Umbrella sampling for nonequilibrium processes

The authors introduce an algorithm for determining the steady-state probability distribution of an ergodic system arbitrarily far from equilibrium. By enforcing equal sampling of different regions of phase space, as in umbrella sampling simulations of systems at equilibrium, low probability regions are explored to a much greater extent than in physically weighted simulations. The algorithm can be used to accumulate joint statistics for an arbitrary number of order parameters for a system governed by any stochastic dynamics. They demonstrate the efficiency of the algorithm by applying it to a model of a genetic toggle switch which evolves irreversibly according to a continuous time Monte Carlo procedure.     

Mass spectral study of substituted allyl aryl and allyl alkyl selenides and some analogous sulfides

The electron impact (EI) mass spectra of allyl aryl selenides showed abundant molecular ions and many fragment ions containing the selenium atom. alpha-Cleavage is the dominant process in the fragmentation of selenides, and cleavage product ions are characteristic of the substituents. In the case of 3-methyl allyl and related aryl selenides, characteristic delta-hydrogen migration to the selenium atom is observed. A McLafferty-type rearrangement is found in benzyl allyl selenides and substituted alkyl allyl selenides. The charge on the rearrangement products preferably remains on the fragments containing the phenyl group. The [M - SeH](+), [M - CH(3)](+) and [M - C(2)H(4)](+) ions are found only in the EI mass spectrum of allyl phenyl selenide, and are attributed to a Claisen rearrangement in the source of the mass spectrometer. All structurally informative fragmentation processes are supported by collision induced dissociation spectra of molecular ions. The fragmentation patterns found in methane chemical ionization (CI) spectra of the selenides were significantly different from those observed in EI. The EI and CI mass spectra of analogous sulfides showed similar behaviour to that observed in the corresponding selenides. Copyright 1999 John Wiley & Sons, Ltd.     

Asymmetric synthesis of a sex pheromone (3S,5R,6S)-3,5-dimethyl-6-isopropyl-3,4,5,6-tetrahydropyran-2-one

An Oppolzer anti-aldol approach for the synthesis of the sex pheromone (3S,5R,6S)-3,5-dimethyl-6-isopropyl-3,4,5,6-tetrahydropyran-2-one is reported.     

Automata and logics over finitely varying functions

We extend some of the classical connections between automata and logic due to Büchi (1960) [5] and McNaughton and Papert (1971) [12] to languages of finitely varying functions or “signals”. In particular, we introduce a natural class of automata for generating finitely varying functions called ’s, and show that it coincides in terms of language definability with a natural monadic second-order logic interpreted over finitely varying functions Rabinovich (2002) [15]. We also identify a “counter-free” subclass of ’s which characterise the first-order definable languages of finitely varying functions. Our proofs mainly factor through the classical results for word languages. These results have applications in automata characterisations for continuously interpreted real-time logics like Metric Temporal Logic (MTL) Chevalier et al. (2006, 2007) [6] and [7].     

Arithmetic coding as a non-linear dynamical system

In order to perform source coding (data compression), we treat messages emitted by independent and identically distributed sources as imprecise measurements (symbolic sequence) of a chaotic, ergodic, Lebesgue measure preserving, non-linear dynamical system known as Generalized Luröth Series (GLS). GLS achieves Shannon’s entropy bound and turns out to be a generalization of arithmetic coding, a popular source coding algorithm, used in international compression standards such as JPEG2000 and H.264. We further generalize GLS to piecewise non-linear maps (Skewed-nGLS). We motivate the use of Skewed-nGLS as a framework for joint source coding and encryption.     

Electrospray ionisation mass spectral studies on hydrolysed products of sulfur mustards

Off-site detection of the hydrolysed products of sulfur mustards in aqueous samples is an important task in the verification of Chemical Weapons Convention (CWC)-related chemicals. The hydrolysed products of sulfur mustards are studied under positive and negative electrospray ionisation (ESI) conditions using an additive with a view to detecting them at trace levels. In the presence of cations (Li(+), Na(+), K(+) and NH(4) (+)), the positive ion ESI mass spectra of all the compounds include the corresponding cationised species; however, only the [M+NH(4)](+) ions form [M+H](+) ions upon decomposition. The tandem mass (MS/MS) spectra of [M+H](+) ions from all the hydrolysed products of the sulfur mustard homologues were distinct and allowed these compounds to be characterised unambiguously. Similarly, the negative ion ESI mass spectra of all the compounds show prominent adducts with added anions (F(-), Cl(-), Br(-), and I(-)), but the [M-H](-) ion can only be generated by decomposition of an [M+F](-) ion. The MS/MS spectra of the [M-H](-) ions from all the compounds result in a common product ion at m/z 77. A precursor ion scan of m/z 77 is shown to be useful in the rapid screening of these compounds in aqueous samples at trace levels, even in the presence of complex masking agents, without the use of time-consuming sample preparation and chromatography steps. An MS/MS method developed to measure the detection limits of the hydrolysed products of sulfur mustards found these to be in the range of 10-500 ppb.     

Adsorption studies of arsenic on Mn-substituted iron oxyhydroxide

Mn-substituted iron oxyhydroxide (Mn(0.13)Fe(0.87)OOH) was prepared by the oxidation of ferrous carbonate precipitated from ferrous sulfate and sodium carbonate solutions. X-ray diffraction analysis led to the conclusion that the sample was basically iron manganese hydroxide with bixbyite structure. The sample exhibited a surface area of 101 m2 g(-1) and a pore volume of 0.35 cm3 g(-1). Batch experiments were conducted to study the adsorption of arsenite and arsenate species onto Mn-substituted iron oxyhydroxide (MIOH) and adsorption equilibrium time was evaluated. The temperature of adsorption was varied from 30 to 60 degrees C. The maximum uptake of arsenite and arsenate was found to be 4.58 and 5.72 mg g(-1), respectively. Zeta potential measurements and FT-IR spectral studies were also conducted to study the nature of adsorption. In both cases, adsorption was best described by Langmuir isotherm and activation energies as calculated from a model-free isoconversional method were found to be on the order of 15-24 and 45-67 kJ mol(-1) for arsenate and arsenite, respectively.     

A DFT study of the mechanism of Ni superoxide dismutase (NiSOD): role of the active site cysteine-6 residue in the oxidative half-reaction

In the present DFT study, the catalytic mechanism of H2O2 formation in the oxidative half-reaction of NiSOD, E-Ni(II) + O2- + 2H+ --> E-Ni(III) + H2O2, has been investigated. The main objective of this study is to investigate the source of two protons required in this half-reaction. The proposed mechanism consists of two steps: superoxide coordination and H2O2 formation. The effect of protonation of Cys6 and the proton donating roles of side chains (S) and backbones (B) of His1, Asp3, Cys6, and Tyr9 residues in these two steps have been studied in detail. For protonated Cys6, superoxide binding generates a Ni(III)-O2H species in a process that is exothermic by 17.4 kcal/mol (in protein environment using the continuum model). From the Ni(III)-O2H species, H2O2 formation occurs through a proton donation by His1 via Tyr9, which relative to the resting position of the enzyme is exothermic by 4.9 kcal/mol. In this pathway, a proton donating role of His1 residue is proposed. However, for unprotonated Cys6, a Ni(II)-O2- species is generated in a process that is exothermic by 11.3 kcal/mol. From the Ni(II)-O2- species, the only feasible pathway for H2O2 formation is through donation of protons by the Tyr9(S)-Asp3(S) pair. The results discussed in this study elucidate the role of the active site residues in the catalytic cycle and provide intricate details of the complex functioning of this enzyme.     

Multiple layer formation of bovine serum albumin on silver nanoparticles revealed by dynamic light scattering and spectroscopic techniques

It is well known that when nanoparticles (NPs) are exposed to biological fluid, it results into formation of nanoparticle protein corona, which has been the subject of extensive studies for the development of targeted drug delivery. In this work, we demonstrated the dynamic light scattering, fluorescence, and UV-visible spectroscopy as quantitative and qualitative tools to monitor adsorption of BSA protein onto silver nanoparticles (AgNPs). The adsorption resulted in significant gradual increase in average hydrodynamic radius of BSA-AgNP corona from 24 to 35 nm and its attainment of equilibrium point (saturation) that correlated with albumin concentration enables condition for bound and unbound protein adsorption to be interpreted. Using DLS, the dissociation constant (K_D) was obtained for soft corona to be 2.09?±?0.30 μM. The UV-visible and fluorescence spectroscopy results were correlated with DLS. Loss of percent helicity in secondary structure of adsorbed BSA was monitored in both coronas as compared to native protein. Both coronas were found to be biocompatible with RBC membrane. Further, the results of adsorption isotherm model were used to validate the multilayer formation of albumin protein on silver nanoparticles. The obtained results would be relevant in the drug design development for tumor-targeted therapy.

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