Biological Physics
Intact-organism imaging of Drosophila larvae reveals and quantifies chromatin-aqueous phase separation. The chromatin can be organized near the lamina layer of the nuclear envelope, conventionally fill the nucleus, be organized centrally,…
Adhesion interactions mediated by multiple bond types are relevant for many biological and soft matter systems, including the adhesion of biological cells and functionalized colloidal particles to various substrates. To elucidate advantages…
Optical coherence tomography offers astounding opportunities to image the complex structure of living tissue, but lacks functional information. We present dynamic full-field optical coherence tomography to image living human induced…
Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we perform polymer simulations, microscopy and mass spectrometry to dissect…
Using geometrical arguments it is shown that Cancer Stem Cells (CSC) must be confined inside solid tumors under natural situations. Aided by an agent-based model and percolation theory, the probability for a CSC to be at the border of a…
By embedding inert tracer particles (TPs) in a growing multicellular spheroid the local stresses on the cancer cells (CCs) can be measured. In order for this technique to be effective the unknown effect of the dynamics of the TPs on the CCs…
Lipid bilayer membranes are flexible thin laterally fluid films consisting of two unimolecular layers of lipids. On spatial scales much larger than the bilayer thickness, the membrane elasticity is well determined by its shape and…
Microbial communities feature an immense diversity of species and this diversity is linked with outcomes ranging from ecosystem stability to medical prognoses. Yet the mechanisms underlying microbial diversity are under debate. While simple…
This is an introduction to the special issue Genome organization: experiments and simulations, published in Chromosome Research, volume 25, issue 1 (2017).
Bacterial colonization ofimplanted biomedical devicesis themain cause of healthcare-associated infections, estimated to be 8.8 million per year in Europe. Many infections originate from damaged skin, which lets microorganisms exploit…
We found that the AYFFF self-assemblies in the chloride solution of some divalent cations ($Zn^{2+}, Mg^{2+},$ and $Cu^{2+}$) display super strong paramagnetism, which may approach the mass susceptibility of ferromagnetism. We attribute the…
We discuss a polymer model for the 3D organization of human chromosomes. A chromosome is represented by a string of beads, with each bead being "colored" according to 1D bioinformatic data (e.g., chromatin state, histone modification, GC…
Organismal phenotypes emerge from a complex set of genotypic interactions. While technological advances in sequencing provide a quantitative description of an organism's genotype, characterization of an organism's physical phenotype lags…
In the last fifteen years a debate emerged about the validity of the famous Hodgkin-Huxley model for nerve impulse. Mechanical models have been proposed. This note reviews the experimental properties of the nerve impulse and discusses the…
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…
Associative polymers with sticker-and-spacer architectures undergo phase transitions that combine phase separation and bond percolation. Here, we generalize mean-field models for bond percolation and extract effective sticker interaction…
We have earlier reported the iMOLSDOCK technique to perform induced-fit peptide-protein docking. iMOLSDOCK uses the mutually orthogonal Latin squares (MOLS) technique to sample the conformation and the docking pose of the small molecule…
The ability of biological and artificial collectives to outperform solitary individuals in a wide variety of tasks depends crucially on the efficient processing of social and environmental information at the level of the collective. Here,…
Tannery wastewater contains large amounts of pollutants that, if directly discharged into ecosystems, can generate an environmental hazard. The present investigation has focused the attention to the remediation of wastewater originated from…
Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and…