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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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Steady Rayleigh-BénardRayleigh-Bénard convection between stress-free boundaries

arXiv

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arXiv 2020年

作者： Wen, Baole Goluskin, David LeDuc, Matthew Chini, Gregory P. Doering, Charles R. Department of Mathematics University of Michigan Ann ArborMI48109-1043 United States Department of Mathematics & Statistics University of Victoria VictoriaBCV8P 5C2 Canada Department of Physics University of Michigan Ann ArborMI48109-1040 United States Program in Integrated Applied Mathematics University of New Hampshire DurhamNH03824 United States Department of Mechanical Engineering University of New Hampshire DurhamNH03824 United States Center for the Study of Complex Systems University of Michigan Ann ArborMI48109-1042 United States

Steady two-dimensional Rayleigh-Bénard convection between stress-free isothermal boundaries is studied via numerical computations. We explore properties of steady convective rolls with aspect ratios π/5 ⩽ Γ ⩽ 4π, where Γ is the width-to-height ratio for a pair of counter-rotating rolls, over eight orders of magnitude in the Rayleigh number, 103 ⩽ Ra ⩽ 1011, and four orders of magnitude in the Prandtl number, 10−2 ⩽ Pr ⩽ 102. At large Ra where steady rolls are dynamically unstable, the computed rolls display Ra → ∞ asymptotic scaling. In this regime, the Nusselt number Nu that measures heat transport scales as Ra1/3 uniformly in Pr. The prefactor of this scaling depends on Γ and is largest at Γ ≈ 1.9. The Reynolds number Re for large-Ra rolls scales as Pr−1Ra2/3 with a prefactor that is largest at Γ ≈ 4.5. All of these large-Ra features agree quantitatively with the semi-analytical asymptotic solutions constructed by Chini & Cox (2009). Convergence of Nu and Re to their asymptotic scalings occurs more slowly when Pr is larger and when Γ is smaller. Copyright © 2020, The Authors. All rights reserved.

关键词： Prandtl number

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A spectral method for solving heat and moisture transfer through consolidated porous media

arXiv

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arXiv 2019年

作者： Gasparin, Suelen Dutykh, Denys Mendes, Nathan LAMA UMR 5127 CNRS Université Savoie Mont Blanc Campus Scientifique F-73376 Le Bourget-du-Lac Cedex France and Thermal Systems Laboratory Mechanical Engineering Graduate Program Pontifical Catholic University of Paraná Rua Imaculada Conceição 1155 Curitiba – ParanáCEP: 80215-901 Brazil Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LAMA Chambéry73000 France LAMA UMR 5127 CNRS Université Savoie Mont Blanc Campus Scientifique Le Bourget-du-Lac CedexF-73376 France Thermal Systems Laboratory Mechanical Engineering Graduate Program Pontifical Catholic University of Paraná Rua Imaculada Conceição 1155 Curitiba – ParanáCEP: 80215-901 Brazil

This work presents an efficient numerical method based on spectral expansions for simulation of heat and moisture diffusive transfers through multilayered porous materials. Traditionally, by using the finite-difference approach, the problem is discretized in time and space domains (Method of lines) to obtain a large system of coupled Ordinary Differential Equations (ODEs), which is computationally expensive. To avoid such a cost, this paper proposes a reduced-order method that is faster and accurate, using a much smaller system of ODEs. To demonstrate the benefits of this approach, tree case studies are presented. The first one considers nonlinear heat and moisture transfer through one material layer. The second case – highly nonlinear – imposes a high moisture content gradient – simulating a rain like condition – over a two-layered domain, while the last one compares the numerical prediction against experimental data for validation purposes. Results show how the nonlinearities and the interface between materials are easily and naturally treated with the spectral reduced-order method. Concerning the reliability part, predictions show a good agreement with experimental results, which confirm robustness, calculation efficiency and high accuracy of the proposed approach for predicting the coupled heat and moisture transfer through porous materials. Copyright © 2019, The Authors. All rights reserved.

关键词： Porous materials

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Characterizing cellular mechanical phenotypes with mechanonode-pore sensing

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Microsystems & Nanoengineering 2018年第1期4卷 438-449页

作者： Junghyun Kim Sewoon Han Andy Lei Masaru Miyano Jessica Bloom Vasudha Srivastava Martha R.Stampfer Zev J.Gartner Mark A.LaBarge Lydia L.Sohn Department of Mechanical Engineering University of California at BerkeleyBerkeleyCA 94720-1740USA Department of Bioengineering University of California at BerkeleyBerkeleyCA 94720-1762USA Department of Population Sciences Beckman Research InstituteCity of HopeDuarteCA 91010USA Department of Pharmaceutical Chemistry University of CaliforniaSan FranciscoSan FranciscoCA 94143USA Biological Systems and Engineering Division Lawrence Berkeley National LaboratoryCA 94720USA Graduate Program in Bioengineering University of CaliforniaBerkeleyand University of CaliforniaSan FranciscoBerkeleyCA 94720USA

The mechanical properties of cells change with their differentiation,chronological age,and malignant ***,these properties may be useful label-free biomarkers of various functional or clinically relevant cell ***,we demonstrate mechano-node-pore sensing(mechano-NPS),a multi-parametric single-cell-analysis method that utilizes a four-terminal measurement of the current across a microfluidic channel to quantify simultaneously cell diameter,resistance to compressive deformation,transverse deformation under constant strain,and recovery time after *** define a new parameter,the whole-cell deformability index(wCDI),which provides a quantitative mechanical metric of the resistance to compressive deformation that can be used to discriminate among different cell *** wCDI and the transverse deformation under constant strain show malignant MCF-7 and A549 cell lines are mechanically distinct from non-malignant,MCF-10A and BEAS-2B cell lines,and distinguishes between cells treated or untreated with cytoskeleton-perturbing small *** categorize cell recovery time,ΔT_(r),as instantaneous(ΔTr~0 ms),transient(ΔT_(r)≤40 ms),or prolonged(ΔT_(r)>40 ms),and show that the composition of recovery types,which is a consequence of changes in cytoskeletal organization,correlates with cellular *** the wCDI and cell-recovery time,mechano-NPS discriminates between sub-lineages of normal primary human mammary epithelial cells with accuracy comparable to flow cytometry,but without antibody ***-NPS identifies mechanical phenotypes that distinguishes lineage,chronological age,and stage of malignant progression in human epithelial cells.

关键词： microfluidics mechanical phenotyping node-pore sensing biosensors label-free

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Molding Compound Effects on Warpage of Fan-out Wafer Level Packaging

Molding Compound Effects on Warpage of Fan-out Wafer Level P...

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International Symposium on Electronic Materials and Packaging

作者： Yan-Cheng Liu Hsien-Chie Cheng Zong-Da Wu Ph.D. Program of Mechanical and Aeronautical Engineering Feng Chia University Taichung Taiwan ROC Department of Aerospace and Systems Engineering Feng Chia University Taichung Taiwan ROC

ISBN: (纸本)9781538656433;9781538656426

Fan-out Wafer-level Packaging (FOWLP) technology has become one of the most rapid packaging technologies which can meet consumer demand for electronic devices. Since there are many advantages to FOWLP, several important issues remain to be addressed, including yield, reliability, thermal performance, die shift, and warpage. Therefore, the main reasons that cause the yield problem of the FOWLP are the mismatch of temperature loading and coefficient of thermal expansion(CTE) among the components of the package, and the other reason is the chemical shrinkage of liquid type epoxy molding compound during the cure process. In this study, the main goal is to assess the process-induced warpage of FOWLP during the fabrication process. To predict the amount of warpage precisely, a process-dependent simulation model which includes the cure-induced shrinkage of the liquid type of molding compound obtained by measurement is proposed. To confirm the validity of the simulation model, the simulation results are compared to the online warpage measurement data. Finally, the influence of the material properties of molding compound parameters on the process-induced warpage is discussed.

关键词： Compounds Semiconductor device modeling Fabrication Packaging Solid modeling Wafer scale integration

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Formation flying techniques for the virtual telescope for X-ray observations 69

Formation flying techniques for the virtual telescope for X-...

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69th International Astronautical Congress: #InvolvingEveryone, IAC 2018

作者： Kyle, Rankin Neerav, Shah John, Krizmanic Steven, Stochaj Asal, Naseri Department of Mechanical and Aerospace Engineering New Mexico State University United States Goddard Space Flight Center NASA United States CRESST NASA GSFC University of Maryland Baltimore County United States Klipsch School of Electrical and Computer Engineering New Mexico State University United States Program Manage/Systems Engineer Space Dynamics Laboratory United States

The Virtual Telescope for X-Ray Observations (VTXO) is an Astrophysics SmallSat mission being developed to demonstrate 10-milliarcsecond X-ray imaging using a Phase Fresnel Lense (PFL)-based space telescope. PFLs promise to provide several orders of magnitude improvement in angular resolution over current state of the art X-ray optics. However, PFLs for astronomical applications requires a very long focal length, for VTXO the focal length is estimated to be in the range of 0.5 km to 4 km. Since these focal lengths are not feasible on a single spacecraft, the proposed solution is to use two separate spacecraft, one with the lense(s), and the second with an X-ray camera. These two spacecrafts will then fly in a formation approximating a single rigid telescope. In order to achieve this configuration, the two spacecraft must maintain the formation a focal length distance apart, with centimeter level control, and sub-millimeter level knowledge requirements. Additionally, for the telescope to achieve sufficient exposure time, the system must keep the telescope axis pointed at a fixed target on the celestial sphere for durations on the order of a few hours. VTXO's system architecture calls for two CubeSats to operate in a highly eccentric Earth orbit with one of the spacecraft's traveling on a natural keplarian orbit. The second spacecraft will then fly on a â€œpseudoâ€¥ orbit maintaining a fixed offset relative to the celestial sphere during observations. Observations with this system will occur near apogee where differential forces on the spacecrafts are minimal which in turn minimizes fuel consumption. The â€œpseudoâ€¥ orbit where the second spacecraft is located is not quite a stable orbit requiring small continuous propulsion to maintain formation. This paper and presentation will overview VTXO's system architecture, additionally it will look in depth at the formation flying techniques, including fuel consumption, and methods for establishing, and maintaining the form

关键词： Orbits

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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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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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Linearization of two-state thruster models

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Journal of Physics: Conference Series 2020年第1期1490卷

作者： Dieky Adzkiya Hendro Nurhadi Teguh Herlambang Department of Mathematics Institut Teknologi Sepuluh Nopember Indonesia Center of Excellence for Mechatronics and Industrial Automation Research Center Institut Teknologi Sepuluh Nopember Indonesia Department of Industrial Mechanical Engineering Institut Teknologi Sepuluh Nopember Indonesia Study Program of Information Systems Universitas Nahdlatul Ulama Surabaya Indonesia

A thruster is a device used for station keeping, attitude control, in the reaction control system, or long-duration, low-thrust acceleration. Thruster is one of the main components in autonomous surface vehicle. In th...

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Performance Management systems for Project Management Offices: A Case-Based Study

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Procedia Manufacturing 2019年 39卷 923-931页

作者： Rafael Duarte Fernando Deschamps Edson Pinheiro de Lima André Pepino Rene Marcel Guzman Clavijo Universidade Positivo R. Prof. Pedro Viriato Parigot de Souza 5300 Curitiba - PR 81280-330 Brazil Industrial and Systems Engineering Graduate Program (PPGEPS) – Pontifical Catholic University of Parana (PUCPR) R. Imac. Conceição 1155 Curitiba - PR 80215-901 Brazil Department of Mechanical Engineering (DEMEC) Federal University of Parana (UFPR) Av. Cel. Francisco H. dos Santos 230 - Centro Politécnico Bloco IV Curitiba - PR 81530-000 Brazil Federal University of Technology – Parana (UTFPR)

Project Management Offices (PMOs) are organizational structures in charge of managing and coordinating several simultaneous projects within companies. Due to the complexity of different projects’ objectives, it’s usual to simplify project indicators and control them by means of the well-known triple constraint or “iron triangle”: scope, cost and time. This approach does not account for the organizational strategy, internal and external stakeholders’ interests, nor other specific indicators. The problems due to the lack of integration caused by this oversimplification are yet amplified in complex project portfolios related to technology development and deployment, since in this kind of scenario the marketing competition demands new features, at lower costs, in no time. These points could be addressed by operations management approaches, such as the Performance Management systems Design Framework (PMSDF). To identify the viability and relevance in using this method in PMOs, this work adopts a mixed methods research. Is begins with a Systematic Literature Review to better understand performance management routine and tools in PMO. It was followed by meetings with two project management consultants, to identify the best practices, habits and advises, to check the differences between practitioner and academic views. Finally, it was conducted interviews with the PMO Director of a trucks’ manufacturer and a PMO Manager in an agrarian-cattle-breeding cooperative, to verify how such companies measure their PMO’s successes. The last step was to adapt the PMSDF to the project management context, evaluating the PMO operation in a medium-sized software development company and propose the restructuration of its Performance Management System.

关键词： PMS PMO KPI Operations Strategy PMSDF

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