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Many tools and techniques measure local structure in materials in contexts ranging from biology to geology. We provide a survey of those tools and metrics that are especially useful for analyzing particulate soft matter. The metrics we…
The diffusion of active microscopic organisms in complex environments plays an important role in a wide range of biological phenomena from cell colony growth to single organism transport. Here, we investigate theoretically and…
Brownian motion is essential for describing diffusion in systems ranging from simple to complex liquids. Unlike simple liquids, which consist of only a solvent, complex liquids, such as colloidal suspensions or the cytoplasm of a cell, are…
Microrheology is the study of the properties of a complex fluid through the diffusion dynamics of small particles, typically latex beads, moving through that material. Currently, it is the dominant technique in the study of the physical…
The connection between the properties of cell tissue and those of the single constituent cells remains to be elucidated. At the purely mechanical level, the degree of rigidity of different cellular components, such as the nucleus and the…
Quantifying the relationship between geometric descriptors of microstructure and effective properties like permeability is essential for understanding and improving the behavior of porous materials. In this paper, we employ a previously…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
Microtubules, major elements of the cell skeleton are, most of the time, well organized in vivo, but they can also show self-organizing behaviors in time and/or space in purified solutions in vitro. Theoretical studies and models based on…
We apply a hybrid Molecular Dynamics and mesoscopic simulation technique to study the dynamics of two dimensional colloidal discs in confined geometries. We calculate the velocity autocorrelation functions, and observe the predicted…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Mechanical properties of the cell are important biomarkers for probing its architectural changes caused by cellular processes and/or pathologies. The development of microfluidic technologies have enabled measuring cell mechanics at…
The movement of intracellular cargo transported by molecular motors is commonly marked by switches between directed motion and stationary pauses. The predominant measure for assessing movement is effective diffusivity, which predicts the…
For the first time the phenomenon of cellular structure coarsening are consistently analysed from the positions of kinetic, hydrodynamic and stochastodynamic theories of nonequilibrium statistical systems. Thereby micro-, meso- and…
The large-scale collective behavior of biological systems can be characterized by macroscopic transport, which arises from the non-equilibrium microscopic interactions among individual constituents. A prominent example is the formation of…
The structure and degree of order in soft matter and other materials is intimately connected to the nature of the interactions between the particles. One important research goal is to find suitable control mechanisms, to enhance or suppress…
Advances in intensity-based microscopy techniques have improved our ability to quantify particle motion at microscopic scales, enabling insight into diffusion and collective dynamics. Building on this foundation, we introduce a novel…
In this work, two-dimensional simulations of the microwave dielectric properties of models with ellipses and realistic models of trabecular bone tissue are performed. In these simulations, finite difference time domain methodology has been…
Open cellular solids usually possess random microstructures that may contain a characteristic length scale, such as the cell size. This gives rise to size dependent mechanical properties where large systems behave differently from small…
The lack of analytical models describing diffusion time dependence at intermediate time scales in complex tissue microstructure limits the accurate quantification of extracellular diffusivity and tissue microstructure. We introduce TRACED,…
Diffusion is a fundamental phenomenon that occurs ubiquitously in nature and remains the subject of continuous research interest. Understanding diffusion is a key to understanding leaving systems. In this Chapter, I discuss diffusion of…