Standard DEB model summary of telepart of DEB

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Standard DEB model summary of tele-part of DEB course 2011 Bas Kooijman Dept theoretical

Standard DEB model summary of tele-part of DEB course 2011 Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam [email protected] vu. nl http: //www. bio. vu. nl/thb/ Lisbon, 2011/04/04

Homeostasis 1. 2 strong homeostasis constant composition of pools (reserves/structures) generalized compounds, stoichiometric contraints

Homeostasis 1. 2 strong homeostasis constant composition of pools (reserves/structures) generalized compounds, stoichiometric contraints on synthesis weak homeostasis constant composition of biomass during growth in constant environments determines reserve dynamics (in combination with strong homeostasis) structural homeostasis constant relative proportions during growth in constant environments isomorphy. work load allocation thermal homeostasis ectothermy homeothermy endothermy acquisition homeostasis supply demand systems development of sensors, behavioural adaptations

Supply-demand spectrum 1. 2. 5

Supply-demand spectrum 1. 2. 5

Maturation 2. 5. 2

Maturation 2. 5. 2

Maturity & its maintenance 2. 5. 3 a DEB implementation is motivated by 4

Maturity & its maintenance 2. 5. 3 a DEB implementation is motivated by 4 observations 1 Contrary to age, volume at birth or puberty hardly depends on food density. So stage transitions cannot be linked to age. 2 Some species continue growing after puberty. Other species, such as birds, only reproduce well after the growth period. So stage transitions cannot be linked to size. 3 Total cumulative energy investment in development at any given size of the individual depends on food density; this can be removed by allowing for maturity maintenance. 4 Ultimate reproduction rate is a continuous function of food density This demonstrates the existence of maturity maintenance.

Macrochemical reaction eq 3. 5

Macrochemical reaction eq 3. 5

Simultaneous Substrate Processing 3. 7 c production Chemical reaction: 1 A + 1 B

Simultaneous Substrate Processing 3. 7 c production Chemical reaction: 1 A + 1 B 1 C Poisson arrival events for molecules A and B blocked time intervals • acceptation event ¤ rejection event Kooijman, 1998 Biophys Chem 73: 179 -188

Interactions of substrates 3. 7. 3 b Kooijman, 2001 Phil Trans R Soc B

Interactions of substrates 3. 7. 3 b Kooijman, 2001 Phil Trans R Soc B 356: 331 -349

Change in body shape 4. 2. 2 Isomorph: surface area volume 2/3 volumetric length

Change in body shape 4. 2. 2 Isomorph: surface area volume 2/3 volumetric length = volume 1/3 Mucor Ceratium V 0 -morph: surface area volume 0 Merismopedia V 1 -morph: surface area volume 1

Weight 1/3, g 1/3 diameter, m Isomorphic growth 2. 6 c Amoeba proteus Prescott

Weight 1/3, g 1/3 diameter, m Isomorphic growth 2. 6 c Amoeba proteus Prescott 1957 Saccharomyces carlsbergensis Berg & Ljunggren 1922 time, h Weight 1/3, g 1/3 length, mm time, h Pleurobrachia pileus Greve 1971 Toxostoma recurvirostre Ricklefs 1968 time, d

volume, m 3 4. 2. 3 a Bacillus = 0. 2 Collins & Richmond

volume, m 3 4. 2. 3 a Bacillus = 0. 2 Collins & Richmond 1962 time, min Fusarium = 0 Trinci 1990 time, h volume, m 3 hyphal length, mm Mixtures of V 0 & V 1 morphs Escherichia = 0. 28 Kubitschek 1990 time, min Streptococcus = 0. 6 Mitchison 1961 time, min

Mixtures of changes in shape 4. 2. 4 a Dynamic mixtures between morphs V

Mixtures of changes in shape 4. 2. 4 a Dynamic mixtures between morphs V 1 - V 0 -morph outer annulus behaves as a V 1 -morph, inner part as a V 0 -morph. Result: diameter increases time Lichen Rhizocarpon V 1 - iso- V 0 -morph

input, output Digestive system 7. 3 a completely stirred reactor stomach model input, output

input, output Digestive system 7. 3 a completely stirred reactor stomach model input, output time plugflow reactor gut model time both reactors in series Stomach • good in buffering • residence times exponentially distributed many short times, few large ones Gut • bad in buffering • residence time constant digestion requires some time

Reserve residence time 2. 3. 1 b

Reserve residence time 2. 3. 1 b

Standard DEB model 2 a Isomorph with 1 reserve & 1 structure feeds on

Standard DEB model 2 a Isomorph with 1 reserve & 1 structure feeds on 1 type of food has 3 life stages (embryo, juvenile, adult) Processes: feeding digestion maintenance storage product formation maturation Balances: mass, energy , entropy, time Extensions: • more types of food and food qualities • more types of reserve (autotrophs) • more types of structure (organs, plants) • changes in morphology • different number of life stages growth reproduction aging

Standard DEB scheme 2 b 1 food type, 1 reserve, 1 structure, isomorph food

Standard DEB scheme 2 b 1 food type, 1 reserve, 1 structure, isomorph food feeding defecation faeces assimilation somatic maintenance growth structure reserve 1 - maturity maintenance maturation reproduction maturity offspring time: searching & handling feeding surface area weak & strong homeostasis κ-rule for allocation to soma maintenance has priority somatic maint structure maturity maint maturity stage transition: maturation embryo: no feeding, reprod juvenile: no reproduction adult: no maturation maternal effect: reserve density at birth equals that of mother initially: zero structure, maturity

1 E, 1 V isomorph 2. 9 c all quantities scaled dimensionless

1 E, 1 V isomorph 2. 9 c all quantities scaled dimensionless

1 E, 1 V isomorph 2. 9 C, continued

1 E, 1 V isomorph 2. 9 C, continued

time, cum. feeding, 10 reprod. hazards, h, h. H acceleration, q maturity, v. H

time, cum. feeding, 10 reprod. hazards, h, h. H acceleration, q maturity, v. H length l, survival S reserve density, e 1 E, 1 V isomorph 2. 9 d time,

scaled flux of NH 3 scaled flux of O 2 scaled flux of H

scaled flux of NH 3 scaled flux of O 2 scaled flux of H 2 O scaled flux of CO 2 1 E, 1 V isomorph 2. 9 D, continued time,

Section VII The Standard Model The Standard ModelSection VII The Standard Model The Standard Model
If not the Standard Model What Standard ModelIf not the Standard Model What Standard Model
Lecture 10 Standard Model Lagrangian The Standard ModelLecture 10 Standard Model Lagrangian The Standard Model
Standard 1 Basics Standard 2 Word Processing StandardStandard 1 Basics Standard 2 Word Processing Standard
Standard 10 1 Standard 10 2 Standard 10Standard 10 1 Standard 10 2 Standard 10
Standard Files C Standard File Device Pointer StandardStandard Files C Standard File Device Pointer Standard
4 4 STANDARD DEVIATION STANDARD DEVIATION The Standard4 4 STANDARD DEVIATION STANDARD DEVIATION The Standard
Standard 10 6 Standard 10 7 Standard 10Standard 10 6 Standard 10 7 Standard 10
STANDARD OPERATIONS 2 Standard Operations DEFINISI STANDARD OPERATIONSSTANDARD OPERATIONS 2 Standard Operations DEFINISI STANDARD OPERATIONS
Pertemuan 7 Standard Costs Standard Costs Predetermined StandardPertemuan 7 Standard Costs Standard Costs Predetermined Standard
Meaning of Standard Standard Cost and Standard CostingMeaning of Standard Standard Cost and Standard Costing
Lecture 2 Outline of basic theory Standard DEBLecture 2 Outline of basic theory Standard DEB
Guardianship JOHN LAFOND AND DEB FEINEN Legal StandardGuardianship JOHN LAFOND AND DEB FEINEN Legal Standard
Exponential Model Logistic Model Compertz Model Bass ModelExponential Model Logistic Model Compertz Model Bass Model
Business Model Business Model Business Model Business ModelBusiness Model Business Model Business Model Business Model
ER Model KAVRAMSAL MODEL KAVRAMSAL MODEL Conceptual ModelER Model KAVRAMSAL MODEL KAVRAMSAL MODEL Conceptual Model
Standard Model of Particles What is the standardStandard Model of Particles What is the standard
AIAA Model exchange standard review requestsinstructions Standard readyAIAA Model exchange standard review requestsinstructions Standard ready
Physics Beyond the Standard Model Summary by DennisPhysics Beyond the Standard Model Summary by Dennis
Using STORET as a Database Design Model DebUsing STORET as a Database Design Model Deb
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Inversion Model Summary of Asteroidal Occultations Historical ModelInversion Model Summary of Asteroidal Occultations Historical Model
Model S Model X Model 3 Longest RangeModel S Model X Model 3 Longest Range
Introduction to simulation model What is model ModelIntroduction to simulation model What is model Model
Measurement model 1 Measurement model 2 Structural modelMeasurement model 1 Measurement model 2 Structural model
Retrieval Model 4 Topic Model Inference Network ModelRetrieval Model 4 Topic Model Inference Network Model
Materi ke 4 Model Data Model Data ModelMateri ke 4 Model Data Model Data Model
Model 1 V 0 Model 2 V ModelModel 1 V 0 Model 2 V Model
MODEL BASIS DATA MODEL BASIS DATA Model basisMODEL BASIS DATA MODEL BASIS DATA Model basis
Distribution Model Meaning Types Transportation Model Assignment ModelDistribution Model Meaning Types Transportation Model Assignment Model
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Station Model Review Station Model Review Station ModelStation Model Review Station Model Review Station Model
IMU Deblur Blur Model Blur Model Blur ModelIMU Deblur Blur Model Blur Model Blur Model
OIS Model TCPIP Model 1 OSI Model TheOIS Model TCPIP Model 1 OSI Model The
Qualitative Response Model probit model logit model probitQualitative Response Model probit model logit model probit
Collective Model Collective Model Shell model fails forCollective Model Collective Model Shell model fails for
PEMODELAN DATA Model Basis Data Model Hirarkis ModelPEMODELAN DATA Model Basis Data Model Hirarkis Model
Model Checking in the Proportional Hazard model ModelModel Checking in the Proportional Hazard model Model
MODEL PROTOTYPE Bahasan Definisi Model Prototype Gambar ModelMODEL PROTOTYPE Bahasan Definisi Model Prototype Gambar Model
MODEL KELAKUAN ORGANISASI Model Kelakuan Organisasi Model diMODEL KELAKUAN ORGANISASI Model Kelakuan Organisasi Model di