The presented Virtual X-ray Laboratories (v-XRLab) have been developed to address the lack of advanced and expensive research equipment for educational purposes, facilitate hands-on practice associated with online science or engineering courses, and enhance students’ knowledge of equipment design and operational principles. Also, in contrast with fully computerized contemporary X-ray equipment, the v-XRLabs help students understand factors affecting data accuracy and method limitations first-hand, and, consequently, better estimate reliability of the experiment results.

During the COVID-19 pandemic, the virtual labs helped instructors minimize drawbacks of lost access to actual physical laboratories.

Integrated cloud-based virtual laboratories (ATeL’s v-Labs) allowed learners to perform authentic research and laboratory experiments online, using highly accurate digital copy of a multifunctional X-Ray Powder Diffractometer (v-XRPD) and X-ray Fluorescence (v-XRF) spectrometer. The v-XRPD realistically imitates the design and operation of a typical flat plate geometry diffractometer, and it also includes educational analytical software.

The v-XRLab includes an open repository of samples available for experiments. The-Diffractometer can work with CIF files obtained from the CCDC CSD, XY formats produced by a vendor's instrument, and some other plain text files as well. The open collection of virtual samples available for online experimentation includes alloys, ceramics, polymers, nanostructured materials, thin films, and even human kidney stones.

Experimental data can be collected and handled manually or automatically. Virtual data can be exported to popular software as well.

The v-XRLabs incorporate self-guided online experiments that couple hands-on practice with efficient contextual ‘just-in-time learning” by integrating simulations with video and voice instructions, manuals, quizzes, references, and other multimedia learning resources. This combines skill development, knowledge acquisition and performance-based assessment into a single process.

A complimentary authoring tool enables instructors to modify existing online experiments and to create new ones, as well as to add new samples in the repository. New samples can be either based on actual XRD patterns or be calculated from known structural data.

The v-XRLabs incorporate an augmented reality (AR) X-Ray diffractometer (AR-XRPD) and its attachments running on a mobile device or smart glasses and synchronized in real time with the main simulated XRPD and the relevant processes. This dramatically enhances student engagement and provides them with unique opportunities for data analysis and deeper exploration of the equipment and processes in augmented reality.

The v-XRLlabs were incorporated into courses on chemistry, materials science, forensics, mineralogy, metallurgy, and materials characterization techniques, among others. They has been used as follows: (i) as the only tool for lab practice on the relevant subjects, by the students who have no access to real equipment including MOOC students; (ii) for hybrid experimentation in combination with equipment; (iii) for preparing students and tech personnel to effective and meaningful hands-on practice in actual X-ray labs; (iv) for performance-based assessment of students’ and trainees understanding, and their ability to apply acquired knowledge and skills for performing experiments, and solving practical tasks; (v) and for lecture demonstrations.

The presenters will share their experience in using the v-XRLabs during the COVID-19 pandemic and beyond it. The v-XRLab can be accessed at the following link: https://atelearning.com/XRLab/index.php

Crystal structures of proteins are three-dimensional, but most depictions of them, in textbooks and in the scientific literature, are not. When students are on campus, they can interact with physical models, discuss structures in the computer lab and experience the properties and functions of proteins in the biochemistry lab. We describe two projects that support interactive, collaborative and experiential learning in a remote setting. In the first project, students explored metabolic enzymes using the visualization software Pymol. Starting with crystal structures in the Protein Data Bank, students learned the basics of Pymol: they superimposed structures representing different stages in the catalytic mechanism, highlighted non-covalent interactions, identified bonds broken and made, and discussed the active sites of these enzymes in the context of the protein fold. In weekly meetings, students shared their progress and setbacks amongst each other, and used peer-to-peer learning to elevate their chemical and graphical design skills. Individually, they created different scenes and made them into a short video for which they provided an explanatory voiceover. Students wrote about their progress in weekly reflections. Many students reported being “excited and challenged” about learning a new technique at the outset. Later, deeper learning strategies emerged such as searching the primary literature or comparing existing videos to see how one might position an active site. The help-seeking behavior also became more sophisticated, for example asking for a video tutorial showing how to add or remove functional groups from a model. Overall, students were actively engaged in their projects and were eager to share what they had learned in discussions with their peers. The second project, housed on the public science site Proteopedia.org, aims at presenting examples of conformational change in a more interactive way. We wrote a series of Jmol scripts (storymorph.spt) to make it easier to superimpose structures and create morphs (fictional trajectories connecting conformational states). Using an algorithm that combines rigid-body movement with linear interpolation, morphs are made on the fly, allowing the visitor to change parameters (such as the timing of distinct parts of the conformational change or the initial superposition) to get a better feel for how the conformation might change. It is also possible to slow down or pause the morph, allowing visitors to explore the suggested intermediates in three-dimensions, including potential clashes or unrealistic bond lengths or angles. Morphs made available through this project include hexokinase binding to glucose, RNA polymerase transitioning from early to late initiation, conformational changes in calmodulin, and the pre-fusion to post-fusion transition of the coronavirus spike protein. Together these two projects highlight simple ways to keep science-learning interactive, collaborative, fun, and — most importantly — three-dimensional in spite of the limitations caused by a pandemic.

Many months of this pandemic brought high concentration on online teaching in basically all levels of education. Of course, the least problematic is such teaching in universities where many things can be transferred to online form without significant losses and in certain cases even with some benefits. Of course, not for the work that should teach students some manual skills. Otherwise, there are no limits for interactive communication during the online teaching. However, it may be easier for the teachers rather than for students who must sit at the computer many hours a day. Universities are supporting different platforms for online teaching. While for organizing of meetings I prefer to use Zoom or similar platforms, for teaching I have decided to prepare everything in MS Teams in the form for education where it is easy to create a team for the subject and assign students from the list of university students.

Our faculty required that all the presentations be recorded, and the records are available, in addition to presentations (ppt, pdf), to all relevant students till the end of semester. Some shared files like Excel or Word ones have possibility of multiple access of teacher and student. Probably the most useful part is Notebook that can contain different folders owned by teacher only, shared for all and owned by each individual student, respectively. In the shared folder, anybody can write formatted text, draw, insert pictures, tables directly in Teams or in One Note application with a few more advanced features. Students cannot see folders and pages of other students while the teacher can see everything. So, the teacher can easily click on the corresponding place of any student any time and see up-to-date information, e.g. where the student is during his/her task. Teacher can also write or draw directly to their documents. Usually, it is working quite quickly if the Internet is not too slow. The system was used for online teaching of fundamentals of crystallography and X-ray diffraction for smaller groups of students up to 10. In addition to simple examples and tests, graphical possibilities were used either with mouse or graphical tablet. The students had different symmetrical periodical 2D patterns with a task to draw elementary cell, corresponding symmetry elements, and determine the plane group from the list. In order, to make their life easier, they could use a portfolio of all symbols and it was then sufficient to move specific symbols to relevant positions. A similar way was used for space groups (complete diagrams of general positions with symmetry elements or vice versa complete diagrams of symmetry elements with general positions, the determination or estimation of the space group). The work was quite smooth.

A little more complicated was the preparation of online practical courses when the entrance of students to the faculty building was completely forbidden. One was the basic problem of powder diffraction – determination of lattice parameter of unknown cubic phase and then also phase analysis of mixture of 3-6 phases. This practical part always begins with a short excursion in X-ray laboratory showing them a few instruments, description of powder diffractometer, preparation of different samples, specimen alignment and automatic measurement in symmetrical scan. So, everything was recorded to videos and what was only missing for students was their own specimen preparation. This is followed by demonstration of fast evaluation of powder pattern and generation of a file with peak parameters. The students used the free program Winplotr. A short video tutorial how to use it quickly for simple fitting of XRD peaks was provided. Students used this output (each with different dataset) to index peaks according to procedure described on web link and determined the lattice parameter considering the instrumental aberrations. This was done in Excel file simultaneously accessible also by the teacher. The first part was closed by looking into the ICDD Powder Diffraction File and trial to find the phase (demo by the teacher). Usually, it was not found because the lattice parameter deviated from the database value from some reason that was discussed. Then the pattern of a mixture of phases was evaluated in commercial software (demo by the teacher), the list of peaks was generated (2q, d, I) and the students obtained scanned education edition (ICDD material) of Hanawalt index and made the search “manually”, again with different datasets. Interaction of the teacher was necessary. Finally, for homework, the students should download 30-days trial of program Match and use it for the phase analysis of the mixture (again a short video tutorial provided. More online “practical” tasks were prepared, for example study of textures and stresses in thin films showing different diffraction geometries and scans.

Real examinations could be realized after the winter semester in February 2021. In general, I have never heard so well-structured and correct answers. I think that the reasons were the following. Students had everything available in their Teams folders. Each student had to go through all the tasks and materials independently but except the direct online teaching in any time that was suitable for him/her, and I did the same. The students could return to some parts of presentations and if something were not clear, they could look at corresponding video part. So, my overall experience was positive.

However, the courses were for smaller groups of students and do not require any manual skills, so they can be adopted quite easily for online form.

In order to address the loss of crystallographic training opportunities resulting from the cancellation of conventional schools around the world due to the COVID-19 pandemic we have started an online crystallography school with live lectures and live Q&A using Zoom Webinar. In 2020 we ran three versions of the school: two 10 one-hour classes on basic topics in crystallography and five 1.5-hour classes on advanced topics. In June 2021 we plan to run a fourth school consisting of 10 1.5 hour classes on advanced topics. We have reported on the execution and results of the two basic schools held in 2020 previously (1).

For the June 2021 school, we have scheduled ten 1.5 hour lectures on advanced topics including: electron diffraction, refinement, twinning, powder and PDF analysis, solution scattering and macromolecular crystallography, non-spherical atom refinement and charge density analysis, and data mining.

This presentation will review the execution and outcomes of the December 2020 and June 2021 advanced topics schools.

1. https://doi.org/10.1063/4.0000078

My objective is to share approaches by which I incorporate structural biology into our biochemistry curriculum at Hampton University. I will also discuss methods to engage K-12 and undergraduate students in crystallographic research and structural biology (since 2001). I will show the successes and failures involved in the process of fully integrating these pre-baccalaureate students in crystallography research. Our outreach efforts have included socioeconomically underserved students or groups underrepresented in STEM. We will present strategies for recruiting and retaining STEM students. We will present the significant barriers to our research programs. We will also discuss potential funding sources. Finally, we will present how structural science has helped COVID-proof our research and biochemistry teaching approach over the past year of remote-learning.

An approach for increasing the impact of undergraduate scientific training with a discovery based X-ray structure determination lab module has been part of the chemistry curriculum at Vassar College since 2010. Just as chemical crystallography and complimentary spectroscopic techniques such as NMR can be fast, effective tools to experimentally determine the structure of molecules and enhance students learning of molecular structure, they can also provide an inspiring opportunity for students to write short, scientific journal style reports that can be edited and published in collaboration with a mentor. This talk will briefly review the X-ray crystallography module and then focus on the experience of conducting this module with remote and hybrid online learning during the pandemic.