Tight-binding Research Articles

Anomalous Crystalline-Electromagnetic Responses in Semimetals

We present a unifying framework that allows us to study the mixed crystalline-electromagnetic responses of topological semimetals in spatial dimensions up to D=3 through dimensional augmentation and reduction procedures. We show how this framework illuminates relations between the previously known topological semimetals and use it to identify a new class of quadrupolar nodal line semimetals for which we construct a lattice tight-binding Hamiltonian. We further utilize this framework to quantify a variety of mixed crystalline-electromagnetic responses, including several that have not previously been explored in existing literature, and show that the corresponding coefficients are universally proportional to weighted momentum-energy multipole moments of the nodal points (or lines) of the semimetal. We introduce lattice gauge fields that couple to the crystal momentum and describe how tools including the gradient expansion procedure, dimensional reduction, compactification, and the Kubo formula can be used to systematically derive these responses and their coefficients. We further substantiate these findings through analytical physical arguments, microscopic calculations, and explicit numerical simulations employing tight-binding models. Published by the American Physical Society 2024

A potent and selective reaction hijacking inhibitor of Plasmodium falciparum tyrosine tRNA synthetase exhibits single dose oral efficacy in vivo.

The Plasmodium falciparum cytoplasmic tyrosine tRNA synthetase (PfTyrRS) is an attractive drug target that is susceptible to reaction-hijacking by AMP-mimicking nucleoside sulfamates. We previously identified an exemplar pyrazolopyrimidine ribose sulfamate, ML901, as a potent reaction hijacking inhibitor of PfTyrRS. Here we examined the stage specificity of action of ML901, showing very good activity against the schizont stage, but lower trophozoite stage activity. We explored a series of ML901 analogues and identified ML471, which exhibits improved potency against trophozoites and enhanced selectivity against a human cell line. Additionally, it has no inhibitory activity against human ubiquitin-activating enzyme (UAE) in vitro. ML471 exhibits low nanomolar activity against asexual blood stage P. falciparum and potent activity against liver stage parasites, gametocytes and transmissible gametes. It is fast-acting and exhibits a long in vivo half-life. ML471 is well-tolerated and shows single dose oral efficacy in the SCID mouse model of P. falciparum malaria. We confirm that ML471 is a reaction hijacking inhibitor that is converted into a tight binding Tyr-ML471 conjugate by the PfTyrRS enzyme. A crystal structure of the PfTyrRS/ Tyr-ML471 complex offers insights into improved potency, while molecular docking into UAE provides a rationale for improved selectivity.

Photoinduced Electron-Nuclear Dynamics of Fullerene and Its Monolayer Networks in Solvated Environments.

The recently synthesized monolayer fullerene network in a quasi-hexagonal phase (qHP-C60) exhibits superior electron mobility and optoelectronic properties compared to molecular fullerene (C60), making it highly promising for a variety of applications. However, the microscopic carrier dynamics of qHP-C60 remain unclear, particularly in realistic environments, which are of significant importance for applications in optoelectronic devices. Unfortunately, traditional ab initio methods are prohibitive for capturing the real-time carrier dynamics of such large systems due to their high computational cost. In this work, we present the first real-time electron-nuclear dynamics study of qHP-C60 using velocity-gauge density functional tight binding, which enables us to perform several picoseconds of excited-state electron-nuclear dynamics simulations for nanoscale systems with periodic boundary conditions. When applied to C60, qHP-C60, and their solvated counterparts, we demonstrate that water/moisture significantly increases the electron-hole recombination time in C60 but has little impact on qHP-C60. Our excited-state electron-nuclear dynamics calculations show that qHP-C60 is extremely unique and enable exploration of time-resolved dynamics for understanding excited-state processes of large systems in complex, solvated environments.

Silane‐treated kapok fiber/epoxy composites for aerospace cabin interiors: Synthesis and characterization

AbstractThis study underscores the potential of silanized kapok fiber (KF) as a lightweight, eco‐friendly reinforcement for aerospace cabin interiors, emphasizing electrical insulation and mechanical resilience. KF/epoxy composites were fabricated via hand lay‐up, and silane treatment improved flexural, tensile, impact, and storage modulus by 131%, 101%, 145%, and 105%, respectively, due to enhanced fiber‐matrix interaction. Dielectric and impedance spectroscopy revealed reduced dielectric constant, loss, and AC conductivity due to the removal of polar groups and compact composite structure. Additionally, 9% silane concentration decreased water absorption by 3.9% over 400 h due to the tight packing and binding between the fiber and epoxy. These findings demonstrate that silane treatment enhances fiber‐matrix compatibility, improving the mechanical and overall performance of KF/epoxy composites.Highlights KFs are treated with silane coupling agents. Silane treatment enhanced interfacial, chemical and mechanical bonding. Mechanical and electrical properties of composites enhanced with silane grafting on KF. Tg of the composites increased after silane treatment. Explored density and demonstrated reduced water absorption properties of the composites.

Electric current through atoms arranged in concentric circles induced by applying static magnetic field

Abstract The induction of electric current between atoms arranged in concentric circles by an external magnetic field is studied using a tight-binding model. In particular, the dependence of electric current on the strength of the magnetic field, number of atoms, and temperature is examined. Substantial changes are observed in the electric current distribution when the difference in the transfer integral along the circumference and between circles is increased. Additionally, the difference in the electric current flow compared with that through a graphene ring is analyzed.

IRF2BP2 binds to a conserved RxSVI motif of protein partners and regulates megakaryocytic differentiation

IRF2BP2 is a transcriptional coregulator that plays diverse regulatory roles in various cellular processes in either IRF2-dependent or IRF2-independent manner through interactions with protein partners via its RING domain; however, the underlying molecular mechanisms remain unclear. In this study, we conduct a motif discovery search on the sequences of interacting proteins IRF2 and VGLL4 of IRF2BP2 and identify a conserved RxSVI motif. Biochemical and structural data reveal that the RING domain binds to the motif-containing peptides of IRF2 and VGLL4 with comparable affinities and in a similar manner. The motif-containing peptides tend to form a short loop along with a short β-strand, which facilitates effective recognition and tight binding by the RING domain. Further exploration of this motif in the human proteome identifies the transcription factor ZBTB16 as an interacting protein of IRF2BP2. Biochemical, structural, and cell biological data demonstrate that the RING domain binds to the motif-containing peptide of ZBTB16 in a manner similar to that of IRF2 and VGLL4. Moreover, IRF2BP2 plays a crucial regulatory role in megakaryocytic differentiation through interaction with ZBTB16. These findings elucidate the molecular basis for how IRF2BP2 can engage with different protein partners, thereby exerting diverse regulatory functions in many cellular processes.

Graphene: Study in Electronic Structure, Superconductivity and Potential in Quantum Information Sciences

Graphene, a two-dimensional lattice of carbon atoms, exhibits remarkable electronic properties due to its Dirac-like electronic excitations. This paper reviews the elementary electronic properties of graphene, including the tight-binding model for single-layer graphene and the band structure formation. The tight-binding Hamiltonian provides a fundamental understanding of graphene’s linear energy dispersion near the Dirac points, leading to unique phenomena such as massless Dirac fermions and chiral tunneling. We explore the potential of superconductivity in graphene using BCS theory. We find that BCS theory cannot explain superconductivity in graphene and its forms. This is in contradiction with the discovery of unconventional superconductivity in twisted bilayer graphene (TBG). The study further explores the potential application of bilayer graphene quantum in quantum information sciences, highlighting the development of states with relaxation times exceeding 500 ms. These valley states, arising from the hexagonal lattice structure, can be used to encode information as robust valley qubits for fault-tolerant quantum computing

Visualization of a multi-turnover Cas9 after product release.

While the most widely used CRISPR-Cas enzyme is the S. pyogenes Cas9 endonuclease (Cas9), it exhibits single-turnover enzyme kinetics which leads to long residence times on product DNA. This blocks access to DNA repair machinery and acts as a major bottleneck during CRISPR-Cas9 gene editing. Although Cas9 can eventually be forcibly removed by extrinsic factors (translocating polymerases, helicases, chromatin modifying complexes, etc), the mechanisms contributing to Cas9 dissociation following cleavage remain poorly understood. Interestingly, it's been shown that Cas9 can be more easily dislodged when complexes collide with the PAM-distal region of the Cas9 complex or when the strength of Cas9 interactions in this region are weakened. Here, we employ truncated guide RNAs as a strategy to weaken PAM-distal nucleic acid interactions and still support Cas9 activity. We find that guide truncation promotes much faster Cas9 turnover and used this to capture previously uncharacterized Cas9 reaction states. Kinetics-guided cryo-EM enabled us to enrich for rare, transient states that are often difficult to capture in standard workflows. From a single dataset, we examine the entire conformational landscape of a multi-turnover Cas9, including the first detailed snapshots of Cas9 dissociating from product DNA. We discovered that while the PAM-distal product dissociates from Cas9 following cleavage, tight binding of the PAM-proximal product directly inhibits re-binding of new targets. Our work provides direct evidence as to why Cas9 acts as a single-turnover enzyme and will guide future Cas9 engineering efforts.

Encoding the lattice in the holography

One of the most wanted features of holography in its condensed matter physics application is to encode the structure of lattice, which is the most direct data of the material. In this paper, we propose a method to encode the lattice structure by embedding the tight binding data into the Dirac equation in the anti–de Sitter bulk. We explicitly worked out the idea for the graphene and Haldane models, and the result shows that some degrees of freedom escape the free-electron on-shell curve, and Green’s function loses the pole structure completely. It implies that the electronic structure is not described by the band structure only, which is consistent with what many angle-resolved photoemission spectroscopy data tell us, and it also implies that the system is in non-Fermi liquid even for the graphene, which is consistent with recent experiments for the clean graphene. Published by the American Physical Society 2024

Three-Dimensional Multiorbital Flat Band Models and Materials.

Flat band (FB) systems are essential for uncovering exotic quantum phenomena associated with strong electron correlations. Here we present a systematic theoretical framework for constructing multiorbital FB models and identifying feasible material candidates. This framework integrates group theory and crystallography into a symmetry-adapted tight-binding model incorporating lattice, site, and orbital degrees of freedom. Using this approach, we unveil a novel three-dimensional (3D) multiorbital FB model in the face-centered-cubic lattice, distinct from well-known single-orbital Lieb and kagome models. Critically, we identify numerous high-quality binary materials with ultraclean 3D FBs near the Fermi level. Furthermore, we explore diverse orbital bases within this model and extend our analysis to other cubic lattices with different space groups, broadening the scope for realizing 3D multiorbital FB systems. Our findings provide a foundational platform for exploring correlated physics in multiorbital FB systems and guiding the discovery of new quantum materials.

In silicon desinging of RANKL-targeting vaccine for protection of osteoporosis based on the epitope of Denosumab

BackgroundLife quality of osteoporosis patients is affected significantly due to the severely complications of fracture and pain. RANKL, indicated as the key mediator of osteoporosis, plays a pathogenic role of osteoclasts induction. To target this program, two medications, bisphosphonate and Denosumab, were developed and achieved remarkable advantages in clinics. Unfortunately, fracture-related side-effects always emerge unavoidably, after either long-term administration of bisphosphonates or Denosumab withdrawing. To address these challenges, vaccine-based approach has been adopted to achieve sustainable protection through induction and maintenance of effective antibodies in mild level over decades. MethodsA Denosumab binding peptide was firstly identified as the basic component of vaccine. This peptide was then fused with diphtheria toxin T domain, a widely used adjuvant protein. Its capabilities to penetrate the autologous tolerance and induce the immune responses was then demonstrated with in-silicon evaluation. Finally, the efficacy of the DR3 vaccine was assessed through immunization on the human RANKL transgenic mice model of osteoporosis. ResultsThe DTT-RANKL(220–245)3 vaccine, termed as DR3, were predicted as highly antigenic and non-allergenicity. This molecule was comprised of 46.5 % of helix, 8.5 % strand and 45.1 % coil, the optimized Z-value of the tertiary structure was 6.39, and the favored area in the Ramachandran plot was 96.1 % after refinement. Molecular docking showed a tight binding of DR3 vaccine to TLR2 (−9.2 kcal/mol) and TLR4 (−9.5 kcal/mol). In addition, the immune stimulation indicated robust responses post administration of DR3 vaccine, including high level production of of antibodies and cytokines, activated T and B lymphocytes, and the long-last immune memory. In agree with the simulation, vaccinated mice generated high titers anti-hRANKL antibodies and elevated levels of IL-4 and IL-10 at 7th week post immunization. ConclusionDR3 vaccine was aroused to benefit the prevention and treatment of osteoporosis, and other bone-resorptive diseases potentially.

Moiré polar vortex, flat bands, and Lieb lattice in twisted bilayer BaTiO3.

Through first-principles calculations based on density functional theory, we investigate the crystal and electronic structures of twisted bilayer BaTiO3. Our findings reveal that large stacking fault energy leads to a chiral in-plane vortex pattern that was recently observed in experiments. We also found nonzero out-of-plane local dipole moments, indicating that the strong interlayer interaction might offer a promising strategy to stabilize ferroelectric order in the two-dimensional limit. The vortex pattern in the twisted BaTiO3 bilayer supports localized electronic states with quasi-flat bands, associated with the interlayer hybridization of oxygen pz orbitals. We found that the associated bandwidth reaches a minimum at ∼19∘ twisting, configuring the largest magic angle in moiré systems reported so far. Further, the moiré vortex pattern bears a notable resemblance to two interpenetrating Lieb lattices and the corresponding tight-binding model provides a comprehensive description of the evolution the moiré bands with twist angle and reveals the topological nature.

Non-adiabatic Couplings in Surface Hopping with Tight Binding Density Functional Theory: The Case of Molecular Motors.

Nonadiabatic molecular dynamics (NAMD) has become an essential computational technique for studying the photophysical relaxation of molecular systems after light absorption. These phenomena require approximations that go beyond the Born-Oppenheimer approximation, and the accuracy of the results heavily depends on the electronic structure theory employed. Sophisticated electronic methods, however, make these techniques computationally expensive, even for medium size systems. Consequently, simulations are often performed on simplified models to interpret the experimental results. In this context, a variety of techniques have been developed to perform NAMD using approximate methods, particularly density functional tight binding (DFTB). Despite the use of these techniques on large systems, where ab initio methods are computationally prohibitive, a comprehensive validation has been lacking. In this work, we present a new implementation of trajectory surface hopping combined with DFTB, utilizing nonadiabatic coupling vectors. We selected the methaniminium cation and furan systems for validation, providing an exhaustive comparison with the higher-level electronic structure methods. As a case study, we simulated a system from the class of molecular motors, which has been extensively studied experimentally but remains challenging to simulate with ab initio methods due to its inherent complexity. Our approach effectively captures the key photophysical mechanism of dihedral rotation after the absorption of light. Additionally, we successfully reproduced the transition from the bright to dark states observed in the time-dependent fluorescence experiments, providing valuable insights into this critical part of the photophysical behavior in molecular motors.

Discovery of Propionic Acid Derivatives with a 5-THIQ Core as Potent and Orally Bioavailable Keap1-Nrf2 Protein-Protein Interaction Inhibitors for Acute Kidney Injury.

Keap1 plays a crucial role in regulating the Nrf2-mediated cytoprotective response and is increasingly targeted for oxidative stress-related diseases. Using small molecules to disrupt the Keap1-Nrf2 protein-protein interaction (PPI) has emerged as a new strategy for developing Nrf2 activators. Through extensive structure-activity relationship studies, we identified compound 56, which features a unique 5-tetrahydroisoquinoline scaffold and acts as a potent inhibitor of the Keap1-Nrf2 PPI. Compound 56 exhibited significant inhibitory activity (IC50 = 16.0 nM) and tight Keap1 binding affinity (Kd = 3.07 nM), along with acceptable oral bioavailability (F = 20%). Notably, 56 enhanced antioxidant defenses in HK-2 renal tubular epithelial cells and significantly reduced plasma creatinine and blood urea nitrogen levels in acute kidney injury (AKI) mice. These findings collectively position compound 56 as a promising candidate for the treatment of AKI.

Topology in a one-dimensional plasmonic crystal: the optical approach

Abstract In this paper we study the topology of the bands of a plasmonic crystal composed of graphene and of a metallic grating. Firstly, we derive a Kronig–Penney type of equation for the plasmonic bands as function of the Bloch wavevector and discuss the propagation of the surface plasmon polaritons on the polaritonic crystal using a transfer-matrix approach considering a finite relaxation time. Second, we reformulate the problem as a tight-binding model that resembles the Su–Schrieffer–Heeger (SSH) Hamiltonian, one difference being that the hopping amplitudes are, in this case, energy dependent. In possession of the tight-binding equations it is a simple task to determine the topology (value of the winding number) of the bands. This allows to determine the existense or absence of topological end modes in the system. Similarly to the SSH model, we show that there is a tunable parameter that induces topological phase transitions from trivial to non-trivial. In our case, it is the distance d between the graphene sheet and the metallic grating. We note that d is a parameter that can be easily tuned experimentally simply by controlling the thickness of the spacer between the grating and the graphene sheet. It is then experimentally feasible to engineer devices with the required topological properties. Finally, we suggest a scattering experiment allowing the observation of the topological states.

Non-Hermitian Skin Effect in Many-Body Thermophotonics.

The tight-binding model, foundational in depicting electronic behaviors in solid-state physics, has recently contributed to the understanding of non-Hermitian skin effects in optics, acoustics, and mechanics. However, tight-binding model is primarily built upon scalar nearest couplings, which in turn does not fit to describe the vectorial long-range interactions inherently in thermophotonics. Here, we report a strategy involving many-body radiative interactions in a two-dimensional thermophotonic lattice, and further reveal two types of orthogonal non-Hermitian skin modes in a reciprocal system. For in-plane modes, a pronounced geometry-dependent skin effect manifests at the edges, while for out-of-plane modes, skin effects induced by many-body interactions emerge at the corners instead. Our work provides a pioneering approach for understanding many-body-driven skin effect and unveils a mechanism for unexpected manipulation in thermophotonics.

Hofstadter Butterflies and Metal/Insulator Transitions for Moiré Heterostructures

AbstractWe consider a tight-binding model recently introduced by Timmel and Mele (Phys Rev Lett 125:166803, 2020) for strained moiré heterostructures. We consider two honeycomb lattices to which layer antisymmetric shear strain is applied to periodically modulate the tunneling between the lattices in one distinguished direction. This effectively reduces the model to one spatial dimension and makes it amenable to the theory of matrix-valued quasi-periodic operators. We then study the charge transport and spectral properties of this system, explaining the appearance of a Hofstadter-type butterfly and the occurrence of metal/insulator transitions that have recently been experimentally verified for non-interacting moiré systems (Wang et al. in Nature 577:42–46, 2020). For sufficiently incommensurable moiré lengths, described by a diophantine condition, as well as strong coupling between the lattices, which can be tuned by applying physical pressure, this leads to the occurrence of localization phenomena.

Topological material in the III–V family: Heteroepitaxial InBi on InAs

InBi(001) is formed epitaxially on InAs(111)-A by depositing Bi onto an In-rich surface. Angle-resolved photoemission measurements reveal topological electronic surface states, close to the M¯ high symmetry point. This demonstrates a heteroepitaxial system entirely in the III–V family with topological electronic properties. InBi shows coexistence of Bi and In surface terminations, in contradiction with other III–V materials. For the Bi termination, the study gives a consistent physical picture of the topological surface electronic structure of InBi(001) terminated by a Bi bilayer rather than a surface formed by splitting to a Bi monolayer termination. Theoretical calculations based on relativistic density functional theory and the one-step model of photoemission clarify the relationship between the InBi(001) surface termination and the topological surface states, supporting a predominant role of the Bi bilayer termination. Furthermore, a tight-binding model based on this Bi bilayer termination with only Bi–Bi hopping terms, and no Bi–In interaction, gives a deeper insight into the spin texture. Published by the American Physical Society 2024

Quantum Valley Hall Effect without Berry Curvature.

The quantum valley Hall effect (QVHE) is characterized by the valley Chern number (VCN) in a way that one-dimensional (1D) chiral metallic states are guaranteed to appear at the domain walls (DW) between two domains with opposite VCN for a given valley. Although in the case of QVHE, the total Berry curvature (BC) of the system is zero, the BC distributed locally around each valley makes the VCN well defined as long as intervalley scattering is negligible. Here, we propose a new type of valley-dependent topological phenomenon that occurs when the BC is strictly zero at each momentum. Such zero Berry curvature (ZBC) QVHE is characterized by the valley Euler number (VEN) which is computed by integrating the Euler curvature around a given valley in two-dimensional (2D) systems with space-time inversion symmetry. 1D helical metallic states can be topologically protected at the DW between two domains with the opposite VENs when the DW configuration preserves either the mirror symmetry with respect to the DW or the combination of the DW space-time inversion and chiral symmetries. We establish the fundamental origin of ZBC QVHE. Also, by combining tight-binding model study and first-principles calculations, we propose stacked hexagonal bilayer lattices including h-BX (X=As, P) and large-angle twisted bilayer graphenes as candidate systems with robust helical DW states protected by VEN.

Electron transport and quantum phase transitions in cumulene-connected C80H20 fulleryne: DFT and tight-binding studies

Molecular bridges are opening up exciting new applications in diverse fields, improving the efficiency of conductive inks, enhancing the performance of devices such as organic light-emitting diodes and low-cost solar cells, and advancing the development of highly sensitive sensors, chemical reactions, drug delivery systems, and more. In this paper, we study the electron transport properties of a C80H20 fulleryne (dodecahedryne) connected to two cumulene electrodes. Using density functional theory (DFT), we determine the optimal molecular bridge structure. Based on the IR vibration spectra, different stable phases of the molecular bridge are obtained. The corresponding tight-binding (TB) parameters of the cage are obtained by assigning appropriate values of the length and type of bonds for the fulleryne cage through matching the HOMO-LUMO gap between the DFT calculations and the TB parameters. The electron transport for the desired structures is investigated using the obtained tight-binding parameters and the non-equilibrium Green's function (NEGF) method. Finally, it is concluded that among the five possible configurations for the cumulene-dodecahedryne -cumulene molecular bridge, only one specific configuration—where the electrodes are one edge apart—exhibits metallic behavior, while other positions act as insulators. In addition, the system exhibits quantum phase transitions from metal to semiconductor and from insulator to metal in the presence of critical electric fields. The ability to control quantum phase transitions in these molecular systems can be leveraged to develop qubits for quantum computing. The unique properties can be utilized to design advanced molecular electronic devices.