Tight-binding Research Articles

#2765 Medium chain fatty acids are potent binding competitors to improve protein-bound uremic toxin clearance in hemodialysis

Abstract Background and Aims Protein-bound uremic toxins (PBUTs) remain a concerning burden in patients with end-stage renal disease (ESRD) since their removal during hemodialysis is limited due to their tight binding to albumin. By increasing their circulating free fraction during HD, “binding competitors” of albumin could be used to increase their dialytic clearance. Medium chain fatty acids (MCFAs, 6 to 12 carbon length) are potent candidates for that purpose. The present study aims to investigate whether MCFAs could serve as potential binding competitors of albumin to enhance the removal of PBUTs, specifically IS and p-CS, during hemodialysis. Method Hexanoate (C6), octanoate (C8), and decanoate (C10) were purchased from Sigma-Aldrich. The binding of MCFAs to albumin was investigated in silico and using fluorescent probes: warfarin (specific of Sudlow's site I) and dansylsarcosine (specific of Sudlow's site II). Indoxyl-sulfate (IS, final concentration 212 µM) and p-cresyl sulfate (p-CS, final concentration 250 µM) were added to a 600 µM bovine serum albumin-phosphate buffered saline solution. The free fractions of IS and p-CS were assayed with or without MCFAs (1-2 mM) using ultrafiltration devices in this solutions and in patients uremic plasma. To mimic the removal of PBUTs during a HD session, batches of 2 liters of fresh bovine blood were loaded with IS and p-CS (final concentration 200 µM). A 2-hours closed-loop HD session was performed using a Fresenius 5008 CorDiax HD generator (Fresenius, Germany). A solution of 224 mM of octanoate was perfused at the rate of 150 µL/min; A solution of saline 0.9% was used as a control. One milliliter of blood was sampled every 15 minutes through the arterial sampling port and concentration of IS and p-CS were assayed by HPLC coupled with fluorescence detection. The hemolytic effect of MCFAs was evaluated in vitro by assaying the free hemoglobin concentration. Results According to the in silico prediction, the binding was predicted to be almost complete for MCFAs ≥ C8 (Fig. 1). The enhanced protein binding appeared to be inversely correlated with water solubility, which became particularly low for MCFAs ≥ C10. Octanoate and decanoate were the more prone to displace dansylsarcosine from Sudlow's site II of albumin (which is the main binding site of IS and p-CS). In vitro, the incubation with 2 mM of octanoate and decanoate increased the free fraction of PBUTs from 12% to 53% for p-CS (4.4 fold, p < 0.05) and from 11% to 45% for IS (4.1 fold, p < 0.05). Octanoate was also able to increase the free fraction of PBUTs in patients uremic plasma (1.6-fold for IS, p < 0.05 and 4.8 fold for p-CS, <0.01). The per-dialytic infusion of octanoate significantly increased the fractional removal of p-CS (from 38% to 88%, p < 0.001) and IS (from 36% to 91%, p < 0.001). No significant hemolysis was observed for concentration of MCFAs lower than 2 mmol/L. Conclusion MCFAs and especially octanoate and decanoate are serious candidates to displace the binding of PBUTs such as p-CS and IS. The per-dialytic administration of octanoate significantly increased the removal of PBUTs and could constitute a new strategy to prevent their accumulation in end-stage kidney disease patients. Due to their good safety profile, MCFAs could be better tolerated than other chemical compounds that has already been tested in a clinical setting such as ibuprofen. Further in vivo studies are however needed to carefully evaluate this potentially new therapeutic option.

A 3D in vitro model for assessing the influence of intraocular lens: Posterior lens capsule interactions on lens epithelial cell responses

Posterior Capsule Opacification (PCO), the most frequent complication of cataract surgery, is caused by the infiltration and proliferation of lens epithelial cells (LECs) at the interface between the intraocular lens (IOL) and posterior lens capsule (PLC). According to the “no space, no cells, no PCO” theory, high affinity (or adhesion force) between the IOL and PLC would decrease the IOL: PLC interface space, hinder LEC migration, and thus reduce PCO formation. To test this hypothesis, an in vitro hemisphere-shaped simulated PLC (sPLC) was made to mimic the human IOL: PLC physical interactions and to assess their influence on LEC responses. Three commercially available IOLs with different affinities/adhesion forces toward the sPLC, including Acrylic foldable IOL, Silicone IOL, and PMMA IOL, were used in this investigation. Using the system, the physical interactions between IOLs and sPLC were quantified by measuring the adhesion force and interface space using an adhesion force apparatus and Optical Coherence Tomography, respectively. Our data shows that high adhesion force and tight binding between IOL and sPLC contribute to a small interface space (or “no space”). By introducing LECs into the in vitro system, we found that, with small interface space, among all IOLs, acrylic foldable IOLs permitted the least extent of LEC infiltration, proliferation, and differentiation (or “no cells”). Further statistical analyses using clinical data revealed that weak LEC responses are associated with low clinical PCO incidence rates (or “no PCO”). The findings support that the in vitro system could simulate IOL: PLC interplays and predict IOLs’ PCO potential in support of the “no space, no cells, no PCO” hypothesis.

Adsorption of Glycine on TiO2 in Water from On-the-fly Free-Energy Calculations and In Situ Electrochemical Impedance Spectroscopy.

We report here an experimental-computational study of hydrated TiO2 anatase nanoparticles interacting with glycine, where we obtain quantitative agreement of the measured adsorption free energies. Ab initio simulations are performed within the tight binding and density functional theory in combination with enhanced free-energy sampling techniques, which exploit the thermodynamic integration of the unbiased mean forces collected on-the-fly along the molecular dynamics trajectories. The experiments adopt a new and efficient setup for electrochemical impedance spectroscopy measurements based on portable screen-printed gold electrodes, which allows fast and in situ signal assessment. The measured adsorption free energy is -30 kJ/mol (both from experiment and calculation), with preferential interaction of the charged NH3+ group which strongly adsorbs on the TiO2 bridging oxygens. This highlights the importance of the terminal amino groups in the adsorption mechanism of amino acids on hydrated metal oxides. The excellent agreement between computation and experiment for this amino acid opens the doors to the exploration of the interaction free energies for other moderately complex bionano systems.

Jiezi: An open-source Python software for simulating quantum transport based on non-equilibrium Green's function formalism

We present a Python-based open-source library named Jiezi, which provides the means of simulating the electronic transport properties of nanoscaled devices on the atomistic level. The key feature of Jiezi lies in its core algorithm, i.e., self-consistent orchestration between the non-equilibrium Green's function (NEGF) method and a Poisson's equation solver. Beyond the construction of the tight-binding (TB) Hamiltonian with empirical parameters for conventional materials, the package offers a comprehensive framework for constructing the Wannier-based Hamiltonian matrix, enabling the investigation of novel materials and their heterostructures. To expedite the solution of NEGF systems, a methodology based on renormalization theory is proposed for reducing the dimension of the Hamiltonian matrix. Additionally, we adopt a non-linear Poisson equation solver with no analytical approximation in this software. The software facilitates seamless integration with external tools for geometry and mesh generation and post-processing. In this paper, we present the main capabilities and workflow by demonstrating with a simulation for the carbon nanotube field-effect transistor (CNTFET). Program summaryProgram Title: JieziCPC Library link to program files:https://doi.org/10.17632/nk79kbtww4.1Developer's repository link:https://github.com/Jiezi-negf/JieziLicensing provisions: GPLv3Programming language: PythonNature of problem: Simulates the quantum transport property of nano-scaled transistors based on the predefined device structure and the material composition.Solution method: Solves the coupled Schrödinger equation and Poisson equation by NEGF and finite element method.

Bounds to electron spin qubit variability for scalable CMOS architectures

Spins of electrons in silicon MOS quantum dots combine exquisite quantum properties and scalable fabrication. In the age of quantum technology, however, the metrics that crowned Si/SiO2 as the microelectronics standard need to be reassessed with respect to their impact upon qubit performance. We chart spin qubit variability due to the unavoidable atomic-scale roughness of the Si/SiO2 interface, compiling experiments across 12 devices, and develop theoretical tools to analyse these results. Atomistic tight binding and path integral Monte Carlo methods are adapted to describe fluctuations in devices with millions of atoms by directly analysing their wavefunctions and electron paths instead of their energy spectra. We correlate the effect of roughness with the variability in qubit position, deformation, valley splitting, valley phase, spin-orbit coupling and exchange coupling. These variabilities are found to be bounded, and they lie within the tolerances for scalable architectures for quantum computing as long as robust control methods are incorporated.

Improvements in thermoelectric features by resonant-tunneling magnetic tunnel junctions with β-Ga2O3 semiconductor

A study was conducted to investigate thermoelectric effects (TEEs) in resonant-tunneling magnetic tunnel junctions (RTMTJs) featuring wide-bandgap semiconductors such as ZnO and β-Ga2O3, along with a non-magnetic metal spacer. The transmission function was determined using the non-equilibrium Green’s function method within a tight-binding model. Significant enhancements in TEEs were observed for the β-Ga2O3 semiconductor compared to other materials, indicating its potential applicability in the emerging field of β-Ga2O3 spincaloritronics.

Engineering complete delocalization of single particle states in a class of one dimensional aperiodic lattices: A quantum dynamical study

We study quantum dynamics of a wave packet on a class of one dimensional decorated aperiodic lattices, described within a tight binding formalism. We look for the possibility of finding extended single particle states even in the absence of any translational periodicity. The chosen lattices are stubbed with one or more atoms, tunnel coupled to the backbone, thereby introducing a minimal quasi-one dimensionality. It is seen that, for a group of such lattices a certain correlation between the numerical values of the hopping amplitudes leads to a complete delocalization of single particle states. In some other cases, a special value of a magnetic flux trapped in the loops present in the geometries delocalize the states, leading to a flux driven insulator to metal transition. The mean square displacement, temporal autocorrelation function, the time dependence of the inverse participation ratio, or the information entropy – the so-called hallmarks of studying localization based on dynamics – all of them indicate such a complete turnover in the nature of the single particle states and the character of the energy spectrum under suitable conditions. The results shown in this work using quasiperiodic lattices of the Fibonacci family are much more general and hold good even for a randomly disordered arrangement of the building blocks of the systems considered, and indicate a subtle universality class under which these lattices can be grouped.

Hydrogenation-controlled band engineering of dumbbell graphene

The stability of the dumbbell structure has been confirmed by previous theory and experiment. Based on first-principles calculations, we proposed hexagonal dumbbell graphene (HDB C10) and rectangular dumbbell graphene (RDB C10) monolayers containing periodically raised C (CR) atoms. They turn out to have high mobility semiconductor properties. By adsorbing H atoms on these CR atoms, their band structures can be widely tuned from semiconductor to semimetal. When considering adsorption of two/four H atoms on the unit cell of the dumbbell structure, the bandgap can be increased, and isolated flat band structures can be obtained by further adding or removing H atoms. Remarkably, two different Dirac band structures can be found in the HDB/RDB C10H2-I monolayers. The HDB C10H2-I shows a Dirac cone with isotropic Fermi velocities, while the RDB C10H2-I monolayer exhibits a quasi-one-dimensional Dirac nodal line with varying Fermi velocities along the XS path. Tight-binding (TB) models are constructed including nearest neighbor (NN) and next NN hopping in order to understand our DFT results. These TB models are related to the Su-Schrieffer-Heeger model, and are able to explain the tunable topological properties of the RDB C10H2-I monolayer. They not only are able to explain the different kinds of Fermi velocity, but also can predict the emergence of topological edge states, providing a good platform for research on Dirac fermions. The HDB/RDB C10 monolayer exhibits more freedom of tunable band structures and more stable hydrogen storage capacity, making it superior to graphene. Finally, possible experimental synthesis paths of these DB monolayers are provided.

BerryEasy: a GPU enabled python package for diagnosis of nth-order and spin-resolved topology in the presence of fields and effects

Multiple software packages currently exist for the computation of bulk topological invariants in both idealized tight-binding models and realistic Wannier tight-binding models derived from density functional theory. Currently, only one package is capable of computing nested Wilson loops and spin-resolved Wilson loops. These state-of-the-art techniques are vital for accurate analysis of band topology. In this paper we introduce BerryEasy, a python package harnessing the speed of graphical processing units to allow for efficient topological analysis of supercells in the presence of disorder and impurities. Moreover, the BerryEasy package has built-in functionality to accommodate use of realistic many-band tight-binding models derived from first-principles.

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.

Seebeck Effect of Dirac Electrons in Organic Conductors under Hydrostatic Pressure Using a Tight-Binding Model Derived from First Principles

Seebeck Effect of Dirac Electrons in Organic Conductors under Hydrostatic Pressure Using a Tight-Binding Model Derived from First Principles

DFTB Simulation of Charged Clusters Using Machine Learning Charge Inference.

We present a modification to self-consistent charge density functional-based tight binding (SCC-DFTB), which allows computation based on approximate atomic charges. We obtain these charges by means of a machine learning (ML) process that combines a Coulomb model with a neural network. This allows us to avoid the SCC cycles in the SCC-DFTB calculation while maintaining its accuracy. The main input of the model is the atomic positions characterized by a set of atom-centered symmetry functions. The charge inference from our ML algorithm is as close as 10-2 units of charge from the exact SCC solution. Our ML-DFTB approach provides a good approximation of the density matrix and of the energy and forces with only a single diagonalization. This is a significant computational saving with respect to the complete SCC algorithm, which allows us to investigate a bigger ensemble of atoms. We show the quality of our approach in the case of charged silicon carbide (SiC) clusters. The ML-DFTB potential energy surface (PES) mimics the SCC-DFTB PES rather well, despite its simplicity. This allows us to obtain the same geometric structure ordering with respect to energy for small clusters. The dissociation barriers for ion emission are well-reproduced, which opens the way to investigating ion field emission and charged cluster stability. The ML-DFTB approach is obviously not limited to charged clusters or SiC materials. It opens a new route to investigate larger clusters than those investigated by standard SCC-DFTB, as well as surface and solid-state chemistry at the atomic level.

Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method.

Recent experimental findings reveal nonconventional fluorescence emission in biological systems devoid of conjugated bonds or aromatic compounds, termed non-aromatic fluorescence (NAF). This phenomenon is exclusive to aggregated or solid states and remains absent in monomeric solutions. Previous studies focused on small model systems in vacuum show that the carbonyl stretching mode along with strong interaction of short hydrogen bonds (SHBs) remains the primary vibrational mode explaining NAF in these systems. In order to simulate larger model systems taking into account the effects of the surrounding environment, in this work we propose using the density functional tight-binding (DFTB) method in combination with non-adiabatic molecular dynamics (NAMD) and the mixed quantum/molecular mechanics (QM/MM) approach. We investigate the mechanism behind NAF in the crystal structure of l-pyroglutamine-ammonium, comparing it with the related nonfluorescent amino acid l-glutamine. Our results extend our previous findings to more realistic systems, demonstrating the efficiency and robustness of the proposed DFTB method in the context of NAMD in biological systems. Furthermore, due to its inherent low computational cost, this method allows for a better sampling of the nonradiative events at the conical intersection which is crucial for a complete understanding of this phenomenon. Beyond contributing to the ongoing exploration of NAF, this work paves the way for future application of this method in more complex biological systems such as amyloid aggregates, biomaterials, and non-aromatic proteins.

Long-range Pairing in Monolayer NbSe2 Facilitates the Emergence of Topological Superconducting States

Abstract NbSe2, which simultaneously exhibits superconductivity and spin-orbit coupling, is anticipated to pave the way for topological superconductivity and unconventional electron pairing. In this paper, we systematically study topological superconducting (TSC) phases in monolayer NbSe2 through mixing on-site s-wave pairing (ps) with long-range pairing (psA1) based on a tight-binding model. We observe rich phases with both fixed and sensitive Chern numbers (CNs) depending on the chemical potential (μ) and out-of-plane magnetic field (Vz). As psA1 increases, the TSC phase manifests matching and mismatching features according to whether there is a bulk-boundary correspondence (BBC). Strikingly, the introduction of long-range pairing significantly reduces the critical Vz to form TSC phases compared with the pure s-wave paring. Moreover, the TSC phase can be modulated even at Vz=0 under appropriate μ and psA1, which is identified by the robust topological edge states (TESs) of ribbons. Additionally, the long-range pairing influences the hybridization of bulk and edge states, resulting in a matching/mismatching BBC with localized/oscillating TESs on the ribbon. Our finding is helpful for realization of TSC states in experiment, as well as designing and regulating TSC materials.

The Role of Spin – Orbit Coupling in the Spin Transport FM-(G/C)N-FM

The spin transport through DNA system formed by a guanine-cytosine is studied extendedly in our work. Hence, theoretical treatment is accomplished for one magnetized active region (includes base pairs and backbone) coupled to ferromagnetic leads in parallel configuration case, throughout magnetic quantum contacts (FM-(G/C)N-FM). Our treatment is based on the tight binding model to derive obvious formula for the spin dependent transmission spectrum which is employed to investigate the spin transport through DNA junction. Our calculations are accomplished in the presence of spin-orbit coupling for strong, weak and "without backbone" regimes. The role the system spin dependent factors of the transport of (G/C)N molecule are investigated in our study. These factors include the molecular length, as well as externally applied bias voltage. Variation of these factors can enhance or suppress spin transport through (G/C)N molecule (with N=10,15,20,25. The transmission spectrum results confirm that the spin transport throughout (G/C)N is originated by a coherent tunneling process between neighboring bases through the overlapping of the LUMO orbitals of the bases. The physical mechanism is raise from quantum interference combination with molecular length and the presence of spin-orbit coupling. The best functional feature for environmental effect, which may induce dephasing such as leads temperature, is investigated. The results showed that the spin-polarized transport can be effectively regulated by the molecular length of (G/C) which can exhibit efficient spin filtering and spin switching

Magic-angle twisted bilayer graphene under orthogonal and in-plane magnetic fields

We investigate the effect of a magnetic field on the band structure of bilayer graphene with a magic twist angle of 1.08∘. The coupling of a tight-binding model and the Peierls phase allows the calculation of the energy bands of periodic two-dimensional systems. For an orthogonal magnetic field, the Landau levels are dispersive, particularly for magnetic lengths comparable to or larger than the twisted bilayer cell size. A high in-plane magnetic field modifies the low-energy bands and gap, which we demonstrate to be a direct consequence of the minimal coupling.

Electronic heat conductivity in a two-temperature state

Heat transport in solids is governed by two fundamental contributions, atomic and electronic. The electronic energy transport in transient excited states is a defining factor in the problem of ultrafast material irradiation. Here, we calculate the electronic heat conductivity at elevated electron temperatures up to 40,000 K. We apply the novel combined method of tight binding formalism to calculate the electron-phonon contribution to the electronic heat conductivity, and the linear response theory (in the single-pole Ritchie-Howie loss function approximation) for its electron-electron counterpart, implemented in the hybrid code XTANT-3. It allows us to evaluate the electronic heat conductivity in a wide range of materials – fcc metals: Al, Ca, Ni, Cu, Sr, Y, Zr, Rh, Pd, Ag, Ir, Pt, Au, and Pb; hcp metals: Mg, Sc, Ti, Co, Zn, Tc, Ru, Cd, Hf, Re, and Os; bcc metals: V, Cr, Fe, Nb, Mo, Ba, Ta, and W; other metals: Sn, Ga, In, Mn, Te, and Se; semimetal graphite; semiconductors – group IV: Si, Ge, and SiC; group III-V: AlAs, AlP, GaP, GaAs, and GaSb; oxides: ZnO, TiO2, and Cu2O; and others: PbI2, ZnS, and B4C.

A DFTB study on the electronic response of encapsulated DNA nucleobases onto chiral CNTs as a sequencer

Sequencing the DNA nucleobases is essential in the diagnosis and treatment of many diseases related to human genes. In this article, the encapsulation of DNA nucleobases with some of the important synthesized chiral (7, 6), (8, 6), and (10, 8) carbon nanotubes were investigated. The structures were modeled by applying density functional theory based on tight binding method (DFTB) by considering semi-empirical basis sets. Encapsulating DNA nucleobases on the inside of CNTs caused changes in the electronic properties of the selected chiral CNTs. The results confirmed that van der Waals (vdW) interactions, π-orbitals interactions, non-bonded electron pairs, and the presence of high electronegative atoms are the key factors for these changes. The result of electronic parameters showed that among the CNTs, CNT (8, 6) is a suitable choice in sequencing guanine (G) and cytosine (C) DNA nucleobases. However, they are not able to sequence adenine (A) and thymine (T). According to the band gap energy engineering approach and absorption energy, the presence of G and C DNA nucleobases decreased the band gap energy of CNTs. Hence selected CNTs suggested as biosensor substrates for sequencing G and C DNA nucleobases.

Influence of the disorder correlation length on localization and quantum state transference in tight-binding channels

We investigate in detail the transference of quantum states in a disordered channel. We consider a one-dimensional tight-binding model consisting of a source S connected to a receiver R throughout a disordered channel. The disorder distribution contains a single tunable spatial correlation length. We demonstrate that the disorder correlation length plays a relevant role within the localization properties of the channel. The hopping parameter between the sites S and R and the channel are also adjustable parameters. We investigate the possibility of transference of quantum states along this quantum channel model and describe the optimal conditions for the occurrence of a high fidelity process.

From topological nodal-line semimetals to quantum spin Hall insulators in tetragonal SnX monolayers (X=F, Cl, Br, I)

Abstract Two-dimensional (2D) topological materials have recently garnered significant interest due to their profound physical properties and promising applications for future quantum nanoelectronics. Achieving various topological states within one type of materials is, however, seldom reported. Based on first-principles calculations and tight-binding models, we investigate topological electronic states in a novel family of 2D halogenated tetragonal stanene (T-SnX, X = F, Cl, Br, I). All the four monolayers are found being unusual topological nodal-line semimetals (NLSs), protected by a glide mirror symmetry. When spin-orbit coupling (SOC) is turned on, T-SnF and TSnCl are still ascertained as topological NLSs due to the remaining band inversion, primarily composed of Sn pxy orbitals, while T-SnBr and T-SnI become quantum spin Hall insulators. The phase transition is ascribed to moving up in energy of Sn s orbitals and increasing of SOC strengths. The topology origin in the materials is uniformly rationalized through elementary band representations. The robust and diverse topological states found in the 2D T-SnX monolayers position them as an excellent material platform for the development of innovative topological electronics.