Publications

Updated: 9 August 2026
* Asterisk indicates corresponding authorship.

2026

• Creon, A.; Scheer, T. E. S.; Reinke, P.; Rahmani, A.; Günther, S.; Niebling, S.; Schamoni-Kast, K.; Uetrecht, C.; Meents, A.; Chapman, H. N.; Sprenger, J.; Lane, T. J.* (2026). Statistical crystallography reveals an allosteric network in SARS-CoV-2 Mpro. Commun Biol 9, 602.

2025

• Fadini, A.*; Apostolopoulou, V.; Lane, T. J.*; van Thor, J. J.* (2025). Denoising and iterative phase recovery reveal low-occupancy populations in protein crystals. Commun Biol 8, 1649.

• Schori, A. et al. (2025). Real-space observation of the dissociation of a transition metal complex and its concurrent energy redistribution. Nat Commun 16, 4767.

• Ma, L. et al. (2025). Revealing the reaction path of UVC bond rupture in cyclic disulfides with ultrafast x-ray scattering. Sci Adv 11, eadp9175.

2024

• Stransky, M.; Lane, T. J.*; Gorel, A.; Boutet, S.; Schlichting, I.*; Mancuso, A. P.; Jurek, Z.; Ziaja, B.* (2024). Ionization by XFEL radiation produces distinct structure in liquid water. Commun Phys 7, 281.

• Fletcher, L. et al. (2024). X-ray diffraction of metastable structures from supercooled liquid hydrogen. Sci Rep 14, 17283.

• Reinke, P. Y. A.; Schubert, R.; et al.; Lane, T. J.* (2024). SARS-CoV-2 Mpro responds to oxidation by forming disulfide and NOS/SONOS bonds. Nat Commun 15, 3827.

2023

• Christou, N.-E.; Apostolopoulou, V.; Melo, D. V. M.; et al.; Lane, T. J.* (2023). Time-resolved crystallography captures light-driven DNA repair. Science 382, 1015-1020.

• Amann-Winkel, K. et al. (2023). Liquid-liquid phase separation in supercooled water from ultrafast heating of low-density amorphous ice. Nat Commun 14, 442.

• Lane, T. J.* (2023). Protein structure prediction has reached the single-structure frontier. Nat Methods 20, 170-173.

• Aithani, L. et al. (2023). Advancing structural biology through breakthroughs in AI. Curr Opin Struct Biol 80, 102601.

• Peck, A.; Lane, T. J.; Poitevin, F. (2023). Modeling diffuse scattering with simple, physically interpretable models. Methods Enzymol 688, 169-194.

• Yang, C. et al. (2023). Melting domain size and recrystallization dynamics of ice revealed by time-resolved x-ray scattering. Nat Commun 14, 3313.

2022

• Al-Haddad, A. et al. (2022). Observation of site-selective chemical bond changes via ultrafast chemical shifts. Nat Commun 13, 7170.

• Chitturi, S. R. et al. (2022). A machine learning photon detection algorithm for coherent x-ray ultrafast fluctuation analysis. Struct Dyn 9, 054302.

• Hammarström, B.; Lane, T. J.; Batili, H.; Sierra, R.; Wiklund, M.; Sellberg, J. A. (2022). Acoustic Focusing of Protein Crystals for In-Line Monitoring and Up-Concentration during Serial Crystallography. Anal Chem 94, 12645-12656.

• Adam, V. et al. (2022). Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement. ChemPhysChem 23, e202200192.

• Srinivasan, V. et al. (2022). Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease. Commun Biol 5, 805.

• Ladd-Parada, M. et al. (2022). Following the Crystallization of Amorphous Ice after Ultrafast Laser Heating. J Phys Chem B 126, 2299.

2021

• Esmaeildoost, N. et al. (2021). Anomalous temperature dependence of the experimental x-ray structure factor of supercooled water. J Chem Phys 155, 214501.

• Sun, Y. et al. (2021). Nonuniform Flow Dynamics Probed by Nanosecond X-Ray Speckle Visibility Spectroscopy. Phys Rev Lett 127, 058001.

• Sorigue, D. et al. (2021). Mechanism and dynamics of fatty acid photodecarboxylase. Science 372, eabd5687.

• Günther, S.; Reinke, P. Y. A.; et al. (2021). X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science 372, 642-646.

• Yun, J.-H. et al. (2021). Early-stage dynamics of chloride ion-pumping rhodopsin revealed by a femtosecond X-ray laser. PNAS 118, e2020486118.

• Pathak, H. et al. (2021). Enhancement and maximum in the isobaric specific-heat capacity measurements of deeply supercooled water using ultrafast calorimetry. PNAS 118, e2018379118.

• Gruenbein, M. L. et al. (2021). Observation of shock-induced protein crystal damage during megahertz serial femtosecond crystallography. Phys Rev Research 3, 013046.

2020

• Coakley, J. et al. (2020). Femtosecond quantification of void evolution during rapid material failure. Sci Adv 6, eabb4434.

• Kim, K.-H.; Amann-Winkel, K.; et al. (2020). Experimental observation of the liquid-liquid transition in bulk supercooled water under pressure. Science 370, 978-982.

• Lane, T. J.*; Ratner, D. (2020). What are the advantages of ghost imaging? Multiplexing for x-ray and electron imaging. Opt Express 28, 5898-5918.

• Kabra, K.; Li, S.; Cropp, F.; Lane, T. J.; Musumeci, P.; Ratner, D. (2020). Mapping photocathode quantum efficiency with ghost imaging. Phys Rev Accel Beams 23, 022803.

• Driver, T. et al. (2020). Attosecond transient absorption spooktroscopy: a ghost imaging approach to ultrafast absorption spectroscopy. Phys Chem Chem Phys 22, 2704-2712.

2019

• Stankus, B. et al. (2019). Ultrafast X-ray scattering reveals vibrational coherence following Rydberg excitation. Nat Chem 11, 716-721.

• Lieske, J. et al. (2019). On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies. IUCrJ 6, 714-728.

• Barmherzig, D.; Sun, J.; Li, P.-N.; Lane, T. J.; Candes, E. J. (2019). Holographic phase retrieval and reference design. Inverse Problems 35, 094001.

• Ratner, D.; Cryan, J. P.; Lane, T. J.; Li, S.; Stupakov, G. (2019). Pump-Probe Ghost Imaging with SASE FELs. Phys Rev X 9, 011045.

• Ruddock, J. et al. (2019). Simplicity beneath Complexity: Counting Molecular Electrons Reveals Transients and Kinetics of Photodissociation Reactions. Angew Chem 58, 6371-6375.

• Sierra, R. G.; Batyuk, A.; Sun, Z.; Aquila, A.; Hunter, M. S.; Lane, T. J.; Liang, M.; et al. (2019). The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source. J Synch Rad 26, 346-357.

• Barmherzig, D.; Sun, J.; Candes, E. J.; Lane, T. J.; Li, P.-N. (2019). Dual-Reference Design for Holographic Coherent Diffraction Imaging. arXiv:1902.02492.

2018

• Yong, H. et al. (2018). Determining Orientations of Optical Transition Dipole Moments Using Ultrafast X-ray Scattering. J Phys Chem Lett 9, 6556-6562.

• Li, S.; Cropp, F.; Kabra, K.; Lane, T. J.; Wetzstein, G.; Musumeci, P.; Ratner, D. (2018). Electron ghost imaging. Phys Rev Lett 121, 114801.

• Barmherzig, D.; Sun, J.; Li, P.-N.; Lane, T. J. (2018). On Block-Reference Coherent Diffraction Imaging. Imaging and Applied Optics 10.1364/COSI.2018.CTH1B.1.

• Nogly, P. et al. (2018). Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser. Science 361, eaat0094.

• Lane, T. J.* (2018). Biomolecular Imaging with Megavolt Electrons: Opportunities and Challenges for an Ultrafast Electron Microscope at SLAC. SLAC SciDocs SLAC-R-1093.

• Perakis, F.; Camisasca, G.; Lane, T. J.; et al. (2018). Coherent x-rays reveal the influence of cage effects on ultrafast water dynamics. Nat Commun 9, 1917.

• Peck, A.; Poitevin, F.; Lane, T. J.* (2018). Intermolecular correlations are necessary to explain diffuse scattering from protein crystals. IUCrJ 5, 211-222.

• Coquelle, N. et al. (2018). Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography. Nat Chem 10, 31-37.

2017

• Shen, X.; Li, R. K.; Lundström, U.; Lane, T. J.; Reid, A. H.; Weathersby, S. P.; Wang, X. J. (2017). Femtosecond mega-electron-volt electron microdiffraction. Ultramicroscopy 184 pt. A, 172-176.

• Herrmann, J. et al. (2017). Environmental Calcium Controls Alternate Physical States of the Caulobacter Surface Layer. Biophys J 112, 1841-1851.

• Shi, J.; Nobrega, R. P.; Schwantes, C.; Kathuria, S. V.; Bilsel, O.; Matthews, C. R.; Lane, T. J.*; Pande, V. S. (2017). Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY. Sci Rep 7, 44116.

• Thayer, J.; Damiani, D.; Ford, C.; Dubrovin, M.; Gaponenko, I.; O’Grady, C. P.; et al. (2017). Data systems for the Linac coherent light source. Adv Struct Chem Imaging 3, 3.

2016

• Stankus, B.; Budarz, J. M.; Kirrander, A.; Rogers, D.; Robinson, J.; Lane, T. J.; et al. (2016). Femtosecond photodissociation dynamics of 1,4-diiodobenzene by gas-phase X-ray scattering and photoelectron spectroscopy. Faraday Discuss 194, 525-536.

• Young, I. D. et al. (2016). Structure of photosystem II and substrate binding at room temperature. Nature 540, 453-457.

• Mendez, D. et al. (2016). Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure. IUCrJ 3, 420-429.

• Hunter, M. S. et al. (2016). Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray Free Electron Laser. Nat Commun 7, 13388.

• Shi, L.; Wetzstein, G.; Lane, T. J. (2016). A Flexible Phase Retrieval Framework for Flux-limited Coherent X-Ray Imaging. arXiv:1606.01195.

• Stan, C. A., Milathianaki, D., Laksmono, H., Sierra, R. G., McQueen, T. A., Messerschmidt, M., Williams, G. J.; Koglin, J. E.; Lane, T. J.; et al. (2016). Liquid explosions induced by X-ray laser pulses. Nat Phys 12, 966-971.

• Damiani, D.; Dubrovin, M.; Gaponenko, I.; Kroeger, W.; Lane, T. J.; Mitra, A.; O’Grady, C.P.; Salnikov, A.; Sanchez-Gonzalez, A.; Schneider, D.; Yoon, C. H. (2016). Linac Coherent Light Source data analysis using psana. J Appl Cryst 49, 672-679.

• Mariani, V.; Morgan, A.; Yoon, C. H.; Lane, T. J.; White, T. A.; O’Grady, C.; et al. (2016). OnDA: online data analysis and feedback for serial X-ray imaging. J Appl Cryst 49, 1073-1080.

2015

• Minitti, M. P.; Budarz, J. M.; Kirrander, A.; Robinson, J. S.; Ratner, D.; Lane, T. J.; Zhu, D.; Glownia, J.M.; Kozina, M.; Lemke, H. T.; Sikorski, M.; Feng, Y.; Nelson S.; Saita, K.; Stankus B.; Northey T.; Hastings, J. B.; Weber, P. M. (2015). Imaging Molecular Motion: Femtosecond X-Ray Scattering of an Electrocyclic Chemical Reaction. Phys Rev Lett 114, 255501.

• McGibbon, R. T.; Beauchamp, K. A.; Schwantes, C. R.; Wang, L.-P.; Hernandez, C. X.; Harrigan, M. P.; Lane, T. J.; Swails, J. M.; Pande, V. S. (2015). MDTraj: a modern, open library for the analysis of molecular dynamics trajectories. Biophys J 109, 1528-1532.

2014

• Lane, T. J.; Schwantes, C. R.; Beauchamp, K. A.; Pande, V. S. (2014). Efficient inference of protein structural ensembles. arXiv:1408.0255.

• Mendez, D.; Lane, T. J.; et al. (2014). Observation of correlated X-ray scattering at atomic resolution. Phil Trans R Soc B 369, 20130315.

2013

• Lane, T. J.; Schwantes, C. R.; Beauchamp, K. A.; Pande, V. S. (2013). Probing the Origins of Two-State Folding. J Chem Phys 139, 145104.

• Lane, T. J.; Pande, V. S. (2013). Inferring the Rate-Length Law of Protein Folding. PLoS ONE 8, e78606.

• Lane, T. J.; Shukla, D.; Beauchamp, K. A.; Pande, V. S. (2013). To milliseconds and beyond: challenges in the simulation of protein folding. Curr Opin Struct Biol 23, 58-65.

• Eastman, P.; Friedrichs, M. S.; Chodera, J. C.; Radmer, R. J.; Bruns, C. M.; Ku, J. P.; Beauchamp, K. A.; Lane, T. J.; Wang, L.-P.; Shukla, D.; Tye, T; Houston, M.; Stich, T.; Klein, C.; Shirts, M. R.; Pande, V. S. (2013). OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. J Chem Theory Comput 9, 461-469.

2012

• Lane, T. J.; Pande, V. S. (2012). A Simple Model Predicts Experimental Folding Rates and a Hub-Like Topology. J Phys Chem B 116, 6764-6774.

• Lane, T. J.; Pande, V. S. (2012). Eigenvalues of the Homogeneous Finite Linear One Step Master Equation: Applications to Downhill Folding. J Chem Phys 137, 215106.

2011

• Lane, T. J.; Bowman, G. R.; Beauchamp, K. A.; Voelz, V. A.; Pande, V. S. (2011). Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long Trajectories. J Am Chem Soc 133, 18413-18419.

• Beauchamp, K. A.; Bowman, G. R.; Lane, T. J.; Maibaum, L.; Haque, I. S.; Pande, V. S. (2011). MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale. J Chem Theory Comput 7, 3412-3419.

• Frau, A. F.; Lane, T. J.; Schlather, A. E.; Park, J. Y.; Advincula, R. C. (2011). Modulating Electrochemical Activity in Polyaniline/Titanium Oxide Hybrid Nanostructured Ultrathin Films. Ind Eng Chem Res 50, 5532-5542.

• Lane, T. J. (2011). Ultrasonic Rheology of Mixed-Phase Systems: Using a QCM as an Effective Rheological Device: Theory and Applications for Combined Surface and Bulk Rheology. Amphiphiles: Molecular Assembly and Applications. Ed. Ramanathan Nagarajan. ACS Symposium Series 1070, Chapter 10, pp 145-174.

2010

• Zwang, T. J.; Fletcher, W. R.; Lane, T. J.; Johal, M. S. (2010). Quantification of the Layer of Hydration of a Supported Lipid Bilayer. Langmuir 26, 4598-4601.

2009

• Kett, P. J.; Casford, M. T.; Yang, A. Y.; Lane, T. J.; Johal, M. S.; Davies, P. B. (2009). Structural Changes in a Polyelectrolyte Multilayer Assembly Investigated by Reflection Absorption Infrared Spectroscopy and Sum Frequency Generation Spectroscopy. J Phys Chem B 113, 1559-1568.

2008

• Lane, T. J. et al. (2008). Dual-Beam Polarization Interferometry Resolves Mechanistic Aspects of Polyelectrolyte Adsorption. Langmuir 24, 10633-10636.

• Lane, T. J. et al. (2008). Ultrasonic Rheology of the Aqueous Phase of SDS Micellar Systems. Anal Chem 80, 7840-7845.