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DOE OSTI2022

Monte Carlo study of the pseudogap and superconductivity emerging from quantum magnetic fluctuations

Abstract The origin of the pseudogap behavior, found in many high- T c superconductors, remains one of the greatest puzzles in condensed matter physics. One possible mechanism is fermionic incoherence, which near a quantum critical point allows pair formation but suppresses superconductivity. Employing quantum Monte Carlo simulations of a model of itinerant fermions coupled to ferromagnetic spin fluctuations, represented by a quantum rotor, we report numerical evidence of pseudogap behavior, emerging from pairing fluctuations in a quantum-critical non-Fermi liquid. Specifically, we observe enhanced pairing fluctuations and a partial gap opening in the fermionic spectrum. However, the system remains non-superconducting until reaching a much lower temperature. In the pseudogap regime the system displays a “gap-filling" rather than “gap-closing" behavior, similar to the one observed in cuprate superconductors. Our results present direct evidence of the pseudogap state, driven by superconducting fluctuations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Hyperfine-to-rotational energy transfer in ultracold atom–molecule collisions of Rb and KRb

Energy transfer between different mechanical degrees of freedom in atom–molecule collisions has been studied and largely understood. However, systems involving spins remain less explored. Here, in this study, we directly observed energy transfer from atomic hyperfine to molecular rotation in the 87 Rb ($| {F}_{a},{M}_{{F}_{a}}\rangle =| 2,2\rangle$) + 40 K 87 Rb (X 1 Σ + , rotational state N = 0) ⟶ Rb ($| 1,1\rangle$) + KRb ( N = 0, 1, 2) collision with state-to-state precision. We also performed quantum scattering calculations that rigorously included the coupling between spin and rotational degrees of freedom at short range under the assumption of rigid-rotor KRb monomers moving along a single potential energy surface. The calculated product rotational state distribution deviates from the observations even after extensive tuning of the atom–molecule potential energy surface. In addition, our ab initio calculations indicate that spin–rotation coupling is enhanced close to a conical intersection that is energetically accessible at short range. This, together with the deviation, suggests that vibrational degrees of freedom and conical intersections play an important part in the coupling. Our observations confirm that spin is coupled to mechanical rotation at short range and establish a benchmark for future theoretical studies.

chemical physics↗

DOE OSTI2023

Changes within the central stalk of E. coli F 1 F o ATP synthase observed after addition of ATP

F 1 F o ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the F o motor that is transferred to the F 1 motor to catalyze ATP production, with flexible F 1 /F o coupling required for efficient catalysis. F 1 F o ATP synthase can also operate in reverse, hydrolyzing ATP and pumping protons, and in bacteria this function can be regulated by an inhibitory ε subunit. Here we present cryo-EM data showing E. coli F 1 F o ATP synthase in different rotational and inhibited sub-states, observed following incubation with 10 mM MgATP. Our structures demonstrate how structural transitions within the inhibitory ε subunit induce torsional movement in the central stalk, thereby enabling its rotation within the F ο motor. This highlights the importance of the central rotor for flexible coupling of the F 1 and F o motors and provides further insight into the regulatory mechanism mediated by subunit ε.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Accurate and reliable thermochemistry by data analysis of complex thermochemical networks using Active Thermochemical Tables: the case of glycine thermochemistry

Active Thermochemical Tables (ATcT) were successfully used to resolve the existing inconsistencies related to the thermochemistry of glycine, based on statistically analyzing and solving a thermochemical network that includes >3350 chemical species interconnected by nearly 35 000 thermochemically-relevant determinations from experiment and high-level theory. Here, the current ATcT results for the 298.15 K enthalpies of formation are −394.70 ± 0.55 kJ mol −1 for gas phase glycine, −528.37 ± 0.20 kJ mol −1 for solid α-glycine, −528.05 ± 0.22 kJ mol −1 for β-glycine, −528.64 ± 0.23 kJ mol −1 for γ-glycine, −514.22 ± 0.20 kJ mol −1 for aqueous undissociated glycine, and −470.09 ± 0.20 kJ mol −1 for fully dissociated aqueous glycine at infinite dilution. In addition, a new set of thermophysical properties of gas phase glycine was obtained from a fully corrected nonrigid rotor anharmonic oscillator (NRRAO) partition function, which includes all conformers. Corresponding sets of thermophysical properties of α-, β-, and γ-glycine are also presented.

Active Thermochemical Tables↗

DOE OSTI2023

Condition monitoring of permanent magnet AC machines for all-electric transportation systems: State of the art

The current state of the art on emerging and efficient techniques for condition monitoring of permanent magnet (PM) alternating-current (AC) machines deployed in electric vehicle (EV) applications is presented. The discussion includes the most common and specific types of faults in PM motors, such as rotor demagnetisation and stator inter-turn faults, respectively. Fault indicators, such as voltage (v s ) and current (i s ) signals and machine signatures based on motor back electromotive force (EMF) (E B ) and magnetic flux (φ), are taken into account as a measuring quantity in diagnosing motor faults. Other signatures, including thermal analysis, acoustic noise, and vibrations, are also illustrated as some of the emerging techniques in estimating the performance of EV motors while under operations. In addition, various fault modelling methods, condition monitoring techniques, and comprehensive approaches applied in diagnosing the effect of machine faults during its incipient stages are illustrated. Since most of the fault diagnostic techniques discussed here include only machine-based quantities as fault indices/indicators, the provided solutions are therefore found to be more reliable and accurate for diagnosing the motor faults. This comprehensive review study is inclusive of the existing fault diagnostic techniques, which are currently employed in industrial and commercial practices, in addition to the new methodologies proposed by the authors. All the given condition monitoring schemes therefore seem significantly vital in estimating the state of health of PM AC machines while under operation in all-electric transportation systems.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2020

Hydrokinetic Turbines in Yawed Conditions: Toward Synergistic Fluvial Installations

Laboratory experiments were performed in critical mobility conditions to study the effects of an in-stream horizontal axis turbine in yawed conditions. The misalignment between the rotor axis and the incoming flow velocity is observed to alter the near and far wake of the turbine, as well as the scour and deposition patterns in the proximity of the monopile support tower. Various hydraulic conditions may lead to such misalignment, e.g., as a result of complex fluvial bathymetries distorting the flow or as a strategy to steer the wake away from downstream units and maximize energy production in a turbine array. The research first investigates the simplest case of a single turbine deployed along the channel centerline and oriented at different yaw angles to study the wake deflection and the turbine performance. A second set of experiments is performed moving the turbine relatively close to a nonerodible lateral wall to explore a potential passive yaw control strategy devoted to protect the banks from erosion by steering the wake toward the channel center and favor deposition along the bank.

42 ENGINEERING↗

DOE OSTI2020

The role of rotation-vibration coupling in symmetric and asymmetric isotopomers of ozone

A theoretical framework and a computer code (SpectrumSDT) are developed for accurate calculations of coupled rotational–vibrational states in triatomic molecules using hyper-spherical coordinates and taking into account the Coriolis coupling effect. Concise final formulas are derived for the construction of the Hamiltonian matrix using an efficient combination of the variational basis representation and discrete variable representation methods with locally optimized basis sets and grids. First, the new code is tested by comparing its results with those of the APH3D program of Kendrick et al. [Kendrick, Pack, Walker, and Hayes, J. Chem. Phys. 110, 6673 (1999)]. Then, accurate calculations of the rovibrational spectra are carried out for doubly substituted symmetric ( 18 O 16 O 18 O) and asymmetric ( 18 O 18 O 16 O) ozone isotopomers for the total angular momentum up to J = 5. Together with similar data recently reported for the singly substituted symmetric ( 16 O 18 O 16 O) and asymmetric ( 16 O 16 O 18 O) ozone isotopomers, these calculations quantify the role of the Coriolis coupling effect in the large mass-independent isotopic enrichment of ozone, observed in both laboratory experiments and the atmosphere of the Earth. It is found that the Coriolis effect in ozone is relatively small, as evidenced by deviations of its rotational constants from the symmetric-top-rotor behavior, magnitudes of parity splittings (Λ-doubling), and ratios of rovibrational partition functions for asymmetric vs symmetric ozone molecules. It is concluded that all of these characteristics are influenced by the isotopic masses as much as they are influenced by the overall symmetry of the molecule. It is therefore unlikely that the Coriolis coupling effect could be responsible for symmetry-driven mass-independent fractionation of oxygen isotopes in ozone.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Experimental and theoretical studies of the doubly substituted methyl-ethyl Criegee intermediate: Infrared action spectroscopy and unimolecular decay to OH radical products

In this work the infrared (IR) action spectrum of the doubly substituted methyl-ethyl Criegee intermediate (MECI) is observed in the CH stretch overtone region with detection of OH products. The MECI exhibits four conformers, all of which undergo unimolecular decay via a 1,4 H-atom transfer mechanism, followed by the rapid release of OH products. Conformers with different orientations of the carbonyl oxide group with respect to the methyl and ethyl substituents (i.e., anti and syn ) decay via distinct transition state barriers (16.1 kcal mol –1 and 15.4 kcal mol –1 , respectively). The observed IR action spectrum is in good agreement with the predicted anharmonic IR absorption spectrum, but exhibits significant congestion, which is attributed to couplings between spectroscopic bright states and nearby dark states. Energy-dependent OH appearance rates are measured upon IR excitation of the strongest features in the IR action spectrum and are found to be on the order of 10 6 –10 7 s –1 . The experimental rates are in good agreement with computed Rice–Ramsperger–Kassel–Marcus rates for the unimolecular decay of MECI at these energies, which incorporate quantum mechanical tunneling and sophisticated hindered rotor treatments, as well as high-level theoretical calculations of the TS barrier heights, rovibrational properties, and torsional barriers associated with the MECI conformers. Master equation modeling is used to predict thermal rates for the unimolecular decay of anti - and syn -MECI of 473 s –1 and 660 s –1 , respectively. Comparison with other previously studied Criegee intermediate systems provides insights into substituent effects on unimolecular decay under both energy-dependent and thermal conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

A review of tidal energy—Resource, feedbacks, and environmental interactions

The ocean contains a variety of renewable energy resources, little of which has been exploited. Here, we review both tidal range and tidal stream energy, with a focus on the resource, feedbacks, and environmental interactions. The review covers a wide range of timescales of relevance to tidal energy, from fortnightly (spring-neap) and semi-diurnal variability, down to array, and device-scale turbulence. When simulating the regional tidal energy resource, and to assess environmental impacts, it is necessary to account for feedbacks between the tidal array and the resource itself. We critically review various methods for simulating energy extraction, from insights gained through theoretical studies of “tidal fences” in idealized channels, to realistic three-dimensional model studies with complex geometry and arrays of turbines represented by momentum sinks and additional turbulence due to the presence of rotors and support structures. We discuss how variability can be reduced by developing multiple (aggregated) sites with a consideration of the enhanced phase diversity offered by exploiting less energetic tidal currents. This leads to future research questions that have not yet been explored in depth at first-generation tidal sites in relatively sheltered channels (e.g., the interaction of waves with currents). Such enhanced understanding of real sea conditions, including the effects of wind and waves, leads to our other identified primary future research direction—reduced uncertainties in turbulence predictions, including the development of realistic models that simulate the interaction between ambient turbulence and the turbulence resulting from multiple wakes, and changes to system-wide hydrodynamics, water quality, and sedimentation.

Environmental impacts↗

DOE OSTI2022

High-resolution CH stretch spectroscopy of jet-cooled cyclopentyl radical: First insights into equilibrium structure, out-of-plane puckering, and IVR dynamics

First, high-resolution sub-Doppler infrared spectroscopic results for cyclopentyl radical (C 5 H 9 ) are reported on the α-CH stretch fundamental with suppression of spectral congestion achieved by adiabatic cooling to T rot ≈ 19(4) K in a slit jet expansion. Surprisingly, cyclopentyl radical exhibits a rotationally assignable infrared spectrum, despite 3N – 6 = 36 vibrational modes and an upper vibrational state density (ρ ≈ 40–90 #/cm –1 ) in the critical regime (ρ ≈ 100 #/cm –1 ) necessary for onset of intramolecular vibrational relaxation (IVR) dynamics. Such high-resolution data for cyclopentyl radical permit detailed fits to a rigid-rotor asymmetric top Hamiltonian, initial structural information for ground and vibrationally excited states, and opportunities for detailed comparison with theoretical predictions. Specifically, high level ab initio calculations at the coupled-cluster singles, doubles, and perturbative triples (CCSD(T))/ANO0, 1 level are used to calculate an out-of-plane bending potential, which reveals a C 2 symmetry double minimum 1D energy surface over a C 2v transition state. Here, the inversion barrier [V barrier ≈ 3.7(1) kcal/mol] is much larger than the effective moment of inertia for out-of-plane bending, resulting in localization of the cyclopentyl wavefunction near its C 2 symmetry equilibrium geometry and tunneling splittings for the ground state too small (<1 MHz) to be resolved under sub-Doppler slit jet conditions. The persistence of fully resolved high-resolution infrared spectroscopy for such large cyclic polyatomic radicals at high vibrational state densities suggests a “deceleration” of IVR for a cycloalkane ring topology, much as low frequency torsion/methyl rotation degrees of freedom have demonstrated a corresponding “acceleration” of IVR processes in linear hydrocarbons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Can lidars assess wind plant blockage in simple terrain? A WRF-LES study

Wind plant blockage reduces wind velocity upstream of wind plants, reducing the power generated by turbines adjacent to the inflow, and potentially throughout the plant as well. The nature of the mechanism that amplifies blockage as well as the velocity reductions in both the induction zone and potentially deeper into the array are not well understood. Field observations can provide valuable insight into the characteristics of the induction zone and the mechanisms that amplify it. However, the relatively small velocity reductions that have been measured experimentally pose a challenge in quantifying blockage, especially in onshore environments with flow heterogeneities that may be of the same scale as the blockage effect itself. We simulate the flow around the King Plains wind plant in the relatively simple terrain of Oklahoma, the location of the American WAKE experimeNt, to evaluate wind plant blockage in this environment. Using numerical simulations, we find the largest velocity deceleration (0.64 m s−1; 8%) immediately upstream of the wind plant, and 1% velocity deficits 24 rotor diameters upstream of the first turbine row. We also use virtual measurements upstream of the wind plant to analyze the uncertainties and difficulties in measuring blockage using a scanning lidar on shore. Based on our virtual lidar study, the induction zone of land-based wind plants can be incorrectly estimated using observations if the effects of nonuniform terrain on the flow are not carefully considered. Changes in terrain elevation produce local variations in wind speed (as measured by a scanning lidar) that exceed in magnitude the deceleration within the induction zone. We refer to these local changes in wind speed as terrain effects. A methodology to differentiate between terrain effects and blockage in experimental settings is proposed and evaluated herein, highlighting the difficulties and uncertainties associated with measurement and simulation of blockage in even relatively simple onshore environments.

17 WIND ENERGY↗

DOE OSTI2023

Coupling turbulent flow with blade aeroelastics and control modules in large-eddy simulation of utility-scale wind turbines

We present a large-eddy simulation framework capable of control co-design of large wind turbines, coupling the turbulent flow environment with blade aeroelastics and turbine controllers. The geometry and aerodynamics of the rotor blades and the turbine nacelle are parameterized using an actuator surface model. The baseline collective pitch control and individual pitch control (IPC) algorithms, consisting of a single-input, single-output proportional–integral controller and two integral controllers, respectively, are incorporated into the simulation framework. Furthermore, a second-order model based on the Euler–Bernoulli beam theory is implemented to describe the blade deformation. Simulations are carried out to investigate the impact of collective and individual pitch control strategies on the deflection of turbine blades. Our results show that the IPC reduces the blade tip deflection fluctuations in the out-of-plane direction, while the fluctuations of the blade tip deflection along the in-plane direction are barely affected by the IPC. Furthermore, the blade out-of-plane deformation fluctuation is underestimated by the one-way coupling approach compared to the two-way coupling approach. Furthermore, the findings of this study reveal the importance of advanced control systems in reducing the dynamic loads on wind turbine blades and underscore the potential of control co-design to reduce the levelized cost of wind energy.

42 ENGINEERING↗

DOE OSTI2024

The Simons Observatory: Cryogenic half wave plate rotation mechanism for the small aperture telescopes

We present the requirements, design, and evaluation of the cryogenic continuously rotating half-wave plate (CHWP) for the Simons Observatory (SO). SO is a cosmic microwave background polarization experiment at Parque Astronómico de Atacama in northern Chile that covers a wide range of angular scales using both small (Ø0.42 m) and large (Ø6 m) aperture telescopes. In particular, the small aperture telescopes (SATs) focus on large angular scales for primordial B-mode polarization. To this end, the SATs employ a CHWP to modulate the polarization of the incident light at 8 Hz, suppressing atmospheric 1/f noise and mitigating systematic uncertainties that would otherwise arise due to the differential response of detectors sensitive to orthogonal polarizations. The CHWP consists of a 505 mm diameter achromatic sapphire HWP and a cryogenic rotation mechanism, both of which are cooled down to ~50 K to reduce detector thermal loading. Under normal operation, the HWP is suspended by a superconducting magnetic bearing and rotates with a constant 2 Hz frequency, controlled by an electromagnetic synchronous motor. We find that the number of superconductors and the number of magnets that make up the superconducting magnetic bearing are important design parameters, especially for the rotation mechanism’s vibration performance. The rotation angle is detected through an angular encoder with a noise level of 0.07 μrad √ $\overline{s}$. During a cooldown process, the rotor is held in place by a grip-and-release mechanism that serves as both an alignment device and a thermal path. In this paper, we provide an overview of the SO SAT CHWP: its requirements, hardware design, and laboratory performance.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Virtual tower measurements during the American WAKE ExperimeNt (AWAKEN)

Dual-Doppler lidar measurements were made during the American WAKE ExperimeNt to provide height-resolved measurements of wind speed and direction at multiple locations immediately south of the leading row turbines in the King Plains wind farm in Oklahoma. These so-called virtual tower measurements were performed to characterize the inflow into the wind farm and to assess possible upwind blockage effects due to the collective action of the wind farm. The campaign was conducted from 12 November 2022 to 17 October 2023, during which time 14 unique virtual tower locations were sampled with heights ranging from 240 to 490 m AGL. The wind retrieval algorithm provided estimates of the horizontal winds and their uncertainties with a vertical resolution of about 10 m, while also accounting for the tilt of the lidar platform. The virtual tower results are compared to collocated lidar wind profiling data at the A1 site, which was located roughly 2.4 rotor diameters south of the nearest turbine. The wind speed difference between the wind profiler and the virtual tower was found to be quite sensitive to atmospheric stability and wind direction below 250 m AGL. The largest differences were observed for inflow under stable conditions, where the profiler wind speeds were observed to be about 22% lower than the virtual tower near hub height. These results suggest that there are persistent horizontal gradients in the flow upwind of the wind farm which result in biased estimates using standard ground-based lidar wind profiling methods.

17 WIND ENERGY↗

DOE OSTI2024

Wind plant wake losses: Disconnect between turbine actuation and control of plant wakes with engineering wake models

Wake losses from neighboring plants may become a major factor in wind plant design and control as additional plants are constructed in areas with high wind resource availability. Because plant wakes span a large range of physical scales, from turbine rotor diameter to tens of kilometers, it is unclear whether conventional wake models or turbine control strategies are effective at the plant scale. Wake steering and axial induction control are evaluated in the current work as means of reducing the impact of neighboring wind plants on power and levelized cost of electricity. FLOw Redirection and Induction in Steady State (FLORIS) simulations were performed with the Gauss–Curl Hybrid and TurbOPark wake models as well as two operation and maintenance models to investigate control setpoint sensitivity to wake representation and economic factors. Both wake models estimate losses across a range of atmospheric conditions, although the wake loss magnitude is dependent on the wake model. Annual energy production and levelized cost of electricity are driven by wind direction frequency, with frequently aligned plants experiencing the greatest losses. However, both wake steering and axial induction are unable to mitigate the impact of upstream plants. Wake steering is constrained by plant geometry, since wake displacement is much less than the plant wake width, while axial induction requires curtailing the majority of turbines in upstream plants. Individual turbine strategies are limited by their effective scale and model representation. New wake models that include plant-scale physics are needed to facilitate the design of effective plant wake control strategies.

Scott, Ryan (ORCID:0000000328107574)↗

DOE OSTI2024

The nonlinear behavior of generic tail fins for small wind turbines

This paper describes analysis and measurements of the yaw response of tail fins for small wind turbines. It is based on an extension of unsteady slender body theory (USBT) to cover non-slender fins and high angles of incidence, both of which make the theory nonlinear. We provide three main additions to the substantial literature on linearized USBT for tail fins. First, USBT is extended to high angles by modeling the nonlinear vortex dynamics. Second, the restriction to slender bodies is removed by modeling the chordwise load variation. Third, we consider the effect of time-varying wind speed. Further, the extended theory is compared to wind tunnel measurements of the yaw behavior of delta, elliptical, and rectangular tail fins without a rotor and nacelle. The fins were released from initial yaw angles of -40° and -80°; the latter is of sufficient magnitude to show the importance of the nonlinear yaw dynamics. Generally good agreement was found between the theory and measurements, and the theory was shown to be more accurate than a “polar” or quasi-steady model which uses only the lift and drag of a delta planform. Of the three planforms, the rectangular one showed the lowest accuracy in terms of frequency but the damping was accurately predicted. Overall, the results demonstrate the importance of nonlinearity in the response of a yawing tail fin, particularly for the higher aspect ratio fins at large yaw angles.

17 WIND ENERGY↗

DOE OSTI2026

Transient hydroperoxyalkyl intermediates (•QOOH) in isopentane oxidation. II. Isomer-resolved unimolecular dynamics

Transient carbon-centered hydroperoxyalkyl intermediates (•QOOH) in isopentane oxidation are characterized by their time- and energy-resolved unimolecular dissociation dynamics to hydroxyl (OH) and cyclic ether products. Two distinct •QOOH isomers are examined with radical sites at a primary carbon of one of the methyl groups (β-Me) or a secondary carbon (β-Et) of the ethyl group. Energy-dependent unimolecular rates are obtained from the time-dependent appearance of OH products for the two isomers and compared with statistical microcanonical rates computed using RRKM theory, including heavy-atom tunneling, based on high-level theoretical calculations. A benchmark-corrected approach is utilized to compute high-accuracy stationary-point energies, most importantly, transition-state barriers, for the •QOOH_Me and •QOOH_Et isomers in isopentane oxidation, building on higher-level reference calculations for the oxidation of ethane (C 2 H 5 O 2 ) and propane (C 3 H 7 O 2 ), respectively. Here, the measured rates are compared with RRKM calculations incorporating the benchmark-corrected transition-state parameters, a vibrationally adiabatic multidimensional hindered-rotor treatment of key torsions, and quantum tunneling. Agreement between experiment and theory validates the statistical description and shows faster decay for •QOOH_Et due to its lower barrier. Both β-QOOH isomers decay almost exclusively to OH + cyclic ether products under the conditions studied.

Oxidation processes↗

DOE OSTI2020

Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling

The CRISPR-Cas9 nuclease has been widely repurposed as a molecular and cell biology tool for its ability to programmably target and cleave DNA. Cas9 recognizes its target site by unwinding the DNA double helix and hybridizing a 20-nucleotide section of its associated guide RNA to one DNA strand, forming an R-loop structure. A dynamic and mechanical description of R-loop formation is needed to understand the biophysics of target searching and develop rational approaches for mitigating off-target activity while accounting for the influence of torsional strain in the genome. Here we investigate the dynamics of Cas9 R-loop formation and collapse using rotor bead tracking (RBT), a single-molecule technique that can simultaneously monitor DNA unwinding with base-pair resolution and binding of fluorescently labeled macromolecules in real time. By measuring changes in torque upon unwinding of the double helix, we find that R-loop formation and collapse proceed via a transient discrete intermediate, consistent with DNA:RNA hybridization within an initial seed region. Using systematic measurements of target and off-target sequences under controlled mechanical perturbations, we characterize position-dependent effects of sequence mismatches and show how DNA supercoiling modulates the energy landscape of R-loop formation and dictates access to states competent for stable binding and cleavage. Consistent with this energy landscape model, in bulk experiments we observe promiscuous cleavage under physiological negative supercoiling. The detailed description of DNA interrogation presented here suggests strategies for improving the specificity and kinetics of Cas9 as a genome engineering tool and may inspire expanded applications that exploit sensitivity to DNA supercoiling.

59 BASIC BIOLOGICAL SCIENCES↗