CO-H2-O2 reaction on a catalytic surface: A computer simulation study

The oxidation of carbon monoxide to form carbon dioxide and the oxidation of hydrogen to form water are the reactions of environmental and industrial importance. These two reactions have been studied independently by Monte Carlo computer simulation using Langmuir-Hinshelwood mechanism but no effort has been made to study the combined CO-H₂-O₂ reaction on these lines. Keeping in view the importance of this 3-component system, the surface coverages and production rates are studied as a function of CO partial pressure for different ratios of H₂ and O₂. The diffusion of reacting species on the surface as well as their desorption from the surface is also introduced to include temperature effects. The phase diagrams of the system are drawn to observe the behavior of these atoms/molecules on the surface and the production of CO₂ and H₂O are determined at different concentrations of H₂. The results are compared with 2-component systems.     

Conformational properties of surfactant-like peptides with variable glycine tails

The three-dimensional structures of surfactant-like peptides containing 4-10 glycines as the components of the hydrophobic tails and aspartic acids as the hydrophilic heads (G₄D₂, G₆D₂, G₈D₂, G₁₀D₂) are investigated by using the multicanonical simulation procedure. The thermodynamically most stable low energy structures of the sequences are determined. Ramachandran plots are prepared and analyzed to predict the secondary structure motifs of the molecules.     

Stochastic simulation of the reaction-diffusion systemA+B→inert in integer and fractal dimensions

We present a stochastic simulation of the reaction-diffusion systemA+Binert based upon the algorithm of the minimal process method. In order to overcome the well known problems of this algorithm when selecting a reaction or diffusion event according to its rate contribution we introduce the concept of logarithmic classes which accelerates the algorithm by an order of magnitude. We simulate the systemA+Binert for integer dimensionsd=1,2,3,4 and confirm the predictions of the scaling theory by Kang and Redner. We extend our simulations to fractal structures, namely the Sierpinski carpet, triangle, the Menger sponge and HLA-clusters. Again we find agreement with the scaling theory if the fractal dimensions are defined as the spectral dimension.     

Transient Non-Thermal Mobility of CO for CO--NO Catalytic Reaction on Square Lattice: Monte Carlo Simulation

We study a model based on precursor mechanism for CO-NO catalytic reaction on square lattice with Monte Carlo simulation. The precursor mechanism clearly demonstrates its impact on the phase diagram. The steady reactive state （SRS） gets established. The width of reactive region increases by increasing the range of precursor mobility. When the precursor mobility is increased to third-nearest neighbourhood, the second-order transition disappears.     

Folding kinetics of two-state proteins based on the model of general random walk in native contact number space

We investigated the folding kinetics of a series of two-state proteins by using the model of general random walk in native contact number space, and derive the observed linear relationship between the logarithms of the folding rate constants and the numbers of native contacts from “kinetic viewpoint”. The protein folding speed limit and stability in this model are consistent with experimental observations.     

Monte Carlo simulation of Ising model on decagonal covering structure

We study the Ising model on a two-dimensional quasilattice developed from the decagonal covering structure. The periodic boundary conditions are applied to a patch of rhombus-like covering pattern. By means of the Monte Carlo simulation and the finite-size scaling analysis the critical temperature is estimated as 2.317±0.002. Two critical exponents are obtained being 1/v=0.992±0.003 and η=0.247±0.002, which are close to the values of the two-dimensional regular lattices as well as the Penrose tilings.     

Mechanism for Alternating Electric Fields Induced-Effects on Cytosolic Calcium

In this work, from the point of calcium ions in the cytosol, we extend a V_m-[Ca²⁺]_cyt model to explain the changes of action potential V_m of the plasma membrane and the calcium concentration in the cytosol [Ca²⁺]_cyt under an alternating electric field in cells. An alternating external electric field may exert an oscillating force to each of the free electrolytes, existing on both sides of the plasma membrane. The mechanism for the alternating electric field induced-effects on V_m and [Ca²⁺]_cyt is elucidated. The simulation results show a correlation between the changes of [Ca²⁺]_cyt and the alternating electric field. When the numerical ratio between the intensity E₀(mV/m) and the frequency υ (Hz) of the field was about 1-2, the [Ca²⁺]_cyt signal is changed dramatically. The bioactive changes of [Ca²⁺]_{_cyt} appear at low frequency, in the range of 0-100Hz.     

Influence of sublayer atoms on Si(100) surface reconstructions

Influence of sublayer atoms on Si(100) surface reconstruction has been examined with density functional theory and molecular dynamic simulation. We found that the displacements of sublayer atoms under the buckled dimer affect the motions of their neighboring atoms and thus play an important role in determining the surface reconstructions. The present results reveal the relationship between the surface dimer reconstruction and the motion of the sublayer atoms and provide an account for experimental observations of Si(100) surface reconstructions at very low temperatures.     

Computer simulation study of the Levy flight process

The random walk simulation of a Levy flight shows a linear relation between the mean square displacement 〈r²〉 and time. We have analyzed different aspects of this linearity. It is shown that the restriction of jump length to a maximum value (l_m) affects the diffusion coefficient, even though it remains constant for l_m greater than 1464. So, this factor has no effect on the linearity. In addition, it is shown that the number of samples does not affect the results. We have demonstrated that the relation between the mean square displacement and time remains linear in a continuous space, while continuous variables just reduce the diffusion coefficient. The results also imply that the movement of a Levy flight particle is similar to the case in which the particle moves in each time step with an average jump length 〈l〉. Finally, it is shown that the non-linear relation of the Levy flight will be satisfied if we use a time average instead of an ensemble average. The difference between the time average and ensemble average results shows that the Levy distribution may be a non-ergodic distribution.     

A Scheme for Information Erasure in a Double-Well Potential

We design an experimental scheme to realize one-bit information erasure and restoring processes by considering an overdamped colloidal particle in a double-well optical trap, which is added by a controllable laser tweezer. Using the Monte Carlo method, we simulate numerically the Langevin equation to calculate the mean work spent during the entire process and validate the entropy production fluctuation theory. Our result shows that the distribution of entropy production becomes narrow with increasing temperature and becomes stationary, represents the diminishing extent of irreversibility.     

Theoretical study on structure of boron nitride fullerenes

We propose the parameters of the Stillinger-Weber potential for hexagonal boron nitride (BN) structures. For the reliability of these parameters, the structural property of BN fullerenes is investigated. The stability of BN fullerenes increases with increasing the number of atoms, due to the reduction of the curvature effect of BN fullerenes. The structures of the relative stable fullerenes are B₁₆N₁₆, B₁₈N₁₈, B₂₂N₂₂, B₂₅N₂₅, and B₂₈N₂₈.     

Distinct conformational properties determined by implicit and explicit representation of protein-solvent interactions. An analytical and computer simulation study

In the protein folding problem, solvent-mediated forces are commonly represented by intra-chain pairwise contact energy. Although this approximation has proven to be useful in several circumstances, it is limited in some other aspects of the problem. Here we show that it is possible to achieve two models to represent the chain-solvent system, one of them with implicit and other with explicit solvent, such that both reproduce the same thermodynamic results. Firstly, lattice models treated by analytical methods, were used to show that the implicit and explicitly representation of solvent effects can be energetically equivalent only if local solvent properties are time and spatially invariant. Following, applying the same reasoning used for the lattice models, two inter-consistent Monte Carlo off-lattice models for implicit and explicit solvent are constructed, being that now in the latter the solvent properties are allowed to fluctuate. Then, it is shown that the chain configurational evolution as well as the globule equilibrium conformation are significantly distinct for implicit and explicit solvent systems. Actually, strongly contrasting with the implicit solvent version, the explicit solvent model predicts: (i) a malleable globule, in agreement with the estimated large protein-volume fluctuations; (ii) thermal conformational stability, resembling the conformational heat resistance of globular proteins, in which radii of gyration are practically insensitive to thermal effects over a relatively wide range of temperatures; and (iii) smaller radii of gyration at higher temperatures, indicating that the chain conformational entropy in the unfolded state is significantly smaller than that estimated from random coil configurations. Finally, we comment on the meaning of these results with respect to the understanding of the folding process.     

Signal propagation in stem-cell niches

Stem cells, maintaining tissue homeostasis, are nurtured in microscopic niches formed of so-called environmental cells. The kinetics of proliferation and differentiation of stem cells in such niches depend on their interaction with the messenger proteins secreted by environmental cells. We propose a generic mean-field kinetic model of the propagation of such signals. To motivate our study, we briefly describe a stem-cell niche in the Drosophila ovary. Our model is however applicable to other niches as well. In particular, it helps one to understand the necessary conditions for the niche function. For example, the model predicts that in the case of the Drosophila ovary each germline stem cell should have in the external membrane at least 700 receptors interacting with the signaling Dpp and Gpp proteins emanating from the cap cells.     

Structural class tendency of polypeptide: A new conception in predicting protein structural class

Prediction of protein domain structural classes is an important topic in protein science. In this paper, we proposed a new conception: structural class tendency of polypeptides (SCTP), which is based on the fact that a given amino acid fragment tends to be presented in certain type of proteins. The SCTP is obtained from an available training data set PDB40-B. When using the SCTP to predict protein structural classes by Intimate Sorting predictive method, we got the predictive accuracy (jackknife test) with 93.7%, 96.5%, and 78.6% for the testing data set PDB40-j, Chou&Maggiora and CHOU. These results indicate that the SCTP approach is quite encouraging and promising. This new conception provides an effective tool to extract valuable information from protein sequences.     

Using 3D fluid-structure interaction model to analyse the biomechanical properties of erythrocyte

This Letter presents a newly developed three-dimensional fluid-structure interaction model of the red blood cell (RBC). The model consists of a deformable liquid capsule modelled as Newtonian fluid enclosed by a hyperelastic membrane with viscoelastic property. Numerical results show that viscosity in the cytoplasm affects the deformed shape of RBC under loading. This observation is contrary to the earlier belief that viscosity of the cytoplasm can be neglected. Numerical simulations carried out to investigate large deformation induced on the RBC model using direct tensile forces show significant improvement in terms of correlation with experimental results. The membrane shear modulus estimated from the model ranges between 3.7 to compares well with results obtained from micropipette aspiration experiments.     

A study of Barstar folding events using boundary value simulations

From extensive biophysical studies of protein folding, two competing mechanisms emerged: hydrophobic collapse and the framework model. Our protein of choice is Barstar—a barnase inhibitor. The approximation algorithm we used to study Barstar folding trajectories is called SDEL—stochastic difference equation in length. Using the native structure as the final boundary value and a collection of unfolded structures as the varying initial boundary value, SDEL calculates an ensemble of least action pathways between these boundaries. The results are atomically detailed folding pathways, with as many intermediate structures as you request in the input. We generated 12 pathways, starting from a structurally wide selection of unfolded conformations. Using the protein's radius of gyration as our primary reaction coordinate, we tracked H-bonds, dihedral angles, native and non-native contacts, and energy along the folding pathways. This paper will follow our findings, with special emphasis on pinpointing hydrophobic collapse as a more appropriate mechanism for Barstar. Comparison with pathway predictions for Barstar using experimental techniques will also be discussed.     

Visualisation of a supersonic free-jet expansion using laser-induced fluorescence spectroscopy: Application to the measurement of rate constants at ultralow temperatures

2 Σ⁺, v^′=0) by air at 26±4 K. A value of 2.56±0.40×10^-10 molecule^-1 cm³ s^-1 was obtained, a factor of more than four higher than at room temperature, and consistent with attractive forces dominating the quenching of OH(A²Σ⁺). A d etailed computational fluid dynamics (CFD) simulation of the supersonic free-jet expansion was performed, providing a two-dimensional visualisation of temperature and density variations throughout the expansion. The CFD calculations reproduced the salient features of the experimental temperature and density profiles along the centreline. Comparison between experiment and computation has allowed validation of CFD codes. Received: 31 January 1997/Revised version: 24 March 1997     

Quantitative evaluation about property of thin-film formation

Chemical vapor deposition (CVD) is gradually emphasized as one promising method for nanomaterial formation. Such growth mechanism has been mainly investigated on basis of experiment. Due to large cost of the equipment of experiment and low level of current measurement, the comprehension about authentic effect of formation condition on properties of nanomaterial is limited in qualitative manner. Three quantitative items: flatness of primary deposition, adhesion between cluster and substrate, and degree of epitaxial growth were proposed to evaluate the property of thin film. In this simulation, three different cluster sizes of 203, 653, 1563 atoms with different velocities (0, 10, 100, 1000, 3000 m/s) were deposited on a Cu(0 0 1) substrate whose temperatures were set between 300 and 1000 K. Within one velocity range, not only the speed of epitaxial growth and adhesion between thin film and substrate were enhanced, but also the degree of epitaxy increased and the shape of thin film became more flat with velocity increasing. Moreover, the epitaxial growth became well as the temperature of substrate was raised within a certain range, and the degree of epitaxy of small cluster was larger than larger cluster. The results indicated that the property of thin film could be controlled if the effect of situations of process was made clear.     

Molecular dynamics simulation about porous thin-film growth in secondary deposition

The thin film growth has been confirmed to be assembled by an enormous number of clusters in experiments of CVD. Sequence of clusters’ depositions proceeds to form the thin film at short time as gas fluids through surface of substrate. In order to grow condensed thin film using series of cluster deposition, the effect of initial velocity, substrate temperature and density of clusters on property of deposited thin film, especially appearance of nanoscale pores inside thin film must be investigated. In this simulation, three different cluster sizes of 203, 653, 1563 atoms with different velocities (0, 10, 100, 1000 and 3000 m/s) were deposited on a Cu(0 0 1) substrate whose temperatures were set between 300 and 1000 K. Four clusters and one cluster were used in primary deposition and secondary deposition, respectively. We have clarified that adhesion between clusters and substrate is greatly influenced by initial velocity. As a result, the exfoliation pattern of deposited thin film is dependent on initial velocity and different between them. One borderline dividing whole region into porous region and nonporous region are obtained to show the effect of growth conditions on appearance of nanoscale pores inside thin film. Moreover, we have also shown that the likelihood of porous thin film is dependent on the point of impact of a cluster relative to previously deposited clusters.     

Study ofA+A→0 with probability of reaction and diffusion in one dimension and in fractal substrata

We present Monte Carlo simulations of annihilation reactionA+A0 in one dimensional lattice and in three different fractal substrata. In the model, the particles diffuse independently and when two of them attempt to occupy the same substratum site, they react with a probabilityp. For different kinds of initial distributions and in the short an intermediate time regimes, the results for 0<p1 show that the density ofA particles approximately behaves as (t)=(t=0)f(t/t ₀), with the scaling functionf(x)1 forx1,f(x)x ^–y forx1. The crossover timet ₀, behaves ast _{0 0eff} ^–1y where theeffective initial density _0eff depends on (t=0) and on the kind of initial distribution. For a given substratum of spreading dimensiond _s, the exponenty(d _s/2<y<1) depends only onp and its value increases asp decreases (y1 whenp0). In the very long time regime it is expected thatp(t)t ^–ds/2 independently ofp.