Nanomechanical and topographical imaging of living cells by Atomic Force Microscopy with colloidal probes

Atomic Force Microscopy (AFM) has a great potential as a tool to characterize mechanical and morphological properties of living cells; these properties have been shown to correlate with cells' fate and patho-physiological state in view of the development of novel early-diagnostic strategies. Although several reports have described experimental and technical approaches for the characterization of cell elasticity by means of AFM, a robust and commonly accepted methodology is still lacking. Here we show that micrometric spherical probes (also known as colloidal probes) are well suited for performing a combined topographic and mechanical analysis of living cells, with spatial resolution suitable for a complete and accurate mapping of cell morphological and elastic properties, and superior reliability and accuracy in the mechanical measurements with respect to conventional and widely used sharp AFM tips. We address a number of issues concerning the nanomechanical analysis, including the applicability of contact mechanical models and the impact of a constrained contact geometry on the measured elastic modulus (the finite-thickness effect). We have tested our protocol by imaging living PC12 and MDA-MB-231 cells, in order to demonstrate the importance of the correction of the finite-thickness effect and the change in cell elasticity induced by the action of a cytoskeleton-targeting drug.Comment: 51 pages, 12 figures, 3 table

Concurrent coupling of atomistic simulation and mesoscopic hydrodynamics for flows over soft multi-functional surfaces

We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an all-atom molecular dynamics (MD) description for specific atomistic details in the vicinity of the functional surface, with a dissipative particle dynamics (DPD) approach that captures mesoscopic hydrodynamics in the domain away from the functional surface. In order to achieve a seamless transition in dynamic properties we endow the MD simulation with a DPD thermostat, which is validated against experimental results by modeling water at different temperatures. We then validate the MD-DPD coupling method for transient Couette and Poiseuille flows, demonstrating that the concurrent MD-DPD coupling can resolve accurately the continuum-based analytical solutions. Subsequently, we simulate shear flows over polydimethylsiloxane (PDMS)-grafted surfaces (polymer brushes) for various grafting densities, and investigate the slip flow as a function of the shear stress. We verify that a "universal" power law exists for the sliplength, in agreement with published results. Having validated the MD-DPD coupling method, we simulate time-dependent flows past an endothelial glycocalyx layer (EGL) in a microchannel. Coupled simulation results elucidate the dynamics of EGL changing from an equilibrium state to a compressed state under shear by aligning the molecular structures along the shear direction. MD-DPD simulation results agree well with results of a single MD simulation, but with the former more than two orders of magnitude faster than the latter for system sizes above one micron.Comment: 11 pages, 12 figure

Diffusive spreading and mixing of fluid monolayers

The use of ultra-thin, i.e., monolayer films plays an important role for the emerging field of nano-fluidics. Since the dynamics of such films is governed by the interplay between substrate-fluid and fluid-fluid interactions, the transport of matter in nanoscale devices may be eventually efficiently controlled by substrate engineering. For such films, the dynamics is expected to be captured by two-dimensional lattice-gas models with interacting particles. Using a lattice gas model and the non-linear diffusion equation derived from the microscopic dynamics in the continuum limit, we study two problems of relevance in the context of nano-fluidics. The first one is the case in which along the spreading direction of a monolayer a mesoscopic-sized obstacle is present, with a particular focus on the relaxation of the fluid density profile upon encountering and passing the obstacle. The second one is the mixing of two monolayers of different particle species which spread side by side following the merger of two chemical lanes, here defined as domains of high affinity for fluid adsorption surrounded by domains of low affinity for fluid adsorption.Comment: 12 pages, 3 figure

Perspectives on Multi-Level Dynamics

As Physics did in previous centuries, there is currently a common dream of extracting generic laws of nature in economics, sociology, neuroscience, by focalising the description of phenomena to a minimal set of variables and parameters, linked together by causal equations of evolution whose structure may reveal hidden principles. This requires a huge reduction of dimensionality (number of degrees of freedom) and a change in the level of description. Beyond the mere necessity of developing accurate techniques affording this reduction, there is the question of the correspondence between the initial system and the reduced one. In this paper, we offer a perspective towards a common framework for discussing and understanding multi-level systems exhibiting structures at various spatial and temporal levels. We propose a common foundation and illustrate it with examples from different fields. We also point out the difficulties in constructing such a general setting and its limitations

Acoustic excitations and elastic heterogeneities in disordered solids

In the recent years, much attention has been devoted to the inhomogeneous nature of the mechanical response at the nano-scale in disordered solids. Clearly, the elastic heterogeneities that have been characterized in this context are expected to strongly impact the nature of the sound waves which, in contrast to the case of perfect crystals, cannot be completely rationalized in terms of phonons. Building on previous work on a toy model showing an amorphisation transition [Mizuno H, Mossa S, Barrat JL (2013) EPL {\bf 104}:56001], we investigate the relationship between sound waves and elastic heterogeneities in a unified framework, by continuously interpolating from the perfect crystal, through increasingly defective phases, to fully developed glasses. We provide strong evidence of a direct correlation between sound waves features and the extent of the heterogeneous mechanical response at the nano-scale

Community detection for correlation matrices

A challenging problem in the study of complex systems is that of resolving, without prior information, the emergent, mesoscopic organization determined by groups of units whose dynamical activity is more strongly correlated internally than with the rest of the system. The existing techniques to filter correlations are not explicitly oriented towards identifying such modules and can suffer from an unavoidable information loss. A promising alternative is that of employing community detection techniques developed in network theory. Unfortunately, this approach has focused predominantly on replacing network data with correlation matrices, a procedure that tends to be intrinsically biased due to its inconsistency with the null hypotheses underlying the existing algorithms. Here we introduce, via a consistent redefinition of null models based on random matrix theory, the appropriate correlation-based counterparts of the most popular community detection techniques. Our methods can filter out both unit-specific noise and system-wide dependencies, and the resulting communities are internally correlated and mutually anti-correlated. We also implement multiresolution and multifrequency approaches revealing hierarchically nested sub-communities with `hard' cores and `soft' peripheries. We apply our techniques to several financial time series and identify mesoscopic groups of stocks which are irreducible to a standard, sectorial taxonomy, detect `soft stocks' that alternate between communities, and discuss implications for portfolio optimization and risk management.Comment: Final version, accepted for publication on PR