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1. Using transition density models to interpret experimental optical spectra of exciton-coupled cyanine (iCy3)2 dimer probes of local DNA conformations at or near functional protein binding sites

   https://doi.org/10.1093/nar/gkad1163  

   Heussman, Dylan ; Enkhbaatar, Lulu ; Sorour, Mohammed I. ; Kistler, Kurt A. ; von Hippel, Peter H. ; Matsika, Spiridoula ; Marcus, Andrew H. ( December 2023 , Nucleic Acids Research)

   Exciton-coupled chromophore dimers are an emerging class of optical probes for studies of site-specific biomolecular interactions. Applying accurate theoretical models for the electrostatic coupling of a molecular dimer probe is a key step for simulating its optical properties and analyzing spectroscopic data. In this work, we compare experimental absorbance and circular dichroism (CD) spectra of ‘internally-labeled’ (iCy3)2 dimer probes inserted site-specifically into DNA fork constructs to theoretical calculations of the structure and geometry of these exciton-coupled dimers. We compare transition density models of varying levels of approximation to determine conformational parameters of the (iCy3)2 dimer-labeled DNA fork constructs. By applying an atomistically detailed transition charge (TQ) model, we can distinguish between dimer conformations in which the stacking and tilt angles between planar iCy3 monomers are varied. A major strength of this approach is that the local conformations of the (iCy3)2 dimer probes that we determined can be used to infer information about the structures of the DNA framework immediately surrounding the probes at various positions within the constructs, both deep in the duplex DNA sequences and at sites at or near the DNA fork junctions where protein complexes bind to discharge their biological functions.

    

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2. RTD Light Emission around 1550 nm with IQE up to 6% at 300 K

   https://doi.org/10.1109/DRC50226.2020.9135175  

   Brown, E. R. ; Zhang, W-D. ; Fakhimi, P. ; Growden, T. A. ; Berger, P.R. ( June 2020 , IEEE Device Research Conference (DRC), Columbus, OH (June 22-24, 2020))

   Resonant tunneling diodes (RTDs) have come full-circle in the past 10 years after their demonstration in the early 1990s as the fastest room-temperature semiconductor oscillator, displaying experimental results up to 712 GHz and fmax values exceeding 1.0 THz [1]. Now the RTD is once again the preeminent electronic oscillator above 1.0 THz and is being implemented as a coherent source [2] and a self-oscillating mixer [3], amongst other applications. This paper concerns RTD electroluminescence – an effect that has been studied very little in the past 30+ years of RTD development, and not at room temperature. We present experiments and modeling of an n-type In0.53Ga0.47As/AlAs double-barrier RTD operating as a cross-gap light emitter at ~300K. The MBE-growth stack is shown in Fig. 1(a). A 15-μm-diam-mesa device was defined by standard planar processing including a top annular ohmic contact with a 5-μm-diam pinhole in the center to couple out enough of the internal emission for accurate free-space power measurements [4]. The emission spectra have the behavior displayed in Fig. 1(b), parameterized by bias voltage (VB). The long wavelength emission edge is at  = 1684 nm - close to the In0.53Ga0.47As bandgap energy of Ug ≈ 0.75 eV at 300 K. The spectral peaks for VB = 2.8 and 3.0 V both occur around  = 1550 nm (h = 0.75 eV), so blue-shifted relative to the peak of the “ideal”, bulk InGaAs emission spectrum shown in Fig. 1(b) [5]. These results are consistent with the model displayed in Fig. 1(c), whereby the broad emission peak is attributed to the radiative recombination between electrons accumulated on the emitter side, and holes generated on the emitter side by interband tunneling with current density Jinter. The blue-shifted main peak is attributed to the quantum-size effect on the emitter side, which creates a radiative recombination rate RN,2 comparable to the band-edge cross-gap rate RN,1. Further support for this model is provided by the shorter wavelength and weaker emission peak shown in Fig. 1(b) around = 1148 nm. Our quantum mechanical calculations attribute this to radiative recombination RR,3 in the RTD quantum well between the electron ground-state level E1,e, and the hole level E1,h. To further test the model and estimate quantum efficiencies, we conducted optical power measurements using a large-area Ge photodiode located ≈3 mm away from the RTD pinhole, and having spectral response between 800 and 1800 nm with a peak responsivity of ≈0.85 A/W at  =1550 nm. Simultaneous I-V and L-V plots were obtained and are plotted in Fig. 2(a) with positive bias on the top contact (emitter on the bottom). The I-V curve displays a pronounced NDR region having a current peak-to-valley current ratio of 10.7 (typical for In0.53Ga0.47As RTDs). The external quantum efficiency (EQE) was calculated from EQE = e∙IP/(∙IE∙h) where IP is the photodiode dc current and IE the RTD current. The plot of EQE is shown in Fig. 2(b) where we see a very rapid rise with VB, but a maximum value (at VB= 3.0 V) of only ≈2×10-5. To extract the internal quantum efficiency (IQE), we use the expression EQE= c ∙i ∙r ≡ c∙IQE where ci, and r are the optical-coupling, electrical-injection, and radiative recombination efficiencies, respectively [6]. Our separate optical calculations yield c≈3.4×10-4 (limited primarily by the small pinhole) from which we obtain the curve of IQE plotted in Fig. 2(b) (right-hand scale). The maximum value of IQE (again at VB = 3.0 V) is 6.0%. From the implicit definition of IQE in terms of i and r given above, and the fact that the recombination efficiency in In0.53Ga0.47As is likely limited by Auger scattering, this result for IQE suggests that i might be significantly high. To estimate i, we have used the experimental total current of Fig. 2(a), the Kane two-band model of interband tunneling [7] computed in conjunction with a solution to Poisson’s equation across the entire structure, and a rate-equation model of Auger recombination on the emitter side [6] assuming a free-electron density of 2×1018 cm3. We focus on the high-bias regime above VB = 2.5 V of Fig. 2(a) where most of the interband tunneling should occur in the depletion region on the collector side [Jinter,2 in Fig. 1(c)]. And because of the high-quality of the InGaAs/AlAs heterostructure (very few traps or deep levels), most of the holes should reach the emitter side by some combination of drift, diffusion, and tunneling through the valence-band double barriers (Type-I offset) between InGaAs and AlAs. The computed interband current density Jinter is shown in Fig. 3(a) along with the total current density Jtot. At the maximum Jinter (at VB=3.0 V) of 7.4×102 A/cm2, we get i = Jinter/Jtot = 0.18, which is surprisingly high considering there is no p-type doping in the device. When combined with the Auger-limited r of 0.41 and c ≈ 3.4×10-4, we find a model value of IQE = 7.4% in good agreement with experiment. This leads to the model values for EQE plotted in Fig. 2(b) - also in good agreement with experiment. Finally, we address the high Jinter and consider a possible universal nature of the light-emission mechanism. Fig. 3(b) shows the tunneling probability T according to the Kane two-band model in the three materials, In0.53Ga0.47As, GaAs, and GaN, following our observation of a similar electroluminescence mechanism in GaN/AlN RTDs (due to strong polarization field of wurtzite structures) [8]. The expression is Tinter = (2/9)∙exp[(-2 ∙Ug 2 ∙me)/(2h∙P∙E)], where Ug is the bandgap energy, P is the valence-to-conduction-band momentum matrix element, and E is the electric field. Values for the highest calculated internal E fields for the InGaAs and GaN are also shown, indicating that Tinter in those structures approaches values of ~10-5. As shown, a GaAs RTD would require an internal field of ~6×105 V/cm, which is rarely realized in standard GaAs RTDs, perhaps explaining why there have been few if any reports of room-temperature electroluminescence in the GaAs devices. [1] E.R. Brown,et al., Appl. Phys. Lett., vol. 58, 2291, 1991. [5] S. Sze, Physics of Semiconductor Devices, 2nd Ed. 12.2.1 (Wiley, 1981). [2] M. Feiginov et al., Appl. Phys. Lett., 99, 233506, 2011. [6] L. Coldren, Diode Lasers and Photonic Integrated Circuits, (Wiley, 1995). [3] Y. Nishida et al., Nature Sci. Reports, 9, 18125, 2019. [7] E.O. Kane, J. of Appl. Phy 32, 83 (1961). [4] P. Fakhimi, et al., 2019 DRC Conference Digest. [8] T. Growden, et al., Nature Light: Science & Applications 7, 17150 (2018). [5] S. Sze, Physics of Semiconductor Devices, 2nd Ed. 12.2.1 (Wiley, 1981). [6] L. Coldren, Diode Lasers and Photonic Integrated Circuits, (Wiley, 1995). [7] E.O. Kane, J. of Appl. Phy 32, 83 (1961). [8] T. Growden, et al., Nature Light: Science & Applications 7, 17150 (2018). 

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3. Extracting correlation effects from Momentum-Resolved Electron Energy Loss Spectroscopy (M-EELS): Synergistic origin of the dispersion kink in Bi 2.1 Sr 1.9 CaCu 2 O 8+x

   Huang, E ; Limtragool, K ; Setty, C. Husain ; Mitrano, M ; Abbamonte, P ; Phillips, P. ( January 2021 , Physical review)

   We employ Momentum-Resolved Electron Energy Loss Spectroscopy (M-EELS) on Bi2.1Sr1.9CaCu2O8+x to resolve the issue of the kink feature in the electron dispersion widely observed in the cuprates. To this end, we utilize the GW approximation to relate the density response function measured in in M-EELS to the self-energy, isolating contributions from phonons, electrons, and the momentum dependence of the effective interaction to the decay rates. The phononic contributions, present in the M-EELS spectra due to electron-phonon coupling, lead to kink features in the corresponding single-particle spectra at energies between 40 meV and 80 meV, independent of the doping level. We find that a repulsive interaction constant in momentum space is able to yield the kink attributed to phonons in ARPES. Hence, our analysis of the M-EELS spectra points to local repulsive interactions as a factor that enhances the spectroscopic signatures of electron-phonon coupling in cuprates. We conclude that the strength of the kink feature in cuprates is determined by the combined action of electron-phonon coupling and electron-electron interactions. 

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4. Observation of chiral surface excitons in a topological insulator Bi 2 Se 3

   https://doi.org/10.1073/pnas.1813514116  

   Kung, H. -H. ; Goyal, A. P. ; Maslov, D. L. ; Wang, X. ; Lee, A. ; Kemper, A. F. ; Cheong, S. -W. ; Blumberg, G. ( February 2019 , Proceedings of the National Academy of Sciences)

   The protected electron states at the boundaries or on the surfaces of topological insulators (TIs) have been the subject of intense theoretical and experimental investigations. Such states are enforced by very strong spin–orbit interaction in solids composed of heavy elements. Here, we study the composite particles—chiral excitons—formed by the Coulomb attraction between electrons and holes residing on the surface of an archetypical 3D TI,${\mathrm{B}\mathrm{i}}_2{\mathrm{S}\mathrm{e}}_3$. Photoluminescence (PL) emission arising due to recombination of excitons in conventional semiconductors is usually unpolarized because of scattering by phonons and other degrees of freedom during exciton thermalization. On the contrary, we observe almost perfectly polarization-preserving PL emission from chiral excitons. We demonstrate that the chiral excitons can be optically oriented with circularly polarized light in a broad range of excitation energies, even when the latter deviate from the (apparent) optical band gap by hundreds of millielectronvolts, and that the orientation remains preserved even at room temperature. Based on the dependences of the PL spectra on the energy and polarization of incident photons, we propose that chiral excitons are made from massive holes and massless (Dirac) electrons, both with chiral spin textures enforced by strong spin–orbit coupling. A theoretical model based on this proposal describes quantitatively the experimental observations. The optical orientation of composite particles, the chiral excitons, emerges as a general result of strong spin–orbit coupling in a 2D electron system. Our findings can potentially expand applications of TIs in photonics and optoelectronics.

    

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5. Wavelength‐decomposition‐based embedded cluster density approximation for systems with nonlocal electron correlation

   https://doi.org/10.1002/qua.26347  

   Huang, Chen ( July 2020 , International Journal of Quantum Chemistry)

   Local correlation methods rely on the assumption that electron correlation is nearsighted. In this work, we develop a method to alleviate this assumption. This new method is demonstrated by calculating the random phase approximation (RPA) correlation energies in several one‐dimensional model systems. In this new method, the first step is to approximately decompose the RPA correlation energy to the nearsighted and farsighted components based on the wavelength decomposition of electron correlation developed by Langreth and Perdew. The short‐wavelength (SW) component of the RPA correlation energy is then considered to be nearsighted, and the long‐wavelength (LW) component of the RPA correlation energy is considered to be farsighted. The SW RPA correlation energy is calculated using a recently developed local correlation method: the embedded cluster density approximation (ECDA). The LW RPA correlation energy is calculated globally based on the system's Kohn‐Sham orbitals. This new method is termedλ‐ECDA, whereλindicates the wavelength decomposition. The performance ofλ‐ECDA is examined on a one‐dimensional model system: aH₂₄chain, in which the RPA correlation energy is highly nonlocal. In this model system, a softened Coulomb interaction is used to describe the electron‐electron and electron‐ion interactions, and slightly stronger nuclear charges (1.2e) are assigned to the pseudo‐H atoms. Bond stretching energies, RPA correlation potentials, and Kohn‐Sham eigenvalues predicted byλ‐ECDA are in good agreement with the benchmarks when the clusters are made reasonably large. We find that the LW RPA correlation energy is critical for obtaining accurate prediction of the RPA correlation potential, even though the LW RPA correlation energy contributes to only a few percent of the total RPA correlation energy.

    

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