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Alireza Baradaran ◽  
Mehdi Ghaffarian

Abstract Using the tight-binding model and density functional theory, the topological invariant of the two-dimensional (2D) group III-V and IV-IV compounds are studied in the absence and the presence of an external perpendicular electric field and spin-orbit coupling. It will be recognized that a critical value of these parameters changes the topological invariant of 2D graphene-like compounds. The significant effects of an external electric field and spin-orbit coupling are considered to the two-center overlap integrals of the Slater-Koster model involved in band structures, changing band-gap, and tuning the topological phase transition between ordinary and quantum spin Hall regime. These declare the good consistency between two theories: tight-binding and density functional. So, this study reveals topological phase transition in these materials. Our finding paves a way to extend an effective Hamiltonian, and may instantly clear some computation aspects of the study in the field of spintronic based on the first-principles methods.

Materials ◽  
2022 ◽  
Vol 15 (2) ◽  
pp. 500
Pablo Álvarez-Rodríguez ◽  
Víctor Manuel García-Suárez

Graphene stands out as a versatile material with several uses in fields that range from electronics to biology. In particular, graphene has been proposed as an electrode in molecular electronics devices that are expected to be more stable and reproducible than typical ones based on metallic electrodes. In this work, we study by means of first principles, simulations and a tight-binding model the electronic and transport properties of graphene nanogaps with straight edges and different passivating atoms: Hydrogen or elements of the second row of the periodic table (boron, carbon, nitrogen, oxygen, and fluoride). We use the tight-binding model to reproduce the main ab-initio results and elucidate the physics behind the transport properties. We observe clear patterns that emerge in the conductance and the current as one moves from boron to fluoride. In particular, we find that the conductance decreases and the tunneling decaying factor increases from the former to the latter. We explain these trends in terms of the size of the atom and its onsite energy. We also find a similar pattern for the current, which is ohmic and smooth in general. However, when the size of the simulation cell is the smallest one along the direction perpendicular to the transport direction, we obtain highly non-linear behavior with negative differential resistance. This interesting and surprising behavior can be explained by taking into account the presence of Fano resonances and other interference effects, which emerge due to couplings to side atoms at the edges and other couplings across the gap. Such features enter the bias window as the bias increases and strongly affect the current, giving rise to the non-linear evolution. As a whole, these results can be used as a template to understand the transport properties of straight graphene nanogaps and similar systems and distinguish the presence of different elements in the junction.

2021 ◽  
Zhixin Cyrillus Tan ◽  
Brian T Orcutt-Jahns ◽  
Aaron S Meyer

Abstract A critical property of many therapies is their selective binding to target populations. Exceptional specificity can arise from high-affinity binding to surface targets expressed exclusively on target cell types. In many cases, however, therapeutic targets are only expressed at subtly different levels relative to off-target cells. More complex binding strategies have been developed to overcome this limitation, including multi-specific and multivalent molecules, creating a combinatorial explosion of design possibilities. Guiding strategies for developing cell-specific binding are critical to employ these tools. Here, we employ a uniquely general multivalent binding model to dissect multi-ligand and multi-receptor interactions. This model allows us to analyze and explore a series of mechanisms to engineer cell selectivity, including mixtures of molecules, affinity adjustments, valency changes, multi-specific molecules and ligand competition. Each of these strategies can optimize selectivity in distinct cases, leading to enhanced selectivity when employed together. The proposed model, therefore, provides a comprehensive toolkit for the model-driven design of selectively binding therapies.

Maryam Mirzaei ◽  
Taraneh Vazifehshenas ◽  
T. Salavati-fard ◽  
Bilal Tanatar

Abstract We investigate the dynamic optical transition of monolayer silicene in the presence of external electric and exchange fields within the low-energy tight-binding model. Applying external electric and exchange fields breaks the silicene band structure spin and valley degeneracies. Three phases of silicene corresponding to different strengths of perpendicular electric field with respect to the spin-orbit coupling (∆z < ∆so, ∆z = ∆so and ∆z > ∆so) are considered. We obtain the spinand valley-dependent optical responses to the incoming circularly polarized light using the Kubo formula. We show and discuss how the magnitude and direction of the transverse and longitudinal optical responses of such a system change with the electric and exchange fields. Our calculations suggest that the intraband part of the longitudinal optical response as well as the initial point of the interband part have strong dependencies on the exchange field. Furthermore, we show that one of the spin subbands plays a dominant role in the response to polarized light. Depending on the type of incident light polarization, the dominant subband may change. Our results shed light on the relation between silicene dynamic optical responses and externally applied fields.

Shoma Arai ◽  
Shingo Kaneta-Takada ◽  
Le Duc Anh ◽  
Masaaki Tanaka ◽  
Shinobu Ohya

Abstract The two-dimensional electron gas formed at interfaces between SrTiO3 and other materials has attracted much attention since extremely efficient spin-to-charge current conversion has been recently observed at these interfaces. This has been attributed to their complicated quantized multi-orbital structures with a topological feature. However, there are few reports quantitatively comparing the conversion efficiency values between experiments and theoretical calculations at these interfaces. In this study, we theoretically explain the experimental temperature dependence of the spin-to-charge current conversion efficiency using an 8×8 effective tight-binding model considering the second dxy subband, revealing the vital role of the quantization of the multi-band structure.

2021 ◽  
Vol 12 ◽  
Wei Hong ◽  
Raphael Nyaruaba ◽  
Xiaohong Li ◽  
Huan Liu ◽  
Hang Yang ◽  

Staphylococcus aureus can produce a multilayered biofilm embedded in extracellular polymeric matrix. This biofilm is difficult to remove, insensitive to antibiotics, easy to develop drug-resistant strains and causes enormous problems to environments and health. Phage lysin which commonly consists of a catalytic domain (CD) and a cell-wall binding domain (CBD) is a powerful weapon against bacterial biofilm. However, the real-time interaction between lysin and S. aureus biofilm is still not fully understood. In this study, we monitored the interactions of three lysins (ClyF, ClyC, PlySs2) against culture-on-chip S. aureus biofilm, in real-time, based on surface plasmon resonance (SPR). A typical SPR response curve showed that the lysins bound to the biofilm rapidly and the biofilm destruction started at a longer time. By using 1:1 binding model analysis, affinity constants (KD) for ClyF, ClyC, and PlySs2 were found to be 3.18 ± 0.127 μM, 1.12 ± 0.026 μM, and 15.5 ± 0.514 μM, respectively. The fact that ClyF and PlySs2 shared the same CBD but showed different affinity to S. aureus biofilm suggested that, not only CBD, but also CD affects the binding activity of the entire lysin. The SPR platform can be applied to improve our understanding on the complex interactions between lysins and bacterial biofilm including association (adsorption) and disassociation (destruction).

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