Discontinuous molecular dynamics for semiflexible and rigid bodies

A general framework for performing event-driven simulations of systems with semiflexible or rigid bodies interacting under impulsive forces is outlined. The method consists of specifying a means of computing the free evolution of constrained motion, evaluating the times at which interactions occur, and determining the consequences of interactions on subsequent motion. Algorithms for computing the times of interaction events and carrying out efficient event-driven simulations are discussed. The semiflexible case and the rigid case differ qualitatively in that the free motion of a rigid body can be computed analytically and need not be integrated numerically.     

Noncentral forces in crystals of charged colloids

The elastic properties of fcc crystals consisting of charge stabilized colloidal particles are determined from real space imaging experiments using confocal microscopy. The normal modes and the force constants of the crystal are obtained from the fluctuations of the particles around their lattice sites using the equipartition theorem. We show that the Cauchy relation is not fulfilled and that only noncentral many-body forces can account for the elastic properties.     

Spinodal decomposition in a model colloid-polymer mixture in microgravity

We study phase separation in a deeply quenched colloid-polymer mixture in microgravity on the International Space Station using small-angle light scattering and direct imaging. We observe a clear crossover from early-stage spinodal decomposition to late-stage, interfacial-tension-driven coarsening. Data acquired over 5 orders of magnitude in time show more than 3 orders of magnitude increase in domain size, following nearly the same evolution as that in binary liquid mixtures. The late-stage growth approaches the expected linear growth rate quite slowly.     

Inhibition of the histone demethylase JMJD2E by 3-substituted pyridine 2,4-dicarboxylates

Based on structural analysis of the human 2-oxoglutarate (2OG) dependent JMJD2 histone N(ε)-methyl lysyl demethylase family, 3-substituted pyridine 2,4-dicarboxylic acids were identified as potential inhibitors with possible selectivity over other human 2OG oxygenases. Microwave-assisted palladium-catalysed cross coupling methodology was developed to install a diverse set of substituents on the sterically demanding C-3 position of a pyridine 2,4-dicarboxylate scaffold. The subsequently prepared di-acids were tested for in vitro inhibition of the histone demethylase JMJD2E and another human 2OG oxygenase, prolyl-hydroxylase domain isoform 2 (PHD2, EGLN1). A subset of substitution patterns yielded inhibitors with selectivity for JMJD2E over PHD2, demonstrating that structure-based inhibitor design can enable selective inhibition of histone demethylases over related human 2OG oxygenases.     

Simulation of tethered oligomers in nanochannels using multi-particle collision dynamics

The effect of a high Reynold's number, pressure-driven flow of a compressible gas on the conformation of an oligomer tethered to the wall of a square channel is studied under both ideal solvent and poor solvent conditions using a hybrid multiparticle collision dynamics and molecular dynamics algorithm. Unlike previous studies, the flow field contains an elongational component in addition to a shear component as well as fluid slip near the walls and results in a Schmidt number for the polymer beads that is less than unity. In both solvent regimes the oligomer is found to extend in the direction of flow. Under the ideal solvent conditions, torsional twisting of the chain and aperiodic cyclical dynamics are observed for the end of the oligomer. Under poor solvent conditions, a metastable helix forms in the end of the chain despite the lack of any attractive potential between beads in the oligomeric chain. The formation of the helix is postulated to be the result of a solvent induced chain collapse that has been confined to a single dimension by a strong flow field.     

Clique analysis of a tolerance relation

The Harary‐Ross clique detection algorithm has often been neglected in analyses of symmetric graphs and tolerance relations because of presumed storage and computation problems. This paper presents a modification of the original algorithm which overcomes these difficulties. The modified algorithm is shown to perform as well as other recent structurally different algorithms. Indeed, for arc densities which might be expected in typical sociometric analyses, the modified algorithm has certain conceptual and operational advantages. The paper also indicates possible applications of the algorithm in the analysis of non‐symmetric functional relations and points out the conceptual similarity with simplicial connectivity analysis.     

Crotonase catalysis enables flexible production of functionalized prolines and carbapenams

The biocatalytic versatility of wildtype and engineered carboxymethylproline synthases (CMPSs) is demonstrated by the preparation of functionalized 5-carboxymethylproline derivatives methylated at C-2, C-3, C-4, or C-5 of the proline ring from appropriately substituted amino acid aldehydes and malonyl-coenzyme A. Notably, compounds with a quaternary center (at C-2 or C-5) were prepared in a stereoselective fashion by engineered CMPSs. The substituted-5-carboxymethyl-prolines were converted into the corresponding bicyclic β-lactams using a carbapenam synthetase. The results demonstrate the utility of the crotonase superfamily enzymes for stereoselective biocatalysis, the amenability of carbapenem biosynthesis pathways to engineering for the production of new bicyclic β-lactam derivatives, and the potential of engineered biocatalysts for the production of quaternary centers.     

Dynamics of drying in 3D porous media

The drying dynamics in three dimensional porous media are studied with confocal microscopy. We observe abrupt air invasions in size from single particle to hundreds of particles. We show that these result from the strong flow from menisci in large pores to menisci in small pores during drying. This flow causes air invasions to start in large menisci and subsequently spread throughout the entire system. We measure the size and structure of the air invasions and show that they are in accord with invasion percolation. By varying the particle size and contact angle we unambiguously demonstrate that capillary pressure dominates the drying process.     

Investigation of high sensitivity GC-FTIR as an analytical tool for structural identification

As part of a detailed investigation into the application of GC-FTIR in industrial and environmental analysis, representative sets of samples have been analyzed in parallel using commercial high-sensitivity instruments. Two of the instruments utilize low temperature storage of the GC eluate to extend the time available for FTIR analysis, yielding greater sensitivity than that possible by conventional ‘light-pipe’ GC-FTIR. In certain circumstances, instruments using both types of sample storage give rise to spectra exhibiting features characteristic of the interface used. Chromatographic resolution was found not to be significantly degraded by use of either sample storage interface. Particular advantages were found in having parallel flame ionization detection and mass spectrometry; this enabled the location of smaller components and gave greater certainty of identification.