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Void distributions reveal structural link between jammed packings and protein cores

Physical Review E 2019年第2期99卷 022416-022416页

作者： John D. Treado Zhe Mei Lynne Regan Corey S. O'Hern Department of Mechanical Engineering & Materials Science Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical & Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Chemistry Yale University New Haven Connecticut 06520 USA Department of Molecular Biophysics & Biochemistry Yale University New Haven Connecticut 06520 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA

Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction ϕ≈0.56, which is the same as dense, random packing of amino-acid-shaped particles. In this article, we compare the structural properties of protein cores and jammed packings of amino-acid-shaped particles in much greater depth by measuring their local and connected void regions. We find that the distributions of surface Voronoi cell volumes and local porosities obey similar statistics in both systems. We also measure the probability that accessible, connected void regions percolate as a function of the size of a spherical probe particle and show that both systems possess the same critical probe size. We measure the critical exponent τ that characterizes the size distribution of connected void clusters at the onset of percolation. We find that the cluster size statistics are similar for void percolation in packings of amino-acid-shaped particles and randomly placed spheres, but different from that for void percolation in jammed sphere packings. We propose that the connected void regions are a defining structural feature of proteins and can be used to differentiate experimentally observed proteins from decoy structures that are generated using computational protein design software. This work emphasizes that jammed packings of amino-acid-shaped particles can serve as structural and mechanical analogs of protein cores, and could therefore be useful in modeling the response of protein cores to cavity-expanding and -reducing mutations.

关键词： Jamming Protein structure Packing & jamming problems Proteins Crystal structures Finite-size scaling Molecular dynamics Percolation theory

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Additive nanomanufacturing of lab-on-a-chip fluorescent peptide nanoparticle arrays for Alzheimer＇s disease diagnosis

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Bio-Design and Manufacturing 2018年第3期1卷 182-194页

作者： Leming Sun Zhen Fan Tao Yues Jun Yin Jianzhong FU Mingjun Zhang Department of Biomedical Engineering College ofEngineering Ohio State University Columbus OH 43210USA School of Life Sciences Northwestern PolytechnicalUniversity Xi'an 710072 Shaanxi China Department of Polymeric Materials School of MaterialScience and Engineering Tongji UniversityShanghai 201804 China Institute for Advanced Study TongjiUniversity Shanghai 200092 China School of Mechatronic Engineering and Automation Shanghai University Shanghai 200444 China The State Key Laboratory of Fluid Power and Mechatronic Systems School of Mechanical Engineering ZhejiangUniversity Hangzhou 310028 China Key Laboratory of 3D Printing Process and Equipment of Zhejiang Province School of Mechanical EngineeringZhejiang University Hangzhou 310028 China Dorothy M. Davis Heart & Lung Research Institute The OhioState University Wexner Medical Center Columbus OH43210 USA Interdisciplinary Biophysics Graduate Program Ohio StateUniversity Columbus OH 43210 USA

This paper proposes an additive nanomanufacturing approach to fabricate a personalized lab-on-a-chip fluorescent peptide nanoparticles （f-PNPs） array for simultaneous multi-biomarker detection that can be used in Alzheimer＇s disease （AD） diagnosis. We will discuss optimization techniques for the additive nanomanufacturing process in terms of reliability, yield and manufacturing efficiency. One contribution of this paper lies in utilization of additive nanomanufacturing techniques to fabricate a patient-specific customize-designed lab-on-a-chip device for personalized AD diagnosis, which remains a major challenge for biomedical engineering. Through the integrated bio-design and bio-manufacturing process, doctor＇s check- up and computer-aided customized design are integrated into the lab-on-a-chip array for patient-specific AD diagnosis. In addition, f-PNPs with targeting moieties for personalized AD biomarkers will be self-assembled onto the customized lab-on-a- chip through the additive nanomanufacturing process, which has not been done before. Another contribution of this research is the personalized lab-on-a-chip f-PNPs array for AD diagnosis utilizing limited human blood. Blood-based AD assessment has been described as ＂the holy grail＂ of early AD detection. This research created the computer-aided design, fabrication through additive nanomanufacturing, and validation of the f-PNPs array for AD diagnosis. This is a highly interdisciplinary research contributing to nanotechnology, biomaterials, and biomedical engineering for neurodegenerative disease. The conceptual work is preliminary with intent to introduce novel techniques to the application. Large-scale manufacturing based on the proposed framework requires extensive validation and optimization.

关键词： Nanomanufacturing Lab-on-a-chip Fluorescent peptide nanoparticle Alzheimer＇s disease Diagnosis

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FES-assisted cycling with cadence tracking control for rehabilitation of hemiparesis

IEEJ Transactions on Electronics, Information and Systems

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IEEJ Transactions on Electronics, Information and systems 2018年第11期138卷 1391-1398页

作者： Kushima, Yoshihiro Kawai, Hiroyuki Murao, Toshiyuki Kawai, Yasunori Kishitani, Miyako Suzuki, Ryoichi Fujita, Masayuki Graduate Program in Mechanical Engineering Kanazawa Institute of Technology 7-1 Nonoichi Ishikawa921-8501 Japan College of Engineering Kanazawa Institute of Technology 7-1 Nonoichi Ishikawa921-8501 Japan Department of Electrical Engineering National Institute of Technology Ishikawa College Kitacyujo Tsubata Ishikawa929-0392 Japan Saiseikai Kanazawa Hospital Ni 13-6 Akatsuchimachi Kanazawa Ishikawa920-0353 Japan School of Engineering Tokyo Institute of Technology 2-12-1 O-okayama Meguro-ku Tokyo152-8550 Japan

This paper considers a functional electrical stimulation (FES) cycling with cadence tracking control for rehabilitation of hemiparesis. A recumbent trike and rider with four muscle groups is modeled as an Euler Lagrange system based on a pedaling force direction. We propose cadence tracking control considering effects of antagonistic bi-articular muscles to stimulate multiple muscle groups continuously at all angles during pedaling motion. Stability of the developed controller is analyzed through Lyapunov-based methods. Experimental results in healthy participants are shown to confirm the validity of the proposed method and the potential for the rehabilitation of hemiparesis patients. © 2018 The Institute of Electrical Engineers of Japan.

关键词： Lagrange multipliers

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A damage sensitive feature: Beam case

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IOP Conference Series: Materials Science and engineering 2019年第1期694卷

作者： Fergyanto E Gunawan Nobumasa Sekishita Industrial Engineering Department BINUS Graduate Program - Master of Industrial Engineering Bina Nusantara University Jakarta Indonesia 11480 Department of Mechanical Engineering Toyohashi University of Technology Toyohashi Aichi 441-8580 Japan

With the adoption of damage tolerance design principle, the health monitoring system has become an integral part of the engineering structure in operation. For the system to work, damage indicator that describes the structural integrity level should be established and monitored. Damage indicator is usually derived from structural responses. Many quantities have been proposed for damage indicator. Some popular damage indicators are natural frequency, mode shape, curvature, strain energy, and t-, F-, and z-statistics. In this paper, we propose a new damage indicator derived from the theory of the strength of materials. We evaluate the proposal for a case involving damage on a simply-supported beam. The required data are established numerically by the finite element method for structure in healthy and damaged conditions. The results suggest that the current proposal is more sensitive to damage than the natural frequency.

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Phase-change metal ink with pH-controlled chemical sintering for versatile and scalable fabrication of variable stiffness electronics

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Science advances 2025年第22期11卷 eadv4921页

作者： Simok Lee Gun-Hee Lee Inho Kang Woojin Jeon Semin Kim Yejin Ahn Choong Yeon Kim Do A Kwon Michael D Dickey Steve Park Seongjun Park Jae-Woong Jeong School of Electrical Engineering Korea Advanced Institute of Science and Technology (KAIST) 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea. Medical Research Center Seoul National University Seoul 03080 Republic of Korea. Departments of Cogno-Mechatronics Engineering and Optics and Mechatronics Engineering Pusan National University Busan 46241 Republic of Korea. Graduate School of Semiconductor Technology Korea Advanced Institute of Science and Technology (KAIST) 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea. KAIST Information and Electronics Research Institute Daejeon 34141 Republic of Korea. Research Laboratory of Electronics Massachusetts Institute of Technology (MIT) Cambridge MA 02139 USA. Department of Mechanical Engineering Massachusetts Institute of Technology (MIT) Cambridge MA 02139 USA. Department of Chemical and Biomolecular Engineering North Carolina State University (NCSU) Raleigh NC 27606 USA. Department of Materials Science and Engineering Korea Advanced Institute of Science and Technology (KAIST) 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea. KAIST Institute for NanoCentury Daejeon 34141 Republic of Korea. Department of Biomedical Sciences College of Medicine Seoul National University Seoul 03080 Republic of Korea. School of Transdisciplinary Innovations Seoul National University Seoul 03080 Republic of Korea. Interdisciplinary Program in Bioengineering College of Engineering Seoul National University Seoul 08826 Republic of Korea. Department of Transdisciplinary Medicine Seoul National University Hospital Seoul 03080 Republic of Korea. KAIST Institute for Health Science and Technology Daejeon 34141 Republic of Korea.

Variable stiffness electronics represent the forefront of adaptive technology, integrating rigid and soft electronics in a single system through dynamic mechanical modulation. While gallium's high modulus tuning ratio and rapid phase transitions make it ideal for transformative electronic systems (TES), its liquid-state instability, high surface tension, and unintended phase transitions during processing pose substantial challenges. Here, we introduce STiffness-Adjustable temperature-Responsive ink (STAR ink), a chemically sinterable gallium composite electronic ink designed to overcome these obstacles. STAR ink enables high-resolution (~50 micrometers) circuit patterning, large-scale batch fabrication, and three-dimensional structure coating at room temperature. Through pH-controlled chemical sintering, STAR ink-based TES exhibits exceptional mechanical tunability (tuning ratio: 1465) and electrical conductivity (2.27 × 10 siemens per meter). Demonstrated applications-from multilayered variable stiffness printed circuit boards (PCBs) matching standard PCBs' complexity to body-temperature responsive neural probe-underscore STAR ink's potential for reconfigurable electronics across consumer electronics and biomedical devices.

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Numerical simulation of coalescence and break-up of drops in shear flow based on the meshless localized radial basis function method

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Journal of Physics: Conference Series 2021年第1期1825卷

作者： Pranowo Agung Tri Wijayanta Yoshinori Itaya Informatics Department Faculty of Industrial Technology Universitas Atma Jaya Yogyakarta Jl. Babarsari 43 Yogyakarta 55281 Indonesia Research Group of Sustainable Thermofluids Engineering Faculty Universitas Sebelas Maret Jl. Ir. Sutami 36A Kentingan Surakarta 57126 Indonesia Mechanical Engineering Department Faculty of Engineering Universitas Sebelas Maret Jl. Ir. Sutami 36A Kentingan Surakarta 57126 Indonesia Environmental and Renewable Energy Systems Division Graduate School of Engineering Gifu University 1-1 Yanagido Gifu-shi Gifu 501-1193 Japan

In the present paper, the meshless localized radial basis function (RBF) is proposed for simulating of two-phase incompressible viscous flow. Due to the velocity of the shear flow is very low, the fluid can modeled by Stokes equations. For more convenience the primitive variables, i.e., pressure and velocity components of the Stokes equations are transformed into stream function formulation. The interface of the fluid system is modeled by using Cahn-Hilliard equation. The spatial terms of the governing equations are discretized numerically by using the RBF method. The temporal term is integrated by using fully implicit Euler method. The nonlinear terms of Cahn-Hilliard equation is linearized using the Picard iteration. The proposed method is applied to simulate coalescence and break-up of drops in shear flow. The numerical results show that the deformation of the interface can be modeled without any difficulties.

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Electromagnetic Optimization Based on Gaussian Crow Search Approach

Electromagnetic Optimization Based on Gaussian Crow Search A...

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2018 International Symposium on Power Electronics, Electrical Drives, Automation and Motion, SPEEDAM 2018

作者： Dos Santos Coelho, Leandro Klein, Carlos Eduardo Mariani, Viviana Cocco Do Nascimento, Carlos Augusto Richter Askarzadeh, Alireza PUCPR Industrial and Systems Eng. Graduate Program PPGEPS Federal University of Parana UFPR Department of Electrical Engineering DEE/PPGEE Pontifical Catholic University of Parana Curitiba PR Brazil PUCPR Mechanical Engineering Graduate Program PPGEM Curitiba Pontifical Catholic University of Parana PR Brazil Department of Energy Management and Optimization Institute of Science and High Technology and Environmental Sciences Graduate University of Advanced Technology Kerman Iran

ISBN: (纸本)9781538649411

Metaheuristic algorithms have provided efficient tools to designers by which it became possible to determine the optimum solutions of optimization problems encountered in several fields such as engineering, finance and computation. Generally metaheuristics are based on metaphors that are taken from nature or some other processes. Recently, an optimization metaheuristic paradigm based on the social behavior of the crows, called crow search algorithm (CSA), has been proposed. The idea of CSA is motivated from the storing process of the excess food in hiding places then restoring it in the necessary time. The CSA has many favorable characteristics, such as ease of implementation, the need to adjust only a few parameters, a favorable balance between search diversification and intensification, and fast convergence and high sensitivity. However, to enhance the performance of the standard CSA approach, this paper proposes to tune the control parameters using population diversity information and normal (Gaussian) probability distribution function. Loney's solenoid benchmark and circular antenna array design problems are used to evaluate the effectiveness of the conventional CSA and the proposed variant. Simulation results and comparisons with the CSA demonstrated that the performance of the proposed MCSA approach is promising in electromagnetics optimization. © 2018 IEEE.

关键词： Optimization

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Studying operations strategy through cause and effect correlation 24

Studying operations strategy through cause and effect correl...

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24th International Conference on Production Research, ICPR 2017

作者： Okoshi, C.Y. de Lima, E. Pinheiro da Costa, S.E. Gouvêa Industrial and Systems Engineering Graduate Program Pontifical Catholic University of Parana Rua Imaculada Conceição 1155 Prado Velho Curitiba Parana Brazil Industrial and Systems Engineering Graduate Program Federal University of Technology - Parana Via do Conhecimento km 1 Pato Branco Parana Brazil

ISBN: (纸本)9781605955070

The companies use the performance results to identify their main problems and to analyse the cause roots in their production systems, supplier network and process technology. The purpose of this paper is to analyze cause and effect relationships among the performance dimensions and decision areas in the framework of operations strategy. The explored dataset is a research project named 4th Round of High Performance Manufacturing Project. The dataset holds indicators from 304 manufacturing companies in 13 countries. The techniques used for the analysis were descriptive statistics, normality test, factor analysis, and Multiple Linear Regression. As main results, the following cause and effect correlations for each manufacture performance dimension were found: innovation, flexibility, quality, cost, speed, and reliability. The results support the building of cause and effect diagrams regarding performance dimensions and decision areas to be used on improvements to the companies. © 2017 DEStech Publications. All rights reserved.

关键词： Manufacture

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Dynamic Active Constraints for Surgical Robots using Vector Field Inequalities

arXiv

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arXiv 2018年

作者： Marinho, Murilo Marques Adorno, Bruno V. Harada, Kanako Mitsuishi, Mamoru The Department of Mechanical Engineering The University of Tokyo Tokyo Japan The Department of Electrical Engineering The Graduate Program in Electrical Engineering Federal University of Minas Gerais Belo Horizonte-MG Brazil

Robotic assistance allows surgeons to perform dexterous and tremor-free procedures, but robotic aid is still underrepresented in procedures with constrained workspaces, such as deep brain neurosurgery and endonasal surgery. In these procedures, surgeons have restricted vision to areas near the surgical tooltips, which increases the risk of unexpected collisions between the shafts of the instruments and their surroundings. In this work, our vector-field-inequalities method is extended to provide dynamic active-constraints to any number of robots and moving objects sharing the same workspace. The method is evaluated with experiments and simulations in which robot tools have to avoid collisions autonomously and in real-time, in a constrained endonasal surgical environment. Simulations show that with our method the combined trajectory error of two robotic systems is optimal. Experiments using a real robotic system show that the method can autonomously prevent collisions between the moving robots themselves and between the robots and the environment. Moreover, the framework is also successfully verified under teleoperation with tool–tissue interactions. Copyright © 2018, The Authors. All rights reserved.

关键词： Neurosurgery

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Developing a big data/analytics project: A case study in the auto industry 67

Developing a big data/analytics project: A case study in the...

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67th Annual Conference and Expo of the Institute of industrial Engineers 2017

作者： De Oliveira Cordeiro, Gabriel Deschamps, Fernando De Lima, Edson Pinheiro Industrial and Systems Engineering Graduate Program Pontifical Catholic University of Parana Curitiba Brazil Department of Mechanical Engineering Federal University of Parana Curitiba Brazil Federal University of Technology Parana Curitiba Brazil

ISBN: (纸本)9780983762461

For an organization to develop a sustainable position in today's competitive and volatile market, efforts in increasing its maturity of Industry 4.0 thinking and implementation need to be performed. Inside the context of Industry 4.0, the Internet of Things (IoT) and Big Data/Analytics are concepts that are receiving an increased attention of both academics and industry practitioners. However, their implementation is challenging and requires a high level of competences, both in skilled labor and financial resources related to technology selection and implementation. There is a diversity of scenarios in which those two concepts can be applied, especially in large manufacturing enterprises, where large amounts of data are generated, and need to be interpreted, helping managers make better decisions. Hence, it is necessary to organize and better structure projects that conceive, manage, develop and implement IoT and Big Data/Analytics technologies. The objective of this study is to develop a case study presenting the architecture of a small IoT and Big Data/Analytics project in an automotive company. Results suggest that to promote such projects in a larger scale, organizations need to greatly enhance their infrastructure to develop the necessary integration between IoT components and Big Data/Analytics tools.

关键词： Big data

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