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Network formation of associative semiflexible fibers and mixtures of fibers and colloidal particles is simulated for the Johnson-Kendall-Roberts (JKR) model of elastic contacts, and a phase diagram in terms of particle elasticity and…
The phenomenon of linear mode connectivity (LMC) links several aspects of deep learning, including training stability under noisy stochastic gradients, the smoothness and generalization of local minima (basins), the similarity and…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…
Soft colloids allow to explore high density states well beyond random close packing. An important open question is whether softness controls the dynamics under these dense conditions. While experimental works reported conflicting results,…
We study the dynamical rheology of spring networks with a percolation model constructed by bond dilution in a two-dimensional triangular lattice. Hydrodynamic interactions are implemented by a Stokesian viscous coupling between the network…
The mechanical properties of biological materials are spatially heterogeneous. Typical tissues are made up of a spanning fibrous extracellular matrix in which various inclusions, such as living cells, are embedded. While the influence of…
Athermal models of disordered fibrous networks are highly useful for studying the mechanics of elastic networks composed of stiff biopolymers. The underlying network architecture is a key aspect that can affect the elastic properties of…
We present a panoramic view of the utility of coarse-grained (CG) models to study folding and functions of proteins and RNA. Drawing largely on the methods developed in our group over the last twenty years, we describe a number of key…
We study the elasticity of fibrous materials composed of generalized stiff polymers. It is shown that in contrast to cellular foam-like structures affine strain fields are generically unstable. Instead, a subtle interplay between the…
Tissues commonly consist of cells embedded within a fibrous biopolymer network. Whereas cell-free reconstituted biopolymer networks typically soften under applied uniaxial compression, various tissues, including liver, brain, and fat, have…
We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is…
One problem of non-crystalline condensed matter (soft matter) is creating the right equilibrium between elasticity and viscosity, referred to as viscoelasticity. Manifestations of that can be found in everyday live, where the…
A networked oscillator based analysis is performed for periodic bluff body flows to examine and control the transfer of kinetic energy. Spatial modes extracted from the flow field with corresponding amplitudes form a set of oscillators…
We investigate the phase behaviour of a two-dimensional colloidal model system of ultra-soft particles on a substrate which varies periodically along one spatial direction. Our calculations are based on mean-field density functional theory…
Two dimensional simulations of non-cohesive granular matter in a biaxial shear tester are discussed. The effect of particle elasticity on the mechanical behavior is investigated using two complementary distinct element methods (DEM): Soft…
For biologically relevant macromolecules such as intrinsically disordered proteins, internal degrees of freedom that allow for shape changes have a large influence on both the motion and function of the compound. A detailed understanding of…
A minimal model for studying the mechanical properties of amorphous solids is a disordered network of point masses connected by unbreakable springs. At a critical value of its mean connectivity, such a network becomes fragile: it undergoes…
Due to its incommensurate nature, moir\'e superlattices host not only acoustic phonons but also another type of soft collective modes called phasons. Here, we investigate the impact of electron-phason scattering on the transport properties…
All biological systems are subject to perturbations: due to thermal fluctuations, external environments, or mutations. Yet, while biological systems are composed of thousands of interacting components, recent high-throughput experiments…
Disordered spring networks that are undercoordinated may abruptly rigidify when sufficient strain is applied. Since the deformation in response to applied strain does not change the generic quantifiers of network architecture - the number…