Multilevel coarse graining and nano-pattern discovery in many particle stochastic systems

In this work we propose a hierarchy of Markov chain Monte Carlo methods for sampling equilibrium properties of stochastic lattice systems with competing short and long range interactions. Each Monte Carlo step is composed by two or more sub-steps efficiently coupling coarse and finer state spaces. The method can be designed to sample the exact or controlled-error approximations of the target distribution, providing information on levels of different resolutions, as well as at the microscopic level. In both strategies the method achieves significant reduction of the computational cost compared to conventional Markov chain Monte Carlo methods. Applications in phase transition and pattern formation problems confirm the efficiency of the proposed methods.     

Study of disulfide reduction and alkyl chloroformate derivatization of plasma sulfur amino acids using gas chromatography-mass spectrometry

Four disulfide-reducing agents, dithiothreitol (DTT), 2,3-dimercaptopropanesulfonate (DMPS), and the newly tested 2-mercaptoethanesulfonate (MESNA) and Tris(hydroxypropyl)phosphine (THP), were investigated in detail for release of sulfur amino acids in human plasma. After protein precipitation with trichloroacetic acid (TCA), the plasma supernatant was treated with methyl, ethyl, or propyl chloroformate via the well-proven derivatization–extraction technique and the products were subjected to gas chromatographic–mass spectrometric (GC–MS) analysis. All the tested agents proved to be rapid and effective reducing agents for the assay of plasma thiols. When compared with DTT, the novel reducing agents DMPS, MESNA, and THP provided much cleaner extracts and improved analytical performance. Quantification of homocysteine, cysteine, and methionine was performed using their deuterated analogues, whereas other analytes were quantified by means of 4-chlorophenylalanine. Precise and reliable assay of all examined analytes was achieved, irrespective of the chloroformate reagent used. Average relative standard deviations at each analyte level were ≤6%, quantification limits were 0.1–0.2 μmol L⁻¹, recoveries were 94–121%, and linearity was over three orders of magnitude (r ² equal to 0.997–0.998). Validation performed with the THP agent and propyl chloroformate derivatization demonstrated the robustness and reliability of this simple sample-preparation methodology.     

Complexation of some univalent organic cations with benzo-18-crown-6 in nitrobenzene saturated with water

From extraction experiments and γ-activity measurements, the exchange extraction constants corresponding to the general equilibrium C⁺(aq) + 1·Na⁺(nb) <=>1·C⁺ (nb) + Na⁺(aq) taking place in the two-phase water-nitrobenzene system (C⁺ = methylammonium, ethylammonium, propylammonium, ethanolammonium, diethanolammonium, triethanolammonium, cation TRIS+, hydrazinium, hydroxylammonium; 1 = benzo-18-crown-6; aq = aqueous phase, nb = nitrobenzene phase) were evaluated. Furthermore, the stability constants of the 1·C⁺ cationic complex species in nitrobenzene saturated with water were calculated; they were found to increase in the following cation order: triethanolammonium < propylammonium < ethylammonium, diethanolammonium < methylammonium < ethanolammonium < cation TRIS⁺ < hydrazinium < hydroxylammonium.      

Secondary processes in atmospheric pressure chemical ionization-ion trap mass spectrometry: a case study of orotic acid

Atmospheric pressure chemical ionization is known for producing unusual artifacts of the ionization process in some cases. In this work, processes occuring in atmospheric pressure chemical ionization/MS of orotic acid that afforded ions accompanying protonated and deprotonated orotic acid molecules in the spectra were studied. Two processes ran in parallel in the ion source: decarboxylation of neutral orotic acid and collision-induced dissociation of its protonated or deprotonated form. A procedure discerning pre-ionization decomposition and post-ionization dissociation by manipulating ion source parameters was proposed. Experiments with isotopically labeled solvents confirmed ion-molecule reactions of the product of collision-induced dissociation of protonated orotic acid with solvent molecules in the ion source and even under vacuum in the ion trap.     

50 Hz magnetic field effect on the morphology of bacteria

Atomic force microscopy was used to distinguish changes in morphology of bacteria induced by 50 Hz 10 mT magnetic field exposure. It is known that alternating magnetic field exposure causes decrease of viability of different bacterial strains. Previously we found that the viability of rod-like bacteria exposed to magnetic field decreased twice more in comparison with the spherical ones. Motivated by this fact we carried out this study with bacterial cells of both shapes. We used Escherichia coli (rod-like) and Paracoccus denitrificans (spherical) bacteria. As a result we have not observed any change in bacterial morphology neither of rod-like nor of spherical bacteria after 1 h, 50 Hz and 10 mT magnetic field exposure.     

Molecular dynamics with restrictions derived from optical spectra

The information about molecular structure coded in the optical spectra must often be deciphered by complicated computational procedures. A combination of spectral modeling with the molecular dynamic simulations makes the process simpler, by implicit accounting for the inhomogeneous band broadening and Boltzmann averaging of many conformations. Ideally, geometries of studied systems can be deduced by a direct confrontation of such modeling with the experiment. In this work, the comparison is enhanced by restrictions to molecular dynamics propagations based on the Raman and Raman optical activity spectra. The methodology is introduced and tested on model systems comprising idealized H(2)O(2), H(2)O(3) molecules, and the alanine zwitterion. An additional gradient term based on the spectral overlap smoothed by Fourier transformation is constructed and added to the molecular energy during the molecular dynamics run. For systems with one prevalent conformation the method did allow to enrich the Boltzmann ensemble by a spectroscopically favored structure. For systems with multiconformational equilibria families preferential conformations can be selected. An alternative algorithm based on the comparison of the averaged spectra with the reference enabling iterative updates of the conformer probabilities provided even more distinct distributions in shorter times. It also accounts for multiconformer equilibria and provided realistic spectra and conformer distribution for the alanine.     

On the protonation of dibenzo-18-crown-6

Abstract  

The stability constant of the dibenzo-18-crown-6·H₃O⁺ cationic complex species dissolved in nitrobenzene saturated with water has been determined from extraction experiments in the two-phase water–nitrobenzene system and from γ-activity measurements. Various structures of protonated dibenzo-18-crown-6 are discussed.     

Phase separation and phase dissolution in poly(ε-caprolactone)/poly(styrene-co-acrylonitrile) blend

A blend of poly(ε-caprolactone) (PCL) and poly(styrene-co-acrylonitrile) (SAN) containing 27.5 wt% of acrylonitrile having the critical composition (80/20 PCL/SAN) was studied. This PCL/SAN blend having a lower critical solution temperature (LCST) phase boundary at 122 °C offered an excellent opportunity to investigate, firstly the kinetics of phase separation above LCST (125-180 °C), and secondly the kinetics of phase dissolution below LCST (50-115 °C). The blend underwent a temperature-jump above LCST where spinodal decomposition (SD) proceeded, yielding a regularly phase-separated structure (SD structure). Then, it was quenched to the temperatures below LCST when the phase dissolution proceeded. Optical microscopy was used to observe the spinodal decomposition qualitatively while light scattering was used to characterize the phase separation and phase dissolution quantitatively. It was found that during phase dissolution the peak maximum moved towards a smaller angle (wavelength of concentration fluctuations increased) while the peak intensity decreased. This behavior was explained by a model. Also it was found that the fastest phase dissolution kinetics at 80 °C, which was characterized by an apparent diffusion coefficient, was about 10 times slower than the kinetics of phase separation at 180 °C.     

Basic properties of solution of the non-steady Navier–Stokes equations with mixed boundary conditions in a bounded domain

In this paper we deal with the system of the non-steady Navier–Stokes equations with mixed boundary conditions. We study the existence and uniqueness of a solution of this system. Suppose that the system is solvable with some given data (the initial velocity and the right hand side). We prove that there exists a unique solution of this system for data which are small perturbations of the previous ones.