Computers and supercomputers in biology

 

Computers and supercomputers in biology
ed. V.D. Lakhno and M.N. Ustinin
Moscow-Izhevsk: 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. X-rays 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 X-ray analysis	55
3.1.2. Present-days problems of macromolecular crystallography	58
3.1.3. Main stages of the X-ray 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 X-ray scattering data	62
3.1.6. How to “see” the functions of three variables	65
3.1.7. Phase problem of X-ray 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 ab-initio 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 pseudo-models	103
3.3.7. Combination of methods. Determinig of low-angular phasis for a ribosomal particle T50S	106
3.3.8. Revealing of the structure of a low-density 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. Quantum-mechanical 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. Long-range 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 Newton-Krylov 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 two-helical B-DNA 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 three-dimensional 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 GIS-technologies 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 protein-encoding 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. Patero-optimal alignment	439
6.3. Recognition ot protein-encoding region in DNA sequence is an important problem of the analysis of the biological sequences	442
6.4. Present-day 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 X-ray system	462
7.4. Main operations of digital X-ray image processing	465
7.5. Approximation of digital X-ray 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. 3D-modelling and animation	490
8.4. Rendering	495
8.5. Conclusions	496
References	497
Glossary	498