Multi-resolution spatial simulation for molecular crowding

Jeschke, Sabina; Uhrmacher,

doi:10.1109/wsc.2008.4736214

Cited by 13 publications

(19 citation statements)

References 27 publications

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“…Special multi-scale methods have been developed to accommodate the heterogeneous process of the cells like crowding with small and large molecules [154] or slow and fast reactions [155], which also involves for instance local mean field closures for interactions [156] and coupling of several simulation methods [14]. …”

Section: Applications and Results Of Spatial Simulationsmentioning

confidence: 99%

Spatial Simulations in Systems Biology: From Molecules to Cells

Klann

Koeppl

2012

IJMS

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Cells are highly organized objects containing millions of molecules. Each biomolecule has a specific shape in order to interact with others in the complex machinery. Spatial dynamics emerge in this system on length and time scales which can not yet be modeled with full atomic detail. This review gives an overview of methods which can be used to simulate the complete cell at least with molecular detail, especially Brownian dynamics simulations. Such simulations require correct implementation of the diffusion-controlled reaction scheme occurring on this level. Implementations and applications of spatial simulations are presented, and finally it is discussed how the atomic level can be included for instance in multi-scale simulation methods.

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Section: Applications and Results Of Spatial Simulationsmentioning

confidence: 99%

Spatial Simulations in Systems Biology: From Molecules to Cells

Klann

Koeppl

2012

IJMS

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“…Their spatio-temporal dynamics are often driven by diffusion processes in environments with impenetrable barriers (excluded volumes) [5]. Here, processes, especially in higher organisms, have attracted particular attention that have obvious structure-forming potential and are significantly important for the progression in healthy, for example, embryonic, as well as unhealthy, for example, cancerous, growth [48].…”

Section: Discussionmentioning

confidence: 99%

“…Molecular diffusion can be hindered by excluded volumes, which we here define as spatial barriers that are impenetrable for diffusing molecules. These excluded volumes can have a strong impact on the molecular distribution [5,6]. Figure 1 gives an abstract presentation of three cases found in cell biology for which our general scheme of an environment with excluded volumes applies.…”

Section: Introductionmentioning

confidence: 99%

An explicit numerical scheme to efficiently simulate molecular diffusion in environments with dynamically changing barriers

Kossow

Rybacki

Millat

et al. 2015

Mathematical and Computer Modelling of Dynamical Systems

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Despite temporal changes in the quantities of molecules, the functioning of cells also depends on their distribution within cells and in their extracellular environment. The dynamics of molecules are often governed by diffusion in heterogeneous environments consisting of dynamically changing impenetrable barriers (excluded volumes). This provides a challenge for efficient simulations of cellular processes with large numbers of molecules. To model the diffusion of molecular mass in consideration of excluded volumes, we here present an explicit numerical scheme that approximates the diffusion equation by using cellular automata. Because this approach represents molecular diffusion at the macroscopic scale, it is more amenable for efficient simulations than comparable microscopic approaches that treat diffusing molecules individually. In contrast to implicit numerical schemes (macroscopic approach), our approach is capable of accounting for excluded volumes, even if those exhibit a dynamic of their own, without increasing computational costs. The presented approach can easily be integrated into certain types of spatio-temporal multiscale models, as demonstrated by an existing model investigating cancer progression. Thereby, it allows to take the spatial effects of a heterogeneous environment on diffusing molecules into account.

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“…Though accomplished without DEVS, a good example of algorithm integration is described in Jeschke and Uhrmacher (2008). This recent work combines the Next Subvolume Method, which tracks the concentrations of chemicals in various subvolumes, with an algorithm that, like the TPS, tracks the positions of relatively large individual particles.…”

Section: Layered Model Designmentioning

confidence: 99%

DEVS-based design of spatial simulations of biological systems

Goldstein

Wainer

2009

Proceedings of the 2009 Winter Simulation Conference (WSC)

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The application of the DEVS formalism to spatial simulations of biological systems is motivated by a need to keep software manageable, even when faced with complex models that may combine algorithms for potential fields, fluid dynamics, the interaction of proteins, or the reaction and diffusion of chemicals. We demonstrate DEVS-based design by applying the formalism to a "tethered particle system" (TPS), a model we designed to capture the motion of deformable biological structures. The paper focuses on the design of DEVS models using hierarchies and layers, and describes a recently-developed simulator that supports our approach. The DEVS-based TPS model, which has been used to simulate certain interactions in nerve cells, demonstrates the formalism's potential as a means of addressing the complexity of spatial biological models.

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Multi-resolution spatial simulation for molecular crowding

Cited by 13 publications

References 27 publications

Spatial Simulations in Systems Biology: From Molecules to Cells

Spatial Simulations in Systems Biology: From Molecules to Cells

An explicit numerical scheme to efficiently simulate molecular diffusion in environments with dynamically changing barriers

DEVS-based design of spatial simulations of biological systems

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