Champs is thrilled to announce that Dr Matthaios Katsanikas, Champs PDRA, has been  elected as researcher C (assistant professor level) in Dynamical Astronomy at Research Center for Astronomy and Applied Mathematics (RCAAM) of Academy of Athens.

The Academy of Athens (Greek: Ακαδημία Αθηνών, Akadimía Athinón) is Greece’s national academy, and the highest research establishment in the country. It was established in 1926, and operates under the supervision of the Ministry of Education. The Academy’s main building is one of the major landmarks of Athens.

Dr Katsanikas duties in his new role will be the research and the supervision of research programs, postdoctoral researchers and Master and PhD theses and the teaching at postgraduate programs. He expects to take up this position in early 2021.

Dr Katsanikas joined the Champs project in 2017, one of our first PDRA cohort, based in Bristol under Professor Wiggins supervision. He has made great progress during his time working on the project, so this next step in his career is well deserved and recognition of what an excellent researcher he is.

We wish Dr Katsanikas all the best for the future.

The rise of machine learning (ML) has led to an explosion in potential strategies which may be used to learn from data in order to make scientific predictions. For physical scientists who wish to apply ML strategies to a particular domain, the vast number of strategies available has made it difficult to make an a priori assessment of what strategy to adopt. This is further complicated when similar domains have not been previously explored in the literature.

Recently, CHAMPS PDRA Dr. Lars Andersen Bratholm and collaborators worked with Kaggle to design a competition which encouraged data scientists around the world to develop ML models for predicting pairwise nuclear magnetic resonance (NMR) properties for synthetically relevant chemical compounds.
The success this strategy has cultivated highlights the potential of crowd-sourced ML approaches across a range of scientific domains and the CHAMPS symposium “Crowd-sourcing machine learning in NMR” took place on the 5th of March to communicate this message to researchers in the Bristol area.

The symposium started off with Professor Craig butts and PhD student Will Gerrard from the University of Bristol presenting how modelling of NMR properties with DFT and ML can accelerate the drug design process. This was followed by Addison Howard from Kaggle introducing the Kaggle platform, background to the company and interesting findings from the CHAMPS competition. The early non-technical session ended with Lars Bratholm conveying the main findings of the competition from the organizers point of view, namely what can be gained from combining all the different approaches, and how the collaborative environment of Kaggle is something that we can learn from in academia.

The afternoon session turned more technical and featured representatives from six of the top performing teams who all presented their approaches to the competition. The talks of Brandon Anderson, Luka Stojanovic, Milos Popovic, Sunghwan Choi, Andres Torrubia and Devin Wilmott all spurred great discussion with audience, which continued the following day with the competition organizers.

Dr. Lars Andersen Bratholm.

CHAMPS Workshop – ‘Chaos Indicators, Phase Space and Chemical Reaction Dynamics’
|  4th – 6th May 2020  |

Organisers | Dr Matthaios Katsanikas, Dr Makrina Agaoglou + Dr Francisco Gonzalez Montoya

Schedule of talks

Day 1 – Monday 4th May 12pm – 2pm (UK Time)
12.00 – 12.10 Introduction
12.10 – 12.40 R. MacKay – (University of Warwick, Coventry)
12.40 – 13.10 T. Komatsuzaki – (Hokkaido University, Japan)
13.10 – 13.40 S. Keshavamurthy – (Indian Inst of Technology Kanpur, India)

Day 2 – Tuesday 5th May 12pm – 2pm (UK Time)
12.00 – 12.10 Introduction
12.10 – 12.40 A. Mancho – (Instituto de Ciencias Matemáticas, CSIC, Madrid)
12.40 – 13.10 V. J. Garcia Garrido – (Universidad de Alcala, Spain)
13.10 – 13.40 Ch. Skokos – (University of Cape Town, South Africa)

Day 3 – Wednesday 6th May 12pm – 2pm (UK Time)
12.00 – 12.10 Introduction
12.10 – 12.40 S. Farantos – (University of Crete, Greece)
12.40 – 13.10 P. Patsis – (RCAAM of Academy of Athens, Greece)
13.10 – 13.40 P. Cincotta – (Universidad Nacional de La Plata, Argentina)

Symposium – Title: Crowd-sourcing Machine Learning in NMR

Following on from the success of the Kaggle competition that Champs PDRA Lars Anderson Bratholm ran last year he is now organising a Symposium to be held on Thursday 5th March 2020.

Title, abstract and schedule below (subject to change):

Crowd-sourcing Machine Learning in NMR

Abstract:
The rise of machine learning (ML) has led to an explosion in potential strategies which may be used to learn from data in order to make scientific predictions. For physical scientists who wish to apply ML strategies to a particular domain, the vast number of strategies available has made it difficult to make an a priori assessment of what strategy to adopt. This is further complicated when similar domains have not been previously explored in the literature.
Recently, we worked with Kaggle to design a competition which encouraged data scientists around the world to develop ML models for predicting pairwise nuclear magnetic resonance (NMR) properties for synthetically relevant chemical compounds. Over 3 months, we received 47,800 ML model submissions from 2700 teams in 84 countries, with the top models outperforming our own previously published methods. The success this strategy has cultivated highlights the potential of crowd-sourced ML approaches across a range of scientific domains.

This symposium will introduce the background and main findings of the competition, including the context of computational NMR, the Kaggle platform and presentations from the top performing teams of the competition.

Location: Lecture Theater 2.41, Fry Building, Bristol BS8 1TH

Schedule – Thursday 5th March:

10:00 – 11:15: Registration
11:15 – 11:50: Craig Butts and Will Gerrard
11:50 – 12:25: Addison Howard and Walter Reade
12:25 – 13:15: Lunch
13:15 – 13:50: Lars Andersen Bratholm
13:50 – 14:25: Brandon Anderson
14:25 – 14:40: Break
14:40 – 15:15: Luka Stojanovic and Milos Popovic
15:15 – 15:50: Youhan Lee and Sunghwan Choi
15:50 – 16:05: Break
16:05 – 16:40: Andres Torrubia
16:40 – 17:15: Devin Wilmott
17:15 – 18:15: Drinks reception
An Eventbrite registration, link below, has been set up. Numbers are limited (due to lecture theatre capacity) and will be allocated on a first come, first served basis.  If you wish to attend please can you complete the form so we can plan for numbers and catering on the day.

CHAMPS Book Sprint

On December 6-9, 2019, CHAMPS PDRAs Makrina Agaoglou, Broncio Aguilar Sanjuan, Rafael Garcia-Meseguer, Francisco Gonzalez-Montoya, Matthaios Katsanikas, Vladimir Krajnak, Shibabrat Naik, PI Stephen Wiggins, and collaborator Victor Jose Garcia-Garrido of the Universidad de Alcala in Spain held a book sprint.

A book sprint is a method of creating a book collaboratively in a short period of time. The book sprint was held at Engineers House in Bristol which afforded an atmosphere promoting intensive collaboration with minimal distractions. The book is an account of our results, approach, and future directions on the phase space approach to chemical reaction dynamics. The book was produced using Jupyter Book and is available at www.chemicalreactions.io. The result is the book entitled “Chemical Reactions: A Journey into Phase Space”. It is our intention that the book will appeal both to mathematicians and to chemists and will serve as an entry into the field. Indeed, the GitHub framework provides a mechanism for scientific collaboration and we invite the interested scientific community to contribute to the further development of the book. Instructions for this are on the GitHub site for the book (https://github.com/champsproject/chem_react_dyn).

On Wednesday the 18th of September a joint CHAMPS and Leeds Physical Chemistry seminar “Quantum Trajectories in Phase Space” took place in Leeds . The talk was given by Prof Craig Martens from University of California, Irvine. Although it is a physical/computational chemistry seminar it was of general interest, as it was focused on unusual formulation of quantum mechanics. We almost always think about quantum mechanics in terms of wave function and waves of probability, but there are other ways of looking at it. But Prof Martens presented one an approach, in which quantum mechanics is formulated very similar to classical mechanics, with the difference that neighbouring classical trajectories are not independent. They are entangled and push each other in a very specific way, as if there were many parallel worlds interacting with each other. The talk was attended not only by physicist, mathematicians and computational chemists, but also by a number of experimental organic and inorganic chemists.

University of Leeds Physical Chemistry seminar “Quantum Trajectories in Phase Space” by Prof. Craig Martens from University of California Irvine Wednesday 18th September 2019.

https://physicalsciences.leeds.ac.uk/events/event/4/school-of-chemistry/911/quantum-trajectories-in-phase-space

Although it is a physical/computational chemistry seminar it can be of general interest, as it will be about an unusual formulation of quantum mechanics. We almost always think about quantum mechanics in terms of wave function and waves of probability, but there are other ways of looking at it. Craig Martens will present one of those approaches, in which quantum mechanics is just like classical, with the difference that neighbouring classical trajectories are not independent. They are entangled and push each other in a very specific way, a bit like there were many parallel worlds interacting with each other.

The CHAMPS Project was pleased to host Professor Joel Bowman, the Samuel Candler Dobbs Professor of Theoretical Chemistry at Emory University in Atlanta, Georgia, for a visit during September 3-5, 2019. Professor Bowman presented a seminar entitled “A Machine Learning Approach for Prediction of Rate Constants”, which described a new application of machine learning in chemistry. Actually, the talk had two independent halves, with the first half of the talk devoted to a discussion of the current “state-of-the art” of the roaming mechanism for chemical reactions, which included some discussion of the manifestation of quantum effects in roaming .The CHAMPS PDRAs (as well as the PI) particularly enjoyed a two hour, informal, round table discussion, covering many aspects of contemporary reaction dynamics, as well as a bit of much appreciated career advice.

Figuring premier @ the Wickham Theatre!
Posted on September 30, 2018 by David R Glowacki

The last couple weeks have seen some interesting outreach developments! With support from Arts Council England, the EPSRC-funded CHAMPS programme, the Leverhulme Trust, and the Royal Society, David Glowacki and team worked on a project called “Figuring” at the Wickham theatre in the University of Bristol’s Department of Drama, with a talented team drawn across artistic, scientific, and technological practices. On 21 Sept, they worked to premier Figuring to an audience of artists, producers, and technologists. This follows on from a previous prototype showing of Figuring at the Knowle West Media Centre, as part of their Commons Sense programme.
The aim of Figuring is to investigate what can be created when moving, sensing bodies are embedded in simulated virtual worlds, and what arises when somatic and movement based practices are combined with Narupa, a state-of-the-art multi-person VR framework for molecular dynamics simulation, which has been developed within the Intangible Realities Laboratory over the last several years.
Figuring takes its name from its intention to explore ‘string figures’, in both the real world and also in the virtual world. String figures are created through simple movements of folding, looping, twisting, and knotting strings between the hands, fingers and thumbs of one or more people.

During our time at the Wickham theatre, members of the CHAMPS project worked with a group of dancers to facilitate experiments with both physical and virtual strings. For the ‘raw material’ of the virtual strings, the team relied on real-time molecular dynamics simulations of proteins: the molecular strings from which life is woven. Narupa enables audiences to reach out and touch simulated proteins: folding, looping, twisting, and knotting them.
Despite their virtuality, Figuring audiences reported ‘felt’ sensations whilst manipulating virtual simulations of molecular strings. Moving forward, we hope to better understand the origins of such sensations, how they map onto their physical and tangible analogues, and how different sensory and somatic practices might enable us to understand perception across real, virtual and imagined environments.

Figuring represents a collaboration between a diverse team with broad interests, led by David Glowacki and somatic/movement artist Lisa May Thomas. Alex Jones, Dr. Tom Mitchell, and Prof. Joseph Hyde helped to devise algorithms for generating sound from the virtual string dynamics. Computer Scientist Mike O’Connor and Mark Wannacott played a key role in developing the VR interaction capabilities and aesthetic, and Helen Deeks provided key advice on human-computer interaction strategies. Somatic and movement practitioners included Laila Diallo, Ben McEwan, Bryn Thomas, Ania Varez, Will Dickie, Fernanda Munoz-Newsome and Anne-Gaëlle Thiriot. Production is by Emma Hughes, dramaturgy by Tanuja Amarasuriya, and set design by Phillipa Thomas. Photos are by Paul Blakemore and Silvia Cardarelli-Gronau, and film by Adam Laity.

Summer Undergraduate Research Opportunities in the CHAMPS Project

The breadth and scale of research in CHAMPS provides opportunities for researchers from a variety of backgrounds and levels, even for undergraduates. This summer Wenyang Lyu , an undergraduate in the School of Mathematics at the University of Bristol, personified these characteristics of CHAMPS. Supported by a bursary from the London Mathematical Society and the School of Mathematics, Wenyang completed a research project that will be useful for the CHAMPS project, as well as researchers in related areas worldwide.

Periodic orbits are universally acknowledged as a fundamental building block for phase space structure in dynamical systems. For general nonlinear dynamical systems discovering the existence and nature of periodic orbits can only be carried out using computational methods. For this reason it is important to have numerical methods for fining periodic orbits that lead to reproducible results. Wenyang implemented two know numerical methods for finding periodic orbits in Python, and further developed a new numerical method. He has tested these methods on benchmark two degree-of-freedom Hamiltonian systems.

He has submitted a paper to the Journal of Open Source Software (JOSS) https://joss.theoj.org/ and his software package is available on Github https://github.com/WyLyu/UPOsHam

Wenyang was supervised by Shibabrat Naik, a postdoctoral research associate in the CHAMPS project, and Stephen Wiggins.

Phase space structures such as dividing surfaces, normally hyperbolic invariant manifolds, and their stable and unstable manifolds in molecular Hamiltonian have been an integral part of computing quantitative results such as the cumulative reaction probability and rate constants in chemical reactions. Thus, methods that can reveal the geometry of these invariant manifolds in high dimensional phase space (4 or more dimensions) need to be benchmarked by comparing with known results. In these articles, we assessed the capability of one such method called Lagrangian descriptor (LD) for revealing the aforementioned high dimensional phase space structures associated with an index-1 saddle in Hamiltonian systems. The LD based approach is applied to two and three degree-of-freedom quadratic Hamiltonian systems where the high dimensional phase space structures are known, that is as closed-form analytical expressions. This leads to a direct comparison of features in the LD contour maps and the phase space structures’ intersection with an isoenergetic two-dimensional surface, and hence provides a verification of the method. Next, the method of LD is applied to classical two and three degrees of freedom Hamiltonians that model features of dissociation reactions. The result of the LD based approach is compared with an established numerical method for computing unstable periodic orbit and tube manifolds of a two degrees of freedom system, and the results are in good agreement. We have also discussed the results in the context of three degrees of freedom extension of the same model Hamiltonian.
References:
Shibabrat Naik, Víctor J. García-Garrido, Stephen Wiggins, Finding NHIM: Identifying high dimensional phase space structures in reaction dynamics using Lagrangian descriptors, Communications in Nonlinear Science and Numerical Simulation, 2019, 79, 104907
https://doi.org/10.1016/j.cnsns.2019.104907

Shibabrat Naik and Stephen Wiggins, Finding normally hyperbolic invariant manifolds in two and three degrees of freedom with Hénon-Heiles-type potential, Phys. Rev. E, 2019, 100 (2), 022204
https://doi.org/10.1103/PhysRevE.100.022204

Related talk: https://doi.org/10.6084/m9.figshare.8131958.v2

Chemistry and molecular dynamics of peptides colloquium.
School of Chemistry University of Leeds.
11.09.2019 Room: 1.53

15:00-15:45 Enzymatic manipulation of peptides to tackle the next generation therapeutic targets: Facilitating cyclisation of peptides and their membrane permeation
Wael Houssen, Institute of Medical Sciences, University of Aberdeen
15:45-16:00 Coffee break
16:00-16:45 Chemistry research with virtual reality: From speeding up molecular dynamics to reaction network discovery.
Robin Shannon, School of Chemistry University of Bristol and School of chemistry University of Leeds
16:45-17:30 Virtual Reality demonstration. Cyclising peptides with your own hands and more.

Abstracts

Enzymatic manipulation of peptides, to tackle the next generation therapeutic targets: Facilitating cyclisation of peptides and their membrane permeation
Dr Wael Houssen
Institute of Medical Sciences, University of Aberdeen

Recent advances in our understanding of disease biology have identified a set of challenging targets for drug discovery. One of these is the protein-protein interactions (PPIs) known to be implicated in many critical diseases that are as yet without an effective treatment option e.g. autoimmune disorders and cancer. Although biological drugs can interact with PPIs but they cannot penetrate cellular membranes because of their large size. There is currently a much growing evidence that cyclic and stapled peptides can modulate PPIs and thus hold a great promise in targeting intracellular PPIs for which the transformational potential is greatest. However, the challenges in their production at large scale and their poor cellular permeability have hampered the development of these remarkable compounds. In this talk, I will explain my insights in using synthetic biology, enzyme engineering and computational chemistry to address these challenges.

Chemistry research with virtual reality: From speeding up molecular dynamics to reaction network discovery.
Dr Robin Shannon
School of Chemistry University of Bristol and School of Chemistry, University of Leeds

With the release of the open source Narupa code (https://gitlab.com/intangiblerealities), it has become possible to interact with dynamical chemistry simulations in virtual reality. You can now submerge yourself into atomistic world where you can push and pull molecules and atoms with your own hands, steering molecular dynamics in a chosen direction. In this talk I will discuss two areas where Narupa is being used to aid or enable research in the general field of rare event simulation. In the first case I show how Narupa can aid the sampling of complex conformation changes, for example in the process of peptide cyclisation or nanotube permeation, in order to obtain quantitative thermodynamic information, and in the second case I will show some initial results where virtual reality and gamification are being used to explore reaction networks. After the talk you will be able to try VR chemistry yourself.

CHAMPS Research Day at the University of Bristol—10 June 2019

CHAMPS held a research day at the University of Bristol on Monday 10th June 2019. The focus of this year’s research day was to give each PDRA an opportunity to discuss the current status of their research and their plans for the future and to obtain feedback from the entire CHAMPS team.

At the end of the we had dinner at Côte Brasserie in Clifton Village, which also provided an opportunity for a timely birthday celebration.

Lars Bratholm – CHAMPS PDRA:

A 1-day workshop, entitled “Recent Developments and Possible Extensions to the World of the Exact Factorization and Bohmian Dynamics” was held at the University of Bristol on Monday 22 April 2019. The workshop comprised a forum of eight 40-minute seminars with four breaks for discussion with world experts in the two related subjects of Bohmian Dynamics (BD) and Exact Factorization. This 1-day scientific encounter was intended to engage the CHAMPS team’s postdocs in these two topics, disseminate the recent work in these two areas performed by members of the CHAMPS team to the visiting world experts and inform all of the participants of the latest advances in these topics in the chemistry community.

To define the topics, Bohmian trajectories are meant to represent classical particle paths corresponding to quantum solutions when the quantum coupling constant h-bar has been set equal to zero in the 1927 Born-Oppenheimer (BO) approximation. J von Neumann’s 1931 approach (described in his textbook) is now called the “Exact Factorization” (EXF). The EXF approach generalised the formulation of the quantum-classical problem which has recently seen an active revival and development in numerical simulations of molecular chemistry.

Sophya Garashchuk discussed finite-dimensional representations of Bohmian trajectories and numerical difficulties in the implementation of Bohmian dynamics.

Salvador Miret-Artes discussed stochastic Bohmian particle trajectories as a possible representation of solutions of the Schrödinger-Langevin equation. In one of the discussion sessions which followed this lecture, the idea of stochasticity as a means of quantifying uncertainty in numerical simulations of the dynamics of molecular chemistry was a prominent topic.

Werner Koch discussed Bohmian trajectories whose space and time parameters and complex. This intriguing concept led to considerable discussion.

Cesare Tronci discussed a new mathematical formulation of EXF in terms of density matrices. In this new formulation, an analogue of the Bohmian trajectories arises as the Lagrangian paths of quantum complex-fluid parcels. The talk was based on a paper co-authored with a CHAMPS co-PI (Holm), which is to appear in Acta Mathematica Applicandae.

Eberhard Gross surveyed the modern development of the EXF approach and many of its successful applications in computational simulations of molecular chemistry processes during the past few years.

Ivano Tavernelli surveyed a series of standard applications of Bohmian trajectories in the BO framework, obtained upon setting the quantum coupling constant h-bar equal to zero.

Basile Curchod surveyed recent applications of the more modern EXF which involved the effects of h-bar at linear order. He also discussed many successful applications of EXF in computational simulations of molecular chemistry and explained the strategy of design of modern computational algorithms for these applications. Also

Mike Robb discussed recent applications of the BO approximation to computational simulations of atto-second processes in quantum molecular chemistry.

The many computational results displayed during the workshop raised the question of quantifying the uncertainty in these solutions. The discussions of these questions among the participants raised issues about how to model the combination of theoretical and computational errors in the quantum-classical interaction problem at the foundations of molecular chemistry which has an intrinsic uncertainty. We hope that the workshop will stimulate our efforts in improving the understanding of mathematical features of Bohmian Dynamics and Exact Factorization and creating new computational simulation techniques for use in chemistry.

Abstracts and slides for the lectures can be found here soon…

Report on the CHAMPS (Chemistry and Mathematics in Phase Space) Workshop

19th March 2019 – “Discovering Phase Space Structure and Reaction Mechanisms from Trajectory Data Sets” held at Engineers House, Clifton Bristol.

 This one day workshop was very much in the spirit of the CHAMPS project in that it brought together a group of chemists, mathematicians, and physicists all concerned with different aspects of the fundamental problem of revealing the phase space structures governing reaction dynamics using trajectory based diagnostics. The trajectory based diagnostic used by most of this group was the method of Lagrangian descriptors.  This method has emerged as a flexible and “easy to code” method that can be used in a wide variety of settings relevant to chemical reaction dynamics.

Ana Mancho gave the first talk and discussed the basic ideas behind the method of Lagrangian descriptors and the different settings in which they can be applied. In particular, it was demonstrated how they could be applied to complex data sets in  geophysical fluid dynamics settings.  She was followed by Victor Garcia Garrido how the method could be applied in higher dimensional settings in order to detect periodic orbits and normally hyperbolic invariant manifolds (NHIMs) in general. Next Florentino Borondo showed how the method of Lagrangian descriptors could be applied to a study of  lithium cyanide isomerization. He showed how the method revealed the stable and unstable manifolds of a hyperbolic periodic orbit that mediated the isomerization reaction. Intriguingly, he demonstrated the existence of a parabolic periodic orbit in the reaction region and argued that it played an important role in the isomerization reaction. The full implications of this observation required further study. Rigoberto Hernandez  showed that the method of Lagrangian descriptors could be extended to completely new situations for reaction dynamics. In particular, he considered dissipative systems where the time dependence is stochastic and driven systems where the  dividing surfaces vary in time. This theme was extended by Fabio Revuelta who considered the situation where the environment exhibits memory effects and is modelled by colored noise. Thomas Bartsch considered the reaction dynamics of a system with three reactive channels that is known to be strongly chaotic at all energies—the monkey saddle.  He discussed the phase space structures controlling reaction dynamics in this situation. Joerg Main  concluded the main talks by discussing  how neural networks could be used to reveal the phase space structures, such as NHIMs,  that  govern the reaction dynamics. He showed how this approach could be used to locate time dependent NHIMs in driven systems and, from this, compute rate constants in multidimensional systems.

The day was concluded by a lively series of “lightning talks” (20 slides, 15 seconds per slide, for a total of 5 minutes) presented by the CHAMPS postdocs.

The small size of the workshop encouraged much interaction amongst the participants and encouraged further collaborations amongst the participants.  We hope to hear more about the fruits of these interactions in a follow-on workshop in the near future.

The Chesnavich Model for Ion-Molecule Reactions: A Rigid Body Coupled to a Particle

Gregory S. Ezra and Stephen Wiggins

International Journal of Bifurcation and Chaos, Vol. 29, No. 2 (2019) 1950025

DOI: 10.1142/S0218127419500251

 In this paper, we present a derivation of Chesnavich’s Hamiltonian for a model ion-molecule reaction. The model system has the basic structure of a rigid body coupled to a structureless particle. Using the form of the potential energy of interaction given by Chesnavich, we derive the equilibria, determine their stability, and construct two, two-dimensional invariant manifolds and determine their stability.

CHAMPS – Workshop on Exact Factorization and Bohmian Mechanics

Engineers House The Promenade Clifton Down, Bristol BS8 3NB

Monday 22nd April 2019

Methodologies for separating nuclear and electronic motions are fundamental to chemistry.

In recent years the notion of “Exact Factorization” has emerged as a compelling approach for analysing and interpreting the complete wave function for a system of nuclei and electrons evolving in a time-dependent external potential.

Another related approach is Bohmian mechanics, which is known for many years, but recently has received much of attention.

The purpose of this workshop is to bring together experts in this area to discuss the current “state-of-the-art” and the prospects for future development.

To register your interest in this event please email the Champs Project Manager for further information – champs-project@bristol.ac.uk

CHAMPS – Workshop on “Discovering Phase Space Structure and Reaction Mechanisms from Trajectory Data Sets” 

Engineers House The Promenade Clifton Down, Bristol BS8 3NB

Tuesday 19th March 2019

Congratulation to CHAMPS PDRA Lars Bratholm for being awarded a Alan Turing Institute Fellowship

We are please that Dr. Lars Bratholm is in the first group of Alan Turing Institute fellows at the University of Bristol. This is a notable accomplishment and we anticipate that this will serve to  further develop links between CHAMPS and the Alan Turing Institute.

https://www.turing.ac.uk/people/researchers/lars-andersen-bratholm

Information about the Alan Turing Institute can be found here:

https://www.turing.ac.uk/about-us

Dr Shibabrat Naik is one of the Champ PDRAs who joined the team in mid 2018.

This is his review of ‘Writing Science’ by Joshua Schimel

https://bristolclear.blogs.bristol.ac.uk/2018/11/21/writing-science-2/.

This review was part of the academic writing month organized during November by Bristol Clear.

Phase Space Structure and Transport in a Caldera Potential Energy Surface

Matthaios Katsanikas and Stephen Wiggins

International Journal of Bifurcation and Chaos, Vol. 28, No. 13 (2018) 1830042

https://doi.org/10.1142/S0218127418300422

We study phase space transport in a 2D caldera potential energy surface (PES) using techniques from nonlinear dynamics. The caldera PES is characterized by a flat region or shallow minimum at its center surrounded by potential walls and multiple symmetry related index one saddle points that allow entrance and exit from this intermediate region. We have discovered four qualitatively distinct cases of the structure of the phase space that govern phase space transport. These cases are categorized according to the total energy and the stability of the periodic orbits associated with the family of the central minimum, the bifurcations of the same family, and the energetic accessibility of the index one saddles. In each case, we have computed the invariant manifolds of the unstable periodic orbits of the central region of the potential, and the invariant manifolds of the unstable periodic orbits of the families of periodic orbits associated with the index one saddles. The periodic orbits of the central region are, for the first case, the unstable periodic orbits with period 10 that are outside the stable region of the stable periodic orbits of the family of the central minimum. In addition, the periodic orbits of the central region are, for the second and third cases, the unstable periodic orbits of the family of the central minimum and for the fourth case the unstable periodic orbits with period 2 of a period-doubling bifurcation of the family of the central minimum. We have found that there are three distinct mechanisms determined by the invariant manifold structure of the unstable periodic orbits that govern the phase space transport. The first mechanism explains the nature of the entrance of the trajectories from the region of the low energy saddles into the caldera and how they may become trapped in the central region of the potential. The second mechanism describes the trapping of the trajectories that begin from the central region of the caldera, their transport to the regions of the saddles, and the nature of their exit from the caldera. The third mechanism describes the phase space geometry responsible for the dynamical matching of trajectories originally proposed by Carpenter and described in [Collins et al., 2014] for the two-dimensional caldera PES that we consider.

V. J. Garcia-Garrido, F. Balibrea-Iniesta, S. Wiggins, A. M. Mancho, and C. Lopesino,  Detection of Phase Space Structures of the Cat Map with Lagrangian Descriptors, Regular and Chaotic Dynamics, 23(6), 751-766 (2018).

https://link.springer.com/article/10.1134/S1560354718060096

In this paper we show that Lagrangian Descriptors (LDs), a technique based on Dynamical Systems Theory (DST), are able to reveal the phase space structures present in the well known Arnold’s cat map. This discrete dynamical system, which represents a classical example of an Anosov diffeomorphism that is strongly mixing,  provides us with a benchmark model to test the performance of LDs and their capability to detect fixed points, periodic orbits and their stable and unstable manifolds present in chaotic maps. In this work we show, both from a theoretical and a numerical perspective, how LDs reveal the invariant manifolds of the periodic orbits of the cat map. The application of this methodology in this setting clearly illustrates the chaotic behaviour of the cat map and highlights some technical numerical difficulties that arise in the identification of its phase space structures.

G. S. Ezra and S. Wiggins, Sampling Phase Space Dividing Surfaces Constructed from Normally Hyperbolic Invariant Manifolds (NHIMs), J. Phys. Chem. A., 122(42), 8354–8362 (2018).

https://pubs.acs.org/doi/10.1021/acs.jpca.8b07205

In this paper, we further investigate the construction of a phase space dividing surface (DS) from a normally hyperbolic invariant manifold (NHIM) and the sampling procedure for the resulting dividing surface described in earlier work (Wiggins, S.; J. Chem. Phys. 2016, 144, 054107). Our discussion centers on the relationship between geometrical structures and dynamics for 2 and 3 degree of freedom (DoF) systems, specifically, the construction of a DS from a NHIM. We show that if the equation for the NHIM and associated DS is known (e.g., as obtained from Poincaré–Birkhoff normal form theory), then the numerical procedure described in Wiggins et al. ( J. Chem. Phys. 2016, 144, 054107) gives the same result as a sampling method based upon the explicit form of the NHIM. After describing the sampling procedure in a general context, it is applied to a quadratic Hamiltonian normal form near an index-one saddle where explicit formulas exist for both the NHIM and the DS. It is shown for both 2 and 3 DoF systems that a version of the general sampling procedure provides points on the analytically defined DS with the correct microcanonical density on the constant-energy DS. Excellent agreement is obtained between analytical and numerical averages of quadratic energy terms over the DS for a range of energies.

V. J. Garcia-Garrido, J. Curbelo, A. M. Mancho, S. Wiggins, and C. R. Mechoso,  The Application of Lagrangian Descriptors to 3D Vector Fields, Regular and Chaotic Dynamics, 23(5), 551-568 (2018).

https://doi.org/10.1134/S1560354718050052

Since the 1980s, the application of concepts and ideas from Dynamical Systems Theory to analyze phase space structures has provided a fundamental framework to understand long-term evolution of trajectories in many physical systems. In this context, for the study of fluid transport and mixing the development of Lagrangian techniques that can capture the complex and rich dynamics of time dependent flows has been crucial. Many of these applications have been to atmospheric and oceanic flows in two-dimensional (2D) relevant scenarios. However, the geometrical structures that constitute the phase space structures in time dependent three-dimensional (3D) flows require further exploration. In this paper we explore the capability of Lagrangian Descriptors (LDs), a tool that has been successfully applied to time dependent 2D vector fields, to reveal phase space geometrical structures in 3D vector fields. In particular we show how LDs can be used to reveal phase space structures that govern and mediate phase space transport. We especially highlight the identification of Normally Hyperbolic Invariant Manifolds (NHIMs) and tori. We do this by applying this methodology to three specific dynamical systems: a 3D extension of the classical linear saddle system, a 3D extension of the classical Duffing system, and a geophysical fluid dynamics f-plane approximation model which is described by analytical wave solutions of the 3D Euler equations. We show that LDs successfully identify and recover the template of invariant manifolds that define the dynamics in phase space for these examples.

Article, “Influence of mass and potential energy surface geometry on roaming in Chesnavich’s CH4+ model,” was published 07 September 2018, in The Journal of Chemical Physics (Vol.149, Issue 9).  Vladimir Krajnak and Stephen Wiggins

It may be accessed via the link below: https://doi.org/10.1063/1.5044532
DOI: 10.1063/1.5044532

Chesnavich’s model Hamiltonian for the reaction CH⁺₄ → CH⁺₃ + H is known to exhibit a range of interesting dynamical phenomena including roaming. The model system consists of two parts: a rigid, symmetric top representing the CH⁺₃ ion and a free H atom. We study roaming in this model with focus on the evolution of geometrical features of the invariant manifolds in phase space that govern roaming under variations of the mass of the free atom m and a parameter a that couples radial and angular motion. In addition, we establish an upper bound on the prominence of roaming in Chesnavich’s model. The bound highlights the intricacy of roaming as a type of dynamics on the verge between isomerisation and nonreactivity as it relies on generous access to the potential wells to allow reactions as well as a prominent area of high potential that aids sufficient transfer of energy between the degrees of freedom to prevent isomerisation.

In July 2018, three of the CHAMPS PDRA’s: Rafael Garcia Meseguer, Matthaios Katsanikas and Vladimir Krajnak, attended the workshop ‘Geometry of Chemical Reaction Dynamics in Gas and Condensed Phases’ at the Telluride Science Research Center in Telluride, CO, USA. The meeting focussed on theoretical aspects of chemical reaction dynamics and forms a platform for discussions about extensions of theory from lower to higher dimensional systems and from gas to condensed phases. Apart from meeting some of the leading researchers in the field and discussing ideas for future work, the PDRA’s also shared their contributions to the field. Rafael gave a talk on the applications of Lagrangian descriptors to finding dividing surfaces and invariant structures, Matthaios shared his findings on phase space transport in the Caldera model and Vladimir reported on the phase space mechanism behind Roaming in Chesnavich’s model and its evolution under parameter variations.

CHAMPS held a research day at Imperial College London on Friday 13th July 2018. This provided an  opportunity for all of the investigators and PDRAs to discuss their research and obtain feedback from the entire CHAMPS team.

Geometry of nonadiabatic quantum hydrodynamics

Michael. S. Foskett, Darryl. D. Holm, Cesare Tronci

(Submitted on 3 Jul 2018)

By using standard momentum maps from geometric mechanics, we collectivize the mean-field (MF) and exact factorization (EF) models of molecular quantum dynamics into two different quantum fluid models. After deriving the corresponding quantum fluid models, we regularize each of their Hamiltonians for finite ℏ by introducing spatial smoothing. The ℏ≠0 dynamics of the Lagrangian paths of the classical nuclear fluid flows for both MF and EF can be written and contrasted as finite dimensional canonical Hamiltonian systems for the evolution in phase space of singular solutions called Bohmions, in which each nucleus follows a Lagrangian path in configuration space. Comparison is also made with the variational dynamics of a new type of Bohmian trajectories, which arise from Hamilton’s principle with spatially smoothed quantum potential with finite ℏ.

https://arxiv.org/abs/1807.01031

The CHAMPS Leeds group just published in the Journal of Chemical Physics two papers related to CHAMPS Work Projects 4 and 5 on quantum dynamics and nonadiabatic dynamics. In the first paper “The effect of sampling techniques used in the multiconfigurational Ehrenfest method” by C.Symonds, J.Kattitzi and D.Shalashilin (https://aip.scitation.org/doi/10.1063/1.5020567) Spin-Boson model was used to assess the samplings of Canonical Coherent States basis sets in the phase space quantum mechanics. The paper validated the sampling techniques used in our simulations of ultrafast photochemical reactions. It has been demonstrated that the techniques really work and for the Spin-Boson model the calculations converge to the exact quantum result.  The Figure below shows quantum wave functions in phase space.

In the second paper “Zombie states for description of structure and dynamics of multi-electron systems” by D.Shalashilin (https://aip.scitation.org/doi/10.1063/1.5023209) a new type of Fermionic Coherent State has been introduced, which potentially can be used in simulations of nonadiabatic dynamics in chemistry and photochemistry. Fermionic Coherent States are well known in mathematics.  However, they require complicated algebra of Grassmann numbers not well suited for numerical simulations in computational chemistry.  The paper introduces a coherent antisymmetrised superposition of “dead” and “alive” electronic states called Zombie State (ZS), which do not need Grassmann algebra.  Instead it is replaced by a very simple sign-changing rule in the definition of creation and annihilation operators.  Zombie States can be used as basis functions for quantum propagation just like Canonical Coherent States for distinguishable particles.  As it is shown at the Figure in standard electronic structure and dynamics theories (left frame) some spin-orbitals are occupied by electrons and some are empty. In Zombie States (right frame) all orbitals are occupied, but some electrons are more “alive” than “dead” or more “dead” than “alive”.  The term “Zombie” for simultaneously “dead” and “alive” electrons was proposed by Liz Clark, Bristol School of Mathematics manager, who is acknowledged in the paper!

Robert G. Bergman Lecture: What is a transition state, and why should I care?

13th March 2018. University of California, Berkeley.

Featured Speaker:  Prof. Barry Carpenter, School of Chemistry, University of Bristol

Since the early days of the development of Transition State Theory, there have been two descriptions of what a transition state (TS) is. The one that most chemists use identifies the TS with a saddle point on the potential energy surface (PES). The other is that it is a dividing surface (DS) in phase space, which reactive trajectories cross only once on their transit from reactant to product. Under limited circumstances, the two descriptors can be shown to be equivalent, but in most practical circumstances they are not. The DS description is the more rigorous, and this talk will focus on cases in which the location of the DS in configuration space is far from any PES saddle point. A common example occurs for reactions in solution that involve substantial changes in shape of the solute. If there are parallel paths to competing products after such an event, then incorrect identification of the true location of the TS can lead to a misunderstanding of what controls the product ratio. That, in turn, has obvious consequences for efforts to control product ratios through change of conditions or design of catalysts.

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.

A goal of CHAMPS is to bring together developments in mathematics with problems in chemistry that reveal a new and unique insight. The method of Lagrangian descriptors is an excellent example of such a synergy.

Lagrangian descriptors are a trajectory diagnostic for revealing phase space structures in dynamical systems. The method was originally developed in the context of Lagrangian transport studies in fluid dynamics (Madrid and Mancho 2009) but the wide applicability of the method has recently been recognized in chemistry, see (Craven and Hernandez 2015, Junginger and Hernandez 2016, Feldmaier, Junginger et al. 2017, Junginger, Duvenbeck et al. 2017, Junginger, Main et al. 2017).

The method is very compelling since it is straightforward to implement computationally, the interpretation is evident, and it provides a “high resolution” method for exploring high dimensional phase space with low dimensional slices. It also applies to both Hamiltonian and non-Hamiltonian systems (Lopesino, Balibrea-Iniesta et al. 2017) as well as to systems with arbitrary, even stochastic, time-dependence (Balibrea-Iniesta, Lopesino et al. 2016). Moreover, Lagrangian descriptors can be applied directly to data sets, without the need of an explicit dynamical system (Mendoza, Mancho et al. 2014).

Briefly, Lagrangian descriptors are implemented as follows. Each point in a chosen grid of initial conditions for trajectories in phase space is assigned a value according to the arclength of the trajectory starting at that initial condition after integration for a fixed, finite time, both backward and forward in time (all initial conditions in the grid are integrated for the same time). The idea is that the influence of phase space structures on trajectories will result in differences in arclength of nearby trajectories near a phase space structure. This has been quantified in terms of the notion of “singular structures’ in the Lagrangian descriptor plots, which are easy to recognize visually (Mancho, Wiggins et al. 2013, Lopesino, Balibrea-Iniesta et al. 2017).

Trajectories are the “primitive objects” that are used to explore phase space structure. In fact, phase space structure is “built” from trajectories. For high dimensional phase space this approach is problematic and prone to issues of interpretation since a tightly grouped set of initial conditions may result in trajectories that become “lost” with respect to each other in phase space. The method of Lagrangian descriptors turns this problem on its head by emphasizing the initial conditions of trajectories, rather than the precise location of their futures and pasts, after a specified amount of time.  A low dimensional “slice” of phase space can be selected and sampled with a grid of initial conditions of high resolution. Since the phase space structure is encoded in the initial conditions of the trajectories, no resolution is lost as the trajectories evolve in time.

We remark that the original Lagrangian trajectory diagnostic is the arclength. This has been modified in (Lopesino, Balibrea et al. 2015, Lopesino, Balibrea-Iniesta et al. 2017) where, effectively, a different type of norm is used as a trajectory diagnostic. This has been shown to have many advantages over the arclength. For example, it allows for a rigorous analysis of the notion of “singular structures” in certain cases and the relation of this notion to invariant manifolds. It also allows a natural decomposition of the Lagrangian descriptor in a way that isolates distinct dynamical effects. This was utilized in (Demian and Wiggins 2017) in order to show that a Lagrangian descriptor could be used to detect the Lyapunov periodic orbits in the two degree-of-freedom Henon-Heiles Hamiltonian system.

This figure is from (Mendoza, Mancho et al. 2014) and shows the results of the  use of the Lagrangian descriptor for revealing flow structures in the Gulf Stream using a geophysical  fluid dynamics data set.

The use and further development of Lagrangian descriptors is a topic underlying many of the themes of CHAMPS: from understanding the role of phase space structure in high dimensional systems to dimensional reduction and as well as for machine learning from data sets.

References

Balibrea-Iniesta, F., et al. (2016). “Lagrangian Descriptors for Stochastic Differential Equations: A Tool for Revealing the Phase Portrait of Stochastic Dynamical Systems.” International Journal of Bifurcation and Chaos 26(13): 1630036.

Craven, G. T. and R. Hernandez (2015). “Lagrangian descriptors of thermalized transition states on time-varying energy surfaces.” Physical review letters 115(14): 148301.

Demian, A. S. and S. Wiggins (2017). “Detection of Periodic Orbits in Hamiltonian Systems Using Lagrangian Descriptors.” International Journal of Bifurcation and Chaos 27(14): 1750225.

Feldmaier, M., et al. (2017). “Obtaining time-dependent multi-dimensional dividing surfaces using Lagrangian descriptors.” Chemical Physics Letters 687: 194-199.

Junginger, A., et al. (2017). “Chemical dynamics between wells across a time-dependent barrier: Self-similarity in the Lagrangian descriptor and reactive basins.” The Journal of chemical physics 147(6): 064101.

Junginger, A. and R. Hernandez (2016). “Lagrangian descriptors in dissipative systems.” Physical Chemistry Chemical Physics 18(44): 30282-30287.

Junginger, A., et al. (2017). “Variational principle for the determination of unstable periodic orbits and instanton trajectories at saddle points.” Physical Review A 95(3): 032130.

Lopesino, C., et al. (2015). “Lagrangian descriptors for two dimensional, area preserving, autonomous and nonautonomous maps.” Communications in Nonlinear Science and Numerical Simulation 27(1): 40-51.

Lopesino, C., et al. (2017). “A theoretical framework for lagrangian descriptors.” International Journal of Bifurcation and Chaos 27(01): 1730001.

Madrid, J. J. and A. M. Mancho (2009). “Distinguished trajectories in time dependent vector fields.” Chaos: An Interdisciplinary Journal of Nonlinear Science 19(1): 013111.

Mancho, A. M., et al. (2013). “Lagrangian descriptors: A method for revealing phase space structures of general time dependent dynamical systems.” Communications in Nonlinear Science and Numerical Simulation 18(12): 3530-3557.

Mendoza, C., et al. (2014). “Lagrangian descriptors and the assessment of the predictive capacity of oceanic data sets.” Nonlinear Processes in Geophysics 21(3): 677-689.

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.

A.S. Demian and S. Wiggins, Detection of Periodic Orbits in Hamiltonian Systems Using Lagrangian Descriptors, International Journal of Bifurcation and Chaos, 27 (4), 1750225 (2017).

http://www.worldscientific.com/doi/abs/10.1142/S021812741750225X

 The purpose of this paper is to apply Lagrangian Descriptors, a concept used to describe phase space structure, to autonomous Hamiltonian systems with two degrees of freedom in order to detect periodic solutions. We propose a method for Hamiltonian systems with saddle-center equilibrium and apply this approach to the classical Hénon–Heiles system. The method was successful in locating the unstable Lyapunov orbits in phase space.

B.K. Carpenter, G.S. Ezra, S. C. Farantos, Z. C. Kramer, and S. Wiggins. Dynamics on the Double Morse Potential: A Paradigm for Roaming Reactions with no Saddle Points, Regular and Chaotic Dynamics, 23(1), 60-79 (2018).

https://link.springer.com/article/10.1134/S1560354718010069

In this paper we analyze a two degree of freedom Hamiltonian system constructed from two planar Morse potentials. The resulting potential energy surface has two potential wells surrounded by an unbounded flat region containing no critical points. In addition, the model has an index one saddle between the potential wells. We study the dynamical mechanisms underlying transport between the two potential wells, with emphasis on the role of the flat region surrounding the wells. The model allows us to probe many of the features of the “roaming mechanism” whose reaction dynamics are of current interest in the chemistry community.

B.K. Carpenter, G.S. Ezra,  S. C. Farantos, Z. C. Kramer, and S. Wiggins. Empirical Classification of Trajectory Data: An Opportunity for the Use of Machine Learning in Molecular Dynamics. J. Phys. Chem. B. DOI: 10.1021/acs.jpcb.7b08707

Publication Date (Web): October 2, 2017.
https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b08707

This paper uses trajectory data and machine learning approaches to “learn” phase space structures. Classical Hamiltonian trajectories are initiated at random points in phase space on a fixed energy shell of a model two degree of freedom potential, consisting of two interacting minima in an otherwise flat energy plane of infinite extent.  Below the energy of the plane, the dynamics are demonstrably chaotic.  However, most of the work in this paper involves trajectories at a fixed energy that is 1% above that of the plane, in which regime the dynamics exhibit behavior characteristic of chaotic scattering.  The trajectories are analyzed without reference to the potential, as if they had been generated in a typical direct molecular dynamics simulation.  The questions addressed are whether one can recover useful information about the structures controlling the dynamics in phase space from the trajectory data alone, and whether, despite the at least partially chaotic nature of the dynamics, one can make statistically meaningful predictions of trajectory outcomes from initial conditions.  It is found that key unstable periodic orbits, which can be identified on the analytical potential, appear by simple classification of the trajectories, and that the specific roles of these periodic orbits in controlling the dynamics are also readily discerned from the trajectory data alone.  Two different approaches to predicting trajectory outcomes from initial conditions are evaluated, and it is shown that the more successful of them has ~90% success.  The results are compared with those from a simple neural network, which has higher predictive success (97%) but requires the information obtained from the “by-hand” analysis to achieve that level.  Finally, the dynamics, which occur partly on the very flat region of the potential, show characteristics of the much-studied phenomenon called “roaming.” On this potential, it is found that roaming trajectories are effectively “failed” periodic orbits, and that angular momentum can be identified as a key controlling factor, despite the fact that it is not a strictly conserved quantity.  It is also noteworthy that roaming on this potential occurs in the absence of a “roaming saddle,” which has previously been hypothesized to be a necessary feature for roaming to occur.

The Champs (Chemistry and mathematics in phase space) Kick off Meeting took place 15th & 16th January 2018.  This two-day conference was held at The Watershed in Bristol and launched the Chemistry and Mathematics in Phase Space project. 70 people from all over the world attended the event which had a stimulating set of talks from eminent speakers.

It brought together an international group of distinguished speakers who gave first class talks to a large audience on a wide range of areas in Mathematics and Chemistry.

The conference dinner was held in the Bristol Museum and Art Gallery

The kick off meeting was the first organized activity of Champs bringing together chemists and mathematicians. The success of this meeting reinforces our optimism that this is an opportune time for such an interdisciplinary collaboration of chemists and mathematicians and we expect that this will be the first of many such successful meetings  of Champs related topics.

Watch as the Voronoi screen is carefully fixed in place on the glass atrium at the new home for the School of Mathematics. For more information on the Voronoi screen, and the Fry building please visit: http://www.bristol.ac.uk/maths/fry-bu…

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.

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.

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.

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, 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.

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.

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.

On 17th June, David Glowacki and Lisa May Thomas led a workshop at Modern Art Oxford entitled Sculpting the Invisible World. The work was part of the gallery’s ‘Future Knowledge’ program of events, curated by Emma Ridgway, and photographed by Stu Allsop. Using a pioneering multi-person virtual reality software framework, visitors were invited to interact within a virtual landscape as embodied energy fields. Methods from rigorous computational molecular physics and real-time digital rendering allowed digitally embodied participants to sculpt the dynamics of a simulated molecular nano-world, for example deforming buckminsterfullerene molecules, passing them back and forth, threading methane molecules through a carbon nanotube, and tying knots in proteins.

Sculpting the Invisible World follows on from the ‘dances with Avatars’ experiments carried out by Lisa May Thomas, which were designed as a sort of embodied Turing Test. During the Modern Art Oxford workshops, we were specifically interested in two aspects of multi-person interaction in VR: (1) what are the conventions which guided human-to-human interaction in virtual spaces, when we are rendered as digital bodies? (2) how do we begin what ‘feeling’ means in an immersive scientific visualisation environment – particularly in order to understand workshop participants’ claims that different molecular structures “feel” different?