Biophysicist (Rockville, Md.)最新文献_第2页

A Torsion-Based Rheometer for Measuring Viscoelastic Material Properties. 用于测量粘弹性材料特性的扭转流变仪

Biophysicist (Rockville, Md.) Pub Date : 2022-12-01 Epub Date: 2022-11-22 DOI: 10.35459/tbp.2020.000172

Merrill Asp, Elise Jutzeler, Jakub Kochanowski, Katherine Kerr, Dawei Song, Sarthak Gupta, Bobby Carroll, Alison Patteson

引用次数: 0

A Semester-Long Learning Path Teaching Computational Skills via Molecular Graphics in PyMOL 在PyMOL中通过分子图形学教授计算技能的一学期学习路径

Biophysicist (Rockville, Md.) Pub Date : 2022-12-01 DOI: 10.35459/tbp.2022.000219

Magnus Kjaergaard, Laura Skak Rasmussen, Johan Nygaard Vinther, Kasper Røjkjær Andersen, E. Andersen, E. Lorentzen, S. Thirup, D. Otzen, D. Brodersen

{"title":"A Semester-Long Learning Path Teaching Computational Skills via Molecular Graphics in PyMOL","authors":"Magnus Kjaergaard, Laura Skak Rasmussen, Johan Nygaard Vinther, Kasper Røjkjær Andersen, E. Andersen, E. Lorentzen, S. Thirup, D. Otzen, D. Brodersen","doi":"10.35459/tbp.2022.000219","DOIUrl":"https://doi.org/10.35459/tbp.2022.000219","url":null,"abstract":"\u0000 Structural biology describes biological processes at the molecular level and is an integral part of undergraduate study programs in molecular biosciences. Students are often fascinated by the visualizations created by molecular graphics software, which allow them to see the molecular world for the first time. Today, molecular visualization and structural analysis do not require expensive high-end computers but can be performed on the students' own laptops and are therefore highly suited for active learning approaches. We have designed a semester-long learning path that integrates molecular graphics and structural analysis using PyMOL into an undergraduate course in biomolecular structure and function. Compared to stand-alone PyMOL introductions, the semester-long learning path allows for an improved pedagogical design. The path progressively introduces more advanced functions in relevant scientific contexts and allows for spaced repetition. Advanced analysis functions in PyMOL are available only via the command line, so the learning path also teaches basic scripting and serves as an accessible introduction to computational thinking because a few lines of code can produce stunning results. Student surveys carried out at the end of the course suggest that the learning path supported the ability to perform structural analysis to a high degree. Moreover, a simulated exam showed that almost all students were able to carry out basic visualization tasks using PyMOL scripts, while three-quarters could undertake advanced structural analysis after following the course. In summary, integration of molecular graphics software with teaching of structural biochemistry allows a hands-on approach to analyzing molecular mechanisms and introduces biologically oriented students to computational thinking.","PeriodicalId":72403,"journal":{"name":"Biophysicist (Rockville, Md.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46813350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

History and Philosophy of a Biophysics Department 生物物理系的历史和哲学

Biophysicist (Rockville, Md.) Pub Date : 2022-09-23 DOI: 10.35459/tbp.2022.000218

N. Düzgüneş

引用次数: 0

Understanding Internal Review Boards and Their Role in Biophysics Education 了解内部审查委员会及其在生物物理教育中的作用

Biophysicist (Rockville, Md.) Pub Date : 2022-09-23 DOI: 10.35459/tbp.2022.000223

A. Feig, Gundula Bosch

引用次数: 0

Dynamical Models of Chemical Exchange in Nuclear Magnetic Resonance Spectroscopy. 核磁共振波谱学中化学交换的动力学模型。

Biophysicist (Rockville, Md.) Pub Date : 2022-07-01 DOI: 10.35459/tbp.2021.000201

Nicolas Daffern, Christopher Nordyke, Meiling Zhang, Arthur G Palmer, John E Straub

{"title":"Dynamical Models of Chemical Exchange in Nuclear Magnetic Resonance Spectroscopy.","authors":"Nicolas Daffern, Christopher Nordyke, Meiling Zhang, Arthur G Palmer, John E Straub","doi":"10.35459/tbp.2021.000201","DOIUrl":"https://doi.org/10.35459/tbp.2021.000201","url":null,"abstract":"Chemical exchange line-broadening is an important phenomenon in nuclear magnetic resonance (NMR) spectroscopy, in which a nuclear spin experiences more than one magnetic environment as a result of chemical or conformational changes of a molecule. The dynamic process of chemical exchange strongly affects the sensitivity and resolution of NMR experiments, and increasingly provides a powerful probe of the inter-conversion between chemical and conformational states of proteins, nucleic acids, and other biological macromolecules. A simple and often used theoretical description of chemical exchange in NMR spectroscopy is based on an idealized two-state jump model (the random-phase or telegraph signal). However, chemical exchange can also be represented as a barrier-crossing event that can be modeled using chemical reaction rate theory. The time scale of crossing is determined by the barrier height, the temperature, and the dissipation modeled as collisional or frictional damping. This tutorial explores the connection between the NMR theory of chemical exchange line-broadening and strong-collision models for chemical kinetics in statistical mechanics. Theoretical modeling and numerical simulation are used to map the rate of barrier-crossing dynamics of a particle on a potential energy surface to the chemical exchange relaxation rate constant. By developing explicit models for the exchange dynamics, the tutorial aims to elucidate the underlying dynamical processes that give rise to the rich phenomenology of chemical exchange observed in NMR spectroscopy. Software for generating and analyzing the numerical simulations is provided in the form of Python and Fortran source codes.","PeriodicalId":72403,"journal":{"name":"Biophysicist (Rockville, Md.)","volume":"3 1","pages":"13-34"},"PeriodicalIF":0.0,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9850547/pdf/nihms-1849913.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9732469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Active Learning Module for Protein Structure Analysis Using Novel Enzymes 利用新型酶进行蛋白质结构分析的主动学习模块

Biophysicist (Rockville, Md.) Pub Date : 2022-04-06 DOI: 10.35459/tbp.2021.000209

Jessica I. Kelz, Gemma R. Takahashi, Fatemeh Safizadeh, Vesta Farahmand, Marquise G. Crosby, Jose L. Uribe, S. H. Kim, Marc A. Sprague-Piercy, Elizabeth M Diessner, B. Norton-Baker, S. Damo, Rachel W. Martin, Pavan Kadandale

{"title":"Active Learning Module for Protein Structure Analysis Using Novel Enzymes","authors":"Jessica I. Kelz, Gemma R. Takahashi, Fatemeh Safizadeh, Vesta Farahmand, Marquise G. Crosby, Jose L. Uribe, S. H. Kim, Marc A. Sprague-Piercy, Elizabeth M Diessner, B. Norton-Baker, S. Damo, Rachel W. Martin, Pavan Kadandale","doi":"10.35459/tbp.2021.000209","DOIUrl":"https://doi.org/10.35459/tbp.2021.000209","url":null,"abstract":"\u0000 A major challenge for science educators is teaching foundational concepts while introducing their students to current research. Here we describe an active learning module developed to teach protein structure fundamentals while supporting ongoing research in enzyme discovery. It can be readily implemented in both entry-level and upper-division college biochemistry or biophysics courses. Preactivity lectures introduced fundamentals of protein secondary structure and provided context for the research projects, and a homework assignment familiarized students with 3-dimensional visualization of biomolecules with UCSF Chimera, a free protein structure viewer. The activity is an online survey in which students compare structure elements in papain, a well-characterized cysteine protease from Carica papaya, to novel homologous proteases identified from the genomes of an extremophilic microbe (Halanaerobium praevalens) and 2 carnivorous plants (Drosera capensis and Cephalotus follicularis). Students were then able to identify, with varying levels of accuracy, a number of structural features in cysteine proteases that could expedite the identification of novel or biochemically interesting cysteine proteases for experimental validation in a university laboratory. Student responses to a postactivity survey were largely positive and constructive, describing points in the activity that could be improved and indicating that the activity was an engaging way to learn about protein structure.","PeriodicalId":72403,"journal":{"name":"Biophysicist (Rockville, Md.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45959150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Control Theory for Physicists by John Bechhoefer John Bechhoefer的物理学家控制理论

Biophysicist (Rockville, Md.) Pub Date : 2022-04-01 DOI: 10.35459/tbp.2022.000217

M. Hinczewski

引用次数: 0

Perspectives on How 1.5 Years of the COVID-19 Pandemic Have Impacted Biophysicists at Primarily Undergraduate Institutions 关于1.5年的COVID-19大流行如何影响主要本科院校的生物物理学家的观点

Biophysicist (Rockville, Md.) Pub Date : 2022-03-11 DOI: 10.35459/tbp.2021.000187

Patricia Soto, Ashley R. Carter, Christos Deligkaris, Duygucan Gül, Kambiz M. Hamadani, J. Knight, D. Matulis, T. N. Ozturk, Y. Rivera-Colón, Elizabeth A. Yates

引用次数: 0

Authentic Science Learning During COVID-19: The Adaptive Design of a SEM Outreach Activity COVID-19期间的真实科学学习:SEM外展活动的适应性设计

Biophysicist (Rockville, Md.) Pub Date : 2022-02-16 DOI: 10.35459/tbp.2021.000206

Ella Yonai, Eyal Shimoni, Keren Kahil, R. Blonder

{"title":"Authentic Science Learning During COVID-19: The Adaptive Design of a SEM Outreach Activity","authors":"Ella Yonai, Eyal Shimoni, Keren Kahil, R. Blonder","doi":"10.35459/tbp.2021.000206","DOIUrl":"https://doi.org/10.35459/tbp.2021.000206","url":null,"abstract":"\u0000 Before March 2020, with the outbreak of the COVID-19 pandemic, remote instruction of science was only moderately developed compared with more traditional approaches for learning science. Since the outbreak, however, all formal education systems have been carried out in remote mode, and outreach activities that take place in a research or academic setting have usually been canceled, or there has been a search for innovative approaches to shift to digital space. Therefore, the development of learning and teaching strategies has currently focused on remote activities. In this study, a design-based approach was applied to transform an existing authentic science activity using a scanning electron microscope (SEM) from face-to-face to remote learning mode. The remote mode activity included the remote operation of the SEM by the participants. The goal was to formulate a general approach to transform authentic outreach activities from face-to-face to remote operation. To evaluate the design, we compared learners' perceived authenticity in the 2 modes and reflected on the process. Data were collected with a Likert-type questionnaire regarding participants' perceived authenticity. The results suggest that items of authenticity related to the experience of learning content have a positive potential for use in remote mode. The learners' experience of connecting with the scientists is an apparent disadvantage in remote mode. However, changes in communication technology or in the pedagogy of remote teaching is a promising direction for improving social experience.","PeriodicalId":72403,"journal":{"name":"Biophysicist (Rockville, Md.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48157681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Online Assignments at Kilimanjaro Christian Medical University College during the COVID-19 Pandemic 2019冠状病毒病大流行期间乞力马扎罗山基督教医科大学的在线作业

Biophysicist (Rockville, Md.) Pub Date : 2022-02-16 DOI: 10.35459/tbp.2021.000194

G. J. M. Stienen, G. Ibrahim, H. Luzinge, A. Mteta, L. Msuya, J. Bartlett

引用次数: 0