Preface	6
	Contents	10
	List of Contributors	12
	Elastic Growth Models	14
	1 Introduction	14
	2 One-dimensional Theory: Elasticity, Visco-elasticity, and Plasticity	15
	3 One-dimensional Theory: Growth Models	18
	4 Three-dimensional Growth	34
	5 Conclusions	53
	References	53
	A Model of Pattern Coupled to Form in Metazoans	58
	1 Introduction	59
	2 Aspects of the Genome	62
	3 The Pattern Model	64
	4 Morphology	77
	5 Notes on Sample Numerical Results	85
	6 Summary and Outlook	88
	Appendix A	91
	Appendix B	93
	References	97
	Mathematical Modeling of HIV-1 Infection and Drug Therapy	100
	1 Introduction	100
	2 Basic Model of Virus Infection	103
	3 Delay Models	105
	4 Age-structured Models	109
	5 Drug Resistance	120
	6 Viral and Latent Reservoir Persistence	135
	7 Discussion	136
	References	139
	Overcoming the Key Challenges in De Novo Protein Design: Enhancing Computational E . ciency and Incorporating True Backbone Flexibility	145
	1 Introduction	145
	2 The Original De Novo Protein Design Framework	148
	3 Improvement of the De Novo Protein Design Framework	153
	4 Case Studies	174
	5 Conclusions	187
	References	188
	An Improved Heuristic for Consistent Biclustering Problems	196
	1 Introduction	196
	2 Consistent Biclustering	198
	3 Supervised Biclustering	201
	4 Heuristic Algorithm	202
	5 Numerical Experiments	204
	6 Conclusion Remarks	206
	References	208
	The Steiner Tree Problem and Its Application to the Modelling of Biomolecular Structures	210
	1 Introduction	210
	2 The Fermat-Steiner Problem. Motivations for Further Study	210
	3 Consecutive Evenly Spaced Points	214
	4 Steiner Points and Steiner Trees	220
	5 Generic Sequences of Points and the Construction of the Steiner Ratio Function	224
	6 An Unconstrained Optimization Problem. The Euclidean Steiner Ratio for Very Large Number of Points	227
	7 Concluding Remarks	229
	References	229
	Phenotypic Switching and Mutation in the Presence of a Biocide: No Replication of Phenotypic Variant	231
	1 Introduction	231
	2 Mutation and Phenotypic Change	232
	3 Di.erent Consumption Functions	238
	4 Numerical Results	244
	5 Discussion and Conclusion	247
	Appendix A: Proofs	248
	References	251
	From Spatial Pattern in the Distribution and Abundance of Species to a Uni . ed Theory of Ecology: The Role of Maximum Entropy Methods	253
	1 Introduction	253
	2 Scaling Metrics in Spatial Ecology	254
	3 Models of Spatial Pattern in Ecology	257
	4 Intercomparisons of the Four Models	267
	5 Tests of Models: an Overview	268
	6 Advantages of the Maximum Entropy Framework in Ecology	272
	7 Toward a Uni.ed Theory of Ecology	275
	References	279
	Protein Structure and Its Folding Rate	283
	1 Introduction	283
	2 Protein Structure	284
	3 Phase Transitions in Protein Molecules	287
	4 Theory of Protein Folding	298
	5 Concluding Remarks	307
	References	308
	Index	312