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At least 1,369 records · Page 76

Mechanistic investigation of SARS-CoV-2 main protease to accelerate design of covalent inhibitors

Targeted covalent inhibition represents one possible strategy to block the function of SARS-CoV-2 Main Protease (M PRO ), an enzyme that plays a critical role in the replication of the novel SARS-CoV-2. Toward the design of covalent inhibitors, we built a covalent inhibitor dataset using deep learning models followed by high throughput virtual screening of these candidates against M PRO . Two top-ranking inhibitors were selected for mechanistic investigations—one with an activated ester warhead that has a piperazine core and the other with an acrylamide warhead. Specifically, we performed a detailed analysis of the free energetics of covalent inhibition by hybrid quantum mechanics/molecular mechanics simulations. Cleavage of a fragment of the non-structured protein (NSP) from the SARS-CoV-2 genome was also simulated for reference. Simulations show that both candidates form more stable enzyme-inhibitor (E-I) complexes than the chosen NSP. It was found that both the NSP fragment and the activated ester inhibitor react with CYS145 of M PRO in a concerted manner, whereas the acrylamide inhibitor follows a stepwise mechanism. Most importantly, the reversible reaction and the subsequent hydrolysis reaction from E-I complexes are less probable when compared to the reactions with an NSP fragment, showing promise for these candidates to be the base for efficient M PRO inhibitors.

60 APPLIED LIFE SCIENCES↗

Selective bond formation triggered by short optical pulses: quantum dynamics of a four-center ring closure

Here we report bond formation induced by an ultrashort UV pulse. The photochemical process is described by quantum dynamics as coherent electronic and nuclear motions during the ultrashort pulse induced ring closure of norbornadiene to quadricyclane. Norbornadiene consists of two ethylene moieties connected by a rigid (CH 2 ) 3 bridge. Upon photoexcitation, two new sigma bonds are formed, resulting in the closure of a four-atom ring. As a medium-sized polyatomic molecule, norbornadiene exhibits a high density of strongly coupled electronic states from about 6 eV above the ground state. We report on inducing the formation of the new bonds using a short femtosecond UV pulse to pump a non-equilibrium electronic density in the open form that evolves towards the closed ring form. As the coherent electronic-nuclear coupled dynamics unfold, the excited states change character through non-adiabatic interactions and become valence states for the two new C–C bonds of quadricyclane. Our three-dimensional fully quantum dynamical grid simulations during the first 200 fs show that short UV pulses of different polarization initiate markedly different initial non-equilibrium electronic densities that follow different dynamical paths to the S 0 /S 1 conical intersection. They lead to different initial relative yields of quadricyclane, thereby opening the way to controlling bond-making with attopulses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bringing discrete-time Langevin splitting methods into agreement with thermodynamics

In light of the recently published complete set of statistically correct Grønbech–Jensen (GJ) methods for discrete-time thermodynamics, we revise a differential operator splitting method for the Langevin equation in order to comply with the basic GJ thermodynamic sampling features, namely, the Boltzmann distribution and Einstein diffusion, in linear systems. This revision, which is based on the introduction of time scaling along with flexibility of a discrete-time velocity attenuation parameter, provides a direct link between the ABO splitting formalism and the GJ methods. This link brings about the conclusion that any GJ method has at least weak second order accuracy in the applied time step. It further helps identify a novel half-step velocity, which simultaneously produces both correct kinetic statistics and correct transport measures for any of the statistically sound GJ methods. Explicit algorithmic expressions are given for the integration of the new half-step velocity into the GJ set of methods. Finally, numerical simulations, including quantum-based molecular dynamics (QMD) using the QMD suite Los Alamos Transferable Tight-Binding for Energetics, highlight the discussed properties of the algorithms as well as exhibit the direct application of robust, time-step-independent stochastic integrators to QMD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Generation of collimated vortex gamma-rays from intense Poincaré beam–plasma interaction

We report on numerical calculations in which a multi-petawatt γ-ray beam is generated using a novel configuration based on fully structured light irradiating an overdense plasma waveguide. We analyze how the relativistic laser pulse efficiently confines and accelerates plasma electrons to GeV-scale energies and drives a quasi-static field that induces magneto-bremsstrahlung radiation. Multiphoton Compton scattering of electrons in the intense part of the laser also occurs although the radiated energy-density is comparatively lower. The emitted γ-rays carry orbital angular momentum, are highly collimated, and account for upwards of 15% of the incident field energy in one particular case. A comparison of the laser-to-particle angular momentum and energy transfer efficiencies is made between the cases of irradiation by a circularly polarized Laguerre–Gauss mode and one type of full Poincaré beam, and it is found that the latter yields an order-of-magnitude enhancement. In conclusion, the essential characteristics of the interaction are validated with three-dimensional particle-in-cell simulations that include quantum electrodynamical effects.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Alkali hydroxide (LiOH, NaOH, KOH) in water: Structural and vibrational properties, including neutron scattering results

Structural and vibrational properties of aqueous solutions of alkali hydroxides (LiOH, NaOH, and KOH) are computed using quantum molecular dynamics simulations for solute concentrations ranging between 1 and 10M. Element-resolved partial radial distribution functions, neutron and x-ray structure factors, and angular distribution functions are computed for the three hydroxide solutions as a function of concentration. The vibrational spectra and frequency-dependent conductivity are computed from the Fourier transforms of velocity autocorrelation and current autocorrelation functions. Our results for the structure are validated with the available neutron data for 17M concentration of NaOH in water [Semrouni et al., Phys. Chem. Chem. Phys. 21, 6828 (2019)]. We found that the larger ionic radius [rLi+

Chemistry↗

Experimental quantum Bernoulli factories via Bell-basis measurements

Randomness processing in the Bernoulli factory framework provides a concrete setting in which quantum resources can outperform classical ones. We experimentally demonstrate quantum randomness processing based on Bell-basis measurements of two identical input quoins prepared on IBM superconducting hardware. Using only the measurement outcomes (and no external classical randomness source), we realize the classically inconstructible Bernoulli doubling primitive f(p)=2p, and, as intermediate outputs from the same Bell-measurement statistics, an exact fair coin f(p)=1/2 and the classically inconstructible function f(p)=4p(1−p). We benchmark the measured output biases against ideal predictions and discuss the impact of device noise. Our results establish a simple resource-efficient experimental primitive for quantum-to-classical randomness processing and support the viability of quantum Bernoulli factories for quantum-enhanced stochastic simulation and sampling tasks.

Roy, Tanay [Fermilab] (ORCID:000000019442862X)↗

Unveiling the catalytic mechanism of GTP hydrolysis in microtubules

Microtubules (MTs) are large cytoskeletal polymers, composed of αβ-tubulin heterodimers, capable of stochastically converting from polymerizing to depolymerizing states and vice versa. Depolymerization is coupled with hydrolysis of guanosine triphosphate (GTP) within β-tubulin. Hydrolysis is favored in the MT lattice compared to a free heterodimer with an experimentally observed rate increase of 500- to 700-fold, corresponding to an energetic barrier lowering of 3.8 to 4.0 kcal/mol. Mutagenesis studies have implicated α-tubulin residues, α:E254 and α:D251, as catalytic residues completing the β-tubulin active site of the lower heterodimer in the MT lattice. The mechanism for GTP hydrolysis in the free heterodimer, however, is not understood. Additionally, there has been debate concerning whether the GTP-state lattice is expanded or compacted relative to the GDP state and whether a “compacted” GDP-state lattice is required for hydrolysis. In this work, extensive quantum mechanics/molecular mechanics simulations with transition-tempered metadynamics free-energy sampling of compacted and expanded interdimer complexes, as well as a free heterodimer, have been carried out to provide clear insight into the GTP hydrolysis mechanism. α:E254 was found to be the catalytic residue in a compacted lattice, while in the expanded lattice, disruption of a key salt bridge interaction renders α:E254 less effective. The simulations reveal a barrier decrease of 3.8 ± 0.5 kcal/mol for the compacted lattice compared to a free heterodimer, in good agreement with experimental kinetic measurements. Additionally, the expanded lattice barrier was found to be 6.3 ± 0.5 kcal/mol higher than compacted, demonstrating that GTP hydrolysis is variable with lattice state and slower at the MT tip.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synthesis and investigation into explosive sensitivity for a series of new picramide explosives

Tailoring the molecular properties that govern energetic material sensitivity is essential to improve safety and help develop new energetic materials. Despite this need, understanding the complex chemistry and physics of explosive initiation and propagation is still a challenge. Recent work by our group has reinforced the view that explosive sensitivity under sub-shock conditions is connected to the strength of the weakest covalent bond in the molecule, that is, its “trigger linkage.” These correlations have been observed with different classes of energetic molecules and indicate that “trigger linkage” bond breaking, and heat of explosion are good indicators for the sensitivity trends. Herein we report the synthesis of aliphatic energetic materials with ethane, propane and neopentane backbones. Experimental and computational studies show that the trigger linkage model, based on results from quantum molecular dynamics simulations, correctly predicts trends observed in the impact sensitivity of the molecules. However, while the model predicts the impact sensitivities of the ethane series, the neopentane series has higher impact sensitivities than predicted, which is presumably influenced by crystal packing effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electric-field-induced crossover of polarization reversal mechanisms in Al 1–x Sc x N ferroelectrics

Scandium-doped aluminum nitride, Al 1–x Sc x N, represents a new class of displacive ferroelectric materials with high polarization and sharp hysteresis along with high-temperature resilience, facile synthesizability and compatibility with standard CMOS fabrication techniques. The fundamental physics behind the transformation of unswitchable piezoelectric AlN into switchable Al–Sc–N ferroelectrics depends upon important atomic properties such as local structure, dopant distributions and the presence of competing mechanism of polarization switching in the presence of an applied electric-field that have not been understood. We computationally synthesize Al 1–x Sc x N to quantify the inhomogeneity of Sc distribution and phase segregation, and characterize its crystal and electronic structure as a function of Sc-doping. Nudged elastic band calculations of the potential energy surface and quantum molecular dynamics simulations of direct electric-field-driven ferroelectric switching reveal a crossover between two polarization reversal mechanisms—inhomogeneous nucleation-and-growth mechanism originating near Sc-rich regions in the limit of low applied fields and nucleation-limited-switching in the high-field regime. Finally, understanding polarization reversal pathways for these two mechanisms as well as the role of local Sc concentration on activation barriers provides design rules to identify other combinations of dopant elements, such as Zr, Mg etc. to synthesize superior AlN-based ferroelectric materials.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Optimal control of large quantum systems: assessing memory and runtime performance of GRAPE

Abstract Gradient Ascent Pulse Engineering (GRAPE) is a popular technique in quantum optimal control, and can be combined with automatic differentiation (AD) to facilitate on-the-fly evaluation of cost-function gradients. We illustrate that the convenience of AD comes at a significant memory cost due to the cumulative storage of a large number of states and propagators. For quantum systems of increasing Hilbert space size, this imposes a significant bottleneck. We revisit the strategy of hard-coding gradients in a scheme that fully avoids propagator storage and significantly reduces memory requirements. Separately, we present improvements to numerical state propagation to enhance runtime performance. We benchmark runtime and memory usage and compare this approach to AD-based implementations, with a focus on pushing towards larger Hilbert space sizes. The results confirm that the AD-free approach facilitates the application of optimal control for large quantum systems which would otherwise be difficult to tackle.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Site-selective correlations in interacting flat-band quasicrystals

Model lattices such as the kagome and Lieb lattices have been widely investigated to elucidate the properties of interacting flat-band systems. While a quasicrystal does not have proper bands, the noninteracting density of states of several of them displays the typical signature of a flat band pinned at the Fermi level: a delta-function zero-energy peak. Here, we employ quantum Monte Carlo simulations to determine the effect of onsite repulsion on these quasicrystals. While global properties such as the antiferromagnetic structure factor and the specific heat behave similarly as in the case of periodic lattices undergoing a Mott transition, the behavior of the local density of states depends on the coordination number of the site. In particular, sites with the smallest coordination number, which give the dominant spectral-weight contribution to the zero-energy peak, are the ones most strongly impacted by the interaction. Besides establishing site-selective correlations in quasicrystals, our work also points to the importance of the real-space structure of flat bands in interacting systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Sub-Doppler Cooling of a Trapped Ion in a Phase-Stable Polarization Gradient

Trapped ions provide a highly controlled platform for quantum sensors, clocks, simulators, and computers, all of which depend on cooling ions close to their motional ground state. Existing methods like Doppler, resolved sideband, and dark resonance cooling balance trade-offs between the final temperature and cooling rate. A traveling polarization gradient has been shown to cool multiple modes quickly and in parallel, but utilizing a stable polarization gradient can achieve lower ion energies, while also allowing tailorable light-matter interactions in the sub-wavelength regime. In this Letter, we demonstrate cooling of a trapped ion below the Doppler limit using a phase-stable polarization gradient created using trap-integrated photonic devices. At an axial frequency of 2⁢𝜋×1.45 MHz we achieve ⟨𝑛⟩=1.56±0.07 in 150 μ⁢s and cooling rates of ∼0.3 quanta/μ⁢s. Here, we examine ion dynamics under different polarization gradient phases, detunings, and intensities, showing reasonable agreement between experimental results and a multilevel model. Cooling is fast and power efficient, with lower average motional Fock state occupation when compared to simulated operation under the corresponding running wave configuration. Our results demonstrate a well-controlled test bed for studying the dynamics of multilevel atomic systems in a phase-stable polarization gradient.

Atom & ion cooling↗

Machine-learned quantum molecular dynamics calculations of warm dense equation of state and ionic transport coefficients of deuterated water

White dwarf models require accurate equations of state and ionic transport coefficients in the warm dense matter regime, where kinetic theory models and tabulated equations of state are often inaccurate. In this work, spectral-partitioned density functional theory and machine-learned interatomic potentials are combined to perform large-scale, first-principles quantum molecular dynamics simulations of deuterated water (D 2 O) near the principal Hugoniot. This approach retains Kohn-Sham accuracy while achieving orders-of-magnitude speedup, yielding converged equation of state and transport properties over a broad pressure and temperature range. The results reveal the thermodynamic conditions under which ionic transport models for interdiffusivity and shear viscosity converge and identify those in closest agreement with density functional theory benchmarks at temperatures in the warm dense matter regime. The present framework extends first-principles transport calculations to higher temperatures than previously achieved, and provides an efficient, scalable, and general approach for studying transport properties in complex multicomponent mixtures.

79 ASTRONOMY AND ASTROPHYSICS↗

New state of matter between the hadronic phase and the quark-gluon plasma?

Lattice-quantum chromodynamics (QCD) simulations and theoretical arguments hint at the existence of an intermediate phase of strongly interacting matter between a confined hadron gas and a deconfined quark-gluon plasma (QGP). We qualitatively and semiquantitatively explore and differentiate the phase structures in the temperature window from the QCD pseudocritical temperature 𝑇 c ≃ 160 MeV to the pure gluonic deconfinement temperature 𝑇 d ≃ 285 MeV. We propose a three-regime picture using a hadron resonance gas description augmented with the exponential spectrum of strings, corresponding to highly excited mesons and glueballs, based on the analysis of a large number 𝑁 c of colors. We estimate the entropy density from our model to confirm that the lattice-QCD data are bracketed with three regimes, i.e., a hadron gas, a QGP, and a new phase for 𝑇 c ≲ 𝑇 ≲ 𝑇 d . In this new phase, which we name a spaghetti of quarks with glueballs (SQGBs), thermal degrees of freedom of quarks are liberated, yet gluons remain confined in glueballs. Since the Hagedorn temperature 𝑇 H ∼ 285 MeV is universal in the meson and the glueball sectors, in the infinite-𝑁 c limit, the phase diagram in the plane of the baryon chemical potential and the temperature is reduced to one with the confined and deconfined phases and quarkyonic matter at high density. At large but finite 𝑁 c , an SQGB window may open between these phases. We point out that the SQGB has interesting similarities with quarkyonic matter and that this matter in the large-𝑁 c limit is confined as measured by the interaction between heavy quarks, but behaves in other respects like a quasifree gas of quarks. As a result of the extrapolation to 𝑁 c = 3, we present a revised phase diagram with the SQGB phase bounded by thermal crossovers. Finally, we give a quantitative analysis of chiral-symmetry restoration in the SQGB phase.

Color confinement↗

Electronic band gaps from quantum Monte Carlo methods

We develop a method for calculating the fundamental electronic gap of semiconductors and insulators using grand canonical quantum Monte Carlo simulations. Further, we discuss the origin of the bias introduced by supercell calculations of finite size and show how to correct the leading and subleading finite size errors either based on observables accessible in the finite-sized simulations or from density-functional theory calculations. Our procedure is applied to carbon, silicon, and molecular hydrogen crystals, and compared to experiment for carbon and silicon.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Direct observation of the momentum distribution and renormalization factor in lithium

We have measured the momentum distribution and renormalization factor $Z_{k_F}$ in liquid and solid lithium by high-resolution Compton scattering. High-resolution data over a wide momentum range exhibit a clear feature of the renormalization and a sharp drop of momentum densities at the Fermi momentum $k_F$. In this work, these results are compared with those computed by quantum Monte Carlo simulation performed both on a disordered crystal and a liquid exhibiting very good agreement. Asymptotic behavior of the experimental and theoretical momentum distributions are examined to estimate $Z_{k_F}$. The experimentally obtained $Z_{k_F} = 0.43^{+0.11}_{–0.01}$ for liquid Li and $0.54^{+0.11}_{–0.02}$ for solid Li are in good agreement with theoretical results of 0.54 ± 0.01 and 0.64 ± 0.01, respectively.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Continuous-time Monte Carlo renormalization group

We implement the Monte Carlo renormalization group approach in the continuous-time Monte Carlo simulation of a quantum system. In this work, we demonstrate numerically the emergent isotropy between space and time at large distances for the systems that exhibit Lorentz invariance at quantum criticality. Here, this allows us to estimate accurately the sound velocity for these quantum systems. $\textit{Q}$-state Potts models in one and two space dimensions are used to illustrate the method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Shock-compressed silicon: Hugoniot and sound speed up to 2100 GPa

In this work, the high-pressure equation of state and isentropic sound speed of fluid silicon were studied using laser-driven shock waves. Principal Hugoniot measurements to 2100 GPa were performed using impedance matching to an α-quartz reference. Sound speed was determined by time correlating imposed shock-velocity perturbations in both the sample (Si) and reference material (α-quartz). A change in shock velocity versus particle velocity (u s –u p ) slope on the fluid silicon principal Hugoniot was detected at 200 GPa. Density functional theory-based quantum molecular dynamics simulations suggest that an increase in ionic coordination and 50% increase in average ionization is coincident with the experimentally observed change in slope.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗