Small-angle Coulomb collision model for particle-in-cell simulations

We construct and investigate a set of stochastic differential equations that incorporate the physics of velocity-dependent small-angle Coulomb collisions among the plasma particles in a particle-in-cell simulation. Each particle is scattered stochastically from all the other particles in a simulation cell modeled as one or more Maxwellians. Total energy and momentum are conserved by linear transformation of the velocity increments. In two test simulations the proposed “particle-moment” collision algorithm performs well with time steps as large as 10% of the relaxation time – far larger than a particle-pairing collision algorithm, in which pairs of particles are scattered from one another, requires to achieve the same accuracy.     

Conjugation and cyclization—two strong driving forces leading to the formation of new chromophores

Novel chromophores formed in the solvent reactions of α-amino acids and small peptides were identified by crystal structure analysis and characterized by UV absorption. The formation of these chromophores in basic solutions was attributed to two strong driving forces—conjugation and cyclization. The discussion of possible reaction pathways could benefit the future design of α-amino acid-based chromophores.     

Quantum chemistry in parallel with PQS

This article describes the capabilities and performance of the latest release (version 4.0) of the Parallel Quantum Solutions (PQS) ab initio program package. The program was first released in 1998 and evolved from the TEXAS program package developed by Pulay and coworkers in the late 1970s. PQS was designed from the start to run on Linux‐based clusters (which at the time were just becoming popular) with all major functionality being (a) fully parallel; and (b) capable of carrying out calculations on large—by ab initio standards—molecules, our initial aim being at least 100 atoms and 1000 basis functions with only modest memory requirements. With modern hardware and recent algorithmic developments, full accuracy, high‐level calculations (DFT, MP2, CI, and Coupled‐Cluster) can be performed on systems with up to several thousand basis functions on small (4‐32 node) Linux clusters. We have also developed a graphical user interface with a model builder, job input preparation, parallel job submission, and post‐job visualization and display. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009     

Real‐Time Nanomicroscopy via Three‐Dimensional Single‐Particle Tracking

We developed a new method for real‐time, three‐dimensional tracking of fluorescent particles. The instrument is based on a laser‐scanning confocal microscope where the focus of the laser beam is scanned or orbited around the particle. Two confocal pinholes are used to simultaneously monitor regions immediately above and below the particle and a feedback loop is used to keep the orbit centered on the particle. For moderate count rates, this system can track particles with 15 nm spatial resolution in the lateral dimensions and 50 nm in the axial dimension at a temporal resolution of 32 ms. To investigate the interaction of the tracked particles with cellular components, we have combined our orbital tracking microscope with a dual‐color, wide‐field setup. Dual‐color fluorescence wide‐field images are recorded simultaneously in the same image plane as the particle being tracked. The functionality of the system was demonstrated by tracking fluorescent‐labeled artificial viruses in tubulin‐eGFP expressing HUH7 cells. The resulting trajectories can be used to investigate the microtubule network with super resolution.     

Topological free entropy dimension in unital C-algebras

The notion of topological free entropy dimension of n-tuple of elements in a unital C^∗ algebra was introduced by Voiculescu. In the paper, we compute topological free entropy dimension of one self-adjoint element and topological free orbit dimension of one self-adjoint element in a unital C^∗ algebra. We also calculate the values of topological free entropy dimensions of any families of self-adjoint generators of some unital C^∗ algebras, including irrational rotation C^∗ algebra, UHF algebra, and minimal tensor product of two reduced C^∗ algebras of free groups.     

A new photostable terrylene diimide dye for applications in single molecule studies and membrane labeling

A new terrylene diimide-based dye (WS-TDI) that is soluble in water has been synthesized, and its photophysical properties are characterized. WS-TDI forms nonfluorescing H-aggregates in water that show absorption bands being blue-shifted with respect to those of the fluorescing monomeric form. The ratio of monomeric WS-TDI to aggregated WS-TDI was determined to be 1 in 14 400 from fluorescence correlation spectroscopy (FCS) measurements, suggesting the presence of a large amount of soluble, nonfluorescent aggregates in water. The presence of a surfactant such as Pluronic P123 or CTAB leads to the disruption of the aggregates due to the formation of monomers in micelles. This is accompanied by a strong increase in fluorescence. A single molecule study of WS-TDI in polymeric films of PVA and PMMA reveals excellent photostability with respect to photobleaching, far above the photostability of other common water-soluble dyes, such as oxazine-1, sulforhodamine-B, and a water-soluble perylenediimide derivative. Furthermore, labeling of a single protein such as avidin is demonstrated by FCS and single molecule photostability measurements. The high tendency of WS-TDI to form nonfluorescent aggregates in water in connection with its high affinity to lipophilic environments is used for the fluorescence labeling of lipid membranes and membrane containing compartments such as artificial liposomes or endosomes in living HeLa cells. The superior fluorescence imaging quality of WS-TDI in such applications is demonstrated in comparison to other well-known membrane staining dyes such as Alexa647 conjugated with dextran and FM 4-64 lipophilic styryl dye.     

Application of SIMSTEX to oligomerization of insulin analogs and mutants

The propensity of various insulins and their analogs to oligomerize was investigated by mass spectrometric methods including measurement of the relative abundances of oligomers in the gas phase and the kinetics of H/D amide exchange. The kinetics of deuterium uptake show a good fit when the exchanging amides are placed in three kinetic groups: fast, intermediate, and slow. r-Human insulin, of the insulins investigated, has fewer amides that exchange at intermediate rates and more that exchange at slow rates, in accord with its higher extent of association in solution. We adapted PLIMSTEX (protein ligand interactions by mass spectrometry, titration, and H/D exchange) to determine protein/ligand affinities in solution, to determine self-association equilibrium constants for proteins, and to apply them to various insulin analogs. We term this adaptation SIMSTEX (self-association interactions using mass spectrometry, self-titration and H/D exchange); it gives affinity constants that compare well with the literature results. The results from SIMSTEX show that some mutants (e.g., GlnB13) have an increased tendency to self-associate, possibly slowing down their action in vivo. Other mutants (e.g., lispro and AspB9) have lower propensities for self-association, thus providing potentially faster-acting analogs for use in controlling diabetes.     

Characterization of self-assembled supramolecular [Ga4L6] host-guest complexes by electrospray ionization mass spectrometry

Self-assembled supramolecular host-guest complexes have been characterized by electrospray ionization mass spectrometry. The spectra obtained by use of a Q-TOF instrument equipped with a Z-spray ion source show primarily the 3- and 4- charge states of the assemblies. The assemblies have the general formula [guest subset Ga4L6]11- where L represents the chelating bidentate catechol ligand 1,5-bis(2',3'-dihydroxy-benzamido)naphthalene and guests are tetramethyl ammonium (Me4N+), tetraethyl ammonium (Et4N+), tetra-n-propyl ammonium (Pr4N+) and decamethylcobaltocenium (Cp*2Co+) cations. For the first time, the mass spectrum of the empty assembly [Ga4L6]12- is reported. This article also reports that provided the electrospray ion source is capable of preserving noncovalent interactions, it is possible to observe host-guest complexes containing both weak binding guests as well as sterically demanding guests in the mass spectra. The present data suggest that electrospray mass spectrometry is a powerful tool for characterization of supramolecular host-guest complexes.     

Asymmetric Diels-Alder reactions of a new enantiomerically pure sulfinylquinone: a straightforward access to functionalized Wieland-Miescher ketone analogues with (R) absolute configuration

An efficient and highly stereocontrolled preparation, on a large scale, of two new Wieland-Miescher-type diketones is described. The approach centers on a diastereoselective Diels-Alder reaction using a new enantiomerically pure sulfinylquinone. Mechanistic investigations of this cycloaddition on several dienes are described.     

Microfluidic technologies for MALDI-MS in proteomics

The field of microfluidics continues to offer great promise as an enabling technology for advanced analytical tools. For biomolecular analysis, there is often a critical need to couple on-chip microfluidic sample manipulation with back-end MS. Though interfacing microfluidics to MS has been most often reported through the use of direct ESI-MS, there are compelling reasons for coupling microfluidics to MALDI-MS as an alternative to ESI-MS for both online and offline analysis. The intent of this review is to provide a summary of recent developments in the integration of microfluidic systems with MALDI-MS, with an emphasis on applications in proteomics. Key points are summarized, followed by a review of relevant technologies and a discussion of outlook for the field.