生物物理
It is well established that gene expression can be modeled as a Markovian stochastic process and hence proper observables might be subjected to large fluctuations and rare events. Since dynamics is often more than statics, one can work with…
Bacteriorhodopsin (bR) is a light-driven proton pump. We use time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry…
The CRISPR (clustered regularly interspaced short palindromic repeats) mechanism allows bacteria to adaptively defend against phages by acquiring short genomic sequences (spacers) that target specific sequences in the viral genome. We…
Understanding the nanoscale structural changes can provide the physical state of cells/tissues. It has been now shown that increases in nanoscale structural alterations are associated with the progress of carcinogenesis in most of the…
Due to over-metabolism, the tumour cells become hypoxic. To overcome this situation tumour cells secret several chemical substrates to attract nearby blood vessels towards it (angiogenesis). Transition from avascular to vascular tumour is…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
In growing plant cells, parallel ordering of microtubules (MTs) along the inner surface of the cell membrane influences the direction of cell expansion and thereby plant morphology. For correct expansion of organs that primarily grow by…
The translocation of double-stranded DNA through a solid-state nanopore may either decrease or increase the ionic current depending on the ionic concentration of the surrounding solution. Below a certain crossover ionic concentration, the…
We analyse transcriptional bursting within a stochastic non-equilibrium model which accounts for the coupling between the dynamics of DNA supercoiling and gene transcription. We find a clear signature of bursty transcription when there is a…
The experimental characterisation of the swimming statistics of populations of microorganisms or artificially propelled particles is essential for understanding the physics of active systems and their exploitation. Here, we construct a…
Near a bifurcation point, the response time of a system is expected to diverge due to the phenomenon of critical slowing down. We investigate critical slowing down in well-mixed stochastic models of biochemical feedback by exploiting a…
The migration of cells is relevant for processes such as morphogenesis, wound healing, and invasion of cancer cells. In order to move, single cells deform cyclically. However, it is not understood how these shape oscillations influence…
Inside cells of living organisms, actin filaments and microtubules self-assemble and dissemble dynamically by incorporating actin or tubulin from the cell plasma or releasing it into their tips' surroundings. Such reaction-diffusion systems…
In biological settings membranes typically interact locally with other membranes or the extracellular matrix in the exterior, as well as with internal cellular structures such as the cytoskeleton. Characterization of the dynamic properties…
We propose an approach to analysing single trajectories of a particle, which moves randomly on a landscape distinct parts of which result in sufficiently various diffusion coefficients. The method based on the mapping the cumulative sum of…
The liver performs critical physiological functions, including metabolizing and removing substances, such as toxins and drugs, from the bloodstream. Hepatotoxicity itself is intimately linked to abnormal hepatic transport and hepatotoxicity…
Effective forces -- derived from experimental or {\it in silico} molecular dynamics time traces -- are critical in developing reduced and computationally efficient descriptions of otherwise complex dynamical problems. Thus, designing…
A biomimetic model of cell-cell communication was developed to probe the passive molecular transport across ion channels inserted in synthetic lipid bilayers formed between contacting droplets arranged in a linear array. Diffusion of a…
Abeta is a disordered peptide central to Alzheimer's Disease. Aggregation of Abeta has been widely explored, but its molecular crowding less so. The synaptic cleft where Abeta locates only holds 60-70 water molecules along its width. We…
We propose an image-based cellular contractile force evaluation method using a machine learning technique. We use a special substrate that exhibits wrinkles when cells grab the substrate and contract, and the wrinkles can be used to…