these are notes from introductory survey lectures given at the institute for studies in theoretical physics and mathematics (ipm), teheran, in 2008 and 2010. we present the definition and the fundamental properties of fomin-zelevinsky’s cluster algebras. then, we introduce quiver representations and show how they can be used to construct cluster variables, which are the canonical generators of ...

The breast and ovarian cancer susceptibility gene product BRCA1 is a tumor suppressor, but its precise biochemical function remains unknown. The BRCA1 COOH terminus acts as a transcription activation domain, and germ-line cancer- predisposing mutations in this region abolish transcription activation, whereas benign polymorphisms do not. These results raise the possibility that loss of transcrip...

A large cellulosomal gene cluster was identified in the recently sequenced genome of Clostridium acetobutylicum ATCC 824. Sequence analysis revealed that this cluster contains the genes for the scaffolding protein CipA, the processive endocellulase Cel48A, several endoglucanases of families 5 and 9, the mannanase Man5G, and a hydrophobic protein, OrfXp. Surprisingly, genetic organization of thi...

Unspecific adhesion of bacteria is usually the first step in the formation of biofilms on abiotic surfaces, yet it is unclear up to now which forces are governing this process. Alongside long-ranged van der Waals and electrostatic forces, short-ranged hydrophobic interaction plays an important role. To characterize the forces involved during approach and retraction of an individual bacterium to...

Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered desolvation barriers. For such transitions, it is thus important characterize and understand the interplay between solvation conformation. Using specialized molecular simulations, here we perform a characterization for polymer solvated in water. We find that an external potentia...

the search for new stationary phases has been one of the predominant concerns in high performance liquid chromatography (hplc) in order to achieve better resolutions, longer column lives, and reduce the time of analysis. a chromatographic packing for separation of underivatized amino acids (aas) were prepared by dynamically coating 2-amino tetraphenyl prophyrin (atpp) on a c-18 reversed-phase p...

As the beneficial effects of curcumin have often been reported to be limited to its small concentrations, we have undertaken a study to find the aggregation properties of curcumin in water by varying the number of monomers. Our molecular dynamics simulation results show that the equilibrated structure is always an aggregated state with remarkable structural rearrangements as we vary the number ...