Related papers: Reverse Coarse-graining for Equation-free Modeling…

We derive a mesoscopic modeling and simulation technique that is very close to the technique known as dissipative particle dynamics. The model is derived from molecular dynamics by means of a systematic coarse-graining procedure. Thus the…

Data-driven reduced-order models often fail to make accurate forecasts of high-dimensional nonlinear dynamical systems that are sensitive along coordinates with low-variance because such coordinates are often truncated, e.g., by proper…

We present an equation-free dynamic renormalization approach to the computational study of coarse-grained, self-similar dynamic behavior in multidimensional particle systems. The approach is aimed at problems for which evolution equations…

Coarse-grained molecular models of proteins permit access to length and time scales unattainable by all-atom models and the simulation of processes that occur on long-time scales such as aggregation and folding. The reduced resolution…

Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…

We present a novel learning framework that consistently embeds underlying physics while bypassing a significant drawback of most modern, data-driven coarse-grained approaches in the context of molecular dynamics (MD), i.e., the availability…

Semi-analytical methods, based on Eulerian perturbation theory, are a promising tool to follow the time evolution of cosmological perturbations at small redshifts and at mildly nonlinear scales. All these schemes are based on two…

Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…

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…

Formulating the QFT's as coarse grained 'low' energy sectors of a postulated complete quantum theory of everything with the 'high' energy modes integrated out or 'clustering' into 'low' energy objects, we can evaluate the Feynman amplitudes…

The extent to which quantum computers can simulate physical phenomena and solve the partial differential equations (PDEs) that govern them remains a central open question. In this work, one of the most fundamental PDEs is addressed: the…

Results are presented from numerical experiments aiming at the computation of stochastic phase-field models for phase transformations by coarse-graining molecular dynamics. The studied phase transformations occur between a solid crystal and…

We have proposed an efficient parameterization method for a recent variant of the Gay-Berne potential for dissimilar and biaxial particles and demonstrated it for a set of small organic molecules. Compared to the previously proposed…

Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…

Conjugated organic molecules play a central role in a wide range of optoelectronic devices, including organic light-emitting diodes, organic field-effect transistors, and organic solar cells. A major bottleneck in the computational design…

We present a loss function for neural networks that encompasses an idea of trivial versus non-trivial predictions, such that the network jointly determines its own prediction goals and learns to satisfy them. This permits the network to…

I briefly review some concepts related to coarse-graining methods for the dynamics of soft matter systems and argue that such schemes will almost always need to telescope down the physical hierarchy of time-scales to a more compressed, but…

Coarse-grained (CG) models parameterized using atomistic reference data, i.e., 'bottom up' CG models, have proven useful in the study of biomolecules and other soft matter. However, the construction of highly accurate, low resolution CG…

Difficult, in particular NP-complete, optimization problems are traditionally solved approximately using search heuristics. These are usually slowed down by the rugged landscapes encountered, because local minima arrest the search process.…

Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to…