Publications

Peer-reviewed articles and preprints.

2026

• Cluster Models for Next‐Generation, Machine‐Learning‐Based Energy Functions for Molecular Simulations
  Small Structures, 7(2), e202500656. Authors: Wang, JingChun, Upadhyay, Meenu, Boittier, Eric D, et al..

• Efficient, Equivariant Predictions of Distributed Charge Models
  arXiv preprint arXiv:2602.07234. Authors: Boittier, Eric D, Meuwly, Markus.

• Explicit, Machine-Learned Two-Body Potentials for Molecular Simulations
  arXiv preprint arXiv:2603.14466. Authors: Chaton, Kham Lek, Boittier, Eric D, Devereux, Mike, Meuwly, Markus.

2025

• Roadmap to CCSD (T)-Quality Machine-Learned Potentials for Condensed Phase Simulations
  Journal of Chemical Theory and Computation, 21(18), 8683-8698. Authors: Boittier, Eric D, Kaser, Silvan, Meuwly, Markus.

• Towards Large-Scale Condensed Phase Simulations using Machine Learned Energy Functions
  arXiv preprint arXiv:2506.23272. Authors: Boittier, Eric D, Käser, Silvan, Meuwly, Markus.

2024

• CHARMM at 45: Enhancements in accessibility, functionality, and speed
  The Journal of Physical Chemistry B, 128(41), 9976-10042. Authors: Hwang, Wonmuk, Austin, Steven L, Blondel, Arnaud, et al..

• Force fields for deep eutectic mixtures: application to structure, thermodynamics and 2D-Infrared spectroscopy
  The Journal of Physical Chemistry B, 128(44), 10937-10949. Authors: Topfer, Kai, Boittier, Eric, Devereux, Mike, et al..

• Kernel-based minimal distributed charges: A conformationally dependent ESP-model for molecular simulations
  Journal of Chemical Theory and Computation, 20(18), 8088-8099. Authors: Boittier, Eric, Töpfer, Kai, Devereux, Mike, Meuwly, Markus.

• Systematic improvement of empirical energy functions in the era of machine learning
  Journal of Computational Chemistry, 45(22), 1899-1913. Authors: Devereux, Mike, Boittier, Eric D, Meuwly, Markus.

2023

• Interaction at a distance: Xenon migration in Mb
  The Journal of Chemical Physics, 158(12). Authors: Turan, Haydar Taylan, Boittier, Eric, Meuwly, Markus.

• Structural investigation of CDCA3‐Cdh1 p rotein–protein interactions using in vitro studies and molecular dynamics simulation
  Protein Science, 32(3), e4572. Authors: Barbhuiya, Tabassum Khair, Fisher, Mark, Boittier, Eric D, et al..

• The first HyDRA challenge for computational vibrational spectroscopy
  Physical Chemistry Chemical Physics, 25(33), 22089-22102. Authors: Fischer, Taija L, Bödecker, Margarethe, Schweer, Sophie M, et al..

2022

• Molecular dynamics with conformationally dependent, distributed charges
  Journal of Chemical Theory and Computation, 18(12), 7544-7554. Authors: Boittier, Eric D, Devereux, Mike, Meuwly, Markus.

• Synthesis of a Gal-ß-(1? 4)-Gal disaccharide as a ligand for the fimbrial adhesin UcaD
  Australian Journal of Chemistry, 76(1), 30-36. Authors: Boittier, Eric D, Wimmer, Norbert, Harris, Alexandria K, et al..

• Uncertainty quantification for predictions of atomistic neural networks
  Chemical science, 13(44), 13068-13084. Authors: Vazquez-Salazar, Luis Itza, Boittier, Eric D, Meuwly, Markus.

2021

• Elevating CDCA3 levels in non-small cell lung cancer enhances sensitivity to platinum-based chemotherapy
  Communications Biology, 4(1), 638. Authors: Kildey, Katrina, Gandhi, Neha S, Sahin, Katherine B, et al..

• Identification of proteins deregulated by platinum-based chemotherapy as novel biomarkers and therapeutic targets in non-small cell lung cancer
  Frontiers in oncology, 11, 615967. Authors: Ryan, Sarah-Louise, Dave, Keyur A, Beard, Sam, et al..

• Impact of the characteristics of quantum chemical databases on machine learning prediction of tautomerization energies
  Journal of chemical theory and computation, 17(8), 4769-4785. Authors: Vazquez-Salazar, Luis Itza, Boittier, Eric D, Unke, Oliver T, Meuwly, Markus.

• Transfer learning to CCSD (T): Accurate anharmonic frequencies from machine learning models
  Journal of Chemical Theory and Computation, 17(6), 3687-3699. Authors: Kaser, Silvan, Boittier, Eric D, Upadhyay, Meenu, Meuwly, Markus.

2020

• Assessing molecular docking tools to guide targeted drug discovery of CD38 inhibitors
  International journal of molecular sciences, 21(15), 5183. Authors: Boittier, Eric D, Tang, Yat Yin, Buckley, McKenna E, et al..

• GlycoTorch Vina: docking designed and tested for glycosaminoglycans
  Journal of Chemical Information and Modeling, 60(12), 6328-6343. Authors: Boittier, Eric D, Burns, Jed M, Gandhi, Neha S, Ferro, Vito.

2019

• Cross-species analysis of glycosaminoglycan binding proteins reveals some animal models are “More Equal” than others
  Molecules, 24(5), 924. Authors: Boittier, Eric D, Gandhi, Neha S, Ferro, Vito, Coombe, Deirdre R.

• Pathway Bifurcation in the (4 + 3)/(5 + 2)-Cycloaddition of Butadiene and Oxidopy- rylium Ylides: The Significance of Molecular Orbital Isosymmetry.
  Journal of Organic Chemistry, 84(10), 5997-6005. Authors: Burns, Jed M, Boittier, Eric D.