Quasi-chemical Potential Research Articles

Mechanism of photo-ionic stoichiometry changes in SrTiO3

The impact of UV light (λ = 365 nm) on defect chemistry and composition of undoped SrTiO3 single crystals was investigated by means of impedance spectroscopy. In-plane conductivity measurements between 280 and 450 °C in air reveal a drastic increase of the bulk conductivity upon UV illumination. The measured time dependence of this increase is in accordance with oxygen chemical diffusion in SrTiO3. The corresponding photo-induced change in defect concentrations is caused by oxygen being pumped from the gas phase into the oxide under UV irradiation. This affects the entire SrTiO3 crystal rather than only the thin UV absorption zone and leads to very high oxygen chemical potentials with nominal oxygen pressures up to 106 bar. After switching the UV light off, the resulting conductivity increase relaxes extremely slowly due to slow surface exchange kinetics. A mechanistic model is introduced to explain the impact of UV light on the oxygen chemical potential as well as on the oxygen vacancy and hole/electron concentrations in semiconducting oxides, here SrTiO3. This model is based on the formation of oxygen quasi-chemical potentials in the illuminated region. It is discussed how the interplay of four kinetic parameters causes the observed time-dependent stoichiometry and thus conductivity changes.

DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking

BackgroundProtein-RNA interactions play fundamental roles in many biological processes. Understanding the molecular mechanism of protein-RNA recognition and formation of protein-RNA complexes is a major challenge in structural biology. Unfortunately, the experimental determination of protein-RNA complexes is tedious and difficult, both by X-ray crystallography and NMR. For many interacting proteins and RNAs the individual structures are available, enabling computational prediction of complex structures by computational docking. However, methods for protein-RNA docking remain scarce, in particular in comparison to the numerous methods for protein-protein docking.ResultsWe developed two medium-resolution, knowledge-based potentials for scoring protein-RNA models obtained by docking: the quasi-chemical potential (QUASI-RNP) and the Decoys As the Reference State potential (DARS-RNP). Both potentials use a coarse-grained representation for both RNA and protein molecules and are capable of dealing with RNA structures with posttranscriptionally modified residues. We compared the discriminative power of DARS-RNP and QUASI-RNP for selecting rigid-body docking poses with the potentials previously developed by the Varani and Fernandez groups.ConclusionsIn both bound and unbound docking tests, DARS-RNP showed the highest ability to identify native-like structures. Python implementations of DARS-RNP and QUASI-RNP are freely available for download at http://iimcb.genesilico.pl/RNP/

Optical properties of III-nitrides in electric fields

The influence of intermediate to high electric fields on the optical properties of direct-gap strongly-polar III-Nitrides is characterized. It is manifested through the dependence on the electric field of the nonequilibrium thermodynamic state of the system, which is characterized by a nonequilibrium effective temperature (quasi-temperature), quasi-chemical potentials and drift velocities of the excited carriers driven away from equilibrium, and the quasi-temperatures of the phonons in the different branches. In particular, we analyze the processes of absorption and luminescence, and a field-dependent Roosbroeck-Shockley relation is derived. It is shown that it is possible to measure the carriers’ drift velocity and quasi-temperature, in the steady state or with ultrafast time resolution, resorting to luminescence together with Raman scattering experiments.

Analysis of effective spin-polarized transport through a ZnO based magnetic p–n junction at room temperature

ZnO based magnetic semiconductors (MSs) are prominent candidates for the spintronic devices because of their high Curie temperatures and low conductance mismatches. In this paper the spin-polarized transport in MS/nonmagnetic semiconductor (NMS) p–n junction is investigated. A model is established based on semiconductor drift–diffusion theory and continuity equation. Boundary conditions are obtained from the quasi-chemical potential (QCP) relations at the junction interface. For a ZnO based magnetic p–n junction, we calculate the distributions of carrier/spin density and spin polarization at room temperature. It is demonstrated that by choosing proper parameters, effective spin-polarized injection from ZnO based MS into ZnO can be achieved at room temperature without external spin-polarized injection (ESPI) or large bias.

Theory of the spin‐Hall effect revisited

Utilizing a general and physically well-founded definition of the spin current, we investigate the spin-Hall effect for the two-dimensional linear and cubic Rashba model taking into account short-range elastic scattering on impurities. In the linear response regime, the kinetic equations for the spin-density matrix are analytically solved. There is a close relationship between the spin accumulation and the spin current mediated by a quasi-chemical potential. In contrast to previous findings derived from the conventional definition of the spin current, we obtain the result that in both pure and disordered infinite samples, there is no intrinsic spin-Hall effect. Only an ac electric field can induce a spin-Hall current for the linear and cubic Rashba model. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Theory of electric-field-induced spin accumulation and spin current in the two-dimensional Rashba model

Based on the spin-density-matrix approach, both the electric-field-induced spin accumulation and the spin current are systematically studied for the two-dimensional Rashba model. Eigenmodes of spin excitations give rise to resonances in the frequency domain. Utilizing a general and physically well-founded definition of the spin current, we obtain results that differ remarkably from previous findings. It is shown that there is a close relationship between the spin accumulation and the spin current, which is due to the prescription of a quasi-chemical potential and which does not result from a conservation law. Physical ambiguities are removed that plagued former approaches with respect to a spin-Hall current that is independent of the electric field. For the clean Rashba model, the intrinsic spin-Hall conductivity exhibits a logarithmic divergency in the low-frequency regime.

Nonlinear transport properties of III-nitrides in electric field

We consider the transport properties of polar direct-gap semiconductors in an electric field, specializing the numerical calculation of the general theory to the case of n-doped III-nitrides, in particular, GaN, AlN, and InN. The nonequilibrium thermodynamic state of these materials—characterized by the variables so-called quasitemperature, quasichemical potential, and drift velocity of the carriers, and the quasitemperatures of longitudinal optical and acoustical phonons—is studied. The evolution equations of these variables—which are highly nonlinear—are derived, and the transient regime and the ensuing steady state are analyzed. The nonlinear transport is characterized and its main properties are discussed. In one case comparison with a recent Monte Carlo calculation is made and good agreement is obtained. In this paper we mainly consider the ultrafast transient, and in the following paper the steady state.

A distance-dependent atomic knowledge-based potential for improved protein structure selection.

A heavy atom distance-dependent knowledge-based pairwise potential has been developed. This statistical potential is first evaluated and optimized with the native structure z-scores from gapless threading. The potential is then used to recognize the native and near-native structures from both published decoy test sets, as well as decoys obtained from our group's protein structure prediction program. In the gapless threading test, there is an average z-score improvement of 4 units in the optimized atomic potential over the residue-based quasichemical potential. Examination of the z-scores for individual pairwise distance shells indicates that the specificity for the native protein structure is greatest at pairwise distances of 3.5-6.5 A, i.e., in the first solvation shell. On applying the current atomic potential to test sets obtained from the web, composed of native protein and decoy structures, the current generation of the potential performs better than residue-based potentials as well as the other published atomic potentials in the task of selecting native and near-native structures. This newly developed potential is also applied to structures of varying quality generated by our group's protein structure prediction program. The current atomic potential tends to pick lower RMSD structures than do residue-based contact potentials. In particular, this atomic pairwise interaction potential has better selectivity especially for near-native structures. As such, it can be used to select near-native folds generated by structure prediction algorithms as well as for protein structure refinement.

Derivation of protein-specific pair potentials based on weak sequence fragment similarity

A method is presented for the derivation of knowledge-based pair potentials that corrects for the various compositions of different proteins. The resulting statistical pair potential is more specific than that derived from previous approaches as assessed by gapless threading results. Additionally, a methodology is presented that interpolates between statistical potentials when no homologous examples to the protein of interest are in the structural database used to derive the potential, to a Go-like potential (in which native interactions are favorable and all nonnative interactions are not) when homologous proteins are present. For cases in which no protein exceeds 30% sequence identity, pairs of weakly homologous interacting fragments are employed to enhance the specificity of the potential. In gapless threading, the mean z score increases from -10.4 for the best statistical pair potential to -12.8 when the local sequence similarity, fragment-based pair potentials are used. Examination of the ab initio structure prediction of four representative globular proteins consistently reveals a qualitative improvement in the yield of structures in the 4 to 6 A rmsd from native range when the fragment-based pair potential is used relative to that when the quasichemical pair potential is employed. This suggests that such protein-specific potentials provide a significant advantage relative to generic quasichemical potentials.

An Equilibrium Based Mean-Field Model for Diffusion in Solids With a Distributed Density of States

ABSTRACTDetermination of transport mechanisms and energetics in amorphous silicon presents an interesting modeling challenge. Transport in amorphous silicon films is likely to involve energetically distributed traps and mobile species, as in the case of hydrogen and electron diffusion. Detailed kinetic models using discrete energy levels have been developed, however, the density of states of the diffusing species in amorphous silicon is likely to be continuous and distributed, due to the amorphous nature of the films. We have developed a mean-field, equilibrium based model which utilizes a continuous density of states for the diffusing species. The transport in amorphous silicon is modeled as a function of a gradient in the quasi-chemical potential, rather than concentration, of the diffusing species. The model is applicable when the local equilibration processes are fast relative to the transport process. This approach is extremely numerically efficient, as well as flexible, allowing for modeling of tracer experiments, such as deuterium diffusion in a-Si:H films, and possible changes in density of states with time, temperature, and diffusing species concentration. We demonstrate the utility of the model by simulating hydrogen evolution from a-Si:H films.

Electrical and chemical potentials in a quantum-mechanical conductor

A time-dependent fully quantum response theory for mesoscopic systems is developed in the Heisenberg representation rather than the usual interaction representation. In the mesoscopic system itself, the difference between μ + and μ - quasi-chemical potentials for forward-direction and backward-direction current carriers is shown to be equal to the electron charge times the line integral of the transport electric field through the system.

Noise in diodes, rigorously deduced from first principles

Interaction between photons, valence band electrons and conduction band electrons are treated according to the well-known Einstein model of stimulated absorption, stimulated emission and spontaneous emission, however, with taking into account a non-zero quasi-chemical potential of the photons[1,2]. It leads to a new d.c.-characteristic of the diode[3,4], an alternative for the classical Shockley characteristic. A method developed in [5] allows us to calculate also the noise behaviour and so leads to a diode model, equivalent to the Nyquist model of linear resistors.