Biological Physics
Microbially Induced Calcium Carbonate Precipitation (MICP) is an eco-friendly technique that enhances soil mechanical properties using urease-producing microorganisms, especially Sporosarcina pasteurii. However, field trials often yield…
To analyze hydration effects on macromolecular diffusion, the friction coefficients of macromolecules were examined using molecular dynamics simulations with an all-atom model. In the present study, a method was introduced to decompose the…
Bacterial cells exhibit a diverse array of shapes and sizes, largely governed by their cell walls in conjunction with cytoskeletal proteins and internal turgor pressure. The present study develops a theoretical framework for modeling the…
At the 2023 Les Houches Summer School on Theoretical Biological Physics, several students asked for some background on information theory, and so we added a tutorial to the scheduled lectures. This is largely a transcript of that tutorial,…
Synchronization phenomena are pervasive in coupled nonlinear systems across the natural world and engineering domains. Understanding how to dynamically identify the parameter space (or network structure) of coupled nonlinear systems in a…
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 need for organisms to regulate their volume and osmolarity when surrounded by freshwater is a basic physical challenge for many bacteria, protists and algae. Taking inspiration from the contractile vacuole complex found in many…
By means of a minimal physical model, we investigate the interplay of two phase transitions at play in chromatin organization: (1) liquid-liquid phase separation (LLPS) within the fluid solvating chromatin, resulting in the formation of…
The monograph summarizes the studies of the temperature limits for the existence of a supercooled liquid phase of the components of nanodisperse structures. Original in situ methods for studying supercooling during crystallization in…
Immunization with an inactivated virus is one of the strategies currently being tested towards developing a SARS-CoV-2 vaccine. One of the methods used to inactivate viruses is exposure to high doses of ionizing radiation to damage their…
Many cells face search problems, such as finding food, mates or shelter, where their success depends on their search strategy. In contrast to other unicellular organisms, the slime mold Physarum polycephalum forms a giant network-shaped…
Excitable systems can exhibit a variety of dynamics with different complexity, ranging from a single, stable spiral to spiral defect chaos (SDC), during which spiral waves are continuously formed and destroyed. The corresponding…
All proteins in living organisms are produced in ribosomes that facilitate the translation of genetic information into a sequence of amino acid residues. During translation, the ribosome undergoes initiation, elongation, termination, and…
We use infrared thermal imaging to remotely monitor the temperature of the leaves and plant which in turn is an indicative of their health and stress; in particular water stress. A series of experiments were conducted using Fluke TiX580…
Designing a model of retinal isomerization in Rhodopsin, the first step in vision, that accounts for both experimental transient and stationary state observables is challenging. Here, multi-objective Bayesian optimization is employed to…
Flagellated bacteria are hydrodynamically attracted to rigid walls, yet past work shows a 'hovering' state where they swim stably at a finite height above surfaces. We use numerics and theory to reveal the physical origin of hovering.…
What is certain is that surface temperatures around the globe vary considerably, regardless of the time scales or underlying causes. Since 1850, we have observed an average increase in global surface temperature anomalies of 1.2$^{\circ}$…
Ion channels orchestrate the communication between cells and their environment. These are special proteins capable of changing their shape to allow ions to pass through membranes in response to stimuli like membrane tension. As the letters…
Reservoir computing (RC) is known as a powerful machine learning approach for learning complex dynamics from limited data. Here, we use RC to predict highly stochastic dynamics of cell shapes. We find that RC is able to predict the steady…
Chemo-mechanical waves on active deformable surfaces are a key component for many vital cellular functions. In particular, these waves play a major role in force generation and long-range signal transmission in cells that dynamically change…