Exponential averaging for traveling wave solutions in rapidly varying periodic media

Reaction diffusion systems on cylindrical domains with terms that vary rapidly and periodically in the unbounded direction can be analyzed by averaging techniques. Here, using iterated normal form transformations and Gevrey regularity of bounded solutions, we prove a result on exponential averaging for such systems, i.e., we show that traveling wave solutions can be described by a spatially homogenous equation and exponentially small remainders. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Cross sections for multi-particle final states at a linear collider

In this paper total cross sections for signals and backgrounds of top- and Higgs-production channels in e ⁺ e^- collisions at a future linear collider are presented. All channels considered are characterized by the emergence of six-particle final states. The calculation takes into account the full set of tree-level amplitudes in each process. Two multi-purpose parton level generators, HELAC/PHEGAS and AMEGIC + + , are used, and their results are found to be in perfect agreement.Received: 26 November 2003, Revised: 15 January 2004, Published online: 3 March 2004     

Standing waves, clustering, and phase waves in 1D simulations of kinetic relaxation oscillations in NO+NH3 on Pt(1 0 0) coupled by diffusion

The Lombardo–Imbihl–Fink (LFI) ODE model of the NO+NH₃ reaction on a Pt(1 0 0) surface shows stable relaxation oscillations with very sharp transitions for temperatures T between 404 and 433 K. Here we study numerically the effect of linear diffusive coupling of these oscillators in one spatial dimension. Depending on the parameters and initial conditions we find a rich variety of spatio-temporal patterns which we group into four main regimes: bulk oscillations (BOs), standing waves (SW), phase clusters (PC), and phase waves (PW). Two key ingredients for SW and PC are identified, namely the relaxation type of the ODE oscillations and a nonlocal (and nonglobal) coupling due to relatively fast diffusion of the kinetically slaved variables NH₃ and H. In particular, the latter replaces the global coupling through the gas phase used to obtain SW and PC in models of related surface reactions. The PW exist only under the assumption of (relatively) slow diffusion of NH₃ and H.     

A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems

The implementation of a hybrid QM-MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree-Fock and density functional methods and varying QM-MM boundaries. Also, the computationally efficient RI-J method has been examined for use in QM-MM applications. A B(12) cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM-MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes.     

A novel technique to specifically analyze the secretome of cells and tissues

The secretome of cells and tissues may reflect a broad variety of pathological conditions and thus represents a rich source of biomarkers. The identity of secreted proteins, usually isolated from cell supernatants or body fluids, is hardly accessible by direct proteome analysis, because these proteins are often masked by high amounts of proteins actually not secreted by the investigated cells. Here, we present a novel method for the specific detection of proteins secreted by human tissue specimen as well as cultured cells and chose liver as a model. The method is based on the metabolic labelling of proteins synthesized during a limited incubation period. Then, the cell supernatant is filtered, precipitated, and subjected to two-dimensional gel electrophoresis. Whereas fluorography detected a large number of proteins derived from residual plasma and dead cells, the autoradiographs selectively displayed genuinely secreted proteins. We demonstrate the feasibility of this approach by means of the secretomes of the hepatocellular carcinoma-derived cell line HepG2 and human liver slices. The selective identification of cell- and tissue-specific protein secretion profiles may help to identify novel sets of biomarkers for wide clinical applications.     

Relativistic effective potential SCF calculations of AgH and AuH

Relativistic effective potentials (REP) are now widely used in molecular electronic structure calculations. Tests of these REP are needed to assess their accuracy. This can now be done for AgH and AuH since Lee and McLean have published Dirac-Fock calculations for these molecules. Comparative SCF calculations have been performed for two types of effective potential. Satisfactory agreement between the effective potential results and Dirac-Fock values is found for spectroscopic constants and dipole moments, which supports the use of these potentials for heavy atom containing molecules.