Related papers: Reverse Coarse-graining for Equation-free Modeling…
The quantum-to-classical transition of a quantum state is a topic of great interest in fundamental and practical aspects. A coarse-graining in quantum measurement has recently been suggested as its possible account in addition to the usual…
We show how the Equation-Free approach for multi-scale computations can be exploited to systematically study the dynamics of neural interactions on a random regular connected graph under a pairwise representation perspective. Using an…
Thermodynamic irreversibility is a fundamental concept in statistical physics, yet its experimental measurement remains challenging, especially for complex systems. We introduce a novel random coarse-graining framework to identify…
Molecular simulations have assumed a paramount role in the fields of chemistry, biology, and material sciences, being able to capture the intricate dynamic properties of systems. Within this realm, coarse-grained (CG) techniques have…
With the birth of quantum information science, many tools have been developed to deal with many-body quantum systems. Although a complete description of such systems is desirable, it will not always be possible to achieve this goal, as the…
We investigate two different types of non-Markovian coarse-grained models extracted from a linear, non-equilibrium microscopic system, featuring a tagged particle coupled to underdamped oscillators. The first model is obtained by…
While existing mathematical descriptions can accurately account for phenomena at microscopic scales (e.g. molecular dynamics), these are often high-dimensional, stochastic and their applicability over macroscopic time scales of physical…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
A coarse-grained water model is developed using multistate iterative Boltzmann inversion. Following previous work, the k-means algorithm is used to dynamically map multiple water molecules to a single coarse-grained bead, allowing the use…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
Understanding the emergence of macroscopic irreversible hydrodynamics from the reversible unitary dynamics of isolated quantum many-body systems remains a fundamental challenge. Conventional approaches often force spin density dynamics into…
We introduce a mesoscopic partition function for classical many-body systems based on a combined spatial and phase-space coarse-graining, replacing the canonical phase-space integral with a discrete sum over occupation numbers. 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…
The contemporary scientific landscape is characterized by a "curse of dimensionality," where our capacity to collect high-dimensional network data frequently outstrips our ability to computationally simulate or intuitively comprehend the…
Variational quantum algorithms (VQAs) are increasingly being applied in simulations of strongly-bound (covalently bonded) systems using full molecular orbital basis representations. The application of quantum computers to the weakly-bound…
The structure of polyelectrolytes is highly sensitive to small changes in the interactions between its monomers. In particular, interactions mediated by counterions play a significant role, and are affected by both specific molecular…
Markov state models (MSMs)---or discrete-time master equation models---are a powerful way of modeling the structure and function of molecular systems like proteins. Unfortunately, MSMs with sufficiently many states to make a quantitative…
We present an extension to the iterative Boltzmann inversion method to generate coarse-grained models with three-body intramolecular potentials that can reproduce correlations in structural distribution functions. The coarse-grained…
With the guidance offered by nonequilibrium statistical thermodynamics, simulation techniques are elevated from brute-force computer experiments to systematic tools for extracting complete, redundancy-free and consistent coarse grained…
A continuum model for the phase separation and coarsening, observed in electrostatically driven granular media, is formulated in terms of a Ginzburg-Landau equation subject to conservation of the total number of grains. In the regime of…