AF
Andrew L. Ferguson
Molecular Dynamics SimulationMachine LearningProteinsPeptidesphysics.chem-phphysics.comp-phstat.MLcs.LGDNAPeptoids
On Valency
published · living versionsW_qspcx4nn·v2 · currentpublished
Quantum-accurate atomistic modeling of enzyme catalysis using a machine learned potential
with Meng Gao, Armin Shayesteh Zadeh, Aniruddha Seal, Siva Dasetty +8
2 versions
Preprints & journals
136 papers in the corpus · 2009–2026Quantum-accurate atomistic modeling of enzyme catalysis using a machine learned potential2609.09293v2 · Meng Gao, Armin Shayesteh Zadeh, Aniruddha Seal et al.2026 · 0 citationsarXivon Valency
Computational Characterization of Solute Permeability in Elastin-Like Polypeptide Membranes for Synthetic Cells.42573348 · Mao, Jianming, Xi, Yongkang, Liu, Allen P et al.2026 · 0 citationsBiomacromolecules. 2026;27(8):5656-5672
Data-driven reconstruction of dynamical systems using Takens' Theorem, manifold learning, and universal function approximators2608.05477v1 · Maximilian Topel, Andrew L. Ferguson2026 · 0 citationsarXiv
Ultra coarse-grained modeling of chiral molecular fluids10.26434/chemrxiv.15005575/v1 · Siva Dasetty, Trung Dac Nguyen, Patrick G. Sahrmann et al.2026 · 0 citationsChemRxiv
Ring sliding dynamics of single-and double-threaded cyclodextrin-polyethylene glycol polyrotaxane slide-ring polymers under tension10.26434/chemrxiv.15005291/v1 · Luna Ramirez, Yufei Chen, Chenfeng Ke et al.2026 · 0 citationsChemRxiv
Computational Design of Functionalized Cyclodextrin Probes for Sensitive and Selective PFAS Detection10.26434/chemrxiv.15004563/v1 · Siddarth K. Achar, Srusti Donapati, Marco Piazzi et al.2026 · 0 citationsChemRxiv
Cytoplasmic abundant heat-soluble proteins from tardigrades protect synthetic cells under stress.42069654 · Xi, Yongkang, Mao, Jianming, Chen, Samuel J et al.2026 · 1 citationNature communications. 2026;17(1)
Computational Characterization of Solute Permeability in ELP Membranes for Synthetic Cells10.26434/chemrxiv.15002583/v1 · Jianming Mao, Yongkang Xi, Allen P. Liu et al.2026 · 0 citationsChemRxiv
Characterizing Defect Dynamics in Silicon Carbide Using Symmetry-Adapted Collective Variables and Machine Learning Interatomic Potentials.42023492 · Dutta, Soumajit, Zhang, Cunzhi, Perez Lemus, Gustavo et al.2026 · 3 citationsJournal of chemical theory and computation. 2026;22(9):4728-4741
Polymorphism in Self-Assembly of Short Peptoid Sequences.41909244 · Zheng, Renyu, Zhao, Mingfei, Zhou, Wenhao et al.2026 · 4 citationsPolymer science & technology (Washington, D.C.). 2026;2(3):176-185
Assembly of small silica nanoparticles using lipid-tethered DNA 'bonds'.41311155 · Chiang, Huat Thart, Kern, Naomi, Wylie, Zachery R et al.2025 · 0 citationsSoft matter. 2025;21(48):9398-9411
Tribute to Athanassios Z. Panagiotopoulos.41163490 · Debenedetti, Pablo G, Errington, Jeffrey R, Ferguson, Andrew L et al.2025 · 0 citationsThe journal of physical chemistry. B. 2025;129(43):11101-11103
Computing Reaction Kinetics with MC-PDFT-OPESf: Combining Multireference Electronic Structure Theory and Enhanced Sampling.41144581 · Seal, Aniruddha, Gagliardi, Laura, Ferguson, Andrew L2025 · 2 citationsThe journal of physical chemistry letters. 2025;16(44):11458-11463
Non-Equilibrium Dynamics and Non-Gaussian Fluctuations of an Optical Matter System Manifesting Pseudorotation.41060893 · Chen, Shiqi, Parker, John A, Linderman, John et al.2025 · 2 citationsACS nano. 2025;19(41):36496-36509
ProT-VAE: Protein Transformer Variational AutoEncoder for functional protein design.41052325 · Sevgen, Emre, Moller, Joshua, Lange, Adrian et al.2025 · 54 citationsProceedings of the National Academy of Sciences of the United States of America. 2025;122(41):e2408737122
High-Throughput Virtual Screening of Protein-Catalyzed Capture Agents for Novel Hydrogel-Nanoparticle Fentanyl Sensors.40998403 · Zadeh, Armin Shayesteh, Winton, Alexander J, Palomba, Joseph M et al.2025 · 2 citationsThe journal of physical chemistry. B. 2025;129(40):10568-10583
Weighted active space protocol for multireference machine-learned potentials.40953275 · Seal, Aniruddha, Perego, Simone, Hennefarth, Matthew R et al.2026 · 9 citationsProceedings of the National Academy of Sciences of the United States of America. 2025;122(38):e2513693122
Publisher Correction: Assembly of short amphiphilic peptoids into nanohelices with controllable supramolecular chirality.40903472 · Zheng, Renyu, Zhao, Mingfei, Du, Jingshan S et al.2025 · 0 citationsNature communications. 2025;16(1):8220
The Future of Artificial Intelligence and the Mathematical and Physical Sciences (AI+MPS)2509.02661v3 · Andrew Ferguson, Marisa LaFleur, Lars Ruthotto et al.2025 · 1 citationarXiv
Prediction of αIIbβ3 integrin structures along its minimum free energy activation pathway.40831062 · Dasetty, Siva, Coffman, Robert E, Bidone, Tamara C et al.2025 · 0 citationsBiophysical journal. 2025;124(19):3148-3160
Influence of thermal processing and doping concentration on phase behaviour of a lithium-transporting organic ionic plastic crystal10.26434/chemrxiv-2025-b2jmw · Nicholas Boynton, Leah Hess, Soumajit Dutta et al.2025 · 1 citationChemRxiv
Computational Design of Polypeptide-Based Compartments for Synthetic Cells10.26434/chemrxiv-2025-bmbp7 · Jianming Mao, Yongkang Xi, Armin Shayesteh Zadeh et al.2025 · 1 citationChemRxiv
Recent advances in machine learning and coarse-grained potentials for biomolecular simulations.40544328 · Poma, Adolfo B, Hinostroza Caldas, Alejandra, Cofas-Vargas, Luis F et al.2026 · 25 citationsBiophysical journal. 2026;125(2):327-343
Structure and Synthesizability of Iron-Sulfur Metal-Organic Frameworks.40378053 · Mao, Jianming, Jiang, Ningxin, Darù, Andrea et al.2025 · 10 citationsJournal of the American Chemical Society. 2025;147(21):17651-17667
PLUMED Tutorials: A collaborative, community-driven learning ecosystem.40035582 · Tribello, Gareth A, Bonomi, Massimiliano, Bussi, Giovanni et al.2025 · 35 citationsThe Journal of chemical physics. 2025;162(9)
Recent Advances in Machine Learning and Coarse-Grained Potentials for Biomolecular Simulations and Their Applications10.26434/chemrxiv-2025-vxjlk · Adolfo B. Poma, Alejandra Hinostroza Caldas, Luis Cofas-Vargas et al.2025 · 1 citationChemRxiv
Data-driven equation-free dynamics applied to many-protein complexes: The microtubule tip relaxation.39825563 · Wu, Jiangbo, Dasetty, Siva, Beckett, Daniel et al.2025 · 6 citationsBiophysical journal. 2025;124(22):3853-3866
FlowBack: A Generalized Flow-Matching Approach for Biomolecular Backmapping.39772562 · Jones, Michael S, Khanna, Smayan, Ferguson, Andrew L2025 · 12 citationsJournal of chemical information and modeling. 2025;65(2):672-692
A modular and extensible CHARMM-compatible model for all-atom simulation of polypeptoids.39714012 · Berlaga, Alex, Torkelson, Kaylyn, Seal, Aniruddha et al.2024 · 5 citationsThe Journal of chemical physics. 2024;161(24)
Reversible ppt-Level Detection of Perfluorooctane Sulfonic Acid in Tap Water using Field-Effect Transistor Sensors10.26434/chemrxiv-2024-6q6q5 · Yuqin Wang, Hyun-June Jang, Max Topel et al.2024 · 3 citationsChemRxiv
Tutorial on Molecular Latent Space Simulators (LSSs): Spatially and Temporally Continuous Data-Driven Surrogate Dynamical Models of Molecular Systems.39540914 · Jones, Michael S, Shmilovich, Kirill, Ferguson, Andrew L2024 · 1 citationThe journal of physical chemistry. A. 2024;128(47):10299-10317
Natural Language Prompts Guide the Design of Novel Functional Protein Sequences.39605414 · Praljak, Nikša, Yeh, Hugh, Moore, Miranda et al.2025 · 4 citationsbioRxiv : the preprint server for biology. 2024
Power dissipation and entropy production rate of high-dimensional optical matter systems.39562965 · Chen, Shiqi, Valenton, Emmanuel, Rotskoff, Grant M et al.2024 · 4 citationsPhysical review. E. 2024;110(4-1):044109
Deep-learning-based design of synthetic orthologs of SH3 signaling domains.39106868 · Lian, Xinran, Praljak, Nikša, Subramanian, Subu K et al.2024 · 8 citationsCell systems. 2024;15(8):725-737.e7
Virtual Special Issue on Machine Learning in Physical Chemistry Volume 2.38988211 · Ferguson, Andrew L, Pfaendtner, Jim2024 · 1 citationThe journal of physical chemistry. A. 2024;128(27):5225-5228
Virtual Special Issue on Machine Learning in Physical Chemistry Volume 2.38988219 · Ferguson, Andrew L, Pfaendtner, Jim2024 · 2 citationsThe journal of physical chemistry. B. 2024;128(27):6435-6438
Assembly of short amphiphilic peptoids into nanohelices with controllable supramolecular chirality.38627405 · Zheng, Renyu, Zhao, Mingfei, Du, Jingshan S et al.2024 · 30 citationsNature communications. 2024;15(1):3264
Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multimolecular and Solvent-Inclusive Collective Variables.38150421 · Herringer, Nicholas S M, Dasetty, Siva, Gandhi, Diya et al.2024 · 23 citationsJournal of chemical theory and computation. 2024;20(1):178-198
Data-driven prediction of αIIbβ3 integrin activation paths using manifold learning and deep generative modeling.38098231 · Dasetty, Siva, Bidone, Tamara C, Ferguson, Andrew L2024 · 6 citationsBiophysical journal. 2024;123(17):2716-2729
ProtWave-VAE: Integrating Autoregressive Sampling with Latent-Based Inference for Data-Driven Protein Design.37988083 · Praljak, Nikša, Lian, Xinran, Ranganathan, Rama et al.2023 · 18 citationsACS synthetic biology. 2023;12(12):3544-3561
DiAMoNDBack: Diffusion-Denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces.37906711 · Jones, Michael S, Shmilovich, Kirill, Ferguson, Andrew L2023 · 30 citationsJournal of chemical theory and computation. 2023;19(21):7908-7923
Data-driven discovery of innate immunomodulators via machine learning-guided high throughput screening.38020385 · Tang, Yifeng, Kim, Jeremiah Y, Ip, Carman K M et al.2024 · 18 citationsChemical science. 2023;14(44):12747-12766
Molecular insight into how the position of an abasic site and its sequence environment influence DNA duplex stability and dynamics.37546925 · Ashwood, Brennan, Jones, Michael S, Lee, Yumin et al.2024 · 10 citationsbioRxiv : the preprint server for biology. 2023
Thermodynamic Basis for the Stabilization of Helical Peptoids by Chiral Sidechains.37379071 · Alamdari, Sarah, Torkelson, Kaylyn, Wang, Xiaoqian et al.2023 · 7 citationsThe journal of physical chemistry. B. 2023;127(27):6171-6183
Molecular Latent Space Simulators for Distributed and Multimolecular Trajectories.37314375 · Jones, Michael S, McDargh, Zachary A, Wiewiora, Rafal P et al.2023 · 9 citationsThe journal of physical chemistry. A. 2023;127(25):5470-5490
Denoising Autoencoder Trained on Simulation-Derived Structures for Noise Reduction in Chromatin Scanning Transmission Electron Microscopy.37396862 · Alvarado, Walter, Agrawal, Vasundhara, Li, Wing Shun et al.2026 · 18 citationsACS central science. 2023;9(6):1200-1212
Computational and Experimental Determination of the Properties, Structure, and Stability of Peptoid Nanosheets and Nanotubes.37141445 · Zhao, Mingfei, Zhang, Shuai, Zheng, Renyu et al.2023 · 10 citationsBiomacromolecules. 2023;24(6):2618-2632
Girsanov Reweighting Enhanced Sampling Technique (GREST): On-the-Fly Data-Driven Discovery of and Enhanced Sampling in Slow Collective Variables.37036804 · Shmilovich, Kirill, Ferguson, Andrew L2023 · 26 citationsThe journal of physical chemistry. A. 2023;127(15):3497-3517
Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs.37090657 · Ashwood, Brennan, Jones, Michael S, Radakovic, Aleksandar et al.2023 · 19 citationsbioRxiv : the preprint server for biology. 2023
Disruption of energetic and dynamic base pairing cooperativity in DNA duplexes by an abasic site.36976762 · Ashwood, Brennan, Jones, Michael S, Ferguson, Andrew L et al.2023 · 19 citationsProceedings of the National Academy of Sciences of the United States of America. 2023;120(14):e2219124120
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