in this study, the effect of the secondary structure of the protein on the acid strength of three structures of random (r), alpha helix (α) and beta sheet (b) were investigated theoretically. these structures are related to the cationic amino acids of histidine and lysine in the polypeptide chain of eight-glycine residue. computational methods at the hf, b3lyp, x3lyp and m05-2x levels in the ga...

An optimization strategy for ternary solvent-strength gradient elution RP chromatography is described in which a two-dimensional model of gradient time (2 levels) against ternary proportions of organic modifiers (4 levels) was constructed. From the resolution surface the optimum ratio of organic modifiers could be selected. Excellent retention time and acceptable peak width and resolution simul...

We establish the equivalence of a recently introduced discrete model of the hydrophobic interaction, as well as its extension to continuous state variables, with the Ising model in a magnetic field with temperature-dependent strength. In order to capture the effect of symmetries of the solvent particles we introduce a generalized multi-state model. We solve this model – which is not of the Isin...

We expand upon our recent, fundamental report on solvent immersion imprint lithography (SIIL) and describe a semi-automated and high-performance procedure for prototyping polymer microfluidics and optofluidics. The SIIL procedure minimizes manual intervention through a cost-effective (∼$200) and easy-to-assemble apparatus. We analyze the procedure's performance specifically for Poly (methyl met...

Coupled folding and binding of intrinsically disordered proteins (IDPs) is prevalent in biology. As the first step toward understanding the mechanism of binding, it is important to know if a reaction is 'diffusion-limited' as, if this speed limit is reached, the association must proceed through an induced fit mechanism. Here, we use a model system where the 'BH3 region' of PUMA, an IDP, forms a...

The adsorption behavior of ions at liquid–vapor interfaces exhibits several unexpected yet generic features. In particular, energy and entropy are both minimum when the solute resides near the surface, for a variety of ions in a range of polar solvents, contrary to predictions of classical theories. Motivated by this generality, and by the simple physical ingredients implicated by computational...

Since biomolecules exist in aqueous and membrane environments, the accurate modeling of solvation, and hydrogen bonding interactions in particular, is essential for the exploration of structure and function in theoretical and computational studies. In this chapter, we focus on alternatives to explicit solvent models and discuss recent advances in generalized Born (GB) implicit solvent theories....

The stability of weak polyelectrolytes end grafted to a planar surface has been studied with a molecular theory. The effective quality of the solvent is found to depend on the interplay between polymer grafting density, acid-base equilibrium, and salt concentration. Our results reveal that increasing salt concentration results in a thermodynamically more stable layer. This reverse salt effect i...

For single-file translocations of a charged macromolecule through a narrow pore, the crucial step of arrival of an end at the pore suffers from free energy barriers, arising from changes in intrachain electrostatic interaction, distribution of ionic clouds and solvent molecules, and conformational entropy of the chain. All contributing factors to the barrier in the initial stage of translocatio...

Clostridium acetobutylicum is an important solvent (acetone-butanol-ethanol) producing bacterium. However, a stringent, effective, and convenient-to-use inducible gene expression system that can be used for regulating the gene expression strength in C. acetobutylicum is currently not available. Here, we report an anhydrotetracycline-inducible gene expression system for solvent-producing bacteri...