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The structural dynamics of a molecule are determined by the underlying potential energy landscape. Conical intersections are funnels connecting otherwise separate energy surfaces. Posited almost a century ago1, conical intersections remain the subject of intense scientific investigation2–4. In biology, they play a pivotal role in vision, photosynthesis, and DNA stability5,6. In ultrafast radiationless de-excitation1,7, they are vital to ameliorating photon-induced damage. In chemistry, they tightly couple the normally separable nuclear and electronic degrees of freedom, precluding the Born-Oppenheimer approximation8. In physics, they manifest a Berry phase, giving rise to destructive interference between clockwise and anti-clockwise trajectories around the conical intersection9. Accurate theoretical methods for examining conical intersections are at present limited to small molecules. Experimental investigations are challenged by the required time resolution and sensitivity. Current structure-dynamical understanding of conical intersections is thus limited to simple molecules with around 10 atoms, on timescales of about 100 fs or longer10. Spectroscopy can achieve better time resolution, but provides only indirect structural information. Here, we present single-femtosecond, atomic-resolution movies of a 2,000-atom protein passing through a conical intersection. These movies, extracted from experimental data by geometric machine learning, reveal the dynamical trajectories of de-excitation via a conical intersection, yield the key parameters of the conical intersection controlling the de-excitation process, and elucidate the topography of the electronic potential energy surfaces involved.

The structural dynamics of a molecule are determined by the underlying potential energy landscape. Conical intersections are funnels connecting otherwise separate potential energy surfaces. Posited almost a century ago1, conical intersections remain the subject of intense scientific interest2–5. In biology, they have a pivotal role in vision, photosynthesis and DNA stability6. Accurate theoretical methods for examining conical intersections are at present limited to small molecules. Experimental investigations are challenged by the required time resolution and sensitivity. Current structure-dynamical understanding of conical intersections is thus limited to simple molecules with around ten atoms, on timescales of about 100 fs or longer7. Spectroscopy can achieve better time resolutions8, but provides indirect structural information. Here we present few-femtosecond, atomic-resolution videos of photoactive yellow protein, a 2,000-atom protein, passing through a conical intersection. These videos, extracted from experimental data by machine learning, reveal the dynamical trajectories of de-excitation via a conical intersection, yield the key parameters of the conical intersection controlling the de-excitation process and elucidate the topography of the electronic potential energy surfaces involved. Serial femtosecond crystallography (SFX) has provided significant understanding of time-resolved processes of various systems in biology, for example, rhodopsin, which underlies our vision. The approach involves femtosecond-length X-ray pulses directed at protein crystals and has been used to study various photoactive proteins. However, the function of proteins such as rhodopsin requires trans–cis isomerization of a chromophore, which involves crossing of a conical intersection—a funnel separating potential energy surfaces—at timescales faster than what can be achieved experimentally. Here, Ourmazd and colleagues report a machine learning analysis of SFX data of photoactive yellow protein, which resolves the protein passing through a conical intersection, providing information about the potential energy surfaces involved and achieving time resolution of less than 10 fs. This approach offers an opportunity to understand some of the fastest processes in biology by extracting even more information from SFX datasets.

Wave transmission media created by a periodically modulated magnetic material are referred to as magnonic crystals [1]. The dynamics of magnonic crystals are described by common concepts of solid state physics, i.e., group velocity, density of states, and band structure. We investigate so-called magnonic vortex crystals created via rectangular arrangements of magnetic vortices. Here we aim at the control of vortex-core polarizations by perpendicularly aligned bias fields and use magnetic force microscopy and broadband-ferromagnetic transmission spectroscopy. In the first step, arrays of CoPt-multilayer disks arranged in a checkerboard pattern are prepared by electron-beam lithography, sputter deposition, and lift-off processing, compare figure 1(a). Two layer types A (Pt/0.7 nm Co/Pt) and B (Pt/2x(0.8 Co/1.1 nm Pt)/Pt) of the pattern differ in the magnetic anisotropy and thus yield different switching fields of the perpendicularly magnetized disks [2]. The switching fields are investigated by Kerr microscopy. After saturation in negative field direction, disks of type B start to switch at a field strength of μ 0 H = +29 mT visible in the hysteresis loop shown in figure 1(b). The switching is completed at +37 mT where the greyscale intensity stays constant. A stable state of antiparallel magnetization of both types of disks persists up to +56 mT, where disks of type A start to switch. At +68 mT the magnetizations of disks of type A and B are aligned parallel with the positive field direction, compare figure 1(c). The switching of the multilayer disks follows a normal distribution and shows no dependence on the interdisk distance. In the next step, permalloy disks are prepared on top of the CoPt disks by electron-beam lithography, thermal evaporation, and lift-off processing. A thin Si interlayer is used to avoid direct contact of the perpendicularly and in-plane magnetized ferromagnets. The magnetization of the CoPt disks is adjusted using a perpendicularly aligned magnetic field. Subsequently an in-plane field is used to nucleate vortices in the permalloy disks. It is expected that due to stray field coupling the polarization of the vortex core in each permalloy disk is determined by the subjacent CoPt disk and coincides with the direction of the magnetization of the CoPt disk. The vortex-core polarizations are investigated using magnetic force microscopy (not shown).