Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems

PP Poier, L Lagardere, JP Piquemal - Journal of Chemical Theory …, 2022 - ACS Publications
We propose a new strategy to solve the key equations of the many-body dispersion (MBD)
model by Tkatchenko, DiStasio Jr., and Ambrosetti. Our approach overcomes the original O …

General formulation of polarizable embedding models and of their coupling

M Nottoli, F Lipparini - The Journal of Chemical Physics, 2020 - pubs.aip.org
We propose a general formalism for polarizable embedding models that can be applied to
either continuum or atomistic polarizable models. After deriving such a formalism for both …

Implicit solvents for the polarizable atomic multipole AMOEBA force field

RA Corrigan, G Qi, AC Thiel, JR Lynn… - Journal of chemical …, 2021 - ACS Publications
Computational protein design, ab initio protein/RNA folding, and protein–ligand screening
can be too computationally demanding for explicit treatment of solvent. For these …

Smooth particle mesh Ewald-integrated stochastic Lanczos many-body dispersion algorithm

PP Poier, L Lagardère, JP Piquemal - The Journal of Chemical Physics, 2023 - pubs.aip.org
We derive and implement an alternative formulation of the Stochastic Lanczos algorithm to
be employed in connection with the Many-Body Dispersion model (MBD). Indeed, this …

A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model

RA Corrigan, AC Thiel, JR Lynn, TL Casavant… - The Journal of …, 2023 - pubs.aip.org
Computational simulation of biomolecules can provide important insights into protein
design, protein-ligand binding interactions, and ab initio biomolecular folding, among other …

Variational formulation of the bond capacity charge polarization model

PP Poier - The Journal of Chemical Physics, 2022 - pubs.aip.org
We present an alternative energy formulation of the bond capacity charge polarization
model to be used in molecular dynamics simulations. The energy expression consists of a …

[BOOK][B] Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field: Application to Small Molecules, Proteins, and Nucleic Acids

RA Corrigan - 2023 - search.proquest.com
Computational protein design, ab initio protein/RNA folding, and protein-ligand screening
can be too computationally demanding for explicit treatment of solvent. For these …

[PDF][PDF] O (N) Stochastic Evaluation of Many-Body van der

Van der Waals dispersion interactions play a crucial role in nature, determining the structure
and functionality of molecular 13 systems and materials, 1, 2 two examples being the …