Damage Accumulation in Silica Glass Nanofibers.

The origin of the brittle-to-ductile transition, experimentally observed in amorphous silica nanofibers as the sample size is reduced, is still debated. Here we investigate the issue by extensive molecular dynamics simulations at low and room temperatures for a broad range of sample sizes, with open and periodic boundary conditions. Our results show that small sample-size enhanced ductility is primarily due to diffuse damage accumulation, that for larger samples leads to brittle catastrophic failure. Surface effects such as boundary fluidization contribute to ductility at room temperature by promoting necking, but are not the main driver of the transition. Our results suggest that the experimentally observed size-induced ductility of silica nanofibers is a manifestation of finite-size criticality, as expected in general for quasi-brittle disordered networks.

Deformation and failure of curved colloidal crystal shells.

Designing and controlling particle self-assembly into robust and reliable high-performance smart materials often involves crystalline ordering in curved spaces. Examples include carbon allotropes like graphene, synthetic materials such as colloidosomes, or biological systems like lipid membranes, solid domains on vesicles, or viral capsids. Despite the relevance of these structures, the irreversible deformation and failure of curved crystals is still mostly unexplored. Here, we report simulation results of the mechanical deformation of colloidal crystalline shells that illustrate the subtle role played by geometrically necessary topological defects in controlling plastic yielding and failure. We observe plastic deformation attributable to the migration and reorientation of grain boundary scars, a collective process assisted by the intermittent proliferation of disclination pairs or abrupt structural failure induced by crack nucleating at defects. Our results provide general guiding principles to optimize the structural and mechanical stability of curved colloidal crystals.

Direct Observation of Percolation in the Yielding Transition of Colloidal Glasses.

When strained beyond the linear regime, soft colloidal glasses yield to steady-state plastic flow in a way that is similar to the deformation of conventional amorphous solids. Because of the much larger size of the colloidal particles with respect to the atoms comprising an amorphous solid, colloidal glasses allow us to obtain microscopic insight into the nature of the yielding transition, as we illustrate here combining experiments, atomistic simulations, and mesoscopic modeling. Our results unanimously show growing clusters of nonaffine deformation percolating at yielding. In agreement with percolation theory, the spanning cluster is fractal with a fractal dimension d_{f}≃2, and the correlation length diverges upon approaching the critical yield strain. These results indicate that percolation of highly nonaffine particles is the hallmark of the yielding transition in disordered glassy systems.

Atomic-Scale Front Propagation at the Onset of Frictional Sliding.

Macroscopic frictional sliding emerges from atomic-scale interactions and processes at the contact interface, but bridging the gap between micro and macro scales still remains an unsolved challenge. Direct imaging of the contact surface and simultaneous measurement of stress fields during macroscopic frictional slip revealed the formation of crack precursors, questioning the traditional picture of frictional contacts described in terms of a single degree of freedom. Here we study the onset of frictional slip on the atomic scale by simulating the motion of an aluminum block pushed by a slider on a copper substrate. We show the formation of dynamic slip front propagation and precursory activity that resemble macroscopic observations. The analysis of stress patterns during slip, however, reveals subtle effects due to the lattice structures that hinder a direct application of linear elastic fracture mechanics. Our results illustrate that dynamic front propagation arises already on the atomic scales and shed light on the connections between atomic-scale and macroscopic friction.

Wrinkle motifs in thin films.

On length scales from nanometres to metres, partial adhesion of thin films with substrates generates a fascinating variety of patterns, such as 'telephone cord' buckles, wrinkles, and labyrinth domains. Although these patterns are part of everyday experience and are important in industry, they are not completely understood. Here, we report simulation studies of a previously-overlooked phenomenon in which pairs of wrinkles form avoiding pairs, focusing on the case of graphene over patterned substrates. By nucleating and growing wrinkles in a controlled way, we characterize how their morphology is determined by stress fields in the sheet and friction with the substrate. Our simulations uncover the generic behaviour of avoiding wrinkle pairs that should be valid at all scales.

Overshoot during phenotypic switching of cancer cell populations.

The dynamics of tumor cell populations is hotly debated: do populations derive hierarchically from a subpopulation of cancer stem cells (CSCs), or are stochastic transitions that mutate differentiated cancer cells to CSCs important? Here we argue that regulation must also be important. We sort human melanoma cells using three distinct cancer stem cell (CSC) markers - CXCR6, CD271 and ABCG2 - and observe that the fraction of non-CSC-marked cells first overshoots to a higher level and then returns to the level of unsorted cells. This clearly indicates that the CSC population is homeostatically regulated. Combining experimental measurements with theoretical modeling and numerical simulations, we show that the population dynamics of cancer cells is associated with a complex miRNA network regulating the Wnt and PI3K pathways. Hence phenotypic switching is not stochastic, but is tightly regulated by the balance between positive and negative cells in the population. Reducing the fraction of CSCs below a threshold triggers massive phenotypic switching, suggesting that a therapeutic strategy based on CSC eradication is unlikely to succeed.

Universal features in the genome-level evolution of protein domains.

BACKGROUND: Protein domains can be used to study proteome evolution at a coarse scale. In particular, they are found on genomes with notable statistical distributions. It is known that the distribution of domains with a given topology follows a power law. We focus on a further aspect: these distributions, and the number of distinct topologies, follow collective trends, or scaling laws, depending on the total number of domains only, and not on genome-specific features. RESULTS: We present a stochastic duplication/innovation model, in the class of the so-called 'Chinese restaurant processes', that explains this observation with two universal parameters, representing a minimal number of domains and the relative weight of innovation to duplication. Furthermore, we study a model variant where new topologies are related to occurrence in genomic data, accounting for fold specificity. CONCLUSIONS: Both models have general quantitative agreement with data from hundreds of genomes, which indicates that the domains of a genome are built with a combination of specificity and robust self-organizing phenomena. The latter are related to the basic evolutionary 'moves' of duplication and innovation, and give rise to the observed scaling laws, a priori of the specific evolutionary history of a genome. We interpret this as the concurrent effect of neutral and selective drives, which increase duplication and decrease innovation in larger and more complex genomes. The validity of our model would imply that the empirical observation of a small number of folds in nature may be a consequence of their evolution.