1,721,052 research outputs found
A non-equilibrium percolation transition in random Ising ferromagnets
No full textWe study the geometrical properties of the domain structure that results when a random Ising ferromagnet is quenched to zero temperature. We define a novel connectivity transition between like spins in the frozen configuration, and show that it is in a new universality class, distinct from that of random percolation. The scaling is robust and independent of model details. The relevance of this transition to spinodal decomposition is discussed
Shapes of hydrophobic thick membranes
No full textWe introduce and study the behavior of a tethered membrane of non-zero thickness embedded in three dimensions subject to an effective self-attraction induced by hydrophobicity arising from the tendency to minimize the area exposed to a solvent. The phase behavior and the nature of the folded conformations are found to be quite distinct in the small and large solvent size regimes. We demonstrate spontaneous symmetry breaking with the membrane folding along a preferential axis, when the solvent molecules are small compared to the membrane thickness. For large solvent molecule size, a local crinkling mechanism effectively shields the membrane from the solvent, even in relatively flat conformations. We discuss the binding/unbinding transition of a membrane to a wall that serves to shield the membrane from the solvent
Protein Sequence and Structure: Is One More Fundamental than the Other?
No full textWe argue that protein native state structures reside in a novel "phase" of matter which confers on proteins their many amazing characteristics. This phase arises from the common features of all globular proteins and is characterized by a sequence-independent free energy landscape with relatively few low energy minima with funnel-like character. The choice of a sequence that fits well into one of these predetermined structures facilitates rapid and cooperative folding. Our model calculations show that this novel phase facilitates the formation of an efficient route for sequence design starting from random peptides
Comment on “No-Slip Condition for a Mixture of Two Liquids”
Full text linkA Comment on the Letter by Joel Koplik and Jayanth R. Banavar, Phys. Rev. Lett. 80, 6125 (1998). The authors of the Letter offer a Reply
Emergence of structural and dynamical properties of ecological mutualistic networks
No full textMutualistic networks are formed when the interactions between two classes of species are mutually beneficial. They are important examples of cooperation shaped by evolution. Mutualism between animals and plants has a key role in the organization of ecological communities. Such networks in ecology have generally evolved a nested architecture independent of species composition and latitude; specialist species, with only few mutualistic links, tend to interact with a proper subset of the many mutualistic partners of any of the generalist species. Despite sustained efforts to explain observed network structure on the basis of community-level stability or persistence, such correlative studies have reached minimal consensus. Here we show that nested interaction networks could emerge as a consequence of an optimization principle aimed at maximizing the species abundance in mutualistic communities. Using analytical and numerical approaches, we show that because of the mutualistic interactions, an increase in abundance of a given species results in a corresponding increase in the total number of individuals in the community, and also an increase in the nestedness of the interaction matrix. Indeed, the species abundances and the nestedness of the interaction matrix are correlated by a factor that depends on the strength of the mutualistic interactions. Nestedness and the observed spontaneous emergence of generalist and specialist species occur for several dynamical implementations of the variational principle under stationary conditions. Optimized networks, although remaining stable, tend to be less resilient than their counterparts with randomly assigned interactions. In particular, we show analytically that the abundance of the rarest species is linked directly to the resilience of the community. Our work provides a unifying framework for studying the emergent structural and dynamical properties of ecological mutualistic networks
Geometry and physics of proteins
No full textA conceptual framework for understanding the protein folding problem has remained elusive in spite of many significant advances. We show that geometrical constraints imposed by chain connectivity, compactness, and the avoidance of steric clashes can be encompassed in a natural way using a three-body potential and lead to a selection in structure space, independent of chemical details. Strikingly, secondary motifs such as hairpins, sheets, and helices, which are the building blocks of protein folds, emerge as the chosen structures for segments of the protein backbone based just on elementary geometrical considerations
An intriguing take on complexity<i>Scale: The Universal Laws of Growth, Innovation, Sustainability, and the Pace of Life in Organisms, Cities, Economies, and Companies</i>, Geoffrey West, Penguin Press, 2017, $30.00
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