Article
Engineering, Civil
A. Evkin
Summary: This paper discusses the important property of localization in buckling of spherical shells under external pressure. It is shown that localization is possible for structures with nonlinear softening. An analytical model of local buckling of spherical shell is developed and calculated using the Rayleigh-Ritz method for small and moderate deflections, and the asymptotic method for large deflections. The response of the structure to different types of local perturbations is studied, with special attention to the energy barrier for structure transition. Energy barrier criterion is used to measure the metastability of the structure and estimate the load level separating high and low sensitivity to local perturbations. Formulae for design buckling load are proposed and discussed based on this pressure value. The similarities and differences between local buckling of spherical shells and axially compressed cylindrical shells under external pressure are also discussed.
THIN-WALLED STRUCTURES
(2023)
Review
Biochemistry & Molecular Biology
Rafayel Petrosyan, Abhishek Narayan, Michael T. Woodside
Summary: Single-molecule force spectroscopy (SMFS) is a powerful tool for studying protein folding dynamics, uncovering energy landscapes of folding, complex folding pathways, mechanisms of chaperones in assisting folding, effects of ribosomes on co-translational folding, and monitoring membrane protein folding.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Engineering, Civil
A. Evkin
Summary: This study applies a simple analytical model of spherical shell buckling to investigate the response of the structure to different perturbations represented as random variables. Factors such as probing radial force, energy barrier, and geometrical imperfections are considered to decrease the uniform buckling pressure. The model is further extended to imperfect shells. Monte Carlo method and the propagation of error formula based on Taylor expansion are used to study the uncertainty propagation of these perturbations and its implications in design buckling pressure estimation are discussed.
THIN-WALLED STRUCTURES
(2023)
Article
Chemistry, Organic
Croix J. Laconsay, Dibyendu Mallick, Sason Shaik
Summary: The presence of a copper cation, Cu+, alters the shape of the energy surface in the degenerate Cope rearrangement of semibullvalene. Orbital and electrostatic interactions play a major role in this alteration, with additional external electric fields inducing significant changes in the energy surface. This study is consistent with recent findings that EEFs more readily stabilize/destabilize systems with larger, more polarizable, dipole moments.
JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Thermodynamics
Hongdan Yu, Chen Lu, Wei Liu, Weizhong Chen, Honghui Li, Jiawei Huang
Summary: This study investigates the thermophysical properties of Tamusu mudstone, an important rock for high-level radioactive waste disposal in China. The results show that the thermophysical parameters exhibit significant anisotropic characteristics and are strongly correlated with temperature. These findings can provide essential input parameters for the safety assessment of high-temperature underground facilities.
CASE STUDIES IN THERMAL ENGINEERING
(2023)
Article
Nanoscience & Nanotechnology
Shotaro Hiraide, Homare Arima, Hideki Tanaka, Minoru T. Miyahara
Summary: This study discussed the influence of polymer binders on the adsorption behavior of flexible MOFs, revealing the phenomenon of gate adsorption slacking and analyzing its thermodynamic characteristics through molecular simulations. The results showed that controlling the external force applied to MOF particles is crucial for shaping pellets that meet the requirements of gate adsorption.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Multidisciplinary Sciences
David R. Jacobson, Thomas T. Perkins
Summary: By using an atomic-force-microscope assay optimized for mechanical force to reversibly unfold local regions of an individual protein, researchers overcame limitations of chemical denaturation assays in understanding the energetics of membrane proteins. This approach provided quantitative insight into the Delta Delta G of single amino acid mutations in membrane proteins and highlighted the contribution of membrane protein-lipid contacts to folding energetics. The platform established allows for determining Delta Delta G for fully folded membrane proteins embedded in their native bilayers.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Nabin Kumar Karna, Jakob Wohlert, Anna Liden, Tuve Mattsson, Hans Theliander
Summary: In this study, it is demonstrated that the wettability of cellulose surface can be altered by applying an external electric field, thereby facilitating the dewatering process. The variation in electric field direction and intensity affects the orientational preference of water molecules and interfacial free energy, subsequently influencing the spreading coefficient and contact angle.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2021)
Article
Mathematics, Applied
Donghyun Kim, Ji-Hun Yoon, Chang-Rae Park
Summary: This paper focuses on pricing external barrier options under a stochastic volatility model with a fast mean-reverting process. Through singular perturbation method and Mellin transform technique, an explicit analytical approximated solution for the option price is derived. Numerical experiments verify the accuracy of the pricing model and investigate the sensitivity of option prices to model parameters.
JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS
(2021)
Article
Cell Biology
Yuichi Kondo, Kazuo Sasaki, Hideo Higuchi
Summary: The stepping of single kinesin molecules was measured using optical tweezers, with an improved optical trap using 200-nm beads. The step size of the forward and backward steps was 8.2 nm across various loads. The dwell times of the backward steps and detachment fit well to exponential equations with fast and slow time constants, indicating the presence of both a fast and a slow step.
Article
Physics, Applied
Zhichuan Huang, Ye Hong, Wuyang Lei, Jianxin Liu, Zigang Deng, Yunhua Shi, David A. Cardwell
Summary: High temperature superconducting (HTS) maglev technology has attracted attention due to its advantages of frictionless transportation, low noise, and environmental protection. This paper reports experiments on the dynamic guidance force of Y-Ba-Cu-O (YBCO) and Gd-Ba-Cu-O (GdBCO) bulk HTS single grains. The results show that GdBCO has better stability and recovery ability of the guidance force compared to YBCO under the same conditions, indicating its greater potential for practical application in HTS maglev.
JOURNAL OF PHYSICS D-APPLIED PHYSICS
(2022)
Article
Engineering, Marine
Tao Li, Peng Xie, Xiaotian Li
Summary: This study presents a universal plastic ring-beam model considering the longitudinal stretching effect in the transition zone. The improved model provides more accurate solutions for the pipe's propagation pressure problem, especially for medium-thick or thin-walled pipes. The proportion of longitudinal stretching effect in propagation pressure decreases with the increase of diameter-thick-ratio.
Article
Computer Science, Artificial Intelligence
Grzegorz Malczyk, Maximilian Brunner, Eugenio Cuniato, Marco Tognon, Roland Siegwart
Summary: To improve the accuracy and stability of interactive aerial robots, understanding the forces acting on the platform is crucial. This study introduces a new extended Kalman filter (EKF) based estimator that can differentiate between external disturbances and interaction forces. The estimator combines information from the system's dynamic model and state with wrench measurements from a Force-Torque sensor, enabling robust interaction control even in the presence of external disturbances. The proposed framework is extensively tested on an omnidirectional aerial manipulator, demonstrating its generality and superiority compared to a state-of-the-art estimator based on momentum.
Article
Physics, Multidisciplinary
Xudong Wang, Yao Chen
Summary: This article investigates the joint influence of expanding medium and constant force on particle diffusion. By starting from the Langevin picture and introducing the effect of external force in two different ways, two models with different force terms are obtained. Detailed analysis and derivation yield the Fokker-Planck equations and moments for the two models. The sustained force behaves as a decoupled force, while the intermittent force changes the diffusion behavior with specific effects depending on the expanding rate of the medium.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
Article
Chemistry, Physical
Lei Fu, Jun Zhou, Jiaming Yang, Qinghao Li, Haomin Guo, Qinyuan Deng, Zihe Zhu, Zixuan Zhang, Haoyu Yu, Kai Wu
Summary: Supported metal-metal oxide heterojunctions are widely used in catalysts for energy conversion and storage devices. The interaction between metal and supports is crucial for developing new catalysts. This study investigates the effect of an external electric field and circumstances on the charge transfer within a Cu/SrTiO3 heterojunction. The results show that the external electric field can switch the specific behavior of charge transfer, and the circumstances surrounding the heterojunction also influence charge transfer.
APPLIED SURFACE SCIENCE
(2022)
Article
Multidisciplinary Sciences
Yuzuru Itoh, Juni Andrell, Austin Choi, Uwe Richter, Priyanka Maiti, Robert B. Best, Antoni Barrientos, Brendan J. Battersby, Alexey Amunts
Summary: The study reveals the mechanism of interaction between human mitoribosomes and the insertase OXA1L, elucidating how membrane delivery is achieved during protein synthesis.
Article
Biochemistry & Molecular Biology
Joan-Emma Shea, Robert B. Best, Jeetain Mittal
Summary: Intrinsically disordered proteins (IDPs) are a special class of proteins that do not fold into specific 3D shapes, making experimental studies challenging and requiring theoretical and computational methods. Recent progress has been made in developing new computational and theoretical approaches to study the structure and dynamics of IDPs, particularly their phase separation into protein-rich condensates.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Chemistry, Physical
Grace H. Taumoefolau, Robert B. Best
Summary: In a two-state molecular system, transition paths involve the trajectories during which the system transitions between stable states. Single-molecule experiments can estimate transition-path durations, although there may be a tendency to underestimate. Greater flexibility in the transition-path model can lead to more accurate extraction of transition-path times.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Thomas Dannenhoffer-Lafage, Robert B. Best
Summary: Recent evidence suggests that liquid-liquid phase separation (LLPS) plays a key role in the formation of membraneless organelles, while the development of a new, data-driven hydrophobicity scale can better predict protein phase separation behavior under physiological conditions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemical Research Methods
Paulo C. T. Souza, Riccardo Alessandri, Jonathan Barnoud, Sebastian Thallmair, Ignacio Faustino, Fabian Grunewald, Ilias Patmanidis, Haleh Abdizadeh, Bart M. H. Bruininks, Tsjerk A. Wassenaar, Peter C. Kroon, Josef Melcr, Vincent Nieto, Valentina Corradi, Hanif M. Khan, Jan Domanski, Matti Javanainen, Hector Martinez-Seara, Nathalie Reuter, Robert B. Best, Ilpo Vattulainen, Luca Monticelli, Xavier Periole, D. Peter Tieleman, Alex H. de Vries, Siewert J. Marrink
Summary: The refined Martini 3 model offers improved interaction balance and expanded ability to include specific interactions, allowing for more accurate predictions of molecular packing and interactions. It has been successfully applied in a wide range of applications, demonstrating its versatility and effectiveness in biomolecular simulations.
Article
Chemistry, Multidisciplinary
Mark F. Nueesch, Milos T. Ivanovic, Jean-Benoit Claude, Daniel Nettels, Robert B. Best, Jerome Wenger, Benjamin Schuler
Summary: The use of nanophotonic fluorescence enhancement in zero-mode waveguides dramatically improves time resolution and reduces data acquisition times, enabling measurement of previously inaccessible low-nanosecond dynamics in biomolecules. This approach allows for better detection of biomolecular dynamics and achieves highly consistent results with all-atom molecular dynamics simulations.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Petur O. Heidarsson, Davide Mercadante, Andrea Sottini, Daniel Nettels, Madeleine B. Borgia, Alessandro Borgia, Sinan Kilic, Beat Fierz, Robert B. Best, Benjamin Schuler
Summary: This article reports a new mechanism of molecular competition that explains the role of highly charged intrinsically disordered proteins in chromatin structure and transcriptional activity regulation. This mechanism utilizes the pronounced dynamical disorder of these proteins and their complexes, allowing a highly negatively charged histone chaperone to efficiently invade and displace a highly positively charged histone bound to a nucleosome, thereby accelerating its dissociation.
Article
Chemistry, Physical
Kathryn M. Lebold, Robert B. Best
Summary: The high concentration of nucleic acids and positively charged proteins in the cell nucleus provides many possibilities for complex coacervation. The variation of the positions of charged residues in proteins can tune the phase separation and affect the local ordering and the ordering of DNA.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Sai Chaitanya Chiliveri, John M. Louis, Robert B. Best, Ad Bax
Summary: This study measured the dynamic equilibrium of the HIV-1 virus envelope glycoprotein gp41 in the presence of lipid mimics and determined the reaction kinetics and energy associated with its lipid-bound intermediate and post-fusion six-helical bundle states. The findings provide important insights into the molecular basis of viral membrane fusion.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Pengfei Tian, Adrien Lemaire, Fabien Senechal, Olivier Habrylo, Viviane Antonietti, Pascal Sonnet, Valerie Lefebvre, Frederikke Isa Marin, Robert B. Best, Jerome Pelloux, Davide Mercadante
Summary: Efficiently designing functional proteins with higher thermal stability is still challenging, especially for highly diverse sequence variants. However, optimizing sequence design based on evolutionary fitness can help improve protein stability. In this study, we used a generative evolution fitness model to design artificial sequences for a proteinaceous inhibitor of pectin methylesterase enzymes. The majority of the designs were functional, and some even showed improved thermal stability. This method has the potential to expand the sequence space of functional proteins with valuable traits for industrial applications and scientific research.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Meeting Abstract
Biophysics
Kathryn M. Lebold, Robert B. Best
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Robert B. Best
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Thomas P. Dannenhoffer-Lafage, Robert B. Best
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Layne B. Frechette, Robert B. Best
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Grace H. Taumoefolau, Robert B. Best
BIOPHYSICAL JOURNAL
(2022)