Peptide models XXIII. Conformational model for polar side‐chain containing amino acid residues: A comprehensive analysis of RHF,DFT, and MP2 properties of HCO‐L‐SER‐NH2

Geometric and energetic properties of a diamide of serine, HCO‐NH‐L ‐CH(CH₂OH)CO‐NH₂, are investigated by standard methods of computational quantum chemistry. Similarly to other amino acid residues, conformational properties of HCO‐L ‐Ser‐NH₂ can be derived from the analysis of its E=E(ϕ,ψ;χ₁,χ₂) hypersurface. Reoptimization of 44 RHF/3‐21G conformers at the RHF/6‐311++G** level resulted in 36 minima. For all conformers, geometrical properties, including variation of H‐bond parameters and structural shifts in the torsional space, are thoroughly investigated. Results from further single‐point energy calculations at the RHF, DFT, and MP2 levels, performed on the entire conformational data set, form a database of 224 energy values, perhaps the largest set calculated so far for any single amino acid diamide. A comprehensive analysis of this database reveals significant correlation among energies obtained at six levels of ab initio theory. Regression parameters provide an opportunity for extrapolation in order to predict the energy of a conformer at a high level by doing explicit ab initio computations only for a few selected conformers. The computed conformational and relative energy data are compared with structural and occurrence results derived from a nonhomologous protein database incorporating 1135 proteins. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 626–655, 2000     

High-content and high-throughput identification of macrophage polarization phenotypes

Macrophages are plastic cells of the innate immune system that perform a wide range of immune- and homeostasis-related functions. Due to their plasticity, macrophages can polarize into a spectrum of activated phenotypes. Rapid identification of macrophage polarization states provides valuable information for drug discovery, toxicological screening, and immunotherapy evaluation. The complexity associated with macrophage activation limits the ability of current biomarker-based methods to rapidly identify unique activation states. In this study, we demonstrate the ability of a 2-element sensor array that provides an information-rich 5-channel output to successfully determine macrophage polarization phenotypes in a matter of minutes. The simple and robust sensor generates a high dimensional data array which enables accurate macrophage evaluations in standard cell lines and primary cells after cytokine treatment, as well as following exposure to a model disease environment.

Phenotyping macrophage activation states using an array-based sensor. FRET complex assembly selectively interacts with the macrophage surface, generating a fingerprint for each polarization state that is further used to identify the activation state.     

Truck routing and scheduling

The problem is part of a complex software solution for truck itinerary construction for one of the largest public road transportation companies in the EU. In practice a minor improvement on the operational cost per tour can decide whether a freight services company is profitable or not. Thus the optimization of routes has key importance in the operation of such companies. Given an initial location and an asset state one must be able to calculate a cost optimal itinerary containing all Point of Interests. Such an itinerary is an executable plan which exactly specifies the location and activity of an asset during the whole timespan of the itinerary. If parking places and gas stations are included in the planning then it is NP hard to find an optimal solution. This means that for long range tours an approximately optimal solution for refueling has to be given within an acceptable running time. Also the corridoring of the trucks is an important problem so that we try to optimize the performance, hence tours cannot be recalculated at each data arrival. The vehicle assignment part of this work is already finished and applied with very good results. The remaining part is subject of an ongoing research which started at January 2014. The company started to apply and test our product in the beginning of 2015 under increased human supervision. As a consequence of the project a large cost saving is anticipated by the company.     

Synthesis of N-picolylcarboxamides via palladium-catalysed aminocarbonylation of iodobenzene and iodoalkenes

A systematic investigation of the palladium-catalysed aminocarbonylation of iodobenzene, 1-iodocyclohexene and 1′-iodostyrene in the presence of N-nucleophiles containing pyridyl moieties (2-, 3- and 4-picolylamine, N-ethyl-4-picolylamine, di-(2-picolyl)amine) was carried out. The two types of iodo substrates differ substantially regarding the selectivity towards carbonylation: while the aminocarbonylation of iodobenzene resulted in the formation of carboxamide and ketocarboxamide mixtures under various conditions, with the predominant formation of ketocarboxamide even at low carbon monoxide pressure, the aminocarbonylation of iodoalkenes under same conditions gave the corresponding unsaturated carboxamide exclusively. Most of the carboxamides and phenylglyoxylamides, obtained via single and double carbon monoxide insertion, respectively, were isolated in yields of synthetic interest (up to 86%). Low reaction rates and unexpected chemoselectivity towards carboxamide formation have been observed with di-(2-picolyl)amine as N-nucleophile in the aminocarbonylation of iodobenzene.     

Small Delay Inertial Manifolds Under Numerics: A Numerical Structural Stability Result

In this paper we formulate a numerical structural stability result for delay equations with small delay under Euler discretization. The main ingredients of our approach are the existence and smoothness of small delay inertial manifolds, the C ¹-closeness of the small delay inertial manifolds and their numerical approximation and M.-C. Li's recent result on numerical structural stability of ordinary differential equations under the Euler method.     

Simulation of plasticity in nanocrystalline silicon

Molecular dynamics investigation of plasticity in a model nanocrystalline silicon system demonstrates that inelastic deformation localizes in intergranular regions. The carriers of plasticity in these regions are atomic environments, which can be described as high-density liquid-like amorphous silicon. During fully developed flow, plasticity is confined to system-spanning intergranular zones of easy flow. As an active flow zone rotates out of the plane of maximum resolved shear stress during deformation to large strain, new zones of easy flow are formed. Compatibility of the microstructure is accommodated by processes such as grain rotation and formation of new grains. Nano-scale voids or cracks may form if stress concentrations emerge which cannot be relaxed by a mechanism that simultaneously preserves microstructural compatibility.     

Stability conditions for a non-linear size-structured model

In this paper we consider a general non-linear size-structured population dynamical model with size- and density-dependent fertility and mortality rates and with size-dependent growth rate. Based on M. Farkas (Appl. Math. Comput. 131 (1) (2002) 107–123) we are able to deduce a characteristic function for a stationary solution of the system in a similar way. Then we establish results about the stability (resp. instability) of the stationary solutions of the system.     

Consistency adjustments for pairwise comparison matrices

This paper is concerned with the development of a ‘best’ rank one transitive approximation to a general paired comparison matrix in a least‐squares sense. A direct attack on the non‐linear problem is frequently replaced by a sub‐optimal linear problem and, here, the best procedure of this kind is obtained. The Newton–Kantorovich method for the solution of the non‐linear problem is also studied, including the role of the best linear approximation as a starting point for this method. Numerical examples are included. Copyright © 2002 John Wiley & Sons, Ltd.