bluuebunny/crossref_metadata_2025 huggingface dataset:
Chaotic feature of silicon melt turbulence and its influence on crystal growth
Authors: Miyano Takaya , Shintani Akira , Kanda Tadashi
Published: July 2002

We investigate the relationship between temperature fluctuations of a silicon melt and silicon crystal growth striations in a Czochralski crystal growth system by means of time series analysis estimating the degrees of visible determinism in observed data. A diagnostic test for smoothness in time evolution of observed fluctuations [Phys. Rev. Lett. 70, 580 (1993)] is applied to time series analysis. The method seems immune to noise contamination of observational data. Temperature fluctuations of the melt are observed at three radial positions along the crystal diameter under the crystal-melt interface. Crystal growth striations of as-grown silicon crystals along the growth axis are observed at the corresponding radial positions. At a low crucible rotational rate, determinism in the flow of the melt becomes less visible toward the center of the crucible. The opposite trends are observed at a high crucible rotational rate. Such dynamical properties of the melt are found to be embedded in the growth striations. The influence of the melt turbulence on crystal growth is discussed in the framework of the previous model for growth interface fluctuations.
Measurement of electrical activation energy in boron-doped diamond using the flatband capacitance method
Authors: Liu Kun , Chu Junhao , Johnston Collin , Roth Siegmar
Published: July 2002

A Schottky barrier structure is fabricated on boron-doped diamond film, which is deposited on a (100) silicon substrate using the microwave enhanced chemical vapor deposition method. After optimizing experimental conditions, the flatband capacitance is measured for the Schottky barrier structure in the temperature range of 307–451 K. An electrical activation energy of about 362.4±15.1 meV is obtained from the experimental data in the temperature range of 373–451 K, which is attributed to boron acceptors in the diamond film. The studies indicate that the flatband capacitance measurement is a feasible and useful tool in the electrical activation energy investigations of wide-gap semiconductors, because the ohmic contact problem inherent to these kinds of semiconductors can be avoided.
Absorption spectra and electronic structure of PrBa2Cu3Oy
Authors: Kakinuma K. , Fueki K. , Takahashi H. , Pittini R. , Sata N. , Ishigame M. , Ikezawa M.
Published: July 2002

We present measurements of the optical transmission and reflection performed at room temperature in the range from 0.2 to 3.5 eV on highly oriented PrBa2Cu3Oy films for oxygen contents between y=6.3 and 6.9. The spectra are discussed in terms of the absorption coefficient, determined directly from the measured transmission and reflection spectra. Three optical absorptions are resolved. For the oxygen content y=6.3, the absorption spectrum shows a gap of 1.1 eV, in good correspondence with the charge transfer gap of 1.21 eV determined from the high temperature conductivity. This energy gap decreases with oxygen content, but still exists for the oxygen content y=6.9. The electronic structure of the PrBa2Cu3Oy system is discussed within a semiconductor model in which the excess oxygen acts as an acceptor.
Computer analysis of the 10 Tesla superconducting magnet system of the Clarendon Laboratory for the purposes of an open-gradient magnetic separation
Authors: Pitel J. , Jones H.
Published: July 2002

The results of a computer simulation of the trajectories of paramagnetic particles in a 240-mm-diameter warm bore of the 10 Tesla (T) superconducting magnet facility of the Clarendon Laboratory, University of Oxford, are reported. Calculations of the magnetic force field distribution of the magnet wound of four cylindrical coaxial sections with a various filling factor but having the same plane of a horizontal symmetry indicate that the magnetic force acting on the paramagnetic particles at the bottom part of the cryostat warm bore has a predominantly axial component which is aimed against the force of gravity. Depending on the value of the particles’ mass susceptibility and the magnet current, the axial magnetic force component can exceed several times the force of gravity and thus dramatically influence the shape of particles’ trajectories.
Magnetically tuned wide-band quantum well infrared photodetectors
Authors: Huang Danhong , Lyo S. K.
Published: July 2002

The electron eigenstates of double quantum well system in an in-plane magnetic field are calculated accurately using the density-functional theory which includes the Coulomb interaction between electrons. The absorption coefficient as a function of the probe photon energy is further calculated using the self-consistent-field theory which takes into account many-body effects on the optical intersubband transitions. The dependence of the absorption spectra on the magnetic field, temperature, electron density, well and middle-barrier widths, quantum-well symmetry, and electric field has been studied extensively. It provides an unconventional approach for designing a tunable wide-band quantum well infrared photodetector by applying an in-plane magnetic field.
Impact ionization in silicon: A microscopic view
Authors: Pacelli A. , Spinelli A. S. , Lacaita A. L.
Published: July 2002

A microscopic, single-particle view of impact ionization in silicon is obtained from a modified full-band Monte Carlo simulation. For each ionization event, the balance between the energies supplied by the electric field and lost to the lattice is plotted as a function of time before ionization. It is shown that two separate mechanisms can be identified. The lucky-electron model describes well impact ionization at very low electric fields. At higher fields, a different form of “lucky scattering” becomes the preferred ionization mechanism, where ionizing electrons suffer a sequence of scattering events with a final velocity directed along the electric field. This process is the microscopic equivalent of the energy-transport theories describing the ensemble dynamics at high fields.
Photoluminescence of C60 nanocrystals embedded in a SiO matrix
Authors: Ohno Takahiro , Matsuishi Kiyoto , Onari Seinosuke
Published: July 2002

Nanometer-sized C60 crystals in a SiO matrix were grown by an inert gas evaporation method. The size of the nanocrystal was varied by changing the evaporation time of the SiO material. We have successfully prepared well-dispersed (C60)n nanocrystals (n∼103) with a narrow size distribution in SiO. The photoluminescence of the C60 nanocrystals in SiO has been investigated and we have found that the photoluminescence spectra were significantly different from that of the C60 solid form (C60 film). Results indicate that the vibronic coupling of the C60 nanocrystals in SiO is strong compared with that of the solid form of C60.
Titanium implantation in bulk and thin film amorphous silica
Authors: Tisserand Stéphane , Flory François , Gatto Alexandre , Roux Laurent , Adamik Miklos , Kovacs Istvan
Published: July 2002

Both bulk and thin film amorphous silica implanted with titanium were investigated. We studied the induced modifications of the microstructure and the consequences on the optical properties. We determined the refractive index profile of implanted materials from guided wave measurements and we show that it matches the distribution of titanium. An increase in refractive index of up to 0.9 can be obtained by high dose implantation. A study of thermal annealing in air shows that the implanted materials exhibit low optical losses.
Elastic scattering under simultaneous excitation of x-ray standing waves in multilayers
Authors: Salditt T. , Metzger T. H. , Peisl J. , Feidenhans’l R.
Published: July 2002

We have measured the structure factor of diffuse scattering and amorphous scattering in a W/Si multilayer under simultaneous excitation of x-ray standing waves. The tuning of the nodes and antinodes to the location of the W and Si sublayers or to the respective interfaces increases the selective sensitivity to the structure of the respective sublayer or interface. The dynamically broadened first multilayer Bragg peak is modeled by the Darwin theory of dynamic diffraction, which allows for the exact determination of the standing wave phase. The decay of diffuse intensity, as measured in a grazing incidence geometry at different standing wave phase shifts, indicates that the height–height self-correlation function is of the same form for both types of interfaces, W/Si and Si/W. The amorphous peaks of the Si sublayer can only be observed if the angles of incidence and exit are optimized to suppress the scattering from the otherwise dominating W layers. The peak positions are the same as for bulk amorphous silicon.
A model for minority carrier lifetime variation in the oxide–silicon structure following 253.7 nm ultraviolet irradiation
Authors: Cheng Z. Y. , Ling C. H.
Published: July 2002

The effective minority carrier lifetime, in the silicon wafer covered with different oxides, is found to increase, or decrease, or decrease and then increase, following ultraviolet (UV) light irradiation. Evidence is presented of injection of UV-generated electrons from the silicon substrate into the oxide. Subsequent trapping occurs at the outer oxide surface for dry or native oxides, but mainly in the bulk of the oxide, in the case of wet or chemical vapor deposited oxides. Recognizing that the lifetime is determined predominantly by carrier recombination at the silicon–silicon oxide interface, and that this recombination rate is controlled by silicon surface band bending, a simple model, based on the postirradiation shift in the location of the Fermi level in the silicon at the interface, is shown to be able to reconcile the apparently conflicting reports in the lifetime behavior. The location of the pre-irradiation Fermi level is determined by the initial oxide charge, assumed to be positive, and also by the interface states.
Magnetocrystalline anisotropy of Pr2(Fe1−xCox)17−yGay compounds with a Th2Zn17-type structure
Authors: Zhang Shao-ying , Shen Bao-gen , Zhang Hong-wei , Liang Bing , Wang Jin-yun , Zhan Wen-shan , Zhao Jian-gao
Published: July 2002

The structure and magnetic properties of Pr2(Fe1−xCox)17−yGay compounds with 0⩽x⩽1 and 0⩽y⩽3 have been investigated using x-ray diffraction (XRD) and magnetization measurements. XRD patterns demonstrate that all samples were single phase with the rhombohedral Th2Zn17-type structure, except for Pr2Fe16.5Ga0.5 with some impurity phases. The replacement of (Fe, Co) by Ga results in an approximately linear increase in the unit cell volume, and decrease in the Curie temperature and saturation magnetization. The substitution of Co for Fe leads to a nonlinear variation in the unit cell volume, the Curie temperature and the saturation magnetization. The magnetic anisotropy phase diagrams of Pr2(Fe1−xCox)16.5Ga0.5 (0⩽x⩽1) and Pr2(Fe0.4Co0.6)17−yGay (0⩽y⩽3) compounds have been determined from the temperature dependence of magnetization and the XRD patterns of magnetically oriented powder samples. Most of the samples exhibit easy plane anisotropy. A small range exists in the magnetic anisotropy phase diagrams of Pr2(Fe1−xCox)17−yGay compounds at 300 K, in which the c axis is the easy magnetization direction, however, small amounts of Ga close the easy c-axis region at y=1.5. The spin-reorientation temperature was found to increase with Co and Ga content for Pr2(Fe1−xCox)16.5Ga0.5 (0.5⩽x⩽1) and Pr2(Fe0.4Co0.6)17−yGay (0⩽y⩽1.5) compounds, respectively. The relationship of the magnetocrystalline anisotropy with the lattice parameters and other magnetic properties were analyzed.
Spectroscopic ellipsometry for characterization of InAs/Ga1−xInxSb superlattices
Authors: Wagner J. , Schmitz J. , Herres N. , Fuchs F. , Walther M.
Published: July 2002

The pseudodielectric function of InAs/Ga1−xInxSb superlattices (SLs) grown by solid-source molecular-beam epitaxy, was measured by spectroscopic ellipsometry (SE) for photon energies ranging from 1.2 to 5 eV. The width of the extrema in the SL pseudodielectric function derived from the E1 and E1+Δ1 interband transitions of the SL constituents InAs and Ga1−xInxSb, was found to depend on the structural quality of the SL. Differences in the SL quality caused by different sequences of InSb- like and GaAs-like interfaces, were easily detected by SE. The formation of the intended interface alternations was verified by Raman spectroscopy. The extrema in the SL pseudodielectric function originating from the E1 and E1+Δ1 interband transitions of Ga1−xInxSb were found to shift to lower energies with increasing In content x. Finally SE has been applied to the analysis of a complete InAs/Ga1−xInxSb SL detector structure.
Electron microscopy studies of ion implanted silicon for seeding electroless copper films
Authors: Muralidhar G. K. , Bhansali S. , Pogany A. , Sood D. K.
Published: July 2002

The feasibility of ion implantation induced electroless copper plating as an effective technique for micro electromechanical systems fabrication was explored by our group recently. This paper aims at investigating such implanted surfaces in order to understand the mechanism assisting the plating. Si was implanted with Pd+ ions at an ion energy of 19 keV in a metal vapour vacuum arc (MEVVA) implanter. The implantation dose ranged between 7×1014 and 2×1017 ions/cm2. The substrates were characterized using scanning electron microscopy (SEM) and transmission electron microscopy (TEM). TEM studies on these substrates indicated that implanted ions tend to form metallic clusters or agglomerates in the substrate. The electroless films nucleate at these clusters. An attempt was made to establish a relationship between implantation dose and cluster size. The topology of the electroless plated films was examined under SEM and the results are discussed in detail.
New method to predict the magnetic properties of thin gauged Si–Fe sheets
Authors: Na J. G. , Park C. H. , Kim J. , Heo N. H. , Lee S. R. , Lee C. S. , Woo J. S.
Published: July 2002

A tertiary crystal growth method was used to fabricate thin gauged 3% Si–Fe sheets in order to reduce the thickness of the sheets without deteriorating soft magnetic properties. During the investigation, the magnetic properties of final annealed sheets were found to be directly related to the magnetic properties of final cold rolled sheets. X-ray and transmission electron microscopy were used to understand the above relation. It was found that the fraction of (110) grains at the surface of the final cold rolled sheets significantly affected the final magnetic properties of the final annealed sheets. On the basis of the above argument, the final magnetic properties of the thin gauged Si–Fe sheets can be predicted by the B10 values of the final cold rolled sheets.
Modified scalar potential solution for three-dimensional magnetostatic problems
Authors: Sivasubramaniam K. , Salon S. , Chari M. V. K. , Mayergoyz I. D.
Published: July 2002

A novel three-dimensional magnetostatic solution based on a modified scalar potential method has been developed. This method has significant advantages over the traditional total scalar, reduced scalar, or vector potential methods. The new method was successfully applied to a three-dimensional geometry of an iron core inductor and a permanent magnet motor. The results obtained are in close agreement with those obtained from traditional methods.
Molecular dynamics simulation of a smectic liquid crystal with atomic detail
Authors: Egberts E. , Berendsen H. J. C.
Published: July 2002

A molecular dynamics simulation of a sodium–decanoate/decanol/water system is reported. The system is treated in full atomic detail, with the exception of CH2 and CH3 groups that are considered to be ‘‘united atoms,’’ and is a refinement of a previous model membrane [Mol. Phys. 11, 1 (1983)]. The long-range Coulomb interactions were included specifically. The order parameters of the chain units of the lipids and diffusion constants of components in the system calculated from the simulation agree well with those reported in experiments on this model membrane. The overall structure of the membrane shows considerable disorder, with a broad lipid–water interface, extending over approximately 1 nm. The distribution of the components is such that an almost complete charge cancellation occurs throughout the system, which is in contradiction with the generally assumed electrical double layer structure for membranes. A counterion condensation of 70% is observed. Both the translational and the rotational motions of water are slowed down compared to bulk water. The penetration of water into the hydrocarbon region of the membrane is substantial. Pair correlations of various atom pairs, and dihedral statistics and transition rates of the dihedrals in the lipids are reported. The distributions of chain segments of the lipids, of water molecules, and of sodium ions are compared with theoretical predictions.
Calculation of scattering wave functions by a numerical procedure based on the Mo/ller wave operator
Authors: Viswanathan Raji , Shi Shenghua , Vilallonga Eduardo , Rabitz Herschel
Published: July 2002

We present a procedure that numerically evaluates the scattering wave function. The solution to the time-independent Schrödinger equation is calculated by a novel combination of: (a) the Mo/ller operator of scattering theory, (b) time-dependent wave packets whose shape is unconstrained, and (c) efficient wave packet propagation on a dynamically-adapted grid. The superposition of packets appropriate to the scattering boundary conditions yields the full wave function, from which scattering amplitudes are then obtained. Since the procedure does not make use of basis-set expansions, its computational cost is independent of the number of open channels. It explicitly calculates the wave function not only in the asymptotic region but also within the interaction region, so it allows one to evaluate additional information beyond the scattering amplitude, as well as the functional sensitivity of transition probabilities with respect to changes in the potential. Applications here are illustrated by two simple examples: one-dimensional tunneling through a potential barrier, and elastic scattering from a one-dimensional periodic surface (i.e., a two-dimensional scattering problem). Extensive applications to imperfect surfaces including sensitivity analysis are separately presented in another article.
A molecular theory of collective orientational relaxation in pure and binary dipolar liquids
Authors: Chandra Amalendu , Bagchi Biman
Published: July 2002

A molecular theory of collective orientational relaxation of dipolar molecules in a dense liquid is presented. Our work is based on a generalized, nonlinear, Smoluchowski equation (GSE) that includes the effects of intermolecular interactions through a mean-field force term. The effects of translational motion of the liquid molecules on the orientational relaxation is also included self-consistently in the GSE. Analytic expressions for the wave-vector-dependent orientational correlation functions are obtained for one component, pure liquid and also for binary mixtures. We find that for a dipolar liquid of spherical molecules, the correlation function φ(k,t) for l=1, where l is the rank of the spherical harmonics, is biexponential. At zero wave-vector, one time constant becomes identical with the dielectric relaxation time of the polar liquid. The second time constant is the longitudinal relaxation time, but the contribution of this second component is small. We find that polar forces do not affect the higher order correlation functions (l>1) of spherical dipolar molecules in a linearized theory. The expression of φ(k,t) for a binary liquid is a sum of four exponential terms. We also find that the wave-vector-dependent relaxation times depend strongly on the microscopic structure of the dense liquid. At intermediate wave vectors, the translational diffusion greatly accelerates the rate of orientational relaxation. The present study indicates that one must pay proper attention to the microscopic structure of the liquid while treating the translational effects. An analysis of the nonlinear terms of the GSE is also presented. An interesting coupling between the number density fluctuation and the orientational fluctuation is uncovered.
How the range of pair interactions governs features of multidimensional potentials
Authors: Braier Paul A. , Berry R. Stephen , Wales David J.
Published: July 2002

By using the pairwise Morse potential as the principle vehicle we have explored the influence of the range of the pair potential on the structure of multidimensional potential-energy surfaces. A scaling relation and a set of reduced units are presented for the homoatomic pairwise-additive Morse potential. The reduced potential has one free parameter, βr0 or ρ0, regulating the range of interaction. Based on several diatomic species, the chemically important range of ρ0 is approximately 2≤ρ0≤7. The number of geometrically distinct minima and transition states depends on ρ0; the larger is ρ0, the narrower is the potential and the greater is the number of geometrically different minima. To illustrate this we found all minima and important low-energy transition states for the Morse six-and seven-particle clusters as functions of ρ0 in its chemically interesting range. From these the dominant mechanisms of isomerization of six- and seven-particle clusters are inferred and compared with experimental and theoretical results for main-group and transition-metal clusters. A nomenclature for saddle points and isomerizations is introduced. The saddle regions of the potentials reveal the dominance of diamond–square–diamond and edge-bridging mechanisms. Knowledge of the stationary points and rearrangement mechanisms allows us to determine the proper molecular symmetry groups and the topologies of the potential-energy surfaces at any arbitrary energy.
Cylindrical manifolds in phase space as mediators of chemical reaction dynamics and kinetics. II. Numerical considerations and applications to models with two degrees of freedom
Authors: De Leon N. , Mehta Manish A. , Topper Robert Q.
Published: July 2002

In Paper I we discussed the existence of cylindrical manifolds embedded in phase space which mediate the dynamics of chemical reactions. A kinetic theory of population decays and decay rate constants was developed which we called ‘‘reactive island’’ (RI) theory. In this paper we discuss the details of the numerical implementation of the theory and then apply it to several molecular models (with two coupled degrees of freedom) representing isomerization between two and three states. Numerical simulations of population decays and asymptotic decay rate constants are compared to the RI theoretical predictions as well as the predictions from the Purely Random Theory (PRT) and Transition State Theory (TST) of reactions. Of the ten systems studied we find that RI theory is generally in good to excellent agreement with the numerical simulations. Only one system exhibits significant deviation between the RI and numerical results. This deviation is seen to be a result of a strong intraconformer dynamical bottleneck. Finally, we compare the theoretical prediction and the numerical simulation for the average n-map mapping time Trxn and find that the agreement, within numerical error, is exact irrespective of the character of the dynamics (i.e., chaotic or regular).
Modeling side chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations
Authors: Roitberg Adrian , Elber Ron
Published: July 2002

A new optimization protocol is proposed which is based on a combination of a mean field approximation and simulated annealing. Instead of optimizing the energy of the real system the energy of a new mean field system is minimized. The global minimum of the new system and the original system is the same. The mean-field optimization is advantageous to the optimization of the real system since (a) More statistics are obtained for alternative solutions and (b) the barrier heights separating the minima are reduced compared to the real system. Computational examples are provided for placement of side chains in tetrapeptides and in a small protein BPTI.
Kinetics and thermodynamics of the reaction SF6⇄SF5+F
Authors: Tsang Wing , Herron John T.
Published: July 2002

A reanalysis of most of the existing data bearing on the strength of the S–F bond in SF6 does not support the generally accepted value of BDE(SF5–F)=390.8±15.1 kJ mol−1 at 298 K. Instead, a new value of BDE(SF5–F)=420±10 kJ mol−1 at 298 K is shown to be compatible with all the existing data. This conclusion is based on a critical examination of earlier shock-tube data on the thermal decomposition of SF6, recent measurements of the rate constant for the reverse reaction, F+SF5, various experiments on ion thermodynamics and photoionization energetics, and studies of the chemiluminescent reactions of Ca and Sr atoms. As a consequence of the present analysis, we find that the rate expressions for SF6 decomposition and the reverse combination rate expressions (at the high pressure limit) are k(SF6→SF5+F)=1.7×1022(1/T)1.9 exp(−50 800/T)s−1, k(SF5+F→SF6)=1×10−11(T/300)−1 cm3 molecule−1 s−1 and the step-size down for collisions of argon with SF6, in the temperature range 1700–2000 K, is about 400 cm−1. We are also able to derive a new value for the appearance energy of SF+5 from SF6 of 14.0 eV, and a new value for ΔfH(SF4)=−746±12 kJ mol−1.
Ab initio calculation of the deuterium quadrupole coupling in liquid water
Authors: Eggenberger Rolf , Gerber Stefan , Huber Hanspeter , Searles Debra , Welker Marc
Published: July 2002

The quadrupole coupling constant and asymmetry parameter for the deuteron in liquid heavy water was determined using purely theoretical methods. Molecular-dynamics simulations with the ab initio potential-energy surface of Lie and Clementi were used to generate snapshots of the liquid. The electric-field gradient at the deuteron was then calculated for these configurations and averaged to obtain the liquid quadrupole coupling constant. At 300 K a quadrupole coupling constant of 256±5 kHz and an asymmetry parameter of 0.164±0.003 were obtained. The temperature dependence of the quadrupole coupling constant was investigated.
Absolute classical densities of states for very anharmonic systems and applications to the evaporation of rare gas clusters
Authors: Weerasinghe Samantha , Amar François G.
Published: July 2002

We have simulated the cluster dissociation reaction Arn→Arn−1+Ar (12≤n≤14) using molecular dynamics (MD) with well defined internal energy and total angular momentum. Reaction rates and kinetic energy release distributions are compared to the predictions of several statistical theories: Rice, Ramsperger, and Kassel (RRK), Engelking, and phase space theory (PST). We employ the Nosé prescription for constant temperature dynamics coupled with the multiple histogram method of Labastie and Whetten to obtain highly accurate vibrational densities of states for the clusters. The absolute densities are determined by the adiabatic switching method of Reinhardt. Incorporation of these accurate anharmonic vibrational densities of states into classical PST allows us to make a direct comparison with the simulation results and eliminates any parameters from the theory. Then PST predictions for the kinetics of evaporation are given for the low energy (long time scale) regime where MD simulations are prohibitively expensive. A critical evaluation of the approximate statistical theories is presented.
A comparative pressure tuning hole burning study of protoporphyrin IX in myoglobin and in a glassy host
Authors: Gafert J. , Friedrich J. , Parak F.
Published: July 2002

We measured the behavior of spectral holes under isotropic pressure changes as a function of burn frequency. We compared a protein sample, namely protoporphyrin IX substituted myoglobin in a glycerol/water glass with a sample where the protoporphyrin IX was directly dissolved in a host glass. The differences are remarkable—holes in the pure glass behave as expected for a homogeneous isotropic material. It is the nonlinear frequency dependence of the pressure shift where the deviation of the protein sample is most obvious. These observations signal a correlation between the structures of the dye probe and the structures of the apoprotein. They further show that global parameters of the apoprotein, such as the isothermal compressibility, depend strongly on the associated conformational substates and are subject to unexpected large variations.
Structural modifications in the amino acid lysine induced by soft x-ray irradiation
Authors: Bozack M. J. , Zhou Y. , Worley S. D.
Published: July 2002

The amino acid DL-lysine has been investigated using the surface-sensitive probe XPS (x-ray photoelectron spectroscopy). The XPS data confirm that solid-state lysine exists in the zwitterionic form. However, during the course of x-ray irradiation in the experiment, the molecule was observed to decompose. A decomposition mechanism consistent with the data has been proposed which involves transformation of the zwitterion to a free base, followed by decarboxylation, to produce 1,5-diaminopentane and CO2 gas. It would appear that caution should be exerted when studying amino acids using XPS if long x-ray irradiation times are employed.
Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations
Authors: Abkevich V. I. , Gutin A. M. , Shakhnovich E. I.
Published: July 2002

The implications of thermodynamics of heteropolymers for their folding kinetics are formulated and discussed. The predictions are tested by Monte Carlo simulation of folding of a lattice model 36-monomer proteins at different temperatures. Using a simulated annealing procedure in sequence space, a number of sequences are designed which have sufficiently low energy in a given target conformation. This conformation plays a role of the native structure for the model proteins. The folding transition is found to be cooperative, and the nature of the free energy barrier is studied. At high temperature the barrier is entropic, and at low temperature it is mainly energetic. This can be explained by transformation of the early partly folded intermediate from the disordered state (belonging to the quasicontinuous part of the energy spectrum) at high temperature to the non-native low-energy frozen conformation at low temperature. The latter plays a role of an off-pathway trap. A parallel folding process has been detected at low temperature where direct folding competes with relaxation of the intermediate. The frozen intermediate must unfold to make it possible to form a folding nucleus, which is the prerequisite of subsequent fast descent to the native state.
Textures and phase transitions in Langmuir monolayers of fatty acids. A comparative Brewster angle microscope and polarized fluorescence microscope study
Authors: Rivière S. , Hénon S. , Meunier J. , Schwartz D. K. , Tsao M.-W. , Knobler C. M.
Published: July 2002

Brewster angle microscopy (BAM) and polarized fluorescence microscopy (PFM) are used to observe the distinctive textures of and the transitions between condensed phases in Langmuir monolayers of n-alkanoic acids. BAM is sensitive to film anisotropy even when the molecules are not tilted as long as the unit cell is anisotropic. Every transition is visible with one or both of the techniques, either as a dramatic change in the degree of contrast or as a sudden alteration of the mosaic domain texture. The two techniques are generally consistent, although the presence of the fluorescent probe impurity (for PFM) causes a subtle difference in the appearance of one transition and small shifts in transition surface pressures.
Chain desorption from a semidilute polymer brush: A Monte Carlo simulation
Authors: Wittmer J. , Johner A. , Joanny J. F. , Binder K.
Published: July 2002

We discuss the dynamic properties of a semidilute grafted polymer layer exposed to pure solvent. When the grafting energy of the head groups of the chains is finite, the chains desorb and are expelled from the layer. We combine Monte Carlo simulations using the bond fluctuation model to self-consistent mean field calculations and a scaling analysis. Chain desorption can be seen as a two step process. For strongly grafted polymers the limiting step is the desorption of the head group. The chain is then expelled by the osmotic pressure gradient. A chain cut off the wall is expelled at a constant velocity of its center of mass. The velocity decreases as the inverse of the molecular weight and increases with the grafting density. In the early stages of the expulsion the tension of the monomers close to the wall relaxes and the chain retracts. The retraction is independent of the molecular weight. Our most important result is that the desorption of the head group is a local process with a characteristic time independent of molecular weight. The desorption time increases exponentially with the grafting energy, it decreases as a power law of the grafting density. The exponent is close to 2 but the precise value is difficult to extract from the simulation.
Impact of global interaction on pattern formation on a disk
Authors: Middya Usuf , Luss Dan
Published: July 2002

Global interaction introduces a new mode of communication among all surface elements and may lead to the formation of a very rich variety of spatiotemporal patterns on a disk some of which cannot exist in its absence. While some of the motions on a disk are analogous to those observed in one-dimensional systems, some, such as targets and spirals, exist only in two-dimensional systems. The global interaction stabilizes motions such as target patterns, which are not stable in its absence. It may, however, destabilize the spiral motion and cause the spiral tip to meander in a rather complex fashion and in some cases to exit the disk. The global interaction also increases the sensitivity of the system to the initial conditions so that qualitatively different patterns may be obtained when different initial conditions are used.
Isomer specific evaporation rates: The case of aniline–Ar2
Authors: Parneix Pascal , Bréchignac Philippe , Amar François G.
Published: July 2002

This paper reports the results of molecular dynamics (MD) simulations of isomerization and evaporation processes of the aniline–Ar2 cluster. The trajectory results are analyzed in terms of a simple unimolecular kinetics scheme in order to extract isomer-specific evaporation rate constants. The less stable isomer, denoted (2/0) is found to have an evaporation rate constant that is about 25% smaller than that for the more stable isomer, (1/1). This result is explained in terms of the densities of states associated with each isomer. We present preliminary results on the aniline–Ar3 cluster and connect this latter system to possible experiments.
Nonergodicity and two subphases in the coexistence region in isomerization dynamics of Ar7-like molecules
Authors: Seko Chihiro , Takatsuka Kazuo
Published: July 2002

It is well-known that a single cluster like Ar7 undergoes ‘‘melting’’ from solidlike to liquidlike states as the energy is increased, the transition of which is not as sudden as the ordinary phase transition though and has a somewhat broad energy range in which solid and liquid coexist. We study a very anomalous dynamics of the coexistence region in the structural isomerization. It is explicitly shown that the time-series of the structural changes both in the purely solidlike and liquidlike phases are stationary, while the coexistence region is found to generate a strongly nonstationary dynamics. The calculated distribution of the residing times for the cluster to stay in one of the possible structures exhibits a nonexponential form having a large hole around the zero lifetime in the coexistence region. Motivated by these strange behaviors, we have calculated the phase-space volumes that are assigned to the individual potential basins, and verified directly that while the pure liquid region is of ergodic nature, the dynamics in the coexistence region is indeed strongly nonergodic. The steep rises of the Lindemann index and the maximum Liapunov exponent in the coexistence region, which were reported before by other authors, are found to be ascribed to the statistical nature rather than the dynamical properties as opposed to the picture suggested by the physical meaning of the indices. It also turns out that the energy range for the coexistence region should be taken wider than considered before and thus extends beyond the ‘‘melting point’’ that is defined usually on the basis of the Lindemann index. Therefore it is appropriate to divide the coexistence region into two subphases. A ‘‘temperature’’ in a microcanonical ensemble is defined so as to characterize the distribution of phase-space volume on a given energy plane. Based on this distribution, we describe a statistical reason why the onset energy of the melting is much higher than those of the transition states.
The reaction between N(4S) and C2H3: Rate constant and primary reaction channels
Authors: Payne Walter A. , Monks Paul S. , Nesbitt Fred L. , Stief Louis J.
Published: July 2002

The rate constant and the product branching ratios have been determined at T=298 K for the reaction between ground state atomic nitrogen (4S) and the vinyl radical (C2H3) at a nominal pressure of 1 Torr He. The kinetic technique employed was discharge-flow coupled to a collision-free sampling mass spectrometer. The rate constant was determined by monitoring the decay of the vinyl radical in the presence of excess [N], yielding a value for k(N+C2H3) of (7.7±2.9)×10−11 cm3 molecule−1 s−1. Three primary reaction channels have been experimentally observed: N+C2H3→C2H2+NH (1a), C2H2N+H (1b), and C2H3N (1c). The lowest energy isomers of the C2H2N radical and the C2H3N adduct molecule are CH2CN and CH3CN, respectively and their identification as products of the reaction is consistent with experimental results. Contributions from the higher energy isomers CH2NC or cyc-C2H2N in channel (1b) and CH3NC or H2C=C=NH in channel (1c) are not consistent with the experimental results and can be ruled out. Contribution from other higher energy isomers such as the radicals HC–CH=N, HC=C=NH and H2C=C=N in channel (1b) and the adduct species vinyl nitrene and 2H-azirine in channel (1c) cannot be ruled out in the absence of knowledge of heats of formation of the radical species and ionization energies for both the radical and adduct species. The following branching ratios were determined at T=298 K: Γ1a=0.16, Γ1c=0.04. No other potential products were detected. It can therefore be inferred that channel (1b) accounts for most if not all of the remaining products, i.e., Γ1b=0.80. The magnitude of the rate constant and the nature of the observed products for N+C2H3 are compared with those for the reactions N+CH3 and N+C2H5. The formation of the adduct molecule is considered in terms of initial formation of vinyl nitrene or 2H-azirine followed by a series of ring openings, ring closings, and an H atom transfer to yield the lowest energy isomer acetonitrile, CH3CN. The possible role of the N+C2H3 reaction in the atmospheric chemistry of Titan, Neptune, and Triton is briefly considered.
Ionic mobility in alcohols: From dielectric friction to the solvent–berg model
Authors: Biswas Ranjit , Bagchi Biman
Published: July 2002

A self-consistent microscopic theory is used to calculate the mobility of rigid univalent ions in methanol, ethanol, and propanol at room temperature. The theoretical predictions are in good agreement with the long-known experimental results. In particular, the theory reproduces the nonmonotonic size dependence of the limiting ionic conductance accurately. The relation between the polar solvation dynamics of an ion and its mobility is clarified. The theory also explains how a dynamical version of the classical solvent–berg model can be recovered for small ions in the limit of slow liquids.
Structural changes of the molecular complexes of pyridines with water and demixing phenomena in aqueous solutions
Authors: Brovchenko Ivan V. , Oleinikova Alla V.
Published: July 2002

Demixing phenomena in the aqueous solutions of organic molecules are considered due to the temperature induced structural changes of the hydrogen bonds between water and organic molecules. The lower and upper critical solution points are attributed to the appearance of the “critical” concentration of the complexes with one hydrogen bond between a single water molecule and single solute molecule. Namely, the hydrogen bonded pair complexes are responsible for the formation of the strongly associated water clusters around solute molecules that may be followed by separation of the homogeneous solution on water-rich and organic-rich phases. The extension of the immiscibility gap upon strengthening of the hydrogen bonds between water and pyridine is obtained. Experimentally observed changes of the lower and upper critical solution temperatures upon the deuteration of water, addition of salts, and presence of the alkyl substituents in the solute pyridine molecules are well reproduced in the framework of the proposed model.
From hydrophobic to hydrophilic behaviour: A simulation study of solvation entropy and free energy of simple solutes
Authors: Lynden-Bell R. M. , Rasaiah J. C.
Published: July 2002

We describe atomistic simulations of the free energy and entropy of hydration of ions in aqueous solution at 25 °C using a simple point charge model (SPC/E) for water and charged spherical Lennard-Jones solutes. We use a novel method with an extended Lagrangian or Hamiltonian in which the charge and the size of the ions are considered as dynamical variables. This enables us to determine thermodynamic properties as continuous functions of solute size and charge and to move smoothly from hydrophilic to hydrophobic solvation conditions. On passing between these extremes, the entropy of solvation goes through maxima. For example it shows a double maximum as a function of charge at constant size and a single maximum as a function of size at constant (non-zero) charge. These maxima correspond to extremes of structure-breaking and are associated with the disappearance of the second solvation shell in the radial distribution function; no anomalies are seen in the first shell. We also present direct evidence of the asymmetry in the free energy, enthalpy and entropy of hydration of ions on charge inversion arising from the asymmetry in the charge distribution in a water molecule. Our calculation only includes local contributions to the thermodynamic functions, but once finite size corrections are applied, the results are in reasonable agreement with experiment.
Layer-by-layer homoepitaxial growth process of MgO(001) as investigated by molecular dynamics, density functional theory, and computer graphics
Authors: Kubo Momoji , Oumi Yasunori , Miura Ryuji , Fahmi Adil , Stirling Andras , Miyamoto Akira , Kawasaki Masashi , Yoshimoto Mamoru , Koinuma Hideomi
Published: July 2002

We applied molecular dynamics, density functional theory, and computer graphics techniques to the investigation of the homoepitaxial growth process of the MgO(001) surface. MgO molecules are deposited over the MgO(001) plane one by one at regular time intervals with definite velocities. Any deposited MgO molecule migrated on the surface, and later a two-dimensional and epitaxial growth of MgO thin layer was observed at 300 K which is in agreement with the experimental result. However, some defects were constructed in the grown film at low temperature of 300 K, which is in remarkable contrast to that at 1000 K. In the latter case, a single flat and smooth MgO layer without defects was formed, which also agreed with the experimental result. Self-diffusion coefficients and activation energy for the surface diffusion of the deposited MgO molecule on the MgO(001) plane were discussed to clarify the temperature-dependency of the epitaxial growth process.
Free energy of hydration of a molecular ionic solute: Tetramethylammonium ion
Authors: Garde Shekhar , Hummer Gerhard , Paulaitis Michael E.
Published: July 2002

We have performed Monte Carlo simulations of the tetramethylammonium ion, hydrated by 256 simple point charge (SPC) water molecules, as a function of total charge on the ion. The total charge was varied between −3e to +3e at intervals of 1e, and was distributed equally on the four methyl sites on the ion. Derivatives of the free energy with respect to charge were related to the fluctuations in the ion–water interaction energies using a cumulant expansion. This derivative information for the different charge states was found to give an accurate description of the free energy of hydration. The calculated hydration free energies were also found to be only weakly dependent on system size and the method used for calculating the electrostatic interactions (Ewald summation or generalized reaction field), when finite system size corrections are applied. The quadratic charge dependence was obtained for the free energy of hydration for both positive and negative ions as expected from the Born model. The hydration is, however, asymmetric. Negative ions are more favorably hydrated compared to positive ions. We relate this asymmetry of hydration to water structure; that is, to differences in the water oxygen and water hydrogen density profiles surrounding positive and negative ions. Another manifestation of this asymmetry is seen in the positive electrostatic potential at the center of methyl sites in the uncharged state of the tetramethylammonium solute.
Molecular tailoring of thermoreversible copolymer gels: Some new mechanistic insights
Authors: Badiger M. V. , Lele A. K. , Bhalerao V. S. , Varghese S. , Mashelkar R. A.
Published: July 2002

We earlier reported the role of hydrophobic and hydrogen bonding interactions on the transition temperatures of thermoreversible copolymer gels. We show here that the chemical structure of the hydrophobe and its concentration determine the transition temperatures [lower critical solution temperature (LCST)] and the heat of transition of new hydrophobically modified poly(N-isopropyl acrylamide) [PNIPAm] copolymer gels. The gels, prepared by copolymerizing NIPAm monomer with hydrophobic comonomers containing increasing lengths of alkyl side groups and a terminal carboxyl acid group, showed lower LCST and lower heat of transition when compared to pure PNIPAm gel. The experimental results were also compared with theoretical calculations based on a lattice-fluid-hydrogen-bond [LFHB] model. We show experimentally and theoretically that a linear correlation exists between the transition temperature and length of the hydrophobic alkyl side group. Also, in apparent contradiction to previous work, we found a reduction in the heat of transition with increasing hydrophobicity. We propose that the presence of the terminal carboxyl acid group on the hydrophobic side chain of the comonomer prevents the association of water molecules around the hydrophobe, thereby causing a reduction in the heat of transition. The LFHB model supports this argument.