Related papers: Stochastic Dynamics of Bionanosystems: Multiscale …

We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…

In standard treatments of open quantum systems, the reduced dynamics is described starting from the assumption that the system and the environment are initially uncorrelated. This assumption, however, is not always guaranteed in realistic…

The intricate process of bubble growth dynamics involves a broad spectrum of physical phenomena from microscale mechanics of bubble formation to macroscale interplay between bubbles and surrounding thermo-hydrodynamics. Traditional bubble…

We introduce a modified molecular dynamics algorithm that allows one to freeze the dynamics of parts of a physical system, and thus concentrate the simulation effort on selected, central degrees of freedom. This freezing, in contrast to…

Macroscopic dynamical descriptions of complex physical systems are crucial for understanding and controlling material behavior. With the growing availability of data and compute, machine learning has become a promising alternative to…

We develop a novel method to analyze the dynamics of stochastic rewriting systems evolving over finitary adhesive, extensive categories. Our formalism is based on the so-called rule algebra framework and exhibits an intimate relationship…

Dynamical systems theory provides powerful methods to extract effective macroscopic dynamics from complex systems with slow modes and fast modes. Here we derive and theoretically support a macroscopic, spatially discrete, model for a class…

Molecular dynamics is based on solving Newton's equations for many-particle systems that evolve along complex, highly fluctuating trajectories. The orbital instability and short-time complexity of Newtonian orbits is in sharp contrast to…

The state of many physical, biological and socio-technical systems evolves by combining smooth local transitions and abrupt resetting events to a set of reference values. The inclusion of the resetting mechanism not only provides the…

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.…

In the infectious disease literature, significant effort has been devoted to studying dynamics at a single scale. For example, compartmental models describing population-level dynamics are often formulated using differential equations. In…

Stochastic evolution underpins several approaches to the dynamics of open quantum systems, such as random modulation of Hamiltonian parameters, the stochastic Schrodinger equation (SSE), and the stochastic Liouville equation (SLE). These…

An approach is suggested for treating multiscale fluctuations in macromolecular systems. The emphasis is on the statistical properties of such fluctuations. The approach is illustrated by a macromolecular system with mesoscopic fluctuations…

Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…

Inference on unknown quantities in dynamical systems via observational data is essential for providing meaningful insight, furnishing accurate predictions, enabling robust control, and establishing appropriate designs for future…

In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of…

The modeling of atomistic biomolecular simulations using kinetic models such as Markov state models (MSMs) has had many notable algorithmic advances in recent years. The variational principle has opened the door for a nearly fully automated…

To directly simulate rare events using atomistic molecular dynamics is a significant challenge in computational biophysics. Well-established enhanced-sampling techniques do exist to obtain the thermodynamic functions for such systems. But…

Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…

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…