The picture we have in our heads about how reactions proceed is often extremely simplified. David Glowacki recently had the pleasure to sit down with Theoretically Speaking, a podcast which is broadcast from Oxford (and which has its origins in the ‘Theory and Modelling in the Chemical Sciences’ Centre for Doctoral Training). The topic was molecular reaction dynamics, and David discussed with the podcast hosts a range of topics, including how to accurately model molecular reaction dynamics in real-world systems, and also about how new developments in virtual reality and GPU-accelerated computing enable us to visualise complex chemical systems in cutting edge research applications. You can listen to the episode here.
Author: David R Glowacki
cloud-streamed interactive Molecular Dynamics in virtual reality
Dr. David Glowacki and co-workers, working with academic colleagues from high-performance computing (HPC) and human-computer interaction (HCI), and industrial collaborators from Interactive Scientific and Oracle, has just published an open-access paper to the arXiv, outlining his group’s latest work in developing and testing a rigorous VR-enabled, multi-person, real-time interactive Molecular Dynamics (iMD) framework.
If you’d like to try it for yourself, visit isci.itch.io/nsb-imd to download a beta version of the app. Once you’ve launched the app, you can initialize a cloud-hosted interactive simulation instance on any of three Oracle cloud servers (at the moment we’re running on servers in Frankfurt, Germany; Phoenix, USA; and Washington DC, USA). Having selected a server & established a connection, you can attempt any of the molecular simulation tasks discussed in the paper (playing with a buckminsterfullerene molecule, threading methane through a nanotube, changing the screw-sense of a helicene molecule, and even tying a knot in a 17-Alanine peptide).
The paper presents the results of HCI experiments showing that VR (we used the HTC Vive setup) enables users to carry out 3d molecular simulation tasks extremely efficiently compared to other platforms. If you don’t have an HTC Vive, then this paper might be the perfect excuse to acquire one! But failing that, don’t worry: the app runs on wide range of architectures, including Android phones/tablets, and also Mac/Windows laptops/desktops. I have it running on my Samsung S6 phone for example: real-time MD streamed from the cloud right to my phone, which I can interactively steer using my phone’s touchcreen! Have fun & feel free to get in touch with David Glowacki if you’re interested in this work.
first contact with the AtMath collaboration
Dr. David Glowacki recently returned from Levi in Finland (way up in Lapland!) where he was invited to give a plenary lecture (entitled “Non-equilibrium reaction dynamics in atmospheric chemistry”) at the kickoff meeting for the Finnish “AtMath” collaboration. AtMath (like CHAMPS) is a funded by a large grant, in order to bring together atmospheric scientists and mathematicians and make progress on difficult problems. David was specifically invited to the conference by Prof. Hanna Vehkamäki, whose group is involved in fundamental modeling of atmospheric particle formation and growth processes using both quantum chemistry and also large non-linear kinetics models. The conference was fantastic: not only was the snow-covered Lapland landscape was amazing, but the relaxed conference programme facilitated great conversations with several of the conference participants who delivered a wide range of fascinating talks across several different areas. There were also a range of speakers invited from beyond the AtMath collaboration, including for example Prof. Jochen Schenk (CSUF) who gave a fascinating talk on the molecular-level transport of water in trees, and also Prof. Eric Vanden-Eijnden (Courant Institute, NYU), who is an applied mathematician who has made very well-known contributions to chemistry for path sampling high-dimensional systems.
molecular graphics & modelling society award
Good news! Dr. David Glowacki has been selected as the recipient of the 10th “Silver Jubilee” award from the molecular graphics and modelling society (MGMS), which aims to recognize contributions to the field of molecular modelling and related areas. As part of this prize, Glowacki will be invited to give a prize lecture. Further details to follow.
efficient excited states in large systems
We recently published a paper titled “Pushing the Limits of EOM-CCSD with Projector-Based Embedding for Excitation Energies” where we calculated the interaction of light with some small molecules that are in solution using state of the art techniques. In this post, I’m planning on giving a general introduction to why we did this research and the ways impact it may have.
The interaction between light and molecules is central to all branches of physical sciences, with our understanding of the physical process involved going back to the quantum revolution 100 years ago. Being able to work out the amount of energy needed for light to affect a molecule and the strength of that interaction is valuable in many areas that affect modern day life, such a photosynthesis, designing better solar cells or even how to build better phone screens.
The use of computers in chemistry makes it possible to predict how chemical reactions occur with little cost or damage to the environment and can be a helpful guide to experiment. Computational chemists aim to find ways to calculate many chemical properties as efficiently as possible without losing accuracy in our predictions.
In the case of light-chemical interactions, two methods that are commonly used are a quick and somewhat rough method called TD-DFT and a more accurate and expensive method called EOM-CCSD. Our work combines the methods in such a way that makes it possible to work our how light interacts with chemicals accurately and quickly.
The approach that we took was to treat different chemicals with different accuracy using a method called “Embedding” (placing one method inside another). By doing this we were able to accurately calculate the effect of light hitting a molecule in solvent between 100x and 1000x faster than possible before.
In the long term, our research may help enable highly accurate predictions of light-chemical interactions in academia and industry. For example, calculating how chlorophyll in plants absorbs light or how to test new solar cell designs without having to actually build them.
interactive MD art installation
CHAMPS has teamed up with one of its industrial partners – the Bristol-based tech startup Interactive Scientific Ltd. – to sponsor installation of the acclaimed real-time interactive molecular dynamics art installation ‘danceroom Spectroscopy’ (dS) at the ‘We the Curious’ science museum in central Bristol. dS – whose architecture is described in a 2014 Faraday Discussion paper – fuses rigorous methods from computational physics, GPU computing, and computer vision to interpret people as fields whose movement creates ripples and waves in an unseen field. The result is a gentle piece comprised of interactive graphics and soundscapes, both of which respond in real-time to people’s movements – enabling them to sculpt the invisible fields in which they are embedded. Offering a unique and subtle glimpse into the beauty of our everyday movements, dS allows us to imagine how we interact with the hidden energy matrix and atomic world which forms the fabric of nature, but is too small for our eyes to see. It’s as much a next-generation digital arts installation as it is an invitation to contemplate the interconnected dynamism of the natural world and processes of emergence, fluctuation, and dissipation – from the microscopic to the cosmic. The installation runs from October through January, and is open to anybody; you can read more about it here.
Chemistry World Feature
Chemistry World, published by the Royal Society of Chemistry, has run a feature on David Glowacki’s research into real-time molecular simulation in virtual reality, with a tagline stating that: “Gaming-style tech is putting the fun into fundamental molecular simulations”. You can look at the article here.
Oracle Open World
During the first week of October, David Glowacki attended the Oracle Open World conference in San Francisco. With Oracle being one of CHAMPS industrial partners, David was invited to give a talk entitled “Collaborative Cloud-Based Virtual Reality for Scientific Research & Education”. In the talk, David outlined the virtual reality framework that he’s been working to develop over the years, focusing on the cloud aspects of the project – particularly those which enable multiple users to simultaneously inhabit the same real-time virtual simulation environment. Using modern cloud architectures, it’s now possible to build real-time interactive simulations that harness the power of cloud supercomputing. And the cloud allows anybody to login to the simulation server remotely. Another highlight of the trip was David’s invitation to a small get-together at Larry Ellison’s private SF residence, where Larry offered his insight into a wide range of different areas, all informed by his perspective as the founder of one of the planet’s biggest tech companies. Amongst his most memorable statements was his claim that, were he to start over again, he’d consider starting a molecular science or biotech company. He also said that computational molecular biosciences is one of his hobbies. It’s an area he’s always been interested in, but wasn’t really a viable discipline back in the day. Things have definitely changed.
bristol machine learning workshop
On Friday 22 Sept, we carried out our first CHAMPS workshop, focussing on machine learning. Led by Dr. David Glowacki, Dr. Lars Bratholm, Rob Arbon, and Silvia Amabilino, there were a number of attendees from a range of backgrounds spanning chemistry, mathematics, and computer science. The material covered during the workshop is available as a series of Jupyter notebooks on Github at this link, available to anybody that might be interested.