September 22, 2018

Using virtual reality to study interactive molecular dynamics

Click on image to see video

Morales, A. (2018) How Virtual Reality Can Change The Way We See Our Molecular World, Forbes, 25 July

O’Connor, M. et al. (2018) Sampling molecular conformations and dynamics in a multiuser virtual reality framework, Science Advances, Vol. 4, No.6, 29 June

The problem

As the authors state in the article (O’Connor et al., 2018):

From a modeling perspective, the nanoscale represents an interesting domain, because the objects of study (for example, molecules) are invisible to the naked eye, and their behavior is governed by physical forces and interactions significantly different from those forces and interactions that we encounter during our day-to-day phenomenological experience. In domains like this, which are imperceptible to the naked eye, effective models are vital to provide the insight required to make research progress….

molecular systems typically have thousands of degrees of freedom. As a result, their motion is characterized by a complicated, highly correlated, and elegant many-body dynamical choreography, which is nonintuitive compared to the more familiar mechanics of objects that we encounter in the everyday physical world. Their combined complexity, unfamiliarity, and importance make molecules particularly interesting candidates for investigating the potential of new digital modeling paradigms.

Until recently, building dynamic models that operate not only in real time but also in three dimensions required not only specialized virtual reality equipment, but more importantly massive amounts of computing power to handle the visual representation and modelling of highly complex and dynamic molecular activity.

The solution

However, through the use of cloud computing and faster networks, building such models has now become a reality, enabling not only such models to be represented but allowing some degree of real-time manipulation by researchers in different locations but within the same time-frame – in other words, distance research and teaching. 

In the Department of Chemistry at the University of Bristol in the U.K., Dr. David Glowacki and his team in their VR laboratory have created an interactive molecular dynamics modelling tool in the form of Nano Simbox VR, which allows anyone to visit and play within the invisible molecular world. This was made possible through a partnership with Oracle which provided the researchers access to its Oracle Cloud Infrastructure with a grant from the Oracle Startup for Higher Education programme.

The main advantage of the use of a cloud platform is to allow the scaling up of modelling from simple to much more complex dynamic nano interactions and the synchronous sharing of the virtual reality experience with multiple users.

The Nano Simbox VR app allows several people to interact at once with the digital models. Users can download the framework and choose the Oracle data center (Frankfurt, Germany; Phoenix, Arizona; Ashburn, Virginia) nearest to them for minimal network latency. 

The main aim of this particular project is to provide an intuitive feeling of the way molecules operate in multiple dimensions to enable researchers and students to have a better understanding of how nano worlds operate.

The paper published by Glowacki and his team in Science Advances describes how the iMD VR app enabled researchers to

  • easily “grab” individual C60 atoms and manipulate their real-time dynamics to pass the C60 back and forth between each other.
  • take hold of a fully solvated benzylpenicillin ligand and interactively guide it to dock it within the active site of the TEM-1 β-lactamase enzyme (with both molecules fully flexible and dynamic) and generate the correct binding mode (33), a process that is important to understanding antimicrobial resistance
  • guide a methane molecule (CH4) through a carbon nanotube, changing the screw sense of an organic helicene molecule,
  • tie a knot in a small polypeptide [17-alanine (17-ALA)].

Glowacki’s team measured how quickly users were able to accomplish these tasks using the iMD VR app compared with other platforms, and found that in all applications the VR application led to faster mastery.

Comment

This is just one instance where VR is operating at the interface of research and teaching. In particular, its value lies in providing a deep, intuitive understanding of phenomena that are otherwise difficult if not impossible to visualise in other ways.

In some ways this reminds me of the impact of the first mathematics television programs developed by the UK Open University in the 1970s, which included simulations and models of mathematical formulae and processes. This enabled students who were often struggling with the abstract nature of numerical and algebraic calculations to understand in more concrete terms what the calculations and formulae meant.

This intuitive understanding is critical not only for deeper understanding but also for breakthroughs in research and applications of science. In other words, it is a great use of media in education. 

Full disclosure

One of the co-authors of the Science Advances paper is my son, Phil Bates, who is the Oracle Computing  cloud architect who suggested Oracle Cloud Infrastructure to Dr. Glowacki.

 

More developments in teaching science online

Screen shot from A101’s Virtual Reality of Human Anatomy (YouTube)

Matthews, D. (2018) Scepticism over Google plan to replace labs with virtual reality, Times Higher Education, June 7

The Harvard Gazette (2018) Virtual lab to extend reach of science education Harvard Gazette, June 6

It was interesting that I came across these two completely separate news announcements on the same day.

Google and Labster

The THE article is about a partnership between Google and the Danish virtual reality company, Labster. Among the 30 ‘virtual reality’ labs planned are ones allowing training in confocal microscopy, gene therapy and cytogenetics.

Arizona State University, one of the major online providers in the USA, will be the first institution to use the labs in VR this autumn, launching an online-only biological sciences degree. It has worked with Labster to develop the VR labs. Students will require access to their own VR headsets such as Google’s Daydream View, which costs US$99, used in combination with specific brands of smartphones. 

Harvard and Amgen

The second article from the Harvard Gazette announces a partnership between the Amgen Foundation and edX at Harvard University to establish a platform called LabXchange, ‘an online platform for global science education that integrates digital instruction and virtual lab experiences, while also connecting students, teachers, and researchers in a learning community based on sharing and collaboration.’ 

The term ‘virtual lab’ is used differently from the Google/Labster sense. Amgen, a major biotechnology company in the USA, is investing $6.5 million in grant funding to Harvard University to develop, launch and grow the LabXchange platform for teachers and students globally. LabXchange will include a variety of science content, such as simulated experiments, but more importantly it will provide an online network to connect students, researchers and instructors to enable ‘learning pathways’ to be built around the online materials.

Comment

It is interesting and perhaps somewhat unnerving to see commercial companies in the USA moving so strongly into online science teaching in partnership with leading universities.

Of course, the THE had to choose a snarky headline suggesting that you can’t teach science wholly online, rather than have the headline focus on the innovation itself. As with all innovation, the first steps are likely to be limited to certain kinds of online teaching or experiments, and in the end it will come down as much to economic factors as to academic validity. Can virtual labs and online science teaching scale economically better than campus-based courses and at the same quality or better?

More importantly I would expect that the technology will lead to new and exciting approaches not only to science teaching, but also to science research. Already some researchers are using virtual reality and mathematical modelling to explore variations in DNA sequences, for instance. Virtual and augmented reality in particular will lead to science being taught differently online than in physical labs, for different purposes.

At the same time, the two developments are very different. The Google/Labster/ASU partnership is pushing hard the technology boundaries in teaching science, using proprietal VR, whereas the Harvard/Amgen/edX partnership is more of a networked open educational resource, providing access to a wide range of online resources in science. Both these developments in turn are different from remote labs, which provide online access to controlling ‘real’ experimental equipment.

Lastly, both new developments are what I call ‘We’re gonna’ projects. They are announcements of projects that have yet to be delivered. It will be interesting to see how much the reality matches the hype in two year’s time. In the meantime, it’s good to see online learning being taken seriously in science teaching. The potential is fascinating.

Stanford University to be fully online by 2025?

A Stanford sophomore experiences the virtual world at its Virtual Human Interaction Lab

Today I have received a tip from a close colleague that Stanford University is planning to build a partnership with Alphabet Inc., the owner of Google, to enable Stanford to become a fully online global university by 2025. 

Because the university is on an Easter break, it was difficult to find anyone at Stanford to verify this rumour, but the planning seems to be quite advanced. Apparently a highly confidential strategic planning committee has been working for some time on a plan to convert all programs at Stanford into a fully online format, using advanced technologies such as Artificial Intelligence (AI), Virtual and Augmented Reality (VR and AR), and data analytics (DA), technologies in which both Stanford and Google are world leaders.

This will enable Stanford to offer fully accredited degrees to many thousands of students worldwide at a fraction of the current tuition fees, which are currently just under $50,000 a year. Once fully online, the low tuition fees, estimated be around $1,000 a year, will be made possible by a highly innovative business plan being worked out jointly by Stanford and Google. Stanford plans to sell that part of the campus that will no longer be needed for teaching purposes. The Farm, as it is affectionately known, is over 8,000 acres, located close to Silicon Valley. With real estate currently selling at approximately $65 million an acre in Stanford, just selling off half the land will provide sufficient capital for the investment needed to convert all programs into an online mode, leaving the other half of the land for research and administrative purposes. The partnership with Google will allow Google to use data analytics from student online activity for commercial purposes, which will more or less cover the operational costs of online delivery.

I did manage to get hold of a couple of the committee, who asked not to be named as they are not authorised to give information on this project. However, both were very excited. ‘We won’t have to sack any of the current professorial staff, as we still need their subject expertise’, said one. The other said he was really looking forward to developing the first fully augmented reality engineering degree. ‘This could have huge implications,’ he said. ‘Imagine designing a whole bridge without actually having to physically test it! It’s only ever been tried once before without VR and it didn’t work.’ The Director of Stanford University’s Division of Continuing Studies said, ‘You know, it’s not such a big deal. We’ve been delivering online courses in our division for nearly 20 years, so we do know what we’re doing.’

Others outside the university I talked to though were not quite so sanguine. A spokesperson from WCET was concerned about how the accreditation or professional bodies would react. ‘It’s one thing for the university to give degrees; it’s quite another to get recognized by the Accreditation Boards for Engineering and Technology, who in the past have not accepted any online qualifications. But, hey, it’s Stanford, so who knows?’

My personal view is that it still has to get through Stanford’s Senate and Board of Governors. This will be the real test. However, if it is successful, this model will be totally disruptive of the rest of post-secondary education worldwide. If Stanford can scale its model, it could be not just a global university, but THE one university for the whole world. How cool would that be? 

In the meantime, enjoy April the first.

Virtual reality for midwives: an Australian example

Connolly, B. (2018) How virtual reality is transforming learning at the University of Newcastle, CIO, 8 March

This article includes a couple of nice, short videos demonstrating the use of AR and VR in a University of Newcastle nurses’ program in Australia.

The first one, below, demonstrates the use for breech positioning and placenta replacement (click image to play):

University of Newcastle, NSW, Australia

The second demonstrates a neonatal resucitation scenario when a newborn baby stops breathing.

University of Newcastle, NSW, Australia

These are very good examples of the power of AR and VR to enable students to practice and learn in a safe environment without danger to patients. The technology is accessible via mobile phones or tablets so students can practice in their own time as well as in the VR studio with an instructor.

What would be useful to know is the cost of producing such VR applications and the number of students that make use of the equipment over the length of a course – in other words, what is the return on investment, compared, with, for example, traditional video? What are the added benefits? Do learning outcomes improve? We need much more research into these questions.

 

Have we reached a tipping point in teaching science and engineering online?

A remote lab used by online physics students at Colorado Community College

This post lists several new developments in delivering science and engineering online. These developments join a list of other efforts that are listed below in the reference section that suggest we may be reaching a tipping point in teaching science and engineering online.

USA: The University of Colorado Boulder’s Master of Science in Electrical Engineering

UC Boulder is offering a Master of Science in Electrical Engineering (MS-EE), a MOOC-based online, asynchronous, on-demand graduate degree in the autumn, with additional curricula rolling out in 2018-19.

The degree will have a “modular and stackable structure”, according to the university, meaning that students can select about 30 subjects that best suit them as they move through the programme. Each of the 100 courses on offer will feature in-depth video content, reading materials and resources and assessments, and many will also “bring the laboratory experience out of the Engineering Center to students around the world” by “inviting students to apply their knowledge using hardware and software kits at home”, the university said.  

The university has already designed kits for the course on embedded systems engineering – a field in which a computer is designed and programmed to perform predefined tasks, usually with very specific requirements. For this course, students will be sent a circuit board with an embedded system that can plug into their laptop and will form the basis of assignments. The results of the tests will then either be sent automatically to the lecturers or entered manually by students. The technology also means that technical assignments can be machine-graded immediately, with students receiving instant feedback. It allows students to retake assignments as many times as they want.

The home kits will cost in the range of “tens of dollars” rather than thousands of dollars. Overall the degree will cost around US$20,000, which is half the price of the equivalent on-campus programme.

Individual courses can be taken for a single academic credit, but they can also be grouped into thematic series of 3-4 credits, stacked into standalone CU Boulder graduate certificates of 9-12 credits, or combined to earn the full 30-credit degree. Each course addresses professional skills while providing content at the same high quality as the university’s traditional on-campus master’s degrees.

CU Boulder faculty have custom designed each course. Courses feature in-depth video content, curated readings and resources, and assessments that challenge students to demonstrate their mastery of the subject area. Many courses bring the laboratory experience out of the Engineering Center to MOOC students around the world, inviting students to apply their knowledge using hardware and software kits at home. 

However, the program has still to be accredited by the Higher Learning Commission (HLC), and no information was given as to whether it will be accepted by ABET, the accreditation agency for professional engineers in the USA. This will be critical, as in the past, very few engineering programs with online components have passed this hurdle

Also the notion of MOOCs being not only open but free seems to be a thing of the past. US$20,000 for a degree may be half the cost of the on-campus course, but I suspect many potential students will want to be sure that they can get full accreditation as a professional engineer before laying out that kind of money.

Nevertheless, this is a bold venture by UC Colorado, building on its previous excellent work in offering open educational resources in science through its PhET project. Founded in 2002 by Nobel Laureate Carl Wieman (now at the University of British Columbia), the PhET Interactive Simulations project at the University of Colorado Boulder creates free interactive math and science simulations. PhET sims are based on extensive education research and engage students through an intuitive, game-like environment where students learn through exploration and discovery. It will be interesting to see how much the MS-EE program draws on these resources.

Queen’s University’s online Bachelor in Mining Engineering Technology

Queen’s University’s new Bachelor of Mining Engineering Technology (BTech) program combines technical expertise with the managerial and problem-solving skills the industry needs from the next generation of mining professionals, in a flexible online learning format. The university provides a very interesting rationale for this program:

Canada’s mining industry is facing a retirement crisis that is only set to worsen over the next five to ten years. With the most experienced part of the mining workforce leaving, new opportunities will open up for the next generation of mining professionals.

This program was developed as a result of discussions between the university and the mining industry in Ontario. The web site indicates the type of position open to graduates with typical salaries.

Graduates of any Engineering Technology or Mining Engineering Technician diploma who have completed their diploma with a minimum 75% average or individuals with at least two years of study in a relevant science field are eligible to enrol. Upon successful completion of the bridging program, students enter the final two years of the four-year degree program. Each year includes a two-week field placement in Kingston and Timmins. Students receive block transfer credits for the first two years of the program.

Students can study full-time, or work full-time and study part-time. This allows students to adjust their course load at any time during the program.

However, the BTech program is unaccredited. Graduates seeking professional licensure will need to apply to write the Board Exams in mining engineering. In Ontario, the application will go to the Professional Engineers Ontario (PEO). As with applications from an accredited program, graduates would also need to write the law and ethics exam, and complete the required supervised work experience program in order to be considered for licensure.

It will be interesting to see how the two programs work out. Both ABET in the U.S. and professional engineering societies in Canada have up to now denied accreditation for any degree programs with a significant online component, a necessary first step to taking the professional exams. But the Queen’s program has been built specifically to respond to the needs of employers. I will be very interested to see how the PEO in particular responds to graduates from this program wanting licensure as professional engineers – or will the employers just ignore the professional association and hire the graduates anyway?

Image: The Fraser Institute

More online virtual labs for science and engineering

Drexel University Online has an excellent series called Virtually Inspired, which like Contact North’s Pockets of Innovation

is an ongoing research project to uncover the best of breed technology-enhanced online courses and programs indicative of the “Online Classroom of the Future.”

Online Virtual Labs for Science and Engineering showcases three examples from Chile, India and Denmark of online virtual labs that provide hands-on experiential learning.

LAB4U, Chile

The Lab4Physics mobile app enables students to use various built-in tools to measure gravity or acceleration in real-time with a built-in accelerometer. They can study speed, velocity, distance or displacement using the built-in speedometer. With the sonometer, students can study waves, amplitude, time and other physics phenomenon.

Coming soon, the Lab4Chemistry app will helps students learn spectrophotometric techniques. Students can use the built-in camera as a spectrophotometer or colorimeter to analyze samples wherever they may be. By taking pictures of droplets of different concentration and optical densities, they can create a calibration plot to measure a material’s transmission or reflection properties.

Each app has pre-designed experiments. For example, a student can swing their phone or tablet like a pendulum to learn how oscillation works.

Students and teachers alike can download the app, experiment, analyze and learn with pre-designed guided lab experiences and step-by-step instructions. For those who lack Internet access, the experiments and tools can be downloaded to use offline, even in airplane mode.

Students, teachers, and institutions from primary, secondary and tertiary institutions across Latin and South America are taking advantage of Lab4U.  Most recently Lab4U has expanded their work to Mexico and the United States.

Virtual labs of India

Virtual labs of India is an initiative of the Indian Ministry of Human Resource Development. Its objectives are:

  • to provide remote-access to labs in various disciplines of Science and Engineering. These Virtual Labs will cater to students at the undergraduate level, post graduate level as well as to research scholars

  • to enthuse students to conduct experiments by arousing their curiosity, helping them learn basic and advanced concepts through remote experimentation 

  • to provide a complete Learning Management System around the Virtual Labs where the students can avail the various tools for learning, including additional web-resources, video-lectures, animated demonstrations and self evaluation.

  • to share costly equipment and resources, which are otherwise available to limited number of users due to constraints on time and geographical distances.

Anywhere from four to twenty-five labs are offered per discipline area. These areas include Computer Science & Engineering, Electrical, Mechanical, Chemical, and Civil Engineering, Biotechnology and Biomedical engineering, and more.

Virtual Labs Simulations from Denmark

Labster is a Danish company with offices in Bali, Zurich, London, and Boston, as well as Copenhagen. 

Labster offers fully interactive advanced lab simulations based on mathematical algorithms that support open-ended investigations. They combine these with gamification elements such as an immersive 3D universe, storytelling and a scoring system which stimulates students’ natural curiosity and highlights the connection between science and the real world. All that is needed is a computer or laptop and a browser to perform advanced experiments and achieve core science learning outcomes. 

Labster currently has more than 60 simulations covering a wide range of topics including Parkinson’s Disease, Viral Gene Therapy, Eutrophication, Lab Safety, Animal Genetics, Tissue Engineering, and Waste Water Treatmen. Some simulations are available in virtual reality with the addition of a VR headset.

Labster is being used for on-campus teaching at many high-reputation universities, including MIT, Harvard an UC Berkeley.

Where is the tipping point for recognising online science and engineering degrees?

We now have a wide range of examples of not only online courses, but online tools that provide experiential learning and experimental situations in science and engineering fully online. When will the professional associations start recognizing that science and engineering can be taught effectively online?

It needs to be remembered that the teaching of science, and in particular the experimental method, was invented, more or less from scratch, by Thomas Huxley in the 1860s. There was so much opposition to the teaching of science by the established universities of Oxford and Cambridge that Huxley had to move to the Government School of Mines, where he began to train teachers in the experimental method. That institute eventually became Imperial College, one of the most prestigious centres of higher education in the world.

However, it is now another century and another time.

The U.K. Open University developed low cost, ingenious experimental kits in the 1970s that were mailed to students, enabling them to do experimental work at home. Today the Open University has the online OpenScienceLaboratory.

Dietmar Kennepohl at Athabasca University, who helped develop and design much of the experimental work for Athabasca University’s distance education programs in science, has written an excellent book about how to teach science online.

Students can now access and control online remote labs and equipment that do actual experiments or demonstrations in real time.

We have online simulation kits that can be downloaded, enabling students to build and test circuits, videos that demonstrate chemical reactions, and virtual reality environments that enable students to explore DNA mutations.

The only thing that stops us offering fully online, high quality science and engineering programs now is the conservatism of the professional associations, and the ignorance about the possibilities of online learning, and the fear and conservatism, of the majority of science and engineering faculty.

Further references

Bates, T. (2014) More developments in online labs, Online learning and distance education resources, May 8

Bates, T. (2013) Can you teach lab science via remote labs?Online learning and distance education resources, April 22

Bates, T. (2009) Can you teach ‘real’ engineering at a distance? Online learning and distance education resources, July 5

Kennepohl, D. and Shaw, L. (2011) Accessible Elements: Teaching Online and at a Distance Edmonton: Athabasca University Press

PhET (2018) Interactive simulations for science and math Boulder CO: University of Colorado

The Open University, The OpenScience Laboratory, accessed 22 February, 2018