Tight-binding Research Articles

Cleaving Folded RNA by Multifunctional DNAzyme Nanomachines.

Both tight and specific binding of folded biological mRNA is required for gene silencing by oligonucleotide gene therapy agents. However, this is fundamentally impossible using the conventional oligonucleotide probes according to the affinity/specificity dilemma. This study addresses this problem for cleaving folded RNA by using multicomponent agents (dubbed 'DNA nanomachine' or DNM). DNMs bind RNA by four short RNA binding arms, which ensure tight and highly selective RNA binding. Along with the improved affinity, DNM maintain the high sequence selectivity of the conventional DNAzymes. DNM enabled up to 3-fold improvement in DNAzymes catalytic efficiency (kcat/Km) by facilitating both RNA substrate binding and product release steps of the catalytic cycle. This study demonstrates that multicomponent probes organized in sophisticated structures can help to achieve the balance between affinity and selectivity in recognizing folded RNA and thus creates a foundation for applying complex DNA nanostructures derived by DNA nanotechnology in gene therapy.

Fraunhofer pattern in the presence of Majorana zero modes

We propose a new platform to detect signatures of the presence of Majorana bound states (MBSs) in the Fraunhofer pattern of Josephson junctions featuring quantum spin Hall edge states on the normal part and Majorana bound states at the NS interfaces. We use a tight-binding model to demonstrate a drastic change in the periodicity of the Fraunhofer pattern when comparing trivial and nontrivial regimes. We explain these results in terms of the presence of additional parallel-spin electron-hole reflections, which due to the spin-momentum locking, occur as cross Andreev reflections, accumulating a different magnetic flux and yielding a change in the Fraunhofer periodicity. We show that this detection scheme exhibits some advantages compared to previous ones as it is robust against disorder and finite temperature and works in equilibrium. Furthermore, we introduce a scattering model that captures the main results of the microscopic calculations with MBSs and extend our discussion to the main differences found using accidental zero-energy Andreev bound states. Published by the American Physical Society 2024

Electric-field-controlled electronic structures and quantum transport in monolayer InSe nanoribbons

Electronic structures and quantum transport properties of the monolayer InSe nanoribbons are studied by adopting the tight-binding model in combination with the lattice Green function method. Besides the normal bulk and edge electronic states, a unique electronic state dubbed as edge-surface is found in the InSe nanoribbon with zigzag edge type. In contrast to the zigzag InSe nanoribbon, a singular electronic state termed as bulk-surface is observed along with the normal bulk and edge electronic states in the armchair InSe nanoribbons. Moreover, the band gap, the transversal electron probability distributions in the two sublayers, and the electronic state of the topmost valence subband can be manipulated by adding a perpendicular electric field to the InSe nanoribbon. Further study shows that the charge conductance of the two-terminal monolayer InSe nanoribbons can be switched on or off by varying the electric field strength. In addition, the transport of the bulk electronic state is delicate to even a weak disorder strength, however, that of the edge and edge-surface electronic states shows a strong robustness against to the disorders. These findings may be helpful to understand the electronic characteristics of the InSe nanostructures and broaden their potential applications in two-dimensional nanoelectronic devices as well.

Unique electronic and optical properties of ABBA tetralayer graphene under external electric fields

In this study, we examine the electronic and optical properties of ABBA-stacked tetralayer graphene (4LG), emphasizing its unique characteristics in contrast to its counterparts. The full tight-binding model elucidates the significance of interlayer couplings in the system. We investigate the influence of gate voltage on the system and uncover alterations in the band structure, the emergence of edge states, and the formation of band gaps. The analysis of the density of states reveals the existence of van Hove singularities, which dynamically evolve with the changing gate voltage, resulting in a transition from semimetallic to semiconductor properties. The optical absorption spectrum demonstrates asymmetrical peaks and step-like structures, further affected by a potential difference. Under a finite electric field, optical excitations in gated 4LG reveal triangular isoenergy loops with significant interaction-induced distortions of up to 100 meV. This study anticipates the potential for tuning optical properties in ABBA-stacked 4LG through external electric fields, offering opportunities for experimental exploration.

Mechanism of Action of Curcumin for Rheumatoid Arthritis Based on Machine Learning, Molecular Dynamics and Cellular Experiments

<i>Objective</i>: Curcumin has been widely used in rheumatoid arthritis (RA) treatment and the previous study also proved its effectiveness. However, the pharmacological mechanism is still not clear. The current study intends to discuss the potential mechanism of action of curcumin in RA treatment through machine learning, network pharmacology, molecular dynamics and cellular experiments.<i>Methods</i>: RA-related microarray data were obtained from three GEO datasets: GSE55235, GSE55457 and GSE77298. Machine learning methods including XGBOOST, LASSO and SVM were adopted to screen out potential targets of RA pathogenesis. Online tools SwissTargetPrediction and Similarity ensemble approach were visited to predict potential targets of action of curcumin. The key target was identified via a Venn diagram and processed for molecular docking and molecular dynamics simulation with curcumin. Fibroblast-like synoviocytes (RA-FLSs) were selected to study the effect of curcumin at different concentrations (20, 40 and 80 μmol/L) on cell proliferation and apoptosis using MTT and flow cytometry assays. In addition, Western blot was used to examine the protein level.<i>Results</i>: Arachidonate 5-Lipoxygenase (ALOX5) was identified as a key target of RA following bioinformatics prediction. Results of molecular docking and molecular dynamics simulation demonstrated the tight binding between curcumin and ALOX5 with stable function. RA-FLSs intervened with different concentrations of curcumin (20, 40 and 80 mol/L) exhibited decreased potential in proliferation while increased apoptosis, which were in a dose-dependent manner. Additionally, with the increase of curcumin concentration, the protein level of ALOX5 gradually decreased. <i>Conclusion</i>: Curcumin may exert its therapeutic effects in RA treatment via down-regulating the expression of ALOX5.

Fermionic and Bosonic Partition Functions at Imaginary Chemical Potential as Bloch Functions

In this work it is pointed out that the phase transitions of the <i>d</i>+1 Gross-Neveu (fermionic) and <I>CP<SUP>N</SUP></I><sup>−1</sup> (bosonic) models at finite temperature and imaginary chemical potential can be mapped to transformations of Hubbard-like regular hexagonal to square lattice with the intermediate steps to be specific surfaces (irregular hexagonal kind) with an ordered construction based on the even indexed Bloch-Wigner-Ramakrishnan polylogarithm function. The zeros and extrema of the Clausen <i>Cl<sub>d</sub></i>(<i>θ</i>) function play an important role to the analysis since they allow us not only to study the fermionic and bosonic theories and their phase transitions but also the possibility to explore the existence of conductors arising from the correspondence between the partition functions of the two models and the Bloch and Wannier functions that play a crucial role in the tight-binding approximation in solid state physics. The main aim of this work is not only to unveil the relevance of the canonical partition functions of a fermionic and a bosonic model to Bloch states by using an imaginary chemical potential but also to examine the overlap between two Bloch wave-functions that differ by a lattice momentum that calculates the momentum transfer of a Bloch wave during the interaction with a lattice point of a hexagonal construction.

Discovery of periplasmic solute binding proteins with specificity for ketone bodies: β-hydroxybutyrate binding proteins.

Polyhydroxyalkanoates are a class of biodegradable, thermoplastic polymers which represent a major carbon source for various bacteria. Proteins which mediate the translocation of polyhydroxyalkanoate breakdown products, such as β-hydroxybutyrate (BHB)-a ketone body which in humans serves as an important biomarker, have not been well characterized. In our investigation to screen a solute-binding protein (SBP) which can act as a suitable recognition element for BHB, we uncovered insights at the intersection of bacterial metabolism and diagnostics. Herein, we identify SBPs associated with putative ATP-binding cassette transporters that specifically recognize BHB, with the potential to serve as recognition elements for continuous quantification of this analyte. Through bioinformatic analysis, we identified candidate SBPs from known metabolizers of polyhydroxybutyrate-including proteins from Cupriavidus necator, Ensifer meliloti, Paucimonas lemoignei, and Thermus thermophilus. After recombinant expression in Escherichia coli, we demonstrated with intrinsic tryptophan fluorescence spectroscopy that four candidate proteins interacted with BHB, ranging from nanomolar to micromolar affinity. Tt.2, an intrinsically thermostable protein from Thermus thermophilus, was observed to have the tightest binding and specificity for BHB, which was confirmed by isothermal calorimetry. Structural analyses facilitated by AlphaFold2, along with molecular docking and dynamics simulations, were used to hypothesize key residues in the binding pocket and to model the conformational dynamics of substrate unbinding. Overall, this study provides strong evidence identifying the cognate ligands of SBPs which we hypothesize to be involved in prokaryotic cellular translocation of polyhydroxyalkanoate breakdown products, while highlighting these proteins' promising biotechnological application.

Orbital Ingredients and Persistent Dirac Surface State for the Topological Band Structure in FeTe0.55Se0.45

FeTe0.55Se0.45 (FTS) occupies a special spot in modern condensed matter physics at the intersections of electron correlation, topology, and unconventional superconductivity. The bulk electronic structure of FTS is predicted to be topologically nontrivial due to the band inversion between the dxz and pz bands along Γ−Z. However, there remain debates in both the authenticity of the Dirac surface states (DSSs) and the experimental deviations of band structure from the theoretical band inversion picture. Here we resolve these debates through a comprehensive angle-resolved photoemission spectroscopy investigation. We first observe a persistent DSS independent of kz. Then, by comparing FTS with FeSe, which has no band inversion along Γ−Z, we identify the spectral weight fingerprint of both the presence of the pz band and the inversion between the dxz and pz bands. Furthermore, we propose a renormalization scheme for the band structure under the framework of a tight-binding model preserving crystal symmetry. Our results highlight the significant influence of correlation on modifying the band structure and make a strong case for the existence of topological band structure in this unconventional superconductor. Published by the American Physical Society 2024

Electronic and transport properties of U-cut edge patterned AGNR superlattice for RTD application

In this paper, we first characterize a superlattice structure created by repeating a heterostructure formed from two armchair graphene nanoribbon (AGNR) segments with different widths. We investigate the electronic and transport properties of this structure by varying its widths and lengths to demonstrate the tunability of its overall band gap. The plot of the local density of states shows the formation of localized states at the low band gap segments of the superlattice. The superlattice is then used as a barrier to create a double barrier quantum well (DBQW) to design a proposed resonant tunneling diode (RTD) structure. We observe this device's negative differential resistance (NDR) operation for a range of bias voltages between the contacts. We study the effect of dimensional parameters on the RTD performance. The non-equilibrium Green's function method, based on a tight-binding model, is employed for numerical computation.

Modified tight-binding model for strain effects in monolayer transition metal dichalcogenides

Modified tight-binding model for strain effects in monolayer transition metal dichalcogenides

Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials

We report the development and testing of new integrated cyberinfrastructure for performing free energy simulations with generalized hybrid quantum mechanical/molecular mechanical (QM/MM) and machine learning potentials (MLPs) in Amber. The Sander molecular dynamics program has been extended to leverage fast, density-functional tight-binding models implemented in the DFTB+ and xTB packages, and an interface to the DeePMD-kit software enables the use of MLPs. The software is integrated through application program interfaces that circumvent the need to perform “system calls” and enable the incorporation of long-range Ewald electrostatics into the external software’s self-consistent field procedure. The infrastructure provides access to QM/MM models that may serve as the foundation for QM/MM–ΔMLP potentials, which supplement the semiempirical QM/MM model with a MLP correction trained to reproduce ab initio QM/MM energies and forces. Efficient optimization of minimum free energy pathways is enabled through a new surface-accelerated finite-temperature string method implemented in the FE-ToolKit package. Furthermore, we interfaced Sander with the i-PI software by implementing the socket communication protocol used in the i-PI client–server model. The new interface with i-PI allows for the treatment of nuclear quantum effects with semiempirical QM/MM–ΔMLP models. The modular interoperable software is demonstrated on proton transfer reactions in guanine-thymine mispairs in a B-form deoxyribonucleic acid helix. The current work represents a considerable advance in the development of modular software for performing free energy simulations of chemical reactions that are important in a wide range of applications.

Molecular Modeling and simulation-based identification of inhibitors against new Delhi Metallo-Lactamase 1: Implications for bacterial antibiotic resistance

ObjectivesBacterial infections expressing New Delhi metallo-lactamase-1 (NDM-1) pose an escalating global threat to healthcare systems. NDM-1 is an enzyme that renders β-lactam antibiotics ineffective, leading to resistance against numerous antibiotics used in clinical practice. Therefore, there is an urgent need to identify and develop a clinically relevant inhibitor for NDM-1. MethodsVitas-M laboratory database was screened for small molecules with abilities to bind NDM-1, by generating structure-based pharmacophore hypothesis. Thereafter, molecular docking was performed between NDM-1 and the potential small molecule inhibitors. The outcomes of molecular docking were validated by molecular dynamics simulation and MM-GBSA protocols. ResultsBased upon initial NDM-1-binding characteristics, two ligands (STK115225 and STK107343) were nominated for further analyses for stability and affinity of protein–ligand interactions. Assessment of conformational change parameters indicated that these showed tight and stable binding to the active site pocket of NDM-1 protein. Principal component analysis (PCA) further illustrated that the protein ligand complexes were highly stable. Molecular dynamics simulation along with high numbers of static hydrogen bonds signifies the potency of STK115225 and STK107343 in inhibiting NDM-1. Further, MM-GBSA-based binding free energy maps verified favorable energy changes for the binding of the two small molecules, indicating their abilities for high affinity-binding with NDM-1. ConclusionsThis study has significant implications for addressing antibiotic resistance mediated by NDM-1. The identification of STK115225 and STK107343 as high-affinity binding ligands against NDM-1 provides a strong foundation for developing new therapeutic agents. However, to fully ascertain their clinical relevance, these findings must be validated through in vitro and in vivo experiments. If successful, these inhibitors could restore the efficacy of β-lactam antibiotics and offer a new approach to combat NDM-1 mediated antibiotic resistance, ultimately improving patient outcomes and reducing the global burden of resistant bacterial infections.

Exploring dielectric properties in atomistic models of amorphous boron nitride

We report a theoretical study of dielectric properties of models of amorphous Boron Nitride, using interatomic potentials generated by machine learning. We first perform first-principles simulations on small (about 100 atoms in the periodic cell) sample sizes to explore the emergence of mid-gap states and its correlation with structural features. Next, by using a simplified tight-binding electronic model, we analyse the dielectric functions for complex three dimensional models (containing about 10.000 atoms) embedding varying concentrations of sp1, sp2 and sp3 bonds between B and N atoms. Within the limits of these methodologies, the resulting value of the zero-frequency dielectric constant is shown to be influenced by the population density of such mid-gap states and their localization characteristics. We observe nontrivial correlations between the structure-induced electronic fluctuations and the resulting dielectric constant values. Our findings are however just a first step in the quest of accessing fully accurate dielectric properties of as-grown amorphous BN of relevance for interconnect technologies and beyond.

Effective model and electron correlations in trilayer nickelate superconductor La4Ni3O10

Recently, signatures of superconductivity with critical temperature from 20 to 30 K have been reported in pressured trilayer nickelate La4Ni3O10 through a pressure-induced structure transition. Here we explore the evolution of electronic structures and electronic correlations in different phases of La4Ni3O10 under corresponding pressure regions, by using density functional theory (DFT) combined with dynamical mean-field theory (DMFT). Similar to bilayer superconductor La3Ni2O7, the electronic bands in superconducting La4Ni3O10 are dominated by Ni-3 dx2−y2 and 3 dz2 orbits near the Fermi level, in contrast, the inner Ni–O plane in La4Ni3O10 generates a doublet hole-pocket Fermi surfaces around the Brillouin-zone corner, meanwhile one branch of the Ni- 3dz2 bands is pushed very close above the Fermi level, which can induce an electron pocket through small electron doping. The DFT+DMFT simulations suggest that the electronic correlations only give minor modification to the Fermi surfaces, meanwhile the Ni- 3dz2 and 3 dx2−y2 states on outer Ni–O layers have considerable greater mass enhancements than on the inner layer. The sensitiveness of electronic structure under doping and unique layer dependence of correlation suggest a distinct superconducting mechanism with respect to bilayer La3Ni2O7. Based on the DFT and DFT+DMFT simulations, we eventually derive a trilayer effective tight-binding model, which can produce rather precise electronic bands and Fermi surfaces, hence can serve as an appropriate model to further study the superconducting mechanism and paring symmetry in trilayer La4Ni3O10.

Superexchange Mechanism in Coupled Triangulenes Forming Spin-1 Chains.

We show that the origin of the antiferromagnetic coupling in spin-1 triangulene chains, which were recently synthesized and measured by Mishra et al. ( Nature 2021, 598, 287-292), originates from a superexchange mechanism. This process, mediated by intertriangulene states, opens the possibility to control parameters in the effective bilinear-biquadratic spin model. We start from the derivation of an effective tight-binding model for triangulene chains using a combination of tight-binding and Hartree-Fock methods fitted to hybrid density functional theory results. Next, correlation effects are investigated within the configuration interaction method. Our low-energy many-body spectrum for NTr = 2 and NTr = 4 triangulene chains agree well with the bilinear-biquadratic spin-1 chain antiferromagnetic model when indirect coupling processes and superexchange coupling between triangulene spins are taken into account.

Quasi-localization and Wannier obstruction in partially flat bands

The localized nature of a flat band is understood by the existence of a compact localized eigenstate. However, the localization properties of a partially flat band, ubiquitous in surface modes of topological semimetals, have been unknown. We show that the partially flat band is characterized by a non-normalizable quasi-compact localized state (Q-CLS), which is compactly localized along several directions but extended in at least one direction. The partially flat band develops at momenta where normalizable Bloch wave functions can be obtained from a linear combination of the non-normalizable Q-CLSs. Outside this momentum region, a ghost flat band, unseen from the band structure, is introduced based on a counting argument. Then, we demonstrate that the Wannier function corresponding to the partially flat band exhibits an algebraic decay behavior. Namely, one can have the Wannier obstruction in a band with a vanishing Chern number if it is partially flat. Finally, we develop the construction scheme of a tight-binding model for a topological semimetal by designing a Q-CLS.

Non-Abelian Braiding of Topological Edge Bands.

Braiding is a geometric concept that manifests itself in a variety of scientific contexts from biology to physics, and has been employed to classify bulk band topology in topological materials. Topological edge states can also form braiding structures, as demonstrated recently in a type of topological insulators known as Möbius insulators, whose topological edge states form two braided bands exhibiting a Möbius twist. While the formation of Möbius twist is inspiring, it belongs to the simple Abelian braid group B_{2}. The most fascinating features about topological braids rely on the non-Abelianness in the higher-order braid group B_{N} (N≥3), which necessitates multiple edge bands, but so far it has not been discussed. Here, based on the gauge enriched symmetry, we develop a scheme to realize non-Abelian braiding of multiple topological edge bands. We propose tight-binding models of topological insulators that are able to generate topological edge states forming non-Abelian braiding structures. Experimental demonstrations are conducted in two acoustic crystals, which carry three and four braided acoustic edge bands, respectively. The observed braiding structure can correspond to the topological winding in the complex eigenvalue space of projective translation operator, akin to the previously established point-gap winding topology in the bulk of the Hatano-Nelson model. Our Letter also constitutes the realization of non-Abelian braiding topology on an actual crystal platform, but not based on the "virtual" synthetic dimensions.

Modeling the electroluminescence of atomic wires from quantum dynamics simulations.

Static and time-dependent quantum-mechanical approaches have been employed in the literature to characterize the physics of light-emitting molecules and nanostructures. However, the electromagnetic emission induced by an input current has remained beyond the realm of molecular simulations. This is the challenge addressed here with the help of an equation of motion for the density matrix coupled to a photon bath based on a Redfield formulation. This equation is evolved within the framework of the driven-Liouville von Neumann approach, which incorporates open boundaries by introducing an applied bias and a circulating current. The dissipated electromagnetic power can be computed in this context from the time derivative of the energy. This scheme is applied in combination with a self-consistent tight-binding Hamiltonian to investigate the effects of bias and molecular size on the electroluminescence of metallic and semiconducting chains. For the latter, a complex interplay between bias and molecular length is observed: there is an optimal number of atoms that maximizes the emitted power at high voltages but not at low ones. This unanticipated behavior can be understood in terms of the band bending produced along the semiconducting chain, a phenomenon that is captured by the self-consistency of the method. A simple analytical model is proposed that explains the main features revealed by the simulations. The methodology, applied here at a self-consistent tight-binding level but extendable to more sophisticated Hamiltonians such as density functional tight binding and time dependent density functional theory, promises to be helpful for quantifying the power and quantum efficiency of nanoscale electroluminescent devices.

Enhanced Seebeck effect in gated O-shaped Kekulé graphene junctions

The Seebeck effect in graphene with uniform Kekulé lattice distortion has been studied using the tight-binding model combined with the nonequilibrium Green's function method. The numerical results of this work show that the Seebeck coefficient of the O-shaped Kekulé graphene can be enhanced by modulating the gate voltage. At room temperature (T≈300 K), the Seebeck coefficient for the armchair nanoribbon is Sc≈1370μV/K and for the zigzag nanoribbon is Sc≈1260μV/K. At low temperature (T≈128 K), the Seebeck coefficient for the armchair nanoribbon is Sc≈2500μV/K. In addition, the nano-structuration of the O-shaped Kekulé graphene layer induces an anisotropic behavior in the Seebeck effect. Our work provides an idea for the fabrication of efficient and controllable thermoelectric effect devices.

Phonon-induced band gap renormalization by dielectric dependent global hybrid density functional tight binding

Phonon-induced band gap renormalization by dielectric dependent global hybrid density functional tight binding