A method and program for mass quantum chemical calculations of protein—ligand docking complexes

A new fast computational method for mass calculations of docking complexes by the AM1/PM3 semiempirical methods is proposed. The computation time is shortened by at least an order of magnitude compared to alternative schemes of quantum chemical calculations. The root-mean-square deviation of the AM1 calculated energies of formation of complexes from the results obtained by conventional diagonalization procedure is at most 0.4 kcal mol⁻¹. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 418–420, February, 2008.     

Absorption measurement of strained SiGe nanostructures deposited by UHV-CVD

In order to obtain a low band gap photocell based on the widely spread silicon technology, e.g. for thermophotovoltaics, SiGe nanostructures can be introduced into a monocrystalline silicon photocell. Beforehand, it is necessary to know the absorption coefficient of the SiGe quantum wells. On a silicon (1 0 0) substrate multiple Si/SiGe quantum well structures were grown by UHV-CVD. The Ge concentration and the well width were used as growth parameters. To obtain significant absorption, the experiment was set up to allow for 200 internal reflections.The total reflection of the light results in a standing electromagnetic wave. The absorption coefficient was obtained from the experimental data taking the geometry and the electric field distribution in the absorbing layer into account. The influence of well width and germanium content on the absorption was investigated with the goal of maximizing the absorption for photons with energies below the band gap energy of silicon. The measurement results are compared with a theoretical model, which takes the band structure of strained SiGe including confinement effects into account.     

Path Integrals in Noncommutative Quantum Mechanics

We consider an extension of the Feynman path integral to the quantum mechanics of noncommuting spatial coordinates and formulate the corresponding formalism for noncommutative classical dynamics related to quadratic Lagrangians (Hamiltonians). The basis of our approach is that a quantum mechanical system with a noncommutative configuration space can be regarded as another effective system with commuting spatial coordinates. Because the path integral for quadratic Lagrangians is exactly solvable and a general formula for the probability amplitude exists, we restrict our research to this class of Lagrangians. We find a general relation between quadratic Lagrangians in their commutative and noncommutative regimes and present the corresponding noncommutative path integral. This method is illustrated with two quantum mechanical systems in the noncommutative plane: a particle in a constant field and a harmonic oscillator.     

Stress Tensor Fluctuations and Passive Quantum Gravity

The quantum fluctuations of the stress tensor of a quantum field are discussed, as are the resulting space-time metric fluctuations. Passive quantum gravity is an approximation in which gravity is not directly quantized, but fluctuations of the space-time geometry are driven by stress tensor fluctuations. We discuss a decomposition of the stress tensor correlation function into three parts, and consider the physical implications of each part. The operational significance of metric fluctuations and the possible limits of validity of semiclassical gravity are discussed.     

On Set-Theoretical Solutions to Quantum Yang-Baxter Equation

The problem on the set-theoretical solutions to the quantum Yang-Baxter equation was presented byDrinfel'd as a main unsolved problem in quantum group theory. The set-theoretical solutions are a natural extensionof the usual (linear) solutions. In this paper, we not only give a further study on some known set-theoretical solutions(the Venkov's solutions), but also find a new kind of set-theoretical solutions which have a geometric interpretation.Moreover, the new solutions lead to the metahomomorphisms in group theory.     

A Reality Proof in PT-Symmetric Quantum Mechanics

We review the proof of a conjecture concerning the reality of the spectra of certain PT-symmetric quantum mechanical systems, obtained via a connection between the theories of ordinary differential equations and integrable models. Spectral equivalences inspired by the correspondence are also discussed.     

Classical Limit of Expectation Values in a Wave Packet Involving Few Stationary States

Expectation values of physical quantities in a wave packet involving few stationary states in an infinite square well are calculated. Explicit results show that the expectation values in the classical limit go over to the corresponding classical quantity in the form of the arithmetic mean (in mathematical term, the Fejér's average) of the partial Fourier series converging to the classical quantity. The number of the stationary states is that of the partial Fourer series in the Fejér's average. The quantum uncertainty is then demonstrated to have a classical counterpart.     

Stochastic resonance in perspective

Summary We outline the historical development of stochastic resonance (SR), a phenomenon in which the signal and/or the signal-to-noise ratio in a nonlinear system increase with increasing intensity of noise. We discuss basic theoretical ideas explaining and describing SR, and we review some revealing experimental data that place SR within the wider context of statistical physics. We emphasize the close relationship of SR to some effects that are well known in condensed-matter physics. Paper presented at the International Workshop ?Fluctuations in Physics and Biology: Stochastic Resonance, Signal Processing and Related Phenomena?, Elba, 5–10 June 1994.     

A density functional theory computational study of the role of ligand on the stability of CuI and CuII species associated with ATRP and SET‐LRP

Atom transfer radical polymerization (ATRP) and single electron‐transfer living radical polymerization (SET‐LRP) both utilize copper complexes of various oxidation states with N‐ligands to perform their respective activation and deactivation steps. Herein, we utilize DFT (B3YLP) methods to determine the preferred ligand‐binding geometries for Cu/N‐ligand complexes related to ATRP and SET‐LRP. We find that those ligands capable of achieving tetrahedral complexes with Cu^I and trigonal bipyramidal with axial halide complexes with [Cu^IIX]⁺ have higher energies of stabilization. We were able to correlate calculated preferential stabilization of [Cu^IIX]⁺ with those ligands that perform best in SET‐LRP. A crude calculation of energy of disproportionation revealed that the same preferential binding of [Cu^IIX]⁺ results in increased propensity for disproportionation. Finally, by examining the relative energies of the basic steps of ATRP and SET‐LRP, we were able to rationalize the transition from the ATRP mechanism to the SET‐LRP mechanism as we transition from typical nonpolar ATRP solvents to polar SET‐LRP solvents. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4950–4964, 2007