Proteome Allocation Models - Revision history

Kate Evans at 13:39, 3 February 2026

2026-02-03T13:39:18Z

← Older revision		Revision as of 06:39, 3 February 2026
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	{{BreadcrumbsCellular}}		{{BreadcrumbsCellular}}

	* [[Page authors\|Page authors]]: [[Naomi Levine]], [[User:Hagi BucknWise\|Hagen Buck-Wiese ~~(Need coauthor)~~]]		* [[Page authors\|Page authors]]: [[Naomi Levine]], [[User:Hagi BucknWise\|Hagen Buck-Wiese]]
	* [[Responsible curator\|Responsible curator]]: [[User:Hagi BucknWise\|Hagen Buck-Wiese]]		* [[Responsible curator\|Responsible curator]]: [[User:Hagi BucknWise\|Hagen Buck-Wiese]]
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Kate Evans at 13:38, 3 February 2026

2026-02-03T13:38:50Z

← Older revision		Revision as of 06:38, 3 February 2026
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	{{BreadcrumbsCellular}}		{{BreadcrumbsCellular}}

	* [[Page authors\|Page authors]]: [[Naomi Levine]], [[User:Hagi BucknWise\|Hagen Buck-Wiese (~~Undergrad~~)]]		* [[Page authors\|Page authors]]: [[Naomi Levine]], [[User:Hagi BucknWise\|Hagen Buck-Wiese (Need coauthor)]]
	* [[Responsible curator\|Responsible curator]]: [[User:Hagi BucknWise\|Hagen Buck-Wiese]]		* [[Responsible curator\|Responsible curator]]: [[User:Hagi BucknWise\|Hagen Buck-Wiese]]
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Kate Evans at 13:38, 3 February 2026

2026-02-03T13:38:10Z

← Older revision		Revision as of 06:38, 3 February 2026
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	{{BreadcrumbsCellular}}		{{BreadcrumbsCellular}}

	* [[Page authors\|Page authors]]: [[Naomi Levine]], [[User:Hagi BucknWise\|Hagen Buck-Wiese]]		* [[Page authors\|Page authors]]: [[Naomi Levine]], [[User:Hagi BucknWise\|Hagen Buck-Wiese (Undergrad)]]
	* [[Responsible curator\|Responsible curator]]: [[User:Hagi BucknWise\|Hagen Buck-Wiese]]		* [[Responsible curator\|Responsible curator]]: [[User:Hagi BucknWise\|Hagen Buck-Wiese]]
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Kate Evans at 22:27, 15 January 2026

2026-01-15T22:27:21Z

← Older revision		Revision as of 15:27, 15 January 2026
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	\| '''Computational demand:''' Local		\| '''Computational demand:''' Local
	\|-		\|-
	\| '''Spatial resolution:''' grid: sub um		\| '''Spatial resolution:''' grid: sub μm

	domain: um		domain: μm
	\|-		\|-
	\| '''Temporal resolution:''' time step & output: steady-state		\| '''Temporal resolution:''' time step & output: steady-state

Kate Evans at 22:26, 15 January 2026

2026-01-15T22:26:41Z

← Older revision		Revision as of 15:26, 15 January 2026
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	\| '''Computational demand:''' Local		\| '''Computational demand:''' Local
	\|-		\|-
	\| '''Spatial resolution:''' grid: sub um; domain: um		\| '''Spatial resolution:''' grid: sub um

			domain: um
	\|-		\|-
	\| '''Temporal resolution:''' time step & output: steady-state		\| '''Temporal resolution:''' time step & output: steady-state

Hagi BucknWise: /* Recent applications */

2026-01-15T21:47:07Z

Recent applications

← Older revision		Revision as of 14:47, 15 January 2026
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	*Molenaar et al. (2009) ''Shifts in growth strategies reflect tradeoffs in cellular economics.''<ref>Molenaar, D., van Berlo, R., de Ridder, D. et al. Shifts in growth strategies reflect tradeoffs in cellular economics. Mol Syst Biol 5, MSB200982 (2009). https://doi.org/10.1038/msb.2009.82</ref>		*Molenaar et al. (2009) ''Shifts in growth strategies reflect tradeoffs in cellular economics.''<ref>Molenaar, D., van Berlo, R., de Ridder, D. et al. Shifts in growth strategies reflect tradeoffs in cellular economics. Mol Syst Biol 5, MSB200982 (2009). https://doi.org/10.1038/msb.2009.82</ref>
	=== Recent applications ===		=== Recent applications ===
	*Leles & Levine (2023) ''Mechanistic constraints on the trade-off between photosynthesis and respiration in response to warming.''<ref name="Leles and Levine"/>		*Leles & Levine (2023) ''Mechanistic constraints on the trade-off between photosynthesis and respiration in response to warming.''<ref name="Leles and Levine"/> e.g. [https://github.com/LevineLab/ProteomePhyto Model's github]

	== Limitations ==		== Limitations ==

Hagi BucknWise: /* Example Studies & Code */

2026-01-09T19:02:43Z

Example Studies & Code

← Older revision		Revision as of 12:02, 9 January 2026
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	=== Classic examples ===		=== Classic examples ===
	*Molenaar et al. 2009 ''Shifts in growth strategies reflect tradeoffs in cellular economics.''<ref>Molenaar, D., van Berlo, R., de Ridder, D. et al. Shifts in growth strategies reflect tradeoffs in cellular economics. Mol Syst Biol 5, MSB200982 (2009). https://doi.org/10.1038/msb.2009.82</ref>		*Molenaar et al. (2009) ''Shifts in growth strategies reflect tradeoffs in cellular economics.''<ref>Molenaar, D., van Berlo, R., de Ridder, D. et al. Shifts in growth strategies reflect tradeoffs in cellular economics. Mol Syst Biol 5, MSB200982 (2009). https://doi.org/10.1038/msb.2009.82</ref>
	=== Recent applications ===		=== Recent applications ===
	*Leles & Levine 2023 ''Mechanistic constraints on the trade-off between photosynthesis and respiration in response to warming.''<ref name="Leles and Levine">		*Leles & Levine (2023) ''Mechanistic constraints on the trade-off between photosynthesis and respiration in response to warming.''<ref name="Leles and Levine"/>

	== Limitations ==		== Limitations ==
	Currently, these models are confined to solving for steady-state and do not include environmental fluctuations.		Currently, these models are confined to solving for steady-state and do not include environmental fluctuations.

Hagi BucknWise at 19:01, 9 January 2026

2026-01-09T19:01:08Z

← Older revision		Revision as of 12:01, 9 January 2026
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	=== Classic examples ===		=== Classic examples ===
			*Molenaar et al. 2009 ''Shifts in growth strategies reflect tradeoffs in cellular economics.''<ref>Molenaar, D., van Berlo, R., de Ridder, D. et al. Shifts in growth strategies reflect tradeoffs in cellular economics. Mol Syst Biol 5, MSB200982 (2009). https://doi.org/10.1038/msb.2009.82</ref>
	=== Recent applications ===		=== Recent applications ===
			*Leles & Levine 2023 ''Mechanistic constraints on the trade-off between photosynthesis and respiration in response to warming.''<ref name="Leles and Levine">
	== Limitations ==		== Limitations ==
	Currently, these models are confined to solving for steady-state and do not include environmental fluctuations.		Currently, these models are confined to solving for steady-state and do not include environmental fluctuations.

Hagi BucknWise at 01:48, 9 January 2026

2026-01-09T01:48:17Z

← Older revision		Revision as of 18:48, 8 January 2026
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	<div class="model-box">		<div class="model-box">
	{\| class="model-ib"		{\| class="model-ib"
	! ~~Proteome Allocation Models~~		! Model type
	\|-		\|-
	\| '''Approach:''' ~~Optimizer~~		\| '''Approach:''' Mechanistic optimized
	\|-		\|-
	\| '''~~Environment~~:''' Local~~/Cluster~~		\| '''Computational demand:''' Local
	\|-		\|-
	\| '''Spatial ~~scale~~:''' ~~Single cell~~		\| '''Spatial resolution:''' grid: sub um; domain: um
	\|-		\|-
	\| '''Temporal ~~scale~~:''' ~~Steady–state~~		\| '''Temporal resolution:''' time step & output: steady-state
	\|}		\|}
	</div>		</div>
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	== Data inputs ==		== Data inputs ==
	Reactions represented in proteome allocation models require input parameters that define stoichiometry and rate constants. In addition, physical parameters such as density or size constraints, molecular weights and metabolite concentration ranges are required as input.		Reactions represented in proteome allocation models require input parameters that define stoichiometry and rate constants. In addition, physical parameters such as density or size constraints, molecular weights and metabolite concentration ranges are required as input.

			== Example Studies & Code ==

			=== Classic examples ===

			=== Recent applications ===

	== Limitations ==		== Limitations ==

Hagi BucknWise at 20:00, 7 January 2026

2026-01-07T20:00:16Z

← Older revision		Revision as of 13:00, 7 January 2026
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	{{BreadcrumbsCellular}}		{{BreadcrumbsCellular}}

	* [[~~Contributors~~\|~~Primary author~~]]: [[User:Hagi BucknWise\|Hagen Buck-Wiese]]		* [[Page authors\|Page authors]]: [[Naomi Levine]], [[User:Hagi BucknWise\|Hagen Buck-Wiese]]
	* [[~~Contributors\|Contributing authors]]: [[Naomi Levine]], [[Kermit the Frog]], [[Paul Fremont]]~~		* [[Responsible curator\|Responsible curator]]: [[User:Hagi BucknWise\|Hagen Buck-Wiese]]
	* [[Contributors\|Responsible curator]]s: [[User:Hagi BucknWise\|Hagen Buck-Wiese]]		----
	----

	__TOC__		__TOC__
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	\| '''Approach:''' Optimizer		\| '''Approach:''' Optimizer
	\|-		\|-
	\| '''Environment:''' Local ~~(mostly)~~		\| '''Environment:''' Local/Cluster
	\|-		\|-
	\| '''Spatial scale:''' Single cell		\| '''Spatial scale:''' Single cell
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	== Model overview ==		== Model overview ==
			These models optimize proteome allocation and cell physiology to maximize cellular growth rate. The models provide mechanistic insights into the trade-offs between resource allocation, respiration, cellular space, and management of environmental conditions that limit the metabolic choices of the cell <ref name="Leles and Levine"> Leles SG, Levine NM. Mechanistic constraints on the trade-off between photosynthesis and respiration in response to warming. Sci Adv. 2023 Sep;9(35):eadh8043. doi: 10.1126/sciadv.adh8043 </ref>.

	== Scales of interest ==		== Scales of interest ==
			Proteome allocation models typically represent a single cell, often including subcellular compartments such as a bacterial periplasm or an alga's vacuole. The modeled cell is commonly placed in a diffusive or advective & diffusive environment from which it acquires resources <ref> Norris N, Levine NM, Fernandez VI, Stocker R. Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria. PLoS Comput Biol. 2021 May 19;17(5):e1009023. doi: 10.1371/journal.pcbi.1009023 </ref>.

	== Data inputs ==		== Data inputs ==
			Reactions represented in proteome allocation models require input parameters that define stoichiometry and rate constants. In addition, physical parameters such as density or size constraints, molecular weights and metabolite concentration ranges are required as input.

	== Limitations ==		== Limitations ==
			Currently, these models are confined to solving for steady-state and do not include environmental fluctuations.

	== References ==		== References ==

	[[Category:Main Pages\|Model types]]		[[Category:Main Pages\|Model types]]