具體描述
內容簡介
《生物數學·第1捲(第3版)》是近代生物數學方麵的名著。這是第一捲,第三版,在原來版本的基礎上做瞭全麵修訂。近年來這個科目的茁壯成長和新知識點的不斷湧現,新的版本將原來的一捲集分成上下兩捲,擴大瞭知識容量,第二捲絕大多數是新增知識點。書中對生物學中的反應擴散方程和形態發生學的數學理論及研究成果作瞭全麵介紹,是學習與研究生物數學的一部不可多得的參考書。 目錄
contents, volume i
preface to the third edition
preface to the first edition
1. continuous population models for single species
1.1 continuous growth models
1.2 insect outbreak model: spruce budworm
1.3 delay models
1.4 linear analysis of delay population models: periodic solutions
1.5 delay models in physiology: periodic dynamic diseases
1.6 harvesting a single natural population
1.7 population model with age distribution
exercises
2. discrete population models for a single species
2.1 introduction: simple models
2.2 cobwebbing: a graphical procedure of solution
2.3 discrete logistic-type model: chaos
2.4 stability, periodic solutions and bifurcations
2.5 discrete delay models
2.6 fishery management model
.2.7 ecological implications and caveats
2.8 tumour cell growth
exercises
3. models for interacting populations
3.1 predator-prey models: lotka-volterra systems
3.2 complexity and stability
3.3 realistic predator-prey models
3.4 analysis of a predator-prey model with limit cycle periodic behaviour: parameter domains of stability
3.5 competition models: competitive exclusion principle
3.6 mutualism or symbiosis
3.7 general models and cautionary remarks
3.8 threshold phenomena
3.9 discrete growth models for interacting populations
3.10 predator-prey models: detailed analysis
exercises
4. temperature-dependent sex determination (tsd)
4.1 biological introduction and historical asides on the crocodilia.
4.2 nesting assumptions and simple population model
4.3 age-structured population model for crocodilia
4.4 density-dependent age-structured model equations
4.5 stability of the female population in wet marsh region l
4.6 sex ratio and survivorship
4.7 temperature-dependent sex determination (tsd) versus genetic sex determination (gsd)
4.8 related aspects on sex determination
exercise
5. modelling the dynamics of marital interaction: divorce prediction and marriage repair
5.1 psychological background and data: gottman and levenson methodology
5.2 marital typology and modelling motivation
5.3 modelling strategy and the model equations
5.4 steady states and stability
5.5 practical results from the model
5.6 benefits, implications and marriage repair scenarios
6. reaction kinetics
6.1 enzyme kinetics: basic enzyme reaction
6.2 transient time estimates and nondimensionalisation
6.3 michaelis-menten quasi-steady state analysis
6.4 suicide substrate kinetics
6.5 cooperative phenomena
6.6 autocatalysis, activation and inhibition
6.7 multiple steady states, mushrooms and isolas
exercises
7. biological oscillators and switches
7.1 motivation, brief history and background
7.2 feedback control mechanisms
7.3 oscillators and switches with two or more species: general qualitative results
7.4 simple two-species oscillators: parameter domain determination for oscillations
7.5 hodgkin-huxley theory of nerve membranes:fitzhugh-nagumo model
7.6 modelling the control of testosterone secretion and chemical castration
exercises
8. bz oscillating reactions
8.1 belousov reaction and the field-koros-noyes (fkn) model
8.2 linear stability analysis of the fkn model and existence of limit cycle solutions
8.3 nonlocal stability of the fkn model
8.4 relaxation oscillators: approximation for the belousov-zhabotinskii reaction
8.5 analysis of a relaxation model for limit cycle oscillations in the belousov-zhabotinskii reaction
exercises
9. perturbed and coupled oscillators and black holes
9.1 phase resetting in oscillators
9.2 phase resetting curves
9.3 black holes
9.4 black holes in real biological oscillators
9.5 coupled oscillators: motivation and model system
9.6 phase locking of oscillations: synchronisation in fireflies
9.7 singular perturbation analysis: preliminary transformation
9.8 singular perturbation analysis: transformed system
9.9 singular perturbation analysis: two-time expansion
9.10 analysis of the phase shift equation and application to coupled belousov-zhabotinskii reactions
exercises
10. dynamics of infectious diseases
10.1 historical aside on epidemics
10.2 simple epidemic models and practical applications
10.3 modelling venereal diseases
10.4 multi-group model for gonorrhea and its control
10.5 aids: modelling the transmission dynamics of the human immunodeficiency virus (hiv)
10.6 hiv: modelling combination drug therapy
10.7 delay model for hiv infection with drug therapy
10.8 modelling the population dynamics of acquired immunity to parasite infection
10.9 age-dependent epidemic model and threshold criterion
10.10 simple drug use epidemic model and threshold analysis
10.11 bovine tuberculosis infection in badgers and caule
10.12 modelling control strategies for bovine tuberculosis in badgers and cattle
exercises
11. reaction diffusion, chemotaxis, and noniocal mechanisms
11.1 simple random walk and derivation of the diffusion equation
11.2 reaction diffusion equations
11.3 models for animal dispersal
11.4 chemotaxis
11.5 nonlocal effects and long range diffusion
11.6 cell potential and energy approach to diffusion and long range effects
exercises
12. oscillator-generated wave phenomena
12. i belousov-zhabotinskii reaction kinematic waves
12.2 central pattern generator: experimental facts in the swimming of fish
12.3 mathematical model for the central pattern generator
12.4 analysis of the phase coupled model system
exercises
13. biological waves: single-species models
13. l background and the travelling waveform
13.2 fisher-kolmogoroff equation and propagating wave solutions
13.3 asymptotic solution and stability of wavefront solutions of the fisher-kolmogoroff equation
13.4 density-dependent diffusion-reaction diffusion models and some exact solutions
13.5 waves in models with multi-steady state kinetics: spread and control of an insect population
13.6 calcium waves on amphibian eggs: activation waves on medaka eggs
13.7 invasion wavespeeds with dispersive variability
13.8 species invasion and range expansion
exercises
14. use and abuse of fractals
14.1 fractals: basic concepts and biological relevance
14.2 examples of fractals and their generation
14.3 fractal dimension: concepts and methods of calculation
14.4 fractals or space-filling?
appendices
a. phase plane analysis
b. routh-hurwitz conditions, jury conditions, descartes'
rule of signs, and exact solutions of a cubic
b.1 polynomials and conditions
b.2 descartes' rule of signs
b.3 roots of a general cubic polynomial
bibliography
index
contents, volume ii
j.d. murray: mathematical biology, ii: spatial models and biomedical applications
preface to the third edition
preface to the first edition
1. multi-species waves and practical applications
1.1 intuitive expectations
1.2 waves of pursuit and evasion in predator-prey systems
1.3 competition model for the spatial spread of the grey squirrel in britain
1.4 spread of genetically engineered organisms
1.5 travelling fronts in the belousov-zhabotinskii reaction
1.6 waves in excitable media
1.7 travelling wave trains in reaction diffusion systems with oscillatory kinetics
1.8 spiral waves
1.9 spiral wave solutions of x-co reaction diffusion systems
2. spatial pattern formation with reaction diffusion systems
2.1 role of pattern in biology
2.2 reaction diffusion (turing) mechanisms
2.3 general conditions for diffusion-driven instability:linear stability analysis and evolution of spatial pattern
2.4 detailed analysis of pattern initiation in a reaction diffusion mechanism
2.5 dispersion relation, turing space, scale and geometry effects in pattern formation models
2.6 mode selection and the dispersion relation
2.7 pattern generation with single-species models: spatial heterogeneity with the spruce budworm model
2.8 spatial patterns in scalar population interaction diffusion equations with convection: ecological control strategies
2.9 nonexistence of spatial patterns in reaction diffusion systems: general and particular results
3. animal coat patterns and other practical applications of reactiondiffusion mechanisms
3.1 mammalian coat patterns--'how the leopard got its spots'
3.2 teratologies: examples of animal coat pattern abnormalities
3.3 a pattern formation mechanism for butterfly wing patterns
3.4 modelling hair patterns in a whorl in acetabularia
4. pattern formation on growing domains: alligators and snakes
4. i stripe pattern formation in the alligator: experiments
4.2 modelling concepts: determining the time of stripe formation
4.3 stripes and shadow stripes on the alligator
4.4 spatial patterning of teeth primordia in the alligator:background and relevance
4.5 biology of tooth initiation
4.6 modelling tooth primordium initiation: background
4.7 model mechanism for alligator teeth patterning
4.8 results and comparison with experimental data
4.9 prediction experiments
4.10 concluding remarks on alligator tooth spatial patterning
4.11 pigmentation pattern formation on snakes
4.12 cell-chemotaxis model mechanism
4.13 simple and complex snake pattern elements
4.14 propagating pattern generation with the celi-chemotaxis system
5. bacterial patterns and chemotaxis
5.1 background and experimental results
5.2 model mechanism for e. coli in the semi-solid experiments
5.3 liquid phase model: intuitive analysis of pattern formation
5.4 interpretation of the analytical results and numerical solutions
5.5 semi-solid phase model mechanism for s. typhimurium
5.6 linear analysis of the basic semi-solid model
5.7 brief outline and results of the nonlinear analysis
5.8 simulation results, parameter spaces, basic patterns
5.9 numerical results with initial conditions from the experiments
5.10 swarm ring patterns with the semi-solid phase model mechanism
5.11 branching patterns in bacillus subtilis
6. mechanical theory for generating pattern and form in development
6.1 introduction, motivation and background biology
6.2 mechanical model for mesenchymal morphogenesis
6.3 linear analysis, dispersion relation and pattern formation potential
6.4 simple mechanical models which generate spatial patterns with complex dispersion relations
6.5 periodic patterns of feather germs
6.6 cartilage condensation in limb morphogenesis and morphogenetic rules
6.7 embryonic fingerprint formation
6.8 mechanochemical model for the epidermis
6.9 formation of microvilli
6.10 complex pattern formation and tissue interaction models
7. evolution, morphogenetic laws, developmental constraints and teratologies
7.1 evolution and morphogenesis
7.2 evolution and morphogenetic rules in cartilage formation in the vertebrate limb
7.3 teratologies (monsters)
7.4 developmental constraints, morphogenetic rules and the consequences for evolution
8.a mechanical theory of vascular network formation
8.1 biological background and motivation
8.2 cell-extracellular matrix interactions for vasculogenesis
8.3 parameter values
8.4 analysis of the model equations
8.5 network patterns: numerical simulations and conclusions
9. epidermal wound healing
9.1 brief history of wound healing
9.2 biological background: epidermal wounds
9.3 model for epidermal wound healing
9.4 nondimensional form, linear stability and parameter values
9.5 numerical solution for the epidermal wound repair model
9.6 travelling wave solutions for the epidermal model
9.7 clinical implications of the epidermal wound model
9.8 mechanisms of epidermal repair in embryos
9.9 actin alignment in embryonic wounds: a mechanical model
9.10 mechanical model with stress alignment of the actin filaments in two dimensions
10. dermal wound healing
10.1 background and motivation---general and biological
10.2 logic of wound healing and initial models
10.3 brief review of subsequent developments
10.4 model for fibroblast-driven wound healing: residual strain and tissue remodelling
10.5 solutions of the model equation solutions and comparison with experiment
10.6 wound healing model of cook (1995)
10.7 matrix secretion and degradation
10.8 cell movement in an oriented environment
10.9 model system for dermal wound healing with tissue structure
10.10 one-dimensional model for the structure of pathological scars
10.11 open problems in wound healing
10.12 concluding remarks on wound healing
11. growth and control of brain tumours
11.1 medical background
11.2 basic mathematical model of glioma growth and invasion
11.3 tumour spread in vitro: parameter estimation
11.4 tumour invasion in the rat brain
11.5 tumour invasion in the human brain
11.6 modelling treatment scenarios: general comments
11.7 modelling tumour resection (removal) in homogeneous tissue
11.8 analytical solution for tumour recurrence after resection
11.9 modelling surgical resection with brain tissue heterogeneity
11.10 modelling the effect of chemotherapy on tumour growth
11.11 modeling tumour polyclonality and cell mutation
12. neural models of pattern formation
12.1 spatial patterning in neural firing with a simple activation-inhibition model
12.2 a mcchanism for stripe formation in the visual cortex
12.3 a model for the brain mechanism underlying visual hallucination patterns
12.4 neural activity model for shell patterns
12.5 shamanism and rock art
13. geographic spread and control of epidemics
13.1 simple model for the spatial spread of an epidemic
13.2 spread of the black death in europe 1347-1350
13.3 brief history of rabies: facts and myths
13.4 the spatial spread of rabies among foxes i: background and simple model
13.5 spatial spread of rabies among foxes ii:three-species (sir) model
13.6 control strategy based on wave propagation into a non-epidemic region: estimate of width of a rabies barrier
13.7 analytic approximation for the width of the rabies control break
13.8 two-dimensional epizootic fronts and effects ot variable fox densitics: quantitative predictions for a rabies outbreak in england
13.9 effect of fox immunity on spatial spread of rabies
14. wolf territoriality, wolf-deer interaction and survival
14.1 introduction and wolf ecology
14.2 models for wolf pack territory formation: single pack--home range model
14.3 multi-wolf pack territorial model
14.4 wolf-deer predator-prey model
14.5 concluding remarks on-wolf territoriality and deer survival
14.6 coyote home range patterns
14.7 chippewa and sioux intertribal conflict c1750-1850
appendix
a. general results for the laplacian operator in bounded domains
bibliography
index 前言/序言
深入探索生命科學的數學視角:《計算生物學導論》 本書特色與定位 《計算生物學導論》旨在為生命科學、生物信息學、數學及計算機科學領域的學生和研究人員提供一個全麵、深入且實用的基礎框架,用以理解和應用現代計算方法解決復雜的生物學問題。本書側重於將抽象的數學原理與具體的生物學案例緊密結閤,強調從數據驅動的角度理解生命係統的動態性與復雜性。不同於傳統生物學教材的定性描述,本書提供瞭一套量化的工具箱,幫助讀者跨越學科壁壘,構建嚴謹的分析能力。 第一部分:基礎數學與統計學迴顧 本部分為後續高級主題的奠定基礎,內容嚴謹且具有針對性,專注於生物學研究中最常遇到的數學工具。 1. 綫性代數在生物數據中的應用: 詳細闡述矩陣運算、特徵值分解、奇異值分解(SVD)在處理高維生物數據集中的核心作用。重點討論主成分分析(PCA)在綫性降維、模式識彆中的應用,例如基因錶達譜的聚類分析和可視化。我們深入探討瞭馬爾可夫鏈(Markov Chains)在基因調控網絡狀態轉移、蛋白質摺疊構象空間探索中的建模潛力。 2. 概率論與統計推斷: 梳理瞭貝葉斯推斷的基本原則,並將其應用於生物學場景,如疾病診斷中的靈敏度與特異性計算,以及基因位點變異的先驗與後驗概率更新。著重講解瞭假設檢驗(Hypothesis Testing)的流程,包括p值解釋、多重檢驗校正(如Bonferroni和FDR方法)在基因組學研究中的必要性。我們還介紹瞭最大似然估計(MLE)在參數擬閤中的應用。 3. 微分方程與動態係統: 聚焦常微分方程(ODE)在描述生物係統變化率上的能力。內容涵蓋瞭從簡單的指數增長/衰減模型,到復雜的Lotka-Volterra捕食者-獵物模型,再到酶促反應的Michaelis-Menten動力學。對於偏微分方程(PDE),本書介紹瞭反應擴散係統在形態發生(Morphogenesis)中的基礎應用,如Turing模式的形成機製,為理解組織和器官的形成提供瞭數學基礎。 第二部分:分子生物學與基因組學中的計算方法 本部分將理論工具應用於當前生物信息學最熱門的領域,強調算法的效率與準確性。 4. 序列比對與數據庫搜索: 詳細解析瞭Needleman-Wunsch(全局比對)和Smith-Waterman(局部比對)算法的動態規劃原理,並探討瞭BLAST(Basic Local Alignment Search Tool)背後的啓發式加速機製。對序列相似性的統計顯著性評估(如E值計算)進行瞭詳盡的數學推導。 5. 從頭組裝與基因組測序: 涵蓋瞭二代測序(NGS)數據的處理流程。重點講解瞭De Bruijn圖在短讀長序列組裝中的核心作用,以及如何利用圖論中的路徑搜索解決序列重疊和歧義問題。此外,還討論瞭重疊群(contig)的質量評估和後續的Scaffolding技術。 6. 係統發育重建: 探討瞭如何從分子序列數據構建物種或基因間的進化關係樹。詳細比較瞭基於距離的方法(如NJ, UPGMA)和基於字符的方法(如最大簡約法和最大似然法)的數學假設和計算復雜度。對貝葉斯方法(如MCMC采樣)在係統發育樹不確定性評估中的應用進行瞭介紹。 第三部分:蛋白質結構與功能計算 本部分關注生物大分子的三維結構信息,是理解分子機製的關鍵。 7. 蛋白質結構預測與比對: 介紹瞭從氨基酸序列預測二級結構(如α螺鏇、β摺疊)的統計模型。在三維結構比對方麵,重點講解瞭鏇轉和平移變換(如Kabsch算法)在最小化RMSD(均方根偏差)中的應用。對於同源建模(Homology Modeling),闡述瞭如何利用模闆結構進行殘基坐標的轉化和優化。 8. 蛋白質相互作用網絡: 將生物學網絡視為圖論問題。介紹瞭節點(分子)、邊(相互作用)的定義,以及網絡拓撲學指標(如度中心性、介數中心性)在識彆關鍵調節因子中的意義。內容延伸至使用隨機模型(如隨機圖模型)來區分真實生物網絡與偶然連接。 第四部分:復雜生物網絡與動力學建模 本部分將視角從單個分子提升到細胞和群體水平,關注係統的湧現行為。 9. 生物網絡動力學模擬: 迴顧瞭使用ODE和SDE(隨機微分方程)來模擬基因調控網絡和信號通路的方法。特彆關注瞭隨機性在低分子數係統中的重要性,引入瞭Gillespie算法(或稱化學主方程模擬)來直接模擬反應事件的隨機演化。 10. 種群遺傳學與進化計算: 探討瞭群體遺傳學中的基本模型,如Wright-Fisher模型,及其在模擬漂變和選擇壓力下的等位基因頻率變化。介紹瞭如何利用計算方法模擬適應度景觀,並評估新突變在種群中的擴散概率。 總結與展望 《計算生物學導論》力求在嚴謹的數學論證和貼近前沿的生物學應用之間取得完美平衡。本書通過豐富的案例研究、清晰的算法描述和配套的僞代碼,確保讀者不僅能理解“是什麼”,更能掌握“如何做”。掌握這些計算工具,是未來生命科學研究人員在海量組學數據時代取得突破的關鍵。 目標讀者: 生物信息學專業本科高年級及研究生、計算生物學交叉學科研究人員、數學或計算機科學背景希望進入生物領域的學生。 必備知識前提: 基礎微積分、綫性代數初步知識,以及基本的生物學概念。