Building on the gas-phase MB-nrg PEF for polyalanine, Ruihan Zhou and Francesco Paesani add machine-learned 2-body terms for each backbone functional group interacting with water, fit to BSSE-corrected DLPNO-CCSD(T)/aug-cc-pVTZ data, then validate the resulting potential against alanine dipeptide-water dimer scans, free-energy surfaces in explicit MB-pol water, and hydration radial distribution functions.
Ruihan Zhou and co-authors extend the MB-nrg many-body formalism to covalently bonded biomolecules by fragmenting polyalanine into functional-group n-mers, fitting permutationally invariant polynomials to DLPNO-CCSD(T)/aug-cc-pVTZ reference energies, and reproducing alanine dipeptide Ramachandran surfaces, harmonic frequencies, and AceAla9Nme secondary-structure dynamics more faithfully than Amber ff14SB and ff19SB.
Proposes Ewald message passing, a Fourier-space scheme inspired by Ewald summation that captures long-range interactions in molecular graphs. The method is architecture-agnostic and improves energy MAEs by 10% on OC20 and 16% on OE62 across four baseline GNN models.
A differentiable point-set alignment library implementing N-dimensional Kabsch, Horn quaternion, and Umeyama scaling algorithms with per-point weights, batch dimensions, and custom autograd across NumPy, PyTorch, JAX, TensorFlow, and MLX.
This paper bridges Molecular Dynamics and Transition State Theory by applying a dynamical corrections formalism to surface diffusion, identifying a low-temperature bounce-back mechanism causing non-Arrhenius behavior.
This 1994 handbook chapter serves as a practical user guide for the Embedded-Atom Method (EAM). It details the theoretical derivation from density-functional theory, synthesizes related methods like the Glue Model, and provides a complete tutorial on fitting potentials, illustrated with a specific implementation for the Ni-Al-B system.
This 1993 review systematizes the Embedded-Atom Method (EAM) as a practical semi-empirical approach for metallic systems. It synthesizes theory, applications, and connections to related methods while addressing the limitations of pair potentials.
This paper validates the homogeneous Evans method for calculating thermal conductivity against experimental Argon data. It demonstrates broad agreement across the phase diagram but identifies significant non-monotonic behavior and enhanced long-time tails near the critical point.
A molecular dynamics investigation using EAM and many-body potentials to elucidate atomic exchange mechanisms on Iridium surfaces, verifying Field Ion Microscope observations.
Proposes the Hyperbolic Algorithm for Euclidean field theory simulations. By adding a second-order fictitious time derivative to the Langevin equation, the method reduces systematic errors from O(ε) down to O(ε²).
Stillinger and Weber propose a 3-body interaction potential that stabilizes the diamond crystal structure of silicon and reproduces liquid properties through molecular dynamics, addressing the inability of standard pair potentials to model tetrahedral semiconductors.
This molecular dynamics study reveals that adatom dimers on fcc(111) surfaces exhibit simultaneous multiple jumps at intermediate temperatures, migrating with mobility comparable to single adatoms.