charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS.

CHARMM is one of the most widely used biomolecular force fields. Although developed in close connection with a dedicated molecular simulation engine of the same name, it is also usable with other codes. GROMACS is a well-established, highly optimized, and multipurpose software for molecular dynamics, versatile enough to accommodate many different force field potential functions and the associated algorithms.

Lipid Polymorphism of the Subchloroplast-Granum and Stroma Thylakoid Membrane-Particles. II. Structure and Functions.

In Part I, by using P-NMR spectroscopy, we have shown that isolated granum and stroma thylakoid membranes (TMs), in addition to the bilayer, display two isotropic phases and an inverted hexagonal (H) phase; saturation transfer experiments and selective effects of lipase and thermal treatments have shown that these phases arise from distinct, yet interconnectable structural entities. To obtain information on the functional roles and origin of the different lipid phases, here we performed spectroscopic measurements and inspected the ultrastructure of these TM fragments. Circular dichroism, 77 K fluorescence emission spectroscopy, and variable chlorophyll-a fluorescence measurements revealed only minor lipase- or thermally induced changes in the photosynthetic machinery.

Poly(Pyridinium Salt)s Containing 2,7-Diamino-9,9'-Dioctylfluorene Moieties with Various Organic Counterions Exhibiting Both Lyotropic Liquid-Crystalline and Light-Emitting Properties.

A series of poly(pyridinium salt)s-fluorene main-chain ionic polymers with various organic counterions were synthesized by using ring-transmutation polymerization and metathesis reactions. Their chemical structures were characterized by Fourier Transform Infrared (FTIR), proton (H), and fluorine 19 (F) nuclear magnetic resonance (NMR) spectrometers. These polymers showed a number-average molecular weight (Ms) between 96.

Interfacial structure of 70% fish oil-in-water emulsions stabilized with combinations of sodium caseinate and phosphatidylcholine.

We report on the structural evaluation of high fat fish oil-in-water emulsions emulsified with sodium caseinate (CAS) and phosphatidylcholine (PC). The microemulsions contained 70% (w/w) fish oil with 1.05-1.