bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimierungsstrategien im Bereich der Formoptimierung bei Massivumformverfahren
Authors: Schellenberg Dirk , Kreißig Reiner , Ihlemann Jörn
Published: November 2010

Zur Lösung von Formoptimierungsproblemen und der Identifikation von Materialparametern wurde an der TU Chemnitz das Programm SPC‐Opt (Scientific Programming and Optimization) entwickelt. Darin werden moderne Aspekte der nichtlinearen FEM und Optimierung umgesetzt. So können beispielsweise die Vorteile paralleler Rechnerarchitekturen genutzt und außer der hauseigenen FEM‐Software auch kommerzielle Programme zur Lösung der notwendigen Anfangs‐Randwert‐Probleme verwendet werden. In der Annahme hinreichend glatter Zielfunktionen werden die Optimierungsprobleme mittels gradientenbasierter Methoden gelöst. Zu diesem Zweck wurden mehrere Trust‐Region‐ und Line‐Search‐Verfahren implementiert. Da diese jedoch lediglich das nächstgelegene lokale Minimum finden, stehen auch verschiedene Verfahren zur Startparametervariation zur Verfügung.

Ein wichtiger Punkt bei der Lösung von Formoptimierungsproblemen stellt die durch die Variation der Designvariablen erforderliche Neuvernetzung des FEM‐Netzes dar. Durch die Nutzung von Bezugskurven konnte ein Verfahren entwickelt werden, welches die bestehende Netztopologie beibehält und eine direkte Neuberechnung der Knotenkoordinaten zulässt. Speziell bei Problemen, welche die Beibehaltung der Knotenanzahl erfordern, können so verfahrensbedingte Diskretisierungsunterschiede bei der Neuvernetzung vermieden werden. Gegenüber anderen auf Formbasisvektoren basierenden Verfahren behalten diese FEM‐Netze auch bei deutlicher Variation ihrer Randkonturen eine gute Qualität. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An alternative way of solving large Lyapunov equations
Authors: Eppler André K. , Bollhöfer Matthias
Published: November 2010

System reduction has become an essential tool in simulating large electrical circuits. Among such methods balanced truncation is in particular popular since it preserves properties like passivity of the underlying descriptor system. One of the main tasks therein consists of solving large scale Lyapunov equations efficiently. In this setting one is looking for a symmetric low rank solution. For this purpose we discuss Krylov‐subspace methods such as the General‐Minimal‐Residual method. To speed up convergence the method is combined with the Low Rank Cholesky‐Factor‐Alternating‐Direct‐Implicit‐Iteration as a structure preserving preconditioner. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Direct Evaluation of Nonlinear Gradient Elasticity in 2D with C1 Continuous Discretization Methods
Authors: Fischer Paul , Mergheim Julia , Steinmann Paul
Published: November 2010

In this contribution, we present a study on the performance of four different subparametric triangular finite element formulations for linear and nonlinear strain gradient elastic continua. Fully C1 and nonconforming C* finite elements are considered for a numerical analysis. The results are demonstrated by means of two computational examples together with the L2, H1 and H2 error norms. An interesting aspect concerning the linear geometry approximation is revealed. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Use of Halley's Method in the Nonlinear Finite Element Analysis
Authors: Plate Carolin , Papadopoulos Panayiotis , Müller Ralf
Published: November 2010

Halley's method is a higher order iteration method for the solution of nonlinear systems of equations. Unlike Newton's method, which converges quadratically in the vicinity of the solution, Halley's method can exhibit a cubic order of convergence. The equations of Halley's method for multiple dimensions are derived using Padé approximants and inverse one‐point interpolation, as proposed by Cuyt. The investigation of the performance of Halley's method concentrates on eight‐node volume elements for nonlinear deformations using Staint Venant‐Kirchhoff's constitutive law, as well as a geometric linear theory of von Mises plasticity. The comparison with Newton's method reveals the sensibility of Halley's method, in view of the radius of attraction but also demonstrates the advantages of Halley's method considering simulation costs and the order of convergence. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
State Trajectory Compression in Optimal Control
Authors: Götschel Sebastian , Weiser Martin
Published: November 2010

In optimal control problems with nonlinear time‐dependent 3D PDEs, the computation of the reduced gradient by adjoint methods requires one solve of the state equation forward in time, and one backward solve of the adjoint equation. Since the state enters into the adjoint equation, the storage of a 4D discretization is necessary. We propose a lossy compression algorithm using a cheap predictor for the state data, with additional entropy coding of prediction errors. Analytical and numerical results indicate that compression factors around 30 can be obtained without exceeding the FE discretization error. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Computation of derivatives for structure preserving optimal control using automatic differentiation
Authors: Ober‐Blöbaum Sina , Walther Andrea
Published: November 2010

In this work we combine a recently developed method, Discrete Mechanics and Optimal Control (DMOC), with the well established Automatic Differentiation package ADOL‐C. DMOC is based on the discretization of the variational structure of the mechanical system which leads to structure (symplectic‐momentum) preserving time‐stepping equations. The discretized equations provide equality constraints for the resulting finite dimensional nonlinear optimization problem. For the solution of this problem standard nonlinear optimization techniques like sequential quadratic programming (SQP) are used. To ensure robustness of these techniques the computation of derivatives of the objective function and the constraints is of great importance. The concept of Automatic Differentiation (AD) is used to improve the performance of the SQP method. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Krylov Subspace Methods for Model Order Reduction of Bilinear Discrete‐Time Control Systems
Authors: Benner Peter , Breiten Tobias , Damm Tobias
Published: November 2010

In this paper, we propose a projection technique for model order reduction of discrete‐time bilinear control systems based on the concept of so‐called multimoments. We will make use of an explicit solution formula of the system and consider its Z‐transform which allows us to characterize the system output by generalized transfer functions. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Invariant tracking control design via integrator backstepping
Authors: Collon Carsten , Rudolph Joachim
Published: November 2010

A tracking control problem for systems in state representation possessing a Lie symmetry group G is considered. By designing an invariant feedback control law based on invariant tracking errors the symmetry group G can be preserved under feedback. An extension of this approach to the popular integrator backstepping design method is presented. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Eddy current measurements of surface roughness
Authors: Dziczkowski Leszek
Published: November 2010

The paper proposes a method for simultaneous measurements of the material conductivity and its surface roughness for non‐ferromagnetic materials. The method takes advantage of the effect exercised by eddy currents onto impedance of a contact coil. The essence of the method is to eliminate the influence of the surface unevenness onto measurements of conductivity by the calculation of a correcting factor that serves as a specific equivalent of the surface roughness. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Tracking of Mechanical System Parameters by Phase‐Locked Loops
Authors: Kern Dominik , Seemann Wolfgang
Published: November 2010

The eigenfrequencies of a mechanical system depend on several parameters such as mass‐, damping‐, stiffness‐distribution and boundary conditions. Variation of these parameters results in variation of the Frequency Response Function (FRF). An eigenfrequency can be tracked by resonant excitation with a Phase‐Locked Loop (PLL) in order to monitor a certain parameter. As an example, a cantilever beam with a time‐variant mass at its end is analyzed. In this contribution, the FRF of this beam will be derived, which is the prerequisite for the following resonant excitation. The modified PLL‐design for the resonant excitation of higher modes will be explained and finally tested at the state‐space model of the beam. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Sliding Mode Control of an Underactuated Two‐Link Manipulator
Authors: Knoll Carsten , Röbenack Klaus
Published: November 2010

We consider a horizontally mounted two‐link manipulator of which only the first joint is actuated and the friction in the second joint is neglected. As a consequence, predefined equilibrium points are difficult to reach and point‐to‐point control is a challenging task. Starting from a partially feedback linearized model, a transformation to Byrnes‐Isidori normal form is presented. Based on this decomposition, the projection into a two‐dimensional subspace reveals certain similarities to a double integrator. Modifying an existing sliding mode approach for that system, a control law which steers the manipulator to an equilibrium point can be deduced. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Some Remarks on Affine Derivative Systems concerning Flatness
Authors: Schöberl Markus , Schlacher Kurt
Published: November 2010

We consider nonlinear implicit control systems and discuss the construction of a system parametrization in the context of flatness. To this end, quasilinear systems will play a prominent role since they are affine in the derivative variables which alleviates the proposed reduction and elimination strategy. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Flux‐corrected‐transport methods for modelling of gas discharge plasmas
Authors: Becker Markus M. , Loffhagen Detlef
Published: November 2010

The hydrodynamic description of gas discharge plasmas leads to a nonlinear coupled system of balance equations for the particle, current and energy densities of electrons and heavy particles as well as Poisson's equation for the electric potential. New implicit flux‐corrected‐transport methods for the numerical solution of the discharge model are proposed and compared with established flux‐corrected‐transport schemes based on finite‐difference as well as finite‐element methods. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A posteriori control of modelling errors in linear elasticity
Authors: Große‐Wöhrmann André , Blum Heribert , Stiemer Marcus
Published: November 2010

The concept of adaptive error control for finite element Galerkin discretizations has more recently been extended from the pure treatment of the discretization errors [1], [2] also to the control of modelling errors [4], [5]. These techniques can be employed for a rigorous justification of the local choice of the model out of a given hierarchy with increasing complexity. In the present paper the concept is exemplified by a hierarchy of linear‐elastic models, consisting of a basic model with constant E modulus and an improved model with oscillating E modulus. Significant reduction of the computational complexity can be achieved by a proper choice of the model in different subdomains, automatically chosen by the error estimators. Several error indicators are investigated in the context of goal oriented error estimation. Their efficiency is compared by means of finite element simulations [3] of an elementary example. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A characterization of the eigenvalues of Schrödinger operators with Dirichlet and Neumann boundary conditions
Authors: Behrndt Jussi , Rohleder Jonathan
Published: November 2010

The eigenvalues of the self‐adjoint Schrödinger operators on a bounded domain with Dirichlet and Neumann boundary conditions are characterized by the singularities of an associated Dirichlet‐to‐Neumann map and its inverse, respectively. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Composite Finite Elements for Elliptic Interface Problems
Authors: Peterseim Daniel
Published: November 2010

We present a Composite Finite Element Method for the approximation of linear elliptic boundary value problems of Dirichlet type with discontinuous coefficients. The challenge is the discontinuity of the coefficient (interface) which is not necessarily resolved by the underlying finite element mesh. The method is non‐conforming in the sense that shape functions preserve continuity across the interface only in an approximative way. However, the construction allows to balance the non‐conformity and the overall discretization error. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Configurational‐Force‐Based Adaptive FE Solver for a Phase Field Model of Fracture
Authors: Welschinger Fabian , Hofacker Martina , Miehe Christian
Published: November 2010

The computational modeling of failure mechanisms in solids due to fracture based on sharp crack discontinuities suffers in situations with complex crack topologies. This can be overcome by diffusive crack modeling, based on the introduction of a crack phase field as outlined in [1, 2]. Following these formulations, we outline a thermodynamically consistent framework for phase field models of crack propagation in elastic solids, develop incremental variational principles and, as an extension to [1, 2], consider their numerical implementations by an efficient h‐adaptive finite element method. A key problem of the phase field formulation is the mesh density, which is required for the resolution of the diffusive crack patterns. To this end, we embed the computational framework into an adaptive mesh refinement strategy that resolves the fracture process zones. We construct a configurational‐force‐based framework for h‐adaptive finite element discretizations of the gradient‐type diffusive fracture model. We develop a staggered computational scheme for the solution of the coupled balances in physical and material space. The balance in the material space is then used to set up indicators for the quality of the finite element mesh and accounts for a subsequent h‐type mesh refinement. The capability of the proposed method is demonstrated by means of a numerical example. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Characterization of the disordered‐to‐α‐helical transition of IA3 by SDSL‐EPR spectroscopy
Authors: Pirman Natasha L. , Milshteyn Eugene , Galiano Luis , Hewlett Justin C. , Fanucci Gail E.
Published: November 2010

Electron paramagnetic resonance (EPR) spectroscopy coupled with site‐directed spin labeling (SDSL) is a valuable tool for characterizing the mobility and conformational changes of proteins but has seldom been applied to intrinsically disordered proteins (IDPs). Here, IA3 is used as a model system demonstrating SDSL‐EPR characterization of conformational changes in small IDP systems. IA3 has 68 amino acids, is unstructured in solution, and becomes α‐helical upon addition of the secondary structural stabilizer 2,2,2‐trifluoroethanol (TFE). Two single cysteine substitutions, one in the N‐terminus (S14C) and one in the C‐terminus (N58C), were generated and labeled with three different nitroxide spin labels. The resultant EPR line shapes of each of the labels were compared and each reported changes in mobility upon addition of TFE. Specifically, the spectral line shape parameters h(+1)/h(0), the local tumbling volume (VL), and the percent change of the h(−1) intensity were utilized to quantitatively monitor TFE‐induced conformational changes. The values of h(+1)/h(0) as a function of TFE titration varied in a sigmoidal manner and were fit to a two‐state Boltzmann model that provided values for the midpoint of the transition, thus, reporting on the global conformational change of IA3. The other parameters provide site‐specific information and show that S14C‐SL undergoes a conformational change resulting in more restricted motion than N58C‐SL, which is consistent with previously published results obtained by studies using NMR and circular dichroism spectroscopy indicating a higher degree of α‐helical propensity of the N‐terminal segment of IA3. Overall, the results provide a framework for data analyzes that can be used to study induced unstructured‐to‐helical conformations in IDPs by SDSL.
Ab initio simulation of a 57‐residue protein in explicit solvent reproduces the native conformation in the lowest free‐energy cluster
Authors: Ikebe Jinzen , Standley Daron M. , Nakamura Haruki , Higo Junichi
Published: November 2010

An enhanced conformational sampling method, multicanonical molecular dynamics (McMD), was applied to the ab intio folding of the 57‐residue first repeat of human glutamyl‐ prolyl‐tRNA synthetase (EPRS‐R1) in explicit solvent. The simulation started from a fully extended structure of EPRS‐R1 and did not utilize prior structural knowledge. A canonical ensemble, which is a conformational ensemble thermodynamically probable at an arbitrary temperature, was constructed by reweighting the sampled structures. Conformational clusters were obtained from the canonical ensemble at 300 K, and the largest cluster (i.e., the lowest free‐energy cluster), which contained 34% of the structures in the ensemble, was characterized by the highest similarity to the NMR structure relative to all alternative clusters. This lowest free‐energy cluster included native‐like structures composed of two anti‐parallel α‐helices. The canonical ensemble at 300 K also showed that a short Gly‐containing segment, which adopts an α‐helix in the native structure, has a tendency to be structurally disordered. Atomic‐level analyses demonstrated clearly that inter‐residue hydrophobic interactions drive the helix formation of the Gly‐containing segment, and that increasing the hydrophobic contacts accompanies exclusion of water molecules from the vicinity of this segment. This study has shown, for the first time, that the free‐energy landscape of a structurally well‐ordered protein of about 60 residues is obtainable with an all atom model in explicit water without prior structural knowledge.
Modeling of the Toll‐like receptor 3 and a putative Toll‐like receptor 3 antagonist encoded by the African swine fever virus
Authors: Henriques Elsa S. , Brito Rui M. M. , Soares Hugo , Ventura Sónia , de Oliveira Vivian L. , Parkhouse R. Michael E.
Published: November 2010

African swine fever virus (ASFV) is a large double‐stranded DNA virus responsible for a lethal pig disease, to which no vaccine has ever been obtained. Its genome encodes a number of proteins involved in virus survival and transmission in its hosts, in particular proteins that inhibit signaling pathways in infected macrophages and, thus, interfere with the host's innate immune response. A recently identified novel ASFV viral protein (pI329L) was found to inhibit the Toll‐like receptor 3 (TLR3) signaling pathway, TLR3 being a crucial “danger detector.” pI329L has been predicted to be a transmembrane protein containing extracellular putative leucine‐rich repeats similar to TLR3, suggesting that pI329L might act as a TLR3 decoy. To explore this idea, we used comparative modeling and other structure prediction protocols to propose (a) a model for the TLR3–Toll‐interleukin‐1 receptor homodimer and (b) a structural fold for pI329L, detailed at atomistic level for its cytoplasmic domain. As this later domain shares only remote sequence relationships with the available TLR3 templates, a more complex modeling strategy was employed that combines the iterative implementation of (multi)threading/assembly/refinement (I‐TASSER) structural prediction with expertise‐guided posterior refinement. The final pI329L model presents a plausible fold, good structural quality, is consistent with the available experimental data, and it corroborates our hypothesis of pI329L being a TLR3 antagonist.
NMR determination of pKa values in α‐synuclein
Authors: Croke Robyn L. , Patil Sharadrao M. , Quevreaux Jason , Kendall Debra A. , Alexandrescu Andrei T.
Published: November 2010

The intrinsically unfolded protein α‐synuclein has an N‐terminal domain with seven imperfect KTKEGV sequence repeats and a C‐terminal domain with a large proportion of acidic residues. We characterized pKa values for all 26 sites in the protein that ionize below pH 7 using 2D 1H‐15N HSQC and 3D C(CO)NH NMR experiments. The N‐terminal domain shows systematically lowered pKa values, suggesting weak electrostatic interactions between acidic and basic residues in the KTKEGV repeats. By contrast, the C‐terminal domain shows elevated pKa values due to electrostatic repulsion between like charges. The effects are smaller but persist at physiological salt concentrations. For α‐synuclein in the membrane‐like environment of sodium dodecylsulfate (SDS) micelles, we characterized the pKa of His50, a residue of particular interest since it is flanked within one turn of the α‐helix structure by the Parkinson's disease‐linked mutants E46K and A53T. The pKa of His50 is raised by 1.4 pH units in the micelle‐bound state. Titrations of His50 in the micelle‐bound states of the E46K and A53T mutants show that the pKa shift is primarily due to interactions between the histidine and the sulfate groups of SDS, with electrostatic interactions between His50 and Glu46 playing a much smaller role. Our results indicate that the pKa values of uncomplexed α‐synuclein differ significantly from random coil model peptides even though the protein is intrinsically unfolded. Due to the long‐range nature of electrostatic interactions, charged residues in the α‐synuclein sequence may help nucleate the folding of the protein into an α‐helical structure and confer protection from misfolding.
Charge transport in organic crystals: Theory and modelling
Authors: Ortmann Frank , Bechstedt Friedhelm , Hannewald Karsten
Published: November 2010

Efficient charge transport in organic semiconductors is the key for their application in Organic Electronics. Therefore the most important design ansatz is directed to improve carrier mobilities by means of available tools such as chemical and/or structural modifications of the organic materials. Thereby theoretical input can provide guidelines towards possible realizations of high‐mobility or, more general, highly functional materials. In particular the structure–property relationship is at the heart of theoretical studies which are extremely helpful if they achieve predictive power. In this paper we systematically review several charge‐transport approaches and illustrate their relationship in order to display their capabilities regarding this goal. Special focus is put on the transport mechanism, the mobility anisotropy and temperature dependence of charge‐carrier transport. As the central concept the inclusion of the strong coupling of the carriers with the vibrating lattice and, hence, the dressing of carriers to polarons is described. The availability of material parameters is tremendously important for transport description. We highlight their computation by ab initio theory in order to arrive at a satisfactory level beyond phenomenological approaches.
Advances in electronic structure methods for defects and impurities in solids
Authors: Van de Walle Chris G. , Janotti Anderson
Published: November 2010

Defects and impurities are often decisive in determining the physical properties of most materials. The process of defect identification and characterization is typically difficult and indirect, usually requiring an ingenious combination of different experimental techniques. First‐principles calculations have emerged as a powerful microscopic tool that complements experiments or sometimes even serves as the sole source of atomistic information due to experimental limitations. Still, first‐principles calculations based on density functional theory in the local density or generalized gradient approximations suffer from serious limitations when describing defects in solids. Recent advances in electronic structure methods, rapid increases in computing power, and the development of efficient algorithms indicate a promising future for computational defect physics. We review recent advances in the theory of defects in solids from the perspective of first‐principles calculations. We focus in particular on methods that improve the description of band gaps, leading to results that can be directly compared to experiments on a quantitative level. We discuss the use of LDA+U in wide‐band‐gap materials, screened hybrid functionals, the quasiparticle GW method, and the use of modified pseudopotentials. Advantages and limitations of these methods are illustrated with examples.
Near‐exact supersymmetric partner potentials: Construction and exploitation
Authors: Mukherjee Neetik , Pathak Ranjit K. , Bhattacharyya Kamal
Published: November 2010

Precise supersymmetric (SUSY) partner potentials can be generated only for exactly solvable problems of the stationary Schrödinger equation. This is a severe restriction, as most problems are not amenable to exact solutions. We employ here a linear variational strategy to explicitly construct approximate SUSY partners of a few common, not exactly solvable potentials and subsequently examine their properties to explore the advantages in practical implementation. The efficacy of our proposed scheme is commendable. We demonstrate that, for symmetric potentials, the constructed partners may be so good that the overall recipe has the nicety of generating the whole eigenspectrum by employing only half of the full Hilbert space functions. A similar strategy is shown to work for the odd states too, with proper boundary conditions. Pilot calculations involve a number of low‐lying states of some mixed oscillator and double‐well potentials. Analysis of the results reveals a few interesting features of the problem of construction of approximate SUSY partners and their practical use. Particularly, we identify places where the operator‐level approximations are involved and how far they affect the bounding properties of energies that are obtained as eigenvalues of a matrix diagonalization problem associated with linear variations. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Determination of the natural abundance δ15N of taurine by gas chromatography–isotope ratio measurement mass spectrometry
Authors: Tea Illa , Antheaume Ingrid , Besnard Jorick , Robins Richard J.
Published: November 2010

The measurement of the nitrogen isotope ratio of taurine (2‐aminoethanesulphonic acid) in biological samples has a large number of potential applications. Taurine is a small water‐soluble molecule which is notoriously difficult to analyze due to its polarity and functionality. A method is described which allows the determination of the natural abundance δ15N values of taurine and structural analogues, such as 3‐amino‐1‐propanesulphonic acid (APSA), by isotope ratio mass spectrometry interfaced to gas chromatography (GC‐irm‐MS). The one‐step protocol exploits the simultaneous derivatization of both functionalities of these aminosulphonic acids by reaction with triethylorthoacetate (TEOA). Conditions have been established which ensure quantitative reaction thus avoiding any nitrogen isotope fractionation during derivatization and workup. The differences in the δ15N values of derivatized and non‐derivatized taurine and APSA all fall within the working range of 0.4‰ (−0.02 to 0.39‰). When applied to four sources of taurine with various δ15N values, the method achieved excellent reproducibility and accuracy. The optimized method enables the determination of the natural abundance δ15N values of taurine over the concentration range 1.5–7.84 µmol.mL−1 in samples of biological origin. Copyright © 2010 John Wiley & Sons, Ltd.
Rapid monitoring of sulfur mustard degradation in solution by headspace solid‐phase microextraction sampling and gas chromatography mass spectrometry
Authors: Creek Jo‐Anne M. , McAnoy Andrew M. , Brinkworth Craig S.
Published: November 2010

A method using headspace solid‐phase microextraction (HS‐SPME) followed by gas chromatography/mass spectrometry (GC/MS) analysis has been developed to gain insight into the degradation of the chemical warfare agent sulfur mustard in solution. Specifically, the described approach simplifies the sample preparation for GC/MS analysis to provide a rapid determination of changes in sulfur mustard abundance. These results were found to be consistent with those obtained using liquid‐liquid extraction (LLE) GC/MS. The utility of the described approach was further demonstrated by the investigation of the degradation process in a complex matrix with surfactant added to assist solvation of sulfur mustard. A more rapid reduction in sulfur mustard abundance was observed using the HS‐SPME approach with surfactant present and was similar to results from LLE experiments. Significantly, this study demonstrates that HS‐SPME can simplify the sample preparation for GC/MS analysis to monitor changes in sulfur mustard abundance in solution more rapidly, and with less solvent and reagent usage than LLE. Copyright © 2010 Commonwealth of Australia. Published by John Wiley & Sons, Ltd.
Bioassay‐directed fractionation for discovery of bioactive neutral lipids guided by relative mass defect filtering and multiplexed collision‐induced dissociation
Authors: Stagliano Michael C. , DeKeyser Joshua G. , Omiecinski Curtis J. , Jones A. Daniel
Published: November 2010

We report a synergistic method using bioassay‐directed liquid chromatography fractionation and time‐of‐flight mass spectrometry to guide and accelerate bioactive compound discovery. To steer purification and assays toward anticipated neutral lipid activators of a constitutive androstane receptor splice variant, a relative mass defect filter was calculated, based on the ratio of the mass defect to the measured ion mass, and used to reduce the number of candidate ion masses. Mass measurements often lack sufficient accuracy to provide unambiguous assignments of elemental compositions, and since the relative mass defect reflects fractional hydrogen content of ions, this value is largely determined by the hydrogen content of a compound's biosynthetic precursors. A relative mass defect window ranging from 600–1000 ppm, consistent with an assortment of lipids, was chosen to assess the number of candidate ions in fractions of fetal bovine serum. This filter reduced the number of candidate ion m/z values from 1345 to 892, which was further reduced to 21 by intensity and isotope filtering. Accurate mass measurements from time‐of‐flight mass spectrometry and fragment ion masses generated using nonselective collision‐induced dissociation suggested dioctyl phthalate as one of few neutral lipid constituents in the active fraction. The identity of this compound was determined to be di(2‐ethylhexyl) phthalate using GC/MS, and it was ranked as a promising candidate for reporter assay screening. Copyright © 2010 John Wiley & Sons, Ltd.
Empirical equations for the temperature dependence of calcite‐water oxygen isotope fractionation from 10 to 70°C
Authors: Demény Attila , Kele Sándor , Siklósy Zoltán
Published: November 2010

Although the temperature dependence of calcite‐water oxygen isotope fractionation seems to have been well established by numerous empirical, experimental and theoretical studies, it is still being discussed, especially due to the demand for increased accuracy of paleotemperature calculations. Experimentally determined equations are available and have been verified by theoretical calculations (considered as representative of isotopic equilibrium); however, many natural formations do not seem to follow these relationships implying either that existing fractionation equations should be revised, or that carbonate deposits are seriously affected by kinetic and solution chemistry effects, or late‐stage alterations. In order to test if existing fractionation‐temperature relationships can be used for natural deposits, we have studied calcite formations precipitated in various environments by means of stable isotope mass spectrometry: travertines (freshwater limestones) precipitating from hot and warm waters in open‐air or quasi‐closed environments, as well as cave deposits formed in closed systems. Physical and chemical parameters as well as oxygen isotope composition of water were monitored for all the investigated sites. Measuring precipitation temperatures along with oxygen isotope compositions of waters and calcites yielded empirical environment‐specific fractionation–temperature equations:

[1] 1000 · lnα = 17599/T – 29.64 [for travertines with a temperature range of 30 to 70°C] and

[2] 1000 · lnα = 17500/T – 29.89 [for cave deposits for the range 10 to 25°C].

Finally, based on the comparison of literature data and our results, the use of distinct calcite‐water oxygen isotopic fractionation relationships and application strategies to obtain the most reliable paleoclimate information are evaluated. Copyright © 2010 John Wiley & Sons, Ltd.
Using a dual inlet atmospheric pressure ionization source as a dynamic reaction vessel
Authors: Campbell J. Larry
Published: November 2010

Atmospheric pressure ionization (API) sources have the ability to serve as dynamic ‘reaction vessels’ and this capability has been rapidly evolving over the past few years. With API sources, many different reagents and source conditions can be rapidly explored with minimal carryover or contamination of the mass spectrometer. While most API applications involve the simple protonation/deprotonation of analyte molecules, a great deal of flexibility and utility is available in almost any API source, provided the reagents and ionization conditions are judiciously selected. Here, the generation of a unique and useful class of reagent ions at atmospheric pressure is demonstrated for the first time. Within the AP gas‐phase environment of a dual inlet ion source, the gas‐phase synthesis of substituted N‐phenylpyridinium cations is demonstrated by establishing conditions favorable to the nucleophilic substitution reaction required for their formation. The flexibility of this API source as a reaction vessel is also demonstrated. Copyright © 2010 John Wiley & Sons, Ltd.
Structural study of acetogenins by tandem mass spectrometry under high and low collision energy
Authors: Allegrand Julie , Touboul David , Schmitz‐Afonso Isabelle , Guérineau Vincent , Giuliani Alexandre , Le Ven Jessica , Champy Pierre , Laprévote Olivier
Published: November 2010

Collision‐induced dissociation experiments of seven annonaceous acetogenins were carried out under high and low collision energy conditions. Each compound was studied as protonated or deprotonated and lithium‐ or sodium‐ cationized molecules, using ElectroSpray Ionisation (ESI) with a hybrid linear trap/orbitrap mass spectrometer (LTQ‐Orbitrap®). The same ion species were studied with a Matrix‐Assisted Laser Desorption Ionisation (MALDI) tandem mass spectrometer in a high collision energy regime (1 or 2 keV). Although each of the techniques showed some limitations in the detection of functional groups, unambiguous structural identification of the acetogenins was obtained. MALDI ToF‐ToF has the advantage over ESI‐based methods to provide mass spectra rich in informative fragments which allows the confirmation of some functional groups position. By contrast, ESI‐LTQ‐Orbitrap® analysis has the advantage over MALDI that the mass spectra are relatively simple with only fragments close to the functional groups. However, this technique needs to carry out experiments both in negative and positive ionization modes. Copyright © 2010 John Wiley & Sons, Ltd.
Diet discrimination factors are inversely related to δ15N and δ13C values of food for fish under controlled conditions
Authors: Dennis Caroline A. , MacNeil M. Aaron , Rosati Jennifer Y. , Pitcher Trevor E. , Fisk Aaron T.
Published: November 2010

A recent literature review reported negative relationships between diet discrimination factors (DDFs = Xfish – Xfood; X = δ15N or δ13C) and the values of δ15N and δ13C in the food of wild organisms but there has been no laboratory‐based confirmation of these relationships to date. Laboratory reared guppies (Poecilia reticulata) fed a series of diets with a range of δ13C (−22.9 to −6.6‰) and δ15N (6.5 to 1586‰) values were used to magnify diet‐tissue dynamics in order to calculate DDFs once the fish had achieved equilibrium with each of the diets. Values of DDFs range widely for δ15N (7.1 to −849‰) and δ13C (1.1 to −7.0‰) and showed a strong negative correlation with the stable isotope value in the food for δ15N (slope = −0.59 ± 0.02, r2 = 0.95) and δ13C (slope = −0.56 ± 0.02, r2 = 0.94). Based on these relationships, the magnitude of DDF change over environmentally relevant values of δ15N or δ13C would be significant and could confound the interpretation of stable isotopes in the environment. Using highly enriched experimental diets, our study adds to a growing number of studies that undermine the consistent trophic enrichment paradigm with results that demonstrate the currently poor mechanistic understanding of how DDFs arise. The results of our study highlight that the magnitude of the stable isotope values in prey must be considered when choosing DDF values. Future laboratory studies should therefore be directed at uncovering the mechanistic basis of DDFs and, like others before, we recommend the determination of diet‐dependent DDFs under laboratory conditions before modeling dietary proportions or calculating trophic positions. Copyright © 2010 John Wiley & Sons, Ltd.
Synthesis, characterization and application of modified Pd nanoparticles as preconcentration probes for selective enrichment/analysis of proteins via hydrophobic interactions from real‐world samples using nanoparticle‐liquid‐liquid microextraction coupled to matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Authors: Bhat Abdul R. , Wu Hui‐Fen
Published: November 2010

We introduce a novel preconcentrating technique by using surface modification of palladium nanoparticles (Pd‐NPs) with octadecane thiol (ODT) prepared in toluene for selective and sensitive extraction of proteins (insulin, ubiquitin, lysozyme) from a variety of real‐world samples including pancreas, mushroom, soybean and milk using nanoparticle‐liquid‐liquid microextraction (NP‐LLME) coupled to matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐MS). The limit of detection (LOD) values obtained for gramicidin D and insulin in water and urine are between 17–37 nM (17–37 fmol) (with RSDs ranging from 5.3–7.2%) which are 10–20‐fold enhancement in detection sensitivity compared with conventional MALDI‐MS. The optimal sample pH for highest extraction efficiency of insulin, ubiquitin and lysozyme from biological samples was observed at sample pH ∼ pI which could be due to the enhancement of hydrophobic interactions between proteins with the hydrophobic ligands of Pd‐ODT NPs. In addition, we also found that with the addition of 1 M NaCl, signals could be significantly enhanced by using the current approach. It is an efficient, straightforward, sensitive and selective nanoprobe which can be widely applied for separation, enrichment and preconcentration of peptides or proteins from complex biological samples in proteome research. Copyright © 2010 John Wiley & Sons, Ltd.
Characterization of [peptide+(Ag)n]+ complexes using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Authors: Jayasekharan T. , Sahoo N. K.
Published: November 2010

Silver ion complexes of peptides [M + (Ag)n]+, M = angiotensin I or substance P where n = 1–8 and 17–23 for angiotensin I and n = 1–5 for substance P, are identified and characterized using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS). The Ag+ coordination number exceeds the number of available amino acid residues in angiotensin I whereas the number of observed complexes in substance P is less than the number of amino acid residues in it. The larger coordination number of angiotensin I with Ag+ indicates the simultaneous binding of several Ag+ ions to the amino acid residue present in it. The lower number of observed complexes in substance P suggests the binding of two or more residues to one Ag+ ion. The presence of trifluoroacetic acid in the peptide samples reduces the Ag+ coordination ability in both the peptides which indicates that the basic residues in it are already protonated and do not participate in the Ag+‐binding process. The Ag+ ion also forms a complex with the α‐cyano‐4‐hydroxycinnamic acid (CHCA) matrix and is observed in the MALDI mass spectra and the formation of [CHCA + Ag]+, [CHCA + AgNO3]+ and [(CHCA)2 + Ag]+ ions is due to the high binding affinity of Ag+ to the CN group of CHCA. Copyright © 2010 John Wiley & Sons, Ltd.
An integrated bioanalytical platform for supporting high‐throughput serum protein binding screening
Authors: Zhang Jun , Shou Wilson Z. , Vath Marianne , Kieltyka Kasia , Maloney Jennifer , Elvebak Larry , Stewart Jeremy , Herbst John , Weller Harold N.
Published: November 2010

Quantification of small molecules using liquid chromatography/tandem mass spectrometry (LC/MS/MS) on a triple quadrupole mass spectrometer has become a common practice in bioanalytical support of in vitro adsorption, distribution, metabolism and excretion (ADME) screening. The bioanalysis process involves primarily three indispensable steps: MS/MS optimization for a large number of new chemical compounds undergoing various screening assays in early drug discovery, high‐throughput sample analysis with LC/MS/MS for those chemically diverse compounds using the optimized MS/MS conditions, and post‐acquisition data review and reporting. To improve overall efficiency of ADME bioanalysis, an integrated system was proposed featuring an automated and unattended MS/MS optimization, a staggered parallel LC/MS/MS for high‐throughput sample analysis, and a sophisticated software tool for LC/MS/MS raw data review as well as biological data calculation and reporting. The integrated platform has been used in bioanalytical support of a serum protein binding screening assay with high speed, high capacity, and good robustness. In this new platform, a unique sample dilution scheme was also introduced. With this dilution design, the total number of analytical samples was reduced; therefore, the total operation time was reduced and the overall throughput was further improved. The performance of the protein binding screening assay was monitored with two controls representing high and low binding properties and an acceptable inter‐assay consistency was achieved. This platform has been successfully used for the determination of serum protein binding in multiple species for more than 4000 compounds. Copyright © 2010 John Wiley & Sons, Ltd.
Stereo‐based all‐terrain obstacle detection using visual saliency
Authors: Santana Pedro , Guedes Magno , Correia Luís , Barata José
Published: November 2010

This paper proposes a hybridization of two well‐known stereo‐based obstacle detection techniques for all‐terrain environments. While one of the techniques is employed for the detection of large obstacles, the other is used for the detection of small ones. This combination of techniques opportunistically exploits their complementary properties to reduce computation and improve detection accuracy. Being particularly computation intensive and prone to generate a high false‐positive rate in the face of noisy three‐dimensional point clouds, the technique for small obstacle detection is further extended in two directions. The goal of the first extension is to reduce both problems by focusing the detection on those regions of the visual field that detach more from the background and, consequently, are more likely to contain an obstacle. This is attained by means of spatially varying the data density of the input images according to their visual saliency. The second extension refers to the use of a novel voting mechanism, which further improves robustness. Extensive experimental results confirm the ability of the proposed method to robustly detect obstacles up to a range of 20 m on uneven terrain. Moreover, the model runs at 5 Hz on 640 × 480 stereo images. © 2010 Wiley Periodicals, Inc.
A permutation approach to validation*
Authors: Magdon‐Ismail Malik , Mertsalov Konstantin
Published: November 2010

We give a permutation approach to validation (estimation of out‐sample error). One typical use of validation is model selection. We establish the legitimacy of the proposed permutation complexity by proving a uniform bound on the out‐sample error, similar to a Vapnik‐Chervonenkis (VC)‐style bound. We extensively demonstrate this approach experimentally on synthetic data, standard data sets from the UCI‐repository, and a novel diffusion data set. The out‐of‐sample error estimates are comparable to cross validation (CV); yet, the method is more efficient and robust, being less susceptible to overfitting during model selection. Copyright © 2010 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 3: 361‐380 2010
Dynamics of isolatedSaponaria bellidifoliaSm. populations at northern range periphery
Authors: Csergő Anna‐Mária , Molnár Edit , García Maria Begoña
Published: November 2010

Four populations ofSaponaria bellidifoliasituated at the species’ northern range periphery (Apuseni Mountains, southeastern Carpathians) were monitored over a period of 5 years. They were chosen to represent different habitat types (rocky, fixed screes, open screes and grassy), disturbance regime (fire), and population sizes (categorized as large and small). The reproductive effort was quantified, and matrix models were used to describe the population dynamics and to assess population viability.Saponaria bellidifoliahad very stable population dynamics in the harsh and stable abiotic conditions of the outcrops where populations occur. Habitat conditions exerted a notable influence on the species’ population reproductive performance, growth rate, and vital rates, whereas population size and climate did not have a clear‐cut effect on the dynamics of the species.Saponaria bellidifoliamaintains viable populations in the southeastern Carpathians, at its northern range periphery.
The Absolute Configurations of Hydroxy Fatty Acids from the Royal Jelly of Honeybees (Apis mellifera)
Authors: Kodai Tetsuya , Nakatani Takafumi , Noda Naoki
Published: November 2010

9‐Hydroxy‐2E‐decenoic acid (9‐HDA) is a precursor of the queen‐produced substance, 9‐oxo‐2E‐decenoic acid (9‐ODA), which has various important functions and roles for caste maintenance in honeybee colonies (Apis mellifera). 9‐HDA in royal jelly is considered to be a metabolite of 9‐ODA produced by worker bees, and it is fed back to the queen who then transforms it into 9‐ODA. Recently we found that 9‐HDA is present in royal jelly as a mixture of optical isomers (R:S, 2:1). The finding leads us to suspect that chiral fatty acids in royal jelly are precursors of semiochemicals. Rather than looking for semiochemicals in the mandibular glands of the queen bee, this study involves the search for precursors of pheromones from large quantities of royal jelly. Seven chiral hydroxy fatty acids, 9,10‐dihydroxy‐2E‐decenoic, 4,10‐dihydroxy‐2E‐decenoic, 4,9‐dihydroxy‐2E‐decenoic, 3‐hydroxydecanoic, 3,9‐dihydroxydecanoic, 3,11‐dihydroxydodecanoic, and 3,10‐dihydroxydecanoic acids were isolated. The absolute configurations of these acids were determined using the modified Mosher's method, and it was revealed that, similar to 9‐HDA, five acids are present in royal jelly as mixtures of optical isomers.