A graphical method to construct a phylogenetic tree

A 3D graphical representation of DNA sequences, which has no circuit or degeneracy, is derived for mathematical denotation of DNA sequence. Based on this graphical representation, we propose a new sequence distance measure. We make use of the corresponding similarity matrix to construct a phylogenic tree by virtue of the fuzzy theory. The examination of phylogenic tree belong to eight species illustrates the utility of our approach. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Reduced-size polarized basis sets for calculations of molecular electric properties. IV. First-row transition metals

Recent studies of the perturbation-dependent basis sets have indicated the possibility of a significant reduction of the size of the usual CGTO sets without considerable loss of accuracy in calculations of molecular electric properties. The resulting (ZPolX) basis sets have been developed for several atoms of the first and second row of the Periodic Table. The same method of the ZPolX basis set generation is extended for the first-row transition metals and the corresponding contracted ZPolX basis sets of the size [6s5p3d1f] are determined for both nonrelativistic and scalar relativistic calculations. The performance of the ZPolX basis sets is verified in calculations on the first-row transition metal oxides at the level of the ROHF, ROHF/CASPT2, and ROHF/CCSD(T) approximations. Also the study of the dipole polarizability of TiCl₄ confirms the excellent features of these very compact basis sets. The ZPolX basis sets for nonrelativistic and relativistic calculations of molecular electric properties are available on the web page http://www.chem.uni.torun.pl/zchk/basis-sets.html.     

The convergence of the Rayleigh-Ritz Method in quantum chemistry

Two sufficient criteria for the convergence of the Rayleigh-Ritz Method (RRM) with respect to the eigenvalues (E-convergence) of non-relativistic electronic Hamiltonians of molecules are discussed and compared. Moreover, a necessary and sufficient criterion is given. By example (Sect. 9) it is shown that the L ²-completeness of the basis is not sufficient to guarantee E-convergence. The convergence of the wave functions in different norms (-convergence) is also investigated. In particular, sufficient conditions for the one-particle basis functions (orbitals) are given, such that a CI calculation in this basis is both E- and -convergent.     

Medium-size Gaussian basis sets for hydrogen through argon

Summary Medium-sized Gaussian basis sets are reoptimized for the ground states of the atoms from hydrogen through argon. The composition of these basis sets is (4s), (5s), and (6s) for H and He, (9s5p) and (12s7p) for the atoms Li to Ne, and (12s8p) and (12s9p) for the atoms Na to Ar. Basis sets for the² P states of Li and Na, and the³ P states of Be and Mg are also constructed since they are useful in molecular calculations. In all cases, our energies are lower than those obtained previously with Gaussian basis sets of the same size.     

Medium-size polarized basis sets for high-level-correlated calculations of molecular electric properties

Summary The first-order polarized basis sets for the use in high-level-correlated investigations of molecular electric properties have been generated for Pb, Bi, Po, and At. The performance of the standard [10.17.14.5/13.11.8.2] and extended [20.17.14.9/13.11.8.4] basis sets has been examined in nonrelativistic and quasirelativistic calculations for atoms and simple closed-shell hydrides. The relativistic contributions to electric dipole properties of those systems have been evaluated by using the recently developed quasirelativistic scheme. The predicted dipole polarizability of At is in good agreement with the results of other relativistic calculations. The calculated quasirelativistic dipole moments of BiH₃ (–0.499 a.u.), PoH₂ (–0.207 a.u.), and AtH (+0.036 a.u.) involve a significant relativistic contribution which amounts to —0.230 a.u., –0.177 a.u., and –0.097 a.u., respectively. The basis set details append this paper. They are also available as a part of the basis set library of the MOLCAS system.     

Reachable and controllable sets for two-dimensional,linear, discrete-time systems

We consider two-dimensional discrete-time linear systems with constrained controls. We propose a simple polynomial time procedure to give an exact external representation of theN-step reachable set and controllable set. The bounding hyperplanes are explicitly derived in terms of the data of the problem. By using a result in computational geometry, all the calculations are made in polynomial time in contrast to classical methods. The limit case asN is also investigated.     

Hypersurfaces of prescribed mean curvature enclosing a given body

Given a smooth domain Ω in ℝ ^m+1 with compact closure and a smooth integrable functionh: ℝ ^m+1→ℝ satisfyingh(x)≥H _∂Ω (x) on ∂Ω whereH _∂ω denotes the mean curvature of ∂Ω calculated w.r.t. the interior unit normal we show that there is a setA⊂ℝ ^m+1 with the properties andH _∂A=h on ∂A.     

Generalizations of Slater's constraint qualification for infinite convex programs

In this paper we study constraint qualifications and duality results for infinite convex programs (P) = inf{f(x): g(x) – S, x C}, whereg = (g ₁,g ₂) andS = S ₁ ×S ₂,S _i are convex cones,i = 1, 2,C is a convex subset of a vector spaceX, andf andg _i are, respectively, convex andS _i -convex,i = 1, 2. In particular, we consider the special case whenS ₂ is in afinite dimensional space,g ₂ is affine andS ₂ is polyhedral. We show that a recently introduced simple constraint qualification, and the so-called quasi relative interior constraint qualification both extend to (P), from the special case thatg = g ₂ is affine andS = S ₂ is polyhedral in a finite dimensional space (the so-called partially finite program). This provides generalized Slater type conditions for (P) which are much weaker than the standard Slater condition. We exhibit the relationship between these two constraint qualifications and show how to replace the affine assumption ong ₂ and the finite dimensionality assumption onS ₂, by a local compactness assumption. We then introduce the notion of strong quasi relative interior to get parallel results for more general infinite dimensional programs without the local compactness assumption. Our basic tool reduces to guaranteeing the closure of the sum of two closed convex cones.