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).
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).
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.
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.
EVENT Schedule inc.talks V.3
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.