Computers and supercomputers in biology
Computers and supercomputers in biology
ed. V.D. Lakhno and M.N. Ustinin
MoscowIzhevsk: Institute of computer investigations, 2002, 528p.
( in Russian )
Contents
PART 1. STRUCTURE AND PHYSICAL PROPERTIES OF DNA AND PROTEINS, CHARGE TRANSFER IN DNA, PHOTOSYNTHETIC REACTION CENTER  13 
Preface to part 1  15 
CHAPTER 1. V.D. Lakhno. Computational problems of computational biology  18 
1.1 Introduction  18 
1.2. Problems of computational biology  18 
1.3. Primary structures  20 
1.4. Xrays proyein analysis  24 
1.5. Protein folding  26 
1.6. Modeling of the structure and dynamics of macromolecules  27 
1.7. Applied problems of computational biology  29 
References  33 
CHAPTER 2. A.A. Zimin, V.D. Lakhno, N.N. Nazipova. Biological macromolecules: structure, shapes and functions  35 
2.1. Introduction  35 
2.2. Nucleic acids (DNA and RNA)  35 
2.3. Proteins  40 
2.4. Spatial structures of biopolymer molecules and methods for their investigation  44 
2.5. Methods for revealing primary structures of DNA, RNA and protein molecules  47 
References  53 
CHAPTER 3. V.Yu. Lunin. Revealing of the spatial structure of biological macromolecules  55 
3.1. Introduction  55 
3.1.1. Fundamentals of the Xray analysis  55 
3.1.2. Presentdays problems of macromolecular crystallography  58 
3.1.3. Main stages of the Xray analysis  59 
3.1.4. Different levels of the description of the protein molecule structure  60 
3.1.5. Main stages of decoding the structure from the Xray scattering data  62 
3.1.6. How to “see” the functions of three variables  65 
3.1.7. Phase problem of Xray analysis  67 
3.2. Phase problem  70 
3.2.1. Terminology and designations  72 
3.2.2. Additional information on the object under study  75 
3.3. Direct phasing at low resolution  86 
3.3.1. Main definitions  87 
3.3.2. Procedure of abinitio phasing  88 
3.3.3. The use of Fourier synthsis histograms  91 
3.3.4. Phasing on the basis of coherence  96 
3.3.5. Phasing on the basis of likelihood minimization  101 
3.3.6. The use of pseudomodels  103 
3.3.7. Combination of methods. Determinig of lowangular phasis for a ribosomal particle T50S  106 
3.3.8. Revealing of the structure of a lowdensity lipoprotein particle (LDL)  107 
3.4. Methods for electron density modication  108 
3.4.1. Presentation of limitations as a functional equation  109 
3.4.2. Structure factor equations  111 
3.4.3. Iteration procedure of phase refining  112 
3.4.4. Phasing as a minimization problem  113 
3.5. N.L. Lunina. The use of FAM method  114 
3.5.1. Fundamentals  114 
3.5.2. Description of FAM method and results of its testing  117 
References  130 
CHAPTER 4. V.D. Lakhno. Dynamics of hole transfer in nucleatide sequences  137 
4.1. Introduction  137 
4.2. Quantummechanical model  139 
4.3. Model parameters  143 
4.4. Hole transfer from the state close to a relaxed one  146 
4.5. Hole transfer from a nonrelaxed state  155 
4.6. Comparison of the theory with the experiment  157 
4.7. Oscillating nature of charge transfer in DNA  161 
4.8. Generalization of the model  164 
4.9. Comparison with ither approaches  165 
4.10. Horizontes of the theory development  167 
References  167 
CHAPTER 5. V.D. Lakhno, N.S. Fialko. Longrange charge transfer in DNA  172 
5.1. Introduction  172 
5.2. Mathematical model  174 
5.3. Some particular cases  176 
5.4. System under consideration  179 
5.5. Stationary solitary wave  181 
5.6. Moving soliton  182 
5.7. Modelling of transfer in a homogeneous chain  184 
5.8. Modelling of a donor and an acceptor  186 
5.9. Discussing of results  191 
References  193 
CHAPTER 6. V.D. Lakhno. Modelling of primary processess of charge transfer in a photosynthetic reaction center  195 
6.1. Introduction  195 
6.2. Primary processess of charge transfer in photosynthetic reaction center  196 
6.3. Mathematical model  197 
6.4. Electron transfere parameters  199 
6.5. Results of numerical calculations  200 
6.6. Possibilities of more comprehensive consideration of structural and dynamical properties of a phtoreaction center  202 
6.7. Further discussioon and comparison with other approaches  205 
6.8. Conclusive remarks  206 
References  206 
CHAPTER 7. D.A. Tikhonov. Method of integral equations of the theory of liquids for the study of a macromolecule hydrotation  209 
7.1. Introduction  209 
7.2. RISM equations for the study of a macromolecule solvation (hydrotation)  211 
7.3. Numerical scheme  213 
7.4. Further approximations in the RISM method which make it more efficeint as to the computational process  221 
7.5. Algorithm for the solution of RISM equations by NewtonKrylov method  222 
7.6. Results of calculations  225 
7.7. Conclusions  229 
Appendix. Nonstationary iteration methods for the solution of SLA equations “Krylov’s subspace methods”  230 
References  233 
CHAPTER 8. A.V. Teplukhin, Yu.S. Lemesheva. The study of the structure of an aqueous shell of twohelical BDNA poly(dA):poly(dT) by parallel processing  234 
8.1. Introduction  234 
8.2. State of the problem  235 
8.3. Methods and algorithms for computer experiments  236 
8.4. Results of investigations  237 
References  239 
Colored illustrations 
PART 2. BIOINFORMATIC, COMPUTATIONAL BIOLOGY AND BIOMEDICINE  241 
Preface to part 2

243 
CHAPTER 1. Yu.E. Elkin. Excitation waves in biological systems and kinematic approach to their study  247 
1.1. Introduction: autoscillations and autowaves in nature  247 
1.2. Autowave imagein a plain and nature heart functioning  250 
1.2.1. Pacemaker  250 
1.2.2. Two pacemaker  250 
1.2.3. Spiral wave  251 
1.3. On mathematical approaches to the study of autowaves  253 
1.4. Kinematic approach  255 
1.4.1. Geometrical description of excitation waves  255 
1.4.2. On the exact solution of stationary kinematic equations  260 
1.4.3. Some results of the use of geometrical methods  263 
1.4.4. Comparison of althernative geometrical approaches  265 
1.4.5. On extending the generalizatied kinematic to the threedimensional case  268 
1.5. Conclusions  269 
References  270 
CHAPTER 2. A.R. Skovoroda. Early noninvasive diagnostic of tissue pathologies as a problem of computational mathematics  274 
2.1. Introduction  274 
2.2. Main relations, mechanical characteristics and experimental data  275 
2.3. Reconstrunction of the displcement modules of the objec under study from the data on its deformed state  283 
2.4. Conclusive remarks  292 
A.N. Klishko. Methods of quatitatie estimstion of elastic chracteristics of soft biological tissues  294 
2.5. Estimation of tissue elastic properties by pressing in a stamp on the basis of testing postoperative materials  294 
2.6. Resonance method of determining the displacement modules of the elatic layer  299 
2.6.1. The problem of the dynamical equilibrium of external forces  299 
2.6.2. The problem of the dynamicalequilibrium of an elastic layer upon axisymmetric loading of one of its boundaries  301 
2.6.3. Determining of resonance frequencies of a their plate lying on an elastic layer and loaded by a periodical external force  309 
References  313 
CHAPTER 3. M.N. Ustinin, S.A. Makhortykh, A.M. Molchanov, M.M. Olshevets, A.N. Pankratov, N.M. Pankratova, V.I. Sukharev, V.V. Sychyov. The problems of the analysis of magnetic encephalography  327 
3.1. Introduction  327 
3.2. Modelling of the biomagnetic activity of the brain  331 
3.3. Solution of the direct and inverse problems of magntic encephalography  338 
3.3.1. Solution of the inverse problem  339 
3.3.2. Momentum fitting procedure  340 
3.3.3. Fitting of the dipole amplitude  341 
3.4. Study of the dynamical characteristic of the magnetic encephalography data  342 
3.4.1. Calculation of the correlation dimensions of a signal  342 
3.4.2. Algorithm for calculation of the attractor dimensions  345 
3.5. Conclusions  347 
References  348 
CHAPTER 4. L.G. Khanina, A.S. Komarov, V.E. Smirnov, M.V. Bobrovskii, I.E.Sizov, E.M.Glukhova. Computational ecology  350 
4.1. Introduction. Computational ecology: definition, main problem  350 
4.2. Databases  351 
4.3. Dynamical modelling  356 
4.3.1. Methodical aspects of the development of imitation models of complicated systems  356 
4.3.2. Modellimg of forest ecosystem  359 
4.3.3. Mathematical plant demography  365 
4.4. Multidimensional analysis of ecological data  371 
4.4.1. Main methods of the multidimensional analysis of ecological data  371 
4.4.2. Classification of flora descriptions  372 
4.4.3. Singling out of functional groups of species  374 
4.5. Spatial anlysis of ecological data  376 
4.5.1. Main methods for statial analysis of ecolgical data  376 
4.5.2. Use of GIStechnologies to assess the vegetation biodiversity  379 
4.6. Visualization  381 
4.7. Conclusions  383 
References  383 
CHAPTER 5. N.N. Nazipova, M.N. Ustinin. Solution of the problem of decoding genetic information contained in biological sequences  392 
5.1. Introduction  392 
5.2. Recognition of proteinencoding regions on an extended genetic sequence  396 
5.2.1. statement of the problem  396 
5.2.2. Methods for recognition of encoding regions with the use of statistical characteristics of the encoding site of genomes  397 
5.2.3. Encoding measures  401 
5.2.4. Efficiency of encoding measures  412 
5.2.5. Mathematical methods for gene recognition used in modern software packages  413 
5.3. Attributing a function to a gene  416 
5.4. Conclusions  419 
References  422 
CHAPTER 6. T.V. Astakhova, N.V. Oleinikova, M.A. Roytberg. Comparative analysis of information biopolymers  433 
6.1. Introduction: Development of methods for biopolymer analysis  433 
6.2. Another approach to the problem of aminoacid sequence alignment. Paterooptimal alignment  439 
6.3. Recognition ot proteinencoding region in DNA sequence is an important problem of the analysis of the biological sequences  442 
6.4. Presentday problems of the comparative analysis of biological sequences, prerequisites for the use of parallel processing  447 
6.5. The study of the certanty of the aminoacid sequence alignment  449 
6.5.1. The soutce of structurally adequate alignment  449 
6.5.2. The measure of sequence similarity  450 
6.5.3. The measure of alignment similarity. The notion of an “island”  451 
6.5.4. The dependence of the extent of structural and sequential alignmetn on the extent of similarity of the studied proteins  452 
6.5.5. Detailed study of alignments. Guessed “islans”  453 
References  455 
CHAPTER 7. M.N. Ustinin, I.A. Nikonov, M.M. Olshevets. Digital diagnostic and telemedicine  458 
7.1. Introduction  458 
7.2. Digital roentgenography  459 
7.3. Software for the digital Xray system  462 
7.4. Main operations of digital Xray image processing  465 
7.5. Approximation of digital Xray images in splash bases  470 
References  474 
CHAPTER 8. S.V. Filippov, E.V. Sobolev. The use of technologies of professional computer graphics for visualization of investigation results  476 
8.1. Introduction  476 
8.2. Composing  477 
8.2.1. Adobe After Effects^{®}  478 
8.2.2. Discreet Combustion^{®}  486 
8.3. 3Dmodelling and animation  490 
8.4. Rendering  495 
8.5. Conclusions  496 
References  497 
Glossary

498 