Manifold learning in atomistic simulations: a conceptual review
Analyzing large volumes of high-dimensional data requires dimensionality reduction: finding
meaningful low-dimensional structures hidden in their high-dimensional observations. Such …
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 …
conditions, including super-hot geothermal reservoirs, has attracted much attention (ie …
Exploring high‐dimensional free energy landscapes of chemical reactions
Molecular dynamics (MD) techniques are widely used in computing free energy changes for
conformational transitions and chemical reactions, mainly in condensed matter systems …
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 …
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
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 …
by analyzing unperturbed segments of a trajectory determined by the additional flat-bottom …
Simple, yet powerful methodologies for conformational sampling of proteins
Several biological functions, such as molecular recognition, enzyme catalysis, signal
transduction, allosteric regulation, and protein folding, are strongly related to conformational …
transduction, allosteric regulation, and protein folding, are strongly related to conformational …
Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling
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 …
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 …
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 …
in experiment is extremely difficult and only a few substrates have been found to be suitable …
Locating landmarks on high-dimensional free energy surfaces
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 …
useful approach for analyzing and understanding key features of these systems in terms of …