Mechanisms of proton-proton inelastic cross-section growth in multi-peripheral model within the framework of perturbation theory. Part 2

We demonstrate a new technique for calculating proton-proton inelastic cross-section, which allows one by application of the Laplace' method replace the integrand in the integral for the scattering amplitude in the vicinity of the maximum point by expression of Gaussian type. This in turn, allows one to overcome the computational difficulties for the calculation of the integrals expressing the cross section to sufficiently large numbers of particles. We have managed to overcome these problems in calculating the proton-proton inelastic cross-section for production (n \le 8) number of secondary particles in within the framework of \phi^3 model. As the result the obtained dependence of inelastic cross-section and total scattering cross-section on the energy \sqrt{s} are qualitative agrees with the experimental data. Such description of total cross-section behavior differs considerably from existing now description, where reggeons exchange with the intercept greater than unity is considered.Comment: 11 pages, 10 figures (v3: some inaccuracies corrected

IVSPlat 1.0: an integrated virtual screening platform with a molecular graphical interface

<p>Abstract</p> <p>Background</p> <p>The virtual screening (VS) of lead compounds using molecular docking and pharmacophore detection is now an important tool in drug discovery. VS tasks typically require a combination of several software tools and a molecular graphics system. Thus, the integration of all the requisite tools in a single operating environment could reduce the complexity of running VS experiments. However, only a few freely available integrated software platforms have been developed.</p> <p>Results</p> <p>A free open-source platform, IVSPlat 1.0, was developed in this study for the management and automation of VS tasks. We integrated several VS-related programs into a molecular graphics system to provide a comprehensive platform for the solution of VS tasks based on molecular docking, pharmacophore detection, and a combination of both methods. This tool can be used to visualize intermediate and final results of the VS execution, while also providing a clustering tool for the analysis of VS results. A case study was conducted to demonstrate the applicability of this platform.</p> <p>Conclusions</p> <p>IVSPlat 1.0 provides a plug-in-based solution for the management, automation, and visualization of VS tasks. IVSPlat 1.0 is an open framework that allows the integration of extra software to extend its functionality and modified versions can be freely distributed. The open source code and documentation are available at <url>http://kyc.nenu.edu.cn/IVSPlat/.</url></p

Let’s not forget tautomers

A compound exhibits tautomerism if it can be represented by two structures that are related by an intramolecular movement of hydrogen from one atom to another. The different tautomers of a molecule usually have different molecular fingerprints, hydrophobicities and pKa’s as well as different 3D shape and electrostatic properties; additionally, proteins frequently preferentially bind a tautomer that is present in low abundance in water. As a result, the proper treatment of molecules that can tautomerize, ~25% of a database, is a challenge for every aspect of computer-aided molecular design. Library design that focuses on molecular similarity or diversity might inadvertently include similar molecules that happen to be encoded as different tautomers. Physical property measurements might not establish the properties of individual tautomers with the result that algorithms based on these measurements may be less accurate for molecules that can tautomerize—this problem influences the accuracy of filtering for library design and also traditional QSAR. Any 2D or 3D QSAR analysis must involve the decision of if or how to adjust the observed Ki or IC50 for the tautomerization equilibria. QSARs and recursive partitioning methods also involve the decision as to which tautomer(s) to use to calculate the molecular descriptors. Docking virtual screening must involve the decision as to which tautomers to include in the docking and how to account for tautomerization in the scoring. All of these decisions are more difficult because there is no extensive database of measured tautomeric ratios in both water and non-aqueous solvents and there is no consensus as to the best computational method to calculate tautomeric ratios in different environments

Gluon Loops in the Inelastic Processes in QCD

Sharf IV, Merkotan KK, Podolyan NA, et al. Gluon Loops in the Inelastic Processes in QCD. 2012.It is shown that inelastic process of the exchange with two massless gluonsis formally equivalent to the process of the exchange with one massiveparticle. Thus, using the Laplace's method, a new mechanism of mass generationin inelastic processes is discovered, which is described by the non-Abeliangauge theory. Furthermore, it is shown that in the QCD perturbation theory, thesame mechanisms of cross-sections growth take place, similar to the onesdiscovered before in the effective scalar theories

Excited-State Dynamics of Cytosine Tautomers

We report the relaxation dynamics of keto and enol or keto-imino cytosine, photoexcited in the wavelength range of 260-290 nm. Three transients with femtosecond to hundreds of picosends lifetimes are observed for the biologically relevant keto tautomer and are assigned to internal conversion and excited-state tautomerization. Only two transients with femtosecond and picosecond lifetimes are identified for the enol or keto-imino tautomer and are assigned to internal conversion processes. The results are discussed in the context of published ab initio theory.close302