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We consider a heat conduction model introduced in \cite{Collet-Eckmann 2009}. This is an open system in which particles exchange momentum with a row of (fixed) scatterers. We assume simplified bath conditions throughout, and give a…
We introduce topological methods for quantifying spatially heterogeneous dynamics, and use these tools to analyze particle-tracking data for a quasi-two-dimensional granular system of air-fluidized beads on approach to jamming. In…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
Quantitative models of associative learning that explain the behavior of real animals with high precision have turned out very difficult to construct. We do this in the context of the dynamics of the thermal preference of C. elegans. For…
We introduce a simple model of active transport for an ensemble of particles driven by an external shear flow. Active refers to the fact that the flow of the particles is modified by the distribution of particles itself. The model consists…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
A complete thermodynamical analysis for a blood model, based on mixture theory, is performed. The model is developed considering the blood as a suspension of red blood cells (solid component) in the plasma (fluid component), and taking into…
Over times shorter than that required for relaxation of enthalpy, a liquid can exhibit striking heterogeneities. The picture of these heterogeneities is complex with transient patches of rigidity, irregular yet persistent, intersected by…
Stochastic Spatio-Temporal processes are prevalent across domains ranging from modeling of plasma to the turbulence in fluids to the wave function of quantum systems. This letter studies a measure-theoretic description of such systems by…
Tracking the behaviour of stochastic systems is a crucial task in the statistical sciences. It has recently been shown that quantum models can faithfully simulate such processes whilst retaining less information about the past behaviour of…
Theoretical approaches are formulated to investigate the molecular mobility under various cooling rates of amorphous drugs. We describe the structural relaxation of a tagged molecule as a coupled process of cage-scale dynamics and…
If the duration of the input pulse resonantly interacting with a system is comparable or smaller than the time required for the system to achieve the steady state, transient effects become important. For complex systems, a quantitative…
Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…
Many numerical studies of blood flow impose a rigid wall assumption due to the simplicity of its implementation compared to a full coupling to a solid mechanics model. In this paper, we present a localised method for incorporating the…
Type 2 diabetes progresses slowly and may be reversed through lifestyle changes, but quantifying the long-term impact of regular physical activity remains challenging due to sparse longitudinal data. Mechanistic models offer a powerful tool…
We find evidence for a continuum limit of a particular causal set dynamics which depends on only a single ``coupling constant'' $p$ and is easy to simulate on a computer. The model in question is a stochastic process that can also be…
We propose a new model based on the Ising model with the aim to study synaptic plasticity phenomena in neural networks. It is today well established in biology that the synapses or connections between certain types of neurons are…
In this article we discuss several aspects of the stochastic dynamics of spin models. The paper has two independent parts. Firstly, we explore a few properties of the multi-point correlations and responses of generic systems evolving in…
We introduce and analyze two general dynamical models for unidirectional movement of particles along a circular chain and an open chain of sites. The models include a soft version of the simple exclusion principle, that is, as the density…