Article
Materials Science, Multidisciplinary
Jacob A. Marks, Michael Schueler, Jan C. Budich, Thomas P. Devereaux
Summary: The study investigates charge pumping near order-obstructed topological phases where quantized charge pumping is still possible even in the presence of strong correlations and spontaneous symmetry breaking. The presence of orbital charge density wave order in the model's ordered phase assists in this quantized charge pumping, demonstrating the collective nature of this order. Additionally, the study shows that the Thouless pump scenario can be used to uncover the underlying topology of order-obstructed phases.
Article
Materials Science, Multidisciplinary
R. Flores-Calderon, A. Martin-Ruiz
Summary: The study demonstrates that a topological electric current can be induced in Weyl semimetals under an external electric field and chemical potential gradient, providing nearly quantized expressions for nonlinear conductivity tensor. When Fermi levels are close to Weyl nodes, the electrochemical response can be quantized in terms of fundamental constants and scattering time under small tilting. This electrochemical chiral current may be derived from an electromagnetic action similar to axion electrodynamics, indicating a direct consequence of the chiral anomaly.
Article
Physics, Multidisciplinary
Constantin Babenko, Frank Goehmann, Karol K. Kozlowski, Jesko Sirker, Junji Suzuki
Summary: A newly developed thermal form factor expansion method is applied to evaluate real-time longitudinal spin-spin correlation functions of the spin-1/2 XXZ chain in the antiferromagnetically ordered regime at zero temperature. The analytical result obtained incorporates all types of excitations in the model, allowing for accurate calculation of real-time correlations in this strongly interacting quantum system for arbitrary distances and times.
PHYSICAL REVIEW LETTERS
(2021)
Article
Optics
Philip Daniel Blocher, Serwan Asaad, Vincent Mourik, Mark A. Johnson, Andrea Morello, Klaus Molmer
Summary: Out-of-time-ordered correlation functions (OTOCs) are crucial in studying quantum information scrambling, but are difficult to measure experimentally. This study proposes an OTOC measurement protocol that does not rely on time reversal and is applicable to various experimental settings and systems.
Article
Physics, Multidisciplinary
K. Ziegler
Summary: This approach processes data from interferometric measurements on a closed quantum system at random times using a time correlation matrix to extract dynamical properties of the system. Through defining a generalized expectation value, distribution of time scales, average transition time, and correlation time are obtained. A classical limit is identified as separate from quantum fluctuations, which are characterized by resonances associated with poles of the generalized expectation value and linked to quantized Berry phase.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2021)
Article
Materials Science, Multidisciplinary
Y. J. Lu, C. C. Guo, H. S. Huang, J. A. Gao, H. R. Qin, W. H. Wang
Summary: The study investigates the aging process of supercooled Cu50Zr50 glass-forming liquid, revealing a multi-mode dynamics accompanied by a quantized hierarchy of mobile clusters. An aging model is proposed to describe the aging dynamics as a weighted average over quantized dynamic modes. This model predicts the heterogeneous dynamics in aging and equilibration of supercooled metallic liquids, shedding light on the intrinsic aspects influencing the aging process.
Article
Multidisciplinary Sciences
Rafael Carballeira, David Dolgitzer, Peng Zhao, Debing Zeng, Yusui Chen
Summary: The study presents a new evolution equation for two-time correlation functions of a generalized non-Markovian open quantum system based on a modified stochastic Schrodinger equation approach. By simplifying and obtaining the two-time reduced propagator, computation costs can be saved and the converging process accelerated. This method can be widely applied to various open quantum models, particularly large-scale systems, and extend quantum regression theory to the non-Markovian case.
SCIENTIFIC REPORTS
(2021)
Article
Mechanics
Carlo Pagani, Leonie Canet
Summary: In this study, the behavior of the two-point correlation function of a scalar field passively advected by a turbulent flow at large wavenumbers is investigated. Through analysis of the Kraichnan model and the Navier-Stokes equation model, it is found that the two-point correlation function of the scalar decays exponentially with time delay at high wavenumbers, and the prefactor is proportional to k(2). The assumption of delta-correlation in time of the stochastic velocity field in the Kraichnan model significantly alters the statistical temporal behavior of the scalar at small times.
Article
Chemistry, Physical
Shreyas Malpathak, Nandini Ananth
Summary: The mixed quantum classical (MQC)-initial value representation (IVR) is a semiclassical framework that selectively quantizes the modes of a complex system. It accurately reproduces nuclear quantum coherences and conserves zero-point energy in the quantum limit, but is less accurate in the classical limit. By modifying the MQC approach, we show analytically that it is exact for all correlation functions at time zero and numerically demonstrate its correctness in capturing the quantum and classical limits of zero-point energy (ZPE) flow. Interestingly, selective quantization of the system allows for prediction and modification of ZPE flow direction.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Erik Fransson, Mattias Slabanja, Paul Erhart, Goran Wahnstrom
Summary: The perturbative treatments of lattice dynamics are limited for strongly anharmonic systems, metastable crystal structures, and liquids. Molecular dynamics simulations using correlation functions can provide access to the full dynamics of these systems, including dynamical structure factors that bridge the gap to experiment. The dynasor package is a flexible and efficient tool that simplifies the analysis of correlation functions, handling input from major MD packages and allowing for easy extension to support additional codes.
ADVANCED THEORY AND SIMULATIONS
(2021)
Article
Astronomy & Astrophysics
R. Mauland, O. Elgaroy
Summary: This research investigates the size and impact of vortices in a Superfluid Dark Matter (SFDM) model as well as explores the parameter space of the model. It is found that the vortices have a small size and are closely spaced. Varying the parameters of the model reveals that reducing the dark matter particle mass results in larger and more energetic vortices. However, none of the parameter combinations explored here produce vortices with both realistic values and enough energy to have an observational impact on the galaxy as a whole.
JOURNAL OF COSMOLOGY AND ASTROPARTICLE PHYSICS
(2022)
Article
Chemistry, Physical
J. P. Wittmer, A. N. Semenov, J. Baschnagel
Summary: The strain correlation functions in two-dimensional isotropic elastic bodies are found to depend on the direction of the field vector and the orientation of the coordinate system. This dependence cannot be used to indicate anisotropy or plastic rearrangement. It is different for the associated strain response field containing information on the localized stress perturbation.
Article
Optics
Massimo Borrelli, Hans Christian Ottinger
Summary: In this study, we investigate the open dynamics of a chain of interacting spins using the quantized version of a classical out-of-equilibrium thermodynamics equation. We focus on both equilibrium and nonequilibrium scenarios for chains of different sizes. The results show that the system reaches thermal equilibration in the equilibrium case, while in the nonequilibrium dynamics, there is a transition from ballistic to diffusive energy current and a scaling consistent with Fourier's law of heat transfer.
Article
Materials Science, Multidisciplinary
Daegwang Choi, Min Park, Byoung Yong Oh, Min-Sik Kwon, Suk In Park, Sooseok Kang, Jin Dong Song, Dogyun Ko, Meng Sun, Ivan G. Savenko, Yong-Hoon Cho, Hyoungsoon Choi
Summary: We report the direct observation of a single quantized vortex vanishing from a microcavity exciton-polariton superfluid. The competition and change in occupation of exciton-polariton vortices were studied through energy-integrated emission image and time-resolved spectroscopy measurements. The experimental findings are consistent with numerical calculations, providing a platform to investigate nonequilibrium vortex dynamics and manipulate multistate polariton condensates.
Article
Meteorology & Atmospheric Sciences
Facundo L. Poblet, Juha Vierinen, Victor Avsarkisov, J. Federico Conte, Harikrishnan Charuvil Asokan, Christoph Jacobi, Jorge L. Chau
Summary: Measurements of kinetic energy in vortical and divergent fluctuations in the mesosphere and lower thermosphere using radar observations of Doppler shifts of specular meteor trails are introduced. Monthly averages show that the kinetic energy is almost evenly distributed between vortical and divergent modes, with higher turbulence during winter months. The horizontal correlation functions exhibit a 2/3 power law in the horizontal lag direction and suggest the potential use of these functions in estimating turbulent energy transfer rates.
JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES
(2023)
Article
Chemistry, Inorganic & Nuclear
Ayaka Sato, Yuta Hori, Yasuteru Shigeta
Summary: This study characterized the geometrical and electronic structures of the [4Fe-4S] cluster in reduced HiPIP and evaluated their effects on the protein environment using density functional theory (DFT). DFT calculations showed that the asymmetry and spin delocalization between iron atoms allowed for the formation of a unique stable structure. The presence of surrounding amino acids was found to stabilize the unique geometrical and electronic structure of the [4Fe-4S] cluster in HiPIP.
INORGANIC CHEMISTRY
(2023)
Article
Chemistry, Medicinal
Ryuhei Harada, Rikuri Morita, Yasuteru Shigeta
Summary: The free-energy profile of a compound is crucial in evaluating membrane permeation and can be calculated using molecular dynamics simulations. However, existing methods often fail to sample rare events in membrane permeation accurately. In this study, a hybrid conformational search method combining rare-event sampling methods and Markov state models was proposed to calculate the free-energy profiles and membrane permeability of seven compounds with good correlation to experimental measurements.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Naphat Loeanurit, Truong Lam Tuong, Van-Kieu Nguyen, Vipanee Vibulakhaophan, Kowit Hengphasatporn, Yasuteru Shigeta, Si Xian Ho, Justin Jang Hann Chu, Thanyada Rungrotmongkol, Warinthorn Chavasiri, Siwaporn Boonyasuppayakorn
Summary: This study aimed to identify lichen-derived depsides and depsidones as inhibitors of dengue virus. It was found that barbatic acid, diffractaic acid, and Parmosidone C from lichens were effective in inhibiting dengue virus, with diffractaic acid showing the highest selectivity index and similar efficacy against other related viruses.
Article
Chemistry, Physical
Masanori Hashimoto, Koichi Miyagawa, Manish Singh, Kota Katayama, Mitsuo Shoji, Yuji Furutani, Yasuteru Shigeta, Hideki Kandori
Summary: Heliorhodopsins (HeRs), a recently discovered family of rhodopsins, have an inverted membrane topology compared to other rhodopsins. ATR-FTIR spectroscopy studies have demonstrated the binding of Zn2+ to HeR, specifically affecting the structure and function. The specific binding site of Zn2+ was found to be located at the cytoplasmic side of TaHeR.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Medicinal
Natsuki Watanabe, Yuta Hori, Mitsuo Shoji, Mauro Boero, Yasuteru Shigeta
Summary: This study investigates the mechanism of racemization of aspartic acid (Asp) catalyzed by salicylaldehyde and acetic acid using computational approaches. The results reveal the dehydration step and the reaction step to change the chirality of Asp as the main stages of the reaction. The calculated energy diagram demonstrates that the dehydration step has the highest energy barrier, followed by the reaction step to change the chirality of Asp.
Article
Agriculture, Multidisciplinary
Yohei Munei, Kowit Hengphasatporn, Yuta Hori, Ryuhei Harada, Yasuteru Shigeta
Summary: This study revealed the relationship between the dynamic behavior of the C-terminal alpha-helix of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and inhibitor sensitivity through free-energy calculations using molecular dynamics simulations. The results showed that Arabidopsis thaliana HPPD preferred the open form of H11 in the absence of the ligand and the closed-like form in complex with mesotrione, while Avena sativa HPPD exhibited the opposite tendency. Important amino acid residues involved in the dynamic behavior of H11 were also identified.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Chemistry, Physical
So Hirata, Yasuteru Shigeta, Sotiris S. Xantheas, Rodney J. Bartlett
Summary: This article presents a new method for studying helical polymers, which can calculate their energy, structure, and vibrational frequencies. It utilizes Gaussian spherical harmonics basis functions with frequency-dependent Dyson self-energy for infinite helical polymers. This method can handle incommensurable structures and can also predict the properties of infinitely catenated chains of nitrogen or oxygen.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Mitsuo Shoji, Yuya Kitazawa, Akimasa Sato, Natsuki Watanabe, Mauro Boero, Yasuteru Shigeta, Masayuki Umemura
Summary: High enantiomeric excesses (ee's) of L-amino acids, including non-proteinogenic amino acid isovaline (Iva), were discovered in the Murchison meteorite. However, the molecular mechanism responsible for their ee remains unclear. By using accurate ab initio calculations, this study shows that the homochirality of amino acids is produced at the aminonitrile precursors stage.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Shinya Sugiura, Takashi Kubo, Yohei Haketa, Yuta Hori, Yasuteru Shigeta, Hayato Sakai, Taku Hasobe, Hiromitsu Maeda
Summary: Quinoidal molecules based on dipyrrolyldiketone boron complexes (QPBs) with partially conjugated pyrrole units as spin coupler were synthesized. The introduction of a benzo unit at the pyrrole beta-positions stabilized QPB, forming a closed-shell tautomer conformation with near-infrared absorption. By adding bases, the deprotonated species monoanion QPB- and dianion QPB2- were formed, showing over 1000 nm absorption and ion pairs with countercations. Ion-pairing with pi -electronic and aliphatic cations modulated the diradical properties of QPB2-, characterized by cation-dependent hyperfine coupling constants. VT NMR, ESR, and theoretical study revealed the higher stability of the singlet diradical compared to the triplet diradical.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Kowit Hengphasatporn, Thitinan Aiebchun, Panupong Mahalapbutr, Atima Auepattanapong, Onnicha Khaikate, Kiattawee Choowongkomon, Chutima Kuhakarn, Jatuporn Meesin, Yasuteru Shigeta, Thanyada Rungrotmongkol
Summary: This study investigated the kinase inhibitory activities of a series of sulfonylated indeno-[1,2-c]-quinolines (SIQs) against EGFR-TK. Among the 23 SIQ derivatives studied, eight compounds showed enhanced EGFR-TK inhibitory activity compared to erlotinib. In cell-based assays, these eight compounds exhibited more significant cytotoxicity against A431 cells with higher EGFR expression. Overall, the potent SIQ compounds obtained in this work could be further optimized for developing novel anticancer drug candidates targeting EGFR-TK.
Article
Chemistry, Multidisciplinary
Takumi Nakanishi, Yuta Hori, Yasuteru Shigeta, Hiroyasu Sato, Ryoji Kiyanagi, Koji Munakata, Takashi Ohhara, Atsushi Okazawa, Rintaro Shimada, Akira Sakamoto, Osamu Sato
Summary: In this study, a novel tridentate ligand and iron(II) complex with a short hydrogen bond were developed, which allows the control of the positions of two protons in the complex by temperature and photoirradiation. This finding offers a promising approach for developing multiple proton transfer systems in crystals.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Takeshi Murakawa, Kazuo Kurihara, Mitsuo Shoji, Naomine Yano, Katsuhiro Kusaka, Yoshiaki Kawano, Mamoru Suzuki, Yasuteru Shigeta, Takato Yano, Motoyasu Adachi, Katsuyuki Tanizawa, Toshihide Okajima
Summary: Determining the precise locations of hydrogen atoms in enzyme active sites is crucial for understanding the structure-function relationships. This study solved the neutron crystallographic structure of a catalytic intermediate of copper amine oxidase and revealed the protonation/deprotonation state of active-site residues. The results showed that substrate binding triggers conformational changes in the enzyme and facilitates subsequent reactions.
Article
Chemistry, Multidisciplinary
Takeshi Hiromoto, Koji Nishikawa, Seiya Inoue, Hideaki Ogata, Yuta Hori, Katsuhiro Kusaka, Yu Hirano, Kazuo Kurihara, Yasuteru Shigeta, Taro Tamada, Yoshiki Higuchi
Summary: This study reports that [NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F can recover its catalytic activity by reacting with H2 under anaerobic conditions after being inactivated in the presence of O2. Neutron structure analysis revealed that a part of the Ni ion dissociates from the active site Ni-Fe complex and forms a new square-planar Ni complex, accompanied by rearrangement of the coordinated thiolate ligands. The analysis also found that the Cys17(S) thiolate forms an unusual hydrogen bond with the main-chain amide N atom of Gly19(S), providing insights into the redox reaction of the Fe-S cluster.
Article
Chemistry, Physical
Natsuki Watanabe, Mitsuo Shoji, Koichi Miyagawa, Yuta Hori, Mauro Boero, Masayuki Umemura, Yasuteru Shigeta
Summary: Enantiomeric excesses (ee) of l-amino acids in meteorites are found to be higher than 10%, especially for isovaline (Iva), indicating the presence of a triggering mechanism that amplifies the ee from an initially small value. In this study, the dimeric molecular interactions of alanine (Ala) and Iva in solution were investigated at a precise first-principles level, revealing the chirality-dependent nature of Iva's dimeric interaction and providing molecular-level insights into the enantioselectivity of amino acids in solution.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Nalinee Kongkaew, Kowit Hengphasatporn, Yuwanda Injongkol, Pitchayathida Mee-udorn, Liyi Shi, Panupong Mahalapbutr, Phornphimon Maitarad, Ryuhei Harada, Yasuteru Shigeta, Thanyada Rungrotmongkol, Alisa S. Vangnai
Summary: Organophosphate pesticides are widely used in agriculture, but they can be lethal to humans. By designing and evaluating a series of analogs, researchers have discovered a new compound with potential for treating organophosphate poisoning, as well as appropriate drug-like properties and blood-brain barrier penetration.
