Article
Physics, Fluids & Plasmas
Kento Yasuda, Kenta Ishimoto
Summary: In this study, the extremum conditions for the most probable transition path of a free active Brownian particle (ABP) on a two-dimensional plane are derived using the Onsager-Machlup integral and its variational principle. The nonuniqueness of these conditions is demonstrated through an analogy with the pendulum equation, indicating the existence of possible multiple paths. The shape of the most probable path changes from an I to a U shape with an increase in the transition process time, as revealed by numerical, theoretical, and Langevin simulation analyses.
Article
Mathematics, Interdisciplinary Applications
Michael Romanovsky
Summary: This study investigates the problem of the most probable distributions on energy in a combinatorial formulation. It considers the natural hypotheses regarding conservation laws and obtains the particle distributions on the maximum and minimum energies, which can be interpreted as a sorting of particles based on their statistical mechanics behavior.
CHAOS SOLITONS & FRACTALS
(2022)
Article
Engineering, Mechanical
Ioannis Petromichelakis, Rubia M. Bosse, Ioannis A. Kougioumtzoglou, Andre T. Beck
Summary: This paper introduces the Wiener path integral (WPI) technique for stochastic response of nonlinear systems, proposes a Newton's optimization scheme for determining the most probable path, and demonstrates the convexity and unique global minimum of the objective function of the system through computational algebraic geometry concepts. The numerical examples show that the proposed scheme converges to the globally optimum most probable path, and comparisons with Monte Carlo simulation data confirm the reliability of the WPI technique.
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
(2021)
Article
Multidisciplinary Sciences
Devin T. Edwards, Marc-Andre Leblanc, Thomas T. Perkins
Summary: Single-molecule force spectroscopy was used to study protein folding dynamics, revealing intrinsic changes in protein folding dynamics and transition state height under different pH conditions. Despite differences in destabilization mechanisms, constant-force landscapes showed minimal differences in transition state height, while force-dependent rates increased as pH decreased. This study provides insights for future AFM-based studies of mechanoresponsive proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Machiko Katori, Shoi Shi, Koji L. Ode, Yasuhiro Tomita, Hiroki R. Ueda
Summary: By analyzing a large-scale dataset of human sleep phenotypes, we identified 16 sleep phenotypes, including social jet lag, chronotypes (morning/night person), and seven different insomnia-like phenotypes. These analyses contribute to the advancement of research on genetic and environmental factors underlying human sleep patterns, and offer potential for the development of digital biomarkers for psychiatric disorders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Medicinal
Karnesh Jain, Othman Ghribi, Jerome Delhommelle
Summary: The misfolding and aggregation of alpha-synuclein play a crucial role in neurodegenerative disorders, with the formation of fibrils involving various intermediates. Simulation results show that conformational rearrangements of alpha-synuclein at physiological temperature mainly exhibit alpha-helix structures. These findings provide valuable insights for understanding the formation of oligomers in neurodegenerative diseases.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Multidisciplinary Sciences
Ze Zhou, Mary-Jane L. Ma, Rebecca W. Y. Chan, W. K. Jacky Lam, Wenlei Peng, Wanxia Gai, Xi Hu, Spencer C. Ding, Lu Ji, Qing Zhou, Peter P. H. Cheung, Stephanie C. Y. Yu, Jeremy Y. C. Teoh, Cheuk-Chun Szeto, John Wong, Vincent W. S. Wong, Grace L. H. Wong, Stephen L. Chan, Edwin P. Hui, Brigette B. Y. Ma, Anthony T. C. Chan, Rossa W. K. Chiu, K. C. Allen Chan, Y. M. Dennis Lo, Peiyong Jiang
Summary: Using a non-negative matrix factorization algorithm, this study identified distinct types of cfDNA cleavage patterns based on different end motifs. These profiles were associated with specific DNA nucleases and could be used to diagnose autoimmune disorders and cancer.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Konstantin Roeder, David J. Wales
Summary: This paper discusses the energy landscape perspective and biomolecules with multiple functions. Understanding the organization of the energy landscape provides new insights into function. Conformational selection and induced fit may serve as alternative routes to achieve multifunctionality.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Physics, Multidisciplinary
Jinlian Jiang, Wei Xu, Ping Han, Lizhi Niu
Summary: This paper explores the effects of stochastic perturbations and periodic excitations on the eutrophicated lake ecosystem. It presents the most probable transition paths to characterize the regime shifts and describes the global transition behavior of the system.
Review
Materials Science, Multidisciplinary
A. R. Jayakrishnan, J. P. B. Silva, K. Kamakshi, D. Dastan, V Annapureddy, M. Pereira, K. C. Sekhar
Summary: Dielectric capacitors offer high-power density and ultrafast discharging times, making them potential candidates for pulsed power technologies. However, low energy density in different dielectric materials limits their real time applications. Relaxor ferroelectrics have emerged as the most promising solution for energy storage capacitors. This review discusses the latest developments on lead-free relaxor ferroelectrics and strategies to enhance their energy storage performance.
PROGRESS IN MATERIALS SCIENCE
(2023)
Article
Engineering, Electrical & Electronic
Zhaowei Zhang, Lin Liu, Hui Liu, Zhenyu Wu, Xiaoye Shi, Su Pan
Summary: In this paper, a comb-search and hierarchical-clustering (CSHC) based Doppler-shift acquisition scheme is proposed to address the energy dispersion problem in space communications. The scheme decreases noise energy by comb-search and increases signal energy by hierarchical-clustering, significantly improving the acquisition probability.
IEEE TRANSACTIONS ON VEHICULAR TECHNOLOGY
(2023)
Article
Materials Science, Multidisciplinary
Xinyi Wang, Francesco Maresca, Penghui Cao
Summary: This study constructs and reports the potential energy landscape governing screw dislocation motion in high-entropy alloys (HEAs). It reveals a hierarchical and multilevel structure, which retards dislocation movement and can be regulated by introducing chemical short-range order.
Article
Multidisciplinary Sciences
Rohit Jain, Khaja Muneeruddin, Jeremy Anderson, Michael J. Harms, Scott A. Shaffer, C. Robert Matthews
Summary: The study revealed the folding mechanisms of bacterial IGPS TIM barrel enzyme using HDX-MS, identifying protected sites and stable cores, and emphasizing the key role of hydrophobicity in stabilizing high-energy folding intermediates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Korak Kumar Ray, Colin D. Kinz-Thompson, Jingyi Fei, Bin Wang, Qiao Lin, Ruben L. Gonzalez
Summary: Biomolecular machines utilize thermal and chemical energy to perform cellular processes, and they require dynamic rearrangements of structural components. The physical and structural mechanisms through which ligands achieve repurposing of these dynamics remain unknown.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Hisashi Ishida, Hidetoshi Kono
Summary: Nucleosome reconstitution is crucial for cellular functions, and the displacement of the H2A-H2B dimer is a key step. In this study, adaptive biased molecular dynamics and umbrella sampling simulations were used to investigate the free energy landscape of the dimer displacement. The docking domain of H2A and the C-terminal of H4 were identified as the main contributors to the free energy. The extent of nucleosomal DNA wrapping determined the different paths for the dimer displacement, suggesting that external factors such as histone chaperones can modulate the displacement path. Additionally, key residues involved in the free energy were found to be related to nucleosome assembly, reassembly, and posttranslational modifications (PTMs) in cancer cells.
JOURNAL OF MOLECULAR BIOLOGY
(2022)