Related papers: Cellular Griffiths-like phase
A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…
Gaussian processes (GPs) offer a flexible, uncertainty-aware framework for modeling complex signals, but scale cubically with data, assume static targets, and are brittle to outliers, limiting their applicability in large-scale problems…
Our report paves the way for insight into a structural disorder and its impact on the physical properties of strongly correlated electron systems (SCESs). In a critical regime, each perturbation, e.g., disorder due to structural defects or…
Understanding how fluctuations propagate across spatial scales is central to our understanding of inanimate matter from turbulence to critical phenomena. In contrast to physical systems, biological systems are organized into a hierarchy of…
The stochastic simulation algorithm commonly known as Gillespie's algorithm is now used ubiquitously in the modelling of biological processes in which stochastic effects play an important role. In well-mixed scenarios at the sub-cellular…
Temporal coherence-persistent alignment across time-can arise between agents with fundamentally distinct dynamics, a behavior that classical diffusion models (e.g., Brownian motion, fractional Brownian motion, generalized Langevin equation)…
Forced granular matter in confined geometries presents phase transitions and coexistence. Depending on the system and forcing parameters, liquid-vapor and liquid-solid co-existing states are possible. For the solid-liquid coexistence that…
In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to…
We introduce a scalable approach to Gaussian process inference that combines spatio-temporal filtering with natural gradient variational inference, resulting in a non-conjugate GP method for multivariate data that scales linearly with…
Partitioned cellular automata are known to be an useful tool to simulate linear and nonlinear problems in physics, specially because they allow for a straightforward way to define conserved quantities and reversible dynamics. Here we show…
The dilute fluid phase of model globular proteins is studied. The model possesses a fluid-fluid transition buried within the fluid-crystal coexistence region, as do some globular proteins. If this fluid-fluid transition is not buried deep…
Rhythmic activity commonly observed in biological systems, occurring from the cellular level to the organismic level, is typically modeled as limit cycle oscillators. Phase reduction theory serves as a useful analytical framework for…
Fluorescence spectroscopy is an image correlation technique to analyze and characterize the molecular dynamics from a sequence of fluorescence images. Many image correlation techniques have been developed for different applications [1]. But…
We theoretically study mixtures of chemically-interacting particles, which produce or consume a chemical to which they are attracted or repelled, in the most general case of many coexisting species. We find a new class of active phase…
The observation of Liquid-Liquid Phase Separation (LLPS) in biological cells has dramatically shifted the paradigm that soluble proteins are uniformly dispersed in the cytoplasm or nucleoplasm. The LLPS region is preceded by a one-phase…
An idea to analyze the fluctuational mode or/and spectrum of water molecules in an inhomogeneous environment around a biomolecule such as protein and DNA is proposed based on the generalized Langevin equation (GLE) for water interacting…
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…
Phase separation, crucial for spatially segregating biomolecules in cells, is well-understood in the simple case of a few components with pairwise interactions. Yet, biological cells challenge the simple picture in at least two ways: First,…
Visual segmentation is a key perceptual function that partitions visual space and allows for detection, recognition and discrimination of objects in complex environments. The processes underlying human segmentation of natural images are…
Mixtures of glass-forming fluids sometimes exhibit glass-glass phase separation at low temperatures. Here, we use a molecular dynamics simulation to study one of the simplest examples of the glass-glass phase separation. We consider a…