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Cell-cell adhesion plays a vital role in the development and maintenance of multicellular organisms. One of its functions is regulation of cell migration, such as occurs, e.g. during embryogenesis or in cancer. In this work, we develop a…
Novel techniques are presented, which identify the power-counting regime (PCR) of chiral effective field theory, and allow the use of lattice quantum chromodynamics results that extend outside the PCR. By analyzing the renormalization of…
We propose that the degree of sweeling of the 30nm chromatin fiber (a "measure" of its transcriptional activity) is mainly determined by the short-ranged electrostatical interaction between different sections of the "folded" DNA chain.…
We propose a continuum model for the theoretical study of hybridized moir\'e excitons in transition metal dichalcogenides heterobilayers, and we use a variational method to solve the exciton wavefunction and calculate the optical absorption…
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…
In this work we propose a physical model of organismal evolution, where phenotype, organism life expectancy, is directly related to genotype i.e. the stability of its proteins which can be determined exactly in the model. Simulating the…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…
Living tissue is able to withstand large stresses in everyday life, yet it also actively adapts to dynamic loads. This remarkable mechanical behaviour emerges from the interplay between living cells and their non-living extracellular…
Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as…
Cell crawling requires the generation of intracellular forces by the cytoskeleton and their transmission to an extracellular substrate through specific adhesion molecules. Crawling cells show many features of excitable systems, such as…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
DNA methylation is a primary layer of epigenetic modification that plays a pivotal role in the regulation of development, aging, and cancer. The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives…
Many practical approximations in physics and engineering invoke a relatively long physical domain with a relatively thin cross-section. In this scenario we typically expect the system to have structures that vary slowly in the long…
Growth-fragmentation processes describe the evolution of systems of cells which grow continuously and fragment suddenly; they are used in models of cell division and protein polymerisation. Typically, we may expect that in the long run, the…
While chiral perturbation theory for mesons is characterized by a momentum expansion in $Q/\Lambda_\chi$ with $\Lambda_\chi \sim 1$ GeV, existing formulations of effective theory for nucleon-nucleon scattering deviate from data at $Q\sim…
Myosin motor proteins drive vigorous steady-state fluctuations in the actin cytoskeleton of cells. Endogenous embedded semiflexible filaments such as microtubules, or added filaments such as single-walled carbon nanotubes are used as novel…
Most models of biological pattern formation are simulated on continuous domains even though cells are discrete objects that provide internal boundaries to the diffusion of regulatory components. In our previous papers on simulating…