Biological Physics
The molecular motion in heterogeneous media displays anomalous diffusion by the mean-squared displacement $\langle X^2(t) \rangle = 2 D t^\alpha$. Motivated by experiments reporting populations of the anomalous diffusion parameters $\alpha$…
Biological systems are remarkably susceptible to relatively small temperature changes. The most obvious example is fever, when a modest rise in body temperature of only few Kelvin has strong effects on our immune system and how it fights…
Adopting a $300 \, \mu$s-long molecular dynamics (MD) trajectory of the reversible folding of villin headpiece (HP35) published by D. E. Shaw Research, we recently constructed a Markov state model (MSM) of the folding process based on…
Biophotons are non-thermal and non-bioluminescent ultraweak photon emissions, first hypothesised by Gurwitsch in 1924 as a regulatory mechanism in cell division, and then experimentally observed in living organisms. Today, two main…
Bacterial genomes are partitioned into kilobases long domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbours. This is made possible by proteins…
The importance of spin-correlated radical pairs in biology is increasingly recognized, with roles in biological effects of weak magnetic fields and emerging quantum spin-based biomedical applications. Fluorescence microscopy offers…
An interacting pair of chemotactic (anti-chemotactic) active colloids, that can rotate their axes of self-propulsion to align {parallel (anti-parallel)} to a chemical gradient, shows dynamical behaviour that varies from bound states to…
The development of multicellular organisms entails a deep connection between time-dependent biochemical processes taking place at the subcellular level, and the resulting macroscopic phenotypes that arise in populations of up to trillions…
We investigate the possibility of usage of the parametric X-ray radiation (PXR) for the selective therapy of superficial sulfur-containing tumor tissues. In these tissues, the concentration of sulfur atoms is significantly higher than in…
Existing research has yet to reach a consensus on whether and how small flying animals utilize elastic energy storage mechanisms to reduce flight energy expenditure, and there is a lack of systematic and universal methods for assessment. To…
Analysing biological spiking neural network models with synaptic plasticity has proven to be challenging both theoretically and numerically. In a network with N all-to-all connected neurons, the number of synaptic connections is on the…
Genetic engineering of cells has a range of applications in treating incurable diseases. Plasmid DNA is a popular choice of nucleic acid for cell engineering due to its low cost and stability. However, plasmid DNA must survive the…
We report in situ single-molecule measurements of proton-induced double-strand breaks (DSBs) in DNA immersed in water, using real-time fluorescence tracking along the entire proton path, including the Bragg peak region. By chemically…
We present a topology grounded, multiscale simulation platform for morphogenesis and biological active matter. Morphogenesis and biological active matter represent keystone problems in biology with additional, far-reaching implications…
Motility-induced phase separation (MIPS) is a paradigmatic non-equilibrium transition in active matter, determined by the P\'eclet number and packing fraction. We investigate the single-phase and phase-separated regimes of MIPS using a…
Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…
Organisms that locomote by propagating waves of body bending can maintain performance across heterogeneous environments by modifying their gait frequency $\omega$ or wavenumber $k$. We identify a unifying relationship between these…
The brain's connectome and the vascular system are examples of physical networks whose tangible nature influences their structure, layout, and ultimately their function. The material resources required to build and maintain these networks…
During the melting transition of dimyristoyl phosphatidylglycerol (DMPG), the order of the lipid chains and the three-dimensional, vesicular structural arrangement change simultaneously. These changes result in peculiar heat capacity…
We demonstrate that internal pivot-like defects, arising from rigor mutant motor proteins that bind without stepping, fundamentally reshape the dynamics of semiflexible filaments in two-dimensional motility assays. Using large-scale…