A New method for Analysis of Biomolecules Using the BSM-SG Atomic Models

Biomolecules and particularly proteins and DNA exhibit some mysterious features that cannot find satisfactory explanation by quantum mechanical modes of atoms. One of them, known as a Levinthal’s paradox, is the ability to preserve their complex three-dimensional structure in appropriate environments. Another one is that they possess some unknown energy mechanism. The Basic Structures of Matter Supergravitation Unified Theory (BSM-SG) allows uncovering the real physical structures of the elementary particles and their spatial arrangement in atomic nuclei. The resulting physical models of the atoms are characterized by the same interaction energies as the quantum mechanical models, while the structure of the elementary particles influence their spatial arrangement in the nuclei. The resulting atomic models with fully identifiable parameters and angular positions of the quantum orbits permit studying the physical conditions behind the structural and bonding restrictions of the atoms connected in molecules. A new method for a theoretical analysis of biomolecules is proposed. The analysis of a DNA molecule leads to formulation of hypotheses about the energy storage mechanism in DNA and its role in the cell cycle synchronization. This permits shedding a light on the DNA feature known as a C-value paradox. The analysis of a tRNA molecule leads to formulation of a hypothesis about a binary decoding mechanism behind the 20 flavors of the complex aminoacyle-tRNA synthetases - tRNA, known as a paradox

Hierarchy of protein loop-lock structures: a new server for the decomposition of a protein structure into a set of closed loops

HoPLLS (Hierarchy of protein loop-lock structures) (http://leah.haifa.ac.il/~skogan/Apache/mydata1/main.html) is a web server that identifies closed loops - a structural basis for protein domain hierarchy. The server is based on the loop-and-lock theory for structural organisation of natural proteins. We describe this web server, the algorithms for the decomposition of a 3D protein into loops and the results of scientific investigations into a structural "alphabet" of loops and locks.Comment: 11 pages, 4 figure

Optimality of the genetic code with respect to protein stability and amino acid frequencies

How robust is the natural genetic code with respect to mistranslation errors? It has long been known that the genetic code is very efficient in limiting the effect of point mutation. A misread codon will commonly code either for the same amino acid or for a similar one in terms of its biochemical properties, so the structure and function of the coded protein remain relatively unaltered. Previous studies have attempted to address this question more quantitatively, namely by statistically estimating the fraction of randomly generated codes that do better than the genetic code regarding its overall robustness. In this paper, we extend these results by investigating the role of amino acid frequencies in the optimality of the genetic code. When measuring the relative fitness of the natural code with respect to a random code, it is indeed natural to assume that a translation error affecting a frequent amino acid is less favorable than that of a rare one, at equal mutation cost. We find that taking the amino acid frequency into account accordingly decreases the fraction of random codes that beat the natural code, making the latter comparatively even more robust. This effect is particularly pronounced when more refined measures of the amino acid substitution cost are used than hydrophobicity. To show this, we devise a new cost function by evaluating with computer experiments the change in folding free energy caused by all possible single-site mutations in a set of known protein structures. With this cost function, we estimate that of the order of one random code out of 100 millions is more fit than the natural code when taking amino acid frequencies into account. The genetic code seems therefore structured so as to minimize the consequences of translation errors on the 3D structure and stability of proteins.Comment: 31 pages, 2 figures, postscript fil

GalPak3D: A Bayesian parametric tool for extracting morpho-kinematics of galaxies from 3D data

We present a method to constrain galaxy parameters directly from three-dimensional data cubes. The algorithm compares directly the data with a parametric model mapped in $x,y,\lambda$ coordinates. It uses the spectral lines-spread function (LSF) and the spatial point-spread function (PSF) to generate a three-dimensional kernel whose characteristics are instrument specific or user generated. The algorithm returns the intrinsic modeled properties along with both an `intrinsic' model data cube and the modeled galaxy convolved with the 3D-kernel. The algorithm uses a Markov Chain Monte Carlo (MCMC) approach with a nontraditional proposal distribution in order to efficiently probe the parameter space. We demonstrate the robustness of the algorithm using 1728 mock galaxies and galaxies generated from hydrodynamical simulations in various seeing conditions from 0.6" to 1.2". We find that the algorithm can recover the morphological parameters (inclination, position angle) to within 10% and the kinematic parameters (maximum rotation velocity) to within 20%, irrespectively of the PSF in seeing (up to 1.2") provided that the maximum signal-to-noise ratio (SNR) is greater than $\sim3$ pixel$^{-1}$ and that the ratio of the galaxy half-light radius to seeing radius is greater than about 1.5. One can use such an algorithm to constrain simultaneously the kinematics and morphological parameters of (nonmerging) galaxies observed in nonoptimal seeing conditions. The algorithm can also be used on adaptive-optics (AO) data or on high-quality, high-SNR data to look for nonaxisymmetric structures in the residuals.Comment: 16 pages, 10 figures, accepted to publication in AJ, revised version after proofs corrections. Algorithm available at http://galpak.irap.omp.e

GATE : a simulation toolkit for PET and SPECT

Monte Carlo simulation is an essential tool in emission tomography that can assist in the design of new medical imaging devices, the optimization of acquisition protocols, and the development or assessment of image reconstruction algorithms and correction techniques. GATE, the Geant4 Application for Tomographic Emission, encapsulates the Geant4 libraries to achieve a modular, versatile, scripted simulation toolkit adapted to the field of nuclear medicine. In particular, GATE allows the description of time-dependent phenomena such as source or detector movement, and source decay kinetics. This feature makes it possible to simulate time curves under realistic acquisition conditions and to test dynamic reconstruction algorithms. A public release of GATE licensed under the GNU Lesser General Public License can be downloaded at the address http://www-lphe.epfl.ch/GATE/

DISPATCH: A Numerical Simulation Framework for the Exa-scale Era. I. Fundamentals

We introduce a high-performance simulation framework that permits the semi-independent, task-based solution of sets of partial differential equations, typically manifesting as updates to a collection of `patches' in space-time. A hybrid MPI/OpenMP execution model is adopted, where work tasks are controlled by a rank-local `dispatcher' which selects, from a set of tasks generally much larger than the number of physical cores (or hardware threads), tasks that are ready for updating. The definition of a task can vary, for example, with some solving the equations of ideal magnetohydrodynamics (MHD), others non-ideal MHD, radiative transfer, or particle motion, and yet others applying particle-in-cell (PIC) methods. Tasks do not have to be grid-based, while tasks that are, may use either Cartesian or orthogonal curvilinear meshes. Patches may be stationary or moving. Mesh refinement can be static or dynamic. A feature of decisive importance for the overall performance of the framework is that time steps are determined and applied locally; this allows potentially large reductions in the total number of updates required in cases when the signal speed varies greatly across the computational domain, and therefore a corresponding reduction in computing time. Another feature is a load balancing algorithm that operates `locally' and aims to simultaneously minimise load and communication imbalance. The framework generally relies on already existing solvers, whose performance is augmented when run under the framework, due to more efficient cache usage, vectorisation, local time-stepping, plus near-linear and, in principle, unlimited OpenMP and MPI scaling.Comment: 17 pages, 8 figures. Accepted by MNRA

CLP-based protein fragment assembly

The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a database of known protein structures that clusters and classifies the fragments according to similarity and frequency. The problem of assembling fragments into a complete conformation is mapped to a constraint solving problem and solved using CLP. The constraint-based model uses a medium discretization degree Ca-side chain centroid protein model that offers efficiency and a good approximation for space filling. The approach adapts existing energy models to the protein representation used and applies a large neighboring search strategy. The results shows the feasibility and efficiency of the method. The declarative nature of the solution allows to include future extensions, e.g., different size fragments for better accuracy.Comment: special issue dedicated to ICLP 201