PubMed · 11802426
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Y Nakayama, M Tomita. 2001. [Towards large-scale simulation of cellular processes].. https://pubmed.ncbi.nlm.nih.gov/11802426/
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Cells are organized through the interactions of proteins with one another, and with phospholipids, nucleic acids and small molecules, suggesting a molecular recognition code for cell assembly. These interactions are mediated by a set of conserved protein interaction domains, which regulate the dynamic behaviour of the cell, and are used to build protein complexes and networks with emergent properties. Cell regulatory proteins have a modular architecture, which may have facilitated the evolution of new signalling pathways, and is exploited by pathogenic micro-organisms and chimeric oncoproteins to re-specify cellular function.
We quantify and ascertain the nature of the second-harmonic generation (SHG) response of amphiphilic push-pull chromophores to a transmembrane electric field. Our technique is based on the application of an alternating field across labeled giant unilamelar vesicles. For chromophore responses that are purely electro-optic, our technique provides an estimate of photoinduced charge shifts based on the observed dispersion of the field response, in accord with a two-level perturbation theory. These results are applicable to the optimization of membrane potential sensors for SHG microscopy.
We study the spectral properties of a diffusion process taking place on the Internet network focusing on the slowest decaying modes. These modes identify an underlying modular structure roughly corresponding to individual countries. For instance, in the slowest decaying mode the diffusion current flows from Russia to U.S. military sites. Quantitatively the modular structure manifests itself in a 10 times larger participation ratio of its slow decaying modes compared to a random scale-free network. We propose to use the fraction of nodes participating in slow decaying modes as a general measure of the modularity of a network. For the 100 slowest decaying modes of the Internet this fraction is approximately 30%. Finally, we suggest that the degree of isolation of an individual module can be assessed by comparing its participation in different diffusion modes.