Related papers: Arbitrarily accurate, nonparametric coarse grainin…
Data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a…
Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or…
Multiscale systems are ubiquitous in science and technology, but are notoriously challenging to simulate as short spatiotemporal scales must be appropriately linked to emergent bulk physics. When expensive high-dimensional dynamical systems…
The emergence of macroscopic variables can be effected through {\it coarse graining}. Despite practical and fundamental benefits conveyed by this partitioning of state space, the apparently subjective nature of the selection of coarse…
We introduce Coarse-Grained Nonlinear Dynamics, an efficient and universal parameterization of nonlinear system dynamics based on the Volterra series expansion. These models require a number of parameters only quasilinear in the system's…
Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…
We demonstrate how the dynamical coarse-graining approach can be systematically extended to higher orders in the coupling between system and reservoir. Up to second order in the coupling constant we explicitly show that dynamical…
We introduce a generalized machine learning framework to probabilistically parameterize upper-scale models in the form of nonlinear PDEs consistent with a continuum theory, based on coarse-grained atomistic simulation data of mechanical…
The classic studies of causal emergence have revealed that in some Markovian dynamical systems, far stronger causal connections can be found on the higher-level descriptions than the lower-level of the same systems if we coarse-grain the…
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…
To study materials phenomena simultaneously at various length scales, descriptions in which matter can be coarse grained to arbitrary levels, are necessary. Attempts to do this in the static regime (i.e. zero temperature) have already been…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a…
Dynamical systems with large state-spaces are often expensive to thoroughly explore experimentally. Coarse-graining methods aim to define simpler systems which are more amenable to analysis and exploration; most current methods, however,…
In typical single-molecule force spectroscopy experiments the mechanical unfolding of molecular complexes or biomolecules is studied applying a force ramp to one end of the system while the other end is kept fixed in space. The…
Many physical systems are described by nonlinear differential equations that are too complicated to solve in full. A natural way to proceed is to divide the variables into those that are of direct interest and those that are not, formulate…
We formulate thermodynamically consistent coarse-graining procedures for molecular systems undergoing thermally and photo-induced transitions: starting from elementary vibronic transitions, we derive effective photo-isomerization reactions…
One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise…
Coarse-grained (CG) molecular dynamics (MD) simulations can simulate large molecular complexes over extended timescales by reducing degrees of freedom. A critical step in CG modeling is the selection of the CG mapping algorithm, which…
We propose an efficient Markov Chain Monte Carlo method for sampling equilibrium distributions for stochastic lattice models, capable of handling correctly long and short-range particle interactions. The proposed method is a Metropolis-type…