Related papers: Cellular Griffiths-like phase
We propose a novel method to reconstruct phase dynamics equations from responses in macroscopic variables to weak inputs. Developing linear and nonlinear response theories in coupled phase-oscillators, we derive formulae which connect the…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…
Coarse-grained (CG) models play a crucial role in the study of protein structures, protein thermodynamic properties, and protein conformation dynamics. Due to the information loss in the coarse-graining process, backmapping from CG to…
We present a new and easy-to-implement sequential sampling method for CGMY processes with either finite or infinite variation, exploiting the time change representation of the CGMY model and a decomposition of its time change. We find that…
We present results from Langevin dynamics simulations of a glassy active-passive mixture of soft-repulsive binary colloidal disks. Activity on the smaller particles is applied according to the quorum sensing scheme, in which a smaller…
Gaussian processes (GPs) are pervasive in functional data analysis, machine learning, and spatial statistics for modeling complex dependencies. Modern scientific data sets are typically heterogeneous and often contain multiple known…
We introduce a Bayesian Gaussian process latent variable model that explicitly captures spatial correlations in data using a parameterized spatial kernel and leveraging structure-exploiting algebra on the model covariance matrices for…
A particle method for reproducing the phase space of collisionless stellar systems is described. The key idea originates in Liouville's theorem which states that the distribution function (DF) at time t can be derived from tracing necessary…
Many physical and biological systems rely on the progression of material through multiple independent stages. In viral replication, for example, virions enter a cell to undergo a complex process comprising several disparate stages before…
We use machine learning methods for an automated classification of experimental XPCS two-time correlation functions from an arrested liquid-liquid phase separation of a protein solution. We couple simulations based on the Cahn-Hilliard…
A simple model for functionalized disordered porous media is proposed and the effects of confinement on self-association, percolation and phase behavior of a fluid of patchy particles are studied. The media is formed by a randomly…
We study a one-dimensional model of microtubule assembly/disassembly in which GTP bound to tubulins within the microtubule undergoes stochastic hydrolysis. In contrast to models that only consider a cap of GTP-bound tubulin, stochastic…
Self-propelled particles that are subject to noise are a well-established generic model system for active matter. A homogeneous alignment field can be used to orient the direction of the self-propulsion velocity and to model systems like…
This paper proposes a physically consistent Gaussian Process (GP) enabling the identification of uncertain Lagrangian systems. The function space is tailored according to the energy components of the Lagrangian and the differential equation…
We consider the systematic numerical approximation of Biot's quasistatic model for the consolidation of a poroelastic medium. Various discretization schemes have been analysed for this problem and inf-sup stable finite elements have been…
Compartmentalization of self-replicating molecules (templates) in protocells is a necessary step towards the evolution of modern cells. However, coexistence between distinct template types inside a protocell can be achieved only if there is…
A physical scenario accounting for the existence of size-limited submicrometric domains in cell membranes is proposed. It is based on the numerical investigation of the counterpart, in lipidic membranes where proteins are diffusing, of the…
We model the spatiotemporal dynamics of cellular protein concentrations near membranes composed of different lipids using a three-variable continuum model for membrane-bound protein, cytosolic protein, and the local composition of a binary…
Several cellular activities, such as directed cell migration, are coordinated by an intricate network of biochemical reactions which lead to a polarised state of the cell, in which cellular symmetry is broken, causing the cell to have a…