Ligand expansion in ligand-based virtual screening using relevance feedback

Query expansion is the process of reformulating an original query to improve retrieval performance in information retrieval systems. Relevance feedback is one of the most useful query modification techniques in information retrieval systems. In this paper, we introduce query expansion into ligand-based virtual screening (LBVS) using the relevance feedback technique. In this approach, a few high-ranking molecules of unknown activity are filtered from the outputs of a Bayesian inference network based on a single ligand molecule to form a set of ligand molecules. This set of ligand molecules is used to form a new ligand molecule. Simulated virtual screening experiments with the MDL Drug Data Report and maximum unbiased validation data sets show that the use of ligand expansion provides a very simple way of improving the LBVS, especially when the active molecules being sought have a high degree of structural heterogeneity. However, the effectiveness of the ligand expansion is slightly less when structurally-homogeneous sets of actives are being sought.     

Diffusion and viscosity of liquid tin: Green-Kubo relationship-based calculations from molecular dynamics simulations

Molecular dynamics (MD) simulations of liquid tin between its melting point and 1600 °C have been performed in order to interpret and discuss the ionic structure. The interactions between ions are described by a new accurate pair potential built within the pseudopotential formalism and the linear response theory. The calculated structure factor that reflects the main information on the local atomic order in liquids is compared to diffraction measurements. Having some confidence in the ability of this pair potential to give a good representation of the atomic structure, we then focused our attention on the investigation of the atomic transport properties through the MD computations of the velocity autocorrelation function and stress autocorrelation function. Using the Green-Kubo formula (for the first time to our knowledge for liquid tin) we determine the macroscopic transport properties from the corresponding microscopic time autocorrelation functions. The selfdiffusion coefficient and the shear viscosity as functions of temperature are found to be in good agreement with the experimental data.     

Laminar bubbly flow in an open capillary channel in microgravity

The study of a bubbly laminar two-phase flow in an open capillary channel under microgravity conditions was conducted aboard the sounding rocket, Texus-45. The channel consists of two parallel plates of width b = 25 mm and distance a = 10 mm. The flow along the length l = 80 mm is confined by a free surface on one side and a plate on the opposite side. The bubbles are injected at the nozzle of the capillary channel via six capillary tubes of 100 μm in inner diameter. Different liquid and gas flow rates were tested leading to different liquid free surface shape and bubble size.     

A dual-dual mixed formulation for nonlinear exterior transmission problems

We combine a dual-mixed finite element method with a Dirichlet-to-Neumann mapping (derived by the boundary integral equation method) to study the solvability and Galerkin approximations of a class of exterior nonlinear transmission problems in the plane. As a model problem, we consider a nonlinear elliptic equation in divergence form coupled with the Laplace equation in an unbounded region of the plane. Our combined approach leads to what we call a dual-dual mixed variational formulation since the main operator involved has itself a dual-type structure. We establish existence and uniqueness of solution for the continuous and discrete formulations, and provide the corresponding error analysis by using Raviart-Thomas elements. The main tool of our analysis is given by a generalization of the usual Babuska-Brezzi theory to a class of nonlinear variational problems with constraints.

     

On metallic ratio in

Metallic ratio is a root of the simple quadratic equation x² = kx + 1 for k is any positive integer which is the characteristic equation of the recurrence relation of k‐Fibonacci (k‐Lucas) numbers. This paper is about the metallic ratio in . We define k‐Fibonacci and k‐Lucas numbers in , and we show that metallic ratio can be calculated in if and only if p≡ ± 1 mod (k² + 4), which is the generalization of the Gauss reciprocity theorem for any integer k. Also, we obtain that the golden ratio, the silver ratio, and the bronze ratio, the three together, can be calculated in for the first time. Moreover, we introduce k‐Fibonacci and k‐Lucas quaternions with some algebraic properties and some identities for them.     

A memetic algorithm for the inventory routing problem

Journal of Heuristics - In this article, we study an Inventory Routing Problem with deterministic customer demand in a two-tier supply chain. The supply chain network consists of a supplier using a...     

Analysis of a new BEM‐FEM coupling for two‐dimensional fluid‐solid interaction

In this work we present a new numerical method, based on a coupling of finite and boundary elements, to solve a fluid‐solid interaction problem in the plane. The discrete method uses classical Lagrange finite elements adapted to curved boundaries for the field variable and spectral approximation of the unknowns on the artificial boundary. We provide error estimates for this Galerkin scheme and propose a full discretization based on elementary quadrature formulae, showing that the perturbation due to numerical integration preserves the optimal rate of convergence. We also suggest an iterative method to solve the complicated linear systems arising from this type of schemes. © 2005 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2005     

A study of atomic iodine and molecular thallium iodide by X-ray photoelectron and auger electron spectroscopy

The I3d5/2 binding energy has been measured in atomic iodine, thallium iodide and cesium iodide by high temperature gas-phase photoelectron spectrscopy using Al K (1486.6 eV) X-rays. The iodine M₅N_4,5N_4,5 (¹G₄) Auger energies for TlI and CsI have also been measured and combined with binding energies to yield extra-atomic relaxation energies of 0.5 and O.3 eV, respectively, after corrections are applied to the Auger parameter. Charges were calculated using the simple potential model, which was also used to obtain an estimate of the atomic T14f binding energy. Two other estimates of the atomic T14f7/2 binding energy have also been calculated, both based on Dirac-Fock ΔSCF binding energies. The results of the three methods suggest a value of 125.3 ± 0.2 eV for T14f7/2.     

Metal-Assisted Oxidative Cyclization of Arylamidrazones I. Synthesis of 3-Acetyl-1,4-dihydro-1-phenyl-1,2,4-benzotriazine

Summary. In the presence of RuCl₃, N-phenylamidrazone underwent oxidative cyclization into 1,4-dihydro-1-phenyl-1,2,4-benzotriazine, the structure of which is established by spectral and X-ray diffraction data.