Brownian dynamics simulations on CPU and GPU with BD_BOX

There has been growing interest in simulating biological processes under in vivo conditions due to recent advances in experimental techniques dedicated to study single particle behavior in crowded environments. We have developed a software package, BD_BOX, for multiscale Brownian dynamics simulations. BD_BOX can simulate either single molecules or multicomponent systems of diverse, interacting molecular species using flexible, coarse-grained bead models. BD_BOX is written in C and employs modern computer architectures and technologies; these include MPI for distributed-memory architectures, OpenMP for shared-memory platforms, NVIDIA CUDA framework for GPGPU, and SSE vectorization for CPU.     

Asymmetric aldol-Tishchenko reaction catalyzed by Yb-complexes with basic amino acid-derived ligands

Simple amino acid-derived esters have been identified as promising chiral sources for the ytterbium-catalyzed aldol-Tishchenko reaction of aromatic aldehydes with aliphatic ketones. The 1,3-anti-diols with three stereogenic centers were isolated in excellent yields, complete anti-diastereocontrol and enantioselectivities of up to 50% ee.     

Faster proton transfer dynamics of water on SnO2 compared to TiO2

Proton jump processes in the hydration layer on the iso-structural TiO(2) rutile (110) and SnO(2) cassiterite (110) surfaces were studied with density functional theory molecular dynamics. We find that the proton jump rate is more than three times faster on cassiterite compared with rutile. A local analysis based on the correlation between the stretching band of the O-H vibrations and the strength of H-bonds indicates that the faster proton jump activity on cassiterite is produced by a stronger H-bond formation between the surface and the hydration layer above the surface. The origin of the increased H-bond strength on cassiterite is a combined effect of stronger covalent bonding and stronger electrostatic interactions due to differences of its electronic structure. The bridging oxygens form the strongest H-bonds between the surface and the hydration layer. This higher proton jump rate is likely to affect reactivity and catalytic activity on the surface. A better understanding of its origins will enable methods to control these rates.     

Structures, electronic properties and solid state luminescence of Cu(I) iodide complexes with 2,9-dimethyl-1,10-phenanthroline and aliphatic aminomethylphosphines or triphenylphosphine

The luminescent complexes of triphenylphosphine and two interesting aminomethylphosphines: P(CH(2)N(CH(2)CH(2))(2)NCH(3))(3) and P(CH(2)N(CH(2)CH(2))(2)O)(3) with copper(I) iodide and 2,9-dimethyl-1,10-phenanthroline (dmp): [CuI(dmp)PPh(3)], [CuI(dmp)P(CH(2)N(CH(2)CH(2))(2)NCH(3))(3)] and [CuI(phen)P(CH(2)N(CH(2)CH(2))(2)O)(3)] are presented in this work. These complexes were characterized in solution by means of NMR spectroscopy and their structures were crystallographically determined in the solid state. All complexes crystallize as the discrete dimers bound by π-stacking interactions between dmp rings. The coordination geometry about the Cu(I) centre is pseudo-tetrahedral showing small flattening and large rocking distortions. The investigated compounds exhibit intense orange photoluminescence in the solid state (emission peaks at r.t.: λ(max) = 588-592 nm; τ = 1.7-2.2 and 6.4-10.0 μs; at 77 K: λ(max) = 605-612 nm; τ = 4.8-6.5 and 32-47 μs), which is several orders higher than the luminescence of the analogous complexes with 1,10-phenanthroline (phen). Electronic and structural properties of the [CuI(dmp/phen)PR(3)] complexes were characterized using DFT methods to interpret their photophysics. On the basis of TDDFT calculations the broad CT bands observed in UV-Vis spectra are interpreted as the two mixed transitions from σ(CuI) bond with a small admixture of σ(CuP) bond to π* phen or dmp ligand: (MX,MPR(3))LCT, while the emissions most probably occur from two triplet states which are in thermal equilibrium.     

On the points realizing the distance to a definable set

We prove a definable/subanalytic version of a useful lemma, presumably due to John Nash, concerning the points realizing the Euclidean distance to an analytic submanifold of Rn. We present a parameter version of the main result and we discuss the properties of the multifunction obtained.     

Quantification of changes in oxygen release from red blood cells as a function of age based on magnetic susceptibility measurements

This study extends the in vitro understanding of the RBC storage lesion by serially analyzing the RBC's magneophoretic mobility, a property dependent on the content and oxygenation or oxidation state of hemoglobin (Hb) iron, during storage. Four prestorage leukoreduced, AS-5 preserved RBC units were stored between 1 and 6 °C for 42 days. Weekly starting on storage day 7, each unit was sampled, divided into 3 aliquots, each subjected to different reactions: one aliquot was exposed to room air to produce oxyhemoglobin (oxyHb), another aliquot was mixed with sodium nitrite to produce methemoglobin (metHb), while the third aliquot was desaturated of oxygen (deoxyhemoglobin, deoxyHb) using nitrogen gas. These aliquots were placed into a cell tracking velocimetry (CTV) apparatus which measured both the settling velocity (u(s)) of the RBCs as well as their magnetically induced velocity (u(m)). The u(m)/u(s) ratio depends on the oxygenation state of the hemoglobin and the quantity of iron within the RBC. The RBC density was measured by percoll centrifugation. There was a significant reduction in the u(m)/u(s) ratio for the deoxyHb RBC aliquot as storage time elapsed, with a smaller but still significant reduction in the u(m)/u(s) ratio for the metHb aliquot. The average RBC density decreased very slightly during storage, as determined by the percoll centrifugation technique, although the average settling velocity (another measure of cell density) seemed to fluctuate during storage. The decrease in magnetophoretic mobility of the deoxyHb portion is explicable either by Hb's increased affinity for oxygen during storage, or else a loss of iron from the cells.     

Light driven reactions of single physisorbed azobenzenes

We present a successful attempt of decoupling a dye molecule from a metallic surface via physisorption for enabling direct photoisomerization. Effective switching between the isomers is possible by exposure to UV light via the rotation pathway.     

A Rapid Gas-Chromatography/Mass-Spectrometry Technique for Determining Odour Activity Values of Volatile Compounds in Plant Proteins: Soy,and Allergen-Free Pea and Brown Rice Protein

Plant-based protein sources have a characteristic aroma that limits their usage in various meat-alternative formulations. Despite being the most popular plant-based protein, the allergenicity of soy protein severely restricts the potential adoption of soy protein as an animal substitute. Thereby, allergen-free plant-protein sources need to be characterized. Herein, we demonstrate a rapid solid-phase-microextraction gas-chromatography/mass-spectrometry (SPME-GC/MS) technique for comparing the volatile aroma profile concentration of two different allergen-free plant-protein sources (brown rice and pea) and comparing them with soy protein. The extraction procedure consisted of making a 1:7 w/v aqueous plant protein slurry, and then absorbing the volatile compounds on an SPME fibre under agitation for 10 min at 40 °C, which was subsequently injected onto a GC column coupled to an MS system. Observed volatile concentrations were used in conjunction with odour threshold values to generate a Total Volatile Aroma Score for each protein sample. A total of 76 volatile compounds were identified. Aldehydes and furans were determined to be the most dominant volatiles present in the plant proteins. Both brown rice protein and pea protein contained 64% aldehydes and 18% furans, with minor contents of alcohols, ketones and other compounds. On the other hand, soy protein consisted of fewer aldehydes (46%), but a more significant proportion of furans (42%). However, in terms of total concentration, brown rice protein contained the highest intensity and number of volatile compounds. Based on the calculated odour activity values of the detected compounds, our study concludes that pea proteins could be used as a suitable alternative to soy proteins in applications for allergen-free vegan protein products without interfering with the taste or flavour of the product.     

Twistor Geometry of a Pair of Second Order ODEs

We discuss the twistor correspondence between path geometries in three dimensions with vanishing Wilczynski invariants and anti-self-dual conformal structures of signature (2, 2). We show how to reconstruct a system of ODEs with vanishing invariants for a given conformal structure, highlighting the Ricci-flat case in particular. Using this framework, we give a new derivation of the Wilczynski invariants for a system of ODEs whose solution space is endowed with a conformal structure. We explain how to reconstruct the conformal structure directly from the integral curves, and present new examples of systems of ODEs with point symmetry algebra of dimension four and greater which give rise to anti–self–dual structures with conformal symmetry algebra of the same dimension. Some of these examples are (2, 2) analogues of plane wave space–times in General Relativity. Finally we discuss a variational principle for twistor curves arising from the Finsler structures with scalar flag curvature.