Dataset Information

Frictional-anisotropy-based systems in biology: structural diversity and numerical model.

ABSTRACT: There is a huge variety in biological surfaces covered with micro- and nanostructures oriented at some angle to the supporting surface. Such structures, for example snake skin, burr-covered plant leaves, cleaning devices and many others cause mechanical anisotropy due to different friction or/and mechanical interlocking during sliding in contact with another surface in different directions. Such surfaces serve propulsion generation on the substrate (or within the substrate) for the purpose of locomotion or for transporting items. We have theoretically studied the dependence of anisotropic friction efficiency in these systems on (1) the slope of the surface structures, (2) rigidity of their joints, and (3) sliding speed. Based on the proposed model, we suggest the generalized optimal set of variables for maximizing functional efficiency of anisotropic systems of this type. Finally, we discuss the optimal set of such parameters from the perspective of biological systems.

SUBMITTER: Filippov A

PROVIDER: S-EPMC3566598 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Frictional-anisotropy-based systems in biology: structural diversity and numerical model.

Filippov Alexander A Gorb Stanislav N SN

Scientific reports 20130207

There is a huge variety in biological surfaces covered with micro- and nanostructures oriented at some angle to the supporting surface. Such structures, for example snake skin, burr-covered plant leaves, cleaning devices and many others cause mechanical anisotropy due to different friction or/and mechanical interlocking during sliding in contact with another surface in different directions. Such surfaces serve propulsion generation on the substrate (or within the substrate) for the purpose of lo ...[more]

PMID: 23393622

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Project description:BackgroundThe success of genome-scale models (GEMs) can be attributed to the high-quality, bottom-up reconstructions of metabolic, protein synthesis, and transcriptional regulatory networks on an organism-specific basis. Such reconstructions are biochemically, genetically, and genomically structured knowledge bases that can be converted into a mathematical format to enable a myriad of computational biological studies. In recent years, genome-scale reconstructions have been extended to include protein structural information, which has opened up new vistas in systems biology research and empowered applications in structural systems biology and systems pharmacology.ResultsHere, we present the generation, application, and dissemination of genome-scale models with protein structures (GEM-PRO) for Escherichia coli and Thermotoga maritima. We show the utility of integrating molecular scale analyses with systems biology approaches by discussing several comparative analyses on the temperature dependence of growth, the distribution of protein fold families, substrate specificity, and characteristic features of whole cell proteomes. Finally, to aid in the grand challenge of big data to knowledge, we provide several explicit tutorials of how protein-related information can be linked to genome-scale models in a public GitHub repository ( https://github.com/SBRG/GEMPro/tree/master/GEMPro_recon/).ConclusionsTranslating genome-scale, protein-related information to structured data in the format of a GEM provides a direct mapping of gene to gene-product to protein structure to biochemical reaction to network states to phenotypic function. Integration of molecular-level details of individual proteins, such as their physical, chemical, and structural properties, further expands the description of biochemical network-level properties, and can ultimately influence how to model and predict whole cell phenotypes as well as perform comparative systems biology approaches to study differences between organisms. GEM-PRO offers insight into the physical embodiment of an organism's genotype, and its use in this comparative framework enables exploration of adaptive strategies for these organisms, opening the door to many new lines of research. With these provided tools, tutorials, and background, the reader will be in a position to run GEM-PRO for their own purposes.

Dataset Information

Frictional-anisotropy-based systems in biology: structural diversity and numerical model.

Publications

Frictional-anisotropy-based systems in biology: structural diversity and numerical model.

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