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Spectrum of bound and quasi-bound states of hydrogen-hydrogen scattering and resonance, using Schroedinger equation
Abstract The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions necessary for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin of replication, catalyzing the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. We report the cryo-electron microscopy structures of Rep68 bound to the adeno-associated virus integration site 1 in different nucleotide-bound states. In the nucleotide-free state, Rep68 forms a heptameric complex around DNA, with three origin-binding domains (OBDs) bound to the Rep-binding element sequence, while three remaining OBDs form transient dimers with them. The AAA+ domains form an open ring without interactions between subunits and DNA. We hypothesize that the heptameric structure is crucial for loading Rep68 onto double-stranded DNA. The ATPγS complex shows that only three subunits associate with the nucleotide, leading to a conformational change that promotes the formation of both intersubunit and DNA interactions. Moreover, three phenylalanine residues in the AAA+ domain induce a steric distortion in the DNA. Our study provides insights into how an SF3 helicase assembles on DNA and provides insights into the DNA melting process.
The evaluation of expectation values Tr[$\rho \mathcal{O}$] for some pure state $\rho$ and Hermitian operator $\mathcal{O}$ is of central importance in a variety of quantum algorithms. Near-optimal techniques have been developed in the past and require a number of measurements N approaching the Heisenberg limit N = O(1/ ε) as a function of target accuracy ε. The use of quantum phase estimation (QPE) requires, however, long circuit depths C = O(1/ ε) making its implementation difficult on near-term noisy devices. The more direct strategy of operator averaging is usually preferred as it can be performed using N = O(1/ε 2 ) measurements and no additional gates aside from those needed for the state preparation. In this work we use a simple but realistic model to describe the bound state of a neutron and a proton (the deuteron) to show that the latter strategy can require an overly large number of measurements in order to achieve a prefixed relative target accuracy ε r . Further, we propose to overcome this problem using a single step of QPE and classical postprocessing. This approach leads to a circuit depth C = O (ε μ ) (with μ ≥ 0) and to a number of measurements N = O (1/ε 2 + ν ) for 0 < ν ≤ 1 and a much smaller prefactor. We provide detailed descriptions of two implementations of our strategy for ν = 1 and ν ≈ 0.5 and derive appropriate conditions that a particular problem instance has to satisfy in order for our method to provide an advantage.
The growing field of correlated nanoelectronics exists at the intersection of two established fields: correlated oxide electronics and semiconductor nanoelectronics. The development of quantum technologies that exploit quantum coherence and entanglement for the purposes of computation, simulation, and sensing will require complex material properties to be controlled at nanoscale dimensions. Heterostructures and nanostructures formed at the interface between LaAlO 3 and SrTiO 3 exhibit striking behavior that arises from the ability to program the conductive behavior at extreme nanoscale dimensions. The active electronic layer, SrTiO 3 , exhibits a wide range of gate-tunable phenomena such as ferroelectricity, ferroelasticity, magnetism, superconductivity, and spin–orbit coupling, all of which can be controlled at the nanoscale using two reversible methods: conductive atomic force microscope lithography and ultra-low-voltage electron beam lithography. Mesoscopic devices such as single-electron transistors and quasi-one-dimensional electron waveguides can be “sketched” using these techniques, and the properties of these devices differ significantly from those created from traditional semiconductors, such as Si or GaAs. The strongly correlated nature of the SrTiO 3 system is evident from superconducting behavior as well as a state in which electrons are paired outside the superconducting state. A highly exotic phase was discovered in which a degenerate quantum liquid is formed from bound states of n = 2, 3, 4, … electrons. Further development of correlated nanoelectronics based on the LaAlO 3 /SrTiO 3 system can potentially lead to a general platform for quantum simulation as well as a pathway for the development of highly entangled states of multiple photons.
Here, we study the honeycomb lattice with a single magnetic impurity modeled by adding imaginary next-nearest-neighbor hopping 𝑖ℎ on a single hexagon. This Haldane defect gives a topological mass term to the gapless Dirac cones and generates chirality. For a small density of defects, Neehus et al. [Phys. Rev. Lett. 135, 126604 (2025)] found that the system's chirality reverses at a critical ℎ 𝑐 ≈ 0.95 associated with an unexpected tricritical point of Dirac fermions at zero defect density. We investigate this zero-density limit by analyzing a single defect and computing two experimentally relevant measures of chirality: (1) orbital magnetization via local Chern marker, a bulk probe of all occupied states; and (2) electronic currents of low-energy states. Both probes show a chirality reversal at a critical ℎ 𝑐 ≈ 0.9–1.0. Motivated by this consistency, we propose a defect-scale toy model whose low-energy states reverse their chirality at ℎ$^{'}_{c}$ ≈ 0.87. Remarkably, the same pair of zero-energy bound states also generates the critical point ℎ 𝑐 in the full impurity projected T-matrix. Our results show how the chirality reversal produced by an impurity can be observed either in local probes or in the global topology, and suggest a possible role of the microscopic defect structure at the critical point.
We formulate large [Formula: see text] duality of [Formula: see text] refined Chern–Simons theory with a torus knot/link in [Formula: see text]. By studying refined BPS states in M-theory, we provide the explicit form of low-energy effective actions of Type IIA string theory with D4-branes on the [Formula: see text]-background. This form enables us to relate refined Chern–Simons invariants of a torus knot/link in [Formula: see text] to refined BPS invariants in the resolved conifold. Assuming that the extra [Formula: see text] global symmetry acts on BPS states trivially, the duality predicts graded dimensions of cohomology groups of moduli spaces of M2–M5 bound states associated to a torus knot/link in the resolved conifold. Thus, this formulation can be also interpreted as a positivity conjecture of refined Chern–Simons invariants of torus knots/links. We also discuss about an extension to non-torus knots.
Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (M pro ) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 Å resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 Å resolution and in its product bound state at 2.0 Å resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on M pro inhibition.
Log-periodic quantum oscillations discovered in transition-metal pentatelluride give a clear demonstration of discrete scale invariance (DSI) in solid-state materials. The peculiar phenomenon is convincingly interpreted as the presence of two-body quasi-bound states in a Coulomb potential. However, the modifications of the Coulomb interactions in many-body systems having a Dirac-like spectrum are not fully understood. Here, we report the observation of tunable log-periodic oscillations and DSI in ZrTe 5 and HfTe 5 flakes. By reducing the flakes thickness, the characteristic scale factor is tuned to a much smaller value due to the reduction of the vacuum polarization effect. The decreasing of the scale factor demonstrates the many-body effect on the DSI, which has rarely been discussed hitherto. Furthermore, the cut-offs of oscillations are quantitatively explained by considering the Thomas-Fermi screening effect. Finally, our work clarifies the many-body effect on DSI and paves a way to tune the DSI in quantum materials.
Sr 2 IrO 4 is an archetypal spin-orbit-coupled Mott insulator with an antiferromagnetic state below 240 K. Here we report results of our study on single crystals of Sr 2 Ir 1–x Fe x O 4 (0 ≤ x < 0.32) and Sr 2 Ir 1–x Co x O 4 (0 ≤ x < 0.22). Fe doping retains the antiferromagnetic state but simultaneously precipitates an emergent metallic state whereas Co doping causes a rapid collapse of both the antiferromagnetic and Mott states, giving rise to a confined metallic state featuring a pronounced linearity of the basal-plane resistivity up to 700 K. The results indicate tetravalent Fe 4+ (3d 4 ) ions in the intermediate spin state with S = 1 and Co 4+ (3d 5 ) ions in the high spin state with S = 5/2 substituting for Ir 4+ (5d 5 ) ions in Sr 2 IrO 4 , respectively. The effective magnetic moment closely tracks the Néel temperature as doping increases, suggesting that the spin state of the dopant predominately determines the magnetic properties in doped Sr 2 IrO 4 . Furthermore, all relevant properties including charge-carrier density (e.g., 10 28 /m 3 ), Sommerfeld coefficient (e.g., 19 mJ / mole K 2 ), and Wilson ratio (e.g., 2.6) consistently demonstrate an emergent metallic state that is both robust and highly correlated in the two systems, arising from the percolation of bound states and the weakening of structural distortions. Furthermore, this study strongly indicates that the antiferromagnetic and Mott states are correlated in an unconventional manner in Sr 2 IrO 4 .
The cross sections for photoionization from the 2 1S, 2 3S, 2 1P and 2 3P excited states of helium are calculated for photoelectron energies below the n = 2 threshold of He(+) using Hylleraas bound state wave functions and 1s-2s-2p close coupling final state wave functions. The resonant structures associated with the lowest-lying 1S, 1P, 3P, and 1D autoionizing states of helium are found to be characterized by large values of the line profile parameter q. The cross sections and the photoelectron angular distribution asymmetry parameters for the P-states are calculated for various polarization states of the target atom and the incident photon. Experiments which would lead to the separate determinations of the S- and D- wave partial photoionization cross sections are discussed.
The basic equations of quantum scattering were translated into the Wigner representation, putting quantum mechanics in the form of a stochastic process in phase space, with real valued probability distributions and source functions. The interpretative picture associated with this representation is developed and stressed and results used in applications published elsewhere are derived. The form of the integral equation for scattering as well as its multiple scattering expansion in this representation are derived. Quantum corrections to classical propagators are briefly discussed. The basic approximation used in the Monte-Carlo method is derived in a fashion which allows for future refinement and which includes bound state production. Finally, as a simple illustration of some of the formalism, scattering is treated by a bound two body problem. Simple expressions for single and double scattering contributions to total and differential cross-sections as well as for all necessary shadow corrections are obtained.
All herpesviruses encode a conserved DNA polymerase that is required for viral genome replication and serves as an important therapeutic target. Currently available herpesvirus therapies include nucleoside and non-nucleoside inhibitors (NNI) that target the DNA-bound state of herpesvirus polymerase and block replication. Here we report the ternary complex crystal structure of Herpes Simplex Virus 1 DNA polymerase bound to DNA and a 4-oxo-dihydroquinoline NNI, PNU-183792 (PNU), at 3.5 Å resolution. PNU bound at the polymerase active site, displacing the template strand and inducing a conformational shift of the fingers domain into an open state. These results demonstrate that PNU inhibits replication by blocking association of dNTP and stalling the enzyme in a catalytically incompetent conformation, ultimately acting as a nucleotide competing inhibitor (NCI). Sequence conservation of the NCI binding pocket further explains broad-spectrum activity while a direct interaction between PNU and residue V823 rationalizes why mutations at this position result in loss of inhibition.
In this article, we use the Halfium R-matrix method to investigate the Rydberg states of the H 2 molecule up to n = 20, filling the gap above the low-lying bound states already calculated with configuration interaction packages. Moreover, we show that the use of Quantum Defect Theory scaling laws, allows for a comprehensive analysis of the regular patterns resulting from the coupling between Rydberg series and doubly excited states. The results should open the door for more efficient quasi-diabatization of the potential energy curves which is required for calculating cross sections and rate coefficients of the (e + H 2 + ) collisional processes, involved in the plasma modeling for fusion devices.
The energy and wave functions of two-particle states in a dense plasma are essentially influenced by the surrounding medium. However, the two-particle bound-state energies may remain unshifted over a large density interval. Two simple examples are given to demonstrate the compensation of many-particle effects such as the self-energy and effective two-particle potentials in hydrogen plasmas. Neglecting self-energy and Pauli blocking, energy values that follow from numerical solutions of the Schroedinger equation with a Debye potential are obtained.
Using an atomistic tight-binding model, we investigate the characteristics of a Josephson junction formed by monolayers of MoS 2 sandwiched between Pb superconducting electrodes. We derive and apply Green's function–based formulation to compute the Josephson current as well as the local density of states in the junction. Our analysis of diagonal and off-diagonal components of the local density of states reveals the presence of triplet superconducting correlations in the MoS 2 monolayers and spin-polarized subgap (Andreev bound) states. Our formulation can be extended to other systems where atomistic details and large scales are needed to obtain accurate modeling of Josephson junction physics.
Abstract Motivation Deep learning has revolutionized protein tertiary structure prediction recently. The cutting-edge deep learning methods such as AlphaFold can predict high-accuracy tertiary structures for most individual protein chains. However, the accuracy of predicting quaternary structures of protein complexes consisting of multiple chains is still relatively low due to lack of advanced deep learning methods in the field. Because interchain residue–residue contacts can be used as distance restraints to guide quaternary structure modeling, here we develop a deep dilated convolutional residual network method (DRCon) to predict interchain residue–residue contacts in homodimers from residue–residue co-evolutionary signals derived from multiple sequence alignments of monomers, intrachain residue–residue contacts of monomers extracted from true/predicted tertiary structures or predicted by deep learning, and other sequence and structural features. Results Tested on three homodimer test datasets (Homo_std dataset, DeepHomo dataset and CASP-CAPRI dataset), the precision of DRCon for top L/5 interchain contact predictions (L: length of monomer in a homodimer) is 43.46%, 47.10% and 33.50% respectively at 6 Å contact threshold, which is substantially better than DeepHomo and DNCON2_inter and similar to Glinter. Moreover, our experiments demonstrate that using predicted tertiary structure or intrachain contacts of monomers in the unbound state as input, DRCon still performs well, even though its accuracy is lower than using true tertiary structures in the bound state are used as input. Finally, our case study shows that good interchain contact predictions can be used to build high-accuracy quaternary structure models of homodimers. Availability and implementation The source code of DRCon is available at https://github.com/jianlin-cheng/DRCon. The datasets are available at https://zenodo.org/record/5998532#.YgF70vXMKsB. Supplementary information Supplementary data are available at Bioinformatics online.
Metabotropic γ-aminobutyric acid G protein–coupled receptors (GABA B ) represent one of the two main types of inhibitory neurotransmitter receptors in the brain. These receptors act both pre- and postsynaptically by modulating the transmission of neuronal signals and are involved in a range of neurological diseases, from alcohol addiction to epilepsy. A series of recent cryo-EM studies revealed critical details of the activation mechanism of GABA B . Structures are now available for the receptor bound to ligands with different modes of action, including antagonists, agonists, and positive allosteric modulators, and captured in different conformational states from the inactive apo to the fully active state bound to a G protein. These discoveries provide comprehensive insights into the activation of the GABA B receptor, which not only broaden our understanding of its structure, pharmacology, and physiological effects but also will ultimately facilitate the discovery of new therapeutic drugs and neuromodulators.
By using scanning tunneling microscopy (STM) we find and characterize dispersive, energy-symmetric in-gap states in the iron-based superconductor FeTe 0.55 Se 0.45 , a material that exhibits signatures of topological superconductivity, and Majorana bound states at vortex cores or at impurity locations. We use a superconducting STM tip for enhanced energy resolution, which enables us to show that impurity states can be tuned through the Fermi level with varying tip-sample distance. We find that the impurity state is of the Yu-Shiba-Rusinov (YSR) type, and argue that the energy shift is caused by the low superfluid density in FeTe 0.55 Se 0.45 , which allows the electric field of the tip to slightly penetrate the sample. We model the newly introduced tip-gating scenario within the single-impurity Anderson model and find good agreement to the experimental data.