Lab for Computational Molecular Engineering

RECENT SELECTED PUBLICATIONS

Collective Variable-Guided Engineering of the Free-Energy Surface of a Small Peptide (2026)

Muralika Medaparambath, Alexander Zhilkin, Dan Mendels

https://arxiv.org/abs/2602.19906

Guiding Peptide Kinetics via Collective-Variable Tuning of Free-Energy Barriers (2026)

Alexander Zhilkin, Muralika Medaparambath, Dan Mendels

https://pubs.acs.org/doi/10.1021/acs.jctc.6c00418

Evaluating the use of a machine learning simulator for structure–property prediction: A case study on disordered elastic networks (2025)

Salman N. Salman, Sergey A. Shteingolts, Ron Levie, Dan Mendels

https://pubs.aip.org/aip/jcp/article/163/12/124115/3364390/

Systematic Modification of Functionality in Disordered Elastic Networks Through Free Energy Surface Tailoring (2023)

D Mendels, F Byléhn, TW Sirk, JJ de Pablo

https://www.science.org/doi/pdf/10.1126/sciadv.adf7541

Collective Variables for Free Energy Surface Tailoring: Understanding and Modifying Functionality in Systems Dominated by Rare Events (2022)

D Mendels and  JJ de Pablo

https://pubs.acs.org/doi/10.1021/acs.jpclett.2c00317

Solubility of organic salts in solvent-antisolvent mixtures: A combined experimental and molecular dynamics simulations approach (2022)

Z Bjelobrk, AK Rajagopalan, D Mendels, T Karmakar, M Parrinello, M Mazzotti

https://pubs.acs.org/doi/10.1021/acs.jctc.2c00304

Solubility prediction of organic molecules with molecular dynamics simulations (2021)

Z Bjelobrk, D Mendels, T Karmakar, M Parrinello, M Mazzotti

https://pubs.acs.org/doi/full/10.1021/acs.cgd.1c00546

Blind search for complex chemical pathways using harmonic linear discriminant analysis (2019)

V Rizzi, D Mendels, E Sicilia, M Parrinello

https://pubs.acs.org/doi/full/10.1021/acs.jctc.9b00358

Folding a small protein using harmonic linear discriminant analysis (2018)

D Mendels, GM Piccini, ZF Brotzakis, YI Yang, M Parrinello

https://aip.scitation.org/doi/full/10.1063/1.5053566

Metadynamics with discriminants: A tool for understanding chemistry (2018)

GM Piccini, D Mendels, M Parrinello

https://pubs.acs.org/doi/full/10.1021/acs.jctc.8b00634

Collective variables from local fluctuations (2018)

D Mendels, GM Piccini, M Parrinello

https://pubs.acs.org/doi/full/10.1021/acs.jpclett.8b00733

Searching for entropically stabilized phases: The case of silver iodide (2018)

D Mendels, J McCarty, PM Piaggi, M Parrinello

https://pubs.acs.org/doi/full/10.1021/acs.jpcc.7b11002