Similar,or dissimilar,that is the question. How different are methods for comparison of compounds similarity?

Comparison of compounds similarity is one of the main strategies of virtual screening protocols. Both similarity and dissimilarity concepts are of great importance during the search for new active compounds. Similarity is important due to the assumption that underlies the process of searching for new drug candidates: structurally similar compounds should induce similar biological response. On the other hand, we are also interested in dissimilarity, as we usually aim to find structurally novel ligands. In the study, we compared several approaches of evaluating compound similarity. Various representations and metrics were applied and we indicated the rate of variation of the results that can occur when shifting from one strategy to another. We compared both general similarity of datasets using different approaches, as well as examined the changes in the set of nearest neighbors when changing one compound representation into another, and the influence of representation/metric settings on the clustering outcome. We hope that the study will be of great help during the preparation of virtual screening experiments, stressing the need for careful selection of the way, the compound similarity is assessed. The differences in the results that can be obtained via the application of particular strategy can significantly influence the outcome of comparison studies; therefore, its settings should be carefully selected beforerunning the comparison.     

Similarity of L-fuzzy Relations Based on L-topologies Induced by L-fuzzy Rough Approximation Operators

This paper proposes similarity of L-fuzzy relations based on L-topologies induced by L-fuzzy rough approximation operators. First, the notion L-fuzzy rough set is generalized and the relationship between generalized L-fuzzy rough sets and L-topologies on an arbitrary universe is investigated. It shows that Alexandrov L-topologies can be induced by L-fuzzy relations without any preconditions. Second, the concept of similarity of L-fuzzy relations is introduced and variations of an L-fuzzy relation are investigated. Third, algebraic structures on similarity of L-fuzzy relations are obtained. Finally, we prove that the subset of the transitive L-fuzzy relations similar to a fixed L-fuzzy relation is a complete distributive lattice.     

Similarity analysis in magnetohydrodynamics: Hall effects on free convection flow and mass transfer past a semi-infinite vertical flat plate

Heat and mass transfer along a semi-infinite vertical flat plate under the combined buoyancy force effects of thermal and species diffusion is investigated in the presence of a strong non-uniform magnetic field and the Hall currents are taken into account. The induced magnetic field due to the motion of the electrically conducting fluid is negligible. This assumption is valid for a small magnetic Reynolds number. The similarity solutions are obtained using the scale group of transformations. These are the only symmetry transformations admitted by the field equations. The non-linear boundary layer equations with the boundary conditions are transferred to a system of non-linear ordinary differential equations with the appropriate boundary conditions. Furthermore, the similarity equations are solved numerically by using a fourth order Runge-Kutta scheme with the shooting method. Numerical results for the velocity profiles, the temperature profiles and the concentration profiles are presented graphically for various values of the magnetic parameter M in the range of 0-1 with the Hall parameter m taking the values 0.5, 1, 2, and 3.     

Heat and brine transport in porous media: the Oberbeck-Boussinesq approximation revisited

This paper discusses the Oberbeck-Boussinesq approximation for heat and solute transport in porous media. In this commonly used approximation all density variations are neglected except for the gravity term in Darcy’s law. However, in the limit of vanishing density differences this gravity term disappears as well. The main purpose of this paper is to give the correct limits in which the gravity term is retained, while other density effects can be neglected. We show that for isothermal brine transport, fluid volume changes can be neglected when a condition is fulfilled for a dimensionless number, which is independent of the density difference and specific discharge. For heat transfer an additional condition is required. One-dimensional examples of simultaneous heat and brine transport are given for which similarity solutions are constructed. These examples are included to elucidate the volume effects and the corresponding induced specific discharge variations. Finally, a two-dimensional example illustrates the relative effects of volume changes and gravity.     

Exact solutions of some general nonlinear wave equations in elasticity

A similarity analysis of a nonlinear wave equation in elasticity is studied; in particular, one with anharmonic corrections. The symmetry transformation give rise to exact solutions via the method of invariants. In some cases, graphical figure of the solutions are presented. Furthermore, we consider some cases wherein the velocities of the longitudinal and transversal plane waves are variable. Finally, a brief discussion on how a symmetry analysis on a perturbation of the elasticity equation can be pursued.     

Flow and heat transfer over a generalized stretching/shrinking wall problem—Exact solutions of the Navier-Stokes equations

In this paper, we investigate the steady momentum and heat transfer of a viscous fluid flow over a stretching/shrinking sheet. Exact solutions are presented for the Navier-Stokes equations. The new solutions provide a more general formulation including the linearly stretching and shrinking wall problems as well as the asymptotic suction velocity profiles over a moving plate. Interesting non-linear phenomena are observed in the current results including both exponentially decaying solution and algebraically decaying solution, multiple solutions with infinite number of solutions for the flow field, and velocity overshoot. The energy equation ignoring viscous dissipation is solved exactly and the effects of the mass transfer parameter, the Prandtl number, and the wall stretching/shrinking strength on the temperature profiles and wall heat flux are also presented and discussed. The exact solution of this general flow configuration is a rare case for the Navier-Stokes equation.     

Numerical similarity reductions of the (1+3)-dimensional Burgers equation

We consider the (1+3)-dimensional Burgers equation u_t = u_xx + u_yy + u_zz + uu_x which has considerable interest in mathematical physics. Lie symmetries are used to reduce it to certain ordinary differential equations. We employ numerical methods to solve a number of these ordinary differential equations.     

Convective heat transfer in a conducting fluid over a permeable stretching surface with suction and internal heat generation/absorption

We consider a convective flow in a porous medium of an incompressible viscous conducting fluid impinging on a permeable stretching surface with suction, and internal heat generation/absorption. Using a similarity transformation the governing equations of the problem are reduced to a coupled third-order nonlinear ordinary differential equations. We first examine a number of special cases for which we may obtain exact solutions. We then obtain analytical solutions (by the Homotopy Analysis Method) and numerical solutions (by a boundary value problem solver), in order to further study the behavior of the nonlinear differential equations, for various values of the physical parameters. Our numerical solutions are shown to agree with the available results in the literature. We then employ the numerical results to bring out the effects of the suction parameter, heat source/sink parameter, stretching parameter, porosity parameter, the Prandtl number and the free convection parameter on the flow and heat transfer characteristics. In the absence of suction and free convection, our findings are in agreement with the corresponding numerical results of Attia [H.A. Attia, On the effectiveness of porosity on stagnation point flow towards a stretching surface with heat generation, Comput. Mater. Sci. 38 (2007) 741-745].     

The solution of Navier equations of classical elasticity using Lie symmetry groups

The analytical solutions of axially-symmetric Navier equations in classical elasticity are found by applying Lie group theory. We investigate two different systems of partial differential equations corresponding elastostatics and elastodynamics problems, and find similarity solutions of both cases by solving the reduced system of ordinary differential equations which have fewer independent variables. As an example of the elastostatics case, the displacements and stress components are obtained for porous, polymeric foam material by using similarity solutions.     

Similarity Solutions for Thawing Processes with a Heat Flux Condition at the Fixed Boundary

Similarity solutions for a mathematical model for thawing in a saturated semi-infinite porous medium is considered when change of phase induces a density jump and a heat flux condition of the type is imposed on the fixed face x=0. Different cases depending on physical parameters are analysed and the explicit solution is obtained if and only if an inequality for the thermal coefficient q ₀ is verified. An improvement for the existence of a similarity solution for the same free boundary problem with a constant temperature on the fixed face x=0 is also obtained. Sommario. Vengono considerate soluzioni di similarità per un modello matematico di disgelo di un mezzo poroso saturo semi-infinito allorquando il cambiamento di fase induce un salto di densità ed una condizione di flusso di calore del tipo viene imposta sulla faccia fissa x=0. Si analizzano differenti casi dipendenti da parametri fisici e la soluzione esplicita viene ottenuta se e solo se risulta verificata una diseguaglianzo per il coefficiente termico q ₀. Si ottiene altresi un miglioramento della condizione di esistenza di una soluzione di similarità per lo stesso problema al contorno libero con temperatura costante sulla faccia fissa x=0.