Manifold learning in atomistic simulations: a conceptual review

J Rydzewski, M Chen, O Valsson - Machine Learning: Science …, 2023 - iopscience.iop.org
Analyzing large volumes of high-dimensional data requires dimensionality reduction: finding
meaningful low-dimensional structures hidden in their high-dimensional observations. Such …

[HTML][HTML] Interfacial tension of carbon dioxide-water under conditions of CO2 geological storage and enhanced geothermal systems: A molecular dynamics study on the …

M Shiga, T Morishita, M Sorai - Fuel, 2023 - Elsevier
In recent years, CO 2 injection into geological formations under a wide range of temperature
conditions, including super-hot geothermal reservoirs, has attracted much attention (ie …

Exploring high‐dimensional free energy landscapes of chemical reactions

S Awasthi, NN Nair - Wiley Interdisciplinary Reviews …, 2019 - Wiley Online Library
Molecular dynamics (MD) techniques are widely used in computing free energy changes for
conformational transitions and chemical reactions, mainly in condensed matter systems …

Correlation between contact angle and water film energetics in carbon dioxide–water–clay mineral interfacial systems: A molecular dynamics study

M Shiga, T Morishita, M Aichi, N Nishiyama… - Energy & …, 2023 - ACS Publications
The wettability of mineral surfaces is an important parameter influencing the fluid flow in
geological formations intended for the storage of carbon dioxide (CO2). Hence, the effects of …

Position-dependent diffusion constant of molecules in heterogeneous systems as evaluated by the local mean squared displacement

T Nagai, S Tsurumaki, R Urano… - Journal of Chemical …, 2020 - ACS Publications
The authors propose a novel method to evaluate the position-dependent diffusion constant
by analyzing unperturbed segments of a trajectory determined by the additional flat-bottom …

Simple, yet powerful methodologies for conformational sampling of proteins

R Harada, Y Takano, T Baba, Y Shigeta - Physical chemistry chemical …, 2015 - pubs.rsc.org
Several biological functions, such as molecular recognition, enzyme catalysis, signal
transduction, allosteric regulation, and protein folding, are strongly related to conformational …

Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling

S Awasthi, NN Nair - The Journal of Chemical Physics, 2017 - pubs.aip.org
Biased sampling of collective variables is widely used to accelerate rare events in molecular
simulations and to explore free energy surfaces. However, computational efficiency of these …

Atomic-scale insights into the phase behavior of carbon dioxide and water from 313 to 573 K and 8 to 30 MPa

M Shiga, T Morishita, N Nishiyama, M Sorai, M Aichi… - ACS …, 2024 - ACS Publications
We performed molecular dynamics (MD) simulations of CO2+ H2O systems by employing
widely used force fields (EPM2, TraPPE, and PPL models for CO2; SPC/E and TIP4P/2005 …

A new surface and structure for silicene: polygonal silicene formation on the Al (111) surface

T Morishita, MJS Spencer, S Kawamoto… - The Journal of …, 2013 - ACS Publications
Seeking a new substrate for fabrication of silicene is of high importance, since its formation
in experiment is extremely difficult and only a few substrates have been found to be suitable …

Locating landmarks on high-dimensional free energy surfaces

M Chen, TQ Yu, ME Tuckerman - Proceedings of the …, 2015 - National Acad Sciences
Coarse graining of complex systems possessing many degrees of freedom can often be a
useful approach for analyzing and understanding key features of these systems in terms of …