Related papers: Cellular Griffiths-like phase
We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy…
Partitioning of (bio)materials in polymeric mixtures is a key phenomenon both in cellular environments, as well as in industrial applications. In cells, several macromolecules are suspended within different biomolecular phases. On the other…
Quantitative modeling of post-transcriptional regulation process is a challenging problem in systems biology. A mechanical model of the regulatory process needs to be able to describe the available spatio-temporal protein concentration and…
Over the last decade, a large variety of clustering algorithms have been developed to detect coregulatory relationships among genes from microarray gene expression data. Model based clustering approaches have emerged as statistically well…
Liquid-liquid phase separation is the mechanism underlying the formation of biomolecular condensates. Disordered protein regions often drive phase separation, but molecular interactions of disordered protein regions are not well understood,…
Phase separation of intrinsically disordered proteins is important for the formation of membraneless organelles, or biomolecular condensates, which play key roles in the regulation of biochemical processes within cells. In this work, we…
In this paper, we present a novel solution strategy for the Cahn-Hilliard-Biot model, a three-way coupled system that features the interplay of solid phase separation, fluid dynamics, and elastic deformations in porous media. It is a…
Recent analyses of multifragmentation in terms of Fisher's model and the related construction of a phase diagram brings forth the problem of the true existence of the vapor phase and the meaning of its associated pressure. Our analysis…
Much work has been devoted to analysing thermodynamic models for solid dispersions with a view to identifying regions in the phase diagram where amorphous phase separation or drug recrystallization can occur. However, detailed partial…
We study variants of hierarchical modular network models suggested by Kaiser and Hilgetag [Frontiers in Neuroinformatics, 4 (2010) 8] to model functional brain connectivity, using extensive simulations and quenched mean-field theory (QMF),…
A combination of cellular contractility and active phase separation in cell-matrix composites is thought to be an enabler of spatiotemporal patterning in multicellular tissues across scales, from somitogenesis to cartilage condensation. To…
Application of quantum principles to living cells requires a new approximation of the full quantum mechanical description of intracellular dynamics. We discuss what principal elements any such good approximation should contain. As one such…
Liquid liquid phase separation (LLPS) of proteins is an intracellular process that is widely used by cells for many purposes. In living cells (in vivo), LLPS occurs in complex and crowded environments. Amino acids (AAs) are vital components…
The Flory-Huggins theory describes the phase separation of solutions containing polymers. Although it finds widespread application from polymer physics to materials science to biology, the concentrations that coexist in separate phases at…
The study of protein mass transport via atomistic simulation requires time and length scales beyond the computational capabilities of modern computer systems. The raspberry model for colloidal particles in combination with the mesoscopic…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…
Glassy dynamics in a confluent monolayer is indispensable in morphogenesis, wound healing, bronchial asthma, and many others; a detailed theoretical framework for such a system is, therefore, important. Vertex model (VM) simulations have…
Optical imaging plays a critical role in advancing our understanding of three dimensional dynamics of biological systems. Coherent imaging (CI) methods exploit spatial phase information, encoded through propagation of coherent signal light…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
A prominent hypothesis in neuroscience proposes that brains achieve optimal performance by operating near a critical point. However, this framework, which often assumes a universal critical point, fails to account for the extensive…