Related papers: Bridging scales in a multiscale pattern-forming sy…

We analyze a spatially extended version of a well-known model of forest-savanna dynamics, which presents as a system of nonlinear partial integro-differential equations, and study necessary conditions for pattern-forming bifurcations.…

Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…

We present a data-driven machine-learning approach for modeling space-time socioeconomic dynamics. Through coarse-graining fine-scale observations, our modeling framework simplifies these complex systems to a set of tractable mechanistic…

The spatiotemporal oscillation patterns of the proteins MinD and MinE are used by the bacterium E. coli to sense its own geometry. Strikingly, both computer simulations and experiments have recently shown that for the same geometry of the…

Coarse-grained (CG) models provide an effective route to reducing the complexity of molecular simulations (MD), but conventional approaches depend heavily on long all-atom MD trajectories to adequately sample configurational space. This…

In this work, we apply phase field simulations to examine the coarsening behavior of morphologically complex two-phase microstructures in which the phases have highly dissimilar mobilities, a condition approaching that found in experimental…

Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…

This work explores the manner in which classical phase space distribution functions converge to the microcanonical distribution. We first prove a theorem about the lack of convergence, then define a generalization of the coarse-graining…

The formation and proliferation of protein aggregates play a central role in a number of devastating neuro-degenerative diseases. Many experimental studies indicate that the ability of existing aggregates to replicate is a key property in…

In general, many dynamic processes are involved with interacting variables, from physical systems to sociological analysis. The interplay of components in the system can give rise to confounding dynamic behavior. Many approaches model…

Realistic physical systems are characterised by emergent interactions across multiple length and time scales, posing a significant challenge for predictive machine learning (ML) models. Most scientific ML models focus on a narrow range of…

The theoretical understanding of pattern formation in active systems remains a central problem of interest. Heterogeneous flocks made up of multiple species can exhibit a remarkable diversity of collective states that cannot be obtained…

Grain microstructures are crucial to the mechanical properties, performance, and often lifetime of metallic components. Hence, the prediction of grain microstructures emerging from solidification processes at relevant macroscopic scale is…

It has recently been discovered that many biological systems, when represented as graphs, exhibit a scale-free topology. One such system is the set of structural relationships among protein domains. The scale-free nature of this and other…

Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…

Continuum models of dislocation plasticity require constitutive closure assumptions, e.g., by relating details of the dislocation microstructure to energy densities. Currently, there is no systematic way for deriving or extracting such…

We study the spatial patterns formed by a system of interacting particles where the mobility of any individual is determined by the population crowding at two different spatial scales. In this way we model the behavior of some biological…

This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential…

Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent…

To develop, calibrate and/or validate continuum models from experimental or numerical data, micro-macro transition methods are required. These methods are used to obtain the continuum fields (such as density, momentum, stress) from the…