Article
Biochemistry & Molecular Biology
Jesus Perez-Juarez, Juana Virginia Tapia-Vieyra, Gabriel Gutierrez-Magdaleno, Nuria Sanchez-Puig
Summary: Mutations in EFL1 and SBDS genes may lead to the occurrence of Shwachman-Diamond Syndrome, affecting the maturation process of ribosomal subunits. The study of yeast Efl1 R1086Q mutation provides insights into its impact on ribosome maturation.
Article
Geriatrics & Gerontology
Xiaoxin Wu, Xiwei Fan, Ross Crawford, Yin Xiao, Indira Prasadam
Summary: The function of articular cartilage relies on the coordinated metabolic regulation in chondrocytes. Dysregulation of cellular metabolism can lead to degenerative diseases like osteoarthritis. Chondrocytes in cartilage have limited access to nutrients and oxygen, as well as pathways for metabolite removal. Central carbon metabolism pathways are crucial for maintaining cartilage homeostasis. Increased understanding of cellular metabolism and its dysregulation in osteoarthritis can provide insights into potential therapeutic opportunities.
Article
Nanoscience & Nanotechnology
Dong Li, Yujie Han, Yanrong Jiang, Guanyu Jiang, Haitao Sun, Zhenrong Sun, Qi-Wei Zhang, Yang Tian
Summary: This study introduces a model for precise manipulation of molecular conformation through host-guest interactions, avoiding side reactions and fatigue accumulation while maintaining excellent reversibility. The molecule's conformation states can be visualized and identified by luminous readout, enabling real-time self-reporting. Additionally, it exhibits valuable functions such as controllable multicolor emission and ratiometric fluorescent thermosensing with high temperature resolution.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Physical
Zhongmin Zhang, Zhiyue Lu
Summary: This research presents a general geometric nonequilibrium theory to explain anomalous catalytic behaviors driven by rapidly oscillating environments. It also proposes a novel design principle for catalysts with oscillation-pumped performances. By encoding the reaction kinetics over a range of control parameters, the control-conjugate landscape simplifies the design principle applicable to large-amplitude environmental oscillations.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Materials Science, Multidisciplinary
John D. Shimanek, Shipin Qin, Shun-Li Shang, Zi-Kui Liu, Allison M. Beese
Summary: A method integrating first-principles calculations is proposed to predict the strain-hardening behavior of pure Ni single crystals. The study found that elastic interactions of pure edge dislocations capture hardening behavior for small strains, while a strain-weighted linear combination of edge and screw flow resistance components captures hardening behavior for larger strains.
Article
Chemistry, Physical
Tokio Watanabe, Hirokazu Yagi, Saeko Yanaka, Takumi Yamaguchi, Koichi Kato
Summary: This research developed a non-linear multivariate analysis using a kernel method to classify the conformations of oligosaccharides, allowing for a systematic comparison and understanding of the contributions of intraresidue conformational factors to their global dynamics. It sheds light on exploring the conformational spaces of oligosaccharides and other molecules with high degrees of motional freedom.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Materials Science, Multidisciplinary
Katherine Inzani, Nabaraj Pokhrel, Nima Leclerc, Zachary Clemens, Sriram P. Ramkumar, Sinead M. Griffin, Elizabeth A. Nowadnick
Summary: Atomic-scale control of spins by electric fields is highly desirable for future technological applications. Magnetically doped Aurivillius-phase oxides present one route to achieve this, with magnetic ions substituted into the ferroelectric structure at dilute concentrations, resulting in spin-charge coupling. However, there has been minimal exploration of the ferroelectric switching pathways in this materials class, limiting predictions of the influence of an electric field on magnetic spins in the structure.
Article
Biochemistry & Molecular Biology
Yu-Cheng Liu, Dah-Yen Yang, Sheh-Yi Sheu
Summary: G-quadruplexes have become attractive drug targets in cancer therapy, but the polymorphic nature of their structures makes understanding their conformational conversion mechanisms challenging. This study used molecular dynamics simulation to show that as salt concentration increases, the mechanism of conformational conversion shifts from multi-pathway to sequential pathways, with conformational conversion being more feasible upon K+ binding compared to Na+ binding in high-salt solutions.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Physics, Applied
Artem Chmeruk, Maribel Nunez-Valdez
Summary: In this study, the magnetic ordering and the effect of pressure on manganese sulfide polymorphs were investigated using first-principles calculations. The results showed good agreement with experimental observations, especially for paramagnetic MnS. It was found that a structural transformation occurred in MnS at a pressure of approximately 21 GPa.
JOURNAL OF APPLIED PHYSICS
(2022)
Article
Neurosciences
Xuan Li, Patrick Friedrich, Kaustubh R. Patil, Simon B. Eickhoff, Susanne Weis
Summary: The study proposes a topography-based predictive framework (TOPF) for identifying individual-specific evoked activity topographies and predicting behavior. The TOPF approach effectively captures individual differences in brain activity and predicts phenotypes across cognition, emotion, and personality. This method is important for advancing our understanding of the brain-behavior relationship.
Article
Physics, Applied
Yuemei Sun, Li Yuan, Xiaoqin Zhu, Weihua Wu, Yifeng Hu, Zhitang Song
Summary: The crystalline-amorphous-crystalline transition process of an oxygen-tuned Sb phase-change material has been studied using ab initio molecular dynamic calculations. The introduction of impurity oxygen atoms breaks the linear arrangement of Sb atoms and changes the electronic structure, improving the amorphous stability and data retention.
JOURNAL OF APPLIED PHYSICS
(2022)
Article
Engineering, Marine
Zhichao Hu, Junmin Mou, Linying Chen, Xuefei Jia, Pengfei Chen
Summary: In this paper, a novel smart tug escorting mode is proposed to achieve energy conservation while ensuring the safe navigation of the serviced ship. A green and smart framework is presented for energy-saving escorting. An escorting model is established to describe the dynamics of the tug and the relation between the tug and the serviced ship. Reference trajectories are planned collaboratively and the Model Predictive Control (MPC) scheme is adopted for tug trajectory tracking. Simulation results show the energy conservation potential of the proposed framework.
Review
Chemistry, Multidisciplinary
Franois Mouvet, Justin Villard, Viacheslav Bolnykh, Ursula Rothlisberger
Summary: This article introduces three methods to improve the efficiency of FPMD simulations, including an efficient implementation of FPMD-QM/MM simulations, specially devised multiple-time-step algorithms, and machine learning models. These methods significantly speed up FPMD simulations while preserving real-time dynamics and accuracy.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Article
Energy & Fuels
Xin Zhang, Yanan Wei, Xingzheng Liu, Linqing Qin, Na Yu, Zheng Tang, Zhixiang Wei, Qinqin Shi, Aidong Peng, Hui Huang
Summary: Isomeric effects were systematically studied on unfused-ring electron acceptors, leading to the discovery of the PBDB-T:NOF-3 based device with higher power conversion efficiency and stable performance. These findings suggest that isomeric effects play a crucial role in designing high-performance UREAs.
Article
Energy & Fuels
Lalitha Subramanian, Vincent Debusschere, Hoay Beng Gooi, Nouredine Hadjsaid
Summary: The research aims to optimize the use of limited heterogeneous flexibilities in the system for grid-support functions and avoid additional investment by proposing a cooperative receding horizon control method. By replacing the conventional linear state-space model with a novel rate-based model, offset errors are eliminated. The proposed cooperative predictive control strategy has been demonstrated on a power hardware-in-the loop platform with a simulated microgrid system, showing the effectiveness of the control solution.
IEEE TRANSACTIONS ON ENERGY CONVERSION
(2021)
Article
Biochemistry & Molecular Biology
Quentin R. Johnson, Richard J. Lindsay, Ricky B. Nellas, Elias J. Fernandez, Tongye Shen
Article
Physics, Multidisciplinary
Emmanuel Trizac, Tongye Shen
Article
Chemistry, Physical
Alexander K. Clark, J. Heath Wilder, Aaron W. Grayson, Quentin R. Johnson, Richard J. Lindsay, Ricky B. Nellas, Elias J. Fernandez, Tongye Shen
JOURNAL OF PHYSICAL CHEMISTRY B
(2016)
Article
Biochemistry & Molecular Biology
Quentin R. Johnson, Richard J. Lindsay, Ricky B. Nellas, Tongye Shen
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2016)
Article
Chemistry, Physical
Richard J. Lindsay, Jan Siess, David P. Lohry, Trevor S. McGee, Jordan S. Ritchie, Quentin R. Johnson, Tongye Shen
JOURNAL OF CHEMICAL PHYSICS
(2018)
Article
Chemistry, Multidisciplinary
Quentin R. Johnson, Richard J. Lindsay, Tongye Shen
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2018)
Article
Biochemistry & Molecular Biology
Richard J. Lindsay, Bill Pham, Tongye Shen, Rachel Patton McCord
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Bill Pham, Richard J. Lindsay, Tongye Shen
Article
Chemistry, Medicinal
Bill Pham, Avery Bancroft Arons, Jeremy G. Vincent, Elias J. Fernandez, Tongye Shen
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2019)
Article
Biochemistry & Molecular Biology
Richard J. Lindsay, Rachael A. Mansbach, S. Gnanakaran, Tongye Shen
Summary: The conformational ensemble of intrinsically disordered proteins, such as α-synuclein, is crucial for understanding and preventing pathologies. Under low pH conditions, neutralization of negatively charged residues leads to compaction of the C-terminal portion of α-synuclein, while internal reorganization allows it to maintain its overall end-to-end distance.
BIOPHYSICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Priyojit Das, Tongye Shen, Rachel Patton McCord
Summary: Chromosome structures vary between different cell types and regions, and are influenced by factors such as epigenetic state.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Bill Pham, Ziju Cheng, Daniel Lopez, Richard J. Lindsay, David Foutch, Rily T. Majors, Tongye Shen
Summary: This study examines the receptor-ligand interaction patterns of the ROR gamma receptor and identifies key contacts essential to its constitutive activity. By analyzing crystal structures and performing computer simulations, the differences between agonist and inverse agonist binding are revealed. These findings have implications for the development of new drugs.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
David Foutch, Bill Pham, Tongye Shen
Summary: Network analysis is a powerful tool for studying structural biology systems, with network centrality measurements and cluster coefficients helping identify key functional residues in proteins. Eigenvector centrality is sensitive in distinguishing structural features, while closeness centrality is less sensitive and more generic with respect to structural specificity. Modifications to protein structure networks (PSNs) can enhance sensitivity to discern structural changes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Priyojit Das, Tongye Shen, Rachel Patton McCord
BMC BIOINFORMATICS
(2020)
Article
Physics, Fluids & Plasmas
Priyojit Das, Rosela Golloshi, Rachel Patton McCord, Tongye Shen