Chemistry and Mathematics in Phase Space
Congratulations to new Champs PDRA Dr Grace Chuang on being a prize winner at the 2021 Chemistry National Meeting in Taiwan. Grace was part of the physical chemistry group and passed the first and second evaluations to get the certification and a prize of £250.
2021化學年會重要時程 研究論文獎（研究生學位論文，大專生專題論文獎）稿截止日：2021 年 01 月 04 日當晚12點前為上傳最後期限Important Dates Online application dea 2021化學年會 2021化學年會 化學年會 2021中國化學年會 2021年化學年會 中央大學化學系 中國化學年會 化學 年會 化學年會地點 化學年會報名 化學年會投稿 …www.2021csnm.tw
Congratulations to Champs PDRA Dr Francisco Gonzalez Montoya who was one of the BMC/BAMC 2021 poster winners.
https://doi.org/10.1021/acs.jpclett.1c00266
A perspective article has been published by JPC Letters which reports implementation of the AIMC method in the Los Alamos NEXMD software used for simulation of energy transfer in organic molecules excited by light. The work was done by an international group of scientists from US, Argentina and UK but the method was originally developed by Dmitry Makhov and Dmitry Shalashilin at the University of Leeds, and was supported largely by the CHAMPS project. The method is based on the idea of using phase space in quantum mechanics and the role of CHAMPS was invaluable.
The paper also made it onto the journal cover:
The Champs team have had a very successful summer with a number of students working closely with the Champs PI and several PDRAs on projects.
Below is a list of names of those who worked on the project over the summer and the titles of their project, a few of which have written papers.
Prof. Stephen Wiggins
Student name – Cate Mandell
Title of Project – “The Role of Time Dependent Phase Space Structures on Reaction Dynamics and the No-Recrossing Property of Dividing Surfaces”
She wrote a paper on her research that has been accepted in the “International Journal of Bifurcation and Chaos”.
Student name – Zara Graham-Jones and Michael Turner, they worked together on the following project
Title of Project – “Lagrangian Descriptors and Bohmian Mechanics” they have written a paper on their project
Dr Shibabrat Naik + Prof. Stephen Wiggins co-advised the following students and their respective topics:
Computation and visualization of phase space structures relevant for chemical reaction dynamics
Student name: Sam Spedding
Title: Two Degree of Freedom Hamiltonian Systems in Chemical Reaction Dynamics – A Phase Space Analysis
Student name: Bing En Gan
Title: Computation and visualization of phase space structures in Reaction Dynamics
Student name: Piero Sarti (LMS summer research award)
Title: Visualizing the 2-Well and 3-Well Deleon-Berne Hamiltonian
Student name: Annie Hu
Title: Poincaré sections, gap times, and directional flux in De Leon-Berne Hamiltonian
Student name: Wenyang Lyu
Title: Classical-quantum correspondence in the saddle-node Hamiltonian
Published paper based on work over winter and spring term: https://link.springer.com/article/10.1134%2FS1560354720050044
There are manuscripts in preparation based on the individual summer project reports.
Dr. Vladimir Krajnak
Student name – Mark Pearson
Title of Project – Phase space structures in the ‘Helium atom’
Dr Francisco Gonzalez Montoya
Student name – Charlotte Quant
Title of Project – The Quantum Inverted Oscillator
Name – Edward Sharp
Title of Project – The Tunnel Effect and the Anderson Localization
Dr Makrina Agaoglou + Dr Matthaios Katsanikas
Student name – Yibin Geng.
Title of Project – “The dynamical matching as a bifurcation effect in caldera potential energy surfaces”
Student name – Rebecca Crossley
Title of Project – “From Poincare Maps to Lagrangian Descriptors: The case of the VRI potential”
Student name – Douglas Haigh
Title of Project – “The time evolution of the selectivity in a symmetric potential energy surface with a post-transition-state bifurcation”
The plan is to submit their drafts in scientific journals in the near future. Some of the titles might change for the submission.
Role of 3D printing technology in dynamical systems applications
Shibabrat Naik, Stephen Wiggins
Understanding chemical reactions using dynamical systems theory is based on using the geometric view of the structures underlying the solutions of the equations of motion. The equations are derived from the potential energy due to the molecular configurations involved in the reaction. In both of these aspects, that is the geometry of the potential energy surfaces and the phase space structures, visualization in the real space of the physical world using 3D printing facility is increasing the educational and hands-on learning experience. In our research project supported by CHAMPS (EPSRC Grant No. EP/P021123/1) we used the 3D-printing facility in the School of Mathematics for prototyping a potential energy surface in the dissociation of ozone available in the literature (dx.doi.org/10.1021/ed500683g). This potential energy function at constant total energy is an 3D volume specified by a function obtained from fitting electronic energies and can be used in dynamical systems analysis of the dissociation.
The CHAMPS (Chemistry and Mathematics in Phase Space) research group is pleased to announce the availability of our latest Jupyter Book, “Lagrangian Descriptors: Discovery and Quantification of Phase Space Structure and Transport” available at
https://champsproject.github.io/lagrangian_descriptors. This book is a companion to our recent Jupyter Book, Chemical Reactions: A Journey into Phase Space, available at http://www.chemicalreactions.io.
Our new Jupyter book contains substantial “computable content” in the form of Jupyter notebooks for computing the Lagrangian descriptors for a variety of dynamical systems.
We view both of our Jupyter books as community resources and we invite all those interested to participate in their further development through GitHub.
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
*REGISTRATION IS NOW OPEN – please register here*
Schedule of talks
Workshop link – https://bluejeans.com/233350403
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)
