Dense regular packings of irregular nonconvex particles

We present a new numerical scheme to study systems of nonconvex, irregular, and punctured particles in an efficient manner. We employ this method to analyze regular packings of odd-shaped bodies, both from a nanoparticle and from a computational geometry perspective. Besides determining close-packed structures for 17 irregular shapes, we confirm several conjectures for the packings of a large set of 142 convex polyhedra and extend upon these. We also prove that we have obtained the densest packing for both rhombicuboctahedra and rhombic enneacontrahedra and we have improved upon the packing of enneagons and truncated tetrahedra.     

Engineered C–N Lyase: Enantioselective Synthesis of Chiral Synthons for Artificial Dipeptide Sweeteners

Aspartic acid derivatives with branched N‐alkyl or N‐arylalkyl substituents are valuable precursors to artificial dipeptide sweeteners such as neotame and advantame. The development of a biocatalyst to synthesize these compounds in a single asymmetric step is an as yet unmet challenge. Reported here is an enantioselective biocatalytic synthesis of various difficult N‐substituted aspartic acids, including N‐(3,3‐dimethylbutyl)‐l ‐aspartic acid and N‐[3‐(3‐hydroxy‐4‐methoxyphenyl)propyl]‐l ‐aspartic acid, precursors to neotame and advantame, respectively, using an engineered variant of ethylenediamine‐N,N′‐disuccinic acid (EDDS) lyase from Chelativorans sp. BNC1. This engineered C–N lyase (mutant D290M/Y320M) displayed a remarkable 1140‐fold increase in activity for the selective hydroamination of fumarate compared to that of the wild‐type enzyme. These results present new opportunities to develop practical multienzymatic processes for the more sustainable and step‐economic synthesis of an important class of food additives.     

Phase diagram of hard snowman-shaped particles

We present the phase diagram of hard snowman-shaped particles calculated using Monte Carlo simulations and free energy calculations. The snowman particles consist of two hard spheres rigidly attached at their surfaces. We find a rich phase behavior with isotropic, plastic crystal, and aperiodic crystal phases. The crystalline phases found to be stable for a given sphere diameter ratio correspond mostly to the close packed structures predicted for equimolar binary hard-sphere mixtures of the same diameter ratio. However, our results also show several crystal-crystal phase transitions, with structures with a higher degree of degeneracy found to be stable at lower densities, while those with the best packing are found to be stable at higher densities.     

Stacking in sediments of colloidal hard spheres

We use computer simulations to investigate the crystallization dynamics of sedimenting hard spheres in large systems (hundreds of thousands of particles). We show that slow sedimentation results primarily in face-centered cubic (fcc) stacked crystals, instead of random hexagonal close packed or hexagonal close packed (hcp) crystals. We also find slanted stacking faults, in the fcc regions. However, we attribute the formation of fcc to the free energy difference between fcc and hcp and not to the presence of these slanted stacking faults. Although the free energy difference between hcp and fcc per particle is small (only 10(-3) times the thermal energy), it can become considerable, when multiplied by the number of particles in each domain. The ratio of fcc to hcp obtained from dynamic simulations is in excellent agreement with well-equilibrated Monte Carlo simulations, in which no slanted stacking faults were found. Our results explain a range of experiments on colloids, in which the amount of fcc increases upon lowering the sedimentation rate or decreasing the initial volume fraction.     

Kinetic pathways for the isotropic-nematic phase transition in a system of colloidal hard rods: a simulation study

We study the kinetic pathways for the isotropic-to-nematic transition in a fluid of colloidal hard rods. In order to follow the formation of the nematic phase, we develop a new cluster criterion that distinguishes nematic clusters from the isotropic phase. Applying this criterion in Monte Carlo simulations, we find spinodal decomposition as well as nucleation and growth depending on the supersaturation. We determine the height of the nucleation barrier and we study the shape and structure of the cluster. More specifically, we find ellipsoidal nematic clusters with an aspect ratio of about 1.7 and a homogeneous nematic director field. Our results are consistent with theoretical predictions on the shape and director field of nematic tactoids. Classical nucleation theory gives reasonable predictions for the height of the nucleation barrier and the critical nucleus size.     

Evidence for out-of-equilibrium crystal nucleation in suspensions of oppositely charged colloids

We report a numerical study of the rate of crystal nucleation in a binary suspension of oppositely charged colloids. Two different crystal structures compete in the thermodynamic conditions under study. We find that the crystal phase that nucleates is metastable and, more surprisingly, its nucleation free-energy barrier is not the lowest one. This implies that, during nucleation, there is insufficient time for subcritical nuclei to relax to their lowest free-energy structure. Such behavior is in direct contradiction with the common assumption that the phase that crystallizes most readily is the one with the lowest free-energy barrier for nucleation. The phenomenon that we describe should be relevant for crystallization experiments where competing solid structures are not connected by an easy transformation.     

Inhibition of cyclin-dependent kinases, GSK-3beta and CK1 by hymenialdisine, a marine sponge constituent

BACKGROUND: Over 2000 protein kinases regulate cellular functions. Screening for inhibitors of some of these kinases has already yielded some potent and selective compounds with promising potential for the treatment of human diseases. RESULTS: The marine sponge constituent hymenialdisine is a potent inhibitor of cyclin-dependent kinases, glycogen synthase kinase-3beta and casein kinase 1. Hymenialdisine competes with ATP for binding to these kinases. A CDK2-hymenialdisine complex crystal structure shows that three hydrogen bonds link hymenialdisine to the Glu81 and Leu83 residues of CDK2, as observed with other inhibitors. Hymenialdisine inhibits CDK5/p35 in vivo as demonstrated by the lack of phosphorylation/down-regulation of Pak1 kinase in E18 rat cortical neurons, and also inhibits GSK-3 in vivo as shown by the inhibition of MAP-1B phosphorylation. Hymenialdisine also blocks the in vivo phosphorylation of the microtubule-binding protein tau at sites that are hyperphosphorylated by GSK-3 and CDK5/p35 in Alzheimer's disease (cross-reacting with Alzheimer's-specific AT100 antibodies). CONCLUSIONS: The natural product hymenialdisine is a new kinase inhibitor with promising potential applications for treating neurodegenerative disorders.     

An Artificial Heme Enzyme for Cyclopropanation Reactions

An artificial heme enzyme was created through self‐assembly from hemin and the lactococcal multidrug resistance regulator (LmrR). The crystal structure shows the heme bound inside the hydrophobic pore of the protein, where it appears inaccessible for substrates. However, good catalytic activity and moderate enantioselectivity was observed in an abiological cyclopropanation reaction. We propose that the dynamic nature of the structure of the LmrR protein is key to the observed activity. This was supported by molecular dynamics simulations, which showed transient formation of opened conformations that allow the binding of substrates and the formation of pre‐catalytic structures.     

STANDARDIZING THE SEGMENTATION INDEX S3

The segmentation index S ₃ of Baerveldt and Snijders (1994) Baerveldt, C. and Snijders, T. 1994. Influences on and from the segmentation of networks: Hypotheses and tests. Social Networks, 16: 213–232. [Crossref], [Web of Science ®] , [Google Scholar] is used in the research of social cohesion. However, as is often the case with network level measures, the index is sensitive to network size and density. Therefore, networks of different size or density are not easily comparable. Of course, this seriously limits the research using this index. In this article we propose a standardization of the segmentation index that solves this problem. The standardization uses the expected value and the maximum value of the index, within certain network types, the so-called network families. We show how these values can be calculated. Furthermore, we present a figure that can be used to derive the expected values and a table for easy determination of the maximum values for all network families existing of 4 to 20 members. This allows the calculation of the standardized index for all networks within these families.     

Effect of excluded volume interactions on the interfacial properties of colloid-polymer mixtures

We report a numerical study of equilibrium phase diagrams and interfacial properties of bulk and confined colloid-polymer mixtures using grand canonical Monte Carlo simulations. Colloidal particles are treated as hard spheres, while the polymer chains are described as soft repulsive spheres. The polymer-polymer, colloid-polymer, and wall-polymer interactions are described by density-dependent potentials derived by Bolhuis and Louis [Macromolecules 35, 1860 (2002)]. We compared our results with those of the Asakura-Oosawa-Vrij model [J. Chem. Phys. 22, 1255 (1954); J. Polym Sci 33, 183 (1958); Pure Appl. Chem. 48, 471 (1976)] that treats the polymers as ideal particles. We find that the number of polymers needed to drive the demixing transition is larger for the interacting polymers, and that the gas-liquid interfacial tension is smaller. When the system is confined between two parallel hard plates, we find capillary condensation. Compared with the Asakura-Oosawa-Vrij model, we find that the excluded volume interactions between the polymers suppress the capillary condensation. In order to induce capillary condensation, smaller undersaturations and smaller plate separations are needed in comparison with ideal polymers.