Related papers: Studying protein assembly with reversible Brownian…
Flexibility governs the many properties of materials and is crucial for the function of proteins and biopolymers. However, how the self-assembly of flexibly bonded particles can lead to larger structures with global reconfigurability is…
Aggregation of protein into bundles is responsible for many neurodegenerative diseases. In this work, we show how two-patch colloidal particles self assemble into chains and a sudden transition to bundles takes place by tuning the patch…
Understanding the influence of activity on dense amorphous assemblies is crucial for biological processes such as wound healing, embryogenesis, or cancer progression. Here, we study the effect of self-propulsion forces of amplitude $f_0$…
The collective properties of a binary mixture of A- and B-type self-steering particles endowed with visual perception are studied by computer simulations. Active Brownian particles are employed with an additional steering mechanism, which…
We perform numerical simulations of athermal repulsive frictionless disks and spheres in two and three spatial dimensions undergoing cyclic quasi-static simple shear to investigate particle-scale reversible motion. We identify three classes…
Behavior of the mixture of particles and dimers moving with different jump rates at reconstructed surfaces is described. Collective diffusion coefficient is calculated by the variational approach. Anisotropy of the collective particle…
In this work we study a two-dimensional system composed by Active Brownian Particles (ABPs) interacting via a repulsive potential with two-length-scales, a soft shell and a hard-core. Depending on the ratio between the strength of the soft…
In many virus families, tens to thousands of proteins assemble spontaneously into a capsid (protein shell) while packaging the genomic nucleic acid. This review summarizes recent advances in computational modeling of these dynamical…
A quantitative model of the mobility of functionalized particles at the interface is pivotal to understanding important systems in biology and nanotechnology. In this work, we investigate the emerging dynamics of particles anchored through…
During the lifecycle of a virus, viral proteins and other components self-assemble to form a symmetric protein shell called a capsid. This assembly process is subject to multiple competing constraints, including the need to form a…
We investigate the phase behavior and kinetics of a monodisperse mixture of active (\textit{i.e.}, self-propelled) and passive isometric Brownian particles through Brownian dynamics simulations and theory. As in a purely active system,…
The actin cytoskeleton is a key component in the machinery of eukaryotic cells, and it selfassembles out of equilibrium into a wide variety of biologically crucial structures. While the molecular mechanisms involved are well characterized,…
Phagocytosis is the process of engulfment and internalization of comparatively large particles by the cell, that plays a central role in the functioning of our immune system. We study the process of phagocytosis by considering a simplified…
Mechanical responses of soft particle packings to quasi-static deformations are determined by the microscopic restructuring of force-chain networks, where complex non-affine displacements of constituent particles cause the irreversible…
We investigate associative-memory behavior in a reconfigurable particle packing programmed by purely local cyclic driving. The system is a two-dimensional bidisperse Lennard--Jones particle assembly with periodic boundaries evolved under…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
In the presence of an obstacle, active particles condensate into a surface "wetting" layer due to persistent motion. If the obstacle is asymmetric, a rectification current arises in addition to wetting. Asymmetric geometries are therefore…
Protein function and activity are a consequence of its three-dimensional structure. Single particle analysis of cryogenic electron micrographs has radically changed structural biology allowing atomic reconstruction of almost any type of…
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…
Brownian dynamics is a popular fine-grained method for simulating systems of interacting particles, such as chemical reactions. Though the method is simple to simulate, it is generally assumed that the dynamics is impossible to solve…