Advantages of using nested collision induced dissociation/post-source decay with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: sequencing of novel peptides from wasp venom

We have examined the applicability of the 'nested' collision induced dissociation/post-source decay (CID/PSD) method to the sequencing of novel peptides from solitary wasps which have neurotoxic venom for paralyzing other insects. The CID/PSD spectrum of a ladder peptide derived from an exopeptidase digest was compared with that of the intact peptide. The mass peaks observed only in the CID/PSD spectrum of a ladder peptide were extracted as C-terminal fragment ions. Assignment of C-terminal fragment ions enabled calculation of N-terminal fragment masses, leading to differentiation between N-terminal fragment ions and internal fragment ions. This methodology allowed rapid and sensitive identification by removing ambiguity in the assignment of the fragment ions, and proved useful for sequencing unknown peptides, in particular those available as natural products with a limited supply. Copyright (C) 2000 John Wiley & Sons, Ltd.

Collision of positronium with atoms, molecules and ions using a modified coupled-channel framework

Scattering of positronium (Ps) from atoms (H, He, Ne, Ar), molecule (H(2)) and ion (He(+)) have been investigated using a coupled-channel (CC) formalism with a regularised non-local exchange potential. The advantage of using such a regularized exchange potential in the close-coupling formalism and the normalizability aspect of the solution at low energies with a minimum effective coupling are discussed. Results for the elastic and total scattering cross-sections, resonance and binding energies in Ps-H, and pick-off annihilation results in Ps-He are found to be in excellent agreement with measurements and variational predictions. (C) 2000 Elsevier B.V. B.V. All rights reserved.

On the Baker-Akhiezer function in the AKNS scheme

Expressions for the Baker-Akhiezer function and their logarithmic space and time derivatives are derived in terms of the matrix elements of U - V matrices and 'squared basis functions'. These expressions generalize the well known formulas for the KdV equation case and establish links between different forms of the Whitham averaging procedure.

Search for single top quarks in the tau plus jets channel using 4.8 fb(-1) of p(p)over-bar collision data

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Search for scalar leptoquarks and T-odd quarks in the acoplanar jet topology using 2.5 fb(-1) of p(p)over-bar collision data at root s=1.96 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Search for squarks and gluinos in events with jets and missing transverse energy using 2.1 fb(-1) of p(p)over-bar collision data at root s=1.96 TeV - D phi Collaboration

A data sample corresponding to an integrated luminosity of 2.1 fb(-1) collected by the D phi detector at the Fermilab Tevatron Collider was analyzed to search for squarks and gluinos produced in p (p) over bar collisions at a center-of-mass energy of 1.96 TeV. No evidence for the production of such particles was observed in topologies involving jets and missing transverse energy, and 95% C.L. lower limits of 379 GeV and 308 GeV were set on the squark and gluino masses, respectively, within the framework of minimal supergravity with tan beta = 3, A(0) = 0, and mu < 0. The corresponding previous limits are improved by 54 GeV and 67 GeV. (c) 2008 Elsevier B.V. All rights reserved.

Extension of the Nambu-Jona-Lasinio model predictions at high densities and temperatures using an implicit regularization scheme

Traditional cutoff regularization schemes of the Nambu-Jona-Lasinio model limit the applicability of the model to energy-momentum scales much below the value of the regularizing cutoff. In particular, the model cannot be used to study quark matter with Fermi momenta larger than the cutoff. In the present work, an extension of the model to high temperatures and densities recently proposed by Casalbuoni, Gatto, Nardulli, and Ruggieri is used in connection with an implicit regularization scheme. This is done by making use of scaling relations of the divergent one-loop integrals that relate these integrals at different energy-momentum scales. Fixing the pion decay constant at the chiral symmetry breaking scale in the vacuum, the scaling relations predict a running coupling constant that decreases as the regularization scale increases, implementing in a schematic way the property of asymptotic freedom of quantum chromodynamics. If the regularization scale is allowed to increase with density and temperature, the coupling will decrease with density and temperature, extending in this way the applicability of the model to high densities and temperatures. These results are obtained without specifying an explicit regularization. As an illustration of the formalism, numerical results are obtained for the finite density and finite temperature quark condensate and applied to the problem of color superconductivity at high quark densities and finite temperature.

Measurement of the W boson helicity in top quark decays using 5.4 fb(-1) of p(p)over-bar collision data

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

SPH simulations of clumps formation by dissipative collision of molecular clouds - I. Non magnetic case

Computer experiments of interstellar cloud collisions were performed with a new smoothed-particle-hydrodynamics (SPH) code. The SPH quantities were calculated by using spatially adaptive smoothing lengths and the SPH fluid equations of motion were solved by means of a hierarchical multiple time-scale leapfrog. Such a combination of methods allows the code to deal with a large range of hydrodynamic quantities. A careful treatment of gas cooling by H, H(2), CO and H II, as well as a heating mechanism by cosmic rays and by H(2) production on grains surface, were also included in the code. The gas model reproduces approximately the typical environment of dark molecular clouds. The experiments were performed by impinging two dynamically identical spherical clouds onto each other with a relative velocity of 10 km s(-1) but with a different impact parameter for each case. Each object has an initial density profile obeying an r(-1)-law with a cutoff radius of 10 pc and with an initial temperature of 20 K. As a main result, cloud-cloud collision triggers fragmentation but in expense of a large amount of energy dissipated, which occurred in the head-on case only. Off-center collision did not allow remnants to fragment along the considered time (similar to 6 Myr). However, it dissipated a considerable amount of orbital energy. Structures as small as 0.1 pc, with densities of similar to 10(4) cm(-3), were observed in the more energetic collision.

A generalized alternating-direction implicit scheme for incompressible magnetohydrodynamic viscous flows at low magnetic Reynolds number

This paper presents numerical simulations of incompressible fluid flows in the presence of a magnetic field at low magnetic Reynolds number. The equations governing the flow are the Navier-Stokes equations of fluid motion coupled with Maxwell's equations of electromagnetics. The study of fluid flows under the influence of a magnetic field and with no free electric charges or electric fields is known as magnetohydrodynamics. The magnetohydrodynamics approximation is considered for the formulation of the non-dimensional problem and for the characterization of similarity parameters. A finite-difference technique is used to discretize the equations. In particular, an extension of the generalized Peaceman and Rachford alternating-direction implicit (ADI) scheme for simulating two-dimensional fluid flows is presented. The discretized conservation equations are solved in stream function-vorticity formulation. We compare the ADI and generalized ADI schemes, and show that the latter is more efficient in simulating low Reynolds number and magnetic Reynolds number problems. Numerical results demonstrating the applicability of this technique are also presented. The simulation of incompressible magneto hydrodynamic fluid flows is illustrated by numerical solution for two-dimensional cases. (c) 2007 Elsevier B.V. All rights reserved.

Possibility of collision between co-orbital asteroids and the Earth

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A critical investigation of the Tanford-Kirkwood scheme by means of Monte Carlo simulations

Monte Carlo simulations are used to assess the adequacy of the Tanford-Kirkwood prescription for electrostatic interactions in macromolecules. Within a continuum dielectric framework, the approach accurately describes salt screening of electrostatic interactions for moderately charged systems consistent with common proteins at physiological conditions. The limitations of the Debye-Huckel theory, which forms the statistical mechanical basis for the Tanford-Kirkwood result, become apparent for highly charged systems. It is shown, both by an analysis of the Debye-Huckel theory and by numerical simulations, that the difference in dielectric permittivity between macromolecule and surrounding solvent does not play a significant role for salt effects if the macromolecule is highly charged. By comparison to experimental data, the continuum dielectric model (combined with either an approximate effective Hamiltonian as in the Tanford-Kirkwood treatment or with exact Monte Carlo simulations) satisfactorily predicts the effects of charge mutation on metal ion binding constants, but only if the macromolecule and solvent are assigned the same or similar permittivities.

Sequencing wasp venom peptides by endopeptidase digestion and nested collision-induced dissociation/post-source decay methods

A method incorporating nested collision-induced dissociation/post-source decay (CID/PSD) combined with endopeptidase digestion is described as an approach to determine the sequence of N-terminally modified peptides. The information from immonium and related ions observed in the CID/PSD spectrum was used for the selection of a suitable endopeptidase for the digestion of peptides. Rapid and reliable assignment of peptide sequence was performed by the comparison of CID/PSD spectra of both intact and endopeptidese-digested peptide fragments, since the assignments of the observed fragment ions to either N- or C-terminal ions can thus be carried out unambiguously. This nested CID/PSD method was applied to the sequence determination of two peptides from the solitary wasps Anoplius samariensis and Batozonellus maculifrons (pompilid wasps), which could not be sequenced by the Edman method due to N-terminal modification. Copyright (C) 2002 John Wiley Sons, Ltd.