Related papers: Dimensionality reduction in bulk-boundary reaction…
Cell polarity and movement are fundamental to many biological functions. Experimental and theoretically studies have indicated that interactions of certain proteins lead to the cell polarization which plays a key role in controlling the…
The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been…
After the recent ground-breaking advances in protein structure prediction, one of the remaining challenges in protein machine learning is to reliably predict distributions of structural states. Parametric models of fluctuations are…
Mechanochemical patterns arising in the actomyosin cortex drive many cellular processes. Here we consider a hydrodynamic model for the actomyosin cortex of cells and study the sensitivity of the emergent patterns to both physical parameters…
For cellular functions like division and polarization, protein pattern formation driven by NTPase cycles is a central spatial control strategy. Operating far from equilibrium, no general theory links microscopic reaction networks and…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…
We introduce a simplified technique for incorporating diffusive phenomena into lattice-gas molecular dynamics models. In this method, spatial interactions take place one dimension at a time, with a separate fractional timestep devoted to…
A number of factors, such as, cell-cell interactions and self-propulsion of cells driven by cytoskeletal forces determine tissue morphologies and dynamics. To explore the interplay between these factors in controlling the dynamics at the…
Soft interfaces formed by lipid membranes are fundamental to living cells, synthetic cells, and membrane-based soft materials. However, a quantitative framework linking molecular organization with nonlinear interfacial mechanics remains…
Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations…
Cellular structures must organize themselves within strict physical constraints, operating with finite resources and well-defined boundaries. Classical systems demonstrate only passive responses to boundaries, from surface energy…
This paper proposes a control theoretic framework to model and analyze the self-organized pattern formation of molecular concentrations in biomolecular communication networks, emerging applications in synthetic biology. In biomolecular…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
For the first time the phenomenon of cellular structure coarsening are consistently analysed from the positions of kinetic, hydrodynamic and stochastodynamic theories of nonequilibrium statistical systems. Thereby micro-, meso- and…
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…
Dimension reduction is a common strategy to study non-linear dynamical systems composed by a large number of variables. The goal is to find a smaller version of the system whose time evolution is easier to predict while preserving some of…
The emergence of spatial patterns and organized growth is a hallmark of developing tissues. While symmetry-breaking and scaling laws govern these processes, how cells coordinate spatial patterning with size regulation remains unclear. Here,…
There has been an increasing recognition of the utility of models of the spatial dynamics of viral spread within tissues. Multicellular models, where cells are represented as discrete regions of space coupled to a virus density surface, are…
Complex dynamical systems are prevalent in various domains, but their analysis and prediction are hindered by their high dimensionality and nonlinearity. Dimensionality reduction techniques can simplify the system dynamics by reducing the…