Observations - Planet Mars in 1967

Visual Mars observations by Volgograd Observatory in 1966-196

The cooperation of Russian and German metal forming scientific schools to develop the new energy-efficient materials and technologies

The future scientific orientation of Katedra PDSS is in the area of materials forming and materials development with a focus on efficient processes regarding the use of energy and resources. Current research in the department PDSS is based on fundamental works on thermo-mechanical treatment of metals and on the modeling of nano-materials, rolled material and medical materials. This includes research on the relevant microstructural and macroscopic effects on the materials behavior. Together with its international research partners PDSS has excellent foundations for experimental research as well. With its international focus and its educational programs for students and skilled employees PDSS is an important partner of the Russian metal processing industry which supports Russian companies to compete on a world-class level

PCA and K-Means decipher genome

In this paper, we aim to give a tutorial for undergraduate students studying statistical methods and/or bioinformatics. The students will learn how data visualization can help in genomic sequence analysis. Students start with a fragment of genetic text of a bacterial genome and analyze its structure. By means of principal component analysis they ``discover'' that the information in the genome is encoded by non-overlapping triplets. Next, they learn how to find gene positions. This exercise on PCA and K-Means clustering enables active study of the basic bioinformatics notions. Appendix 1 contains program listings that go along with this exercise. Appendix 2 includes 2D PCA plots of triplet usage in moving frame for a series of bacterial genomes from GC-poor to GC-rich ones. Animated 3D PCA plots are attached as separate gif files. Topology (cluster structure) and geometry (mutual positions of clusters) of these plots depends clearly on GC-content.Comment: 18 pages, with program listings for MatLab, PCA analysis of genomes and additional animated 3D PCA plot

Principal manifolds and graphs in practice: from molecular biology to dynamical systems

We present several applications of non-linear data modeling, using principal manifolds and principal graphs constructed using the metaphor of elasticity (elastic principal graph approach). These approaches are generalizations of the Kohonen's self-organizing maps, a class of artificial neural networks. On several examples we show advantages of using non-linear objects for data approximation in comparison to the linear ones. We propose four numerical criteria for comparing linear and non-linear mappings of datasets into the spaces of lower dimension. The examples are taken from comparative political science, from analysis of high-throughput data in molecular biology, from analysis of dynamical systems.Comment: 12 pages, 9 figure

The Mystery of Two Straight Lines in Bacterial Genome Statistics. Release 2007

In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial genomes available in Genbank in April 2007, belong to these lines with high accuracy. The main challenge now is to explain the observed high accuracy. The new phenomenon of complementary symmetry for codon position--specific nucleotide frequencies is observed. The results of analysis of several codon usage models are presented. We demonstrate that the mean--field approximation, which is also known as context--free, or complete independence model, or Segre variety, can serve as a reasonable approximation to the real codon usage. The first two principal components of codon usage correlate strongly with genomic G+C content and the optimal growth temperature respectively. The variation of codon usage along the third component is related to the curvature of the mean-field approximation. First three eigenvalues in codon usage PCA explain 59.1%, 7.8% and 4.7% of variation. The eubacterial and archaeal genomes codon usage is clearly distributed along two third order curves with genomic G+C content as a parameter.Comment: Significantly extended version with new data for all the 348 distinct bacterial genomes available in Genbank in April 200

Translational control of gene expression via interacting feedback loops

Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover how translation may be controlled via interacting feedback loops. Our results reveal that this interplay gives rise to a remarkable range of protein synthesis dynamics, including oscillations, step-change and bistability. This suggests that cells may have recourse to a much richer set of control mechanisms than was previously understood.Comment: Supplementary Material Available on Reques