AtomNet PoseRanker: Enriching Ligand Pose Quality for Dynamic Proteins in Virtual High-Throughput Screens.

Structure-based, virtual High-Throughput Screening (vHTS) methods for predicting ligand activity in drug discovery are important when there are no or relatively few known compounds that interact with a therapeutic target of interest. State-of-the-art computational vHTS necessarily relies on effective methods for pose sampling and docking and generating an accurate affinity score from the docked poses. However, proteins are dynamic; in vivo ligands bind to a conformational ensemble. In silico docking to the single conformation represented by a crystal structure can adversely affect the pose quality. Here, we introduce AtomNet PoseRanker (ANPR), a graph convolutional network trained to identify and rerank crystal-like ligand poses from a sampled ensemble of protein conformations and ligand poses. In contrast to conventional vHTS methods that incorporate receptor flexibility, a deep learning approach can internalize valid cognate and noncognate binding modes corresponding to distinct receptor conformations, thereby learning to infer and account for receptor flexibility even on single conformations. ANPR significantly enriched pose quality in docking to cognate and noncognate receptors of the PDBbind v2019 data set. Improved pose rankings that better represent experimentally observed ligand binding modes improve hit rates in vHTS campaigns and thereby advance computational drug discovery, especially for novel therapeutic targets or novel binding sites.

Observation of Density-Dependent Gauge Fields in a Bose-Einstein Condensate Based on Micromotion Control in a Shaken Two-Dimensional Lattice.

We demonstrate a density-dependent gauge field, induced by atomic interactions, for quantum gases. The gauge field results from the synchronous coupling between the interactions and micromotion of the atoms in a modulated two-dimensional optical lattice. As a first step, we show that a coherent shaking of the lattice in two directions can couple the momentum and interactions of atoms and break the fourfold symmetry of the lattice. We then create a full interaction-induced gauge field by modulating the interaction strength in synchrony with the lattice shaking. When a condensate is loaded into this shaken lattice, the gauge field acts to preferentially prepare the system in different quasimomentum ground states depending on the modulation phase. We envision that these interaction-induced fields, created by fine control of micromotion, will provide a stepping stone to model new quantum phenomena within and beyond condensed matter physics.

Predicting molecular properties with covariant compositional networks.

Density functional theory (DFT) is the most successful and widely used approach for computing the electronic structure of matter. However, for tasks involving large sets of candidate molecules, running DFT separately for every possible compound of interest is forbiddingly expensive. In this paper, we propose a neural network based machine learning algorithm which, assuming a sufficiently large training sample of actual DFT results, can instead learn to predict certain properties of molecules purely from their molecular graphs. Our algorithm is based on the recently proposed covariant compositional networks framework and involves tensor reduction operations that are covariant with respect to permutations of the atoms. This new approach avoids some of the representational limitations of other neural networks that are popular in learning from molecular graphs and yields promising results in numerical experiments on the Harvard Clean Energy Project and QM9 molecular datasets.

Density Waves and Jet Emission Asymmetry in Bose Fireworks.

A Bose condensate, subject to periodic modulation of the two-body interactions, was recently observed to emit matter-wave jets resembling fireworks [Nature (London) 551, 356 (2017)NATUAS0028-083610.1038/nature24272]. In this Letter, combining experiment with numerical simulation, we demonstrate that these "Bose fireworks" represent a late stage in a complex time evolution of the driven condensate. We identify a "density wave" stage which precedes jet emission and results from the interference of matter waves. The density waves self-organize and self-amplify without breaking long range translational symmetry. This density wave structure deterministically establishes the template for the subsequent patterns of the emitted jets. Moreover, our simulations, in good agreement with experiment, address an apparent asymmetry in the jet pattern, and show that it is fully consistent with momentum conservation.

Direct Lattice Shaking of Bose Condensates: Finite Momentum Superfluids.

We address band engineering in the presence of periodic driving by numerically shaking a lattice containing a bosonic condensate. By not restricting to simplified band structure models we are able to address arbitrary values of the shaking frequency, amplitude, and interaction strengths g. For "near-resonant" shaking frequencies with moderate g, a quantum phase transition to a finite momentum superfluid is obtained with Kibble-Zurek scaling and quantitative agreement with experiment. We use this successful calibration as a platform to support a more general investigation of the interplay between (one particle) Floquet theory and the effects associated with arbitrary g. Band crossings lead to superfluid destabilization, but where this occurs depends on g in a complicated fashion.

Quasicondensation in Two-Dimensional Fermi Gases.

In this paper we follow the analysis and protocols of recent experiments, combined with simple theory, to arrive at a physical understanding of quasi-condensation in two dimensional Fermi gases. A key signature of quasi-condensation, which contains aspects of Berezinskii-Kosterlitz-Thouless behavior, is a strong zero momentum peak in the pair momentum distribution. Importantly, this peak emerges at a reasonably well defined onset temperature. The resulting phase diagram, pair momentum distribution, and algebraic power law decay are compatible with recent experiments throughout the continuum from BEC to BCS.

Roton-maxon excitation spectrum of Bose condensates in a shaken optical lattice.

We present experimental evidence showing that an interacting Bose condensate in a shaken optical lattice develops a roton-maxon excitation spectrum, a feature normally associated with superfluid helium. The roton-maxon feature originates from the double-well dispersion in the shaken lattice, and can be controlled by both the atomic interaction and the lattice modulation amplitude. We determine the excitation spectrum using Bragg spectroscopy and measure the critical velocity by dragging a weak speckle potential through the condensate-both techniques are based on a digital micromirror device. Our dispersion measurements are in good agreement with a modified Bogoliubov model.

Half-quantum vortex molecules in a binary dipolar Bose gas.

We study the ground state phases of a rotating two-component, or binary, Bose-Einstein condensate, wherein one component possesses a large permanent magnetic dipole moment. A variety of nontrivial phases emerge in this system, including a half-quantum vortex (HQV) chain phase and a HQV molecule phase, where HQVs bind at short distances. We attribute these phases to the development of a minimum in the HQV interaction potential, which emerges without coherent coupling or attractive interactions between the components. Thus, we show that the presence of dipolar interactions in this system provides a unique mechanism for the formation of HQV molecules and results in a rich ground state phase diagram.

Meron ground state of Rashba spin-orbit-coupled dipolar bosons.

We study the effects of dipolar interactions on a Bose-Einstein condensate with synthetically generated Rashba spin-orbit coupling. The dipolar interaction we consider includes terms that couple spin and orbital angular momentum in a way perfectly congruent with the single-particle Rashba coupling. We show that this internal spin-orbit coupling plays a crucial role in the rich ground-state phase diagram of the trapped condensate. In particular, we predict the emergence of a thermodynamically stable ground state with a meron spin configuration.

Magnetically generated spin-orbit coupling for ultracold atoms.

We present a new technique for producing two- and three-dimensional Rashba-type spin-orbit couplings for ultracold atoms without involving light. The method relies on a sequence of pulsed inhomogeneous magnetic fields imprinting suitable phase gradients on the atoms. For sufficiently short pulse durations, the time-averaged Hamiltonian well approximates the Rashba Hamiltonian. Higher order corrections to the energy spectrum are calculated exactly for spin-1/2 and perturbatively for higher spins. The pulse sequence does not modify the form of rotationally symmetric atom-atom interactions. Finally, we present a straightforward implementation of this pulse sequence on an atom chip.

Synthetic 3D spin-orbit coupling.

We describe a method for creating a three-dimensional analogue to Rashba spin-orbit coupling in systems of ultracold atoms. This laser induced coupling uses Raman transitions to link four internal atomic states with a tetrahedral geometry, and gives rise to a Dirac point that is robust against environmental perturbations. We present an exact result showing that such a spin-orbit coupling in a fermionic system always gives rise to a molecular bound state.