Web server to identify similarity of amino acid motifs to compounds (SAAMCO)

Protein-protein interactions are fundamental in mediating biological processes including metabolism, cell growth, and signaling. To be able to selectively inhibit or induce protein activity or complex formation is a key feature in controlling disease. For those situations in which protein-protein interactions derive substantial affinity from short linear peptide sequences, or motifs, we can develop search algorithms for peptidomimetic compounds that resemble the short peptide's structure but are not compromised by poor pharmacological properties. SAAMCO is a Web service ( http://bioware.ucd.ie/ approximately saamco) that facilitates the screening of motifs with known structures against bioactive compound databases. It is built on an algorithm that defines compound similarity based on the presence of appropriate amino acid side chain fragments and a favorable Root Mean Squared Deviation (RMSD) between compound and motif structure. The methodology is efficient as the available compound databases are preprocessed and fast regular expression searches filter potential matches before time-intensive 3D superposition is performed. The required input information is minimal, and the compound databases have been selected to maximize the availability of information on biological activity. "Hits" are accompanied with a visualization window and links to source database entries. Motif matching can be defined on partial or full similarity which will increase or reduce respectively the number of potential mimetic compounds. The Web server provides the functionality for rapid screening of known or putative interaction motifs against prepared compound libraries using a novel search algorithm. The tabulated results can be analyzed by linking to appropriate databases and by visualization.     

Monotone clones and congruence modularity

We investigate the relationship between the local shape of an ordered set P=(P; ) and the congruence-modularity of the variety V generated by an algebra A=(P; F) each of whose operations is order-preserving with respect to P. For example, if V is k-permutable (k2) then P is an antichain; if P is both up and down directed and V is congruence-modular, then V is congruence-distributive; if A is a dual discriminator algebra, then either P is an antichain or a two-element chain. We also give a useful necessary condition on P for V to be congruence-modular. Finally a class of ordered sets called braids is introduced and it is shown that if P is a braid of length 1, in particular if P is a crown, then the variety V is not congruence-modular.     

Analytical solutions for heat transfer on fractal and pre-fractal domains

Fractals can be used to represent intricate self-similar geometries, but their application to the representation of physical systems is beset with difficulties which stem from an inability to define traditionally derived-physical quantities such as stress, pressure, strain, heat etc. This paper describes a method for the determination of analytical heat-transfer solutions on pre-fractal and fractal domains. The approach requires the construction of maps from pre-fractal domains to the continuum, which facilitate the application of traditional continuum solution methods. Solutions on fractal domains are achievable with this approach, and are defined to be the limit solution of analytical solutions obtained on the pre-fractals approximating the fractal of interest. This approach avoids many of the complications and technical difficulties arising from the use of measure theory and fractional derivatives, but also infers that the governing heat transfer equations are valid on all pre-fractals. The fractals considered are necessarily deterministic and relatively simple in form to demonstrate the solution methodology. The solutions presented are limited to one and two-dimensional domains and, in 1-D, are applied to an idealised composite material consisting of relatively small particles of infinitely low thermal conductivity embedded in a relatively large matrix of infinitely high thermal conductivity. The fractal composite system is thus not truly representative of a realistic physical system, but the methods presented do serve to demonstrate how analytical solutions can be attained on dust-like fractal domains. It is demonstrated that a measurable temperature is possible on a fractal structure along with finite measures of heat flux and energy. Transient and steady state thermal solutions are presented. The solutions on a selection of the pre-fractals are compared against finite element predictions to reinforce the validity of the approach.     

A solution methodology for contacting domains in pressure die casting

Multi-domain elastostatic problems can often be efficiently solved using coupled single domain iterative techniques. A particular difficulty however is the decrease in convergence rate associated with the increase in number of solution domains. Further convergence difficulties are encountered for multi-domain problems where contacting domains suffer variable contact conditions. Problems of this type are evident in pressure die casting with die blocks coupled together prior and subsequent to thermal loading. Particular interest in this paper is the development of an efficient solution methodology for prediction of gaps at block interfaces in pressure die casting.     

An analytical solution for the unidirectional solidification problem

The extraction of heat from a molten casting is resisted by an imperfect thermal contact at the mold-casting interface. The nature of the contact varies throughout the casting process and has the effect of increasing the thermal resistance at the interface. This can be modelled by incorporating a gaseous gap at the mold-casting interface that grows with increasing time.

This paper is concerned with an analytical solution of the unidirectional solidification problem, which incorporates movement of the casting at the interface. The derivation of the analytical solution requires the simultaneous solution of the transient heat equations, for the mold, gaseous gap, and solid and liquid parts of the melt. The analytical solution is extended so that contamination layers on the mold and casting can be incorporated as well as an initial gap. This is achieved by introducing virtual layers of mold, gas, and casting. Using the extended solution, the effects of interfacial resistance, air conductivity, and gap variation on solidification rates are examined.