Mass spectrometry of N-(Pyrimidin-2-yl)amino acids and their methyl esters

N(Pyrimidin-2-yl)-glycine, -alanine and -phenylalanine (1-3) and their methyl esters (4-6) were investigated using electron impact (EI) mass Spectrometry. The results showed that EI-induced decomposition occurs on the carboxylic group or involves the loss of R₂OH. In contrast to earlier investigations on N-(pyrimidin-4-yl)amino acids, elimination of water (in 1-3) or methanol (in 4-6) was found to be of EI-induced nature. The loss of 'COOH from M⁺ of ester 4 suggests the occurrence of a skeletal rearrangement leading to the isomeric N-methylamino acid.     

On the Brownian motion of a massive sphere suspended in a hard-sphere fluid. I. Multiple-time-scale analysis and microscopic expression for the friction coefficient

The Fokker-Planck equation governing the evolution of the distribution function of a massive Brownian hard sphere suspended in a fluid of much lighter spheres is derived from the exact hierarchy of kinetic equations for the total system via a multiple-time-scale analysis akin to a uniform expansion in powers of the square root of the mass ratio. The derivation leads to an exact expression for the friction coefficient which naturally splits into an Enskog contribution and a dynamical correction. The latter, which accounts for correlated collisions events, reduces to the integral of a time-displaced correlation function of dynamical variables linked to the collisional transfer of momentum between the infinitively heavy (i.e., immobile) Brownian sphere and the fluid particles.     

Simple global minimization algorithm for one-variable rational functions

Sturm's chain technique for evaluation of a number of real roots of polynomials is applied to construct a simple algorithm for global optimization of polynomials or generally for rational functions of finite global minimal value. The method can be applied both to find the global minimum in an interval or without any constraints. It is shown how to use the method to minimize globally a truncated Fourier series. The results of numerical tests are presented and discussed. The cost of the method scales as the square of the degree of the polynomial.     

Matrix-assisted laser desorption/ionization-mass spectrometry of cuticular lipid profiles can differentiate sex, age, and mating status of Anopheles gambiae mosquitoes

Malaria is a devastating mosquito-borne disease, which affects hundreds of millions of people each year. It is transmitted predominantly by Anopheles gambiae, whose females must be >10 days old to become infective. In this study, cuticular lipids from a laboratory strain of this mosquito species were analyzed using a mass spectrometry method to evaluate their utility for age, sex and mating status differentiation. Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS), in conjunction with an acenaphthene/silver nitrate matrix preparation, was shown to be 100% effective in classifying A. gambiae females into 1, 7–10, and 14 days of age. MALDI-MS analysis, supported by multivariate statistical methods, was also effective in detecting cuticular lipid differences between the sexes and between virgin and mated females. The technique requires further testing, but the obtained results suggest that MALDI-MS cuticular lipid spectra could be used for age grading of A. gambiae females with precision greater than with other available methods.     

Photodynamical simulations of cytosine: characterization of the ultrafast bi-exponential UV deactivation

Deactivation of UV-excited cytosine is investigated by non-adiabatic dynamics simulations, optimization of conical intersections, and determination of reaction paths. Quantum chemical calculations are performed up to the MR-CISD level. Dynamics simulations were performed at multiconfigurational level with the surface hopping method including four electronic states. The results show the activation of four distinct reaction pathways at two different subpicosecond time scales and involving three different conical intersections. Most trajectories relax to a minimum of the S(1) state and deactivate with a time constant of 0.69 ps mainly through a semi-planar conical intersection along the n(O)π* surface. A minor fraction deactivate along ππ* regions of the S(1) surface. Sixteen percent of trajectories do not relax to the minimum and deactivate with a time constant of only 13 fs.     

An instrumented vehicle for offroad dynamics testing

The paper presents an instrumented vehicle that was equipped with measuring systems to perform complete dynamics tests, especially in off-road conditions. The equipment consists of four wheel dynamometers, a steering robot, and a differential GPS system together with an inertial platform, a non-contact vehicle speed sensor, and an on-board computer with software to control the devices and collect experimental data. The four wheel dynamometers measure six elements; based on strain gage force transducers, it measures three orthogonal forces and three moments. The steering robot can control the steering wheel of the vehicle at a variety of excitation modes; it can carry out typical vehicle dynamics tests (ISO 7401, ISO 4138, ISO/TR3888, etc.) as well as custom engineered tests at a wide range of setting parameters (steer angle rate up to 1600 deg/s). The differential GPS system gives true time vehicle kinematics data (velocities, accelerations, angles, etc.) at 10-ns sample rate and 20-mm accuracy. The base vehicle, a Suzuki Vitara 4 × 4, required no special modifications or changes to install the measuring equipment. The paper also describes typical tests performed with the use of the instrumented vehicle together with sample results.     

Nonlinear vibrations and time delay control of an extensible slowly rotating beam

Nonlinear Dynamics - This paper investigates the time-varying formation tracking (TVFT) problem of multiple heterogeneous Euler–Lagrange agents (MHELAs) with predefined-time convergence...     

On the transferability of folding and threading potentials and sequence-independent filters for protein folding simulations

Significant progress has recently been made in de novo protein structure prediction. The Rosetta method by Baker and colleagues, which is based on the idea of assembling putative models from a library of k-mer fragments derived from known three-dimensional protein structures, proved to be particularly successful. Critical components of the Rosetta approach are various sequence-dependent as well as sequence-independent measures that are used to rank alternative models and to enhance sampling of native-like conformations. In the present work we revisit several sequence-independent filters that have been used to enhance the discrimination of native and native-like structures from misfolded structures, such as the overall compactness of the structure and its contact order. We also propose a novel sequence-independent filter, based on the shape of the mean inter-residue radial distribution function. Using the Rosetta, Park–Levitt and CASP4 sets of decoys it is shown that sequence-independent filters are in fact more successful in distinguishing native structures in Rosetta and CASP4 tests than commonly used knowledge-based pairwise potentials. The latter are typically designed to distinguish native structures in a population of well-folded alternatives, and they fail to discriminate between native-like and non-physically packed misfolded structures from Rosetta simulations. Moreover, a rigorous attempt to optimize pairwise potentials for recognition of homologous structures in threading by using a linear programming approach leads to further deterioration of performance in terms of recognition of native structures from the Rosetta set. These findings shed light onto the success of tailored scoring functions used in the Rosetta protocol and provide support for explicit inclusion of both sequence dependent and sequence independent measures in the design of scoring functions. A Web server that enables ranking of decoy structures according to sequence independent filters considered here is available at http://sift.chmcc.org.