Calculation of Two-Center Nuclear Attraction Integrals over Integer and Noninteger n-Slater Type Orbitals in Nonlined-Up Coordinate Systems

Two-center nuclear attraction integrals over Slater type orbitals with integer and noninteger principal quantum numbers in nonlined up coordinate systems have been calculated by means of formulas in our previous work (T. Özdoan and M. Orbay, Int. J. Quant. Chem. 87 (2002) 15). The computer results for integer case are in best agreement with the prior literature. On the other hand, the results for noninteger case are not compared with the literature due to the scarcity of the literature, but also compared with the limit of integer case and good agreements are obtained. The proposed algorithm for the calculation of two-center nuclear attraction integrals over Slater type orbitals with noninteger principal quantum numbers in nonlined-up coordinate systems permits to avoid the interpolation procedure used to overcome the difficulty introduced by the presence of noninteger principal quantum numbers. Finally, numerical aspects of the presented formulae are analyzed under wide range of quantum numbers, orbital exponents and internuclear distances.     

Ab initio Tertiary Structure Prediction of Proteins

A daunting challenge in the area of computational biology has been to develop a method to theoretically predict the correct three-dimensional structure of a protein given its linear amino acid sequence. The ability to surmount this challenge, which is known as the protein folding problem, has tremendous implications. We introduce a novel ab initio approach for the protein folding problem. The accurate prediction of the three-dimensional structure of a protein relies on both the mathematical model used to mimic the protein system and the technique used to identify the correct structure. The models employed are based solely on first principles, as opposed to the myriad of techniques relying on information from statistical databases. The framework integrates our recently proposed methods for the prediction of secondary structural features including helices and strands, as well as -sheet and disulfide bridge formation. The final stage of the approach, which culminates in the tertiary structure prediction of a protein, utilizes search techniques grounded on the foundations of deterministic global optimization, powerful methods which can potentially guarantee the correct identification of a protein's structure. The performance of the approach is illustrated with bovine pancreatic trypsin inhibitor protein and the immunoglobulin binding domain of protein G.     

On 2x2 conservation laws with large data

We deal with a strictly hyperbolic system of two conservation laws in one spatial dimension. One of the eigenvalues of the system is of Temple type (rarefaction and shock curves coincide), the other eigenvalue is only required to be genuinely nonlinear.We consider the initial value problem for data of the following kind: the total variation of the Temple component is bounded, possibly large, while the total variation of the other component is small. For such data we prove global existence, uniqueness and L⊃-Lipschitz continuous dependence of solutions.AMS Subject Classification: Primary 35L65; Secondary 35D05, 35L45.     

A Point Balance Algorithm for the Spherical Code Problem

The Spherical Code (SC) problem has many important applications in such fields as physics, molecular biology, signal transmission, chemistry, engineering and mathematics. This paper presents a bilevel optimization formulation of the SC problem. Based on this formulation, the concept of balanced spherical code is introduced and a new approach, the Point Balance Algorithm (PBA), is presented to search for a 1-balanced spherical code. Since an optimal solution of the SC problem (an extremal spherical code) must be a 1-balanced spherical code, PBA can be applied easily to search for an extremal spherical code. In addition, given a certain criterion, PBA can generate efficiently an approximate optimal spherical code on a sphere in the n-dimensional space ⁿ. Some implementation issues of PBA are discussed and putative global optimal solutions of the Fekete problem in 3, 4 and 5-dimensional space are also reported. Finally, an open question about the geometry of Fekete points on the unit sphere in the 3-dimensional space is posed.     

The asymptotic behavior of a class of nonlinear delay difference equations

The asymptotic behavior of difference equations of type 0, \end{equation*}">is studied, where and each are continuous real functions with decreasing and increasing. Results include sufficient conditions for permanence, oscillations and global attractivity.

     

On Convergence of Minimization Methods: Attraction, Repulsion, and Selection

In this paper, we revisit the convergence properties of the iterationprocess x^k+1=x^k–(x^k)B(x^k)^–1f(x^k)for minimizing a function f(x). After reviewing some classic results andintroducing the notion of strong attraction, we give necessary andsufficient conditions for a stationary point of f(x) to be a point of strongattraction for the iteration process. Not only this result gives a newalgorithmic interpretation to the classic Ostrowski theorem, but alsoprovides insight into the interesting phenomenon called selectiveminimization. We present also illustrative numerical examples for nonlinearleast squares problems.     

Global Optimization: On Pathlengths in Min-Max Graphs

Let f be a smooth nondegenerate real valued function on a finite dimensional, compact and connected Riemannian manifold. The bipartite min-max graph is defined as follows. Its nodes are formed by the set of local minima and the set of local maxima. Two nodes (a local minimum and a local maximum) are connected in by means of an edge if some trajectory of the corresponding gradient flow connects them. Given a natural number k, we construct a function f such that the length of the shortest path in between two specific local minima exceeds k. The latter construction is independent of the underlying Riemannian metric.     

Adaptive extremal optimization by detrended fluctuation analysis

Global optimization is one of the key challenges in computational physics as several problems, e.g. protein structure prediction, the low-energy landscape of atomic clusters, detection of community structures in networks, or model-parameter fitting can be formulated as global optimization problems. Extremal optimization (EO) has become in recent years one particular, successful approach to the global optimization problem. As with almost all other global optimization approaches, EO is driven by an internal dynamics that depends crucially on one or more parameters. Recently, the existence of an optimal scheme for this internal parameter of EO was proven, so as to maximize the performance of the algorithm. However, this proof was not constructive, that is, one cannot use it to deduce the optimal parameter itself a priori. In this study we analyze the dynamics of EO for a test problem (spin glasses). Based on the results we propose an online measure of the performance of EO and a way to use this insight to reformulate the EO algorithm in order to construct optimal values of the internal parameter online without any input by the user. This approach will ultimately allow us to make EO parameter free and thus its application in general global optimization problems much more efficient.     

Attractors for a Three-Dimensional Thermo-Mechanical Model of Shape Memory Alloys

Abstract In this note, we consider a Frémond model of shape memory alloys. Let us imagine a piece of a shape memory alloy which is fixed on one part of its boundary, and assume that forcing terms, e.g., heat sources and external stress on the remaining part of its boundary, converge to some time-independent functions, in appropriate senses, as time goes to infinity. Under the above assumption, we shall discuss the asymptotic stability for the dynamical system from the viewpoint of the global attractor. More precisely, we generalize the paper [12] dealing with the one-dimensional case. First, we show the existence of the global attractor for the limiting autonomous dynamical system; then we characterize the asymptotic stability for the non-autonomous case by the limiting global attractor. * Project supported by the MIUR-COFIN 2004 research program on “Mathematical Modelling and Analysis of Free Boundary Problems”.     

Modeling of chemical tracer transport in the atmospheric environment and its impact on the global climate

Continental regions are experiencing rapid environmental changes due to expansion of industrial activities and land uses in different types of agricultural productions, burning of fossil fuels, etc., which lead to the emanation of huge amount of smog aerosol particulates and chemicals in the atmosphere. Information about these chemical tracers has been found from Indian Ocean Experiment (INDOEX), Intergovernmental Panel for Climate Change (IPCC) assessment reports as well as from other sources. The results of these computations may be interpreted by the chemical tracer transport model. In this paper, we have used a global atmospheric model in which the optical properties and the concentrations of the chemical tracers and aerosols have been incorporated. The aerosols and chemicals are transported in the atmospheric environment by the model cumulus convection and through the model semi-Lagrangian advection process . Thus, they are globally distributed along with the wind flow. The model has been used in studying the impact of the tropospheric chemical perturbations on the global environment.