Modeling the vibrational structure of linear carbon chains has proved to be a difficult task with present first-principles calculations. This limits their applicability for the interpretation of experimental data, such as Raman scattering experiments on linear carbon chains within nanotubes. These limitations can be overcome by means of a simple tight binding scheme for pi-electrons. In this work a force field for the calculation of longitudinal phonon dispersion branches is built on the basis of bond-bond polarizabilities and just three parameters. The so obtained phonon dispersion branches are in very good agreement with the experimental data on carbynes in different environments and polyynes of any length. The model is discussed in relation to the importance of long range vibrational interactions in carbynes. The physical phenomena affecting their vibrational properties (i.e., Kohn anomaly, electron-phonon coupling) can be accurately and analytically described by the present approach.
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http://dx.doi.org/10.1063/1.2831507 | DOI Listing |
J Vis Exp
January 2025
Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Henry and Allison McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Harvard Medical School;
A method to quantitate the stabilization of Mitochondria-Associated endoplasmic reticulum Membranes (MAMs) in a 3-dimensional (3D) neural model of Alzheimer's disease (AD) is presented here. To begin, fresh human neuro progenitor ReN cells expressing β-amyloid precursor protein (APP) containing familial Alzheimer's disease (FAD) or naïve ReN cells are grown in thin (1:100) Matrigel-coated tissue culture plates. After the cells reach confluency, these are electroporated with expression plasmids encoding red fluorescence protein (RFP)-conjugated mitochondria-binding sequence of AKAP1(34-63) (Mito-RFP) that detects mitochondria or constitutive MAM stabilizers MAM 1X or MAM 9X that stabilize tight (6 nm ± 1 nm gap width) or loose (24 nm ± 3 nm gap width) MAMs, respectively.
View Article and Find Full Text PDFMater Horiz
January 2025
Department of Materials Science, University of Michigan, Ann Arbor, Michigan 48109, USA.
It is difficult to intuit how electronic structure features-such as band gap magnitude, location of band extrema, effective masses, -arise from the underlying crystal chemistry of a material. Here we present a strategy to distill sparse and chemically-interpretable tight-binding models from density functional theory calculations, enabling us to interpret how multiple orbital interactions in a 3D crystal conspire to shape the overall band structure. Applying this process to silicon, we show that its indirect gap arises from a competition between first and second nearest-neighbor bonds-where second nearest-neighbor interactions pull the conduction band down from Γ to X in a cosine shape, but the first nearest-neighbor bonds push the band up near X, resulting in the characteristic dip of the silicon conduction band.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.
We present a hybrid semiempirical density functional tight-binding (DFTB) model with a machine learning neural network potential as a correction to the repulsive term. This hybrid model, termed machine learning tight-binding (MLTB), employs the standard self-consistent charge (SCC) DFTB formalism as a baseline, enhanced by the HIP-NN potential as an effective many-body correction for short-range pairwise repulsive interactions. The MLTB model demonstrates significantly improved transferability and extensibility compared to the SCC-DFTB and HIP-NN models.
View Article and Find Full Text PDFRNA
January 2025
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
Neisseria meningitidis minimal ProQ is a global RNA binding protein belonging to the family of FinO-domain proteins. The N. meningitidis ProQ consists only of the FinO domain accompanied by short N- and C-terminal extensions.
View Article and Find Full Text PDFPhotosynth Res
January 2025
Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.
Red algae are photosynthetic eukaryotes whose light-harvesting complexes (LHCs) associate with photosystem I (PSI). In this study, we examined characteristics of PSI-LHCI, PSI, and LHCI isolated from the red alga Galdieria sulphuraria NIES-3638. The PSI-LHCI supercomplexes were purified using anion-exchange chromatography followed by hydrophobic-interaction chromatography, and finally by trehalose density gradient centrifugation.
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