexanol, has also been investigated. The results showed that RhB--CDen has a stronger interaction with 1-borneol than with cyclohexanol. Borneol could push the three aromatic-rings of rhodamine B out of the CD cavity, while the cyclohexanol could not. The interactive sites of host and guest are also presented.     

Dynamics of joint adsorption of mutually soluble substances by activated carbons

A model for the dynamics of isothermal absorption of a binary mixture of an organic substance, soluble in water, and water vapor in a fixed bed of activated carbon was proposed. It includes the equations of material balance and the Myers—Prausnitz model for equilibrium adsorption. The possibility of formation of the condensed phase during the adsorption of an organic substance on moist activated carbon was shown. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1491–1495, August, 1998.     

Molecular dynamics and phase transitions in phospholipid monolayers at liquid-liquid interfaces

Stablen-hexadecane/water andn-tetradecane/water macroemulsions containing monolayers of natural (egg yolk lecithin, EY) and synthetic (dimyristoylphosphatidylcholine, DMPC) phospholipids at liquid-liquid interfaces were prepared. The existence of the monolayers was proved by studying the reduction kinetics of a surface-active spin probe with ascorbate anions. Spin labeled derivatives of stearic acid in which the nitroxide group is locared at different distances from the polar head (5-, 12-, and 16-doxylstearic acids) were used to study the temperature dependences of the molecular ordering, rotational mobility, and local polarity in the monolayers in emulsions and also in bilayers in liposomes obtained from the same lipids. In the EY monolayers, the degree of spin probe solubilization is higher, while the order parameters (S) and rotational correlation times (τ) are lower than those in EY bilayers. The differences between these parameters for mono- and bilayers increase with an increase in the distance of the reporter group from the aqueous phase. In the DMPC monolayers, a first-order phase transition was detected by measuring the temperature dependences ofS and τ. The temperature region of the phase transition in monolayers is shifted to lower temperatures with respect to that for bilayers and depends on the nature of the oil phase. It was concluded that the phospholipid monolayers in emulsions incorporate hydrocarbon molecules, whose concentration in the DMPC monolayers increases on going from the low-temperature (gel) to the high-temperature (liquid crystal) phase. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 418–425, March, 1998.     

Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics

The present study describes an extensive conformational search of substance P using two different computational methods. On the one hand, the peptide was studied using the iterative simulated annealing, and on the other, molecular dynamics simulations at 300 and 400 K. With the former method, the peptide was studied in vacuo with a dielectric constant of 80, whereas using the latter study the peptide was studied in a box of TIP3P water molecules. Analysis of the results obtained using both methodologies was carried out using an in-house methodology using a cluster analysis method based on information theory. Comparison of the two sampling methodologies and the different environment used in the calculations is also analyzed. Finally, the conformational motifs that are characteristic of substance P in a hydrophilic environment are presented and compared with the experimental results available in the literature.