1,721,032 research outputs found
Exemplars of proteins
No full textA unified framework for understanding proteins is presented, which provides links between the fields of protein science, polymer physics and the physics of liquid crystals
Physics of proteins
No full textPeptides and proteins exhibit a common tendency to assemble into highly ordered fibrillar aggregates, whose formation proceeds in a nucleation-dependent manner that is often preceded by the formation of oligomeric assemblies. This process has received much attention because disordered oligomeric aggregates have been associated with neurodegenerative disorders such as Alzheimer's and Parkinson's disease. Here we describe a self-templated nucleation mechanism that determines the transition between the initial condensation of polypeptide chains into disordered assemblies and their reordering into fibrillar structures. The results that we present show that at the molecular level this transition is due to the ability of polypeptide chains to reorder within oligomers into fibrillar assemblies whose surfaces act as templates that stabilize the disordered assemblies
Geometry, topology, and universality of random surfaces.
No full textPrevious simulations of a self-avoiding, closed random surface with restricted topology (without handles) on a three-dimensional lattice have shown that its behavior on long length scales is consistent with that of a branched-polymer. It is shown analytically that such a surface with an unrestricted number of handles has a qualitatively different geometry and therefore is in a different universality class. The effect of a net external pressure is to suppress the handles and collapse the surface into a branched polymer-like configuration. Topology is thus shown to be a key factor in determining the universality class of the system
Organization of ecosystems in the vicinity of a novel phase transition
No full textIt is shown that an ecosystem in equilibrium is generally organized in a state which is poised in the vicinity of a novel phase transition
Comment on "Computational improvements reveal great bacterial diversity and high metal toxicity in soil"
No full textBased on analysis of the reassociation kinetics of bacterial DNA in soil, Gans et al. (Reports, 26 August 2005, p. 1387) claimed that millions of microbe species existed in 10 grams of pristine soil and that 99.9% of the diversity was lost as a result of toxic metals. We show that the data do not support these startling conclusions unambiguously
The origami of life
No full textAll living organisms rely upon networks of molecular interactions to carry out their vital processes. In order for a molecular system to display the properties of life, its constituent molecules must themselves be endowed with several features: stability, specificity, self-organization, functionality, sensitivity, robustness, diversity and adaptability. We argue that these are the emergent properties of a unique phase of matter, and we demonstrate that proteins, the functional molecules of terrestrial life, are perfectly suited to this phase. We explore, through an understanding of this phase of matter, the physical principles that govern the operation of living matter. Our work has implications for the design of functionally useful nanoscale devices and the ultimate development of-physically based artificial life
Anisotropic effective interactions in a coarse-grained tube picture of proteins
No full textRecent studies have shown that a coarse-grained description of a protein backbone represented as a tube of non-zero thickness captures many of the common characteristics of small globular proteins. Here we argue that such a physical picture leads to a prediction of inherently anisotropic amino acid interactions. In order to test this prediction, we have carried out an extensive analysis of a data bank made up of 600 proteins with low sequence homology and covering many different three-dimensional folds. This analysis, based on the study of the geometrical properties of the vectors joining next-nearest neighbor C-alpha atoms along the chain, shows clearly that when amino acids are in contact, the distribution of their relative orientations is not random but exhibits peaks at specific angles whose values reflect, in general, the tubular nature of proteins and, more specifically, the nature of the secondary structure motifs, which are the building blocks of protein structures. Our results suggest that the incorporation of the relative orientation of amino acids in contact could play a vital role in simplified coarse-grained schemes for determining effective interaction parameters for use in folding, threading, and docking
Trees, networks, and hydrology
No full textThis paper reviews theoretical and observational material on form and function of natural networks appeared in somewhat disparate contexts from physics to biology, whose study is related to hydrologic research. Moving from the exact result that drainage network configurations minimizing total energy dissipation are stationary solutions of the general equation describing landscape evolution, we discuss the properties and the dynamic origin of the scale-invariant structure of river patterns and its relation to optimal selection. We argue that at least in the fluvial landscape, nature works through imperfect searches for dynamically accessible optimal configurations and that purely random or deterministic constructs are clearly unsuitable to properly describe natural network forms. We also show that optimal networks are spanning loopless configurations only under precise physical requirements that arise under the constraints imposed by continuity. In the case of rivers, every spanning tree proves a local minimum of total energy dissipation. This is stated in a theorem form applicable to generic networks, suggesting that other branching structures occurring in nature (e.g., scale-free and looping) may possibly arise through optimality to different selective pressures. We thus conclude that one recurrent self-organized mechanism for the dynamic origin of fractal forms is the robust strive for imperfect optimality that we see embedded in many natural patterns, chief and foremost hydrologic ones
Size and form in efficient transportation networks
No full textMany biological processes, from cellular metabolism to population dynamics, are characterized by allometric scaling (power-law) relationships between size and rate(1-10). An outstanding question is whether typical allometric scaling relationships-the power-law dependence of a biological rate on body mass-can be understood by considering the general features of branching networks serving a particular volume. Distributed networks in nature stern from the need for effective connectivity(11), and occur both in biological systems such as cardiovascular and respiratory networks(1-8) and plant vascular and root systems(1,9,10), and in inanimate systems such as the drainage network of river basins(12), Here we derive a general relationship between size and flow rates in arbitrary networks with local connectivity. Our theory accounts in a general way for the quarter-power allometric scaling of living organisms(1-10), recently derived(8) under specific assumptions for particular network geometries. It also predicts scaling relations applicable to all efficient transportation networks, which we verify from observational data on the river drainage basins. Allometric scaling is therefore shown to originate from the general features of networks irrespective of dynamical or geometric assumptions
ECOLOGY Towards a theory of biodiversity
No full textThe article presents a study which investigates the ecological effects on the loss of biodiversity. It notes that life is non-equilibrium phenomenon that involves a dual-diffusion process. It mentions that the evolution of an ecological community corresponds to the dynamics of the distribution of occupied regions in real space and genome space. Moreover, they found out that models on ecological communities that incorporate mutation and spatial dispersal can yield results that explains the researchers observation
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