Biological Physics
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop…
Aging, as defined in terms of the slope of the probability of death versus time (hazard curve), is a generic phenomenon observed in nearly all complex systems. Theoretical models of aging predict hazard curves that monotonically increase in…
A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and…
A wide array of biological systems can navigate in shallow gradients of chemoattractant with remarkable precision. Whilst previous approaches model such systems using coarse-grained chemical density profiles, we construct a dynamical model…
Nanopore-based sensing platforms have transformed single-molecule detection and analysis. The foundation of nanopore translocation experiments lies in conductance measurements, yet existing models, which are largely phenomenological, are…
We propose a polymer model for the dynamics of chromatin replication in three dimensional space. Our simulations indicate that both immobile and tracking replisomes may self-assemble during the process, reconciling previous apparently…
The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can…
Recent experimental studies suggest that wet-dry cycles and coexisting phases can each strongly alter chemical processes. The mechanisms of why and to which degree chemical processes are altered when subject to evaporation and condensation…
Self-assembly is a key process in living systems - from the microscopic biological level (e.g. assembly of proteins into fibrils within biomolecular condensates in a human cell) through to the macroscopic societal level (e.g. assembly of…
Biological active matter is typically tightly coupled to chemical reaction networks affecting its assembly-disassembly dynamics and stress generation. We show that localized states can emerge spontaneously if assembly of active matter is…
Rapid mapping of the mechanical properties of soft biological tissues from light microscopy to macroscopic imaging could transform fundamental biophysical research by providing clinical biomarkers to complement in vivo elastography. We here…
Heterogeneous mechanical dyskinesis during acute myocardial ischaemia is thought to contribute to arrhythmogenic alterations to cardiac electrophysiology. Various forms of mechano-electric coupling (MEC) mechanisms have been suggested to…
Osteoarthritis (OA) is a widespread, debilitating joint disease associated with articular cartilage degradation. It is driven via mechano-inflammatory catabolic pathways, presumed up-regulated due to increased shear stress on the…
Collective cell motions underlie structure formation during embryonic development. Tissues exhibit emergent multicellular characteristics such as jamming, rigidity transitions, and glassy dynamics, but there remain questions about how those…
Weak magnetic field exposure can affect many biological processes across a wide range of living organisms. Recently, it has been observed that weak magnetic fields can modulate reactive oxygen species (ROS) concentration, affecting…
In cystic fibrosis (CF), impaired mucociliary clearance leads to chronic infection and inflammation. However, cilia beating features in a CF altered environment, consisting of dehydrated airway surface liquid layer and abnormal mucus, has…
Due to the potential applications in biomedical engineering, it becomes more and more important to understand the process of engulfment and internalization of nanoparticles (NPs) by cell membranes. Despite the fact that the interaction…
Patterns in ecological systems such as mussel beds have been of considerable interest for a long time. Several physicochemical mechanisms have been proposed for their formation. Here, we propose a novel framework based on economics and game…
Our evolving understanding of the heterocellular cardiac environment demands innovative tools for its study. While murine models are lauded for their versatility and accessibility, they are constrained by scale; tools designed for larger…