Publications

2026

• Structural insight into sodium-dependent bile acid transport by members of the SLC10 family. Li, C. Y., Grob, A., Repa, L., Huxley, O., Brotherton, D. H., Becker, P., Dadzie, R., Beckstein, O., & Cameron, A. D. February 2026. bioRxiv.
• Endosome maturation is orchestrated by inside-out proton signaling through a Na+/H+ exchanger and pH-dependent Rab GTPase cycling. Morrow, E.; Lee, Y.; Ouyang, Q.; Ma, L.; Fleishman, M.; Riaz, H.; Schmidt, M.; Dupree, J.; Mondal, A.; Mohanty, P.; Mittal, J.; Beckstein, O.; and Lambright, D. February 2026. Research Square.

2025

• Bayesian Nonparametric Analysis of Residence Times for Protein–Lipid Interactions in Molecular Dynamics Simulations. Sexton, R.; Fazel, M.; Schweiger, M.; Pressé, S.; and Beckstein, O. Journal of Chemical Theory and Computation, 21(8): 4203–4220. April 2025.
• Chloride binding does not influence prestin motor speed at very high frequencies in the mouse outer hair cell. Bai, J.; Zhang, C.; Bahader, I.; Strenzke, N.; Renigunta, V.; Oliver, D.; Navaratnam, D.; Beckstein, O.; and Santos-Sacchi, J. Structure, 33(8): 1417–1424.e3. August 2025.

2024

• Zarrtraj: A Python package for streaming molecular dynamics trajectories from cloud services. Woods, L.; MacDermott-Opeskin, H.; Jakupovic, E.; Zhuang, Y.; Gowers, R.; and Beckstein, O. November 2024.
• alchemlyb: the simple alchemistry library. Wu, Z.; Dotson, D. L.; Alibay, I.; Allen, B. K.; et al.; and Beckstein, O. Journal of Open Source Software, 9(101): 6934. September 2024.
• Kinetic Diagram Analysis: A Python Library for Calculating Steady-State Observables of Biochemical Systems Analytically. Awtrey, N. C.; and Beckstein, O. Journal of Chemical Theory and Computation. August 2024.
• Chloride binding and cholesterol effects on high frequency complex nonlinear capacitance in the mouse outer hair cell. Bai, J.; Zhang, C.; Renigunta, V.; Oliver, D.; Navaratnam, D. S.; Beckstein, O.; and Santos-Sacchi, J. January 2024. bioRxiv.

2024

• Buffer-Dependent Photophysics of 2-Aminopurine: Insights into Fluorescence Quenching and Excited-State Interactions. Souvik Poddar, Marcia Levitus. J. Phys. Chem. B 2024, 128, 2640–2651.

2024

• Linear and Nonlinear Dielectric Response of Intrinsically Disordered Proteins. J. Phys. Chem. Lett. 2024, 15, 20, 5420–5427.
• Electrophoretic Mobility of Nanoparticles in Water. J. Phys. Chem. B 2024, 128, 12, 2930–2938.
• Electron Tunneling in Biology: When Does it Matter? ACS Omega (2024) 8, 30, 27355–27365.

2024

• Dissecting Allosteric Mutations for Antibiotic Resistance by Time-Dependent Linear Response Theory. P Campitelli, T Modi, SB Ozkan. Journal of Chemical Theory and Computation.
• Evidence that the cold-and menthol-sensing functions of the human TRPM8 channel evolved separately. Dustin D Luu, Nikhil Ramesh, I Can Kazan, Karan H Shah, Gourab Lahiri, Miyeko D Mana, S Banu Ozkan, Wade D Van Horn. Science Advances.
• RNA-induced Allosteric Coupling Drives Viral Capsid Assembly. S Hamilton, T Modi, P Šulc, SB Ozkan. PRX Life 2(1), 013012.
• Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. NJ Ose, P Campitelli, T Modi, IC Kazan, S Kumar, SB Ozkan. eLife.
• Enhancing deep learning model design through protein dynamics information integration. J Lu, ICJ Kazan, BK Kartchner, N Huynh, JH Mills, SB Ozkan. Biophysical Journal 123(3).
• Engineering gain-of-function mutants of a WW domain by dynamics and structural analysis. ICJ Kazan, J Lu, MI Rahman, N Halloran, AA Bobkov, SB Ozkan. Biophysical Journal 123(3).
• Probing impact of allosteric (or distal) mutations on protein function through time-dependent linear response theory. P Campitelli, T Modi, SB Ozkan. Biophysical Journal 123(3).

2025

• A cautious user's guide in applying HMMs to physical systems. Max Schweiger, Ayush Saurabh, Steve Pressé. Journal of Chemical Physics (2025).
• Substrate-interacting pore loops of two ATPase subunits determine the degradation efficiency of the 26S proteasome. Erika M. López-Alfonzo, Ayush Saurabh, Sahar Zarafshan, Steve Pressé, Andreas Martin. Nature Communications (2025, accepted).
• Avoiding subtraction and division of stochastic signals using normalizing flows: NFdeconvolve. Pedro Pessoa, Max Schweiger, Lance W.Q. Xu, Tristan Manha, Ayush Saurabh, Julian Antolin Camarena, Steve Pressé. iScience (2025).
• Perspective: An outlook on fluorescence tracking. Lance W.Q. Xu, Steve Pressé. J. Chem. Phys. (2025).
• Mamba time series forecasting with uncertainty quantification. Pedro Pessoa, Paul Campitelli, Douglas P Shepherd, S Banu Ozkan, Steve Pressé. Machine Learning: Science and Technology (2025).
• Approaching Maximum Resolution in Structured Illumination Microscopy via Accurate Noise Modeling. Ayush Saurabh, Peter T. Brown, J. Shepard Bryan IV, Zachary R. Fox, Rory Kruithoff, Douglas P. Shepherd, Steve P. Pressé. NPJ Imaging (2025).
• Bayesian Inference of Binding Kinetics from Fluorescence Time Series. J. Bryan IV, Stanimir Asenov Tashev, Mohamadreza Fazel, Michael Scheckenbach, Philip Tinnefeld, Dirk-Peter Herten, Steve Pressé. J. Phys. Chem. B. (2025).
• Single-Molecule Reaction-Diffusion. Lance W.Q. Xu, Sina Jazani, Zeliha Kilic, Steve Pressé. Biophys. J. (2025).
• Perspectives: Comparison of Deep Learning Segmentation Models on Biophysical and Biomedical Data. J. Shepard Bryan IV, Pedro Pessoa, Meysam Tavakoli, Steve Pressé. Biophys. J. (2025).
• Bayesian Nonparametric Analysis of Residence Times for Protein–Lipid Interactions in Molecular Dynamics Simulations. Ricky Sexton, Mohamadreza Fazel, Max Schweiger, Steve Pressé, Oliver Beckstein. JCTC (2025).

2024

• DiffMAP-GP: Continuous 2D Diffusion Maps from Particle Trajectories without Data Binning using Gaussian Processes. Vishesh Kumar, J. Shepard Bryan IV, Alex Rojewski, Carlo Manzo, Steve Pressé. Biophys. Rep. (2024).
• BNP-Track: A framework for multi-particle superresolved tracking. I. Sgouralis, L. W. Q. Xu, A. P. Jalihal, Z. Kilic, N. G. Walter, S. Pressé. Nat. Methods (2024).
• Fluorescence Microscopy: a statistics-optics perspective. Mohamadreza Fazel, Kristin S. Grussmayer, Boris Ferdman, Aleksandra Radenovic, Yoav Shechtman, Jörg Enderlein, Steve Pressé. Rev. Mod. Phys. (2024).
• On the statistical foundation of a recent single molecule FRET benchmark. Ayush Saurabh, Lance W.Q. Xu, and Steve Pressé. Nat. Commun. (2024).
• Avoiding matrix exponentials for large transition rate matrices. Pedro Pessoa, Max Schweiger, Steve Pressé. J. Chem. Phys. (2024).
• An accurate probabilistic step finder for time-series analysis. Alex Rojewski, Max Schweiger, Ioannis Sgouralis, Matthew Comstock, Steve Pressé. Biophys. J. (2024).

2024

• Electric field modulation of ERK dynamics shows dependency on waveform and timing. Scientific Reports (2024).

2025

• TN Huynh, S Setayeshgar, A Shrivastava, J Engel. Forging new paths in bacterial motility and sensory transduction: highlights from BLAST XVIII. FEMS Microbiology Reviews. 2025. fuaf042.
• AM Migueles-Lozano et al.; A Shrivastava, J Yan, S Mukherjee. Regulatory plasticity and metabolic trade-offs drive adaptive evolution of alternative flagellar configurations in Pseudomonas aeruginosa. bioRxiv, 2025.07.29.667523.
• A Trivedi, JA Miratsky, EC Henderson, A Singharoy, A Shrivastava. A molecular conveyor belt-associated protein controls the rotational direction of the bacterial type 9 secretion system. mBio, e01125-25.
• S Sen, I Vairagare, J Gosai, A Shrivastava. RABiTPy: an open-source Python software for rapid, AI-powered bacterial tracking and analysis. BMC Bioinformatics, 127.
• P Dadi, CW Pauling, A Shrivastava, DD Shah. Synthesis of versatile neuromodulatory molecules by a gut microbial glutamate decarboxylase. iScience, 28(4).
• ST Rocha, DD Shah, Q Zhu, A Shrivastava. The prevalence of motility-related genes within the human oral microbiota. Microbiology Spectrum, e01264-24.
• AM Zdimal, G Di Dio, W Liu, T Aftab, T Collins, R Colin, A Shrivastava. Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions. The ISME Journal, wrae263.

2024

• ST Rocha, DD Shah, A Shrivastava. Ecological, beneficial, and pathogenic functions of the Type 9 Secretion System. Microbial Biotechnology, e14516.

2026

• DNA-templated Chiral Metamaterial Array as Information Bits. Deeksha Satyabola, Shuai Feng, Prathamesh Chopade, Abhay Prasad, et al.; Petr Sulc, Rizal F Hariadi, Hao Yan, Sui Yang. bioRxiv preprint, 2026.

2025

• High-speed 3D DNA-PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography. G. Bimananda M. Wisna, Daria Sukhareva, Jonathan Zhao, Deeksha Satyabola, Michael Matthies, Subhajit Roy, Petr Šulc, Hao Yan, Rizal F. Hariadi. Nature Communications (2025).
• Repeats Mimic Immunostimulatory Viral Features Across a Vast Evolutionary Landscape. P. Šulc, A. Di Gioacchino, A. Solovyov, et al. Cell Genomics (2025).
• DNA-Templated Spatially Controlled Proteolysis Targeting Chimera for Cyclin D1–CDK4/6 Complex Protein Degradation. Rong Zheng, Abhay Prasad, Deeksha Satyabola, Yang Xu, Subhajit Roy, Yichen Yan, Petr Šulc, Hao Yan. JACS (2025).
• Controlling DNA-RNA strand displacement kinetics with base distribution. Eryk Ratajczyk, Jonathan Bath, Petr Sulc, Jonathan Doye, Ard Louis, Andrew Turberfield. PNAS (2025).
• Falsifiability Test for Classical Nucleation Theory. Camilla Beneduce, Diogo EP Pinto, Lorenzo Rovigatti, Flavio Romano, Petr Šulc, Francesco Sciortino, John Russo. Phys. Rev. Lett. (2025).
• How we simulate DNA origami. Sarah Haggenmueller, Michael Matthies, Matthew Sample, Petr Šulc. Small Methods (2025).
• Automating Blueprints for Colloidal Quasicrystal Assembly. Diogo Pinto, Petr Šulc, Francesco Sciortino, John Russo. ACS Nano (2025).
• Mismatch-Assisted Toehold Exchange Cascades for Magnetic Nanoparticle-Based Nucleic Acid Diagnostics. Rebecca Sack, Joshua Evans, Florian Wolgast, Meinhard Schilling, Thilo Viereck, Petr Šulc, Aidin Lak. JACS Au (2025).
• Inverse Thermodynamics: Designing Interactions for Targeted Phase Behavior. Camilla Beneduce, Giuseppe Mastriani, Petr Šulc, Francesco Sciortino, John Russo. J. Phys. Chem. B (2025).
• Universal 3D Nanoscale Assembly with DNA Polycubes. Thong Diep, Hao Liu, Joshua Evans, Michael Matthies, Matthew Sample, et al.; Petr Šulc. chemRxiv preprint (2025).
• High-endurance mechanical switching in a DNA origami snap-through mechanism. Florian Rothfischer, Lennart J. K. Weiß, Niccolò Tedeschi, Michael Matthies, et al.; Petr Šulc, Tim Liedl, Enzo Kopperger, Friedrich C. Simmel. arXiv preprint (2025).

2024

• Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments. Hao Liu, Michael Matthies, John Russo, et al.; Petr Šulc. Science, 384, 6697, 741–742 (2024).
• Hairygami: Analysis of DNA Nanostructures' Conformational Change Driven by Functionalizable Overhangs. Matthew Sample, Thong Diep, Hao Liu, Michael Matthies, Petr Šulc. ACS Nano (2024).
• Combination of Coevolutionary Information and Supervised Learning Enables Generation of Cyclic Peptide Inhibitors. Ylenia Mazzocato, Nicola Frasson, Matthew Sample, et al.; Petr Šulc, Alessandro Angelini. ACS Central Science (2024).
• Evolving to find optimizations humans miss: using evolutionary computation to improve GPU code for bioinformatics applications. Jhe-Yu Liou, Muaaz Awan, Kirtus Leyba, Petr Šulc, et al. ACM Transactions on Evolutionary Learning (2024).
• ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems. F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti. J. Chem. Phys. 160, 205102 (2024).
• A rhythmically pulsing leaf-spring nanoengine that drives a passive follower. M. Centola, E. Poppleton, J. Valero, S. Ray, R. Welty, Nils G. Walter, P. Šulc, M. Famulok. Nature Nanotechnology 19, 226–236 (2024).
• Coarse-grained modeling of DNA-protein interactions helps elucidate DNA compaction. Petr Sulc. Biophysical Journal (2024). New and Notable perspective.
• Coarse-grained modelling of DNA-RNA hybrids. Eryk J. Ratajczyk, Petr Šulc, Andrew J. Turberfield, Jonathan P.K. Doye, Ard A. Louis. J. Chem. Phys. 160, 115101 (2024).
• Inverse design of self-folding 3D shells. Diogo Pinto, Nuno Araújo, Petr Šulc, John Russo. Phys. Rev. Lett. 132, 118201 (2024).
• RNA-induced allosteric coupling drives viral capsid assembly. Sean Hamilton, Tushar Modi, Petr Šulc, Banu Ozkan. PRX Life (2024).
• Designing 3D multicomponent self-assembling systems with signal-passing building blocks. Joshua Evans, Petr Šulc. J. Chem. Phys. 160, 084902 (2024).
• DNA-Nanostructure-Guided Assembly of Proteins into Programmable Shapes. Qinyi Lu, Yang Xu, Erik Poppleton, Kun Zhou, Petr Sulc, Nicholas Stephanopoulos, Yonggang Ke. Nano Lett. (2024).
• Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement. Andreas Walbrun, Tianhe Wang, Michael Matthies, Petr Šulc, Friedrich Simmel, Matthias Rief. Nature Communications 15 (2024).

2025

• Building the bacterial flagellum: coordinating regulation, dynamic assembly, and function. Einenkel et al. J. MMBR. 2025.
• Swashing Motility: A Propulsion-Independent form of Bacterial Surface Migration. Panich et al. J. Bacteriol. 2025.
• PREPRINT: Long-range coupling regulates stator dynamics in the bacterial flagellar motor. Sawant et al. bioRxiv. 2025.
• PREPRINT: Osmotic stress triggers fast and reversible PMF collapse in Escherichia coli. Meneses et al. bioRxiv. 2025.
• Fourier synthesis optical diffraction tomography for kilohertz rate volumetric imaging. Brown et al. Science Advances 2025.