Related papers: Cellular Griffiths-like phase
In the past few decades, the development of fluorescent technologies and microscopic techniques has greatly improved scientists' ability to observe real-time single-cell activities. In this paper, we consider the filtering problem associate…
In the effort to aid cytologic diagnostics by establishing automatic single cell screening using high throughput digital holographic microscopy for clinical studies thousands of images and millions of cells are captured. The bottleneck lies…
A theory for sequence dependent liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) in the study of biomolecular condensates is formulated by extending the random phase approximation (RPA) and field-theoretic…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
Modeling stochasticity in gene regulatory networks is an important and complex problem in molecular systems biology. To elucidate intrinsic noise, several modeling strategies such as the Gillespie algorithm have been used successfully. This…
Clustering is a popular data mining technique that aims to partition an input space into multiple homogeneous regions. There exist several clustering algorithms in the literature. The performance of a clustering algorithm depends on its…
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
Asymmetric segregation of key proteins at cell division -- be it a beneficial or deleterious protein -- is ubiquitous in unicellular organisms and often considered as an evolved trait to increase fitness in a stressed environment. Here, we…
Multiple biological processes are driven by oscillatory gene expression at different time scales. Pulsatile dynamics are thought to be widespread, and single-cell live imaging of gene expression has lead to a surge of dynamic, possibly…
We propose an exactly solvable self-consistent kinetic model of polymerization-induced phase separation (PIPS) via spinodal decomposition. Using modified Cahn-Hilliard and Glotzer-Coniglio theories for early and late stages of spinodal…
We propose a comprehensive dynamical model for cooperative motion of self-propelled particles, e.g., flocking, by combining well-known elements such as velocity-alignment interactions, spatial interactions, and angular noise into a unified…
The application of an external field often renders empirical criteria for identifying liquid-gas phase transitions ambiguous. Here, we demonstrate that the finite-size scaling of the density profile provides a definitive criterion to…
The fundamental aim of clustering algorithms is to partition data points. We consider tasks where the discovered partition is allowed to vary with some covariate such as space or time. One approach would be to use fragmentation-coagulation…
The regulatory process of Drosophila is thoroughly studied for understanding a great variety of biological principles. While pattern-forming gene networks are analysed in the transcription step, post-transcriptional events (e.g.…
Liquid-liquid phase separation (LLPS) is currently of great interest in cell biology. LLPS is an example of what is called an emergent phenomenon -- an idea that comes from condensed-matter physics. Emergent phenomena have the…
Physical mechanisms of phase separation in living systems can play key physiological roles and have recently been the focus of intensive studies. The strongly heterogeneous and disordered nature of such phenomena in the biological domain…
Coherent ptychographic imaging experiments often discard over 99.9 % of the flux from a light source to define the coherence of an illumination. Even when coherent flux is sufficient, the stability required during an exposure is another…
The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide…
I present a new approach to recover the primordial density fluctuations and the cosmic web structure underlying a galaxy distribution. The method is based on sampling Gaussian fields which are compatible with a galaxy distribution and a…