Structure Of Bound States Research Articles

Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering.

The structures of RNA:RNA complexes regulate many biological processes. Despite their importance, protein-free RNA:RNA complexes represent a tiny fraction of experimentally-determined structures. Here, we describe a joint small-angle X-ray and neutron scattering (SAXS/SANS) approach to structurally interrogate conformational changes in a model RNA:RNA complex. Using SAXS, we measured the solution structures of the individual RNAs in their free state and of the overall RNA:RNA complex. With SANS, we demonstrate, as a proof-of-principle, that isotope labeling and contrast matching (CM) can be combined to probe the bound state structure of an RNA within a selectively deuterated RNA:RNA complex. Furthermore, we show that experimental scattering data can validate and improve predicted AlphaFold 3 RNA:RNA complex structures to reflect its solution structure. Our work demonstrates that in silico modeling, SAXS, and CM-SANS can be used in concert to directly analyze conformational changes within RNAs when in complex, enhancing our understanding of RNA structure in functional assemblies.

Plasmonic Bound States in the Continuum to Tailor Exciton Emission of MoTe2.

Plasmon resonances can greatly enhance light-matter interactions of two-dimensional van der Waals materials. However, the quality factor of plasmonic resonances is limited. Here, we demonstrate a plasmonic quasi-bound state in the continuum (quasi-BIC), which is composed of gold nanorod pairs. Through controlling the rotation angle of the nanorods, the quality factor of the plasmonic BIC mode can be tuned. Simulation results show that the plasmonic BIC combines the advantages of high-quality factor from the BIC effect and small mode volume from plasmonic resonance. Experiment results show that the designed plasmonic BIC mode exhibits a quality factor higher than 15 at the wavelength of around 1250 nm. Through integrating the plasmonic bound state structure with monolayer molybdenum ditelluride (MoTe2), the exciton emission of MoTe2 in the PL spectrum split into two exciton-polariton modes, which is attributed to the high Q factor and strong interaction between the BIC mode and excitons of MoTe2.

Ballistic spin transport in DC-bias single top gate p-type narrow channel device with Zeeman–Rashba effects

The ballistic transport of holes in a p-type quasi-one-dimensional channel system is investigated without considering the coupling effect of the light and heavy holes. A top gate (TG) is used to form a potential barrier in the quantum channel with Zeeman–Rashba (ZR) effects. The Luttinger Hamiltonian and propagation matrix method are used to examine the relationship between the conductance and the incident hole energy. The results show that when the gate width L is large, an electron-like bound state (E-BS) structure is formed at the inflection point of the spin-down branch. When a positive gate potential energy is applied (U0>0), the light and heavy hole spins form an electron-like quasi-bound state (E-QBS) at the top of the branch under the hole spin. Conversely, when a negative gate potential energy (U0<0) is applied, the light and heavy hole spins form a hole-like quasi-bound state (H-QBS) structure at the bottom of the branch.

Low information NMR data guided protein-peptide complex structure determination with MELDXMD.

About 40% of the protein-protein interactions are mediated through small peptide epitope. Knowledge of how a peptide or an intrinsically disordered protein fragment interact with a protein would widen of the understanding of gene regulation, transcription and finally drug discovery. However, the folding upon binding nature of majority of the peptide interacting partner, limits the ability of modeling tools to predict structures of such complexes. To address this problem, we show an integrative approach combining cost-effective NMR chemical shift data and physics based molecular simulations to determine structures of protein-peptide complexes. Here in this presentation, we demonstrate our approach for polypeptide complexes formed with the extraterminal (ET) domain of bromo and extraterminal domain (BET) proteins, which exhibit a high degree of binding plasticity. This system is particularly challenging as the binding process includes allosteric changes across the ET receptor upon binding, and the polypeptide binding partners can form different conformations (e.g., helices and hairpins) in the complex. In a blind study, the new approach successfully predicts bound-state structure, using only backbone chemical shift data, in excellent agreement with experimental structure. We show, this approach is successful on not only strongly interacting complexes, but also in the case of weak binder, this method has been successful. MELD+NMR also predicts relative binding affinities of different peptides, consistent with the experimental values. The hybrid MELD+NMR approach provides a powerful new tool for structural analysis of protein-polypeptide complexes involving disorder to order transitions upon complex formation which are not successfully modeled with most other complex predication methods including state of the art docking methods, providing 3D atomistic structures of complexes as well as their relative binding affinities.

Spin quantum transport in double top-gate system

The quantum transport in an n-type two-dimensional electron gas (2DEG) with a double top gate system is investigated. A propagation matrix method is used to derive the band structure and obtain the conductance of the considered system. The results show that in the presence of the Rashba and the Zeeman interactions, resonance peaks and hole-like bound state structure are formed in the conductance spectra influenced by the gate potential and gate distance. While, under the influence of the Rashba–Dresselhaus and the Zeeman interactions, resonance peaks and inner-mode resonance conductance peaks are formed reflecting the gate potential and the gate distance. Notably, when the Dresselhaus interaction reaches a certain strength, the partial conductance of the spin-preservation internal mode becomes significant. Finally, a simple transcendental equation is found to estimate the energy of a bound state.

Novel alpha6 preferring GABA-A receptor ligands based on loreclezole

The family of GABA-A receptors contains nineteen mammalian subunits from which pentameric, GABA gated anion channels are assembled. The subunit encoded by the GABRA6 gene is highly expressed in the cerebellum and the receptors to which it contributes have recently been demonstrated to be a promising candidate as a novel drug target. Here we examined a series of loreclezole derivatives for potentially selective action at α6β3γ2 receptors with the help of computational methods and functional testing with the two-electrode voltage clamp technique. The synthetic routes to some previously published ligands were improved, and a new derivative was synthesized based on computational docking results. This new loreclezole derivative, [3-(2-chloro-4-methylphenyl)-3-methylbutanenitrile (40)], was shown to display stronger modulatory action in concatenated α6β3γ2 receptors compared to their α1β3γ2 counterpart. The hypothetical bound state structure provides valuable guidance for future design of selective therapeutics.

A solvable contact potential based on a nuclear model

We extend previous works on the study of a particle subject to a three-dimensional spherical singular potential including a delta –delta ' contact interaction. In this case, to have a more realistic model, we add a Coulombic term to a finite well and a radial delta –delta ' contact interaction just at the edge of the well, which is where the surface of the nucleus would be. We first prove that the we are able to define the contact potential by matching conditions for the radial function, fixing a self-adjoint extension of the non-singular Hamiltonian. With these matching conditions, we are able to find analytic solutions of the wave function and focus the analysis on the bound state structure characterizing and computing the number of bound states. For this approximation for a mean-field Woods–Saxon model, the Coulombic term enables us to complete the previous study for neutrons analyzing the proton energy levels in some doubly magic nuclei. In particular, we find the appropriate delta ' contribution fitting the available data for the neutron- and proton-level schemes of the nuclei {}^{{208}}Pb, {}^{{40}}Ca, and {}^{{16}}O.

Gauge-invariant description of the Higgs resonance and its phenomenological implications

We investigate the phenomenological consequences of a strict gauge-invariant formulation of the Higgs particle. This requires a description of the observable scalar particle in terms of a bound state structure. Although this seems to be at odds with the common treatment of electroweak particle physics at first glance, the properties of the bound state can be described in a perturbative fashion due to the Fr\"ohlich-Morchio-Strocchi (FMS) framework. In particular a relation between the bound-state Higgs and the elementary Higgs field is obtained within $R_{\xi}$ gauges such that the main quantitative properties of the conventional description reappear in leading order of the FMS expansion. Going beyond leading order, we show that the pole structure of the elementary and the bound-state propagator coincide to all orders in a perturbative expansion. However, slight deviations of scattering amplitudes containing off-shell Higgs contributions can be caused by the internal bound state structure. We perform a consistent perturbative treatment to all orders in the FMS expansion to quantify such deviations and demonstrate how gauge-invariant expressions arrange in a natural way at the one-loop level. This also provides a gauge-invariant Higgs spectral function which is not plagued by positivity violations or unphysical thresholds. Furthermore, the mass extracted from the gauge-invariant bound state is only logarithmically sensitive to the scale of new physics at one-loop order in contrast to its elementary counterpart.

Transport properties in quantum dot-Majorana bound state structure with ferromagnetic and superconductor leads

Abstract We study an effective transport and Andreev reflection through a quantum dot-Majorana bound state (QD-MBS) hybrid nanostructure coupling between ferromagnetic and superconductor leads. Due to MBSs, the Andreev conductance spectrum experience the transition in the configuration of different lineshape geometry such as spin split and Fano effect. The spin-flip scattering process can suppress the electron and hole reflection. Spin polarization decreases electron reflection but increases the conductance.

Implementation of the 8-Nucleon Yakubovsky Formalism for Halo Nucleus &amp;lt;sup&amp;gt;8&amp;lt;/sup&amp;gt;He

In order to study the bound-state structure of the Helium halo nuclei, the 8-nucleon Yakubovsky formalism has been implemented for ⁸He in a 5-body sub-cluster model, <i>i.e. α+n+n+n+n</i>. In this case, the 8-nucleon Yakubovsky equations have been obtained in the form of two coupled equations, based on the two independent components. In addition, by removing the contribution interactions of the 8 and 7’s bound nucleons in the formalism, the obtained equations explicitly reduce to the 6-nucleon Yakubovsky equations for ⁶He, in the case of effective 3-body model, <i>i.e. α+n+n</i>. In view of the expectation for the dominant structure of ⁸He, namely an inert α-core and four loosely-bound neutrons, Jacobi configurations of the two components in momentum space have been represented to provide technicalities which were considered useful for a numerical performance, such as bound-state calculations and momentum density distributions for halo-bound neutrons.

Bound state structure and electromagnetic form factor beyond the ladder approximation

We investigate the response of the bound state structure of a two-boson system, within a Yukawa model with a scalar boson exchange, to the inclusion of the cross-ladder contribution to the ladder kernel of the Bethe-Salpeter equation. The equation is solved by means of the Nakanishi integral representation and light-front projection. The valence light-front wave function and the elastic electromagnetic form factor beyond the impulse approximation, with the inclusion of the two-body current, generated by the cross-ladder kernel, are computed. The valence wave function and electromagnetic form factor, considering both ladder and ladder plus cross-ladder kernels, are studied in detail. Their asymptotic forms are found to be quite independent of the inclusion of the cross-ladder kernel, for a given binding energy. The asymptotic decrease of form factor agrees with the counting rules. This analysis can be generalized to fermionic systems, with a wide application in the study of the meson structure.

Few-body quantum physics with strongly interacting Rydberg polaritons

We present an extension of our recent paper [Bienias et al., Phys. Rev. A 90, 053804 (2014)] in which we demonstrated the scattering properties and bound-state structure of two Rydberg polaritons, as well as the derivation of the effective low-energy many-body Hamiltonian. Here, we derive a microscopic Hamiltonian describing the propagation of Rydberg slow light polaritons in one dimension. We describe possible decoherence processes within a Master equation approach, and derive equations of motion in a Schroedinger picture by using an effective non-Hermitian Hamiltonian. We illustrate diagrammatic methods on two examples: First, we show the solution for a single polariton in an external potential by exact summation of Feynman diagrams. Secondly, we solve the two body problem in a weakly interacting regime exactly.

Nonautonomous solitons, breathers and rogue waves for the cubic-quintic nonlinear Schrödinger equation in an inhomogeneous optical fibre

Under investigation in this paper is a cubic-quintic nonlinear Schrödinger equation which can describe the propagation of ultrashort pulses in an inhomogeneous optical fibre. Lax pair and conservation laws are constructed from which the integrability of the equation can be verified. Through a gauge transformation, spectral problem for the equation is converted to an Ablowitz–Kaup–Newell–Segur spectral problem. Nonautonomous solitons and breathers are derived based on the Darboux transformation (DT), while nonautonomous rogue waves are obtained via the generalized DT. Influence of the group-velocity dispersion, gain-or-loss coefficient and group-velocity coefficient on the propagation and interaction of the nonautonomous solitons, breathers and rogue waves is also discussed. The gain-or-loss coefficient influences the amplitude of nonautonomous soliton. The characteristic line and velocity for the nonautonomous soliton are dependent on the group-velocity dispersion and group-velocity coefficient, but independent of the gain-or-loss coefficient. For the second-order nonautonomous soliton, if the two spectral parameters have the same real part, the bound-state structure can be formed, and the intensity becomes amplified in the attractive procedure. There exist two types of the nonautonomous breathers. Quasi-periods for the nonautonomous breathers are given, and effects of those coefficients on the quasi-periods are also discussed: The group-velocity dispersion can influence the trajectories of the nonautonomous breathers and rogue waves, while the gain-or-loss coefficient affects the backgrounds for the nonautonomous breathers and rogue waves

Bethe–Salpeter bound-state structure in Minkowski space

The quantitative investigation of the scalar Bethe–Salpeter equation in Minkowski space, within the ladder-approximation framework, is extended to include the excited states. This study has been carried out for an interacting system composed by two massive bosons exchanging a massive scalar, by adopting (i) the Nakanishi integral representation of the Bethe–Salpeter amplitude, and (ii) the formally exact projection onto the null plane. Our analysis, on one hand, confirms the reliability of the method already applied to the ground state and, on the other one, extends the investigation from the valence distribution in momentum space to the corresponding quantity in the impact-parameter space, pointing out some relevant features, like (i) the equivalence between Minkowski and Euclidean transverse-momentum amplitudes, and (ii) the leading exponential fall-off of the valence wave function in the impact-parameter space.

Nonautonomous solitons in terms of the double Wronskian determinant for a variable-coefficient Gross–Pitaevskii equation in the Bose–Einstein condensate

Under investigation in this paper is a variable-coefficient Gross–Pitaevskii equation which describes the Bose–Einstein condensate. Lax pair, bilinear forms and bilinear Bäcklund transformation for the equation under some integrable conditions are derived. Based on the Lax pair and bilinear forms, double Wronskian solutions are constructed and verified. The [Formula: see text]th-order nonautonomous solitons in terms of the double Wronskian determinant are given. Propagation and interaction for the first- and second-order nonautonomous solitons are discussed from three cases. Amplitudes of the first- and second-order nonautonomous solitons are affected by a real parameter related to the variable coefficients, but independent of the gain-or-loss coefficient [Formula: see text] and linear external potential coefficient [Formula: see text]. For Case 1 [Formula: see text], [Formula: see text] leads to the accelerated propagation of nonautonomous solitons. Parabolic-, cubic-, exponential- and cosine-type nonautonomous solitons are exhibited due to the different choices of [Formula: see text]. For Case 2 [Formula: see text], if the real part of the spectral parameter equals 0, stationary soliton can be formed. If we take the harmonic external potential coefficient [Formula: see text] as a positive constant and let the real parts of the two spectral parameters be the same, bound-state-like structures can be formed, but there are only one attractive and two repulsive procedures. For Case 3 [[Formula: see text] and [Formula: see text] are taken as nonzero constants], head-on interaction, overtaking interaction and bound-state structure can be formed based on the signs of the two spectral parameters.

Characterization of the Free State Ensemble of the CoRNR Box Motif by Molecular Dynamics Simulations

Intrinsically disordered proteins (IDPs) and regions are highly prevalent in eukaryotic proteomes, and like folded proteins, they perform essential biological functions. Interaction sites in folded proteins are generally formed by tertiary structures, whereas IDPs use short segments called linear motifs (LMs). Despite their short length and lack of stable structure, LMs may have considerable structural propensities, which often resemble bound-state conformations with targets. Structural data is crucial for understanding the molecular basis of protein interactions and development of targeted pharmaceuticals, but IDPs present considerable challenges to experimental techniques. As a result, IDPs are largely underrepresented in the Protein Data Bank. In the face of experimental challenges, molecular dynamics (MD) simulations have proven to be a useful tool for structural characterization of IDPs. Here, the free state ensemble of the nuclear receptor corepressor 1 (NCOR1) CoRNR box 3 motif, which is important for binding to nuclear receptors to control gene expression, is studied using MD simulations of a total of 8 μs. Transitions between disordered and α-helical conformations resembling a bound-state structure were observed throughout the trajectory, indicating that the motif may have a natural conformational bias toward bound-state structures. The data shows that the disordered and folded populations are separated by a low energy (4-6 kJ/mol) barrier, and the presence of off-pathway intermediates, leading to a C-terminally folded species that cannot efficiently transition into a completely folded conformation. Structural transitions and folding pathways within the free state ensemble were well-described by principal component analysis (PCA) of the peptide backbone dihedral angles, with the analysis providing insight for increasing structural homogeneity of the ensemble.

Using chemical shifts to generate structural ensembles for intrinsically disordered proteins with converged distributions of secondary structure.

A short segment of the disordered p53 transactivation domain (p53TAD) forms an amphipathic helix when bound to the E3 ubiquitin ligase, MDM2. In the unbound p53TAD, this short segment has transient helical secondary structure. Using a method that combines broad sampling of conformational space with re-weighting, it is shown that it is possible to generate multiple, independent structural ensembles that have highly similar secondary structure distributions for both p53TAD and a P27A mutant. Fractional amounts of transient helical secondary structure were found at the MDM2 binding site that are very similar to estimates based directly on experimental observations. Structures were identified in these ensembles containing segments that are highly similar to short p53 peptides bound to MDM2, even though the ensembles were re-weighted using unbound experimental data. Ensembles were generated using chemical shift data (alpha carbon only, or in combination with other chemical shifts) and cross-validated by predicting residual dipolar couplings. We think this ensemble generator could be used to predict the bound state structure of protein interaction sites in IDPs if there are detectable amounts of matching transient secondary structure in the unbound state.

Candidate for laser cooling of a negative ion: observations of bound-bound transitions in La(-).

Despite the tremendous advances in laser cooling of neutral atoms and positive ions, no negatively charged ion has been directly laser cooled. The negative ion of lanthanum, La(-), has been proposed as the best candidate for laser cooling of any atomic anion [ and , Phys. Rev. A 81, 032503 (2010)]. Tunable infrared laser photodetachment spectroscopy is used to measure the bound-state structure of La(-), revealing a spectrum of unprecedented richness with multiple bound-bound electric dipole transitions. The potential laser-cooling transition ((3)F(2)(e)→(3)D(1)(o)) is identified and its excitation energy is measured. The results confirm that La^{-} is a very promising negative ion for laser-cooling applications.

The Importance of Intrinsic Order in a Disordered Protein Ligand

The Importance of Intrinsic Order in a Disordered Protein Ligand

An equilateral model for the 4He trimer

Abstract A scaled He–He potential is used in conjunction with a model involving the radial motion of an equilateral array of three 4 He atoms to study the bound state structure of the trimer. The separations between ground and first excited states are found to be considerably larger than some previous predictions.