Bound State Research Articles

Bound state of asymmetric pure-quartic solitons in motion

In this Letter, we investigate the binding mechanism and motion dynamics of the bound state consisting of two pure-quartic solitons (PQSs) with unequal intensities and find that their movement occurs as an entity under the Raman self-frequency shift. By calculating the forces that induce the relative motion between the unequal PQSs, we derive the balanced conditions for maintaining a near-constant separation and the constant phase profile between them. The predictions are validated by the numerical simulations. Our work provides insights into the intrinsic features of symmetry-broken localized structures in nonlinear–dispersive systems, stimulating interest in asymmetric multi-soliton states with intriguing dynamics.

Site-specific incorporation of 19F-nulcei at protein C-terminus to probe allosteric conformational transitions of metalloproteins

Allosteric conformational change is an important paradigm in the regulation of protein function, which is typically triggered by the binding of small cofactors, metal ions or protein partners. Here, we found those conformational transitions can be effectively monitored by 19F NMR, facilitated by a site-specific 19F incorporation strategy at the protein C-terminus using asparaginyl endopeptidase (AEP). Three case studies show that C-terminal 19F-nuclei can reveal protein dynamics not only adjacent but also distal to C-terminus, including those occurring in a hemoprotein neuroglobin (Ngb), calmodulin (CaM), and a cobalt metalloregulator (CoaR) responding to both cobalt and tetrapyrrole. In Ngb, the heme orientation disorder is affected by missense mutations that perturb backbone rigidity or surface charges close to the heme axial ligands. In CaM, the C-terminal 19F-nuclei is an ideal probe for detecting the binding states of Ca2+, peptides and inhibitors. Furthermore, multiple 19F-moieties were incorporated into the two domains of CoaR, revealing the intrinsically disordered C-terminal metal binding tail might be an allosteric conformational switch to maintain cobalt homeostasis and balance corrinoid biosynthesis. This study demonstrates that the AEP-based 19F-modification strategy can be applied to various targets to study allosteric regulation, especially for those biological processes modulated by the protein C-terminus.

Efficient application of an all-fiber saturable absorber for the generation of heterogeneous and vector dissipative solitons in fiber lasers

A fully fiber-based structural saturable absorber (SA) incorporating graded-index multimode fiber, stepped-index multimode fiber, and graded-index multimode fiber (GIMF–SIMF–GIMF) has been fabricated and applied to a fiber laser. The modulation depth and saturation intensity are measured to be 1.32 % and 26.79 MW/cm2, respectively. A heterogeneous soliton with an adjustable optical spectrum interval with 4.6 nm and 3 nm is generated in the anomalous dispersion regime. The main pulse widths are approximately 41.80 ps and 35.56 ps. Additionally, a switchable single vector soliton and bound states of vector dissipative solitons are achieved in the normal dispersion regime. The pulse width of the single vector soliton is measured to be 6.16 ps, while the bound state exhibits a pulse width of 6.49 ps with a temporal separation of 15.22 ps. By employing external cavity compression, the minimum pulse widths for the single and bound states of vector dissipative solitons are reduced to 2.18 ps and 1.55 ps, respectively. These experimental results demonstrate that the GIMF–SIMF–GIMF SA exhibits unique nonlinear optical effects and offers promising potential for soliton generation applications.

A finger that gets in the way: When binding isn’t just about the bound state

In this issue of Structure, Viennet etal.1 report a study characterizing the DNA binding by a three-zinc-finger fragment from the transcription factor BCL11A, with the unusual feature that an interfinger interaction in the free protein is disrupted during binding, which provides a positive entropic contribution that enhances the affinity.

A new solution to the Callan Rubakov effect

In this paper we study the scattering of massive fermions off of smooth, spherically symmetric monopoles in 4d SU(2) gauge theory. We propose a complete physical picture of the monopole-fermion interaction which encompasses all angular momentum modes. We show that as an in-going fermion scatters off a monopole, it excites trapped W-bosons in the monopole core by a version of the Witten effect so that the monopole can accrue charge and transform into a dyon at parametrically low energies. The imparted electric charge is then protected from decay by an emergent ℤN generalized global symmetry, creating a stable dyon. At sufficiently low energies, the scattered fermion can be trapped by the dyon’s electrostatic potential, forming a bound state, which can decay into spherically symmetric fermion modes subject to the preserved ℤN global symmetry. We propose that monopole-fermion scattering can be described in this way without needing to add “new” states to the Hilbert space, thereby eliminating a long standing confusion in the Callan Rubakov effect.

Possible mixing of a diquark-antidiquark with a pp¯ hadronic molecule

We discuss the possibility that the two nearby resonances observed by BESIII partially below the pp¯ threshold might be due to mixing between two metastable states with the same JPC=0−+ quantum numbers, but rather different internal structure. One is a pp¯ hadronic molecule and the other a bound state of a light-quark diquark and an antidiquark, both with spin 1 and isospin 0, a composite color antitriplet and triplet, respectively. The doubling of resonances, one of which may be interpreted as a hadronic molecule, while the other arises from qq¯ annihilation in a state with vacuum quantum numbers, may be a more general feature than the specific case considered here. Published by the American Physical Society 2024

Infrared Photoactivation Enables nano-DESI MS of Protein Complexes in Tissue on a Linear Ion Trap Mass Spectrometer.

Native mass spectrometry analysis of proteins directly from tissues can be performed by using nanospray-desorption electrospray ionization (nano-DESI). Typically, supplementary collisional activation is essential to decluster protein complex ions from solvent, salt, detergent, and lipid clusters that comprise the ion beam. As an alternative, we have implemented declustering by infrared (IR) photoactivation on a linear ion trap mass spectrometer equipped with a CO2 laser (λ = 10.6 μm). The prototype system demonstrates declustering of intact protein complex ions up to approximately 50 kDa in molecular weight that were sampled directly from brain and eye lens tissues by nano-DESI. For example, signals for different metal binding states of hSOD1G93A homodimers (approximately 32 kDa) separated by only approximately 6 Th (10+ ions) were resolved with IR declustering, but not with collisional activation. We found IR declustering to outperform collisional activation in its ability to reduce chemical background attributable to nonspecific clusters in the nano-DESI ion beam. The prototype system also demonstrates in situ native MS on a low-cost mass spectrometer and the potential of linear ion trap mass spectrometers for this type of analysis.

Acoustic enhancement and weak signal detection based on quasibound states in the continuum

Acoustic signal detection is important in several fields of research. However, realizing weak-signal detection remains a challenge. Recently, the bound state in continuum (BIC) has attracted considerable attention because of its ultrahigh quality-factor (Q-factor) and strong field enhancement. In this study, we achieved two Fabry–Perot BICs (bonding and anti-bonding BICs) in a coupled-resonator system and a mirror-induced BIC in a single-resonator system. And the acoustic enhancement from quasi-BICs of the coupled-resonator system and single-resonator system was investigated in the simulation. Compared to the coupled-resonator system, the amplification performance of the single-resonator system was better and verified in the experiment. The experimental results agreed with the numerical results, and the maximum pressure magnification was approximately 28×. Furthermore, the single-resonator system enhanced the weak harmonic signal, weak periodic impulse signal, and weak modulated signal in the presence of strong background noise, making signal detection much easier. We believe that this work provides a new method to realize weak signal detection based on acoustic enhancement.

Reconstitution of SPO11-dependent double-strand break formation.

Homologous meiotic recombination starts with DNA double-strand breaks (DSBs) generated by SPO11 protein 1 . SPO11 is critical for meiosis in most species but the DSBs it makes are also dangerous because of their mutagenic 2 and gametocidal 3 potential, so cells must foster SPO11's beneficial functions while minimizing its risks 4 . SPO11 mechanism and regulation remain poorly understood. Here we report reconstitution of DNA cleavage in vitro with purified recombinant mouse SPO11 bound to its essential partner TOP6BL. Similar to their yeast orthologs 5,6 , SPO11- TOP6BL complexes are monomeric (1:1) in solution and bind tightly to DNA. Unlike in yeast, however, dimeric (2:2) assemblies of mouse SPO11-TOP6BL cleave DNA to form covalent 5' attachments requiring SPO11 active site residues, divalent metal ions, and SPO11 dimerization. Surprisingly, SPO11 can also manifest topoisomerase activity by relaxing supercoils and resealing DNA that it has nicked. Structure modeling with AlphaFold3 7 illuminates the protein-DNA interface and suggests that DNA is bent prior to cleavage. Deep sequencing of in vitro cleavage products reveals a rotationally symmetric base composition bias that partially explains DSB site preferences in vivo. Cleavage is inefficient on complex DNA substrates, partly because SPO11 is readily trapped in DSB-incompetent (presumably monomeric) binding states that exchange slowly. However, cleavage is improved by using substrates that favor DSB-competent dimer assembly, or by fusing SPO11 to an artificial dimerization module. Our results inform a model in which intrinsically feeble dimerization restrains SPO11 activity in vivo, making it exquisitely dependent on accessory proteins that focus and control DSB formation so that it happens only at the right time and the right places.

Doubly heavy tetraquark bound and resonant states

We calculate the energy spectrum of the S-wave doubly heavy tetraquark systems, including the QQ(′)q¯q¯, QQ(′)s¯q¯, and QQ(′)s¯s¯ (Q(′)=b, c and q=u, d) systems within the constituent quark model. We use the complex scaling method to obtain bound states and resonant states simultaneously, and the Gaussian expansion method to solve the complex-scaled four-body Schrödinger equation. With a novel definition of the root-mean-square radii, we are able to distinguish between meson molecules and compact tetraquark states. The compact tetraquarks are further classified into three different types with distinct spatial configurations: compact even tetraquarks, compact diquark-antidiquark tetraquarks, and compact diquark-centered tetraquarks. In the I(JP)=0(1+) QQq¯q¯ system, there exists the D*D molecular bound state with a binding energy of −14 MeV, which is the candidate for Tcc(3875)+. The shallow B¯*B¯ molecular bound state is the bottom analog of Tcc(3875)+. Moreover, we identify two resonant states near the D*D* and B¯*B¯* thresholds. In the JP=1+ bbq¯q¯(I=0) and bbs¯q¯ systems, we obtain deeply bound states with a compact diquark-centered tetraquark configuration and a dominant χ3¯c⊗3c component, along with resonant states with similar configurations as their radial excitations. These states are the QCD analog of the helium atom. We also obtain some other bound states and resonant states with “QCD hydrogen molecule” configurations. Moreover, we investigate the heavy quark mass dependence of the I(JP)=0(1+) QQq¯q¯ bound states. We strongly urge the experimental search for the predicted states. Published by the American Physical Society 2024

Unleashing Giant Förster Resonance Energy Transfer by Bound State in the Continuum.

Förster resonance energy transfer (FRET), driven by dipole-dipole interactions (DDIs), is widely utilized in chemistry, biology, and nanophotonics. However, conventional FRET is ineffective at donor-acceptor distances exceeding 10 nm and measurements suffer from low signal-to-noise ratios. In this study, we demonstrate significant FRET enhancement and extended interaction distances under ambient conditions by utilizing a bound state in the continuum (BIC) mode within a dielectric metasurface cavity. This enhancement is achieved by leveraging the ultrahigh quality factors, minimal material absorption, and nonlocal effects associated with the BIC mode. Spectrally and angularly resolved photoluminescence (PL) lifetime measurements reveal that the BIC mode significantly increases the FRET rate and interaction distance. The FRET rate is enhanced by up to 70-fold, and the interaction distance is significantly boosted by over an order of magnitude, reaching ∼100 nm. These findings offer valuable insights for achieving long-range, high-efficiency FRET and collective DDIs using loss-less dielectric metasurfaces.

Unitarization of electron scattering with an external potential at NLO in QED

We have calculated the one-loop scattering amplitude of an electron by an external Coulomb potential in QED free of infrared divergences. This feature is achieved by applying the Faddeev-Kulish formalism, which implies a redefinition of both the asymptotic electronic states and of the S matrix. Additionally, we have also derived the infrared-finite one-loop partial-wave amplitudes for this process by applying a recent method in the literature. Next, these partial-wave amplitudes are unitarized based on analyticity and unitarity by employing three different methods of unitarization: the algebraic N/D method, the Inverse Amplitude Method and the first-iterated N/D method. Then, we have studied several partial waves both for physical momentum and for complex ones to look for bound-state poles. The binding momentum for the fundamental bound state in S wave is discussed with special detail. This is a wide-ranging method for calculating nonperturbative partial-wave amplitudes for infinite-range interactions that could be applied to many other systems.

Relativistic bound state solutions and quantum information theory in D dimensions under exponential-type plus Yukawa potentials

The bound-state solution of the radial Klein-Gordon equation has been obtained under the interaction of an exponential-type and Yukawa potential functions. The Greene-Aldrich approximation has been used to overcome the centrifugal barrier and enable the analytical solutions of the energy and wave functions in closed form. The momentum space wave function in D dimensions has been constructed using the Fourier transform. The mean values have been conjectured for the position and momentum spaces using two equivalent equations. The effects of the potential parameters on the expectation values and quantum information measurement have been investigated. For the 1D case, the results obey the Heisenberg uncertainty principle, Fisher, Shannon, Onicescu, and the Rényi entropic inequalities. Other information complexities measures, such as Shannon Power, Fisher-Shannon, and Lopez-Ruiz-Mancini-Calbet, have been verified. For the ground state, the 1D momentum expectation value \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\langle p^{2} \\rangle_{00}$$\\end{document} coincides with the 3D \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\langle p^{2} \\rangle_{000}$$\\end{document} values, which is an indication of degeneracy. The total energy of a particle in both 1D and 3D space may be degenerate due to the inter-dimensional degeneracy of the quantum numbers. However, in this present result, the degeneracy in 1D and 3D occurred for fixed quantum states at different momentum intervals. Thus, in 1D, a particle may transit an entire space (\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\:-\\infty\\:<p<\\infty\\:)$$\\end{document} with a certain kinetic energy, which must be equal to its kinetic energy if it moves through the interval \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\:0<p<\\infty\\:$$\\end{document} in 3D space. This may have implications for kinetic energy degeneracy in higher dimensions.

Structural aspects of CEACAM1 interactions.

Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) is a membrane protein that plays an important role in a variety of immune and non-immune functions. Such functions are regulated by its activity as a homophilic ligand but also through its ability to interact as a heterophilic ligand with various host proteins. These include CEACAM5, T cell immunoglobulin-mucin like protein-3 (TIM-3) and, potentially, protein death protein 1 (PD-1). Furthermore, CEACAM1 is targeted by various pathogens to allow them to invade a host and bypass an effective immune response. Clinically, CEACAM1 plays an important role in infectious diseases, autoimmunity and cancer. In this review, we describe the structural basis for CEACAM1 interactions as a homophilic and heterophilic ligand. We discuss the regulation of its monomeric, dimeric and oligomeric states in cis and trans binding as well as the consequences for eliciting downstream signalling activities. Furthermore, we explore the potential role of avidity in determining CEACAM1's activities.

Prediction of Molar Entropy of Gaseous Molecules for a New Pὃschl‐Teller Potential Model

ABSTRACTThe Pὃschl–Teller potential is a molecular potential energy function that has only been reported for bound state. This Pὃschl–Teller potential is a good representation of many molecules and has not been examined for any thermodynamic property irrespective of its fitness for molecular study. In this study, the molar entropy of four molecules (Pbr, BBr, CsCl, and CsO molecules) is calculated via the molar partition function. The predicted results are compared with the experimental data recorded in the National Institute of Standards and Technology (NIST) database. It is noted that the predicted values for the studied molecules perfectly agree with the experimental results with the following average absolute percentage deviation, PBr is 0.0158%, BBr is 0.0053%, CsCl is 0.0020%, and CsO is 0.0052%. The present model reproduces better results for CsCl and CsO molecules compared to the shifted Tietz–Wei potential and improved Tietz‐oscillator previously reported whose average absolute percentage deviation are 0.361% and 0.284% for CsCl and 0.272% and 0.228% for CsO, respectively.

VP28 interacts with PmRab7 irrespective of its nucleotide state

In shrimp aquaculture, white spot syndrome virus (WSSV) infections severely impact production. Previous research highlighted the crucial role of the Penaeus monodon Rab7 (PmRab7) protein in WSSV entry, specifically its interaction with the viral envelope protein VP28. PmRab7 exists in two conformations: GDP-bound (inactive) and GTP-bound (active). This study, using ELISA and isothermal titration calorimetry (ITC), reveals that the PmRab7-VP28 interaction occurs irrespective of the nucleotide binding state of PmRab7. Comparing the binding affinity between VP28 and different PmRab7 conformations, including wild-type (WT, 22.5 nM), a fast nucleotide exchange (L129F, 128 nM), a GDP-bound form (T22N, 334 nM), and a favorably GTP-bound form (Q67L, 1990 nM), PmRab7-WT exhibits the strongest binding affinity, especially at a lower temperature (25 °C). The binding of PmRab7-WT and VP28 in the presence of excess nucleotide (WT with excess GDP, 924 nM, and WT with excess GTP, 826 nM) shows a 2-fold higher binding affinity than in the absence (WT, 1920 nM) indicating that the addition of excess nucleotide for PmRab7-WT enhanced the affinity for VP28. Together, these findings support the potential of PmRab7-WT as a promising therapeutic candidate for WSSV control in shrimp. Furthermore, from an industrial point of view, the ITC platform developed to study the VP28-PmRab7 interactions provides a high-throughput method for screening additives for shrimp feed that can inhibit this interaction.

L-band wavelength-switchable bound states in a hybrid mode-locked fiber laser

This paper presents a hybrid mode-locked fiber laser based on the nonlinear polarization rotation (NPR) and the nanomaterial saturable absorber. Due to the presence of the NPR filter, we obtain L-band wavelength-switchable conventional solitons (CSs) and bound states (BSs). The tightly BSs and loosely BS, as well as the "2 + 1" type BS, are also experimentally observed. We study the formation of CSs and BSs by numerical simulations, the results of which are consistent with the experimental results. Our work deepens the understanding of the formation of BSs in hybrid mode-locked fiber lasers and provides new solutions for L-band light sources.

Condensation of Exciton-Polaritons in a Bound State in the Continuum: Effects of the Excitation Spot Size and Polariton Transport.

We report the formation of polariton condensates from strongly coupled molecules to bound states in the continuum with quadrupolar character in a metasurface of silicon nanoparticles. Our experiments demonstrate a strong dependence of the condensation threshold on the excitation spot size. The condensation threshold decreases as the excitation spot size increases, achieving thresholds below 3 μm cm-2 for spot sizes of around 1 mm2 and condensate lifetimes exceeding 20 ps. The strong dependence of the condensation threshold on the spot size is caused by the long propagation length of the polaritons. We reproduce this dependence in simulations by including a term for the ballistic transport of exciton-polaritons in the rate equations describing the condensation. These results illustrate the critical role that polariton transport plays in condensation and highlight the relevance of considering the size of the excitation in condensation experiments.

Fate of Two-Particle Bound States in the Continuum in Non-Hermitian Systems.

We unveil the existence of a two-particle bound state in the continuum (BIC) in a one-dimensional interacting nonreciprocal lattice with a generalized boundary condition. By applying the Bethe-ansatz method, we can exactly solve the wave function and eigenvalue of the bound state in the continuum band, which enable us to precisely determine the phase diagrams of BIC. Our results demonstrate that the nonreciprocal hopping can delocalize the bound state and thus shrink the region of BIC. By analyzing the wave function, we identify the existence of two types of BICs with different spatial distributions and analytically derive the corresponding threshold values for the breakdown of BICs. The BIC with similar properties is also found to exist in another system with an impurity potential.

Tetraquarks made of sufficiently unequal-mass heavy quarks are bound in QCD

Tetraquarks, bound states composed of two quarks and two antiquarks, have been the subject of intense study but are challenging to understand from first principles. We apply variational and Green’s function Monte Carlo methods to compute tetraquark ground-state energies in potential nonrelativistic QCD using a wide range of color and spatial wave functions. We find no evidence for bound tetraquarks composed of equal-mass quarks and antiquarks. Conversely, we find clear evidence for the existence of bound tetraquarks for sufficiently unequal quark/antiquark mass ratios at all overall mass scales where our effective theory results are applicable. We predict the critical mass ratios for bound state formation and study tetraquark bound states’ spatial and color structure at leading order and next-to-leading order in potential nonrelativistic QCD. Published by the American Physical Society 2024