How to foster STEM learning during Covid-19 remote schooling: Combining virtual and video experiments.

Understanding scientific concepts is a fundamental aim of science education. Conceptual understanding can be fostered through inquiry learning with experiments. However, during the Covid-19 pandemic school closures hands-on experiments could hardly be realized. Fortunately, digital technologies allow for conducting experiments virtually by using interactive simulations or observing video recordings of hands-on experiments. In the present study, 154 seventh graders in remote schooling were involved in inquiry learning using either a combination of virtual and video experiments in two different orders or only virtual experiments. We hypothesized that in general inquiry learning fosters students' conceptual understanding in physics, which could be confirmed. Moreover, we expected the combinations to be more effective than learning with virtual experiments only due to the complementary roles of the prior, which was, however, not the case. We conclude that virtual and video experiments can be recommended to teachers if hands-on experimentation is not possible.

Designing a Simulation Lab: The Process that Led to Action Potentials Explored and Extended, Two Simulation-Based Neurobiology Labs.

Simulations have long played an important role in neurobiology education. This paper describes the design-research process that led to development of two popular simulation-based neurobiology modules used in undergraduate biology classes. Action Potentials Explored, and the more in-depth and quantitative Action Potentials Extended, are the third generation of neurobiology teaching simulations the author has helped develop. The paper focuses on how we used the idea of constraining simulations as a way of tuning the modules to different student populations. Other designers of interactive educational materials may also find constraint a useful lens through which to view designs.

NeuroLab: A Set of Graphical Computer Simulations to Support Neuroscience Instruction at the High School and Undergraduate Level.

Young students struggle with concepts that involve the parallel activity of large numbers of similar entities, precisely the kind of concepts that abound in neuroscience. While a direct experience to laboratory work cannot be replaced, such activities include a steep learning curve and may be impractical in certain course settings. This article describes a set of computer simulations of a number of neural processes using NetLogo (Wilensky, 1999), a software environment for the design and implementation of multi-agent simulations that has an intuitive graphical interface and minimal learning curve. NeuroLab is a group of graphical simulations that portray ions, molecules, synapses or cells as individual recognizable agents with particular behaviors, depending on the level at which the particular process is simulated. On a typical assignment, students run the simulation a few times manipulating specific variables by means of buttons, switches and sliders and observe the results of their manipulations on the main window. Many simulations include one or more plots that help visualize statistical data in real time and allow for the testing of experimental hypotheses. Students may repeat the simulation as many times as they wish and collect data or answer questions based on their observations. Assignments may take just a few minutes to perform, but could conceivably be part of more involved activities as designed by the instructor.

Shape2SAS: a web application to simulate small-angle scattering data and pair distance distributions from user-defined shapes.

Shape2SAS is a web application that allows researchers and students to build intuition about and understanding of small-angle scattering. It is available at https://somo.chem.utk.edu/shape2sas. The user defines a model of arbitrary shape by combining geometrical subunits, and Shape2SAS then calculates and displays the scattering intensity and the pair distance distribution, as well as a visualization of the user-defined shape. Simulated data with realistic noise are also generated. Here, it is demonstrated how Shape2SAS can calculate and display the different scattering patterns for various geometrical shapes, such as spheres and cylinders. It is also shown how the effect of structure factors can be visualized. Finally, it is indicated how multi-contrast particles can readily be generated, and how the calculated scattering may be used to validate and visualize analytical models generated in analysis software for fitting small-angle scattering data.

Teaching Neurophysiology to Undergraduates using Neurons in Action.

Neurons in Action, a set of 25 hyperlinked tutorials and interactive simulations on CD-ROM, provides the student with a completely different approach to neurophysiology from that of textbooks. Guided by the tutorials, by their professor, by the urge to test their understanding, or simply by curiosity, students specify the parameters of a patch of membrane, an axon, a postsynaptic membrane, or a cell and run virtual experiments. Parameters include geometry, the number and type of ion channels in the membrane, the number of myelin wraps of the axon, the ion concentrations inside and out, synaptic variables, and temperature. Hyperlinked explanations, historical information, and classic papers on the CD provide the "textbook" material. This article describes this learning tool and details several ways in which it is being used at the undergraduate level.

Development of an Online Experiment Platform for High School Biology.

We developed a novel online platform, Rex (Real experiments) that immerses students in a scientific investigative process. Rex is a virtual web-based biological science experiment platform, hosted by real scientists, and uses actual lab experiments that generate real data for students to collect, analyze, and interpret. Seven neuroscience experiments use zebrafish and rats as model systems to study the effects of drugs such as tetrahydrocannabinol (THC), caffeine, alcohol, and cigarette smoke, which are of interest to high school students. We carried out a small field-test of Rex in a variety of high school biology classrooms (e.g., standard, honors, AP, anatomy/physiology) to obtain student and teacher feedback about the implementation and usability of the program. We also assessed student situational interest (SI) to determine whether the Rex experiment captured students' attention, and whether it was an enjoyable and meaningful experience. Overall, students reported a moderate level of SI after participating in the Rex experiments. Situational interest did not differ across teachers, class section, class level, or the type of experiment. In addition, we present details of the technical issues encountered in the classroom, and we provide guidance to readers who may want to use the resource in their classrooms.

A consistent full-field integrated DIC framework for HR-EBSD.

A general, transparent, finite-strain Integrated Digital Image Correlation (IDIC) framework for high angular resolution EBSD (HR-EBSD) is proposed, and implemented through a rigorous derivation of the optimization scheme starting from the fundamental brightness conservation equation in combination with a clear geometric model of the Electron BackScatter Pattern (EBSP) formation. This results in a direct one-step correlation of the full field-of-view of EBSPs, which is validated here on dynamically simulated patterns. Strain and rotation component errors are, on average, (well) below 10-5 for small (Eeq=0.05%) and medium (Eeq=0.2%) strain, and below 3×10-5 for large strain (Eeq=1%), all for large rotations up to 10° and 2% image noise. High robustness against poor initial guesses (1° misorientation and zero strain) and typical convergence in 5 iterations is consistently observed for, respectively, image noise up to 20% and 5%. This high accuracy and robustness rivals, when comparing validation on dynamically simulated patterns, the most accurate HR-EBSD algorithms currently available which combine sophisticated filtering and remapping strategies with an indirect two-step correlation approach of local subset ROIs. The proposed general IDIC/HR-EBSD framework lays the foundation for future extensions towards more accurate EBSP formation models or even absolute HR-EBSD.

MioLab, a rat cardiac contractile force simulator: Applications to teaching cardiac cell physiology and biophysics.

INTRODUCTION: Understanding the basic concepts of physiology and biophysics of cardiac cells can be improved by virtual experiments that illustrate the complex excitation-contraction coupling process in cardiac cells. The aim of this study is to propose a rat cardiac myocyte simulator, with which calcium dynamics in excitation-contraction coupling of an isolated cell can be observed. This model has been used in the course "Mathematical Modeling and Simulation of Biological Systems". In this paper we present the didactic utility of the simulator MioLab(®). METHODS: The simulator enables virtual experiments that can help studying inhibitors and activators in the sarcoplasmic reticulum sodium-calcium exchanger, thus corroborating a better understanding of the effects of medications, which are used to treat arrhythmias, on these compartments. The graphical interfaces were developed not only to facilitate the use of the simulator, but also to promote a constructive learning on the subject, since there are animations and videos for each stage of the simulation. The effectiveness of the simulator was tested by a group of graduate students. RESULTS: Some examples of simulations were presented in order to describe the overall structure of the simulator. Part of these virtual experiments became an activity for Biomedical Engineering graduate students, who evaluated the simulator based on its didactic quality. As a result, students answered a questionnaire on the usability and functionality of the simulator as a teaching tool. All students performed the proposed activities and classified the simulator as an optimal or good learning tool. In their written questions, students indicated as negative characteristics some problems with visualizing graphs; as positive characteristics, they indicated the simulator's didactic function, especially tutorials and videos on the topic of this study. CONCLUSIONS: The results show that the simulator complements the study of the physiology and biophysics of the cardiac cell.

A call for virtual experiments: accelerating the scientific process.

Experimentation is fundamental to the scientific method, whether for exploration, description or explanation. We argue that promoting the reuse of virtual experiments (the in silico analogues of wet-lab or field experiments) would vastly improve the usefulness and relevance of computational models, encouraging critical scrutiny of models and serving as a common language between modellers and experimentalists. We review the benefits of reusable virtual experiments: in specifying, assaying, and comparing the behavioural repertoires of models; as prerequisites for reproducible research; to guide model reuse and composition; and for quality assurance in the translational application of models. A key step towards achieving this is that models and experimental protocols should be represented separately, but annotated so as to facilitate the linking of models to experiments and data. Lastly, we outline how the rigorous, streamlined confrontation between experimental datasets and candidate models would enable a "continuous integration" of biological knowledge, transforming our approach to systems biology.

Set of Simulators of the Electrophysiology of the A-Type Potassium Current (IA) in Neurons / Conjunto de Simuladores de la Electrofisiología de la Corriente de Potasio Tipo-A (IA) en Neuronas

Abstract The A-type potassium current (IA) participates in important brain functions, including neuronal excitability, synaptic integration, and regulation of action potential patterns and firing frequency. Based on the characterization of its electrophysiological properties by current and voltage clamp techniques, mathematical models have been developed that reproduce IA function. For such models, it is necessary to numerically solve equations and utilize hardware with special speed and performance characteristics. Since specific software for studying IA is not found on the Internet, the aim of this work was to develop a set of simulators grouped into three computer programs: (1) IA Current, (2) IA Constant-V Curves and (3) IA AP Train. These simulators provide a virtual reproduction of experiments on neurons with the possibility of setting the current and voltage, which allows for the study of the electrophysiological and biophysical characteristics of IA and its effect on the train of action potentials. The mathematical models employed were derived from the work of Connor et al., giving rise to Hodgkin-Huxley type models. The programs were developed in Visual Basic® and the differential equation systems were simultaneously solved numerically. The resulting system represents a breakthrough in the ability to replicate IA activity in neurons.

Resumen La corriente de potasio tipo-A (IA) tiene importantes funciones cerebrales como: excitabilidad neuronal, integración sináptica y regulación de patrones de potenciales de acción y la frecuencia de disparo. Sus propiedades electrofisiológicas se han caracterizado mediante técnicas de fijación de corriente y de voltaje. A partir de estos conocimientos se desarrollaron modelos matemáticos que reproducen su función. La cantidad de ecuaciones a resolver hace que se requiera de hardware con velocidad y potencia especiales. Un software específico para el estudio propio de la corriente IA no se ha encontrado en Internet. En este trabajo se presenta un conjunto de simuladores agrupados en tres programas de cómputo: (1) Corriente IA, (2) Curvas Constante-V y (3) Tren-IA, que permiten reproducir los experimentos con técnicas de fijación de corriente y de voltaje para estudiar las características electrofisiológicas y biofísicas de la corriente IA, e investigar el efecto que tiene en el tren de potenciales de acción. Los modelos matemáticos utilizados fueron derivados de los trabajos de Connor et al., dando origen a modelos tipo Hodgkin y Huxley. Los programas fueron desarrollados en Visual Basic®. Los sistemas de ecuaciones diferenciales fueron resueltos simultáneamente de forma numérica. Los programas desarrollados contribuyen a solucionar la carencia de este tipo de programas.

Desarrollo de un Simulador de los Experimentos Clásicos y Actualizados de Fijación de Voltaje de Hodgkin y Huxley / Developing a simulation program for classic and updated Hodgkin and Huxley's voltage clamp experiments

Resumen: Los estudios de Hodgkin y Huxley fueron el punto de partida de la generación de modelos matemáticos que explican, reproducen y predicen los resultados experimentales del comportamiento de los canales iónicos sensibles a voltaje del axón. Los altos costos de estos experimentos impiden su implementación en la práctica docente de licenciatura. Una alternativa didáctica son los experimentos virtuales mediante simuladores computacionales. En este trabajo se presenta el desarrollo de un simulador que reproduce paso a paso los experimentos clásicos de Hodgkin y Huxley sobre las conductancias de los canales dependientes de voltaje del axón gigante de calamar. El simulador fue desarrollado en lenguaje Visual Basic ver 5.0 para ambiente Wiindows® . Está formado de cuatro módulos: (1) simulación de corrientes iónicas; (2) experimentos clásicos de Hodgkin y Huxley; (3) versión actual del modelo; (4) potenciales de acción. Consta de pantallas de interfaz que permiten simular y calcular los valores de las variables relacionadas con la conductancia de los canales. El usuario puede realizar una cantidad ilimitada de experimentos virtuales que le facilitarán la comprensión del tema.

Abstract: Hodgkin and Huxley ́s works were the starting point to generating mathematical models for explain, reproduce the experimental results and predict the behavior of voltage-sensitive ion channels in the axon. The high costs of these experiments avoid its implementation in teaching degree. An educational alternative is virtual experiments using computer simulations. In this work the development of a simulator that reproduces step by step the classic experiments of Hodgkin and Huxley on the conductance of voltage-dependent channels in squid giant axon is presented. The simulator was developed in Visual Basic language, ver 5.0 for Windows environment. It consists of four modules: (1) ionic currents simulation; (2) classical Hodgkin and Huxley ́s experiments; (3) current version model; (4) action potentials. It comprises connecting interface screens that allow simulate and compute the values of the variables associated with the channel conductance. The user can perform an unlimited number of virtual experiments that will facilitate the understanding of the subject.