Exploration of the high-order harmonic generation from periodic potentials by Bohmian trajectories

Pan, Xue-Fei; Li, Bo; Qi, Tong; Zhang, Jun; Liu, Xue‐Shen

doi:10.1088/1361-6455/abcede

Cited by 7 publications

(4 citation statements)

References 44 publications

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“…The movement of atoms in a chemical complex is determined by keeping the temperature, volume and pressure parameters fixed for a set amount of time. The trajectories for atoms and molecules were calculated with respect to Newton's equations of motion for a system of interacting particles, in which the potential energies and forces involving the particles are acquired through inter atomic potentials and molecular mechanic force fields (87)(88)(89).…”

Section: Molecular Dynamics Simulation Studiesmentioning

confidence: 99%

Lead generation of UPPS inhibitors targeting MRSA: Using 3D- QSAR pharmacophore modeling, virtual screening, molecular docking, and molecular dynamic simulations

Qandeel,

Mowafy,

Abouzid

et al. 2023

Preprint

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Due to the threat of emerging antibiotic resistance, the quest for new antibacterial agents remains an essential endeavor in drug discovery. Bacterial resistance can be combated by using inhibitors that work on a different mechanism than current antibiotics thus avoiding cross-resistance by targeting new enzymes in the same pathway. Undecaprenyl Pyrophosphate Synthase (UPPS) is a vital target enzyme located in the very early steps of bacterial cell wall biosynthesis. UPPS inhibitors were found to have anti-bacterial activity on resistant strains such as MRSA and VRE when used alone or in combination with current agents. We used several consecutive computer-based protocols to identify novel UPPS inhibitors. The 3D QSAR pharmacophore generation (HypoGen algorithm) methodology in Discovery studio 4.1 was adopted to generate a valid predictive pharmacophore model utilizing a set of UPPS inhibitors with known reported activity. The generated model consists of four features: one Hydrogen Bond Acceptor (HBA), two Hydrophobic (HYD), and one Ring Aromatic (RA). It had a correlation coefficient of 0.86 and a null cost difference of 191.39 reflecting its high predictive power. Hypo1 was proven statistically significant using Fischer's randomization at 95% confidence level. The validated pharmacophore model was used for the virtual screening of several databases (ZINC15 library, drug-like Diverse, Mini Maybridge, and scPDB). The resulting hits were filtered using SMART and Lipinski's filters. The hits were docked into the binding site of the UPPS protein (PDB ID: 5KH5) affording 70 hits with higher docking affinities than the reference compound (6TC, − 21.17 Kcal/mol). The top five hits were eventually elected through extensive docking analysis and visual inspection based on docking affinities, fit values, and key residue interactions with the UPPS receptor. Molecular dynamic simulations of the top five hit-protein complexes were performed using Discovery Studio (DS) to confirm the stability of the protein-ligand complexes. As a result, these promising five hit molecules may be considered as promising novel UPPS inhibitors.

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Section: Molecular Dynamics Simulation Studiesmentioning

confidence: 99%

Lead generation of UPPS inhibitors targeting MRSA: Using 3D- QSAR pharmacophore modeling, virtual screening, molecular docking, and molecular dynamic simulations

Qandeel,

Mowafy,

Abouzid

et al. 2023

Preprint

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show abstract

“…[21][22][23] Furthermore, the model potential has been widely used to study solid HHG by solving the time-dependent Schrödinger equation (TDSE) based on the single active electron approximation. [24][25][26][27][28] Lu et al employed the model potential to intuitively study the dynamic process of HHG in solids via time-dependent population imaging. [24] Dixit et al discussed the impact of vacancy defects in solid HHG, which can broaden the energy cutoff of the harmonic spectrum.…”

mentioning

confidence: 99%

“…[27] Liu et al demonstrated the applicability of Bohmian trajectory analysis in investigating the recombination process in solid HHG. [28] In a word, researchers have demonstrated the intricate electron dynamics present in solid HHG based on the one-dimensional monochromatic periodic potential.…”

mentioning

confidence: 99%

Modifying the Electron Dynamics in High-Order Harmonic Generation via a Two-Color Laser Field

Zhang 张,

Miao 苗

2023

Chinese Phys. Lett.

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The harmonic emission from bichromatic periodic potential has been investigated by numerically solving the time-dependent Schrödinger equation in velocity gauge. The results show that the harmonic minimum is sensitive to the wavelength. Moreover, distinct crystal momentum states contribute differently to harmonic generation. In momentum space, the electron dynamics reveals a close relationship between the spectral minimum and the electron distribution in higher conduction bands. Additionally, by introducing an ultraviolet pulse to the fundamental laser field, the suppression of harmonic minimum occurs as a result of heightened electron populations in higher conduction bands. This work can shed light on the harmonic emission originating from solid with a two-atom basis.

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“…As we know, the move processes of the electrons in a solid can be observed by Bohmian trajectories [39]. Although the solution process is based on classical mechanics (eq.…”

mentioning

confidence: 99%

Investigation of the high-order harmonic generation for a solid with a defect by Bohmian trajectories

Pan

et al. 2022

EPL

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We theoretically investigate the high-order harmonic generation (HHG) for solid by solving the one-dimensional time-dependent Schrödinger equation. The numerical results with the potential well depth of the defect V1 = 0.35 a.u. and V1 = 0.31 a.u. are demonstrated. The intensity of the second plateau of the harmonic spectra can be enhanced with the small potential well depth of the defect. We investigate the emission time of harmonics in terms of the time-frequency analysis, which shows that, with the potential well depth of the defect V1 = 0.31 a.u., one emission peak is weakened and other is enhanced. By analyzing the time evolution of the electronic probability density distribution and the Bohmian trajectories, the electrons ionized in the negative-x direction will directly through the defect to the positive-x direction, which is diﬀerent from the potential well depth of the defect V1 = 0.35 a.u.. In addition, we show a velocity curve to illustrate further the movement process of the ionized electrons.

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Exploration of the high-order harmonic generation from periodic potentials by Bohmian trajectories

Cited by 7 publications

References 44 publications

Lead generation of UPPS inhibitors targeting MRSA: Using 3D- QSAR pharmacophore modeling, virtual screening, molecular docking, and molecular dynamic simulations

Lead generation of UPPS inhibitors targeting MRSA: Using 3D- QSAR pharmacophore modeling, virtual screening, molecular docking, and molecular dynamic simulations

Modifying the Electron Dynamics in High-Order Harmonic Generation via a Two-Color Laser Field

Investigation of the high-order harmonic generation for a solid with a defect by Bohmian trajectories

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