Exploration of Gibbs-Laguerre Tessellations for Three-Dimensional Stochastic Modeling

Random tessellations are well suited for probabilistic modeling of three-dimensional (3D) grain microstructures of polycrystalline materials. The present paper is focused on so-called Gibbs-Laguerre tessellations, in which the generators of the Laguerre tessellation form a Gibbs point process. The goal is to construct an energy function of the Gibbs point process such that the resulting tessellation matches some desired geometrical properties. Since the model is analytically intractable, our main tool of analysis is stochastic simulation based on Markov chain Monte Carlo. Such simulations enable us to investigate the properties of the models, and, in the next step, to apply the knowledge gained to the statistical reconstruction of the 3D microstructure of an aluminum alloy extracted from 3D tomographic image data.

     

Complexes H2CO:PXH2 and HCO2H : PXH2 for X=NC,F, Cl,CN, OH,CCH, CH3, and H: Pnicogen Bonds and Hydrogen Bonds

Ab initio MP2/aug’-cc-pVTZ calculations have been carried out to investigate H₂CO : PXH₂ pnicogen-bonded complexes and HCO₂H : PXH₂ complexes that are stabilized by pnicogen bonds and hydrogen bonds, with X=NC, F, Cl, CN, OH, CCH, CH₃, and H. The binding energies of these complexes exhibit a second-order dependence on the O−P distance. DFT-SAPT binding energies correlate linearly with MP2 binding energies. The HCO₂H : PXH₂ complexes are stabilized by both a pnicogen bond and a hydrogen bond, resulting in greater binding energies for the HCO₂H : PXH₂ complexes compared to H₂CO : PXH₂. Neither the O−P distance across the pnicogen bond nor the O−P distance across the hydrogen bond correlates with the binding energies of these complexes. The nonlinearity of the hydrogen bonds suggests that they are relatively weak bonds, except for complexes in which the substituent X is either CH₃ or H. The pnicogen bond is the more important stabilizing interaction in the HCO₂H : PXH₂ complexes except when the substituent X is a more electropositive group. EOM-CCSD spin-spin coupling constants ^1pJ(O−P) across pnicogen bonds in H₂CO:PXH₂ and HCO₂H : PXH₂ complexes increase as the O−P distance decreases, and exhibit a second order dependence on that distance. There is no correlation between ^2hJ(O−P) and the O−P distance across the hydrogen bond in the HCO₂H : PXH₂ complexes. ^2hJ(O−P) coupling constants for complexes with X=CH₃ and H have much greater absolute values than anticipated from their O−P distances.     

Analysis of cell surface molecular distributions and cellular signaling by flow cytometry

Flow cytometry is a fast analysis and separation method for large cell populations, based on collection and processing of optical signals gained on a cell-by-cell basis. These optical signals are scattered light and fluorescence. Owing to its unique potential ofStatistical data analysis and sensitive monitoring of (micro)heterogeneities in large cell populations, flow cytometry—in combination with microscopic imaging techniques—is a powerful tool to study molecular details of cellular signal transduction processes as well. The method also has a widespread clinical application, mostly in analysis of lymphocyte subpopulations for diagnostic (or research) purposes in diseases related to the immune system. A special application of flow cytometry is the mapping of molecular interactions (proximity relationships between membrane proteins) at the cell surface, on a cell-by-cell basis. We developed two approaches to study such questions; both are based ondistance-dependent quenching of excited state fluorophores (donors) by fluorescent or dark (nitroxide radical) acceptors via Förstertype dipole-dipole resonance energy transfer (FRET) and long-range electron transfer (LRET) mechanisms, respectively. A critical evaluation of these methods using donor- or acceptor-conjugated monoclonal antibodies (or their Fab fragments) to select the appropriate cell surface receptor or antigen will be presented in comparison with other approaches for similar purposes. The applicability of FRET and LRET for two-dimensional antigen mapping as well as for detection of conformational changes in extracellular domains of membrane-bound proteins is discussed and illustrated by examples of several lymphoma cell lines. Another special application area of flow cytometry is the analysis of different aspects of cellular signal transduction, e.g., changes of intracellular ion (Ca²⁺, H⁺, Na⁺) concentrations, regulation of ion channel activities, or more complex physiological responses of cell to external stimuli via correlated fluorescence and scatter signal analysis, on a cell-by-cell basis. This way different signaling events such as changes in membrane permeability, membrane potential, cell size and shape, ion distribution, cell density, chromatin structure, etc., can be easily and quickly monitored over large cell populations with the advantage of revealing microheterogeneities in the cellular responses. Flow cytometry also offers the possibility to follow the kinetics of slow (minute- and hour-scale) biological processes in cell populations. These applications are illustrated by the example of complex flow cytometric analysis of signaling in extracellular ATP-triggered apoptosis (programmed cell death) of murine thymic lymphocytes.     

Factors affecting interaction of radiostrontium with river sediments

Uptake of radiostrontium by sediments from two small streams was studied as a function of pH and composition of aqueous phase, of the concentration of strontium, of contact time, temperature and liquid-to-solid ratio (V/m), using laboratory model experiments. Between pH 5 and 12 the uptake increased with pH and shifted to higher pH values with increasing V/m ratio. Addition of cations suppressed the uptake in the order Na⁺<K⁺<Ca²⁺. Increase in strontium concentration had negligible effect up to 10^–5–10^–4 mol·dm^–3 concentration due to high concentrations of dissolved and exchangeable strontium present in the systems. The V/m ratio had no influence on K_d in the range of V/m=20–446 cm³ · g^–1 but K_d value for V/m=0.79 cm³ · g^–1 was significantly lower. Two-step kinetics of the uptake was observed in most cases with a rapid first step (<100 min) followed by a slow increase. No difference was found between the uptake at 10°C and 22°C. Adsorbed radiostrontium could be easily desorbed with river water. The easiness of desorption decreased with repeated desorption. Drying of sediment did not affect the first desorption, repeated desorptions slightly decreased. Conclusions were drawn on the mechanism of radiostrontium uptake and on the importance of the factors studied for modelling of radiostrontium migration in rivers.     

Probing the proton-transfer coordinate of complexes with F--H...P hydrogen bonds using one- and two-bond spin-spin coupling constants

Scalar coupling constants have been computed using the EOM-CCSD method for equilibrium structures of complexes stabilized by F--H...P hydrogen bonds, as well as structures along the proton-transfer coordinates of these complexes. Variations in the signs and absolute values of (1)J(F--H), (1h)J(H--P) and (2h)J(F--P) have been analyzed and interpreted in terms of changing hydrogen bond type. Of the three phosphorus bases (phosphine, trimethylphosphine and phosphinine) investigated in this study, trimethylphosphine forms the strongest complex with FH, and has the largest two-bond F--P coupling constant. Among the relatively simple phosphorus bases, it would appear to be a leading candidate for experimental NMR study. Similarities and differences are noted between the corresponding coupling constants (J) and the reduced coupling constants (K) across F--H...P and F--H...N hydrogen bonds.     

Does the A.T or G.C base-pair possess enhanced stability? Quantifying the effects of CH...O interactions and secondary interactions on base-pair stability using a phenomenological analysis and ab initio calculations

An empirically based relationship between overall complex stability (-DeltaG degrees ) and various possible component interactions is developed to probe the question of whether the A.T/U and G.C base-pairs exhibit enhanced stability relative to similarly hydrogen-bonded complexes. This phenomenological approach suggests ca. 2-2.5 kcal mol-1 in additional stability for A.T owing to a group interaction containing a CH...O contact. Pairing geometry and the role of the CH...O interaction in the A.T base-pair were also probed using MP2/6-31+G(d,p) calculations and a double mutant cycle. The ab initio studies indicated that Hoogsteen geometry is preferred over Watson-Crick geometry in A.T by ca. 1 kcal mol-1. Factors that might contribute to the preference for Hoogsteen geometry are a shorter CH...O contact, a favorable alignment of dipoles, and greater distances between secondary repulsive sites. The CH...O interaction was also investigated in model complexes of adenine with ketene and isocyanic acid. The ab initio calculations support the result of the phenomenological approach that the A.T base-pair does have enhanced stability relative to hydrogen-bonded complexes with just N-H...N and N-H...O hydrogen bonds.     

HC[triple bond]P and H3C-C[triple bond]P as proton acceptors in protonated complexes containing two phosphorus bases: structures, binding energies, and spin-spin coupling constants

Ab initio calculations at the MP2/aug'-cc-pVTZ level have been carried out to investigate the structures and binding energies of cationic complexes involving protonated sp, sp2, and sp3 phosphorus bases as proton donor ions and the sp-hybridized phosphorus bases H-C[triple bond]P and H3C-C[triple bond]P as proton acceptors. These proton-bound complexes exhibit a variety of structural motifs, but all are stabilized by interactions that occur through the pi cloud of the acceptor base. The binding energies of these complexes range from 6 to 15 kcal/mol. Corresponding complexes with H3C-C[triple bond]P as the proton acceptor are more stable than those with H-C[triple bond]P as the acceptor, a reflection of the greater basicity of H3C-C[triple bond]P. In most complexes with sp2- or sp3-hybridized P-H donor ions, the P-H bond lengthens and the P-H stretching frequency is red-shifted relative to the corresponding monomers. Complex formation also leads to a lengthening of the C[triple bond]P bond and a red shift of the C[triple bond]P stretching vibration. The two-bond coupling constants 2pihJ(P-P) and 2pihJ(P-C) are significantly smaller than 2hJ(P-P) and 2hJ(P-C) for complexes in which hydrogen bonding occurs through lone pairs of electrons on P or C. This reflects the absence of significant s electron density in the hydrogen-bonding regions of these pi complexes.     

Global optimization numerical strategies for rate-independent processes

This paper presents an approach to numerical solution of problems posed in the framework of quasi-static rate-independent processes. As soon as a problem allows for an energetic formulation there are known methods of its time discretization by time incremental minimization problems, which demand for global optimization of a non-convex functional. Moreover the two-sided energy inequality, a necessary condition for optimization, can be formulated. Here we present an algorithm for finding solutions of rate-independent processes that verifies this condition and uses the strategy of backtracking if it is violated. We present the selectivity of the mentioned necessary condition in general and give numerical examples of the efficiency of such an algorithm, but also of situations that are beyond its limits. For those we propose a second strategy relying on wisely chosen combinations of spatial discretizations.     

Novel, highly selective gold nanoparticle patterning on surfaces using pure water

We present a simple, novel procedure to selectively deposit gold nanoparticles using pure water. It enables patterning of nanoparticle monolayers with a remarkably high degree of selectivity on flat as well as microstructured oxide surfaces. We demonstrate that water molecules form a thin "capping" layer on exposed thiol molecules within the mercaptan self-assembled layer. This reversible capping of water molecules locally "deactivates" the thiol groups, therewith inhibiting the binding of metallic gold nanoparticles to these specific areas. This amazing role of water molecules can be used as a tool to pattern flat as well as structured surfaces with gold nanoparticles.