Investigation of a new GRASP-based clustering algorithm applied to biological data

A large amount of biological data has been produced in the last years. Important knowledge can be extracted from these data by the use of data analysis techniques. Clustering plays an important role in data analysis, by organizing similar objects from a dataset into meaningful groups. Several clustering algorithms have been proposed in the literature. However, each algorithm has its bias, being more adequate for particular datasets. This paper presents a mathematical formulation to support the creation of consistent clusters for biological data. Moreover. it shows a clustering algorithm to solve this formulation that uses GRASP (Greedy Randomized Adaptive Search Procedure). We compared the proposed algorithm with three known other algorithms. The proposed algorithm presented the best clustering results confirmed statistically. (C) 2009 Elsevier Ltd. All rights reserved.

D*D rho vertex from QCD sum rules

We calculate the form factors and the coupling constant in the D*D rho vertex in the framework of QCD sum rules. We evaluate the three-point correlation functions of the vertex considering D, rho and D* mesons off-shell. The form factors obtained are very different but give the same coupling constant: g(D*D rho) = 4.3 +/- 0.9 GeV(-1). (C) 2011 Elsevier B.V. All rights reserved.

QCD sum rules for the production of the X(3872) as a mixed molecule-charmonium state in B meson decay

We use QCD sum rules to calculate the branching ratio for the production of the meson X(3872) in the decay B -> X(3872)K, assumed to be a mixture between charmonium and exotic molecular vertical bar c (q) over bar vertical bar vertical bar q (c) over bar vertical bar states with J(PC) = 1(++). We find that in a small range for the values of the mixing angle, 5 degrees <= theta <= 13 degrees, we get the branching ratio B(B -> XK) = (1.00 +/- 0.68) x 10(-5), which is in agreement with the experimental upper limit. This result is compatible with the analysis of the mass and decay width of the mode J/psi(n pi) and the radiative decay mode J/psi gamma performed in the same approach. (C) 2011 Elsevier B.V. All rights reserved.

A QCD sum rule calculation for the Y(4140) narrow structure

We use the QCD sum rules to evaluate the mass of a possible scalar mesonic state that couples to a molecular D(s)*(D) over bar (s)* current. We find a mass m(Ds)*(Ds)* = (4.14 +/- 0.09) GeV, which is in an excellent agreement with the recently observed Y(4140) charmonium state. We consider the contributions of condensates up to dimension-eight, we work at leading order in alpha(s) and we keep terms which are linear in the strange quark mass m(s). We also consider a molecular D*(D) over bar* current and we obtain m m(D)*(D)* = (4.13 +/- 0.10), around 200 MeV above the mass of the Y(3930) charmonium state. We conclude that it is possible to describe the Y(4140) structure as a D(s)*(D) over bar (s)* molecular state or even as a mixture of D(s)*(D) over bar (s)* and D*(D) over bar* molecular states. (C) 2009 Elsevier B.V. All rights reserved.

QCD sum rule calculation for the charmonium-like structures in the J/psi phi and J/psi omega invariant mass spectra

Using the QCD sum rules we test if the charmonium-like structure Y(4274), observed in the J/psi phi invariant mass spectrum, can be described with a D(s)(D) over bar (s0)(2317)+ h.c. molecular current with J(PC) = 0(-+). We consider the contributions of condensates up to dimension ten and we work at leading order in alpha(s). We keep terms which are linear in the strange quark mass m(s). The mass obtained for such state is mD(s)D(s0) = (4.78 +/- 0.54) GeV. We also consider a molecular 0(-+) D (D) over bar (0)(2400)+ h.c. current and we obtain m(DD0) = (4.55 +/- 0.49) GeV. Our study shows that the newly observed Y(4274) in the J/psi phi invariant mass spectrum can be, considering the uncertainties, described using a molecular charmonium current. (C) 2011 Elsevier B.V. All rights reserved.

QCD sum rules study of the J(PC)=1(- -) charmonium Y mesons

We use QCD sum rules to test the nature of the recently observed mesons Y(4260), Y(4350) and Y(4660), assumed to be exotic four-quark (c (c) over barq (q) over bar) or (c (c) over bars (s) over bar) states with J(PC)= 1(--). We work at leading order in alpha(s), consider the contributions of higher dimension condensates and keep terms which are linear in the strange quark mass m(s). We find for the (c (c) over bars (s) over bar) state a mass in m(Y) = (4.65 +/- 0.10) GeV which is compatible with the experimental candidate Y (4660), while for the (c (c) over barq (q) over bar) state we find a mass in m(Y) = (4.49 +/- 0.11) GeV, which is still consistent with the mass of the experimental candidate Y(4350). With the tetraquark structure we are working we cannot explain the Y(4260) as a tetraquark state. We also consider molecular D(s0)(D) over bar (s)* and D(0)(D) over bar* states. For the D(s0)(D) over bar (s)* molecular state we get m(Ds0 (D) over bars*) = (4.42 +/- 0.10) GeV which is consistent, considering the errors, with the mass of the meson Y(4350) and for the D(0)(D) over bar* molecular state we get m(D0 (D) over bar*) = (4.27 +/- 0.10) GeV in excellent agreement with the mass of the meson Y(4260). (C) 2008 Elsevier B.V. All rights reserved.

QCD sum rules study of the meson Z(+)(4430)

We use QCD sum rules to study the recently observed meson Z(+)(4430), considered as a D*D-1 molecule with J(P) = 0(-). We consider the contributions of condensates up to dimension eight and work at leading order in alpha(s). We get m(Z) = (4.40 +/- 0.10) GeV in a very good agreement with the experimental value. We also make predictions for the analogous mesons Z(s) and Z(bb) considered as D-s*D-1 and B*B-1 molecules, respectively. For Z(s) we predict mZ(s) = (4.70 +/- 0.06) GeV, which is above the D-s* D-1 threshold, indicating that it is probably a very broad state and, therefore, difficult to observe experimentally. For Z(bb) we predict m(Zbb) = (10.74 +/- 0.12) GeV, in agreement with quark model predictions. (c) 2008 Elsevier B.V. All rights reserved.

rho D*D* vertex from QCD sum rules

We calculate the form factors and the coupling constant in the rho D*D* vertex in the framework of QCD sum rules. We evaluate the three point correlation functions of the vertex considering both rho and D* mesons off-shell. The form factors obtained are very different but give the same coupling constant: g rho D*D* = 6.60 +/- 0.31. This number is 50% larger than what we would expect from SU(4) estimates. (c) 2007 Elsevier B.V. All rights reserved.

Quantum States Allowing Minimum Uncertainty Product of phi and L(z)

We provide necessary and sufficient conditions for states to have an arbitrarily small uncertainty product of the azimuthal angle phi and its canonical moment L(z). We illustrate our results with analytical examples.

The degree of polydispersity in micellar dispersions: A sum rule approach

Statistical properties of a two-dimensional ideal dispersion of polydisperse micelles are derived by analyzing the convergence properties of a sum rule set by mass conservation. Internal micellar degrees of freedom are accounted for by a microscopic model describing small displacements of the constituting amphiphiles with respect to their equilibrium positions. The transfer matrix (TM) method is employed to compute internal micelle partition function. We show that the conditions under which the sum rule is saturated by the largest eigenvalue of the TM determine the value of amphiphile concentration above which the dispersion becomes highly polydisperse and micelle sizes approach a Schultz distribution. (C) 2011 Elsevier B.V. All rights reserved.

Molecular Ordering of Layer-by-Layer Polyelectrolyte Films Studied by Sum-Frequency Vibrational Spectroscopy

The molecular arrangement in organic thin films is crucial for their increasing technological applications. Here, we use vibrational spectroscopy by sum-frequency generation (SFG) to study the ordering of polyelectrolyte layers adsorbed on silica for all steps of layer-by-layer (LbL) self-assembly. In situ measurements during adsorption and rinsing showed that the adsorbed polymer has a disordered conformation and confirmed surface charge overcompensation upon polyelectrolyte adsorption by probing the interfacial electric field. In dry films, the polymer chains acquired a net orientational ordering, which was affected, however, by the adsorption of subsequent layers. Such a detailed characterization may allow the control of LbL film structure and functionality with unprecedented power.

Molecular Ordering in Layer-by-Layer Polyelectrolyte Films Studied by Sum-Frequency Vibrational Spectroscopy: The Effects of Drying Procedures

Sum-Frequency Vibrational Spectroscopy (SFVS) has been used to investigate the effect of nitrogen-flow drying on the molecular ordering of Layer-by-Layer (LbL) films of poly(allylamine hydrochloride) (PAH) alternated with poly(styrene sulfonate) (PSS). We find that films dried by spontaneous water evaporation are more ordered and homogeneous than films dried by nitrogen flow. The latter are quite inhomogeneous and may have regions with highly disordered polymer conformation. We propose that drying by spontaneous water evaporation reduces the effect of drag by the drying front, while during nitrogen-flow drying the fast evaporation of water ""freezes"" the disordered conformation of adsorbed polyelectrolyte molecules. These findings are important for many applications of LbL films, since device performance usually depends on film morphology and its molecular structure.

Minimum cycle cover and Chinese postman problems on mixed graphs with bounded tree-width

Let M = (V, E, A) be a mixed graph with vertex set V, edge set E and arc set A. A cycle cover of M is a family C = {C(1), ... , C(k)} of cycles of M such that each edge/arc of M belongs to at least one cycle in C. The weight of C is Sigma(k)(i=1) vertical bar C(i)vertical bar. The minimum cycle cover problem is the following: given a strongly connected mixed graph M without bridges, find a cycle cover of M with weight as small as possible. The Chinese postman problem is: given a strongly connected mixed graph M, find a minimum length closed walk using all edges and arcs of M. These problems are NP-hard. We show that they can be solved in polynomial time if M has bounded tree-width. (C) 2008 Elsevier B.V. All rights reserved.

Polynomial identities for the ternary cyclic sum

We simplify the results of Bremner and Hentzel [J. Algebra 231 (2000) 387-405] on polynomial identities of degree 9 in two variables satisfied by the ternary cyclic sum [a, b, c] abc + bca + cab in every totally associative ternary algebra. We also obtain new identities of degree 9 in three variables which do not follow from the identities in two variables. Our results depend on (i) the LLL algorithm for lattice basis reduction, and (ii) linearization operators in the group algebra of the symmetric group which permit efficient computation of the representation matrices for a non-linear identity. Our computational methods can be applied to polynomial identities for other algebraic structures.

New material for orthopedic implants: Electrochemical study of nickel free P558 stainless steel in minimum essential medium

Nickel, a component of stainless steels (SS) applied in orthopedic implants may cause allergic processes in human tissues P558 nickel free SS was studied to verify its viability as a substitute for stainless steel containing nickel Its performance is compared to ISO 5832-9 and F138 most used nowadays grades in implants fabrications, in minimum essential medium. MEM, at 37 degrees C. Potentiodynamic polarization curves, electrochemical impedance spectroscopy (EIS), scanning electron microscopy (SEM) and ""in vitro"" cytotoxicity were used as techniques. From the electrochemical point of view P558 SS is comparable to ISO 5832-9 SS in MEM It remains passivated until the transpassivation potential, above which generalized corrosion occurs F138 presents pitting corrosion at 370 mV/SCE. The cytotoxicity results showed that P558. ISO 5832-9 and F138 do not present cytotoxic character Therefore, these results suggest that P558 SS can be applied in orthopedic implants (C) 2010 Elsevier BV All rights reserved