Related papers: From proteins to grains: a journey through simple …
Inspired from human cognition, machine learning systems are gradually revealing advantages of sparser and more modular architectures. Recent work demonstrates that not only do some modular architectures generalize well, but they also lead…
We review a few representative examples of granular experiments or models where phase separation, accompanied by domain coarsening, is a relevant phenomenon. We first elucidate the intrinsic non-equilibrium, or athermal, nature of granular…
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex…
In this review we summarize theoretical progress in the field of active matter, placing it in the context of recent experiments. Our approach offers a unified framework for the mechanical and statistical properties of living matter:…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…
We study nucleation dynamics of Ising model in a topology that consists of two coupled random networks, thereby mimicking the modular structure observed in real-world networks. By introducing a variant of a recently developed forward flux…
Digestion in the small intestine is the result of complex mechanical and biological phenomena which can be modelled at different scales. In a previous article, we introduced a system of ordinary differential equations for describing the…
The objective of this work is the investigation of complexity, asymmetry, stochasticity and non-linearity of the financial and economic systems by using the tools of statistical mechanics and information theory. More precisely, this thesis…
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…
A key overall goal of biomolecular simulations is the characterization of "mechanism" -- the pathways through configuration space of processes such as conformational transitions and binding. Some amount of heterogeneity is intrinsic to the…
In this paper, we examine how to build coarse-grain transport models consistently from the kinetic to fluid regimes. The internal energy of the gas particles is described through a state-to-state approach. A kinetic equation allows us to…
Coarse graining techniques play an essential role in accelerating molecular simulations of systems with large length and time scales. Theoretically grounded bottom-up models are appealing due to their thermodynamic consistency with the…
Considering the flexibility and applicability of Bayesian modeling, in this work we revise the main characteristics of two hierarchical models in a regression setting. We study the full probabilistic structure of the models along with the…
We present a simple physical model that recapitulates several features of biological evolution, while being based only on thermally-driven attachment and detachment of elementary building blocks. Through its dynamics, this model samples a…
Granular intrusions, such as dynamic impact or wheel locomotion, are complex multiphase phenomena where the grains exhibit solid-like and fluid-like characteristics together with an ejected gas-like phase. Despite decades of modeling…
The two most commonly used methods to model the behaviour of granular flows are discrete element and continuum mechanics simulations. These approaches concentrate on the deterministic description of particle or bulk material motion. Unlike…
The global population increase leads to a high food demand, and to reach this target products such as pesticides are needed to protect the crops. Research is focusing on the development of new products that can be less harmful to the…
This essay provides a critical overview of the mathematical kinetic theory of active particles, which is used to model and study collective systems consisting of interacting living entities, such as those involved in behavior and evolution.…