Article
Chemistry, Physical
Sapana V. Shedge, Tim J. Zuehlsdorff, Ajay Khanna, Stacey Conley, Christine M. Isborn
Summary: This research focuses on simulating the linear and nonlinear spectra of chromophores in condensed phase systems, combining various methods to overcome challenges in capturing vibronic transitions and specific chromophore-environment interactions. Three approaches of different computational costs are presented for simulating linear spectra, with two analogous approaches for nonlinear spectra. Results include simulated absorption spectra and two-dimensional electronic spectra for the Nile red chromophore in different solvent environments.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Xuan Leng, Peng Lei, Wen-zhao Zhang
Summary: The absorption and two-dimensional rephasing spectra of the Fenna-Matthews-Olson (FMO) complex at 77K were simulated using hierarchical equations of motion method. Three cases of vibrational coupling were studied in the FMO complex model, showing that the vibrational mode significantly weakens the intensity of the absorption peak of high-energy electronic transitions. It was also observed that long-lived quantum beatings originate from vibration, while short-lived electronic coherence still exists. Furthermore, the speed-up of rephasing dynamics by electronic resonance mode is not directly proportional to the coupling strength, and the low-energy electronic-vibrational resonance dimer exhibits a greater speed-up.
Article
Environmental Sciences
Ruisi Huang, Hongyu Cao, Ting Huang, Hongjiang Li, Qian Tang, Lihao Wang, Xuefang Zheng
Summary: The abuse of fluoroquinolones antibiotics causes resistance and pollution. This study investigates the photodegradation mechanisms and environmental factors affecting the degradation of fleroxacin. Six possible photodegradation reaction paths were proposed and simulated. The main reactions involve the departure of the piperazine ring and the substitution of fluorine atom. Factors such as pH and substances like NaN3 and Ca2+ were found to influence the photodegradation process.
Article
Chemistry, Multidisciplinary
Yuta Yamamoto, Yasuteru Shigeta
Summary: In this study, the authors conducted conformational analysis of hCtBP2 using a machine learning-based method called random-forest fragment molecular orbital (RF-FMO). RF-FMO identified three important amino acid residues that play a role in the conformational changes during the transition between the open and closed states of hCtBP2, through molecular dynamic simulations and FMO calculations.
Article
Chemistry, Physical
Vladislav Slama, Frank Mueh, Thomas Renger, Torng Mancal
Summary: We proposed an extension of the QM/MM approach to investigate the excited state properties of embedded systems under environmental effects. Our model, based on perturbation theory, allows a more general description of the environment, considering frequency-dependent atomic polarizabilities. By comparing with full quantum chemistry calculations and standard polarizable QM/MM approach, we demonstrated the importance of frequency dependence for accurately treating the effects of the environment on transition energy shifts and interaction energies.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Materials Science, Ceramics
Buda Li, Menglu Li, Hangbo Qi, Siqin Zhao, Shan Feng, Xiaotao Zu, Liang Qiao, Haiyan Xiao
Summary: In this research, the effects of tungsten doping on the structural, electronic, and mechanical properties of Bi2O2Se were investigated using the first-principles method. It was found that tungsten doping had a significant impact on the electronic structure and mechanical properties of Bi2O2Se. The doped Bi2O2Se exhibited metallic-like character with electrons distributed on the Fermi level. Additionally, tungsten doping improved the ductility and toughness of Bi2O2Se while reducing its lattice thermal conductivity. This study demonstrates the effectiveness of tungsten doping in engineering the physical properties of Bi2O2Se.
JOURNAL OF THE AMERICAN CERAMIC SOCIETY
(2023)
Article
Chemistry, Physical
Aleena Mustafai, Ajaz Hussain, Muhammad Yar, Riaz Hussain, Khurshid Ayub, Muhammad Imran, Mohammed A. Assiri
Summary: The physisorption of pollutant gases (NH3, HCN, H2S and PH3) on TQBQ-COF has been studied using DFT calculations. Various analysis methods were used to determine the strength and nature of interactions, including interaction energy, NCI-RDG plots, FMO, NBO, EDD, and QTAIM analysis. The results showed that TQBQ-COF exhibited high sensitivity towards H2S and NH3 adsorption, and weak van der Waals forces were present in all complexes.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Business, Finance
Jun Huang, Feifei Han, Yun Li
Summary: This study examines how the government's participation in the product market as a customer affects supplier firms' environmental, social, and governance (ESG) practices. Using a sample of Chinese listed firms from 2010 to 2020, we find that firms with major government customers exhibit higher ESG performance than those without them. Further analysis shows that female managers, institutional ownership, media coverage, and public attention enhance the positive relationship between major government customers and ESG performance. Overall, the findings suggest that as an important public policy, government procurement can significantly affect stakeholders' value by improving supplier firms' ESG performance.
FINANCE RESEARCH LETTERS
(2023)
Article
Materials Science, Multidisciplinary
Y. Zhao, T. Suzuki, T. Iimori, H-W Kim, J. R. Ahn, M. Horio, Y. Sato, Y. Fukaya, T. Kanai, K. Okazaki, S. Shin, S. Tanaka, F. Komori, H. Fukidome, I Matsuda
Summary: The carrier dynamics in various types of epitaxial graphene layers on SiC substrates were studied using TARPES. Layer-dependent electron doping was observed in the Dirac bands of quasicrystalline bilayer graphene, resulting in the generation of transient voltage between the upper and lower layers. The amount of photoinduced carrier transport depends on the distance from the substrate. Comparison of TARPES results between flat and stepped SiC substrates suggests that the doping carriers likely originate from interface step states.
Article
Business
Chenxiao Wang, Israr Qureshi, Feng Guo, Qingpu Zhang
Summary: This study explores how corporate social responsibility (CSR) affects disruptive innovation under various degrees of environmental turbulence. The empirical results indicate that CSR (external and internal CSR) positively affects disruptive innovation, with technological turbulence positively moderating this relationship. However, market turbulence negatively moderates the relationship between external CSR and disruptive innovation.
JOURNAL OF BUSINESS RESEARCH
(2022)
Article
Physics, Fluids & Plasmas
Alejandro Almodovar, Tobias Galla, Cristobal Lopez
Summary: The effects of stochastic birth and death processes on the structural phases of systems of active and passive Brownian particles subject to volume exclusion were studied. Liquid, hexatic, and solid phases were found as the birth and death parameters varied. Motility-induced phase separation occurred for active particles at large activity and sufficiently small birth rates, while the phases for passive particles were spatially homogeneous. A reentrant transition to the hexatic phase was observed when the birth rate was increased.
Article
Materials Science, Multidisciplinary
Geoffrey Pirard, Francesco Basso Basset, Sergio Bietti, Stefano Sanguinetti, Rinaldo Trotta, Gabriel Bester
Summary: We used atomistic, million-atom screened pseudopotential theory and experimental characterization to study self-assembled GaAs/AlxGa1-xAs(111) quantum dots. Our numerical calculations showed that random alloy disorder in the barrier can cause symmetry breaking and result in a nonzero exciton fine structure splitting (FSS). However, we found that the emission wavelength and FSS can be simultaneously tuned without affecting the radiative lifetime by varying the concentration of aluminum in the alloyed barrier. Additionally, the optical properties of the quantum dots are robust against shape elongation.
Article
Physics, Multidisciplinary
Ze Ruan, Xiu-Cai Jiang, Ze-Yi Song, Yu-Zhong Zhang
Summary: The study revisits the groundstate magnetism of the one-band Hubbard model on the frustrated square lattice considering both nearest-neighbour and next-nearest-neighbour hoppings at half-filling within mean field approximation. Two new magnetic phases, named double-stripe and plaquette antiferromagnetic states, are detected at intermediate Hubbard U strength and relative strong frustration of hopping ratios, which are metallic and stable even at finite temperature and electron doping. The analysis of phase transitions between different phases and properties of the new states suggests that the observed distinct antiferromagnetism in cuprates and iron-based superconductors may have a unified microscopic origin despite orbital degrees of freedom or further hopping distances.
NEW JOURNAL OF PHYSICS
(2021)
Article
Psychology, Clinical
Min Tan, Mei Li, Hui'e Li, Jin Li, You Chang, Guanfei Zhang, Yiping Zhong
Summary: The study showed that in private situations, individuals low in materialism were more likely to engage in pro-environmental behaviors involving other-benefit appeals compared to those high in materialism. However, in public situations, the effects of self-benefit and other-benefit appeals on the pro-environmental behavior of materialistic individuals were similar.
PSYCHOLOGY RESEARCH AND BEHAVIOR MANAGEMENT
(2022)
Article
Materials Science, Multidisciplinary
Muhammad Haroon, Muhammad Khalid, Zahid Shafiq, Muhammad Usman Khan, Muhammad Ramzan Saeed Ashraf Janjua
Summary: Thiazoline derivatives have been synthesized and characterized, exhibiting excellent concurrence between experimental and computational results. The molecules showed promising NLO characteristics, with 5a being the most reactive and 5c the most stable among the investigated compounds. Overall, these derivatives are suitable for applications in NLO properties and optoelectronic devices for the next generation.
MATERIALS TODAY COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Leopoldo Mejia, Ulrich Kleinekathoefer, Ignacio Franco
Summary: Under resonant transport conditions, the accuracy of the Landauer approximation depends on intramolecular interactions, while under nonresonant conditions, the emergence of transport routes beyond Landauer is determined by charging and discharging processes at the electrode-molecule interface. In both cases, decreasing the rate of charge exchange between the electrodes and molecule and increasing the interaction strength with the thermal environment result in decreased accuracy of Landauer.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Pooja Sarngadharan, Sayan Maity, Ulrich Kleinekathoefer
Summary: This study evaluates the excitation energy, spectral density, and linear absorption spectra of the core antenna complex CP43 in photosystem II using a multiscale approach. It combines quantum mechanics/molecular mechanics molecular dynamics simulations and time-dependent long-range-corrected DFTB scheme. The results show good agreement with experimental findings, highlighting the importance of combining diverse techniques for obtaining first-principle results.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Abhishek Acharya, Jigneshkumar Dahyabhai Prajapati, Ulrich Kleinekathofer
Summary: Biological nanopores are important in biological processes and technological applications. Recent studies have focused on antibiotic permeation and analyte sensing, using atomistic simulations to understand solute dynamics and protein interactions. However, successful utilization of nanopores is still limited.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
K. Rajput, B. R. Mehta, U. Kleinekathofer, T. Frauenheim, D. R. Roy
Summary: This study proposes an alternative to conventional silicon technology by studying the potential of inorganic analogues in molecular electronics. The structure, electronic, and transport properties of nitride analogues are analyzed and compared with organic counterparts. The results demonstrate the potential advantages of inorganic analogues in nanoelectronics applications.
MATERIALS TODAY CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Esha V. Shah, Ulrich Kleinekathoefer, Thomas Frauenheim, Debesh R. Roy
Summary: This study proposes a novel pathway of observing transverse transport through nucleobase-pairs of a DNA molecule and finds that the single base-pair G-C and its parallel circuit exhibit superior transport in DNA wires. In comparison with a short DNA molecule, the parallel base-pair circuits enhance transport through quantum interference.
MATERIALS TODAY CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Jiajun Wang, Jigneshkumar Dahyabhai Prajapati, Fan Gao, Yi-Lun Ying, Ulrich Kleinekathoefer, Mathias Winterhalter, Yi-Tao Long
Summary: Chirality is important but often overlooked in biological and chemical processes due to technical limitations. Researchers have used an electrostatically asymmetric membrane channel to successfully identify chiral amino acids in single peptides. This study provides a new approach for developing chiral recognition and protein sequencing methods.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Review
Plant Sciences
Sayan Maity, Ulrich Kleinekathoefer
Summary: This mini review focuses on recent advances in the atomistic modeling of biological light-harvesting (LH) complexes. Multiscale methods are required to investigate the dynamical and spectroscopic properties of LH complexes due to their size and sophisticated electronic structures. The recently developed multiscale approach based on the density functional tight-binding framework has shown superior performance in describing the internal vibrational dynamics of pigment molecules and yields spectral densities in good agreement with experimental data.
PHOTOSYNTHESIS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Smrithi R. Krishnan, Kalyanashis Jana, Amina H. Shaji, Karthika S. Nair, Anjali Devi Das, Devika Vikraman, Harsha Bajaj, Ulrich Kleinekathoefer, Kozhinjampara R. Mahendran
Summary: In this study, a transmembrane pore DpPorA was developed based on the natural pore PorACj using D-amino acid alpha-helical peptides. The DpPorA peptides were found to self-assemble into uniform cation-selective pores in lipid membranes and exhibited properties distinct from their L-amino acid counterparts. Molecular dynamics simulations further revealed the specific structure and conformation of the D-pores. These findings provide valuable insights for the design of complex pores for single-molecule sensing technologies.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Claudio Piselli, Vinaya Kumar Golla, Roland Benz, Ulrich Kleinekathoefer
Summary: This study focuses on the characterization of the lysine cluster in OprO, a porin protein in the outer membrane of Pseudomonas aeruginosa. The importance of lysine residues in ion conductance and phosphate ion flow was demonstrated through experiments and simulations. The results suggest that an improved understanding of lysine residues and ion mobility could lead to the development of more effective antibiotics for P. aeruginosa.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2023)
Article
Chemistry, Medicinal
Abhishek Acharya, Ishan Ghai, Claudio Piselli, Jigneshkumar Dahyabhai Prajapati, Roland Benz, Mathias Winterhalter, Ulrich Kleinekathoefer
Summary: In this study, the molecular mechanism of an antibiotic permeating through a bacterial channel is revealed, with a focus on the role of conformational dynamics of the constriction loop. The dynamics of the L3 loop, specifically the F118 to S125 segment, at the constriction regions of the OmpF porin is investigated using temperature accelerated sliced sampling approach. The importance of hydrogen-bond stabilization in the conformational dynamics of the L3 loop is demonstrated through single channel electrophysiology experiments and applied-field simulations. The findings suggest that conformational dynamics of the constriction loop may play a general role in antibiotic permeation through porins.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biophysics
Abhishek Acharya, Kalyanashis Jana, Dominik Gurvic, Ulrich Zachariae, Ulrich Kleinekathofer
Summary: Predicting molecular permeability and evaluating the effect of molecular transformations on permeation rates are critical for the development of effective antibiotics. In this study, a computational approach using Brownian dynamics is proposed to obtain estimates of molecular permeability through a porin channel within hours. The method is significantly faster compared with previous approaches and shows good correlation with experimental results. The potential applications of this method in high-throughput screening for fast permeators are discussed.
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Physical
Yannick Holtkamp, Markus Kowalewski, Jens Jasche, Ulrich Kleinekathofer
Summary: The theory of open quantum systems is important for understanding various processes in nature. Machine learning techniques have been developed to reduce computational effort in accurately describing dissipative quantum dynamics. However, previous methods require expensive training datasets, limiting their use for larger systems. In this study, a new machine-learned correction term is introduced, trained on data from numerically feasible small systems. It outperforms a previously handcrafted correction and improves the determination of dissipative quantum dynamics for larger systems.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Vivin Vinod, Sayan Maity, Peter Zaspel, Ulrich Kleinekathoefer
Summary: Accurate and fast calculation of molecular excited states remains a challenging topic. This study proposes a multifidelity machine learning approach that combines a small amount of highly accurate training data with cheaper and less accurate data to achieve high accuracy. The approach is applied to predict vertical excitation energies for three molecules, benzene, naphthalene, and anthracene, and achieves comparable accuracy to a machine learning model built solely on high-cost training data.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Jan P. Goetze, Sayan Maity, Ulrich Kleinekathoefer
Summary: This study investigates the FRET between the FMO protein complex and the CBP using an idealized model. It is found that the FRET efficiency is independent of the FMO trimer orientation, indicating that FMO acts as a robust spatial funnel for CBP excitation harvesting.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Multidisciplinary Sciences
Javier Abellon-Ruiz, Kalyanashis Jana, Augustinas Silale, Andrew M. Frey, Arnaud Basle, Matthias Trost, Ulrich Kleinekathoefer, Bert van den Berg
Summary: The uptake of vitamin B-12 is important for the colonization of the gut by Bacteroides species. In this study, the authors investigate the B-12 uptake in Bacteroides thetaiotaomicron, showing that it is mediated by stable outer membrane protein complexes consisting of surface-exposed BtuG lipoproteins and BtuB TonB-dependent transporters.
NATURE COMMUNICATIONS
(2023)
