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arXiv 2020年

作者： Grigas, Alex T. Mei, Zhe Treado, John D. Levine, Zachary A. Regan, Lynne O'Hern, Corey S. Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Pathology Yale University New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Institute of Quantitative Biology Biochemistry and Biotechnology Centre for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical features that specify a real protein. For example, it has long been appreciated that the hydrophobic cores of proteins contribute signifficantly to their stability. As a dataset of decoys to compare with real protein structures, we studied submissions to the bi-annual CASP competition (speciffically CASP11, 12, and 13), in which researchers attempt to predict the structure of a protein only knowing its amino acid sequence. Our analysis reveals that many of the submissions possess cores that do not recapitulate the features that define real proteins. In particular, the model structures appear more densely packed (because of energetically unfavorable atomic overlaps), contain too few residues in the core, and have improper distributions of hydrophobic residues throughout the structure. Based on these observations, we developed a deep learning method, which incorporates key physical features of protein cores, to predict how well a computational model recapitulates the real protein structure without knowledge of the structure of the target sequence. By identifying the important features of protein structure, our method is able to rank decoys from the CASP competitions equally well, if not better than, state-of-the-art methods that incorporate many additional features. Copyright © 2020, The Authors. All rights reserved.

关键词： Proteins

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Bridging particle deformability and collective response in soft solids

arXiv

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arXiv 2020年

作者： Treado, John D. Wang, Dong Boromand, Arman Murrell, Michael P. Shattuck, Mark D. O’Hern, Corey S. Department of Mechanical Engineering & Materials Science Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Department of Biomedical Engineering Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Systems Biology Institute Yale University West HavenCT06516 United States Benjamin Levich Institute and Physics Department The City College of New York New YorkNY10031 United States Department of Applied Physics Yale University New HavenCT06520 United States

Soft, amorphous solids such as tissues, foams, and emulsions are composed of deformable particles. However, the effect of single-particle deformability on the collective behavior of soft solids is still poorly understood. We perform numerical simulations of two-dimensional jammed packings of explicitly deformable particles to study the mechanical response of model soft solids. We find that jammed packings of deformable particles with excess shape degrees of freedom possess low-frequency quartic vibrational modes that stabilize the packings even though they possess fewer interparticle contacts than the nominal isostatic value. Adding intra-particle constraints can rigidify the particles, but these particles undergo a buckling transition and gain an effective shape degree of freedom when their preferred perimeter is above a threshold value. We find that the mechanical response of jammed packings of deformable particles with shape degrees of freedom differs significantly from that of jammed packings of rigid-shape particles, which emphasizes the importance of particle deformability in modelling soft solids. © 2020, CC BY.

关键词： Degrees of freedom (mechanics)

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Correction: The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions

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Soft matter 2022年第19期18卷 3815页

作者： Dong Wang John D Treado Arman Boromand Blake Norwick Michael P Murrell Mark D Shattuck Corey S O'Hern Department of Mechanical Engineering & Materials Science Yale University New Haven Connecticut 06520 USA. corey.ohern@yale.edu. Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut 06520 USA. Department of Physics Yale University New Haven Connecticut 06520 USA. Department of Biomedical Engineering Yale University New Haven Connecticut 06520 USA. Systems Biology Institute Yale University West Haven Connecticut 06516 USA. Benjamin Levich Institute and Physics Department The City College of New York New York New York 10031 USA. Department of Applied Physics Yale University New Haven Connecticut 06520 USA.

Correction for 'The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions' by Dong Wang , , 2021, , 9901-9915, DOI: 10.1039/D1SM01228B.

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Current md forcefields fail to capture key features of protein structure and fluctuations: a case study of cyclophilin a and t4 lysozyme

arXiv

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arXiv 2020年

作者： Mei, Zhe Grigas, Alex T. Treado, John D. Corres, Gabriel Melendez Vuorte, Maisa Sammalkorpi, Maria Regan, Lynne Levine, Zachary A. O’Hern, Corey S. Department of Chemistry Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Biology UPR Humacao Puerto RicoHumacao00792 Puerto Rico Department of Chemistry and Materials Science School of Chemical Engineering Aalto University Aalto Finland Department of Bioproducts and Biosystems School of Chemical Engineering Aalto University Aalto Finland Institute of Quantitative Biology Biochemistry and Biotechnology Center for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh Edinburgh United Kingdom Department of Pathology Yale School of Medicine New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways when they are solved by x-ray crystallography versus solution-based NMR spectroscopy. Given these discrepancies, it is unclear whether molecular dynamics (MD) simulations can accurately recapitulate protein conformations. We therefore perform extensive MD simulations across multiple force fields and sampling techniques to investigate the degree to which computer simulations can capture the ensemble of conformations observed in experiments. By analyzing fluctuations in the atomic coordinates and core packing, we show that conformations sampled in MD simulations both move away from and sample a larger conformational space than the ensemble of structures observed in NMR experiments. However, we find that adding inter-residue distance restraints that match those obtained via Nuclear Overhauser Effect measurements enables the MD simulations to sample more NMR-like conformations, though significant differences between the core packing features in restrained MD and the NMR ensemble remain. Given that the protein structures obtained from the MD simulations possess smaller and less dense protein cores compared to those solved by NMR, we suggest that future improvements to MD forcefields should aim to increase the packing of hydrophobic residues in protein cores. © 2020, CC BY.

关键词： Molecular dynamics

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Imaging real-time amorphization of hybrid perovskite solar cells under electrical biasing

arXiv

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arXiv 2020年

作者： Kim, Min-Cheol Ahn, Namyoung Cheng, Diyi Xu, Mingjie Pan, Xiaoqing Kim, Suk Jun Luo, Yanqi Fenning, David P. Tan, Darren H.S. Zhang, Minghao Ham, So-Yeon Jeong, Kiwan Choi, Mansoo Meng, Ying Shirley Department of NanoEngineering University of California San Diego 9500 Gilman Drive San diegoCA92093 United States Global Frontier Center for Multiscale Energy Systems Seoul National University Seoul08826 Korea Republic of Materials Science and Engineering Program University of California San Diego 9500 Gilman Drive San diegoCA92093 United States Irvine Materials Research Institute University of California Irvine IrvineCA92697 United States Department of Materials Science and Engineering University of California Irvine IrvineCA92697 United States Department of Physics and Astronomy University of California Irvine IrvineCA92697 United States School of Energy Materials and Chemical Engineering Korea University of Technology and Education Cheonan31253 Korea Republic of University of California San Diego San diegoCA92093 United States Department of Mechanical Engineering Seoul National University Seoul08826 Korea Republic of

Perovskite solar cells have drawn much attention in recent years, owing to its world-record setting photovoltaic performances. Despite its promising use in tandem applications and flexible devices, its practicality is still limited by its structural instability often arising from ion migration and defect formation. While it is generally understood that ion instability is a primary cause for degradation, there is still a lack of direct evidence of structural transformation at the atomistic scale. Such an understanding is crucial to evaluate and pin-point how such instabilities are induced relative to external perturbations such as illumination or electrical bias with time, allowing researchers to devise effective strategies to mitigate them. Here, we designed an in-situ TEM setup to enable real-time observation of amorphization in double cation mixed perovskite materials under electrical biasing at 1 V. It is found that amorphization occurs along the (001) and (002) planes, which represents the observation of in-situ facet-dependent amorphization of a perovskite crystal. To reverse the degradation, the samples were heated at 50 oC and was found to recrystallize, effectively regaining its performance losses. This work is vital toward understanding fundamental ion-migration phenomena and address instability challenges of perovskite optoelectronics. Copyright © 2020, The Authors. All rights reserved.

关键词： Perovskite

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Unifying femtosecond and picosecond single-pulse magnetic switching in GdFeCo

arXiv

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arXiv 2020年

作者： Jakobs, F. Ostler, T.A. Lambert, C.-H. Yang, Y. Salahuddin, S. Wilson, R.B. Gorchon, J. Bokor, J. Atxitia, U. Dahlem Center for Complex Quantum Systems and Fachbereich Physik Freie Universität Berlin Berlin14195 Germany LiégeB-4000 Belgium College of Business Technology and Engineering Sheffield Hallam University Howard Street SheffieldS1 1WB United Kingdom Department of Electrical Engineering and Computer Sciences University of California BerkeleyCA94720 United States Department of Materials Science and Engineering University of California BerkeleyCA94720 United States Lawrence Berkeley National Laboratory 1 Cyclotron Road BerkeleyCA94720 United States Department of Mechanical Engineering and Materials Science and Engineering Program University of California RiversideCA92521 United States ETH Zurich Hönggerbergring 64 Zürich8093 Switzerland Portland Technology Development Department Intel Corp. HillsboroOR97006 United States Universite de Lorraine CNRS IJL NancyF-54000 France

Many questions are still open regarding the physical mechanisms behind the magnetic switching in GdFeCo alloys by single optical pulses. Phenomenological models suggest a femtosecond scale exchange relaxation between sublattice magnetization as the driving mechanism for switching. The recent observation of thermally induced switching in GdFeCo by using both several picosecond optical laser pulse as well as electric current pulses has questioned this previous understanding. This has raised the question of whether or not the same switching mechanics are acting at the femoand picosecond scales. In this work, we aim at filling this gap in the understanding of the switching mechanisms behind thermal single-pulse switching. To that end, we have studied experimentally thermal single-pulse switching in GdFeCo alloys, for a wide range of system parameters, such as composition, laser power and pulse duration. We provide a quantitative description of the switching dynamics using atomistic spin dynamics methods with excellent agreement between the model and our experiments across a wide range of parameters and timescales, ranging from femtoseconds to picoseconds. Furthermore, we find distinct element-specific damping parameters as a key ingredient for switching with long picosecond pulses and argue, that switching with pulse durations as long as 15 picoseconds is possible due to a low damping constant of Gd. Our findings can be easily extended to speed up dynamics in other contexts where ferrimagnetic GdFeCo alloys have been already demonstrated to show fast and energy-efficient processes, e.g. domain-wall motion in a track and spin-orbit torque switching in spintronics devices. Copyright © 2020, The Authors. All rights reserved.

关键词： Ternary alloys

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Optimising phase change materials for ventilated building components in sustainable building design: a comprehensive review

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Energy and Buildings 2025年 343卷

作者： Farhan Lafta Rashid Mudhar A. Al-Obaidi Wadhah Amer Hatem Najah M.L. Al Maimuri Arman Ameen Shabbir Ahmad Ephraim Bonah Agyekum Saif Ali Kadhim Karrar A. Hammoodi Petroleum Engineering Department College of Engineering University of Kerbala Karbala 56001 Iraq Technical Instructor Training Institute Middle Technical University Baghdad 10074 Iraq Middle Technical University Technical Institute of Baquba Baquba Diyala 32001 Iraq Building and Construction Techniques Engineering Department College of Engineering and Engineering Techniques Al-Mustaqbal University Hillah Babylon 51001 Iraq Department of Building Engineering Energy Systems and Sustainability Science University of Gävle 801 76 Gävle Sweden Graduate Program of Ocean Engineering School of Engineering Universidade Federal do Rio Grande Rio Grande Italia Avenue km 8 96201-900 Brazil Institute of Geophysics and Geomatics China University of Geosciences Wuhan 430074 China Department of Nuclear and Renewable Energy Ural Federal University Named after the First President of Russia Boris Yeltsin 19 Mira Street Ekaterinburg 620002 Russia Western Caspian University 31 Istiglaliyyat Street AZ1001 Baku Azerbaijan Istanbul Okan University Tuzla Campus 34959 Tuzla Istanbul Turkey College of Mechanical Engineering University of Technology – Iraq Baghdad Iraq College of Engineering University of Al Maarif Al Anbar Iraq

The rise in energy-efficient, sustainable building operations necessitates the development of advanced innovations that reduce heating and cooling demands while maintaining comfortable indoor thermal conditions. Phase change materials (PCMs) demonstrate significant potential as a stabilization mechanism through latent heat storage for managing residential indoor temperatures; however, their integration into systems requires further optimisation. This review examines PCM-assisted ventilation technologies—specifically ventilated façades, roofs, and windows—highlighting their energy performance, which ranges from 7.7 % to 32.8 %, and their capacity to reduce peak temperatures by 2.5 °C to 7.02 °C. These improvements are influenced by PCM thickness of 15–35 mm and melting temperatures of 15–37 °C. The combination of PCM-enhanced hybrid systems with natural or mechanical ventilation has shown greater operational effectiveness, particularly in hot climates and when integrated with adaptive control systems to achieve optimal performance. Despite their benefits, widespread adoption of PCM technologies is hindered by high material costs, hysteresis effects, and limited discharge cycle efficiency. Nevertheless, PCM-enhanced ventilation systems have proven capable of supporting sustainable, low-energy buildings. Continued research is needed to develop cost-effective design strategies, automated control mechanisms, and climate-responsive optimisations to fully realize their potential.

关键词： Energy-efficient ventilation systems Phase change materials (PCMs) Residential buildings Sustainable thermal management

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Considering discrepancy when calibrating a mechanistic electrophysiology model

arXiv

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arXiv 2020年

作者： Lei, Chon Lok Ghosh, Sanmitra Whittaker, Dominic G. Aboelkassem, Yasser Beattie, Kylie A. Cantwell, Chris D. Delhaas, Tammo Houston, Charles Novaes, Gustavo Montes Panfilov, Alexander V. Pathmanathan, Pras Riabiz, Marina Weber dos Santos, Rodrigo Worden, Keith Mirams, Gary R. Wilkinson, Richard D. Computational Biology & Health Informatics Dept. of Computer Science University of Oxford United Kingdom MRC Biostatistics Unit University of Cambridge United Kingdom Centre for Mathematical Medicine & Biology School of Mathematical Sciences University of Nottingham United Kingdom Department of Bioengineering University of California San Diego United States Systems Modeling and Translational Biology GlaxoSmithKline R&D Stevenage United Kingdom ElectroCardioMaths Programme Centre for Cardiac Engineering Imperial College London United Kingdom CARIM School for Cardiovascular Diseases Maastricht University Netherlands Graduate Program in Computational Modeling Universidade Federal de Juiz de Fora Brazil Department of Physics and Astronomy Ghent University Belgium Laboratory of Computational Biology and Medicine Ural Federal University Ekaterinburg Russia U.S. Food and Drug Administration Center for Devices and Radiological Health Office of Science and Engineering Laboratories United States Department of Biomedical Engineering King’s College London Alan Turing Institute United Kingdom Dynamics Research Group Department of Mechanical Engineering University of Sheffield United Kingdom School of Mathematics and Statistics University of Sheffield United Kingdom

Uncertainty quantification (UQ) is a vital step in using mathematical models and simulations to take decisions. The field of cardiac simulation has begun to explore and adopt UQ methods to characterise uncertainty in model inputs and how that propagates through to outputs or predictions. In this perspective piece we draw attention to an important and under-addressed source of uncertainty in our predictions — that of uncertainty in the model structure or the equations themselves. The difference between imperfect models and reality is termed model discrepancy, and we are often uncertain as to the size and consequences of this discrepancy. Here we provide two examples of the consequences of discrepancy when calibrating models at the ion channel and action potential scales. Furthermore, we attempt to account for this discrepancy when calibrating and validating an ion channel model using different methods, based on modelling the discrepancy using Gaussian processes (GPs) and autoregressive-moving-average (ARMA) models, then highlight the advantages and shortcomings of each approach. Finally, suggestions and lines of enquiry for future work are provided. Copyright © 2020, The Authors. All rights reserved.

关键词： Uncertainty analysis

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Modelling and reducing fuel flow pulsation of a fuel-metering system during pump mode switching in a turbofan engine

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IOP Conference Series: Earth and Environmental science 2019年第5期240卷

作者： S Masuda F Shimizu M Fuchiwaki K Tanaka Control Systems Engineering Department Research & Engineering Division Aero Engines Space & Defense Business Area IHI Corporation 229 Tonogaya Mizuho-machi Nishitama-gun Tokyo 190-1297 Japan Department of Computer Science and Systems Engineering Doctoral Program Graduate School of Computer Science and Systems Engineering Kyushu Institute of Technology 680-4 kawazu Iizuka-shi Fukuoka 820-8502 Japan Department of Mechanical Information Science and Technology School of Computer Science and Systems Engineering Kyushu Institute of Technology 680-4 kawazu Iizuka-shi Fukuoka 820-8502 Japan

In this research, the transient characteristics of a new type fuel metering system for aircraft turbofan engines using two types of pumps, a gear pump and a centrifugal pump, were studied by modelling and simulation. This new fuel metering system is capable of hydraulically unloading the operating state of each pump by the pump mode switching mechanism within the permissible range of the pump rotation speed and the fuel flow rate and it is possible to reduce the fuel temperature rise due to the pressure loss in the circuit in the operation region of the entire fuel system. In addition to this, by using a small centrifugal pump that can realize high discharge flow rate, it is possible to reduce weight compared to the conventional fuel system. However, when the pump mode is switched, unexpected fluctuation in the fuel flow rate can occur when a large change in the inlet pressure of the system occurs, the pressure control unit cannot follow the change, and the transient phenomenon cannot be suppressed. At this time, the pressure waveform generated at the time of changing the pump mode includes a high frequency component such that the pressure control unit, which plays a role of keeping the metering valve differential pressure constant, cannot follow up. Therefore, in this paper, we focused on the frequency of the pressure change waveform when the pump mode was changed and studied the model of the fuel system inlet pressure in the gear pump mode. Based on that model, we propose a method to reduce the frequency characteristics of the pressure change occurring at the time of pump mode change.

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The control of brain network dynamics across diverse scales of space and time

arXiv

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arXiv 2019年

作者： Tang, Evelyn Baum, Graham L. Roalf, David R. Satterthwaite, Theodore D. Pasqualetti, Fabio Bassett, Danielle S. Department of Bioengineering School of Engineering & Applied Science University of Pennsylvania PA19104 United States Max Planck Institute for Dynamics and Self-Organization Göttingen37079 Germany Neuroscience Graduate Program Perelman School of Medicine University of Pennsylvania PA19104 United States Department of Psychiatry Perelman School of Medicine University of Pennsylvania PA19104 United States Department of Mechanical Engineering University of California Riverside RiversideCA92521 United States Department of Physics & Astronomy College of Arts & Sciences University of Pennsylvania PA19104 United States Department of Electrical & Systems Engineering School of Engineering & Applied Science University of Pennsylvania PA19104 United States Department of Neurology Perelman School of Medicine University of Pennsylvania PA19104 United States

The human brain is composed of distinct regions that are each associated with particular functions and distinct propensities for the control of neural dynamics. However, the relation between these functions and control profiles is poorly understood, as is the variation in this relation across diverse scales of space and time. Here we probe the relation between control and dynamics in brain networks constructed from diffusion tensor imaging data in a large community based sample of young adults. Specifically, we probe the control properties of each brain region and investigate their relationship with dynamics across various spatial scales using the Laplacian eigenspectrum. In addition, through analysis of regional modal controllability and partitioning of modes, we determine whether the associated dynamics are fast or slow, as well as whether they are alternating or monotone. We find that brain regions that facilitate the control of energetically easy transitions are associated with activity on short length scales and slow time scales. Conversely, brain regions that facilitate control of difficult transitions are associated with activity on long length scales and fast time scales. Built on linear dynamical models, our results offer parsimonious explanations for the activity propagation and network control profiles supported by regions of differing neuroanatomical structure. Copyright © 2019, The Authors. All rights reserved.

关键词： Brain

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