Strain-induced alignment in collagen gels

Collagen is the most abundant extracellular-network-forming protein in animal biology and is important in both natural and artificial tissues, where it serves as a material of great mechanical versatility. This versatility arises from its almost unique ability to remodel under applied loads into anisotropic and inhomogeneous structures. To explore the origins of this property, we develop a set of analysis tools and a novel experimental setup that probes the mechanical response of fibrous networks in a geometry that mimics a typical deformation profile imposed by cells in vivo. We observe strong fiber alignment and densification as a function of applied strain for both uncrosslinked and crosslinked collagenous networks. This alignment is found to be irreversibly imprinted in uncrosslinked collagen networks, suggesting a simple mechanism for tissue organization at the microscale. However, crosslinked networks display similar fiber alignment and the same geometrical properties as uncrosslinked gels, but with full reversibility. Plasticity is therefore not required to align fibers. On the contrary, our data show that this effect is part of the fundamental non-linear properties of fibrous biological networks.Comment: 12 pages, 7 figures. 1 supporting material PDF with 2 figure

In Silico Assembly And Nanomechanical Characterization Of Carbon Nanotube Buckypaper

Carbon nanotube sheets or films, also known as 'buckypaper', have been proposed for use in actuating, structural and filtration systems, based in part on their unique and robust mechanical properties. Computational modeling of such a fibrous nanostructure is hindered by both the random arrangement of the constituent elements as well as the time- and length-scales accessible to atomistic level molecular dynamics modeling. Here we present a novel in silico assembly procedure based on a coarse-grain model of carbon nanotubes, used to attain a representative mesoscopic buckypaper model that circumvents the need for probabilistic approaches. By variation in assembly parameters, including the initial nanotube density and ratio of nanotube type (single- and double-walled), the porosity of the resulting buckypaper can be varied threefold, from approximately 0.3 to 0.9. Further, through simulation of nanoindentation, the Young's modulus is shown to be tunable through manipulation of nanotube type and density over a range of approximately 0.2–3.1 GPa, in good agreement with experimental findings of the modulus of assembled carbon nanotube films. In addition to carbon nanotubes, the coarse-grain model and assembly process can be adapted for other fibrous nanostructures such as electrospun polymeric composites, high performance nonwoven ballistic materials, or fibrous protein aggregates, facilitating the development and characterization of novel nanomaterials and composites as well as the analysis of biological materials such as protein fiber films and bulk structures.National Science Foundation (U.S.) (MRSEC Program under award number DMR- 0819762

Do theoretical physicists care about the protein-folding problem?

The prediction of the biologically active native conformation of a protein is one of the fundamental challenges of structural biology. This problem remains yet unsolved mainly due to three factors: the partial knowledge of the effective free energy function that governs the folding process, the enormous size of the conformational space of a protein and, finally, the relatively small differences of energy between conformations, in particular, between the native one and the ones that make up the unfolded state. Herein, we recall the importance of taking into account, in a detailed manner, the many interactions involved in the protein folding problem (such as steric volume exclusion, Ramachandran forces, hydrogen bonds, weakly polar interactions, coulombic energy or hydrophobic attraction) and we propose a strategy to effectively construct a free energy function that, including the effects of the solvent, could be numerically tractable. It must be pointed out that, since the internal free energy function that is mainly described does not include the constraints of the native conformation, it could only help to reach the 'molten globule' state. We also discuss about the limits and the lacks from which suffer the simple models that we, physicists, love so much.Comment: 27 pages, 4 figures, LaTeX file, aipproc package. To be published in the book: "Meeting on Fundamental Physics 'Alberto Galindo'", Alvarez-Estrada R. F. et al. (Ed.), Madrid: Aula Documental, 200

The Physics of Communicability in Complex Networks

A fundamental problem in the study of complex networks is to provide quantitative measures of correlation and information flow between different parts of a system. To this end, several notions of communicability have been introduced and applied to a wide variety of real-world networks in recent years. Several such communicability functions are reviewed in this paper. It is emphasized that communication and correlation in networks can take place through many more routes than the shortest paths, a fact that may not have been sufficiently appreciated in previously proposed correlation measures. In contrast to these, the communicability measures reviewed in this paper are defined by taking into account all possible routes between two nodes, assigning smaller weights to longer ones. This point of view naturally leads to the definition of communicability in terms of matrix functions, such as the exponential, resolvent, and hyperbolic functions, in which the matrix argument is either the adjacency matrix or the graph Laplacian associated with the network. Considerable insight on communicability can be gained by modeling a network as a system of oscillators and deriving physical interpretations, both classical and quantum-mechanical, of various communicability functions. Applications of communicability measures to the analysis of complex systems are illustrated on a variety of biological, physical and social networks. The last part of the paper is devoted to a review of the notion of locality in complex networks and to computational aspects that by exploiting sparsity can greatly reduce the computational efforts for the calculation of communicability functions for large networks.Comment: Review Article. 90 pages, 14 figures. Contents: Introduction; Communicability in Networks; Physical Analogies; Comparing Communicability Functions; Communicability and the Analysis of Networks; Communicability and Localization in Complex Networks; Computability of Communicability Functions; Conclusions and Prespective

Cytoskeleton and Cell Motility

The present article is an invited contribution to the Encyclopedia of Complexity and System Science, Robert A. Meyers Ed., Springer New York (2009). It is a review of the biophysical mechanisms that underly cell motility. It mainly focuses on the eukaryotic cytoskeleton and cell-motility mechanisms. Bacterial motility as well as the composition of the prokaryotic cytoskeleton is only briefly mentioned. The article is organized as follows. In Section III, I first present an overview of the diversity of cellular motility mechanisms, which might at first glance be categorized into two different types of behaviors, namely "swimming" and "crawling". Intracellular transport, mitosis - or cell division - as well as other extensions of cell motility that rely on the same essential machinery are briefly sketched. In Section IV, I introduce the molecular machinery that underlies cell motility - the cytoskeleton - as well as its interactions with the external environment of the cell and its main regulatory pathways. Sections IV D to IV F are more detailed in their biochemical presentations; readers primarily interested in the theoretical modeling of cell motility might want to skip these sections in a first reading. I then describe the motility mechanisms that rely essentially on polymerization-depolymerization dynamics of cytoskeleton filaments in Section V, and the ones that rely essentially on the activity of motor proteins in Section VI. Finally, Section VII is devoted to the description of the integrated approaches that have been developed recently to try to understand the cooperative phenomena that underly self-organization of the cell cytoskeleton as a whole.Comment: 31 pages, 16 figures, 295 reference