TSpred: a web server for the rational design of temperature-sensitive mutants

Temperature sensitive (Ts) mutants of proteins provide experimentalists with a powerful and reversible way of conditionally expressing genes. The technique has been widely used in determining the role of gene and gene products in several cellular processes. Traditionally, Ts mutants are generated by random mutagenesis and then selected though laborious large-scale screening. Our web server, TSpred (http://mspc.bii.a-star.edu.sg/TSpred/), now enables users to rationally design Ts mutants for their proteins of interest. TSpred uses hydrophobicity and hydrophobic moment, deduced from primary sequence and residue depth, inferred from 3D structures to predict/identify buried hydrophobic residues. Mutating these residues leads to the creation of Ts mutants. Our method has been experimentally validated in 36 positions in six different proteins. It is an attractive proposition for Ts mutant engineering as it proposes a small number of mutations and with high precision. The accompanying web server is simple and intuitive to use and can handle proteins and protein complexes of different sizes.

Use of side-chain for rational design of n-type diketopyrrolopyrrole-based conjugated polymers: what did we find out?

The primary role of substituted side chains in organic semiconductors is to increase their solubility in common organic solvents. In the recent past, many literature reports have suggested that the side chains play a critical role in molecular packing and strongly impact the charge transport properties of conjugated polymers. In this work, we have investigated the influence of side-chains on the charge transport behavior of a novel class of diketopyrrolopyrrole (DPP) based alternating copolymers. To investigate the role of side-chains, we prepared four diketopyrrolopyrrole-diketopyrrolopyrrole (DPP-DPP) conjugated polymers with varied side-chains and carried out a systematic study of thin film microstructure and charge transport properties in polymer thin-film transistors (PTFTs). Combining results obtained from grazing incidence X-ray diffraction (GIXD) and charge transport properties in PTFTs, we conclude side-chains have a strong influence on molecular packing, thin film microstructure, and the charge carrier mobility of DPP-DPP copolymers. However, the influence of side-chains on optical properties was moderate. The preferential ``edge-on'' packing and dominant n-channel behavior with exceptionally high field-effect electron mobility values of >1 cm(2) V-1 s(-1) were observed by incorporating hydrophilic (triethylene glycol) and hydrophobic side-chains of alternate DPP units. In contrast moderate electron and hole mobilities were observed by incorporation of branched hydrophobic side-chains. This work clearly demonstrates that the subtle balance between hydrophobicity and hydrophilicity induced by side-chains is a powerful strategy to alter the molecular packing and improve the ambipolar charge transport properties in DPP-DPP based conjugated polymers. Theoretical analysis supports the conclusion that the side-chains influence polymer properties through morphology changes, as there is no effect on the electronic properties in the gas phase. The exceptional electron mobility is at least partially a result of the strong intramolecular conjugation of the donor and acceptor as evidenced by the unusually wide conduction band of the polymer.

Rational molecular dynamics scheme for predicting optimum concentration loading of nano-additive in phase change materials

The present study deals with the diffusion and phase transition behaviour of paraffin reinforced with carbon nano-additives namely graphene oxide (GO) and surface functionalized single walled carbon nanotubes (SWCNT). Bulk disordered systems of paraffin hydrocarbons impregnated with carbon nano-additives have been generated in realistic equilibrium conformations for potential application as latent heat storage systems. Ab initio molecular dynamics(MD) in conjugation with COMPASS forcefield has been implemented using periodic boundary conditions. The proposed scheme allows determination of optimum nano-additive loading for improving thermo-physical properties through analysis of mass, thermal and transport properties; and assists in determination of composite behaviour and related performance from microscopic point of view. It was observed that nanocomposites containing 7.8% surface functionalised SWCNT and 55% GO loading corresponds to best latent heat storage system. The propounded methodology could serve as a by-pass route for economically taxing and iterative experimental procedures required to attain the optimum composition for best performance. The results also hint at the large unexplored potential of ab-initio classical MD techniques for predicting performance of new nanocomposites for potential phase change material applications. (C) 2015 Author(s).

Moduli spaces of vector bundles on a singular rational ruled surface

We study moduli spaces M-X (r, c(1), c(2)) parametrizing slope semistable vector bundles of rank r and fixed Chern classes c(1), c(2) on a ruled surface whose base is a rational nodal curve. We showthat under certain conditions, these moduli spaces are irreducible, smooth and rational (when non-empty). We also prove that they are non-empty in some cases. We show that for a rational ruled surface defined over real numbers, the moduli space M-X (r, c(1), c(2)) is rational as a variety defined over R.