Implementing and using high-order finite element methods

We present theoretical analyses of and detailed timings for two programs which use high-order finite element methods to solve the Navier- Strokes equations in two and three dimensions. The analyses show that algorithms popular in low-order finite element implementations are not always appropriate for high-order methods. The timings show that with the proper algorithms high-order finite element methods are viable for solving the Navier-Stokes equations. We show that it is more efficient, both in time and storage, not to precompute element matrices as the degree of approximating functions increases. We also study the cost of assembling the stiffness matrix versus directly evaluating bilinear forms in two and three dimensions. We show that it is more efficient not to assemble the full stiffness matrix for high-order methods in some cases. We consider the computational issues with regard to both Euclidean and isoparametric elements. We show that isoparametric elements may be used with higher-order elements without increasing the order of computational complexity.     

A First-Passage Kinetic Monte Carlo algorithm for complex diffusion–reaction systems

We develop an asynchronous event-driven First-Passage Kinetic Monte Carlo (FPKMC) algorithm for continuous time and space systems involving multiple diffusing and reacting species of spherical particles in two and three dimensions. The FPKMC algorithm presented here is based on the method introduced in Oppelstrup et al. [10] and is implemented in a robust and flexible framework. Unlike standard KMC algorithms such as the n-fold algorithm, FPKMC is most efficient at low densities where it replaces the many small hops needed for reactants to find each other with large first-passage hops sampled from exact time-dependent Green’s functions, without sacrificing accuracy. We describe in detail the key components of the algorithm, including the event-loop and the sampling of first-passage probability distributions, and demonstrate the accuracy of the new method. We apply the FPKMC algorithm to the challenging problem of simulation of long-term irradiation of metals, relevant to the performance and aging of nuclear materials in current and future nuclear power plants. The problem of radiation damage spans many decades of time-scales, from picosecond spikes caused by primary cascades, to years of slow damage annealing and microstructure evolution. Our implementation of the FPKMC algorithm has been able to simulate the irradiation of a metal sample for durations that are orders of magnitude longer than any previous simulations using the standard Object KMC or more recent asynchronous algorithms.     

Aluminum Chloride (Alcl3) Promotes Selective Oxidative Deprotection of Benzylic Trimethylsilyl and Tert- Butyldimethylsilyl Ethers to the Corresponding Carbonyl Compounds with Manganese Dioxide (Mno2)

Various types of trimethylsilyl and tert-butyldimethylsilyl ethers of primary and secondary benzylic alcohols could be selectively converted to their corresponding carbonyl compounds with MnO₂ in the presence of AlCl₃ in good to excellent yields.     

Molecular dynamics simulation of ferronanofluid behavior in a nanochannel in the presence of constant and time-dependent magnetic fields

Journal of Thermal Analysis and Calorimetry - For the first time, double phosphates(V) Zn3Cr4(PO4)6 and Mg3Cr4(PO4)6 were synthesized by non-waste solid-state reaction, performed in the temperature...     

A new, efficient, and simple method for the synthesis of thiiranes from epoxides under solvent-free conditions

A simple, efficient, and new method has been developed for the synthesis of thiiranes from epoxides through a one-pot reaction of epoxides with diethyl phosphite in the presence of ammonium acetate or ammonium hydrogen carbonate/sulfur/ and acidic alumina under solvent-free conditions using microwave irradiation.     

‘Fixed charge’ chemical derivatization and data dependant multistage tandem mass spectrometry for mapping protein surface residue accessibility

Protein surface accessible residues play an important role in protein folding, protein-protein interactions and protein-ligand binding. However, a common problem associated with the use of selective chemical labeling methods for mapping protein solvent accessible residues is that when a complicated peptide mixture resulting from a large protein or protein complex is analyzed, the modified peptides may be difficult to identify and characterize amongst the largely unmodified peptide population (i.e., the ‘needle in a haystack’ problem). To address this challenge, we describe here the development of a strategy involving the synthesis and application of a novel ‘fixed charge’ sulfonium ion containing lysine-specific protein modification reagent, S,S′-dimethylthiobutanoylhydroxysuccinimide ester (DMBNHS), coupled with capillary HPLC-ESI-MS, automated CID-MS/MS, and data-dependant neutral loss mode MS³ in an ion trap mass spectrometer, to map the surface accessible lysine residues in a small model protein, cellular retinoic acid binding protein II (CRABP II). After reaction with different reagent:protein ratios and digestion with Glu-C, modified peptides are selectively identified and the number of modifications within each peptide are determined by CID-MS/MS, via the exclusive neutral loss(es) of dimethylsulfide, independently of the amino acid composition and precursor ion charge state (i.e., proton mobility) of the peptide. The observation of these characteristic neutral losses are then used to automatically ‘trigger’ the acquisition of an MS³ spectrum to allow the peptide sequence and the site(s) of modification to be characterized. Using this approach, the experimentally determined relative solvent accessibilities of the lysine residues were found to show good agreement with the known solution structure of CRABP II.     

Adsorption of triton X-100 on silica gel: effects of temperature and alcohols

Adsorption of Triton X-100 (TX-100) on silica gel has been studied as a function of temperature (308–328 K) and composition for mixtures of water with ethanol or t-butanol. The adsorption capacity of silica gel for TX-100 decreases with increase in alcohol content. Adsorption isotherms of TX-100 on silica gel are four-region and were analyzed using the ARIAN (adsorption isotherm regional analysis) model. Data in regions 2, 3 and 4 were fitted to the Temkin, bilayer and reverse desorption isotherms, respectively. The results show that adsorption of TX-100 on silica gel in water and alcohol-water binary mixtures occurs mainly through formation of monolayer surface aggregates or low bilayer coverage.