Publications

Updated: 18 May 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. Comms Bio 9, 602.

2025

• Fadini, A.*; Apostolopoulou, V.; Lane, T. J.*; van Thor, J. J.* (2025) Denoising Reveals Low-Occupancy Populations in Protein Crystals Comms Bio 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. Science Advances 11 (3), 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), 1-9.

• 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 (6674), 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 Op Struct Biol 80, 102601.

• 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. Structural Dynamics,  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, 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 (11) 2299.

2021

• Esmaeildoost, N. et al (2021) Anomalous temperature dependence of the experimental x-ray structure factor of supercooled water. J Chem Phys, 155 (21) 214501.

• Sun, Y. et al (2021) Nonuniform Flow Dynamics Probed by Nanosecond X-Ray Speckle Visibility Spectroscopy. Phys Rev Lett, 127 (5) 058001.

• Sorigue, D. et al (2021) Mechanism and dynamics of fatty acid photodecarboxylase. Science, 372 (6538), eabd5687

• Günther, S.; Reinke, P., et al (2021) X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science, 372 (6542) 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 (13) 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 (6) e2018379118.

• Gruenbein, M. L. et al (2021) Observation of shock-induced protein crystal damage during megahertz serial femtosecond crystallography. Phys Rev Research, 3, (1) 013046.

2020

• Coakley J. et al (2020) Femtosecond quantification of void evolution during rapid material failure. Sci Advances, 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 (6519) 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 (5), 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, DOI: 10.1039/c9cp03951a.

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(4), 714-728.

• Barmherzig, D; Sun, J.; Li, P-N; Lane, T. J. and Candes, E. J (2019). Holographic Phase Retrieval and Reference Design. Inverse Problems, IP-102044.R1.

• 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(10), 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(2),  346-357.

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

• Barmherzig, D; Sun, J; Candes, E. J.; Lane, T. J. and Li, P-N (2019) Holographic Phase Retrieval and Optimal Reference Design. arXiv:1901.06453.

2018

• Yong, H. et al. (2018). Determining Orientations of Optical Transition Dipole Moments Using Ultrafast X-ray Scattering. J Phys Chem Lett, 9(22), 6556-6562. 

• S. Li; F. Cropp; K. Kabra; Lane, T. J.; Weitzstein, G; Musumeci, P.; Ratner, D. (2018) Electron ghost imaging. Phys Rev Lett 121(11), 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 et al. (2018) Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser. Science, 361, 194 (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 Comm, 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.

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 184PA, 172-176.

• Coquelle et al. (2017) Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography. Nat Chem, 10(1), 31-37.

• Herrmann, J.; et al. Environmental Calcium Controls Alternate Physical States of the Caulobacter Surface Layer. (2017) 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. Scientific Reports, 1-13. 

• 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 Imag, 1-13. 

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 Discussions, 194, 525-536.

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

• Mendez, D.; et al. Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure. (2016) 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 Comm, 7, 13388.

• Shi, L.; Wetzstein, G.; Lane, T. J. (2016). A Flexible Phase Retrieval Framework for Flux-limited Coherent X-Ray Imaging. arXiv:1606.01195v1.

• 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, 1-7.

• 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, 1-8.

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. Biophysical J 109(8), 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 Royal 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. and Pande V. S. (2013) Inferring the Rate-Length Law of Protein Folding. PLoS ONE DOI: 10.1371/journal.pone.0078606

• Lane, T. J.;  Shukla, D.; Beauchamp, K. A.; Pande V. S. (2013) To milliseconds and beyond: challenges in the simulation of protein folding. Curr Op Struct Biol, 23(1) 58-65.

• Lane, T. J. and Pande V. S. (2013) Eigenvalues of the Homogeneous Finite Linear One Step Master Equation: Applications to Downhill Folding. J Chem Phys, 6(12) 137, 215106.

• 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(1) 461-469.

2012

• Lane, T. J. and Pande, V. S. (2012) A Simple Model Predicts Experimental Folding Rates and a Hub-Like Topology. J Phys Chem B, 116(23) 6764-6774.

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(45) 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(10) 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(9) 5532-5542.

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

2009

• Zwang, T. J.; Fletcher, W. R.; Lane, T. J.; Johal, M. S. (2009) Characterization of the Layer of Hydration of a Supported Lipid Bilayer. Langmuir, 26(7) 4598-4601.

2008

• Kett, P.; Casford, M.; Yang, A.; Johal, M.; Lane, T. J.; Davies, P. (2008) Structural Changes in a Polyelectrolyte Multilayer Assembly Investigated by Reflection Absorption Infrared Spectroscopy and Sum Frequency Generation Spectroscopy. J Phys Chem B, 113(6) 1559-1568.

• Lane, T. J. et al. (2008) Dual-Beam Polarization Interferometry Resolves Mechanistic Aspects of Polyelectrolyte Adsorption. Langmuir, 24(19) 10633-10636.

• Lane, T. J. et al. (2008) Ultrasonic Rheology of the Aqueous Phase of SDS Micellar Systems. Anal Chemistry, 80(20), 7840-7845.