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Diffusion of colloidal particles in a complex environment such as polymer networks or biological cells is a topic of high complexity with significant biological and medical relevance. In such situations, the interaction between the…
We consider composite quantum-dynamical systems that can be partitioned into weakly interacting subsystems, similar to system-bath type situations. Using a factorized wave function ansatz, we mathematically characterize dynamical scale…
Recently several authors studied the segregation of particles for a system composed of mono-dispersed inelastic spheres contained in a box divided by a wall in the middle. The system exhibited a symmetry breaking leading to an…
Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the…
This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random 3D fiber orientation and…
A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…
Active matter systems being in a non-equilibrium state, exhibit complex behaviors such as self-organization and giving rise to emergent phenomena. There are many examples of active particles with biological origins, including bacteria and…
We study segregation of a binary mixture of similarly charged particles under shear using particle-based simulations. We simulate particle dynamics using a discrete-element model including electrostatic interactions and find that particles…
Active matter exhibits various forms of non-equilibrium states in the absence of external forcing, including macroscopic steady-state currents. Such states are often too complex to be modelled from first principles and our understanding of…
Self-organized dynamic patterns in dense active matter are striking manifestations of non-equilibrium physics. A prominent example is the macroscopic elliptical motion observed in quasi-2D bacterial suspensions, which has lacked a physical…
A driven diffusive model of three types of particles that exhibits phase separation on a ring is introduced. The dynamics is local and comprises nearest neighbor exchanges that conserve each of the three species. For the case in which the…
This paper proposes a mathematical model for replicating a simple dynamics in an aquarium with two components; bacteria and organic matter. The model is based on a system of partial differential equations (PDEs) with four components: the…
The dynamic of complex ordering systems with active rotational degrees of freedom exemplified by protein self-assembly is explored using a machine learning workflow that combines deep learning-based semantic segmentation and rotationally…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
Recent findings suggest that shell protein distribution and morphology of bacterial microcompartments regulate the chemical fluxes facilitating reactions which dictate their biological function. We explore how the morphology and component…
The cellular cytoplasm is organized into compartments. Phase separation is a simple manner to create membrane-less compartments in order to confine and localize particles like proteins. In many cases these particles are bound to fluctuating…
We theoretically study mixtures of chemically-interacting particles, which produce or consume a chemical to which they are attracted or repelled, in the most general case of many coexisting species. We find a new class of active phase…
We demonstrate that a conditional wavefunction theory enables a unified and efficient treatment of the equilibrium structure and nonadiabatic dynamics of correlated electron-ion systems. The conditional decomposition of the many-body…
Understanding flow and transport of bacteria in porous media is crucial to technologies such as bioremediation, biomineralization or enhanced oil recovery. While physicochemical bacteria filtration is well-documented, recent studies showed…
The development of intense high-energy radiation sources and the improvement of techniques for detecting charged fragments have made possible experiments on multiple ionization of a molecule with registration of the momentum and charge of…