NMscatt: a program for calculating inelastic scattering from large biomolecular systems using classical force-field simulations

Computational tools for normal mode analysis, which are widely used in physics and materials science problems, are designed here in a single package called NMscatt (Normal Modes & scattering) that allows arbitrarily large systems to be handled. The package allows inelastic neutron and X-ray scattering observables to be calculated, allowing comparison with experimental data produced at large scale facilities. Various simplification schemes are presented for analyzing displacement vectors, which are otherwise too complicated to understand in very large systems.

Program summary

Title of program:NMscattCatalogue identifier:ADZA_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZA_v1_0.htmlProgram obtainable from:CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions:noNo. of lines in distributed program, including test data, etc.:573 535No. of bytes in distributed program, including test data, etc.:4 516 496Distribution format:tar.gzProgramming language:FORTRAN 77Computer:x86 PCOperating system:GNU/Linux, UNIXRAM:Depends on the system size to be simulatedWord size:32 or 64 bitsClassification:16.3External routines:LAPACKNature of problem: Normal mode analysis, phonons calculation, derivation of incoherent and coherent inelastic scattering spectra.Solution method: Full diagonalization (producing eigen-vectors and eigen-values) of dynamical matrix which is obtained from potential energy function derivation using finite difference method.Running time: About 7 hours per one k-point evaluation in sampling all modes dispersion curves for a system containing 3550 atoms in the unit cell on AMD Athlon 64 X2 Dual Core Processor 4200+.     

Desynchronization and inhibition of Kuramoto oscillators by scalar mean-field feedback

Motivated by neuroscience applications, and in particular by the deep brain stimulation treatment for Parkinson’s disease, we have recently derived a simplified model of an interconnected neuronal population under the effect of its mean-field proportional feedback. In this paper, we rely on that model to propose conditions under which proportional mean-field feedback achieves either oscillation inhibition or desynchronization. More precisely, we show that for small natural frequencies, this scalar control signal induces an inhibition of the collective oscillation. For the closed-loop system, this situation corresponds to a fixed point which is shown to be almost globally asymptotically stable in the fictitious case of zero natural frequencies and all-to-all coupling and feedback. In the case of an odd number of oscillators, this property is shown to be robust to small natural frequencies and heterogencities in both the coupling and feedback topology. On the contrary, for large natural frequencies, we show that scalar proportional mean-field feedback is able to induce desynchronization. After having recalled a formal definition for desynchronization, we show how it can be induced in a network of originally synchronized oscillators.     

Optimization of cutting conditions during cutting by using neural networks

Optimum selection of cutting conditions importantly contribute to the increase of productivity and the reduction of costs, therefore utmost attention is paid to this problem in this contribution. In this paper, a neural network-based approach to complex optimization of cutting parameters is proposed. It describes the multi-objective technique of optimization of cutting conditions by means of the neural networks taking into consideration the technological, economic and organizational limitations. To reach higher precision of the predicted results, a neural optimization algorithm is developed and presented to ensure simple, fast and efficient optimization of all important turning parameters. The approach is suitable for fast determination of optimum cutting parameters during machining, where there is not enough time for deep analysis. To demonstrate the procedure and performance of the neural network approach, an illustrative example is discussed in detail.     

Simulation of cutting forces in ball-end milling

The paper presents a simulation system (SCP) that determines the cutting forces in the ball-end milling process. The system is based on numerical methods, computer programme, theoretical knowledge of technological processes, machining and tests performed. The system for simulation of the cutting process combines the technological data base, the analytical and experimental model and the data base SCP. The experimental model contains a collection of variables of the cutting process by means of sensors and transformation of those data into numerical values, which are a starting point for data calculation of characteristic coefficients of materials. The analytical model is used to estimate the tangential, radial and axial cutting forces, along with a material data base obtained from cutting experiments. Ball-end milling test has been conducted to verify simulation results. The simulation results, are the basis for the development of the tool-designing model and for the model of optimization of the machining process cutting parameters.     

Optical and electrical characterization of carbon nanoparticles produced in laminar premixed flames

Optical and electrical properties of carbonaceous particles produced in laboratory scale, premixed ethylene/air flames are obtained. Light absorption and Raman spectroscopy show that the change in particle nanostructure follows a graphitization trajectory as the flame richness increases. The optical band gap decreases and the size of the aromatic network in the particle increases, while the interlayer spacing between parallel layers decreases. The electrical conductivity of the materials increases by increasing flame richness in agreement to the graphitization trajectory. A non-ohmic behavior has been found and explained in terms of electron tunneling in a percolative network. Our results show that the electrical properties of flame formed carbon nanoparticles are strongly dependent on their nanostructure, and hence they have to be used carefully for the determination of particle concentration with conductometric sensors. Moreover, the dependence of the electrical properties of combustion formed particles might be useful for the development of cheap sensors for the selective detection of different classes of combustion aerosols.     

Wild Prunus Fruit Species as a Rich Source of Bioactive Compounds

Sugars, organic acids, carotenoids, tocopherols, chlorophylls, and phenolic compounds were quantified in fruit of 4 wild growing Prunus species (wild cherry, bird cherry, blackthorn, and mahaleb cherry) using HPLC‐DAD‐MSn. In wild Prunus, the major sugars were glucose and fructose, whereas malic and citric acids dominated among organic acids. The most abundant classes of phenolic compounds in the analyzed fruit species were anthocyanins, flavonols, derivatives of cinnamic acids, and flavanols. Two major groups of anthocyanins measured in Prunus fruits were cyanidin‐3‐rutinoside and cyanidin‐3‐glucoside. Flavonols were represented by 19 derivatives of quercetin, 10 derivatives of kaempferol, and 2 derivatives of isorhamnetin. The highest total flavonol content was measured in mahaleb cherry and bird cherry, followed by blackthorn and wild cherry fruit. Total phenolic content varied from 2373 (wild cherry) to 11053 mg GAE per kg (bird cherry) and ferric reducing antioxidant power antioxidant activity from 7.26 to 31.54 mM trolox equivalents per kg fruits.     

Surface-initiated atom transfer radical polymerization of polyhedral oligomeric silsesquioxane (POSS) methacrylate from flat silicon wafer

A polyhedral oligomeric silsesquioxane (POSS) methacrylate monomer, i.e. 3-(3,5,7,9,11,13,15-heptacyclopentyl-pentacyclo [9.5.1.1.^3,91.^5,151^7,13]-octasiloxane-1-yl) propyl methacrylate (POSS-MA), was directly grafted from flat silicon wafers using surface-initiated atom transfer radical polymerization (ATRP). Two methods were used to improve the system livingness and control of polymer molecular weights. By ‘adding free initiator’ method, a linear relationship between the grafted poly(POSS-MA) layer thickness and monomer conversion was observed. By ‘adding deactivator’ method, the poly(POSS-MA) thickness increased linearly with reaction time. Poly(POSS-MA) layers up to 40 nm were obtained. The chemical compositions measured by X-ray photoelectron spectroscopy (XPS) agreed well with their theoretical values. Water contact angle measurements revealed that the grafted poly(POSS-MA) was extremely hydrophobic. The surface morphologies of the grafted polymer layers were studied by an atom force microscopy (AFM).     

Effect of water vapour partial pressure on the chromia (Cr2O3)-based scale stability

The kinetics of the Cr₂O₃-based scale oxidation and volatilisation were studied in the presence of water vapour (H₂O). A commercial Cr₂O₃-based scale forming Type 310S stainless steel was examined at the ambient pressure (0.1?MPa) and 550°C in relatively low and high H₂O-containing environments of air-10% H₂O and air-70% H₂O, respectively. The increase in the partial pressure of H₂O (p_H2O) from 10 to 70% resulted in the transition of the oxidation and volatilisation kinetics from the parabolic rate law in air-10% H₂O to the paralinear rate law in air-70% H₂O. The kinetics transition was attributed to the increase in the Cr loss rate from the base scale after coupons exposure in air-70% H₂O. The significant role of Mn alloying element in the base scale protectiveness was also discussed in the context of the Cr₂O₃-based scale stability.     

AXL Receptor in Breast Cancer: Molecular Involvement and Therapeutic Limitations

Breast cancer was one of the first malignancies to benefit from targeted therapy, i.e., treatments directed against specific markers. Inhibitors against HER2 are a significant example and they improved the life expectancy of a large cohort of patients. Research on new biomarkers, therefore, is always current and important. AXL, a member of the TYRO-3, AXL and MER (TAM) subfamily, is, today, considered a predictive and prognostic biomarker in many tumor contexts, primarily breast cancer. Its oncogenic implications make it an ideal target for the development of new pharmacological agents; moreover, its recent role as immune-modulator makes AXL particularly attractive to researchers involved in the study of interactions between cancer and the tumor microenvironment (TME). All these peculiarities characterize AXL as compared to other members of the TAM family. In this review, we will illustrate the biological role played by AXL in breast tumor cells, highlighting its molecular and biological features, its involvement in tumor progression and its implication as a target in ongoing clinical trials.