Crystal nucleation in liquids: Open questions and future challenges in molecular dynamics simulations

GC Sosso, J Chen, SJ Cox, M Fitzner… - Chemical …, 2016 - ACS Publications
The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing
an important role in areas such as climate change and the production of drugs. As the early …

Colloidal hard spheres: Triumphs, challenges, and mysteries

CP Royall, P Charbonneau, M Dijkstra, J Russo… - Reviews of Modern …, 2024 - APS
The simplicity of hard spheres as a model system is deceptive. Although the particles
interact solely through volume exclusion, that nevertheless suffices for a wealth of static and …

Adaptive Monte Carlo augmented with normalizing flows

M Gabrié, GM Rotskoff… - Proceedings of the …, 2022 - National Acad Sciences
Many problems in the physical sciences, machine learning, and statistical inference
necessitate sampling from a high-dimensional, multimodal probability distribution. Markov …

On the biophysics and kinetics of toehold-mediated DNA strand displacement

N Srinivas, TE Ouldridge, P Šulc… - Nucleic acids …, 2013 - academic.oup.com
Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for
controlling reaction kinetics. Although the dependence of strand displacement kinetics on …

From metadynamics to dynamics

P Tiwary, M Parrinello - Physical review letters, 2013 - APS
Metadynamics is a commonly used and successful enhanced sampling method. By the
introduction of a history dependent bias which depends on a restricted number of collective …

Progress in accurate chemical kinetic modeling, simulations, and parameter estimation for heterogeneous catalysis

S Matera, WF Schneider, A Heyden, A Savara - Acs Catalysis, 2019 - ACS Publications
Chemical kinetic modeling in heterogeneous catalysis is advancing in its ability to provide
qualitatively or even quantitatively accurate prediction of real-world behavior because of …

Molecular enhanced sampling with autoencoders: On‐the‐fly collective variable discovery and accelerated free energy landscape exploration

W Chen, AL Ferguson - Journal of computational chemistry, 2018 - Wiley Online Library
Macromolecular and biomolecular folding landscapes typically contain high free energy
barriers that impede efficient sampling of configurational space by standard molecular …

Enhancing important fluctuations: Rare events and metadynamics from a conceptual viewpoint

O Valsson, P Tiwary, M Parrinello - Annual review of physical …, 2016 - annualreviews.org
Atomistic simulations play a central role in many fields of science. However, their usefulness
is often limited by the fact that many systems are characterized by several metastable states …

Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation

H Sidky, W Chen, AL Ferguson - Molecular Physics, 2020 - Taylor & Francis
Classical molecular dynamics simulates the time evolution of molecular systems through the
phase space spanned by the positions and velocities of the constituent atoms. Molecular …

The many faces of heterogeneous ice nucleation: Interplay between surface morphology and hydrophobicity

M Fitzner, GC Sosso, SJ Cox… - Journal of the American …, 2015 - ACS Publications
What makes a material a good ice nucleating agent? Despite the importance of
heterogeneous ice nucleation to a variety of fields, from cloud science to microbiology, major …