SVSBI: Sequence-based virtual screening of biomolecular interactions

Virtual screening (VS) is an essential technique for understanding biomolecular interactions, particularly, drug design and discovery. The best-performing VS models depend vitally on three-dimensional (3D) structures, which are not available in general but can be obtained from molecular docking. However, current docking accuracy is relatively low, rendering unreliable VS models. We introduce sequence-based virtual screening (SVS) as a new generation of VS models for modeling biomolecular interactions. The SVS model utilizes advanced natural language processing (NLP) algorithms and optimizes deep $K$-embedding strategies to encode biomolecular interactions without invoking 3D structure-based docking. We demonstrate the state-of-art performance of SVS for four regression datasets involving protein-ligand binding, protein-protein, protein-nucleic acid binding, and ligand inhibition of protein-protein interactions and five classification datasets for the protein-protein interactions in five biological species. SVS has the potential to dramatically change the current practice in drug discovery and protein engineering

Antiferromagnetic magnonic charge current generation via ultrafast optical excitation

N\'eel spin-orbit torque allows a charge current pulse to efficiently manipulate the N\'eel vector in antiferromagnets, which offers a unique opportunity for ultrahigh density information storage with high speed. However, the reciprocal process of N\'eel spin-orbit torque, the generation of ultrafast charge current in antiferromagnets has not been demonstrated. Here, we report the experimental observation of charge current generation in antiferromagnetic metallic Mn2Au thin films using ultrafast optical excitation. The ultrafast laser pulse excites antiferromagnetic magnons, resulting in instantaneous non-equilibrium spin polarization at the antiferromagnetic spin sublattices with broken spatial symmetry. Then the charge current is generated directly via spin-orbit fields at the two sublattices, which is termed as the reciprocal phenomenon of N\'eel spin-orbit torque, and the associated THz emission can be detected at room temperature. Besides the fundamental significance on the Onsager reciprocity, the observed magnonic charge current generation in antiferromagnet would advance the development of antiferromagnetic THz emitter.Comment: 15 pages, 4 figures, this work was submitted to Nature Communications on Jan. 4th, 2023, now is under the 3rd review proces

Terahertz Spin Current Dynamics in Antiferromagnetic Hematite

An important vision of modern magnetic research is to use antiferromagnets (AFMs) as controllable and active ultrafast components in spintronic devices. Hematite (α-Fe2O3) is a promising model material in this respect because its pronounced Dzyaloshinskii-Moriya interaction leads to the coexistence of antiferromagnetism and weak ferromagnetism. Here, femtosecond laser pulses are used to drive terahertz (THz) spin currents from α-Fe2O3 into an adjacent Pt layer. Two contributions to the generation of the spin current with distinctly different dynamics are found: the impulsive stimulated Raman scatting that relies on the AFM order and the ultrafast spin Seebeck effect that relies on the net magnetization. The total THz spin current dynamics can be manipulated by a medium-strength magnetic field below 1 T. The control of the THz spin current achieved in α-Fe2O3 opens the pathway toward tailoring the exact spin current dynamics from ultrafast AFM spin sources

Defect-induced helicity-dependent terahertz emission in Dirac semimetal PtTe2 thin films

Nonlinear transport enabled by symmetry breaking in quantum materials has aroused considerable interest in condensed matter physics and interdisciplinary electronics. However, the nonlinear optical response in centrosymmetric Dirac semimetals via the defect engineering has remained highly challenging. Here, we observe the helicity-dependent terahertz (THz) emission in Dirac semimetal PtTe2 thin films via circular photogalvanic effect (CPGE) under normal incidence. This is activated by artificially controllable out-of-plane Te-vacancy defect gradient, which is unambiguously evidenced by the electron ptychography. The defect gradient lowers the symmetry, which not only induces the band spin splitting, but also generates the giant Berry curvature dipole (BCD) responsible for the CPGE. Such BCD-induced helicity-dependent THz emission can be manipulated by the Te-vacancy defect concentration. Furthermore, temperature evolution of the THz emission features the minimum of the THz amplitude due to the carrier compensation. Our work provides a universal strategy for symmetry breaking in centrosymmetric Dirac materials for efficient nonlinear transport and facilitates the promising device applications in integrated optoelectronics and spintronics.Comment: 27 pages, 5 figure

Reconfiguration of magnetic domain structures of ErFeO3 by intense terahertz free electron laser pulses

Understanding the interaction between intense terahertz (THz) electromagnetic fields and spin systems has been gaining importance in modern spintronics research as a unique pathway to realize ultrafast macroscopic magnetization control. In this work, we used intense THz pulses with pulse energies in the order of 10 mJ/pulse generated from the terahertz free electron laser (THz-FEL) to irradiate the ferromagnetic domains of ErFeO3 single crystal. It was found that the domain shape can be locally reconfigured by irradiating the THz - FEL pulses near the domain boundary. Observed domain reconfiguration mechanism can be phenomenologically understood by the combination of depinning effect and the entropic force due to local thermal gradient exerted by terahertz irradiation. Our finding opens up a new possibility of realizing thermal-spin effects at THz frequency ranges by using THz-FEL pulses.publishe