Publications

2020

Gerrard W, Bratholm L, Packer M, Mulholland A, Glowacki D, Butts C. (2020). IMPRESSION – prediction of NMR parameters for 3-dimensional chemical structures using machine learning with near quantum chemical accuracy. Chemical Science, https://doi.org/10.1039/C9SC03854J

Enrico Lavagna, Jonathan Barnoud, Giulia Rossi, Luca Monticelli Size-dependent aggregation of hydrophobic nanoparticles in lipid membranes. https://doi.org/10.1039/D0NR00868K

 

2019

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

R.Garcia-Meseguer, B.K.Carpenter, S.Wiggins. “The influence of the solvent’s mass on the location of the dividing surface for a model Hamiltonian”  Chemical Physics Letters. 2019. https://doi.org/10.1016/j.cpletx.2019.100030

R.Garcia-Meseguer, B.K.Carpenter. “Re‐Evaluating the Transition State for Reactions in Solution” European Journal of Organic Chemistry. 2019, Issue 2-3, p254-266. https://doi.org/10.1002/ejoc.201800841

M.Katsanikas, S.Wiggins (2019). Phase Space Analysis of the Nonexistence of Dynamical Matching in a Stretched Caldera Potential Energy Surface International Journal of Bifurcation and Chaos Vol. 29, No. 04, 1950057 (2019)

C. Symonds, D. V. Makhov, N. C. Cole-Filipiak, J. A. Green, V. Stavros and D. V. Shalashilin (2019). “Ultrafast Photodissociation Dynamics of Pyrazole, Imidazole and their Deuterated Derivatives using Ab Initio Multiple Cloning.” Physical Chemistry Chemical Physics, Accepted Manuscript.

J. A. Green, D. V. Makhov, N. C. Cole-Filipiak, C. Symonds, V. G. Stavros and D. V. Shalashilin (2019). “Ultrafast photodissociation dynamics of 2-ethylpyrrole: adding insight to experiment with ab initio multiple cloning.” Physical Chemistry Chemical Physics 21(7): 3832-3841.

V. M. Freixas, D. Ondarse-Alvarez, S. Tretiak, D. V. Makhov, D. V. Shalashilin and S. Fernandez-Alberti (2019). “Photoinduced non-adiabatic energy transfer pathways in dendrimer building blocks.” Journal of Chemical Physics 150(12): 10.

Gregory S. Ezra and Stephen Wiggins, The Chesnavich Model for Ion-Molecule Reactions: A Rigid Body Coupled to a Particle, International Journal of Bifurcation and Chaos, Vol. 29, No. 2 (2019) 1950025

Ezra GS, Wiggins S. (2018). Sampling Phase Space Dividing Surfaces Constructed from Normally Hyperbolic Invariant Manifolds (NHIMs).. The journal of physical chemistry. A, 122 (42), pp. 8354-8362

Makhov D, Shalashilin D. (2018). Floquet Hamiltonian for incorporating electronic excitation by a laser pulse into simulations of non-adiabatic dynamics. Chemical Physics, https://doi.org/10.1016/j.chemphys.2018.07.048

Freixas VM, Ondarse-Alvarez D, Tretiak S, Makhov DV, Shalashilin DV, Fernandez-Alberti S. (2019). Photoinduced non-adiabatic energy transfer pathways in dendrimer building blocks.. The Journal of chemical physics, 150 (12), pp. 124301. https://doi.org/10.1021/acs.jpca.9b01006

Hare S, Bratholm L, Glowacki D, Carpenter B. (2019). Low dimensional representations along intrinsic reaction coordinates and molecular dynamics trajectories using interatomic distance matrices. Chemical Science, https://doi.org/10.1142/S0218127419500573

Green J, Shalashilin D. (2019). Simulation of the quantum dynamics of indistinguishable bosons with the method of coupled coherent states. Physical Review A, https://doi.org/10.1016/j.cpletx.2019.100030

Shannon RJ, Hornung B, Tew DP, Glowacki DR. (2019). Anharmonic Molecular Mechanics: Ab Initio Based Morse Parametrizations for the Popular MM3 Force Field.. The journal of physical chemistry. A, 123 (13), pp. 2991-2999  https://doi.org/10.1142/S0218127419500251

Amabilino S, Bratholm LA, Bennie SJ, Vaucher AC, Reiher M, Glowacki DR. (2019). Training Neural Nets To Learn Reactive Potential Energy Surfaces Using Interactive Quantum Chemistry in Virtual Reality.. The journal of physical chemistry. A, 123 (20), pp. 4486-4499  https://doi.org/10.1063/1.5092590

O’Connor MB, Bennie SJ, Deeks HM, Jamieson-Binnie A, Jones AJ, Shannon RJ, Walters R… Glowacki DR. (2019). Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework.. The Journal of chemical physics, 150 (22), pp. 220901  https://doi.org/10.1063/1.5100145

Bramley O, Symonds C, Shalashilin D. (2019). Quantum system-bath dynamics with quantum superposition sampling and coupled generalized coherent states. The Journal of Chemical Physics, https://doi.org/10.1021/acs.jchemed.9b00181

Bennie S, Ranaghan K, Deeks H, Goldsmith H, O’Connor M, Mulholland A, Glowacki D. (2019). Teaching Enzyme Catalysis Using Interactive Molecular Dynamics in Virtual Reality. Journal of Chemical Education,

Foskett M, Holm D, Tronci C. (2019). Geometry of Nonadiabatic Quantum Hydrodynamics. Acta Applicandae Mathematicae, https://doi.org/10.1007/s10440-019-00257-1

Krajňák V, Wiggins S. (2019). Dynamics of the Morse Oscillator: Analytical Expressions for Trajectories, Action-Angle Variables, and Chaotic Dynamics. International Journal of Bifurcation and Chaos,  https://doi.org/10.1142/S0218127419501578

 

2018

V. M. Freixas, S. Fernandez-Alberti, D. V. Makhov, S. Tretiak and D. Shalashilin (2018). “An ab initio multiple cloning approach for the simulation of photoinduced dynamics in conjugated molecules.” Physical Chemistry Chemical Physics 20(26): 17762-17772.

D. V. Makhov and D. V. Shalashilin (2018). “Floquet Hamiltonian for incorporating electronic excitation by a laser pulse into simulations of non-adiabatic dynamics.” Chemical Physics 515: 46-51.

M. Katsanikas and S. Wiggins, Phase Space Structure and Transport in a Caldera Potential Energy Surface, International Journal of Bifurcation and Chaos, Vol. 28, No. 13 (2018) 1830042

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).

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

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).

V. Krajňák and S. Wiggins. Influence of mass and potential energy surface geometry on roaming in Chesnavich’s CH4+ model. The Journal of Chemical Physics 149(9), 094109 (2018).

R. E. Arbon, A. J. Jones, L. Bratholm, T. Mitchell, and D. R. Glowacki, “Sonifying stochastic walks on biomolecular energy landscapes”, arxiv:1803.05805, 2018, International Conference on Auditory Displays (ICAD 2018), accepted

M. O Connor, H. M. Deeks, E. Dawn, O. Metatla, A. Roudaut, M. Sutton, B. R. Glowacki, R. Sage, P. Tew, M. Wonnacott, P. Bates, A. J. Mulholland, D. R. Glowacki, “Sampling molecular conformations and dynamics in a multi-user virtual reality framework”, arXiv:1801.02884, 2018, Science Advances, accepted

X. Zhang, S. J. Bennie, M.W. van der Kamp, D. R. Glowacki, F. R. Manby, A. J. Mulholland, “Multiscale analysis of enantioselectivity in enzyme-catalysed ‘lethal synthesis’ using projector-based embedding”, Royal Society Open Science, 2018

R. Shannon and D. R. Glowacki, “A Simple ‘Boxed Molecular Kinetics’ Approach to Accelerate Rare Events in the Stochastic Kinetic Master Equation”, J Phys Chem A, 2018, articles ASAP

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).

Shalashilin DV, (2018). Zombie states for description of structure and dynamics of multi-electron systems.. The Journal of chemical physics, 148 (19), pp. 194109 https://doi.org/10.1063/1.5023209

Thomas L, Glowacki D. (2018). Seeing and feeling in VR: bodily perception in the gaps between layered realities. International Journal of Performance Arts and Digital Media, https://doi.org/10.1080/14794713.2018.1499387

Shannon RJ, Amabilino S, O’Connor M, Shalishilin DV, Glowacki DR. (2018). Adaptively Accelerating Reactive Molecular Dynamics Using Boxed Molecular Dynamics in Energy Space.. Journal of chemical theory and computation, 14 (9), pp. 4541-4552 https://doi.org/10.1021/acs.jctc.8b00515

2017

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).

S. J. Bennie, B. F. E. Curchod, F. R. Manby, D. R. Glowacki, “Pushing the limits of EOM-CCSD with projector-based embedding for excitation energies”, J. Phys Chem Letters, 2017, 8, pp 5559

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 . The original data on which this paper is based are available at DOI:10.5523/bris.35tigri6toah32f6txz3z8euo3