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At least 343 records · Page 19

Computational tools for the simulation and analysis of spin-polarized EPR spectra

The EPR spectra of paramagnetic species induced by photoexcitation typically exhibit enhanced absorptive and emissive features resulting from sublevel populations that differ from thermal equilibrium. The populations and the resulting spin polarization of the spectra are dictated by the selectivity of the photophysical process generating the observed state. Simulation of the spin-polarized EPR spectra is crucial in the characterization of both the dynamics of formation of the photoexcited state as well as its electronic and structural properties. EasySpin, the simulation toolbox for EPR spectroscopy, now includes extended support for the simulation of the EPR spectra of spin-polarized states of arbitrary spin multiplicity and formed by a variety of different mechanisms, including photoexcited triplet states populated by intersystem crossing, charge recombination or spin polarization transfer, spin-correlated radical pairs created by photoinduced electron transfer, triplet pairs formed by singlet fission and multiplet states arising from photoexcitation in systems containing chromophores and stable radicals. In this paper, we highlight EasySpin’s capabilities for the simulation of spin-polarized EPR spectra on the basis of illustrative examples from the literature in a variety of fields ranging across chemistry, biology, material science and quantum information science.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Visible-Light Photoinitiation of (Meth)acrylate Polymerization with Autonomous Post-Conversion

Conversion plateaus rapidly in radical photopolymerizations (RPPs) following discontinuation of irradiation due to rapid termination of reactive radicals, which restricts the wider use of RPPs in applications that involve nonuniform light access including those with attenuated light transmission or irregular surfaces. Based on our recent report of a radical dark-curing photoinitiator (DCPI) that continues polymerization beyond the cessation of irradiation by enabling latent redox initiation with photo-released amine in the presence of a suitable oxidant, we developed a new DCPI with an absorption spectrum that extends well into the visible range. Our design process involved a series of computational investigations of candidate molecules, including a systematic study of substituents and their position-dependent effects on absorption characteristics, electronic transitions, and the photochemical mechanism and its associated energetics. Our quantum chemical computations identified the target compound 5,7-dimethoxy-6-bromo-3-aroylcoumarin-DMPT/BPh4 and predicted that it would facilitate the dark-curing mechanism by concurrent photo-radical generation and photo-induced release of an efficient redox reductant under visible irradiation. This reductant-tethered chromophore was then synthesized and optically characterized with UV–vis spectroscopy that revealed its strong visible-light absorption with a molar absorptivity of 5710 M–1 cm–1 at 405 nm and 50 M–1 cm–1 at 455 nm. We then demonstrated extensive dark-curing of >35% additional conversion over 25 min following brief activation of the shelf-stable one-part system by irradiation with a 455 nm LED that was ceased at 20% conversion. In contrast, shuttering irradiation of the control formulation at that same point resulted in immediate cessation of conversion, which plateaued at 20%. We determined a remarkable initiator efficiency of 2.82 that results from the additional redox-generated radicals with a 77% photo-reductant generation quantum yield. The combination of superior photo- and dark-curing efficiencies of this new visible DCPI is expected to open new application opportunities in RPP, especially those involving resins that are highly light attenuating, surfaces that possess irregular features that produce uneven irradiance, and production lines where continued dark-curing downstream of the light activation step enhances line efficiencies.

absorption spectrum↗

Singlet fission for quantum information and quantum computing: the parallel JDE model

Abstract Singlet fission is a photoconversion process that generates a doubly excited, maximally spin entangled pair state. This state has applications to quantum information and computing that are only beginning to be realized. In this article, we construct and analyze a spin-exciton hamiltonian to describe the dynamics of the two-triplet state. We find the selection rules that connect the doubly excited, spin-singlet state to the manifold of quintet states and comment on the mechanism and conditions for the transition into formally independent triplets. For adjacent dimers that are oriented and immobilized in an inert host, singlet fission can be strongly state-selective. We make predictions for electron paramagnetic resonance experiments and analyze experimental data from recent literature. Our results give conditions for which magnetic resonance pulses can drive transitions between optically polarized magnetic sublevels of the two-exciton states, making it possible to realize quantum gates at room temperature in these systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Formation and Microwave Losses of Hydrides in Superconducting Niobium Thin Films Resulting from Fluoride Chemical Processing

Abstract Superconducting niobium (Nb) thin films have recently attracted significant attention due to their utility for quantum information technologies. In the processing of Nb thin films, fluoride‐based chemical etchants are commonly used to remove surface oxides that are known to affect superconducting quantum devices adversely. However, these same etchants can also introduce hydrogen to form Nb hydrides, potentially negatively impacting microwave loss performance. Here, comprehensive materials characterization of Nb hydrides formed in Nb thin films as a function of fluoride chemical treatments is presented. In particular, secondary‐ion mass spectrometry, X‐ray scattering, and transmission electron microscopy reveal the spatial distribution and phase transformation of Nb hydrides. The rate of hydride formation is determined by the fluoride solution acidity and the etch rate of Nb 2 O 5, which acts as a diffusion barrier for hydrogen into Nb. The resulting Nb hydrides are detrimental to Nb superconducting properties and lead to increased power‐independent microwave loss in coplanar waveguide resonators. However, Nb hydrides do not correlate with two‐level system loss or device aging mechanisms. Overall, this work provides insight into the formation of Nb hydrides and their role in microwave loss, thus guiding ongoing efforts to maximize coherence time in superconducting quantum devices.

36 MATERIALS SCIENCE↗

Computational methods based on density functional theory for reactions and processes involving electronic spin (Final Technical Report)

This award supports one post-doctoral researcher for 1.5 years. Publications that acknowledge this grant: Refs. 1–14. Refs. 3,10,12 assess current methodology for the evaluation of magnetic exchange couplings in transition metal complexes. In particular, Ref. 10 validates the use of an approximate (non-iterative) Green’s function approach for the calculation of magnetic exchange couplings and will be the foundation for Thrust 2 in this proposal. Refs. 3 and 12 focus on widely used density functional approaches based on the standard energy differences methodology for the particular case of oxo-bridged Fe(III) complexes. Refs. 2,4–7,11 apply current methodologies to problems of practical interest in molecular magnetism. Ref. 13 presents a methodology to explicitly simulate the dynamics of open quantum systems within density functional theory (DFT) calculations based on the Liouville-von Neumann equation of motion for quantum systems driven out-of-equilibrium. Ref. 8 uses non-collinear spin DFT to explain the mechanical behavior of magnetic mono-atomic Pt wires produced in break-junction experiments in the presence of a magnetic field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multiple fermion scattering in the weakly coupled spin-chain compound YbAlO 3

The Heisenberg antiferromagnetic spin-1/2 chain, originally introduced almost a century ago, is one of the best studied models in quantum mechanics due to its exact solution, but nevertheless it continues to present new discoveries. Its low-energy physics is described by the Tomonaga-Luttinger liquid of spinless fermions, similar to the conduction electrons in one-dimensional metals. In this work we investigate the Heisenberg spin-chain compound YbAlO3 and show that the weak interchain coupling causes Umklapp scattering between the left- and right-moving fermions and stabilizes an incommensurate spin-density wave order at q = 2k F under finite magnetic fields. These Umklapp processes open a route to multiple coherent scattering of fermions, which results in the formation of satellites at integer multiples of the incommensurate fundamental wavevector Q = nq. Our work provides surprising and profound insight into bandstructure control for emergent fermions in quantum materials, and shows how neutron diffraction can be applied to investigate the phenomenon of coherent multiple scattering in metals through the proxy of quantum magnetic systems.

36 MATERIALS SCIENCE↗

Parametrized process characterization with reduced resource requirements

Quantum process tomography (QPT) is a powerful tool to characterize quantum operations, but it requires considerable resources, making it impractical for more than two-qubit systems. This study proposes an alternative approach that requires significantly fewer resources for unitary process characterization with a built-in method for state preparation and measurement error mitigation. By measuring the quantum process as rotated through the X and Y axes on the Bloch sphere, we can acquire enough information to reconstruct the quantum process matrix χ and measure its fidelity. We test the algorithm's performance against standard QPT using simulated and physical experiments on several IBM quantum processors and compare the resulting process matrices. We demonstrate with numerical experiments that the method can improve gate fidelity via a noise reduction in the imaginary part of the process matrix, along with a stark decrease in the number of experiments needed to perform the characterization.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Photonic Interrogation and Control of Nano Processes

My research activities for the summer of 2003 consisted of two projects: One project was concerned with determining a method for predicting the static and dynamic assembly properties of nano-structures using laser tweezers. The other project was to investigate the generation of Laguerre-Gaussian modes using a spatial light modulator incorporated into an optical tweezers system. Concerning the first project, I initially pursued the approach suggested by my NASA colleague Dr. Art Decker. This approach involved mimicking the model of the structure of atomic nucleus for the assembly of 1 to 100 atoms using allowed quadruple transitions induced by orbital angular momentums of a Laguerre- Gaussian (Doughnut) laser mode. After realizing the inaptness of the nuclear model with the nanostructure model as far as the binding forces and transitions were concerned, I focused on using quantum dot modei. This model was not attuned also for the host lattice influences the electronic structure of the quantum dot. Thus one other option that I decided to pursue was the approach of molecular quantum mechanics. In this approach the nanostructure is treated as a large (10-100 nm) molecule constructed from single element or multi-elements. Subsequent to consultation with Dr. Fred Morales, a chemical engineer at NASA GRC, and Dr. David Ball, a computational chemist at Cleveland State University, I acquired a molecular-quantum computation software, Hyperchem 7.0. This software allows simulation of different molecular structures as far as their static and dynamic behaviors are concerned. The time that I spent on this project was about eight weeks. Once this suitable approach was identified, I realized the need to collaborate with a computational quantum chemist to pursue searching for stable nanostructures in the range of 10-100 nm that we can be assembled using laser tweezers. The second project was about generating laser tweezers that possess orbital angular momentum. As shown, we were able to generate laser tweezers modes of different orbital angular momentum using a spatial light modulator incorporated into a laser tweezers system. The motivation for investigating these types of modes stems from being able to spin particles at high speeds and also to orient two particles in separate traps and then join them together. Also, there has been recent intense interest on fundamental physics research on orbital angular momentum of light. The fact that circularly polarized light may have associated with it angular momentum that relates to the spin of individual photons (spin 0 for the plane polarized light, spin +1 for the right-circularly polarized light and spin -1 for the left-circularly polarized light) was first demonstrated by Beth in 1936. Orbital angular momentum is, however, distinct from spin in that the spin angular momentum of light is intrinsically linked to the behavior of the electric field in the light whereas orbital angular momentum is a consequence of inclined wavefronts. In 1992 L. Allen, et al showed that the Laguerre-Gaussian (LG) modes could possess well-defined orbital angular momentum that can exceed 1 planck's constant, i.e. l plancks constant per photon, where l is the azimuthal index of the mode.

Jassemnejad, Baha↗

Universal crossed beam imaging studies of polyatomic reaction dynamics

The marriage between high level quantum calculations and experimental advances in laser technology, quantum state control, and detection techniques have opened the door to the study of molecular collision dynamics at a new level of detail. However, one current challenge lies in adapting these powerful strategies to address questions beyond the scope of the small ground state systems that have largely been the focus of reaction dynamics investigations to-date. For molecules with intermediate or large size (more than 6 atoms), lack of spectroscopic information and spectral congestion limit quantum state preparation, control and detection for experiment, and the large number of degrees of freedom of the system makes accurate quantum dynamics calculations prohibitively expensive. Nevertheless, studies of the chemical dynamics of such systems can reveal novel aspects of reactivity not anticipated based upon the behavior of smaller model systems. This Perspective will highlight applications of soft vacuum ultraviolet photoionization at 157 nm as a universal probe in combination with crossed beams and DC slice velocity map ion imaging to study bimolecular reaction dynamics of molecules of intermediate or large size, illuminated with support of high-level ab initio calculations. In this work, we report on the chemical dynamics of atomic oxygen or chlorine reactions with organic compounds: propanol isomers, alkylamines (N(CH 3 ) 3 and NH(CH 3 ) 2 ), and isobutene ((CH 3 ) 2 CCH 2 ) studied using this approach. The polyatomic radical products from the hydrogen abstraction process have been detected by 157 nm photoionization and their slice ion images embody translational energy and angular information that directly reflect the underlying collision dynamics. Various reaction mechanisms (such as direct abstraction and addition–elimination) along with the involvement of roaming dynamics and novel intersystem crossing pathways are presented. These demonstrate the power of this technique to reveal fundamentally new aspects of reaction dynamics that arise in larger reaction systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Benchmarking Information Scrambling

Information scrambling refers to the rapid spreading of initially localized information over an entire system, via the generation of global entanglement. This effect is usually detected by measuring a temporal decay of the out-of-time order correlators. However, in experiments, decays of these correlators suffer from fake positive signals from various sources, e.g., decoherence due to inevitable couplings to the environment, or errors that cause mismatches between the purported forward and backward evolutions. Here, in this Letter, we provide a simple and robust approach to single out the effect of genuine scrambling. This allows us to benchmark the scrambling process by quantifying the degree of the scrambling from the noisy backgrounds. We also demonstrate our protocol with simulations on IBM cloud-based quantum computers.

97 MATHEMATICS AND COMPUTING↗

Development and Progress in Enabling the Photocatalyst Ti02 Visible-Light-Active

Photocatalytic oxidation (PCO) of organic contaminants is a promising air and water quality management approach which offers energy and cost savings compared to thermal catalytic oxidation (TCO). The most widely used photocatalyst, anatase TiO2, has a wide band gap (3.2 eV) and is activated by UV photons. Since solar radiation consists of less than 4% UV, but contains 45% visible light, catalysts capable of utilizing these visible photons need to be developed to make peo approaches more efficient, economical, and safe. Researchers have attempted various approaches to enable TiO2 to be visible-light-active with varied degrees of success'. Strategies attempted thus far fall into three categories based on their electrochemical' mechanisms: 1) narrowing the band gap of TiO2 by implantation of transition metal elements or nonmetal elements such as N, S, and C, 2) modifying electron-transfer processes during PCO by adsorbing sensitizing dyes, and 3) employing light-induced interfacial electron transfer in the heteronanojunction systems consisting of narrow band gap semiconductors represented by metal sulfides and TiO2. There are diverse technical approaches to implement each of these strategies. This paper presents a review of these approaches and results of the photocatalytic activity and photonic efficiency of the end .products under visible light. Although resulting visible-light-active (VLA) photocatalysts show promise, there is often no comparison with unmodified TiO2 under UV. In a limited number of studies where such comparison was provided, the UV-induced catalytic activity of bare TiO2 is much greater than the visible-light-induced catalytic activity of the VLA catalyst. Furthermore, VLA-catalysts have much lower quantum efficiency compared to the approx.50% quantum efficiency of UV-catalysts. This stresses the need for continuing research in this area.

Levine, Lanfang H.↗

Unraveling Triplet Formation Mechanisms in Acenothiophene Chromophores

The evolution of molecular platforms for singlet fission (SF) chromophores has fueled the quest for new compounds capable of generating triplets quantitatively at fast time scales. As the exploration of molecular motifs for SF has diversified, a key challenge has emerged in identifying when the criteria for SF have been satisfied. Here, we show how covalently bound molecular dimers uniquely provide a set of characteristic optical markers that can be used to distinguish triplet pair formation from processes that generate an individual triplet. These markers are contained within (i) triplet charge-transfer excited state absorption features, (ii) kinetic signatures of triplet-triplet annihilation processes, and (iii) the modulation of triplet formation rates using bridging moieties between chromophores. Our assignments are verified by time-resolved electron paramagnetic resonance (EPR) measurements, which directly identify triplet pairs by their electron spin and polarization patterns. Here we apply these diagnostic criteria to dimers of acenothiophene derivatives in solution that were recently reported to undergo efficient intermolecular SF in condensed media. While the electronic structure of these heteroatom-containing chromophores can be broadly tuned, the effect of their enhanced spin-orbit coupling and low-energy nonbonding orbitals on their SF dynamics has not been fully determined. We find that SF is fast and efficient in tetracenothiophene but that anthradithiophene exhibits fast intersystem crossing due to modifications of the singlet and triplet excited state energies upon functionalization of the heterocycle. We conclude that it is not sufficient to assign SF based on comparisons of the triplet formation kinetics between monomer and multichromophore systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

HTMT-class Latency Tolerant Parallel Architecture for Petaflops Scale Computation

Computational Aero Sciences and other numeric intensive computation disciplines demand computing throughputs substantially greater than the Teraflops scale systems only now becoming available. The related fields of fluids, structures, thermal, combustion, and dynamic controls are among the interdisciplinary areas that in combination with sufficient resolution and advanced adaptive techniques may force performance requirements towards Petaflops. This will be especially true for compute intensive models such as Navier-Stokes are or when such system models are only part of a larger design optimization computation involving many design points. Yet recent experience with conventional MPP configurations comprising commodity processing and memory components has shown that larger scale frequently results in higher programming difficulty and lower system efficiency. While important advances in system software and algorithms techniques have had some impact on efficiency and programmability for certain classes of problems, in general it is unlikely that software alone will resolve the challenges to higher scalability. As in the past, future generations of high-end computers may require a combination of hardware architecture and system software advances to enable efficient operation at a Petaflops level. The NASA led HTMT project has engaged the talents of a broad interdisciplinary team to develop a new strategy in high-end system architecture to deliver petaflops scale computing in the 2004/5 timeframe. The Hybrid-Technology, MultiThreaded parallel computer architecture incorporates several advanced technologies in combination with an innovative dynamic adaptive scheduling mechanism to provide unprecedented performance and efficiency within practical constraints of cost, complexity, and power consumption. The emerging superconductor Rapid Single Flux Quantum electronics can operate at 100 GHz (the record is 770 GHz) and one percent of the power required by convention semiconductor logic. Wave Division Multiplexing optical communications can approach a peak per fiber bandwidth of 1 Tbps and the new Data Vortex network topology employing this technology can connect tens of thousands of ports providing a bi-section bandwidth on the order of a Petabyte per second with latencies well below 100 nanoseconds, even under heavy loads. Processor-in-Memory (PIM) technology combines logic and memory on the same chip exposing the internal bandwidth of the memory row buffers at low latency. And holographic storage photorefractive storage technologies provide high-density memory with access a thousand times faster than conventional disk technologies. Together these technologies enable a new class of shared memory system architecture with a peak performance in the range of a Petaflops but size and power requirements comparable to today's largest Teraflops scale systems. To achieve high-sustained performance, HTMT combines an advanced multithreading processor architecture with a memory-driven coarse-grained latency management strategy called "percolation", yielding high efficiency while reducing the much of the parallel programming burden. This paper will present the basic system architecture characteristics made possible through this series of advanced technologies and then give a detailed description of the new percolation approach to runtime latency management.

Sterling, Thomas↗

Surface chemistry models for GaAs epitaxial growth and hydride cracking using reacting flow simulations

Hydride vapor phase epitaxy (HVPE) is a promising technology that can aid in the cost reduction of III-V materials and devices manufacturing, particularly high-efficiency solar cells for space and terrestrial applications. However, recent demonstrations of ultrafast growth rates (~500 µm/h) via uncracked hydrides are not well described by present models for the growth. Therefore, it is necessary to understand the kinetics of the growth process and its coupling with transport phenomena, so as to enable fast and uniform epitaxial growth. In this work, we derive a kinetic model using experimental data and integrate it into a computational fluid dynamics simulation of an HVPE growth reactor. We also modify an existing hydride cracking model that we validate against numerical simulations and experimental data. Here, we show that the developed growth model and the improved cracking model are able to reproduce experimental growth measurements of GaAs in an existing HVPE system.

CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS↗

Optimal polynomial based quantum eigenstate filtering with application to solving quantum linear systems

We present a quantum eigenstate filtering algorithm based on quantum signal processing (QSP) and minimax polynomials. The algorithm allows us to efficiently prepare a target eigenstate of a given Hamiltonian, if we have access to an initial state with non-trivial overlap with the target eigenstate and have a reasonable lower bound for the spectral gap. We apply this algorithm to the quantum linear system problem (QLSP), and present two algorithms based on quantum adiabatic computing (AQC) and quantum Zeno effect respectively. Both algorithms prepare the final solution as a pure state, and achieves the near optimal $\mathcal{\tilde{O}}$(dκlog(1/ϵ)) query complexity for a d -sparse matrix, where κ is the condition number, and ϵ is the desired precision. Neither algorithm uses phase estimation or amplitude amplification.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

From lab to lamp: Understanding downconverter degradation in LED packages

Downconverters, primarily inorganic phosphors, are critical components in white solid-state LED-based lighting and liquid crystal display backlights. Research efforts have led to a fundamental understanding of a downconverter's absorption, photoluminescence, and efficiency as a function of composition, structure, and processing conditions. However, considerably less work has focused on the reliability of phosphors once they are incorporated into LED packages. Solving these issues is often the final step before the commercialization of new materials, but the significant resources and time required to evaluate and mitigate materials failure are rarely discussed in the literature. In this Perspective, we discuss the need for conducting downconverter reliability testing and the potential of accelerating, screening, and understanding downconverter failure modes. Our focus highlights the mechanisms of failure and discusses how this influences materials selection and the design of different LED packages. We also stress the potential for accelerated reliability testing protocols and note the potential role first-principles calculations and data-driven models could play in establishing the compositional-processing trends for different aspects of downconverter reliability. In conclusion, we close with possible research directions that could improve downconverter reliability and emphasize the importance of assessing a material's (chemical) stability where multiple manufacturing and processing steps can dictate system performance.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Fission with Exotic Nuclei (Abbreviated Report)

Nuclear fission is a key mechanism involved in the synthesis of heavy elements in the Cosmos and is the primary explanation for the stability of superheavy elements. Nevertheless, our knowledge of fission remains extremely fragmented. Most experiments have been conducted only on a tiny number of stable actinide nuclei and are often incomplete, leading to gaps in our basic understanding of the process. For many radioactive isotopes, basic fission data such as the charge or mass distribution of the fragments is unknown. These gaps cannot always be filled by simulation alone. Common fission models contain too many free parameters and lack predictive power. In contrast, the fundamental theory of fission under development at LLNL is much more predictive, but its current computational cost is too high to be used extensively for data evaluations. A unique window of opportunity to resolve these limitations has recently opened: the U.S. nuclear science community is ramping up major experimental programs at the Facility for Rare Isotope Beams (FRIB, the DOE flagship facility in low-energy nuclear science), and techniques from machine learning have shown great potential to simplify the use of a fundamental, quantum-mechanical theory of fission. This project has two components. On the experimental side, we acquired and deployed at the HIGS facility a new dual Frisch-Grid ionization chamber to measure correlated fragment-mass, kinetic energy, and angular distributions of fission fragments from induced fission. This new device was used to perform measurements of charge, mass and total kinetic energy of fission fragments in the photofission of 238 U and eight gamma-ray beam energies between 6.2 and 13 MeV, which allowed extracting high-precision independent yields for this reaction. The device was also used to perform measurements of the same quantities in the neutron-induced fission of 234 U with monoenergetic beams of energy between 5 and 8 MeV. In parallel, we collaborated with a team at Commissariat à l’énergie atomique et aux énergies alternatives (CEA) to perform a series of measurements of fission yields in inverse kinematics for the two isotopes of 236 U and 240 Pu. The experiment took place at the Grand Accélérateur National d’Ions Lourds in France in June 2023. The deployment of the VAMOS spectrometer with a new array called PISTA allowed determining the excitation energy of the fissioning system within 1 Mega-electronvolts. The second component of the project involved using deep neural networks to build fast and reliable emulators of our current fission models. In an invited paper published in Frontier in Physics, we showed that autoencoders could successfully compress nuclear wavefunctions in nuclear density functional theory. We achieved a dimensionality reduction of the order of two orders of magnitude while keeping the error in the total energy to less than 0.01%. In a second paper submitted to Physical Review Letters in June 2023 with our collaborators at CEA, we showed that variational autoencoders can learn the collective degrees of freedom driving the fission process.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Ultra-large-scale ab initio quantum chemical computation of bio-molecular systems: The case of spike protein of SARS-CoV-2 virus

The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intramolecular bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

59 BASIC BIOLOGICAL SCIENCES↗