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Using virtual reality to study interactive molecular dynamics

July 26, 2018 by 1 Comment

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.

 

Filed Under: active learning, Bibliography, chemistry, cloud-based applications, creativity, developing intellectual skills, experiential learning, networked learning, research, science, selection of media and technologies, subject areas, Teaching and learning, Technology, virtual worlds/Second Life Tagged With: , , , , , , ,

More developments in teaching science online

June 8, 2018 by 1 Comment

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.

Filed Under: Bibliography, experiential learning, science, selection of media and technologies, simulations, animations and games, subject areas, Teaching and learning, Technology, virtual worlds/Second Life Tagged With: , , , , , , , , , , , , , ,

Free online courses on English for Syrian refugees

June 8, 2018 by Leave a Comment

FutureLearn’s Basic English 1: Elementary. Click on image to access course.

FutureLearn (2018) New free online courses launched to help Syrian refugees continue their education FE News.co.uk, June 8

Kings College, the University of London, has partnered with FutureLearn, the U.K. Open University’s MOOC platform, to deliver a series of twelve new free online courses to assist refugees affected by conflict in the Middle East. The first two courses, Basic English 1: Elementary, and Basic English 2: Pre-Intermediate, start on June 18.

The courses are a result of an interesting project called PADILEA, which stands for The Partnership for Digital Learning and Increased Access, whose partners are King’s College, London, Kiron Open Higher Education (Germany), FutureLearn in the UK, Al al-Bayt University in Jordan and the American University of Beirut, Lebanon. The PADILEA project will provide blended academic programmes, including Massive Online Open Courses (MOOCs), targeted online learning, and classroom-based learning to displaced students who are in refugee camps and other communities.

While the course content is specifically designed for people affected by the Syrian crisis, they are open to all people in the region and beyond for free. Learners can join the courses from any device, computer or smartphone with an internet connection. The courses will also have Arabic translations.

Comment

This is an example of the huge potential of MOOCs to improve accessibility to education and meet some very pressing needs. The PADILEA MOOCs are more focused and targeted than many other MOOCs but still have a large potential audience and have a very important goal. Professor Bronwyn Parry at King’s College perfectly captured the significance of this project:

In the scale of the enormity of the ongoing conflict in the region, English courses may seem a relatively small affair but access to education is absolutely vital and offers opportunity and hope for an entire generation whose lives have been devastated by war and displacement.

I have already reported on Kiron University’s efforts to help refugees with online learning. In some ways, online learning for refugees is like a band-aid for someone who is bleeding to death. It can only help reduce some of the effects caused by more fundamental political and economic issues that still need to be urgently addressed, but nevertheless band-aids are still useful when you are bleeding.

I hope though that eventually a more long-term and stable solution will be found for the education of the millions still stuck in refugee camps hoping to transition to a more normal existence – or better still, remove the need for refugee camps in the first place. 

Filed Under: Bibliography, English, Events, MOOCs, online programs, subject areas Tagged With: , , , , , ,

Open and remote labs from the UK Open University

May 20, 2018 by Leave a Comment

The Open University’s remote access electron microscope set-up

On my recent visit to the UK Open University, I had the privilege of a guided tour of the Open University’s remote labs. These allow students to log on from anywhere and conduct experiments remotely. The tour was courtesy of Professor Nick Braithwaite, Associate Dean (Academic Excellence), Faculty of Science, Technology, Engineering & Mathematics.

Note that remote labs are somewhat different from simulated online experiments, where students interact by entering data or clicking and dragging on screen items. With remote labs, the equipment being operated is real, with the students actually controlling the equipment in real time as well as recording and interpreting data. 

The OpenScience Laboratory

The OpenScience Laboratory is a means of conducting authentic and rigorous investigations using real data and is globally available. It is an initiative of the Open University and the Wolfson Foundation. It includes:

  • Remote Experiments
  • Virtual instruments and interactive screen experiments
  • Online field investigations
  • 3D Immersive environments
  • Citizen Science
  • Research and development 

There are altogether more than 50 self-contained open educational resource modules in experimental science, in the OpenScience Laboratory, each taking somewhere between one to three hours of study to complete.

As an example, there is an experiment to identify what causes variation in species of heather on English moorland. It is a combination of an online video recorded on site in English moorland and guided student activities, such as taking simulated measurements and calculating and interpreting data. The video is divided in to 23 parts, showing how measurements are made in the field, how to calculate slope, water flow, and organic soil depth, and how to take simulated measurements, to test the hypothesis that different types of heather are associated with different levels of slope in moorlands. This took me a couple of hours to complete.

The heather hypothesis

The OpenSTEM labs

The Open STEM Labs are part of the OpenScience Laboratory project.

The OpenSTEM Labs connect students to state-of-the-art instrumentation and equipment for practical enquiries over the internet, where distance is no barrier and where access to equipment is available 24 hours a day.

Students and teachers access the equipment via a web browser through which they can view the experiment, send real-time control commands, monitor real-time performance and download data for subsequent analysis. Using remotely accessible hardware for laboratory and exploratory studies, ranging from electronics to chemical synthesis and from microscopes to telescopes, students are able to access the various instruments and other remote controlled resources virtually anytime from anywhere with an internet connection.

The new facilities are available to students studying Open University modules and may be available by subscription to other institutions of higher education.

Figure 1 below indicates the relationship between the Open Science Labs, OpenSTEM Labs and remote labs.

The Open University’s remote labs

Below are links to some of the diverse range of equipment available. Simply click on a link and this will take you to that experiment’s landing page, as seen by the OU’s students. Here you will then be able to access the equipment. Please note that you may have to book a session if all pieces of that equipment are being used by others. If you do book a session you should enter the experiment through the booking system at the allotted time. This will take you straight through to the equipment. (Not all these are currently operational at any one time and you may need to register first to get access).

The OU also has scanning electron microscopes, an auto-titrator, and a radio telescope available on request from those with direct experience of these curriculum areas. Please email OpenSTEM to arrange access and further briefing.

A student’s desktop view of the eye of a fly seen through the OU’s electron microscope. The student can manipulate the electron microscope to get different degrees of magnitude.

Many of the remote lab experiments are part of the Open University’s MSc in Space Science and Technology.  This includes student remote control of a model ‘Mars Rover’ operated in a mock-up of the surface of Mars.

The OU’s model of the Mars Rover

Comments

The Open University has added a new set of quality online resources in experimental science and technology to those currently offered by, among others:

I would welcome suggestions for other sources for high quality OER in experimental science and technology..

However, many more are still needed. We are still a long way from being able to build an entire high quality experimental science or technology curriculum with open educational resources. As well as increasing quantity, we need better quality resources that enable student activity and engagement, that include clearly understandable instructions, and that result in a high level of scientific inquiry. The Open University resources meet these standards, but not all other OER in this field do. Also there are issues of scalability. One needs enough students to justify the investment in software, production and equipment, especially for remote labs and quality simulations. Sharing of resources between institutions, and between departments within institutions, is therefore highly desirable.

Thus there is still a long way to go in this field, but progress is being made. If you teach science or engineering I recommend you look carefully at the Open University’s resources. It may stimulate you not only to integrate some of these resources into your own teaching, but also to create new resources for everyone.

Filed Under: agriculture, biology, Blogs, chemistry, course design, engineering, experiential learning, open content, physics, remote labs, science, simulations, animations and games, subject areas, Teaching and learning, Tony's Blog, Tweets Tagged With: , , , , , , ,

The current madness in online learning: case no. 1

March 13, 2018 by 1 Comment

Goldsmiths College

Coughlan, S. (2018) University offers science degree online for £5,650 per year, BBC News, March 6

If you want to know what the very opposite of an open higher education system is, look no further than that country of privilege, class, and isolationism called England. 

This is a report of a new Bachelor of Science degree being offered fully online in the United Kingdom by one of my old alma maters, Goldsmiths College, the University of London, where I did a wonderful post-graduate certificate in education that set me up for life in teaching. The new Goldsmiths B. Sc. (actually a three-year bachelor in computer science) is deliberately targeted at part-time, working students.

Great – so far. It’s good to see a full bachelor’s degree in science being made available fully online, targeted at part-time students. 

But the mad part is that the tuition cost for this three year degree is – wait for it – £16,950 (£5,650 a year). That is roughly C$30,000, or C$10,000 a year. 

What makes it even more crazy is that this is an attempt to provide a lower cost alternative to the regular fees now being paid by students for on-campus education in England and Wales, for which tuition fees alone are around C$16,000 a year. This is because the U.K. government in 2010 cut funding for the costs of teaching in English universities, requiring the universities to recover the teaching costs through tuition fees alone. In parallel, part-time students were no longer eligible for government-backed student loans.

And why, you may ask, is the University of London offering this fully online B.Sc. when the U.K’s Open University has been offering at least a distance one since 1971? (And a full science degree at that, covering all the basic sciences.)  

As a result of government policy, the UK Open University has had to triple its tuition fees over this period, to roughly – wait for it – £17,184 for its full three year Bachelor of Natural Sciences. What a co-incidence that Goldsmith’s fees for their new online B. Sc. are £16,950, just £200 below the OU’s! 

The government policies on tuition fees and student loans have been devastating for the UK OU, which is targeted mainly at part-time students, and which had no tuition fees when it was founded in 1971. Its numbers have fallen by 30% between 2010-11 and 2015-16. 

The latest figures from the Higher Education Statistics Agency show that part-time student numbers in England have fallen 56% since 2010, from 243,355 in 2010-11 to just 107,325 in 2015-16. In terms of economic development, this is madness in government policy. In a digital society, lifelong learning is not a luxury but a necessity, and will not just benefit the individual but the whole economy. I shudder to think of the long term implications for English prosperity in the future – even without Brexit.

Why do I feel so strongly about this? I have four grand-children living in England, but their parents, who, like me, are wealthy middle class now, are willing and just about able to support their children at university. However, in 1959 I was working full time at what would now be called a minimum wage and desperate to get any form of post-secondary education. I found out that although I was 21 and had been working for several years, because of my low salary and the low income of my parents, I was eligible for a grant from the London County Council. Not only were my fees covered, but I even got a small maintenance grant that with work in the vacations enabled me to study full time. I got a place in Sheffield University, and the rest is history. However, without that support, not only would I not have succeeded in my life, nor would my children be where they are today.

I have no problem with a minimal level of tuition fees, as in Canada, provided that there is some kind of financial support to allow those on low incomes or who are unemployed to take full advantage of post-secondary educational opportunities. But no-one should be denied the opportunity of a post-secondary education because they cannot afford it. England is more backward today than it was in 1959 in this respect, which is why I am so angry. All that blood, sweat and tears that the working class suffered during and after the Second World War – and for what?

‘It’s the rich what gets the gravy and the poor what gets the blame.’ Was it ever thus in England?

Filed Under: Bibliography, costs and benefits, national, regional and international strategies, science, Strategies, planning and management, subject areas, Teaching and learning, United Kingdom Tagged With: , , , , , ,
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