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arXiv 2024年

作者： Santiago, Paulo Roberto Pereira Chinaglia, Abel Gonçalves Flanagan, Kira Bedo, Bruno L.S. Mochida, Ligia Yumi Aceros, Juan Bononi, Aline Cesar, Guilherme Manna Biomechanics and Motor Control Laboratory School of Physical Education and Sport USP Brazil Graduate Program in Rehabilitation and Functional Performance Medical School USP Brazil Technology and Sports Performance Analysis Laboratory School of Physical Education USP Brazil Laboratory of Applied Biomechanics and Engineering Brooks College of Health UNF United States Department of Physical Therapy Brooks College of Health UNF United States College of Computing Engineering and Construction UNF United States Municipal Pharmacy Ribeirão Preto Brazil

Human movement analysis is crucial in health and sports biomechanics for understanding physical performance, guiding rehabilitation, and preventing injuries. However, existing tools are often proprietary, expensive, and function as "black boxes", limiting user control and customization. This paper introduces vailá—Versatile Anarcho Integrated Liberation Ánalysis in Multimodal Toolbox—an open-source, Python-based platform designed to enhance human movement analysis by integrating data from multiple biomechanical systems. vailá supports data from diverse sources, including retroreflective motion capture systems, inertial measurement units (IMUs), markerless video capture technology, electromyography (EMG), force plates, and GPS/GNSS systems, enabling comprehensive analysis of movement patterns. Developed entirely in Python 3.11.9, which offers improved efficiency and long-term support, and featuring a straightforward installation process, vailá is accessible to users without extensive programming experience. In this paper, we also present several workflow examples that demonstrate how vailá allows the rapid processing of large batches of data, independent of the type of collection method. This flexibility is especially valuable in research scenarios where unexpected data collection challenges arise, ensuring no valuable data point is lost. We demonstrate the application of vailá in analyzing sit-to-stand movements in pediatric disability, showcasing its capability to provide deeper insights even with unexpected movement patterns. By fostering a collaborative and open environment, vailá encourages users to innovate, customize, and freely explore their analysis needs, potentially contributing to the advancement of rehabilitation strategies and performance optimization. For more details in GitHub repository: https://***/vaila-multimodaltoolbox/vaila and the online documentation: https://*** Codes 92C10, 68U10, 65D18, 65K10 © 2024, CC BY-SA.

关键词： Electromyography

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Study of the effect of dynamic viscosity on the performance of a portable microinjector for severe dry eye treatment using a glycerol-water mixture as a test fluid 11

Study of the effect of dynamic viscosity on the performance ...

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11th International Congress of Physics engineering, CIIF 2021

作者： Babakidi, Narcisse Meni Gamboa, Gonzalo Viramontes Ibarra Bracamontes, Laura Alicia Reyes, Israel Luna Graduate Program in Physical Engineering Universidad Michoacana de San Nicolás de Hidalgo 403 Santiago Tapia Morelia58000 Mexico Faculty of Mechanical Engineering Universidad Michoacana de San Nicolás de Hidalgo 403 Santiago Tapia Morelia58000 Mexico Faculty of Electrical Engineering Universidad Michoacana de San Nicolás de Hidalgo 403 Santiago Tapia Morelia58000 Mexico

This article presents the experimental results of a series of performance tests performed on a microinjector designed to deliver different artificial tear solutions to patients with severe dry eye syndrome. The device is intended to aid in the treatment of this syndrome by providing a continuous injection of artificial tears as needed that overcomes many of the deficiencies inherent in dripping from the manual method. In this work, a set of experiments were carried out to quantify the temporal error that allow determining the dynamic behavior of the viscosity of the glycerol/water mixture as a suitable test solution for the device and then comparing it with the use of commercial artificial tears to define an acceptable viscosity range with a lower temporal error for the correct operation of the system. The experimental method of viscosity measurement was used by means of an Ostwald viscometer that allows determining the times that flow the volume of various percentages by volume of glycerol/water and drops. In addition, the gravimetric density method was used to determine the density and subsequently by the Poiseuille relationship with respect to the densities of percentages in volume of glycerol/water and drops, the different times that flow through a capillary tube, the dynamic viscosity. The results obtained during the operation of the tested microinjector suggest that the microinjector can function correctly without problem in a range of evaluated dynamic viscosity of 1 to 1500 mP a.s with a maximum temporal error of ∼5 %. The temporal error evaluated is a parameter that is necessary to know for the well-being of patients using this device and the viscosities of the products used do not significantly influence the performance of the microinjector. © 2022 Published under licence by IOP Publishing Ltd.

关键词： Viscosity

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An Adaptive Oscillators-Based Approach to Achieve Transparent Control of a Six DoF Lower-Limb Exoskeleton

An Adaptive Oscillators-Based Approach to Achieve Transparen...

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IEEE/ASME International Conference on Mechtronic and Embedded Systems and Applications, MESA

作者： Rafhael Milanezi de Andrade Benito Lorenzo Pugliese Abolfazl Mohebbi Paolo Bonato Graduate Program of Mechanical Engineering Universidade Federal do Espírito Santo Vitória ES Brazil Department of Electronics and Telecommunication Politecnico di Torino Turin Italy Department of Mechanical Engineering Polytechnique Montreal Montreal Canada Department of Physical Medicine & Rehabilitation Harvard Medical School Spaulding Rehabilitation Hospital Boston MA USA

ISBN: (数字)9798331516239

ISBN: (纸本)9798331516246

Lower-limb exoskeletons have been effectively used in rehabilitation to reduce gait impairments. However, making the exoskeleton transparent to provide suitable net interaction torques and assist patient’s movements is yet an open challenge. In this study, we designed a torque control method based on adaptive oscillators (AOs) to reduce interaction forces with a six degree-of-freedom exoskeleton, named the ExoRoboWalker. A synchronization layer was designed with a pool of AOs to estimate user’s gait phase, and a baseline torque controller was introduced to generate a torque profile based on user-robot interaction during the previous gait cycles. A zero-torque controller was used in parallel to the main torque controller with the objective of improving users’ control of the system and their balance. The proposed controller was experimentally evaluated in six healthy subjects who walked with the exoskeleton for 200 gait strides at different walking speeds. A transparent controller we previously implemented based on a zero-impedance model was also evaluated and results were compared with the new controller. The controller based on AOs was able to reduce the average interaction torques by 40% at the highest gait speed of 0.8 m/s relative to the zero-impedance controller we previously implemented.

关键词： Knee Ankle Torque Exoskeletons Torque control Control systems Stability analysis Synchronization Hip Standards

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engineering FRET biosensor for H3K9 acetylation imaging in single living cells

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Med-X 2024年第1期2卷 446-461页

作者： Shitian Li Chang Sun Reed E.S.Harrison Leonardo Cheng Li Gao Longwei Liu Yingxiao Wang Qin Peng Department of Bioengineering Institute of Engineering in MedicineUniversity of CaliforniaSan DiegoLa JollaCA 92093USA Biological Sciences Graduate Program University of CaliforniaSan DiegoLa JollaCA 92093USA Institute of Systems and Physical Biology Shenzhen Bay LaboratoryShenzhen 518132China Alfred E.Mann Department of Biomedical Engineering University of Southern CaliforniaLos AngelesCA 90089USA School of Chemical Engineering and Technology North University of ChinaTaiyuanShanxi 030051China

Histone acetylation is an important epigenetic modification that governs gene expression,chromatin changes in stress response,and cell fate *** biosensors have been developed for various epigenetic events to enable spatiotemporal tracking of sub-cellular signaling *** reported histone H3 acetylation biosensor recognizing two acetyl residues lacked *** this study,using a single bromodomain of the BRD4,we have developed a genetically encoded H3K9ac *** systematically investigated different combinations of the BET family protein as binding domains and performed site-saturated mutagenesis to optimize the biosensor,achieving a dynamic FRET change up to 30%under TSA *** the application of the optimized H3K9ac biosensor,we revealed different basal active chromatin architectures in invasive tumor cells compared to benign tumor ***,we found that H3K9ac level increased dramatically when cancer cells passed through microchannels,which models the physical constraints and mechanical microenvironmental conditions that cancer cells encounter when passing through narrow spaces within the *** result highlights the chromatin plasticity in response to external mechanical *** summary,our H3K9ac biosensor provides a versatile tool for mechanistic investigation of cell fate transition in cancer and mechanotransduction.

关键词： FRET biosensor H3K9 acetylation Nuclear deformation Cancer cell migration

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The effect of stereochemical constraints on the radius of gyration of folded proteins

arXiv

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arXiv 2025年

作者： Logan, Jack A. Sumner, Jacob Grigas, Alex T. Shattuck, Mark D. O'Hern, Corey S. Department of Mechanical Engineering Yale University New HavenCT06520 United States Graduate Program in Computational Biology & Biomedical Informatics Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 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 Department of Physics Yale University New HavenCT06520 United States

Proteins are composed of linear chains of amino acids that fold into complex three-dimensional structures. A general feature of folded proteins is that they are compact with a radius of gyration Rg(N) ∼ Nν that obeys power-law scaling with the number of amino acids N in each protein and ν ∼ 1/3. In this study, we investigate the internal scaling of the radius of gyration Rg(n) versus the chemical separation n between amino acids for all subchains of length n. We show that for globular proteins Rg(n) ∼ nν1,2 with a larger exponent ν1 > 1/3 for small n and a smaller exponent ν2 g(N) ∝ Nν. To describe this scaling behavior for Rg(n), we carry out folding simulations for a series of coarse-grained models for proteins beginning with the freely-jointed and freely-rotating chain models composed of spherical monomers and varying degrees of stereochemical constraints. We show that a minimal model, which coarse-grains amino acids into a single spherical backbone atom and one variable-sized spherical side-chain atom, and enforces bend- and dihedral-angle constraints, can recapitulate Rg(n) for x-ray crystal structures of globular proteins. In addition, this model predicts the correct average packing fraction and size of the hydrophobic core, which are two key physical features that can be used to distinguish between computational 'decoys' and correctly folded proteins in protein design applications. © 2025, CC BY.

关键词： Spheres

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Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling

arXiv

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arXiv 2024年

作者： Liu, Zhuoyi Grigas, Alex T. Sumner, Jacob Knab, Edward Davis, Caitlin M. O’Hern, Corey S. Department of Mechanical Engineering and Materials Science 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 Chemistry 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

Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized, non-physiological environments, the effects of realistic cellular environments on protein structure are largely unexplored. Recently, Förster resonance energy transfer (FRET) has been shown to be an effective experimental method for investigating protein structure in vivo. Inter-residue distances measured in vivo can be incorporated as restraints in molecular dynamics (MD) simulations to model protein structural dynamics in vivo. Since most FRET studies only obtain inter-residue separations for a small number of amino acid pairs, it is important to determine the minimum number of restraints in the MD simulations that are required to achieve a given root-mean-square deviation (RMSD) from the experimental structural ensemble. Further, what is the optimal method for selecting these inter-residue restraints? Here, we implement several methods for selecting the most important FRET pairs and determine the number of pairs Nr that are needed to induce conformational changes in proteins between two experimentally determined structures. We find that enforcing only a small fraction of restraints, Nr/N 0.08, where N is the number of amino acids, can induce the conformational changes. These results establish the efficacy of FRET-assisted MD simulations for atomic scale structural modeling of proteins in vivo. © 2024, CC BY.

关键词： Conformations

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Effect of loops on the mean-square displacement of Rouse-model chromatin

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physical Review E 2024年第4期109卷 044502-044502页

作者： Tianyu Yuan Hao Yan Mary Lou P. Bailey Jessica F. Williams Ivan Surovtsev Megan C. King Simon G. J. Mochrie 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 Applied Physics Yale University New Haven Connecticut 06520 USA Department of Cell Biology Yale School of Medicine New Haven Connecticut 06520 USA Department of Molecular Cell and Developmental Biology Yale University New Haven Connecticut 06511 USA

Chromatin polymer dynamics are commonly described using the classical Rouse model. The subsequent discovery, however, of intermediate-scale chromatin organization known as topologically associating domains (TADs) in experimental Hi-C contact maps for chromosomes across the tree of life, together with the success of loop extrusion factor (LEF) model in explaining TAD formation, motivates efforts to understand the effect of loops and loop extrusion on chromatin dynamics. This paper seeks to fulfill this need by combining LEF-model simulations with extended Rouse-model polymer simulations to investigate the dynamics of chromatin with loops and dynamic loop extrusion. We show that loops significantly suppress the averaged mean-square displacement (MSD) of a gene locus, consistent with recent experiments that track fluorescently labeled chromatin loci. We also find that loops reduce the MSD's stretching exponent from the classical Rouse-model value of 1/2 to a loop-density-dependent value in the 0.45–0.40 range. Remarkably, stretching exponent values in this range have also been observed in recent experiments [Weber et al., Phys. Rev. Lett. 104, 238102 (2010); Bailey et al., Mol. Biol. Cell 34, ar78 (2023)]. We also show that the dynamics of loop extrusion itself negligibly affects chromatin mobility. By studying static “rosette” loop configurations, we also demonstrate that chromatin MSDs and stretching exponents depend on the location of the locus in question relative to the position of the loops and on the local friction environment.

关键词： Chromatin Chromosomes DNA Polymers Brownian dynamics Langevin equation Rouse model

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Mechanical plasticity of cell membranes enhances epithelial wound closure

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physical Review Research 2024年第1期6卷 L012036-L012036页

作者： Andrew T. Ton Arthur K. MacKeith Mark D. Shattuck Corey S. O'Hern Department of Physics Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Mechanical Engineering & Materials Science Yale University New Haven Connecticut 06520 USA Benjamin Levich Institute and Physics Department City College of New York New York New York 10031 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA

During epithelial wound healing, cell morphology near the healed wound and the healing rate vary strongly among different developmental stages even for a single species like Drosophila. We develop deformable particle (DP) model simulations to understand how variations in cell mechanics give rise to distinct wound closure phenotypes in the Drosophila embryonic ectoderm and larval wing disc epithelium. We find that plastic deformation of the cell membrane can generate large changes in cell shape consistent with wound closure in the embryonic ectoderm. Our results show that the embryonic ectoderm is best described by cell membranes with an elasto-plastic response, whereas the larval wing disc is best described by cell membranes with an exclusively elastic response. By varying the mechanical response of cell membranes in DP simulations, we recapitulate the wound closure behavior of both the embryonic ectoderm and the larval wing disc.

关键词： Cell mechanics Jamming Cell membrane Epithelial cells

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Designing the pressure-dependent shear modulus using tessellated granular metamaterials

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physical Review E 2023年第3期108卷 034901-034901页

作者： Jerry Zhang Dong Wang Weiwei Jin Annie Xia Nidhi Pashine Rebecca Kramer-Bottiglio Mark D. Shattuck Corey S. O'Hern Department of Mechanical Engineering & Materials Science Yale University New Haven Connecticut 06520 USA Benjamin Levich Institute and Physics Department The City College of New York New York New York 10031 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut 06520 USA

Jammed packings of granular materials display complex mechanical response. For example, the ensemble-averaged shear modulus 〈G〉 increases as a power law in pressure p for static packings of soft spherical particles that can rearrange during compression. We seek to design granular materials with shear moduli that can either increase or decrease with pressure without particle rearrangements even in the large-system limit. To do this, we construct tessellated granular metamaterials by joining multiple particle-filled cells together. We focus on cells that contain a small number of bidisperse disks in two dimensions. We first study the mechanical properties of individual disk-filled cells with three types of boundaries: periodic boundary conditions (PBC), fixed-length walls (FXW), and flexible walls (FLW). Hypostatic jammed packings are found for cells with FLW, but not in cells with PBC and FXW, and they are stabilized by quartic modes of the dynamical matrix. The shear modulus of a single cell depends linearly on p. We find that the slope of the shear modulus with pressure λc<0 for all packings in single cells with PBC where the number of particles per cell N≥6. In contrast, single cells with FXW and FLW can possess λc>0, as well as λc<0, for N≤16. We show that we can force the mechanical properties of multicell granular metamaterials to possess those of single cells by constraining the end points of the outer walls and enforcing an affine shear response. These studies demonstrate that tessellated granular metamaterials provide a platform for the design of soft materials with specified mechanical properties.

关键词： Jamming Granular solids Mechanical metamaterials

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Implementation of VR-based personal basketball team-practice equipment

Implementation of VR-based personal basketball team-practice...

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IEEE Global Conference on Life Sciences and Technologies (LifeTech)

作者： Hiroki Honma Yoshiaki Iida Yasuyuki Okumura Katsuyuki Fujii Yuki Kuno Graduate Program of Mechatronics Graduate School of Science and Engineering Nanzan University Nagoya Japan Physical Education Center Nanzan University Nagoya Japan Faculty of Science and Engineering Nanzan University Nagoya Japan

ISBN: (数字)9781665418751

ISBN: (纸本)9781665448086

In basketball, the next motion can be instantaneously determined with an accurate understanding of the surrounding conditions. Therefore, it is necessary to develop the ability to judge a situation accurately and perform appropriate actions. Development of such decision-making ability in individual practice can lead to higher efficiency. The purpose of this study is to construct an environment closely resembling interpersonal practice by arranging players in a virtual space using VR technology. As this device is used for practice, the sense of distance from the VR player is important. Hence, this study measures the error between VR players and users.

关键词： Performance evaluation Space technology Image edge detection Conferences Measurement uncertainty Decision making Life sciences

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