2024
Automatic feature selection and weighting using Differentiable Information Imbalance Journal Article
In: arXiv preprint arXiv:2411.00851, 2024.
Boosting Ensemble Refinement with Transferable Force-Field Corrections: Synergistic Optimization for Molecular Simulations Journal Article
In: The Journal of Physical Chemistry Letters, vol. 15, no. 5, pp. 1204–1210, 2024.
Molecular dynamics simulations reveal the parallel stranded d (GGGA) 3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble Journal Article
In: International Journal of Biological Macromolecules, vol. 261, pp. 129712, 2024.
RNA Dynamics from Experimental and Computational Approaches Journal Article
In: Structure, vol. 32, pp. 1281, 2024.
Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction Journal Article
In: The Journal of Physical Chemistry B, vol. 128, no. 37, pp. 8896–8907, 2024.
The need to implement FAIR principles in biomolecular simulations Journal Article
In: arXiv preprint arXiv:2407.16584, 2024.
Molecular dynamics simulations reveal how vinculin refolds partially unfolded talin rod helices to stabilize them against mechanical force Journal Article
In: PLOS Computational Biology, vol. 20, no. 8, pp. e1012341, 2024.
2023
Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks Journal Article
In: The Journal of Chemical Physics, vol. 158, no. 7, 2023.
Nonequilibrium thermodynamics of DNA nanopore unzipping Journal Article
In: Physical Review Letters, vol. 130, no. 4, pp. 048101, 2023.
Protein folds vs. protein folding: Differing questions, different challenges Journal Article
In: Proceedings of the National Academy of Sciences, vol. 120, no. 1, pp. e2214423119, 2023.
Linear catenanes in channel confinement Journal Article
In: Macromolecules, vol. 56, no. 7, pp. 2736–2746, 2023.
RNA folding pathways from all-atom simulations with a variationally improved history-dependent bias Journal Article
In: Biophysical Journal, vol. 122, no. 15, pp. 3089–3098, 2023.
Topological entanglement of linear catenanes: Knots and threadings Journal Article
In: ACS Macro Letters, vol. 12, no. 9, pp. 1231–1236, 2023.
Quantum-inspired encoding enhances stochastic sampling of soft matter systems Journal Article
In: Science Advances, vol. 9, no. 43, pp. eadi0204, 2023.
Viral RNA as a branched polymer Book Section
In: Physical Virology: From the State-of-the-Art Research to the Future of Applied Virology, pp. 1–26, Springer International Publishing Cham, 2023.
Topological Analysis and Recovery of Entanglements in Polymer Melts Journal Article
In: Macromolecules, vol. 56, no. 9, pp. 3354–3362, 2023.
Scaling properties of RNA as a randomly branching polymer Journal Article
In: The Journal of Chemical Physics, vol. 158, no. 23, 2023.
Spatial Organization of Slit-Confined Melts of Ring Polymers with Nonconserved Topology: A Lattice Monte Carlo Study Journal Article
In: Macromolecules, vol. 56, no. 19, pp. 7860–7869, 2023.
Phase behaviour of semiflexible lattice polymers in poor-solvent solution: Mean-field theory and Monte Carlo simulations Journal Article
In: The Journal of Chemical Physics, vol. 159, no. 15, 2023.
Intrinsic dimension estimation for discrete metrics Journal Article
In: Physical Review Letters, vol. 130, no. 6, pp. 067401, 2023.
Do machine-learning atomic descriptors and order parameters tell the same story? The case of liquid water Journal Article
In: Journal of Chemical Theory and Computation, vol. 19, no. 14, pp. 4596–4605, 2023.
The geometry of hidden representations of large transformer models Journal Article
In: Advances in Neural Information Processing Systems, vol. 36, pp. 51234–51252, 2023.
Optimal transfer protocol by incremental layer defrosting Journal Article
In: arXiv preprint arXiv:2303.01429, 2023.
Solvation thermodynamics from cavity shapes of amino acids Journal Article
In: PNAS nexus, vol. 2, no. 8, pp. pgad239, 2023.
Agnostic detection of large-scale weather patterns in the northern hemisphere: from blockings to teleconnections Journal Article
In: arXiv preprint arXiv:2309.06833, 2023.
Redundant representations help generalization in wide neural networks Journal Article
In: Journal of Statistical Mechanics: Theory and Experiment, vol. 2023, no. 11, pp. 114011, 2023.
Molecular dynamics simulations with grand-canonical reweighting suggest cooperativity effects in RNA structure probing experiments Journal Article
In: Journal of chemical theory and computation, vol. 19, no. 12, pp. 3672–3685, 2023.
Molecular dynamics simulations of chemically modified ribonucleotides Book Section
In: RNA Structure and Function, pp. 595–612, Springer International Publishing Cham, 2023.
Integrating experimental data with molecular simulations to investigate RNA structural dynamics Journal Article
In: Current Opinion in Structural Biology, vol. 78, pp. 102503, 2023.
Unraveling disease mechanisms using molecular modeling of bio-interfaces Journal Article
In: Biophysical Journal, vol. 122, no. 3, pp. 481a, 2023.
Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations Journal Article
In: Journal of Chemical Information and Modeling, vol. 63, no. 9, pp. 2794–2809, 2023.
Simultaneous refinement of molecular dynamics ensembles and forward models using experimental data Journal Article
In: The Journal of Chemical Physics, vol. 158, no. 21, 2023.
2022
DNA knots Book Section
In: Topological Polymer Chemistry: Concepts and Practices, pp. 115–133, Springer Nature Singapore Singapore, 2022.
Effect of ring rigidity on the statics and dynamics of linear catenanes Journal Article
In: Macromolecules, vol. 55, no. 11, pp. 4523–4532, 2022.
Density-tunable pathway complexity in a minimalistic self-assembly model Journal Article
In: Soft Matter, vol. 18, no. 42, pp. 8106–8116, 2022.
Tuning Knotted Copolyelectrolyte Conformations via Solution Properties Journal Article
In: Macromolecules, vol. 55, no. 23, pp. 10761–10772, 2022.
The Physical Behavior of Interphase Chromosomes: Polymer Theory and Coarse-Grain Computer Simulations. Journal Article
In: Methods in Molecular Biology (Clifton, NJ), vol. 2301, pp. 235–258, 2022.
Entanglement Length Scale Separates Threading from Branching of Unknotted and Non-concatenated Ring Polymers in Melts Journal Article
In: Macromolecules, vol. 55, no. 23, pp. 10723–10736, 2022.
Unfolding and identification of membrane proteins in situ Journal Article
In: Elife, vol. 11, pp. e77427, 2022.
Ranking the information content of distance measures Journal Article
In: PNAS nexus, vol. 1, no. 2, pp. pgac039, 2022.
Redundant representations help generalization in wide neural networks Journal Article
In: Advances in Neural Information Processing Systems, vol. 35, pp. 19659–19672, 2022.
When kinetics plays strange tricks Journal Article
In: Proceedings of the National Academy of Sciences, vol. 119, no. 4, pp. e2122078119, 2022.
Multiple-allele MHC class II epitope engineering by a molecular dynamics-based evolution protocol Journal Article
In: Frontiers in immunology, vol. 13, pp. 862851, 2022.
DADApy: Distance-based analysis of data-manifolds in Python Journal Article
In: Patterns, vol. 3, no. 10, 2022.
Prune and distill: similar reformatting of image information along rat visual cortex and deep neural networks Journal Article
In: Advances in Neural Information Processing Systems, vol. 35, pp. 30206–30218, 2022.
Monte Carlo approach to the conformal bootstrap Journal Article
In: Physical Review D, vol. 106, no. 2, pp. 025019, 2022.
Dpcfam: unsupervised protein family classification by density peak clustering of large sequence datasets Journal Article
In: PLOS Computational Biology, vol. 18, no. 10, pp. e1010610, 2022.
The generalized ratios intrinsic dimension estimator Journal Article
In: Scientific Reports, vol. 12, no. 1, pp. 20005, 2022.
Do Machine-Learning Atomic Descriptors and Order Parameters Tell the Same Story? The Case of Liquid Water Journal Article
In: arXiv e-prints, pp. arXiv–2211, 2022.
High dimensional feature selection using informative distance measures: Application to COVID-19 severity prediction Journal Article
In: 2022.