Biological Physics
In this paper we develop a model for nematic alignment of self-propelled rods interacting through binary collisions. We avoid phenomenological descriptions of rod interaction in favor of rigorously using a set of microscopic-level rules.…
Colonies of rod-shaped bacteria constitute a system of colloidal active matter with nematic properties. As a single initial bacterium multiplies through repeated divisions, the resulting colony quickly loses long-range orientational order,…
Thrombosis under high-shear conditions is mediated by the mechanosensitive blood glycoprotein von Willebrand Factor (vWF). vWF unfolds in response to strong flow gradients and facilitates rapid recruitment of platelets in flowing blood.…
X-ray free-electron lasers (XFELs) with megahertz repetition rate can provide novel insights into structural dynamics of biological macromolecule solutions. However, very high dose rates can lead to beam-induced dynamics and structural…
We present a thermodynamically consistent model describing the dynamics of a multi-component mixture where one enzyme component catalyzes a reaction between other components. We find that the catalytic activity alone can induce phase…
Coordinated and cooperative motion of cells is essential for embryonic development, tissue morphogenesis, wound healing and cancer invasion. A predictive understanding of the emergent mechanical behaviors in collective cell motion is…
We present two methods to reveal protein-ligand unbinding mechanisms in biased unbinding simulations by clustering trajectories into ensembles representing unbinding paths. The first approach is based on a contact principal component…
The process of ligand-protein unbinding is crucial in biophysics. Water is an essential part of any biological system and yet, many aspects of its role remain elusive. Here, we simulate with state-of-the-art enhanced sampling techniques the…
Developing antiviral drugs is an exigent task since viruses mutate to overcome the effect of antiviral drugs. As a result, the efficacy of most antiviral drugs is short-lived. To include this effect, we modify the Neumann and Dahari model.…
Regulating cell growth, extracellular matrix deposition and mineralization of artificial implants are some important parameters that decide the longevity of implants in the body. Picosecond laser induced hybrid groove structures have been…
The adaptive immune system constantly remodels its lymphocyte repertoire for better protection against future pathogens. Its ability to improve antigen recognition on the fly relies on somatic mutation and selective expansion of B…
Bioprinting of living cells can cause major shape deformations, which may severely affect cell survival and functionality. While the shear stresses occurring during cell flow through the printer nozzle have been quantified to some extent,…
Recent empirical observations of three-dimensional bird flocks and human crowds have challenged the long-prevailing assumption that a metric interaction distance rules swarming behaviors. In some cases, individual agents are found to be…
Controllability of complex networks has been the focal point of many recent studies in the field of complexity. These landmark advances shed a new light on the dynamics of natural and technological complex systems. Here, we analyze the…
Many eukaryotic cells are able to perform directional mechanosensing by directly measuring minute spatial differences in the mechanical stress on their membranes. Here, we explore the limits of a single mechanosensitive channel activation…
Stochastic Schr\"odinger equations that govern the dynamics of open quantum systems are given by the equations for signal processing. In particular, the Brownian motion that drives the wave function of the system does not represent noise,…
The suberized netting tissue on the surface of muskmelons is a remnant of the rind fragmentation caused by the mechanical imbalance between the expanding flesh meat and the solidified epidermis during growth. The appearance of this netting…
Chemically active droplets provide simple models for cell-like systems that can grow and divide. Such active droplet systems are driven away from thermodynamic equilibrium and turn over chemically, which corresponds to a simple metabolism.…
$TiO_{2}$ nanoparticles (NPs) are widely used in the environmental engineering, medicine, chemical and food industries due to their unique photocatalytic and biocidal properties. NPs may generate reactive oxygen species and, hence, have the…
The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spurred unprecedented and concerted worldwide research to curtail and eradicate this pathogen. SARS-CoV-2 has four structural proteins:…