Biological Physics
Chaperone-assisted translocation through a nanopore embedded in membrane holds a prominent role in the transport of biopolymers. Inspired by classical Brownian ratchet, we develop a theoretical framework characterizing such translocation…
Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed…
The response of microbes to external signals is mediated by biochemical networks with intrinsic time scales. These time scales give rise to a memory that impacts cellular behaviour. Here we study theoretically the role of cellular memory in…
The extra-cellular microenvironment has a fundamental role in tumor growth and progression, strongly affecting the migration strategies adopted by single cancer cells during metastatic invasion. In this study, we use a novel microfluidic…
The hydrodynamic drag at a lipid bilayer surface determines in part the flow properties of suspensions of cells and liposomes. Given the fluidity of lipid bilayers, it is not obvious a priori whether solid-like no-slip, liquid-like…
While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven…
Inspired by recent experiments on the effects of cytosolic crowders on the organization of bacterial chromosomes, we consider a "feather-boa" type model chromosome in the presence of non-additive crowders, encapsulated within a cylindrical…
The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which…
Multistable non-equilibrium systems are abundant outcomes of nonlinear dynamics with feedback but still relatively little is known about what determines the stability of the steady states and their switching rates in terms of entropy and…
We devise a method to detect and estimate forces in a heterogeneous environment based on experimentally recorded stochastic trajectories. In particular, we focus on systems modeled by the heterogeneous overdamped Langevin equation. Here,…
We present an analytic and numerical study of noise-assisted quantum exciton (electron) transfer (ET) in a bio-complex, consisting of an electron donor and acceptor (a dimer), modeled by interacting continuous electron bands of finite…
We demonstrate numerically that superradiance could play a significant role in nonphotochemical quenching (NPQ) in light-harvesting complexes. Our model consists of a network of five interconnected sites (discrete excitonic states) that are…
In analogy to the development of fluorescent proteins, innovative tools for screening optoacoustic cell labels could lead to tailored protein labels for OA, imparting novel ways to visualize biological structure and function. Optoacoustic…
Lipid rafts are heterogeneous dynamic lipid domains of the cell membranes that are involved in several biological processes, like protein and lipids specific transport and signaling. Our understanding of lipid raft formation is still…
Key to collective cell migration is the ability of cells to rearrange their position with respect to their neighbors. Recent theory and experiments demonstrated that cellular rearrangements are facilitated by cell shape, with cells having…
We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
Outer hair cells in the inner ear is important for the sensitivity, frequency selectivity, and dynamic range of the mammalian ear. Such a physiological role of outer hair cells is thought to be based an amplifying effect of those cells,…
Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients…
A model of coupled molecular oscillators is proposed to study nonequilibrium thermodynamics of synchronization. We find that synchronization of nonequilibrium oscillators costs energy even when the oscillator-oscillator coupling is…
For a first principles understanding of macromolecular processes, a quantitative understanding of the underlying free energy landscape and in particular its entropy contribution is crucial. The stability of biomolecules, such as proteins,…