Accès ouvert
2026
article
OpenAlex
Sachin Shivakumar, Giorgia Frumenzio, Francesco Musiani, Fabio Affinito et autres
Force matching (FM) algorithms develop force fields to dramatically extend the time scales of quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. Here, we present MiMiCPy-FM, an implementation of the generalized QM/MM FM approach for the automated parametrization of biomolecular force fields. …
de, se, it, us, fr
(code pays fourni par la source)
2026
article
OpenAlex
Sachin Shivakumar, Amritam Das, Matthew Peet
We consider$H_{\infty }$-optimal state-feedback control of the class of linear Partial Differential Equations (PDEs) which admit a Partial Integral Equation (PIE) representation. While linear matrix inequalities are commonly used for optimal control of Ordinary Differential Equations (ODEs), the absence of a universal …
us, nl
(code pays fourni par la source)
Accès ouvert
2026
article
OpenAlex
Sachin Shivakumar, Giorgia Frumenzio, Francesco Musiani, Fabio Affinito et autres
Atomistic molecular dynamics (MD) simulations were performed on isocitrate dehydrogenase 1 (IDH1), a dimeric, magnesium-dependent enzyme that catalyzes the oxidative decarboxylation of isocitrate to 2-oxoglutarate (αKG). The force field parameters used to simulate the chain B monomer were derived from QM/MM calculations …
it, de
(code pays fourni par la source)
Accès ouvert
2026
article
OpenAlex
Sachin Shivakumar, Giorgia Frumenzio, Francesco Musiani, Fabio Affinito et autres
Atomistic molecular dynamics (MD) simulations were performed on isocitrate dehydrogenase 1 (IDH1), a dimeric, magnesium-dependent enzyme that catalyzes the oxidative decarboxylation of isocitrate to 2-oxoglutarate (αKG). The force field parameters used to simulate the chain B monomer were derived from QM/MM calculations …
it, de
(code pays fourni par la source)
Accès ouvert
2026
article
OpenAlex
Sachin Shivakumar, Giorgia Frumenzio, Francesco Musiani, Fabio Affinito et autres
Force matching (FM) algorithms develop force fields to dramatically extend the time scales of quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. Here, we present MiMiCPy-FM, an implementation of the generalized QM/MM FM approach for the automated parametrization of biomolecular force fields. …
de
(code pays fourni par la source)
Accès ouvert
2025
dataset
OpenAlex
Sachin Shivakumar, Giorgia Frumenzio, Francesco Musiani, Fabio Affinito et autres
Dataset for the article: "MiMiCPy-FM: a user-friendly force matching tool for extending the time scale of QM/MM MD MiMiC simulations."
de, se, it, us
(code pays fourni par la source)
Accès ouvert
2025
dataset
OpenAlex
Sachin Shivakumar, Giorgia Frumenzio, Francesco Musiani, Fabio Affinito et autres
Dataset for the article: "MiMiCPy-FM: a user-friendly force matching tool for extending the time scale of QM/MM MD MiMiC simulations."
de, se, it, us
(code pays fourni par la source)
2025
article
OpenAlex
Danilo Braghini, Sachin Shivakumar
The H<inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> norm is a commonly used performance metric in the design of estimators. However, H<inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf>-optimal estimation of most PDEs is complicated by the lack of transfer function and state-space representations. To address this problem, we first re-characterize …
us
(code pays fourni par la source)