Biophysicist (Rockville, Md.)最新文献

英文中文

Reflections on COVID-19–induced online teaching in biophysics courses 新冠肺炎诱发生物物理在线教学的思考

Biophysicist (Rockville, Md.)

Pub Date : 2021-06-29 DOI: 10.35459/tbp.2021.000183

S. Klumpp, Sarah Köster, A. Pawsey, Yvonne Lips, M. Wenderoth, P. Klein

引用次数: 1

Updating MoonProt From Home: An Online Student Research Project During the COVID-19 Pandemic 在家更新MoonProt: COVID-19大流行期间的在线学生研究项目

Biophysicist (Rockville, Md.)

Pub Date : 2021-06-29 DOI: 10.35459/tbp.2021.000190

C. Jeffery

During the spring of 2020, labs around the world suddenly closed to help slow the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the deadly COVID-19 pandemic. Among the many effects on science and education, the lab closures resulted in undergraduates losing the opportunity to work on research projects during that spring and summer and throughout the 2020–2021 academic year. Participating directly in a research project is important for undergraduate students to gain research experience and with it the mentoring and training needed to prepare them for graduate school or professional school and a future career in science. To address this need during the pandemic, I organized an online, remote, collaborative project for a team of undergraduates at the University of Illinois at Chicago (UIC) that grew to include additional undergraduates from other universities as well as several high school students and their teachers. My experience in organizing this project could serve as a model for organizing online student research projects in the future.

2020年春季，在致命的COVID-19大流行期间，世界各地的实验室突然关闭，以帮助减缓严重急性呼吸综合征冠状病毒2 (SARS-CoV-2)的传播。在对科学和教育的诸多影响中，实验室关闭导致本科生在春季和夏季以及整个2020-2021学年失去了从事研究项目的机会。直接参与研究项目对本科生获得研究经验非常重要，同时也为他们进入研究生院或专业学校以及未来的科学职业生涯做好了必要的指导和培训。为了在大流行期间满足这一需求，我为伊利诺伊大学芝加哥分校(UIC)的一个本科生团队组织了一个在线、远程协作项目，其中包括来自其他大学的本科生以及几名高中生和他们的老师。我组织这个项目的经验可以作为将来组织在线学生研究项目的一个模式。

引用次数: 1

An Interactive Framework for Teaching Viscoelastic Modeling 一个交互式的粘弹性建模教学框架

Biophysicist (Rockville, Md.)

Pub Date : 2021-06-25 DOI: 10.35459/tbp.2020.000169

Delf Kah, B. Fabry, Richard C. Gerum

Rheologic models consisting of combinations of linear elements, such as springs and dashpots, are widely used in biophysics to describe the mechanical and, in particular, the viscoelastic behavior of proteins, cells, tissue, and soft matter. Even simple arrangements with few elements often suffice to recapitulate the experimental data and to provide biophysical insights, making them an ideal subject for educational purposes. To provide students with an intuitive understanding of the mechanical behavior of spring and dashpot models, we describe a computer simulation tool, elastic viscous system simulator (ElViS), written in the JavaScript programming language for designing viscoelastic models via a graphical user interface and simulating the mechanical response to various inputs. As an example application, we designed a virtual laboratory course using ElViS that teaches the basic principles of viscoelastic modeling in a gamelike manner. We then surveyed 50 undergraduate students of a 1-semester course in biophysics who participated in the virtual laboratory course. Students felt that the course was a helpful addition to the lecture and that it improved learning success.

流变性模型由线性元素的组合组成，如弹簧和阻尼器，在生物物理学中被广泛用于描述力学，特别是蛋白质、细胞、组织和软物质的粘弹性行为。即使是很少元素的简单安排也足以概括实验数据，并提供生物物理学的见解，使它们成为教育目的的理想主题。为了让学生对弹簧和阻尼器模型的力学行为有一个直观的理解，我们描述了一个用JavaScript编程语言编写的计算机仿真工具，弹性粘性系统模拟器(ElViS)，用于通过图形用户界面设计粘弹性模型并模拟各种输入的力学响应。作为一个示例应用程序，我们设计了一个虚拟实验室课程，使用ElViS以类似游戏的方式教授粘弹性建模的基本原理。然后，我们调查了50名参加虚拟实验室课程的生物物理学一学期课程的本科生。学生们觉得这门课是对讲课的有益补充，提高了学习的成功率。

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引用次数: 0

Reaching Behind the Black Screen 触及黑屏背后

Biophysicist (Rockville, Md.)

Pub Date : 2021-06-25 DOI: 10.35459/tbp.2021.000179

Shira Passentin

Shira Passentin is a MSc student in the Department of Science Teaching at the Weizmann Institute of Science. She also is a teacher of science and technology in a middle school (junior high school) in Israel. In this article, she describes a simple biophysical activity, performed by her students at home during coronavirus disease 2019 (COVID-19) lockdowns, which explicates the meaning and importance of surface area in a biologic context.

Shira Passentin是魏茨曼科学研究所科学教学系的一名硕士研究生。她也是以色列一所中学(初中)的科学技术教师。在这篇文章中，她描述了一个简单的生物物理活动，这是她的学生在2019冠状病毒病(COVID-19)封锁期间在家中进行的，这说明了表面积在生物学背景下的意义和重要性。

引用次数: 0

Report on BASICS: Lesson Plan on Aerosols and Infection BASICS报告：气溶胶和感染课程计划

Biophysicist (Rockville, Md.)

Pub Date : 2021-05-27 DOI: 10.35459/TBP.2021.000176

Rebecca D. Hogewood, S. Endow

From online lectures to virtual lab assignments to Zoom breakout rooms, COVID-19 has changed the way students are learning around the world. The goal of the BASICS: Lesson Plan on Aerosols & Infection is to help students understand the biophysics underlying aerosols to explain why the SARS-CoV-2 virus has taken over our lives. The Lesson Plan explains how aerosols travel through air and demonstrates how masks can effectively prevent aerosol transmission and, by extension, viral infection. In this Report, we discuss how we developed this Lesson Plan and what students can learn about infectious virus spread in relation to aerosols.

从在线讲座到虚拟实验室作业再到Zoom分组会议室，新冠肺炎改变了学生在世界各地的学习方式。BASICS：气溶胶与感染课程计划的目标是帮助学生理解气溶胶背后的生物物理，以解释为什么严重急性呼吸系统综合征冠状病毒2型病毒占据了我们的生活。该课程计划解释了气溶胶如何在空气中传播，并展示了口罩如何有效防止气溶胶传播，进而防止病毒感染。在本报告中，我们讨论了我们是如何制定本课程计划的，以及学生可以了解到与气溶胶有关的传染性病毒传播。

引用次数: 0

What Worked, What Did Not: University Instruction during a Pandemic 什么有效，什么无效：大流行病期间的大学教学

Biophysicist (Rockville, Md.)

Pub Date : 2021-05-14 DOI: 10.35459/TBP.2021.000181

Neil A. Manson, R. M. Wadkins

In this report, we discuss the experience of both lecturing and teaching laboratory classes during a pandemic at the University of Mississippi (UM). UM is a relatively rural university with approximately 20 000 students. The instructional approaches that we attempted would be significantly more difficult to implement at universities with larger class sizes, geographically more restricted with regard to climate, or more urban with confined space, yet we observed many failures, even at a rural, spacious campus. Here, we note the various models of instruction that—in our case—could be separated into three approaches: in-person (i.e., traditional face-to-face instruction), online only, and a hybrid model with some component of the two (1). We discuss our experiences of what went right and what went wrong with each approach. Given that similar approaches have been undertaken around the globe, we use this report to relate what we observed as both effective and noneffective for our style of university, with special emphasis on physical biochemical laboratory training of students.

在本报告中，我们讨论了密西西比大学（UM）在疫情期间讲授和教授实验室课程的经验。UM是一所相对乡村的大学，有大约2万名学生。我们尝试的教学方法在班级规模较大、地理位置受气候限制更大或空间有限的城市大学要实施起来要困难得多，但我们观察到许多失败，即使在农村宽敞的校园也是如此。在这里，我们注意到，在我们的案例中，各种教学模式可以分为三种方法：面对面教学（即传统的面对面教学）、仅在线教学和包含两者的混合模式（1）。我们讨论了每种方法的正确之处和错误之处。鉴于全球各地都采取了类似的方法，我们用这份报告来说明我们观察到的对我们的大学风格既有效又无效的东西，特别强调学生的物理-生物化学实验室培训。

引用次数: 0

Beyond Ticking Boxes: Holistic Assessment of Travel Award Programs is Essential for Inclusivity 超越复选框:全面评估旅游奖励计划对包容性至关重要

Biophysicist (Rockville, Md.)

Pub Date : 2021-05-10 DOI: 10.31219/osf.io/fsrpb

C. Etson, Kirsten F. Block, Michael D. Burton, Ashanti Edwards, Sonia C. Flores, Catherine Fry, Ashley N. Guillory, S. Ingram, Richard McGee, D. Neely-Fisher, Stephanie Paxson, Laura Phelan, C. Primus, Kirsta Suggs, Leticia Vega, Elizabeth Vuong, L. Hammonds-Odie, Michael J. Leibowitz, M. Zavala, J. Lujan, M. Ramirez-Alvarado, Verónica A. Segarra

Many professional societies utilize travel awards programs to foster inclusion and facilitate the professional development of underrepresented minority (URM) scientists. All member societies that participate in the Alliance to Catalyze Change for Equity in STEM Success (ACCESS) do so to some degree. Members of this meta-organization recently came together to share their different approaches to URM travel award program assessment. The practices of the Biophysical Society (BPS), one of the ACCESS member societies, is used as a case study to discuss the highlights of our findings. We share and discuss a framework for URM travel award program assessment.

许多专业协会利用旅行奖励计划来促进未被充分代表的少数民族(URM)科学家的包容和专业发展。参与促进STEM成功公平变革联盟(ACCESS)的所有成员协会都在一定程度上这样做。这个元组织的成员最近聚在一起分享了他们对URM旅游奖励计划评估的不同方法。以ACCESS成员学会之一的生物物理学会(BPS)的实践为例，讨论了我们研究结果的亮点。我们分享并讨论了URM差旅奖励计划评估的框架。

引用次数: 3

Quantifying Planarian Behavior as an Introduction to Object Tracking and Signal Processing 量化Planarian行为作为目标跟踪和信号处理的引子

Biophysicist (Rockville, Md.)

Pub Date : 2021-04-27 DOI: 10.35459/TBP.2020.000159

N. Stowell, Tapan Goel, Vir Shetty, Jocelyne Noveral, Eva-Maria S. Collins

Answers to mechanistic questions about biological phenomena require fluency in a variety of molecular biology techniques and physical concepts. Here, we present an interdisciplinary approach to introducing undergraduate students to an important problem in the areas of animal behavior and neuroscience—the neuronal control of animal behavior. In this lab module, students explore planarian behavior by quantitative image and data analysis with freely available software and low-cost resources. Planarians are ∼1–2-cm-long aquatic free-living flatworms famous for their regeneration abilities. They are inexpensive and easy to maintain, handle, and perturb, and their fairly large size allows for image acquisition with a webcam, which makes this lab module accessible and scalable. Our lab module integrates basic physical concepts such as center of mass, velocity and speed, periodic signals, and time series analysis in the context of a biological system. The module is designed to attract students with diverse disciplinary backgrounds. It challenges the students to form hypotheses about behavior and equips them with a basic but broadly applicable toolkit to achieve this quantitatively. We give a detailed description of the necessary resources and show how to implement the module. We also provide suggestions for advanced exercises and possible extensions. Finally, we provide student feedback from a pilot implementation.

要回答有关生物现象的机械问题，需要熟练掌握各种分子生物学技术和物理概念。在这里，我们提出了一种跨学科的方法，向本科生介绍动物行为和神经科学领域的一个重要问题——动物行为的神经元控制。在本实验模块中，学生将使用免费软件和低成本资源，通过定量图像和数据分析来探索涡虫的行为。涡虫是一种长约1 - 2厘米的水生自由生活扁虫，以其再生能力而闻名。它们价格低廉，易于维护，处理和扰动，并且它们相当大的尺寸允许使用网络摄像头进行图像采集，这使得该实验室模块易于访问和扩展。我们的实验模块集成了基本的物理概念，如质心，速度和速度，周期信号和时间序列分析在生物系统的背景下。该模块旨在吸引具有不同学科背景的学生。它挑战学生形成对行为的假设，并装备他们一个基本的，但广泛适用的工具包来实现这一定量。我们给出了必要资源的详细描述，并展示了如何实现该模块。我们还为高级练习和可能的扩展提供建议。最后，我们从试点实施中提供学生反馈。

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引用次数: 2

Introductory Models of COVID-19 in the United States 美国COVID-19的介绍模型

Biophysicist (Rockville, Md.)

Pub Date : 2021-04-18 DOI: 10.35459/tbp.2021.000200

P. Nelson

Students develop and test simple kinetic models of the spread of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Microsoft Excel is used as the modeling platform because it is nonthreatening to students and it is widely available. Students develop finite difference models and implement them in the cells of preformatted spreadsheets following a guided inquiry pedagogy that introduces new model parameters in a scaffolded step-by-step manner. That approach allows students to investigate the implications of new model parameters in a systematic way. Students fit the resulting models to reported cases per day data for the United States using least squares techniques with Excel's Solver. Using their own spreadsheets, students discover for themselves that the initial exponential growth of COVID-19 can be explained by a simplified unlimited growth model and by the susceptible-infected-recovered (SIR) model. They also discover that the effects of social distancing can be modeled using a Gaussian transition function for the infection rate coefficient and that the summer surge was caused by prematurely relaxing social distancing and then reimposing stricter social distancing. Students then model the effect of vaccinations and validate the resulting susceptible-infected-recovered-vaccinated (SIRV) model by showing that it successfully predicts the reported cases per day data from Thanksgiving through the holiday period up to 14 February 2021. The same SIRV model is then extended and successfully fits the fourth peak up to 1 June 2021, caused by further relaxation of social distancing measures. Finally, students extend the model up to the present day (27 August 2021) and successfully account for the appearance of the delta variant of the SARS-CoV-2 virus. The fitted model also predicts that the delta variant peak will be comparatively short, and the cases per day data should begin to fall off in early September 2021, counter to current expectations. This case study makes an excellent capstone experience for students interested in scientific modeling.

学生开发和测试由严重急性呼吸综合征冠状病毒2 (SARS-CoV-2)病毒引起的2019冠状病毒病(COVID-19)传播的简单动力学模型。采用Microsoft Excel作为建模平台，因为它对学生没有威胁，而且使用广泛。学生开发有限差分模型，并在预格式化电子表格的单元格中实现它们，遵循指导式探究教学法，以循序渐进的方式引入新的模型参数。这种方法允许学生以系统的方式研究新模型参数的含义。学生们使用最小二乘技术和Excel的求解器将结果模型与美国每天报告的病例数据拟合。学生们使用自己的电子表格发现，COVID-19最初的指数增长可以用简化的无限增长模型和易感感染康复模型来解释。他们还发现，社交距离的影响可以使用感染率系数的高斯过渡函数来建模，夏季的激增是由于过早放松社交距离，然后重新实施更严格的社交距离造成的。然后，学生们对疫苗接种的效果进行建模，并验证由此产生的易感感染-恢复接种疫苗(SIRV)模型，证明该模型成功预测了从感恩节到2021年2月14日假期期间每天报告的病例数据。然后对相同的SIRV模型进行扩展，并成功拟合到2021年6月1日的第四个峰值，这是由进一步放松社交距离措施造成的。最后，学生们将模型扩展到今天(2021年8月27日)，并成功地解释了SARS-CoV-2病毒的δ变体的出现。拟合的模型还预测，delta变异峰值将相对较短，每天的病例数据将在2021年9月初开始下降，这与目前的预期相反。本案例研究为对科学建模感兴趣的学生提供了极好的顶点体验。

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引用次数: 0

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design. PyRosetta Jupyter笔记本教授生物分子结构预测和设计。

Biophysicist (Rockville, Md.)

Pub Date : 2021-04-01 Epub Date: 2021-04-14 DOI: 10.35459/tbp.2019.000147

Kathy H Le, Jared Adolf-Bryfogle, Jason C Klima, Sergey Lyskov, Jason Labonte, Steven Bertolani, Shourya S Roy Burman, Andrew Leaver-Fay, Brian Weitzner, Jack Maguire, Ramya Rangan, Matt A Adrianowycz, Rebecca F Alford, Aleexsan Adal, Morgan L Nance, Yuanhan Wu, Jordan Willis, Daniel W Kulp, Rhiju Das, Roland L Dunbrack, William Schief, Brian Kuhlman, Justin B Siegel, Jeffrey J Gray

Biomolecular structure drives function, and computational capabilities have progressed such that the prediction and computational design of biomolecular structures is increasingly feasible. Because computational biophysics attracts students from many different backgrounds and with different levels of resources, teaching the subject can be challenging. One strategy to teach diverse learners is with interactive multimedia material that promotes self-paced, active learning. We have created a hands-on education strategy with a set of sixteen modules that teach topics in biomolecular structure and design, from fundamentals of conformational sampling and energy evaluation to applications like protein docking, antibody design, and RNA structure prediction. Our modules are based on PyRosetta, a Python library that encapsulates all computational modules and methods in the Rosetta software package. The workshop-style modules are implemented as Jupyter Notebooks that can be executed in the Google Colaboratory, allowing learners access with just a web browser. The digital format of Jupyter Notebooks allows us to embed images, molecular visualization movies, and interactive coding exercises. This multimodal approach may better reach students from different disciplines and experience levels as well as attract more researchers from smaller labs and cognate backgrounds to leverage PyRosetta in their science and engineering research. All materials are freely available at https://github.com/RosettaCommons/PyRosetta.notebooks.

生物分子结构驱动功能，计算能力的进步使得生物分子结构的预测和计算设计越来越可行。由于计算生物物理学吸引了来自不同背景和不同资源水平的学生，因此教学这门学科可能具有挑战性。教授不同学习者的一种策略是使用交互式多媒体材料，促进自主学习和主动学习。我们创建了一套实践教学策略，包含16个模块，教授生物分子结构和设计的主题，从构象采样和能量评估的基础知识到蛋白质对接、抗体设计和RNA结构预测等应用。我们的模块基于PyRosetta，这是一个Python库，它封装了Rosetta软件包中的所有计算模块和方法。讲习班风格的模块被实现为Jupyter笔记本，可以在Google协作实验室中执行，允许学习者仅通过网络浏览器访问。Jupyter notebook的数字格式允许我们嵌入图像、分子可视化电影和交互式编码练习。这种多模式的方法可以更好地接触到来自不同学科和经验水平的学生，并吸引更多来自小型实验室和同类背景的研究人员利用PyRosetta进行科学和工程研究。所有材料均可在https://github.com/RosettaCommons/PyRosetta.notebooks免费获取。

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