Tunneling Dynamics Research Articles

Impact of water models on the structure and dynamics of enzyme tunnels

Protein hydration plays a vital role in many biological functions, and molecular dynamics simulations are frequently used to study it. However, the accuracy of these simulations is often sensitive to the water model used, a phenomenon particularly evident in intrinsically disordered proteins. Here, we investigated the extent to which the choice of water model alters the behavior of complex networks of tunnels within proteins. Tunnels are essential because they allow the exchange of substrates and products between buried enzyme active sites and the bulk solvent, directly affecting enzyme efficiency and selectivity, making the study of tunnels crucial for a holistic understanding of enzyme function at the molecular level. By performing simulations of haloalkane dehalogenase LinB and its two variants with engineered tunnels using TIP3P and OPC models, we investigated their effects on the overall tunnel topology. We also analyzed the properties of the primary tunnels, including their conformation, bottleneck dimensions, sampling efficiency, and the duration of tunnel openings. Our data demonstrate that all three proteins exhibited similar conformational behavior in both models but differed in the geometrical characteristics of their auxiliary tunnels, consistent with experimental observations. Interestingly, the results indicate that the stability of the open tunnels might be sensitive to the water model used. Because TIP3P can provide comparable data on the overall tunnel network, it is a valid choice when computational resources are limited or compatibility issues impede the use of OPC. However, OPC seems preferable for calculations requiring an accurate description of transport kinetics.

Observation of Discrete Charge States of a Coherent Two-Level System in a Superconducting Qubit.

We report observations of discrete charge states of a coherent two-level system (TLS) that is strongly coupled to an offset-charge-sensitive superconducting transmon qubit. We measure an offset charge of 0.072e associated with the two TLS eigenstates, which have a transition frequency of 2.9GHz and a relaxation time exceeding 3ms. Combining measurements in the strong dispersive and resonant regime, we quantify both transverse and longitudinal coupling of the TLS-qubit interaction. We further perform joint tracking of TLS transitions and quasiparticle tunneling dynamics but find no intrinsic correlations. This Letter demonstrates microwave-frequency TLS as a source of low-frequency charge noise.

Data-Driven Method for Nonlinear Modal Interaction Identification in Fighter Aircraft

The purpose of this paper is to report a new data-driven analysis methodology for identifying nonlinear modal interactions and its application to aeroelastic wind-tunnel data from a generic fighter configuration, which reveals global modal interactions in this system caused by multiple resonance capture events initiated by local nonlinearities. It is shown that during supersonic testing at the Transonic Dynamics Tunnel, vibro-impacts at the embedded external fuel tank shakers on the inboard underwing stations of the generic fighter introduce strong nonlinearity that gives rise to nonlinear modal interactions. Specifically, time–frequency analysis of the acceleration data demonstrates that 6∶5 and 7∶6 transient resonance captures occur across the aircraft exclusively during this vibro-impact forcing window. Further analysis suggests that these resonance captures are dependent on Mach number. These results show experimentally that local vibro-impacts can cause global nonlinear effects in an aeroelastic system and that these effects can be identified using the new methodology herein. The data-driven analysis scheme employed shows applicability to full-aircraft flight test data for identifying nonlinear modal interactions without knowledge of the precise nonlinear contributors.

Enzyme Tunnel Dynamics and Catalytic Mechanism of Norcoclaurine Synthase: Insights from a Combined LiGaMD and DFT Study.

This study conducts a systematic investigation into the catalytic mechanism of norcoclaurine synthase (NCS), a key enzyme in the biosynthesis of tetrahydroisoquinolines (THIQs) with therapeutic applications. By integration of LiGaMD and DFT calculations, the reaction pathway of NCS is mapped, providing detailed insights into its catalytic activity and selectivity. Our findings underscore the critical role of E103 in substrate capture and reveal the hitherto unappreciated influence of nonpolar residues M183 and L76 on tunnel dynamics. A prominent discovery is the identification of a high-energy barrier (44.2 kcal/mol) associated with the aromatic electrophilic attack, which pinpoints the rate-limiting step. Moreover, we disclose the existence of dual transition states leading to different products with the energetically favored six-membered ring formation consistent with experimental evidence. These mechanistic revelations not only refine our understanding of NCS but also advocate for a renewed emphasis on enzyme tunnel engineering for optimizing THIQs biosynthesis. The research sets the stage for translating these findings into practical enzyme modifications. Our results highlight the potential of NCS as a biocatalyst to overcome the limitations of current synthetic methodologies, such as low yields and environmental impacts, and provide a theoretical contribution to the efficient, eco-friendly production of THIQs-based pharmaceuticals.

A flow-field integrated flight control: dynamic wind tunnel testing and simulation

Abstract Abrupt changes in aircraft attitude due to encountering terrain turbulence or wind shear at low altitudes can directly lead to serious accidents. Therefore, a highly responsive and reliable active attitude stabiliser on board is necessary to counteract low-level severe atmospheric disturbances. However, gust environments caused by local terrain and structures are difficult to represent with typical models, such as the Dryden continuous gust model in free space. As a result, an optimal model-based control design cannot be applied. To address this problem, this paper introduces an adaptive mechanism for updating motion equations based on atmospheric conditions using in-flight surface pressure-field sensing. Additionally, a dynamic wind tunnel experiment system, which can be constructed at universities at a low cost, is developed and described in detail. The effectiveness of the proposed scheme is evaluated through wind tunnel experiments and numerical simulations using a large number of gust samples.

Coulomb focusing in attosecond angular streaking

Angular streaking technique employs a close-to-circularly polarized laser pulse to build a mapping between the instant of maximum ionization and the most probable emission angle in the photoelectron momentum distribution, thereby enabling the probe of laser-induced electron dynamics in atoms and molecules with attosecond temporal resolution. Here, through the jointed experimental observations and improved Coulomb-corrected strong-field approximation statistical simulations, we identify that electrons emitted at different initial ionization times converge to the most probable emission angle due to the previously-unexpected Coulomb focusing triggered by the nonadiabatic laser-induced electron tunneling. We reveal that the Coulomb focusing induces the observed nonintuitive energy-dependent trend in the angular streaking measurements on the nonadiabatic tunneling, and that tunneling dynamics under the classically forbidden barrier can leave fingerprints on the resulting signals. Our findings have significant implications for the decoding of the intricate tunneling dynamics with attosecond angular streaking.

Numerical Study on Explosion Risk and Building Structure Dynamics of Long-Distance Oil and Gas Tunnels

To comprehensively understand the explosion risk in underground energy transportation tunnels, this study employed computational fluid dynamics technology and finite element simulation to numerically analyze the potential impact of an accidental explosion for a specific oil and gas pipeline in China and the potential damage risk to nearby buildings. Furthermore, the study investigated the effects of tunnel inner diameter (d = 4.25 m, 6.5 m), tunnel length (L = 4 km, 8 km, 16 km), and soil depth (primarily Lsoil = 20 m, 30 m, 40 m) on explosion dynamics and on structural response characteristics. The findings indicated that as the tunnel length and inner diameter increased, the maximum explosion overpressure gradually rose and the peak arrival time was delayed, especially when d = 4.25 m; with the increase in L, the maximum explosion overpressure rapidly increased from 1.03 MPa to 2.12 MPa. However, when d = 6.5 m, the maximum explosion overpressure increased significantly by 72.8% from 1.25 MPa. Evidently, compared to the change in tunnel inner diameter, tunnel length has a more significant effect on the increase in explosion risk. According to the principle of maximum explosion risk, based on the peak explosion overpressure of 2.16 MPa under various conditions and the TNT equivalent calculation formula, the TNT explosion equivalent of a single section of the tunnel was determined to be 1.52 kg. This theoretical result is further supported by the AUTODYN 15.0 software simulation result of 2.39 MPa (error < 10%). As the soil depth increased, the distance between the building and the explosion source also increased. Consequently, the vibration peak acceleration and velocity gradually decreased, and the peak arrival time was delayed. In comparison to a soil depth of 10 m, the vibration acceleration at soil depths of 20 m and 30 m decreased by 81.3% and 91.7%, respectively. When the soil depth was 10 m, the building was at critical risk of vibration damage.

Exploring the conformational landscape through rotational spectroscopy and computational modelling: The tunneling dynamics in 2,6-diethylphenol

Phenol and some of its derivatives exhibit interesting tunneling motions consisting of two groups of transitions separated by a few hundred MHz. Recently, one of its derivatives, 2,6-di-tert-butylphenol, has shown additional hyperfine tunneling components, the origin of which remains unclear. In this work, another member of the family, 2,6-diethylphenol, has been investigated through its rotational spectrum. The jet-cooled broadband chirped-pulse Fourier transform microwave spectra in the 2–8 GHz frequency region revealed the presence of two conformers. The comparison with the equilibrium structure obtained by computational calculations at the B3LYP-D3(BJ)/Def2-TZVP level validates the structural determination and the orientation of the lateral ethyl groups. Additional observation of all the singly-substituted 13C isotopologues for the most stable ones allowed the determination of the substitution structure by means of the Kraitchman equations. Both conformers exhibited tunneling that was reproduced using an advanced 1D model, which provides an estimate of the barrier height for both conformers.

Study on Deformation of New Tunnels Overcrossing Existing Tunnels Underneath Operating Railways

With the increasing utilization of urban underground space, new tunnels frequently intersect with existing tunnels and operational railways. However, sometimes the excavation and unloading of new tunnels can cause deformation of adjacent existing tunnels and railways, significantly affecting their normal operation. We used finite element software to predict the influence of new tunnel construction on overcrossing existing tunnels and down-traversing operational railways by a dynamic tunneling model based on a connection channel project of the east and west squares of a railway station. This article is not only control the distance between the two tunnels, but the new tunnel and the existing tunnel, as well as the new tunnel and the operation of the railway, the positional relationship between the three, the deformation laws of existing tunnels and operational railways during the construction of new tunnels with different buried depths are analyzed. The results show that the deformation curves of existing tunnels and operational railways present a normal distribution. The maximum deformation position is at the intersection with the new tunnel upon completion of the new tunnel excavation construction. Moreover, an increase in the buried depth of the new tunnel increases the deformation of the operational railway and the existing tunnel. The influence of the depth change of the new tunnel on the settlement of the operational railway is greater than that of the existing tunnel.

Tunneling Currents in the Hyperbolic Phase Space.

We introduce the quantum currents for quantum systems with an SU(1,1) dynamic symmetry group whose evolution is governed by a non-linear Hamiltonian possessing a continuous spectrum and apply them to the analysis of the tunneling dynamics on the hyperbolic phase space.

Promoting Proton Donation through Hydrogen Bond Breaking on Carbon Nitride for Enhanced H2O2 Photosynthesis.

Photocatalytic H2O2 production has attracted much attention as an alternative way to the industrial anthraquinone oxidation process but is limited by the weak interaction between the catalysts and reactants as well as inefficient proton transfer. Herein, we report on a hydrogen-bond-broken strategy in carbon nitride for the enhancement of H2O2 photosynthesis without any sacrificial agent. The H2O2 photosynthesis is promoted by the hydrogen bond formation between the exposed N atoms on hydrogen-bond-broken carbon nitride and H2O molecules, which enhances proton-coupled electron transfer and therefore the photocatalytic activity. The exposed N atoms serve as proton buffering sites for the proton transfer from H2O molecules to carbon nitride. The H2O2 photosynthesis is also enhanced through the enhanced adsorption and reduction of O2 gas toward H2O2 on hydrogen-bond-broken carbon nitride because of the formation of nitrogen vacancies (NVs) and cyano groups after the intralayer hydrogen bond breaking on carbon nitride. A high light-to-chemical conversion efficiency (LCCE) value of 3.85% is achieved. O2 and H2O molecules are found to undergo a one-step two-electron reduction pathway by photogenerated hot electrons and a four-electron oxidation process to produce O2 gas, respectively. Density functional theory (DFT) calculations validate the O2 adsorption and reaction pathways. This study elucidates the significance of the hydrogen bond formation between the catalyst and reactants, which greatly increases the proton tunneling dynamics.

Error-Tolerant Amplification and Simulation of the Ultrastrong-Coupling Quantum Rabi Model.

Cat-state qubits formed by photonic cat states have a biased noise channel, i.e., one type of error dominates over all the others. We demonstrate that such biased-noise qubits are also promising for error-tolerant simulations of the quantum Rabi model (and its varieties) by coupling a cat-state qubit to an optical cavity. Using the cat-state qubit can effectively enhance the counterrotating coupling, allowing us to explore several fascinating quantum phenomena relying on the counterrotating interaction. Moreover, another benefit from biased-noise cat qubits is that the two main error channels (frequency and amplitude mismatches) are both exponentially suppressed. Therefore, the simulation protocols are robust against parameter errors of the parametric drive that determines the projection subspace. We analyze three examples: (i)collapse and revivals of quantum states; (ii)hidden symmetry and tunneling dynamics; and (iii)pair-cat-code computation.

Dynamics of proton tunneling in Hydrogen-Bonded systems through Green's function formalism

This study proposes a new theoretical model based on Green's function formalism for studying proton tunneling via hydrogen bonding. This approach allows calculating the tunneling probability and the tunneling energy that proton transfer occurs along a given path inferred a priori. The method is extended to multiple protons tunneling, characterizing the behaviour of some biological molecules. Specifically, the cases of the proton transfer in the Fujicurin A molecule and the double proton tunneling in the Guanine-Cytosine base-pair are investigated. The new approach is an alternative to those present in the literature. It allows straightforwardly predicting the mechanisms of intramolecular and intermolecular proton transfers involving the rearrangement of conjugated electrons.

Efficiency enhancement in Aspergillus niger α-L-rhamnosidase reverse hydrolysis by using a tunnel site rational design strategy

There has been ongoing interest in improving the efficiency of glycoside hydrolase for synthesizing glycoside compounds through protein engineering, given the potential applications of glycoside compounds. In this study, a strategy of modifying the substrate access tunnel was proposed to enhance the efficiency of reverse hydrolysis catalyzed by Aspergillus niger α-L-rhamnosidase. Analysis of the tunnel dynamics identified Tyr299 as a key modifiable residue in the substrate access tunnel. The location of Tyr299 was near the enzyme surface and at the outermost end of the substrate access tunnel, suggested its role in substrate recognition and throughput. Based on the properties of side chains, six mutants were designed and expressed by Pichia pastoris. Compared to WT, the reverse hydrolysis efficiencies of mutants Y299P and Y299W were increased by 21.3 % and 11.1 %, respectively. The calculation results of binding free energy showed that the binding free energy was inversely proportional to the reverse hydrolysis efficiency. Further, when binding free energy levels were comparable, the mutants with shorter side chains displayed a higher reverse hydrolysis efficiency. These results proved that substrate access tunnel modification was an effective method to improve the reverse hydrolysis efficacy of α-L-rhamnosidase and also provided new insights for modifying other glycoside hydrolases.

Effect of Reynolds Number and Aeroelastic Scaling Upon Launch-Vehicle Ground-Wind Loads

NASA conducted a launch vehicle ground-wind-loads investigation at the NASA Langley Transonic Dynamics Tunnel to investigate wind-induced oscillations (WIOs) of a launch vehicle when exposed to ground winds before launch. Previous publications from this effort have documented the effects of an atmospheric-boundary-layer profile on WIO response and the correlation process between model-scale and full-scale wind characteristics and resulting structural loads. This paper will focus on the importance of aeroelastic scaling and the impact of Reynolds number on WIO response. As described in the literature and confirmed in the present investigation, aeroelastic effects can significantly increase the magnitude of measured loads. Additionally, vortex shedding is sensitive to nuances of the flow in the shear layer, which is governed by Reynolds number. Many wind-tunnel facilities are not capable of producing flight Reynolds numbers for the ground-wind-loads problem. At very low Reynolds numbers, laminar shear layers exhibit different behavior, resulting in different vortex frequencies, oscillating lift magnitudes, and motion sensitivities. This investigation demonstrated that low Reynolds number testing can yield substantially lower dynamic loads with less aeroelastic coupling than those acquired at flight-representative Reynolds numbers for a resonant WIO event. Additionally, a resonant response phenomenon present at flight Reynolds number was absent at low Reynolds number. Conversely, for nonresonant WIO response conditions, similar dynamic load coefficients were obtained for similar test velocities at either Reynolds number condition. These findings impact many large launch vehicles, including the NASA Space Launch System series of vehicles.

Global optimization in variational quantum algorithms via dynamic tunneling method

We present a global optimization routine for the variational quantum algorithms, which utilizes the dynamic tunneling flow. Originally designed to leverage information gathered by a gradient-based optimizer around local minima, we adapt the conventional dynamic tunneling flow to exploit the distance measure of quantum states, resolving issues of extrinsic degeneracy arising from the parametrization of quantum states. Our global optimization algorithm is applied to the variational quantum eigensolver for the transverse-field Ising model to demonstrate the performance of our routine while comparing it with the conventional dynamic tunneling method, which is based on the Euclidean distance measure on the parameter space.

Nuclear-Electronic Orbital Time-Dependent Configuration Interaction Method.

Combining real-time electronic structure with the nuclear-electronic orbital (NEO) method has enabled the simulation of complex nonadiabatic chemical processes. However, accurate descriptions of hydrogen tunneling and double excitations require multiconfigurational treatments. Herein, we develop and implement the real-time NEO time-dependent configuration interaction (NEO-TDCI) approach. Comparison to NEO-full CI calculations of absorption spectra for a molecular system shows that the NEO-TDCI approach can accurately capture the tunneling splitting associated with the electronic ground state as well as vibronic progressions corresponding to double electron-proton excitations associated with excited electronic states. Both of these features are absent from spectra obtained with single reference real-time NEO methods. Our simulations of hydrogen tunneling dynamics illustrate the oscillation of the proton density from one side to the other via a delocalized, bilobal proton wave function. These results indicate that the NEO-TDCI approach is highly suitable for studying hydrogen tunneling and other inherently multiconfigurational systems.

Quaternion-Based Attitude Estimation of an Aircraft Model Using Computer Vision.

Investigating aircraft flight dynamics often requires dynamic wind tunnel testing. This paper proposes a non-contact, off-board instrumentation method using vision-based techniques. The method utilises a sequential process of Harris corner detection, Kanade-Lucas-Tomasi tracking, and quaternions to identify the Euler angles from a pair of cameras, one with a side view and the other with a top view. The method validation involves simulating a 3D CAD model for rotational motion with a single degree-of-freedom. The numerical analysis quantifies the results, while the proposed approach is analysed analytically. This approach results in a 45.41% enhancement in accuracy over an earlier direction cosine matrix method. Specifically, the quaternion-based method achieves root mean square errors of 0.0101 rad/s, 0.0361 rad/s, and 0.0036 rad/s for the dynamic measurements of roll rate, pitch rate, and yaw rate, respectively. Notably, the method exhibits a 98.08% accuracy for the pitch rate. These results highlight the performance of quaternion-based attitude estimation in dynamic wind tunnel testing. Furthermore, an extended Kalman filter is applied to integrate the generated on-board instrumentation data (inertial measurement unit, potentiometer gimbal) and the results of the proposed vision-based method. The extended Kalman filter state estimation achieves root mean square errors of 0.0090 rad/s, 0.0262 rad/s, and 0.0034 rad/s for the dynamic measurements of roll rate, pitch rate, and yaw rate, respectively. This method exhibits an improved accuracy of 98.61% for the estimation of pitch rate, indicating its higher efficiency over the standalone implementation of the direction cosine method for dynamic wind tunnel testing.

Chaos-Assisted Dynamical Tunneling in Flat Band Superwires.

Recent theoretical investigations have revealed unconventional transport mechanisms within high Brillouin zones of two-dimensional superlattices. Electrons can navigate along channels we call superwires, gently guided without brute force confinement. Such dynamical confinement is caused by weak superlattice deflections, markedly different from the static or energetic confinement observed in traditional wave guides or one-dimensional electron wires. The quantum properties of superwires give rise to elastic dynamical tunneling, linking disjoint regions of the corresponding classical phase space, and enabling the emergence of several parallel channels. This paper provides the underlying theory and mechanisms that facilitate dynamical tunneling assisted by chaos in periodic lattices. Moreover, we show that the mechanism of dynamical tunneling can be effectively conceptualized through the lens of a paraxial approximation. Our results further reveal that superwires predominantly exist within flat bands, emerging from eigenstates that represent linear combinations of conventional degenerate Bloch states. Finally, we quantify tunneling rates across various lattice configurations and demonstrate that tunneling can be suppressed in a controlled fashion, illustrating potential implications in future nanodevices.

The slopes of sub-barrier heavy-ion fusion excitation functions shed light on the dynamics of quantum tunnelling

Quantum tunnelling plays a crucial role in heavy-ion fusion reactions at sub-barrier energies, especially in the context of nuclear physics and astrophysics. The nuclear structure of the colliding nuclei and nucleon transfer processes represent intrinsic degrees of freedom. They are coupled to the relative ion motion and, in general, increase the probability of tunnelling. The influence of couplings to nucleon transfer channels relatively to inelastic excitations, on heavy-ion fusion cross sections, is one of the still open problems in this field. We present a new analysis of several systems, based on the combined observation of the energy-weighted excitation functions Eσ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$E\\sigma $$\\end{document} in relation to their first energy derivatives d(Eσ)/dE\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$d(E\\sigma )/dE$$\\end{document}. The relation between d(Eσ)/dE\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$d(E\\sigma )/dE$$\\end{document} and Eσ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$E\\sigma $$\\end{document} removes the basic differences due to the varying Coulomb barrier when comparing different systems. We show that, depending on the nuclear structure and/or the presence of strong transfer channels, this representation reveals characteristic features below the barrier. The possible presence of cross section oscillations makes this analysis less clear for light- or medium-light systems.