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

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.

University of Leeds Physical Chemistry seminar “Quantum Trajectories in Phase Space” Craig Marten

CHAMPS Visitor: Professor Joel Bowman, the Samuel Candler Dobbs Professor of Theoretical Chemistry at Emory University in Atlanta.

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!

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

The last couple weeks have been amazing! With support from Arts Council England, the EPSRC-funded CHAMPS programme, the Leverhulme Trust, and the Royal Society, I’ve been working 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, we premiered 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 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. They have evolved as a generational mechanism for the transmission of stories, knowledge and value systems. String figures offer a mechanism for connecting bodies like nodes within a network, enabling bodies to feel the dynamics of other bodies through space.

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Figuring team members experimenting with the dynamics of physical strings

During our time at the Wickham theatre, a talented group of dancers facilitated experiments with both physical and virtual strings, enabling us to better understand the dynamics that operate between bodies embedded in both real and virtual environments. For the ‘raw material’ of our virtual strings, we relied on real-time 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 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.

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Figuring team members experimenting with the dynamics of virtual strings

Figuring represents a collaboration between a diverse team with broad interests, led by myself 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

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.

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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.

 

Finding high dimensional phase space structures that mediate chemical reactions using Lagrangian descriptors

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 – 11.09.19

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 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.

A copy of the schedule for the day can be found here: Research Day 10.06.19 Schedule.

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