A Monte Carlo simulation of the heterogeneous adsorption of hydrogen ions on metal oxides: Effect of inert electrolyte

Charging of the surface of an oxide caused by the adsorption of hydrogen ions and ions of inert 1:1 electrolyte was investigated by using grand canonical Monte Carlo simulation technique. In particular, adsorption isotherms of protons as well as of ions of the electrolyte together with the resulting charge density of the surface were obtained for different system parameters. Also, the effect of the surface energetic heterogeneity and the concentration of the background electrolyte on the isotherms and the charge density curves was examined. Furthermore, lateral interactions in the mixed adsorbed phase were taken into account in the modeling of the system behavior. The obtained results, in general, suggest that the three factors mentioned above may have substantial influence on the charging mechanism at the liquid/oxide interface.     

Unique edge structure and stability of fabricated dimer islands on Si(001)

The edge structure and stability of monolayer-high islands fabricated on Si(001) surfaces by scanning tunneling microscopy have been analyzed theoretically. In contrast to the edges of similar islands grown by depositing Si, the properties of edges of fabricated islands are determined by the length of the trench of dimers that are removed to create the island. We demonstrate the possibility of controlling the edge structure, and thus the stability, through a selective process of atom removal.     

Combined X-ray-electron imaging techniques: Limitations on lateral resolution

Capabilities of the imaging techniques, in which X-rays are converted to electrons and then the emitted electrons are registered by means of an electron microscope, are analyzed, the focus being on the factors limiting lateral resolution at the stage of electron emission. Bearing in mind the tendency to use harder synchrotron X-rays for some combined X-ray-electron microscopy methods, calculations were made for two significantly different X-ray energies: E = 1.828 keV (K-edge of Si) and E = 11.923 keV (L₃-edge of Au). By using Monte Carlo simulations of the electron trajectories beneath the surface of the sample we show that the radius of the spot from which photoelectrons are emitted could be as small as 1 nm. However, when proper account is taken of an entire electron cascade associated with the re-building of electron shells after photoelectron emission, spots more than one order of magnitude larger result, limiting the best lateral resolution to 20–30 nm.     

The phase diagram of a single polymer chain: New insights from a new simulation method

We present simulation results for the phase behavior of a single chain for a flexible lattice polymer model using the Wang-Landau sampling idea. Applying this new algorithm to the problem of the homopolymer collapse allows us to investigate not only the high temperature coil–globule transition but also an ensuing crystallization at lower temperature. Performing a finite size scaling analysis on the two transitions, we show that they coincide for our model in the thermodynamic limit corresponding to a direct collapse of the random coil into the crystal without intermediate coil–globule transition. As a consequence, also the many chain phase diagram of this model can be predicted to consist only of gas and crystal phase in the limit of infinite chain length. This behavior is in agreement with findings on the phase behavior of hard-sphere systems with a relatively short-ranged attractive square well. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2542–2555, 2006     

Incubation period in the 2,2,4,4‐tetramethyl‐1‐piperidinyloxy‐mediated thermal autopolymerization of styrene: Kinetics and simulations

Mechanisms and simulations of the induction period and the initial polymerization stages in the nitroxide‐mediated autopolymerization of styrene are discussed. At 120–125 °C and moderate 2,2,4,4‐tetramethyl‐1‐piperidinyloxy (TEMPO) concentrations (0.02–0.08 M), the main source of radicals is the hydrogen abstraction of the Mayo dimer by TEMPO [with the kinetic constant of hydrogen abstraction (k_h)]. At higher TEMPO concentrations ([N?] > 0.1 M), this reaction is still dominant, but radical generation by the direct attack against styrene by TEMPO, with kinetic constant of addition k_ad, also becomes relevant. From previous experimental data and simulations, initial estimates of k_h ≈ 1 and k_ad ≈ 6 × 10^?7 L mol^?1 s^?1 are obtained at 125 °C. From the induction period to the polymerization regime, there is an abrupt change in the dominant mechanism generating radicals because of the sudden decrease in the nitroxide radicals. Under induction‐period conditions, the simulations confirm the validity of the quasi‐steady‐state assumption (QSSA) for the Mayo dimer in this regime; however, after the induction period, the QSSA for the dimer is not valid, and this brings into question the scientific basis of the well‐known expression k_th[M]³ (where [M] is the monomer concentration and k_th is the kinetic constant of autoinitiation) for the autoinitiation rate in styrene polymerization. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 6962‐6979, 2006     

Theoretical and computational studies of vectorial processes in biomolecular systems

Efficient vectorial processes such as the transduction of bioenergy and signals are characteristics that strikingly distinguish living systems from inanimate materials. Recent developments in biophysical and biochemical techniques have provided new information about the structure, dynamics and interaction of biomolecules involved in vectorial life processes at multiple length and temporal scales. This wealth of data makes it possible to carry out theoretical and computational studied of key mechanistic questions associated with complex life processes at an unprecedented level. Using two “vectorial biomolecular machines”, myosin and cytochrome c oxidase, as examples, we discuss the identification of interesting and biologically relevant questions that require thorough theoretical analysis. Technical challenges and recent progress related to these theoretical investigations are briefly summarized     

Superdegenerate point in FCC phase diagram: CVM and Monte Carlo investigations

We investigate the topology of the phase diagram of binary alloys on the fee lattice with first-neighbor antiferromagnetic interactions around the superdegenerate point, where the L1₀ and L1₂ phases meet. We treat the system as a hard-constraint lattice gas, following a procedure previously described by Lebowitzet al. We perform cluster variation method calculations in theT0 limit and Monte Carlo simulations directly atT=0 K on the ground states of the superdegenerate point. We find that: (i) there is no disordered phase in the neighborhood of this point; (ii) a phase L for which two of the four cubic sublattices have the same average occupancy and each of the two others are different appears between L1₀ and L1₂; (iii) the transition L/L1₂ is of first order.     

多晶顺磁共振谱的拟合

对电子自旋1/2≤S<3.5,核自旋1/2≤I<4.5和配体少于10个的顺磁体系的多晶EPR谱的拟合进行研究。在VAX-11/785计算机上用FORTRAN语言建立EPR谱模拟程序包,计算了多个例子,获得较为满意的结果。     

Electrostatics of phosphatidic acid monolayers: Insights from computer simulations

In this paper, we argue that many of the fascinating electrostatic effects that take place in amphiphilic systems are strongly related to the particular organization of the oxygen atoms within each individual molecule. In particular, we focus on two effects: charge inversion and dielectric overscreening. For that purpose, we present molecular dynamics simulations of phosphatidic acid (DMPA²⁻) in the presence of divalent counterions. Our results show that the many oxygens present in DMPA²⁻ cooperatively create strong binding sites for counterions, which in some cases lead to charge inversion. We also present an analysis of the role of interfacial water and relate our analysis to the phenomenon of dielectric overscreening. Several experimental implications are discussed in the conclusions.     

Short range photoinduced electron transfer in proteins: QM-MM simulations of tryptophan and flavin fluorescence quenching in proteins

Hybrid quantum mechanical-molecular mechanics (dynamics) were performed on flavin reductase (Fre) and flavodoxin reductase (Fdr), both from Escherichia coli. Each was complexed with riboflavin (Rbf) or flavin mononucleotide (FMN). During 50 ps trajectories, the relative energies of the fluorescing state (S₁) of the isoalloxazine ring and the lowest charge transfer state (CT) were assessed to aid prediction of fluorescence lifetimes that are shortened due to quenching by electron transfer from tyrosine. The simulations for the four cases display a wide range in CT–S₁ energy gap caused by the presence of phosphate, other charged and polar residues, water, and by intermolecular separation between donor and acceptor. This suggests that the Gibbs energy change (ΔG₀) and reorganization energy (λ) for the electron transfer may differ in different flavoproteins.