orbital method
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Atoms ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 5
Author(s):  
Anand K. Bhatia

The excitation cross-sections of the nS states of atomic hydrogen, n = 2 to 6, by electron impact on the ground state of atomic hydrogen were calculated using the variational polarized-orbital method at various incident electron energies in the range 10 to 122 eV. Converged excitation cross-sections were obtained using sixteen partial waves (L = 0 to 15). Excitation cross-sections to 2S state, calculated earlier, were calculated at higher energies than before. Results obtained using the hybrid theory (variational polarized orbital method) are compared to those obtained using other approaches such as the Born–Oppenheimer, close-coupling, R-matrix, and complex-exterior scaling methods using only the spherical symmetric wave functions. Phase shifts and elastic cross-sections are given at various energies and angular momenta. Excitation rate coefficients were calculated at various electron temperatures, which are required for plasma diagnostics in solar and astrophysics to infer plasma parameters. Excitation cross-sections are compared with those obtained by positron impact excitation.


Author(s):  
Koji Okuwaki ◽  
Kazuki Akisawa ◽  
Ryo Hatada ◽  
Yuji Mochizuki ◽  
Kaori Fukuzawa ◽  
...  

Abstract In large biomolecular systems such as protein complexes, there are huge numbers of combinations of inter-residue interactions whose comprehensive analyses are often beyond the intuitive processing by researchers. Here we propose a computational method to allow for a systematic analysis of these interactions based on the fragment molecular orbital calculations, in which the inter-fragment interaction energies are comprehensively processed by the singular value decomposition. For a trimer complex of SARS-CoV-2 spike protein, three-body interactions among residues belonging to three chains are analyzed to elicit a small number of essential interaction modes or networks crucial for the structural stability of complex.


Author(s):  
Ryoya Hiramatsu ◽  
Daisuke Miura ◽  
Akimasa SAKUMA

Abstract We propose a first-principles calculation method for the Gilbert damping constants α at finite temperatures. α is described by the torque correlation model in which the electronic structure is computed by the tight-binding linear muffin-tin orbital method. We include the finite-temperature effect as the transverse spin fluctuation in the disordered local moment picture within the coherent potential approximation. Applying the present method to bcc-Fe and L10-FePt, we demonstrate these temperature-dependent α. By comparing our calculated results with experimental results, we find the calculated values are less than half of the experimental values, reflecting the characteristics of the torque correlation model.


2021 ◽  
Vol 922 (2) ◽  
pp. 100
Author(s):  
A. M. Velasco ◽  
J. L. Alonso ◽  
P. Redondo ◽  
C. Lavín

Abstract We have theoretically determined the absorption oscillator strengths and wavenumbers for rotationally resolved transitions of the c4′1Σu + (6)-X1Σg +(0–9) bands of N2, which are relevant to analyze the spectra of planetary atmospheres. The Molecular Quantum Defect Orbital method has been used in our calculations. The interaction between the c4′1Σu + (6) Rydberg state and the b′1Σu + valence states has been considered using an adequate rovibronic energy matrix. In addition, we have calculated the lifetimes of the rotational levels of the c4′1Σu + (6) state. We hope that the reported data, most of them for the first time, can be useful in the interpretation of planetary atmospheres where N2 is present.


Atoms ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 82
Author(s):  
Robert P. McEachran ◽  
Kathryn R. Hamilton ◽  
Klaus Bartschat

We reinvestigate a key process in electron-atom collision physics, the elastic scattering of electrons from helium atoms. Specifically, results from a special-purpose relativistic polarized-orbital method, which is designed to treat elastic scattering only, are compared with those from a very extensive, fully ab initio, general-purpose B-spline R-matrix (close-coupling) code.


Author(s):  
Iva Lukac ◽  
Paul G. Wyatt ◽  
Ian H. Gilbert ◽  
Fabio Zuccotto

AbstractWater molecules play a crucial role in protein–ligand binding, and many tools exist that aim to predict the position and relative energies of these important, but challenging participants of biomolecular recognition. The available tools are, in general, capable of predicting the location of water molecules. However, predicting the effects of their displacement is still very challenging. In this work, a linear-scaling quantum mechanics-based approach was used to assess water network energetics and the changes in network stability upon ligand structural modifications. This approach offers a valuable way to improve understanding of SAR data and help guide compound design.


Cancers ◽  
2021 ◽  
Vol 13 (16) ◽  
pp. 4246
Author(s):  
Jongwan Kim ◽  
Hocheol Lim ◽  
Sungho Moon ◽  
Seon Yeon Cho ◽  
Minhye Kim ◽  
...  

The Hippo pathway is an important signaling pathway modulating growth control and cancer cell proliferation. Dysregulation of the Hippo pathway is a common feature of several types of cancer cells. The modulation of the interaction between yes-associated protein (YAP) and transcriptional enhancer associated domain (TEAD) in the Hippo pathway is considered an attractive target for cancer therapeutic development, although the inhibition of PPI is a challenging task. In order to investigate the hot spots of the YAP and TEAD1 interacting complex, an ab initio Fragment Molecular Orbital (FMO) method was introduced. With the hot spots, pharmacophores for the inhibitor design were constructed, then virtual screening was performed to an in-house library. Next, we performed molecular docking simulations and FMO calculations for screening results to study the binding modes and affinities between PPI inhibitors and TEAD1. As a result of the virtual screening, three compounds were selected as virtual hit compounds. In order to confirm their biological activities, cellular (luciferase activity, proximity ligation assay and wound healing assay in A375 cells, qRT-PCR in HEK 293T cells) and biophysical assays (surface plasmon resonance assays) were performed. Based on the findings of the study, we propose a novel PPI inhibitor BY03 and demonstrate a profitable strategy to analyze YAP–TEAD PPI and discover novel PPI inhibitors.


Author(s):  
Shigenori Tanaka ◽  
Shusuke Tokutomi ◽  
Ryo Hatada ◽  
Koji Okuwaki ◽  
Kazuki Akisawa ◽  
...  

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