Realistic Energies Research Articles

Study of fragmentation using clusterization algorithm with realistic binding energies

We here study fragmentation using a simulated annealing clusterization algorithm (SACA) with binding energy at a microscopic level. In an earlier version, a constant binding energy (4 MeV/nucleon) was used. We improve this binding energy criterion by calculating the binding energy of different clusters using a modified Bethe–Weizsäcker mass (BWM) formula. We also compare our calculations with experimental data of the ALADiN group. Nearly no effect of this modification is visible.

Theoretical study of PTCDA adsorbed on the coinage metal surfaces, Ag(111), Au(111) and Cu(111)

A thorough understanding of the adsorption of molecules on metallic surfaces is a crucial prerequisite for the development and improvement of functionalized materials. A prominent representative within the class of π-conjugated molecules is 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) which, adsorbed on the Ag(111), Au(111) or Cu(111) surfaces, shows characteristic trends for work-function modification, alignment of molecular levels with the substrate Fermi energy and binding distances. We carried out density functional theory (DFT) calculations to investigate to what extent these trends can be rationalized on a theoretical basis. We used different density functionals (DF) including a fully non-local van der Waals (vdW) DF capable of describing dispersion interactions. We show that, rather independent of the DF, the calculations yield level alignments and work-function modifications consistent with ultra-violet photoelectron spectroscopy when the monolayer is placed onto the surfaces at the experimental distances (as determined from x-ray standing wave experiments). The lowest unoccupied molecular orbital is occupied on the Ag and Cu surfaces, whereas it remains unoccupied on the Au surface. Simultaneously, the work function increases for Ag but decreases for Cu and Au. Adsorption distances and energies, on the other hand, depend very sensitively on the choice of the DF. While calculations in the local density approximation bind the monolayer consistently with the experimental trends, the generalized gradient approximation in several flavors fails to reproduce realistic distances and energies. Calculations employing the vdW-DF reveal that substantial bonding contributions arise from dispersive interactions. They yield reasonable binding energies but larger binding distances than the experiments.

Thermal-Diffusive Instability of Premixed Flames for a Simple Chain-Branching Chemistry Model with Finite Activation Energy

A linear stability of freely propagating, adiabatic premixed flames is investigated in the context of a thermal-diffusive or constant density model, together with a simple two-step chain-branching model of the chemistry. This study considers the case of realistic, finite activation energy of the chain-branching step, and emphasis is on comparing with previous high activation energy asymptotic results. It is found that for realistic activation energies, a pulsating instability is absent in regimes predicted to be unstable by the asymptotic analysis. For the cellular instability, however, the finite activation energy results are in qualitative agreement with the asymptotic results, in that the flame is unstable only below a critical Lewis number of the fuel and becomes more unstable as the Lewis number is decreased. However, it is shown that very high activation energies would be required for the asymptotic analysis to be quantitatively predictive. The flame is less unstable for finite activation energies t...

Mechanism of Superconductivity in Quasi-Two-Dimensional Organic Conductor β-(BDA-TTP) Salts

We investigate theoretically the superconductivity of two-dimensional organic conductors, β-(BDA-TTP) 2 SbF 6 and β-(BDA-TTP) 2 AsF 6 , to understand the role of the spin and charge fluctuations. The transition temperature is estimated by applying random phase approximation to an extended Hubbard model wherein realistic transfer energies are estimated by extended Huckel calculation. We find a gapless superconducting state with a d x y -like symmetry, which is consistent with the experimental results obtained by specific heat and scanning tunneling microscope. In the present model with an effectively half-filled triangular lattice, spin fluctuation competes with charge fluctuation as a mechanism of pairing interaction since both fluctuations have the same characteristic momentum q =(π,0) for V being smaller than U . This is in contrast to a model with a quarter-filled square lattice, wherein both fluctuations contribute cooperatively to pairing interaction due to fluctuations having different characteristi...

Numerical study of steady state melting of a binary alloy

Using an extension of a recently developed model describing phase transformations based on a sharp interface [M. Buchmann, M. Rettenmayr, Scripta Mater. 57 (2007) 169], steady-state melting of an Al–Cu alloy is numerically modelled. The conditions are varied such that the ‘contact conditions’ range from local equilibrium to pronounced deviations thereof, corresponding to ‘solute trapping’ conditions during solidification. The rigorously derived model that includes realistic free energies ensures physical consistency and allows for the treatment of non-ideal systems. Aspects of the asymmetry between melting and solidification become apparent in the contact conditions, i.e. the concentrations at the interface in the liquid and solid phase, respectively, at elevated velocities.

Chemisorbed and Physisorbed Structures for 1,10-Phenanthroline and Dipyrido[3,2-a:2‘,3‘-c]phenazine on Au(111)

Scanning tunneling microscopy (STM) images of 1,10-phenanthroline (PHEN) and dipyrido[3,2-a:2‘,3‘-c]phenazine (DPPZ) on Au(111) are recorded using both in situ and ex situ techniques. The images of PHEN depict regimes of physisorption and chemisorption, whereas DPPZ is only physisorbed. All physisorbed structures are not pitted and fluctuate dynamically, involving aligned (4 × 4) surface domains with short-range (ca. 20 molecules) order for PHEN but unaligned chains with medium-range (ca. 100 molecules) order for DPPZ. In contrast, the chemisorbed PHEN monolayers remain stable for days, are associated with surface pitting, and form a (4 × √13)R46° lattice with long-range order. The density of pitted atoms on large gold terraces is shown to match the density of chemisorbed molecules, suggesting that gold adatoms link PHEN to the surface. For PHEN, chemisorbed and physisorbed adsorbate structures are optimized using plane-wave density-functional theory (DFT) calculations for the surface structure. Realistic binding energies are then obtained adding dispersive corrections determined using complete-active-space self-consistent field calculations using second-order perturbation theory (CASPT2) applied to cluster-interaction models. A fine balance between the large adsorbate−adsorbate dispersive forces, adsorbate−surface dispersive forces, gold ligation energy, and surface mining energy is shown to dictate the observed phenomena, leading to high surface mobility and substrate/surface lattice incommensurability. Increasing the magnitude of the dispersive forces through use of DPPZ, rather than PHEN, to disturb this balance produced physisorbed monolayers without pits and/or surface registration but with much longer-range order. Analogies are drawn with similar but poorly understood processes involved in the binding of thiols to Au(111).

Non-equilibrium transients during solidification – A numerical study

In an extension of a recently developed model [M. Buchmann, M. Rettenmayr, Scripta Mater. 57 (2007) 169] non-equilibrium transients during solidification of a binary metal alloy are studied. Interface velocity and interface concentrations are calculated during the transient towards interface equilibrium in an undercooled alloy. The rigorously derived model includes realistic free energies and real concentration gradients in both phases. The evolution of the interface concentrations and velocity is modelled as a function of the initial driving force on the phase boundary. The time necessary for re-equilibration of the interface is quantified.

Theoretical analysis of breakdown probabilities and jitter in single-photon avalanche diodes

A simple random ionization path length model is used to investigate the breakdown probabilities and jitter in single photon avalanche diodes (SPADs) with submicron multiplication widths. The simulation results show that increasing the multiplication width may not necessarily increase the breakdown probability relative to the breakdown voltage, as the effect of dead space becomes more dominant in thinner multiplication regions at realistic ionization threshold energies for GaAs. On the other hand, reducing the multiplication width results in smaller breakdown time and jitter, despite the increased dead space. The effect of dead space in degrading breakdown time and jitter is relatively weak and further compensated by the stronger influence of large feedback ionization at high fields. Thus, SPAD designs that can minimize the dark count rate may potentially benefit from enhanced breakdown probability, breakdown time, and jitter by reducing the thickness of the multiplication region.

Rapid solidification theory revisited – A consistent model based on a sharp interface

Based on recent progress in the thermodynamics of migrating interfaces, the contact conditions (equilibrium concentrations and deviations thereof) at a solid/liquid interface during rapid solidification are modelled numerically. Possible interface concentrations are calculated as a function of interface velocity. Two processes are assumed to dissipate Gibbs Free Energy: the migration of the interface and the redistribution of solute atoms across the interface. Predicted interface concentrations are in reasonable agreement with available experimental data and earlier models. The rigorously derived model that includes realistic free energies ensures physical consistency and allows for the treatment of non-ideal systems.

Elasticity ofα-Helical Coiled Coils

Predicting large scale conformations of protein structures is computationally demanding. Here we compute the conformation and elasticity of double-stranded coiled coils using a simple coarse-grained elastic model. By maximizing the contact between hydrophobic residues and minimizing the elastic energy, we show that the minimum energy structure of a coiled coil is a supercoiled double helix of alpha helices. For realistic binding energies, the elastic energy of the alpha helices requires binding every 7th residue, which leads to a pitch and helix angle for the structure that is consistent with experimental measurements. Analysis of the model equations shows how the pitch varies with the helical repeat of the hydrophobic residues and with the ratio of the twisting modulus to the bending modulus and provides an estimate of the persistence length of around 150 nm, in agreement with previous experimental estimates.

Ionic dimers in He droplets: Interaction potentials for Li2+–He,Na2+–He, and K2+–He and stability of the smaller clusters

We present post Hartree-Fock calculations of the potential energy surfaces (PESs) for the ground electronic states of the three alkali dimer ions Li(2) (+),Na(2) (+), and K(2) (+) interacting with neutral helium. The calculations were carried out for the frozen molecular equilibrium geometries and for an extensive range of the remaining two Jacobi coordinates, R and theta, for which a total of about 1000 points is generated for each surface. The corresponding raw data were then fitted numerically to produce analytic expressions for the three PESs, which were in turn employed to evaluate the bound states of the three trimers for their J=0 configurations: The final spatial features of such bound states are also discussed in detail. The possible behavior of additional systems with more helium atoms surrounding the ionic dopants is gleaned from further calculations on the structural stability of aggregates with up to six He atoms. The validity of a sum-of-potential approximation to yield realistic total energies of the smaller cluster is briefly discussed vis-a-vis the results from many-body calculations.

Partition function and base pairing probabilities of RNA heterodimers.

BackgroundRNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms.MethodsThe standard dynamic programming algorithms for computing secondary structures of linear single-stranded RNA molecules are extended to the co-folding of two interacting RNAs.ResultsWe present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures.AvailabilityRNAcofold is distributed as part of the Vienna RNA Package, .ContactStephan H. Bernhart – berni@tbi.univie.ac.at

Unified kinetic model of dopant segregation during vapor-phase growth

We develop a unified kinetic model for surface segregation during vapor phase growth that concisely and quantitatively describes the observed behavior in silicon-based systems. A simple analytic function for the segregation length is derived by treating terrace-mediated and step-edge-mediated mechanisms in parallel. The predicted behavior of this parameter is examined through its temperature, flux, and terrace length dependence. Six distinct temperature regimes are predicted for the segregation length that depend on the relative segregation energies and activation barriers of the two mechanisms. The model is compared to reported behavior of Sb and P in Si(001) and excellent agreement is obtained using realistic energies and preexponential factors. The model accounts for the experimentally observed anomalous low-temperature segregation of Sb as a consequence of the competition between step-edge-mediated segregation, dominant at low temperatures, and terrace-mediated segregation, dominant at higher temperatures. The generalized treatment of segregation mechanisms in the model makes it applicable to other segregating systems, including metals and III-V semiconductors.

Generalizing the MTF and DQE to include x-ray scatter and focal spot unsharpness: Application to a new microangiographic system

Detector characterization with modulation transfer function (MTF) and detective quantum efficiency (DQE) inadequately predicts image quality when the imaging system includes focal spot unsharpness and patient scatter. The concepts of MTF, noise power spectrum, noise equivalent quanta and DQE were referenced to the object plane and generalized to include the effect of geometric unsharpness due to the finite size of the focal spot and the effect of the spatial distribution and magnitude of x-ray scatter due to the patient. The generalized quantities provide performance characteristics that consider the complete imaging system, but reduce to a description of the detector properties without magnification or scatter. We have evaluated a new neurovascular angiography imaging system based on a region of interest (ROI) microangiographic detector using these generalized quantities. A uniform head-equivalent phantom was used as a filter and x-ray scatter source. This allowed the study of all properties of the detector under clinically relevant x-ray spectra and x-ray scatter conditions. Realistic focal spots (0.8 mm nominal), beam energies (60-100 kVp), and detector exposures (0.8-2.3 mR) were used, and the effects of different scatter fractions (0-0.62) resulting from changing the beam size (0-100 cm2) were investigated. The generalized MTF and DQE were found to have very little dependence on the tube voltage and the detector entrance exposure. Magnification, with the focal spot used, results in a large decrease of the generalized DQE at higher frequencies (about 100-fold at 10 cycles/mm), but a significantly smaller decrease at lower frequencies. Scatter on the other hand, causes a constant drop in the generalized DQE (factor of 3 for scatter fraction 0.3) for all frequencies. Our results show that there are tradeoffs in the choice of the different system parameters; therefore this methodology of studying the imaging system as a whole could provide guidance in system design.

Three model-Free methods for calculation of activation energy in TG

Two well-known isoconversion methods, the first one developed by Ozawa-Flynn-Wall and the second one developed by Friedman, are confronted with calculations made using modulated thermogravimetry (MTG). The latter variant is free from a number of assumptions and restrictions made in the isoconversion computations. In particular, it allows the use of a single decomposition curve and it remains in force even in the case of multistage decomposition with conjugated processes. To obtain the model-fitting methods from the model-free methods one should replace some functions averaged over isoconversion levels by the functions calculated on the basis of kinetic models. In the Ozawa-Flynn-Wall method it is the averaged reduced time (integral of Arrhenius exponential over time). In the method of Friedman it is the averaged differential conversion function. In MTG, the perturbations caused by the sinusoidal temperature modulation are connected with derivatives of mass loss by simple scaling, where activation energy plays a role of a scaling parameter. The ratio of the experimentally measured perturbations to the experimental derivative is used for the model-free computation of activation energy. If a theoretical derivative replaces the experimental one, this procedure leads to the model-fitting method. Even a rough approximation of the experimental derivative should not lead to an excessive error in activation energy. If in a vicinity of peaks' maxima in derivatives of mass loss the decomposition is controlled by single rate-limiting processes, modulated thermogravimetry should give realistic activation energies for these processes. Inasmuch as the results of MTG are weakly sensitive to selection of kinetic models, this method should have a high predictive force.

A Visco-Hypoplastic Constitutive Relation for Soft Soils

ABSTRACT Soils with soft angular particles are markedly viscoplastic. For constitutive modelling with hypoplasticity, the granulate hardness is replaced by a rate-dependent (argotropic) solid hardness hs. Use is made of the viscosity index IV. The state limits of isotropic compression, stationary shearing (critical state) and cyclic shearing are thus argotropic. They are asymptotic solutions of the proposed visco-hypoplastic relation, the core of which is a viscosity factor fv depending on an overconsolidation ratio pe/p’. It resembles a theory by Niemunis (1996), but has a wider variety of asymptotic solutions (attractors). For constant effective stress, the familiar volumetric creep is obtained, and a dependency of strain rate ratio on stress ratio as observed. The response to strain rate jumps is obtained realistically, and also the relaxation. The material parameters can be easily determined from standard tests and estimated from index tests. Further explanation is given with a back analysis of Henkel’s (1956) triaxial test results. Deviations are due to non-uniform sample deformations. Peak stress conditions are derived from instantaneous state values including strain rate. Extensions are briefly outlined: tensorial formulation, intergranular strain and polar terms. The microphysical background is explained with Persson’s (2000) theory of thermally activated shear melting. Realistic dislocation energies are thus obtained from observed Iv values.

Combined energy–diffraction data refinement of decagonal AlNiCo

We incorporate realistic pair-potential energies directly into a non-linear least-square fit of diffraction data to quantitatively compare structure models with experimental data for the Ni-rich d(AlNiCo) quasicrystal. The initial structure models are derived from a few a priori assumptions (gross features of the Patterson function) and the pair-potentials. In place of the common hyperspace approach to the structure refinement of quasicrystals, we use a real-space tile-decoration scheme, which does not rely on strict quasiperiodicity, and makes it easy to enforce sensible local arrangements of the atoms. Inclusion of the energies provides information complementary to the diffraction data and protects the fit procedure from converging on spurious solutions. The method pinpoints sites that are likely to break the symmetry of their local environment.

Atomic-scale modelling of primary damage and properties of radiation defects in metals

Considerable success has been achieved in recent years in the understanding of radiation damage production in high-energy displacement cascades, the properties of the defects and evolution of radiation damage in metals. Two main reasons form the basis of this success. First, the significant increase in computing power has allowed simulation of realistic cascade energies with good statistics and relatively long-time evolution of defects to be carried out. Second, new experimental findings and corresponding theoretical calculations have allowed interpretation of a number of mechanisms and phenomena crucial for understanding and prediction of practically important radiation effects, such as void swelling, radiation growth, matrix hardening and plastic flow localisation. In this paper we review the most significant results in atomic-scale computer modelling related to these issues, mainly focusing on new achievements such as the formation of extended defect clusters, the dynamic properties of defect clusters, interaction between radiation defects and strengthening of material due to radiation defects.

Limited conductivity in an octagonal quasicrystal

Conductivity of an s-band model on the octagonal tiling is studied. Using perturbation theory it is shown that there is only one channel available for electronic transport, when the kinetic term in the Hamiltonian is small. This feature is independent of the size of the approximant and reveals a microscopic mechanism that is capable of severely limiting conduction processes in a quasicrystal. Numerical evidence indicates that the same result is valid even in case of realistic kinetic energies at some values of the Fermi energy.

Microscopic Description of Odd- and Even-Mass Er Isotopes

The pseudo-SU(3) shell model is used to describe rotational bands and B(E2) electromagnetic transition strengths in the even- and odd-mass rare earth isotopes 164,165,166,167,168Er. The building blocks of the model are the pseudo-SU(3) proton and neutron states with pseudo-spin zero and 1/2, which describe even and odd numbers of nucleons, respectively. The many-particle states are built as linear combinations of pseudo-SU(3) coupled states with well-defined particle number and total angular momentum. The Hamiltonian includes spherical Nilsson single-particle energies, quadrupole—quadrupole and pairing interactions, as well as rotor terms that are diagonal in the SU(3) basis. The use of realistic single-particle energies has a fundamental importance in the appropriate description of odd-mass nuclei.