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The measurement of cellular traction forces on soft elastic substrates has become a standard tool for many labs working on mechanobiology. Here we review the basic principles and different variants of this approach. In general, the…
Being motivated by the delivery of drugs and vaccines through subcutaneous (SC) injection in human bodies, a theoretical investigation is performed using a two-dimensional mathematical model in the cartesian coordinate. In general, a large…
From cytoskeletal networks to tissues, many biological systems behave as active materials. Their composition and stress-generation is affected by chemical reaction networks. In such systems, the coupling between mechanics and chemistry…
The fracture simulation of random particle reinforced composite structures remains a challenge. Current techniques either assumed a homogeneous model, ignoring the microstructure characteristics of composite structures, or considered a…
Coiled Carbon Nanotubes (CCNTs) are increasingly set to become a vital factor in the new generation of nanodevices and energy-absorbing materials due to their outstanding properties. In the following work, the multi-objective optimization…
We report ab initio density functional calculations of the structural and magnetic properties, and the electronic structure of CrAs. To simulate the observed pressure-driven experimental results, we perform our analysis for different…
Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements.…
Emergence of collective dynamical chirality (CDC) at mesoscopic scales plays a key role in many formation processes of chiral structures in nature, which may also provide possible routines for people to fabricate complex chiral…
A molecular-level model is used to study the mechanical response of empty cowpea chlorotic mottle virus (CCMV) and cowpea mosaic virus (CPMV) capsids. The model is based on the native structure of the proteins that consitute the capsids and…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
We describe experimentally observed collective dynamics in colloidal suspensions of model hard-sphere particles using a modified mode coupling theory (MCT). This rescaled MCT is capable to describe quantitatively the wave-vector and…
Here we study a driven lattice gas model for microtubule depolymerizing molecular motors, where traffic jams of motors induce stochastic switching between microtubule growth and shrinkage. We term this phenomenon \enquote{traffic dynamic…
Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…
In this article we give our perspective on the successes and promise of various molecular and coarse-grained simulation approaches to probing the effect of mechanical forces in the actin cytoskeleton.
Microstructural changes in solids, driven by energy flows, do not develop in a static continuous space, such as the space considered in conventional plasticity models. The applied forces create an evolving internal energy landscape, which…
The mesoscopic concept is a way to deal with complex materials with an internal structure within continuum mechanics. It consists of extending the domain of the balance equations by mesoscopic variables and of introducing a local…
It has recently been shown that identical, isotropic particles can form complex crystals and quasicrystals. In order to understand the relation between the particle interaction and the structure, which it stabilizes, the phase behavior of a…
The structure and mechanical properties of a simple two-dimensional model of a cohesive powder are investigated by molecular dynamics simulations. Micromechanical ingredients involve elasticity, friction, a short range attraction and,…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
We consider mechanics of composite materials in which thin inclusions are modeled by lower-dimensional manifolds. By successively applying the dimensional reduction to junctions and intersections within the material, a geometry of…