Automated data reduction for hydrogen/deuterium exchange experiments,enabled by high-resolution fourier transform ion cyclotron resonance mass spectrometry

Mass analysis of proteolytic fragment peptides following hydrogen/deuterium exchange offers a general measure of solvent accessibility/hydrogen bonding (and thus conformation) of solution-phase proteins and their complexes. The primary problem in such mass analyses is reliable and rapid assignment of mass spectral peaks to the correct charge state and degree of deuteration of each fragment peptide, in the presence of substantial overlap between isotopic distributions of target peptides, autolysis products, and other interferant species. Here, we show that at sufficiently high mass resolving power (m/Δm_50% ≥ 100,000), it becomes possible to resolve enough of those overlaps so that automated data reduction becomes possible, based on the actual elemental composition of each peptide without the need to deconvolve isotopic distributions. We demonstrate automated, rapid, reliable assignment of peptide masses from H/D exchange experiments, based on electrospray ionization FT-ICR mass spectra from H/D exchange of solution-phase myoglobin. Combined with previously demonstrated automated data acquisition for such experiments, the present data reduction algorithm enhances automation (and thus expands generality and applicability) for high-resolution mass spectrometry-based analysis of H/D exchange of solution-phase proteins.     

SKATE: A docking program that decouples systematic sampling from scoring

SKATE is a docking prototype that decouples systematic sampling from scoring. This novel approach removes any interdependence between sampling and scoring functions to achieve better sampling and, thus, improves docking accuracy. SKATE systematically samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. Efficient systematic sampling is achieved by pruning the combinatorial tree using aggregate assembly, discriminant analysis, adaptive sampling, radial sampling, and clustering. Because systematic sampling is decoupled from scoring, the poses generated by SKATE can be ranked by any published, or in‐house, scoring function. To test the performance of SKATE, ligands from the Asetex/CDCC set, the Surflex set, and the Vertex set, a total of 266 complexes, were redocked to their respective receptors. The results show that SKATE was able to sample poses within 2 Å RMSD of the native structure for 98, 95, and 98% of the cases in the Astex/CDCC, Surflex, and Vertex sets, respectively. Cross‐docking accuracy of SKATE was also assessed by docking 10 ligands to thymidine kinase and 73 ligands to cyclin‐dependent kinase. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Modulated spin waves and robust quasi-solitons in classical Heisenberg rings

We investigate the dynamical behavior of finite rings of classical spin vectors interacting via nearest-neighbor isotropic exchange in an external magnetic field. Our approach is to utilize the solutions of a continuum version of the discrete spin equations of motion (EOM) which we derive by assuming continuous modulations of spin wave solutions of the EOM for discrete spins. This continuum EOM reduces to the Landau-Lifshitz equation in a particular limiting regime. The usefulness of the continuum EOM is demonstrated by the fact that the time-evolved numerical solutions of the discrete spin EOM closely track the corresponding time-evolved solutions of the continuum equation. It is of special interest that our continuum EOM possesses soliton solutions, and we find that these characteristics are also exhibited by the corresponding solutions of the discrete EOM. The robustness of solitons is demonstrated by considering cases where initial states are truncated versions of soliton states and by numerical simulations of the discrete EOM equations when the spins are coupled to a heat bath at finite temperatures.     

Slow-light enhanced correlated photon pair generation in a silicon photonic crystal waveguide

We report the generation of correlated photon pairs in the telecom C-band at room temperature from a dispersion-engineered silicon photonic crystal waveguide. The spontaneous four-wave mixing process producing the photon pairs is enhanced by slow-light propagation enabling an active device length of less than 100?μm. With a coincidence to accidental ratio of 12.8 at a pair generation rate of 0.006 per pulse, this ultracompact photon pair source paves the way toward scalable quantum information processing realized on-chip.     

Spectral parameter dependent Lax pairs for systems of Calogero–Moser type

Presentation of a method for generating Lax pairs for systems obtained by means of Hamiltonian reduction.     

Predictive modeling of positive mode IMS gas-phase ionization: is 2nd-order Møller-Plesset perturbation theory adequate?

Low level ab initio Quantum Chemistry (QC) is shown to be a promising technique for predicting the relative ordering of a wide variety of potential analyte, dopant, and interferent molecules, by their proton affinities (PA). Computed PAs, using a single level of chemical theory, are summarized for 53 compounds and when compared to literature reference data have a mean unsigned error of ∼9.5 kJ/mol. Where applicable, multiple conformations of the protonated species were explored. In these cases, the Boltzmann weighted PA is reported. Finally, examples are shown in which QC modeling is used to predict potential fragmentation products initiated by the positive mode ionization.     

Global Existence of Plasma Ion-Sheaths and Their Dynamics

 When a negative high voltage pulse is applied to a target material immersed in a plasma, a boundary layer (sheath) forms around the target and the motion of cold ions in the plasma is governed by the Euler-Poisson system. In this paper, by simplifying the Euler-Poisson system on suitable physical regimes, we present a theory for the existence and dynamics of time-dependent sheaths with planar, cylindrical and spherical symmetry. For the construction of ion-sheaths, we employ the method of characteristics and study the dynamic behavior of a plasma-sheath edge based on ODEs which are formally derived from the Euler-Poisson system. Received: 9 December 2002 / Accepted: 16 January 2003 Published online: 28 May 2003 Communicated by P. Constantin     

The reaction of OH with acetaldehyde and deuterated acetaldehyde: Further insight into the reaction mechanism at both low and elevated temperatures

The pulsed laser photolysis/laser‐induced fluorescence technique has been used to conduct additional measurements of the gas‐phase CH₃CHO + OH reaction. These measurements were conducted to verify the complex temperature dependence previously observed by the authors and to acquire mechanistic information about the reaction mechanism in the form of primary kinetic isotope effects. Primary kinetic isotope effect measurements at temperatures of 297, 383, 600, and 860 K indicate that H abstraction from the acetyl group dominates that of the methyl group at low to modest temperatures (?600 K) and H abstraction from the methyl group dominates that from the acetyl group at higher temperatures (860 K). A bi‐exponential © 2006 Wiley Periodicals, Inc. Int J Chem Kinet 38: 489–495, 2006