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Adaptive Skin Meshes Coarsening for Biomolecular Simulation.

ABSTRACT: In this paper, we present efficient algorithms for generating hierarchical molecular skin meshes with decreasing size and guaranteed quality. Our algorithms generate a sequence of coarse meshes for both the surfaces and the bounded volumes. Each coarser surface mesh is adaptive to the surface curvature and maintains the topology of the skin surface with guaranteed mesh quality. The corresponding tetrahedral mesh is conforming to the interface surface mesh and contains high quality tetrahedral that decompose both the interior of the molecule and the surrounding region (enclosed in a sphere). Our hierarchical tetrahedral meshes have a number of advantages that will facilitate fast and accurate multigrid PDE solvers. Firstly, the quality of both the surface triangulations and tetrahedral meshes is guaranteed. Secondly, the interface in the tetrahedral mesh is an accurate approximation of the molecular boundary. In particular, all the boundary points lie on the skin surface. Thirdly, our meshes are Delaunay meshes. Finally, the meshes are adaptive to the geometry.

SUBMITTER: Shi X

PROVIDER: S-EPMC3138625 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature

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Adaptive Skin Meshes Coarsening for Biomolecular Simulation.

Shi Xinwei X Koehl Patrice P

Computer aided geometric design 20110601 5

In this paper, we present efficient algorithms for generating hierarchical molecular skin meshes with decreasing size and guaranteed quality. Our algorithms generate a sequence of coarse meshes for both the surfaces and the bounded volumes. Each coarser surface mesh is adaptive to the surface curvature and maintains the topology of the skin surface with guaranteed mesh quality. The corresponding tetrahedral mesh is conforming to the interface surface mesh and contains high quality tetrahedral th ...[more]

PMID: 21779137

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Project description:Cellular responses to maladaptive environmental changes—stresses—allow for organismal adaptation to diverse and dynamic conditions. Across the tree of life, cells upregulate a highly conserved transcriptional program in response to so-called proteotoxic stresses such as heat shock. Correspondingly, in eukaryotes, these stresses induce the formation of biomolecular condensates, clusters of mRNA and protein which are referred to as stress granules under severe stress. However, major questions remain about this stress-induced response. How conserved is the condensation response relative to the transcriptional response? How does it vary across environmental niches, and to what extent does it correspond with the conserved transcriptional response? To answer these fundamental questions, we studied the growth, transcriptional, and condensation heat-induced stress responses in three fungal species adapted to thrive in different thermal environments: cryophilic S. kudriavzevii, mesophilic S. cerevisiae, and thermotolerant K. marxianus. Here we show that transcriptional heat shock responses track each species’ evolved temperature range of growth. Further, orthologous proteins—including poly(A)-binding protein, Pab1, a core marker of stress granules—form condensates in vivo at temperatures systematically tuned to the temperature at which the organisms activate the transcriptional heat shock response and slow their growth. In vitro, purified Pab1 from each species condenses autonomously at niche-specific temperatures. Homologous mutations in Pab1 cause similar shifts in relative condensation temperature across species, and crucially, mutations which suppress condensation in vitro also reduce fitness during heat stress. Our findings indicate that stress-induced protein condensation is adaptive, conserved, integrated with the growth and transcriptional responses, and tuned to features of the cellular and organismal environment to initiate at niche-specific levels.

Dataset Information

Adaptive Skin Meshes Coarsening for Biomolecular Simulation.

Publications

Adaptive Skin Meshes Coarsening for Biomolecular Simulation.

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