Publications

2021

V. M. Freixas, A. J. White, T. Nelson, H. Song, D. V. Makhov, D. Shalashilin, S. Fernandez-Alberti,  S. Tretiak, “Nonadiabatic Excited-State Molecular Dynamics Methodologies: Comparison and Convergence”, J. Phys. Chem. Lett. 12, 2970 (2021); https://doi.org/10.1021/acs.jpclett.1c00266

D. V. Makhov, D. V. Shalashilin, “Simulation of the effect of vibrational pre-excitation on the dynamics of pyrrole photo-dissociation”, J. Chem. Phys. 154, 104119 (2021); https://doi.org/10.1063/5.0040178

2020

M.Katsanikas, V. Garcia-Garrido, and S. Wiggins: Detection of dynamical matching in a caldera Hamiltonian system using Lagrangian Descriptors, International Journal of Bifurcation and Chaos, 30,
2030026 (2020)  https://arxiv.org/abs/1911.11811

Gonzalez Montoya F, Wiggins S. (2020). Phase space structure and escape time dynamics in a Van der Waals model for exothermic reactions.. Physical review. E, 102 (6-1), pp. 062203
PubMed DOI http://dx.doi.org/10.1103/physreve.102.062203

Deeks HM, Walters RK, Barnoud J, Glowacki DR, Mulholland AJ. (2020). Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease.. Journal of chemical information and modeling,
PubMed DOI  http://dx.doi.org/10.1021/acs.jcim.0c01030

Juárez-Jiménez J, Tew P, O Connor M, Llabrés S, Sage R, Glowacki D, Michel J. (2020). Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes.. Journal of chemical information and modeling,
PubMed DOI http://dx.doi.org/10.1021/acs.jcim.0c00221

Amabilino S, Bratholm L, Bennie S, O’Connor M, Glowacki D. (2020). Training atomic neural networks using fragment-based data generated in virtual reality. The Journal of Chemical Physics,
PubMed DOI http://dx.doi.org/10.1063/5.0015950

Christensen AS, Bratholm LA, Faber FA, Anatole von Lilienfeld O. (2020). FCHL revisited: Faster and more accurate quantum machine learning.. The Journal of chemical physics, 152 (4), pp. 044107
PubMed DOI http://dx.doi.org/10.1063/1.5126701

Katsanikas M, García-Garrido V, Wiggins S. (2020). The dynamical matching mechanism in phase space for caldera-type potential energy surfaces. Chemical Physics Letters,
DOI http://dx.doi.org/10.1016/j.cplett.2020.137199

Lavagna E, Barnoud J, Rossi G, Monticelli L. (2020). Size-dependent aggregation of hydrophobic nanoparticles in lipid membranes.. Nanoscale, 12 (17), pp. 9452-9461
PubMed DOI  http://dx.doi.org/10.1039/D0NR00868K

García-Garrido V, (2020). Unveiling the fractal structure of Julia sets with Lagrangian descriptors. Communications in Nonlinear Science and Numerical Simulation,
DOI http://dx.doi.org/10.1016/j.cnsns.2020.105417

Rawlinson J, Tronci C. (2020). Regularized Born-Oppenheimer molecular dynamics. Physical Review A,
DOI http://dx.doi.org/10.1103/PhysRevA.102.032811

Mykuliak VV, Sikora M, Booth JJ, Cieplak M, Shalashilin DV, Hytönen VP. (2020). Mechanical Unfolding of Proteins-A Comparative Nonequilibrium Molecular Dynamics Study.. Biophysical journal, 119 (5), pp. 939-949
PubMed DOI http://dx.doi.org/10.1016/j.bpj.2020.07.030

Glowacki D, Mueller F, Verweij D, Andres J, McGrenere J, Cockburn A, Avellino I… Metatla O. (2020). Isness: Using Multi-Person VR to Design Peak Mystical Type Experiences Comparable to Psychedelics.
DOI http://dx.doi.org/10.1145/3313831.3376649

Naik S, Wiggins S. (2020). Detecting reactive islands in a system-bath model of isomerization.. Physical chemistry chemical physics : PCCP, 22 (32), pp. 17890-17912
PubMed DOI  http://dx.doi.org/10.1039/D0CP01362E

García-Garrido V, Katsanikas M, Agaoglou M, Wiggins S. (2020). Tuning the branching ratio in a symmetric potential energy surface with a post-transition state bifurcation using external time dependence. Chemical Physics Letters,
DOI  http://dx.doi.org/10.1016/j.cplett.2020.137714

Agaoglou M, García-Garrido V, Katsanikas M, Wiggins S. (2020). The phase space mechanism for selectivity in a symmetric potential energy surface with a post-transition-state bifurcation. Chemical Physics Letters,
DOI  http://dx.doi.org/10.1016/j.cplett.2020.137610

García-Garrido V, Naik S, Wiggins S. (2020). Tilting and Squeezing: Phase Space Geometry of Hamiltonian Saddle-Node Bifurcation and its Influence on Chemical Reaction Dynamics. International Journal of Bifurcation and Chaos,
DOI  http://dx.doi.org/10.1142/S0218127420300086

Montoya F, Wiggins S. (2020). Revealing roaming on the double Morse potential energy surface with Lagrangian descriptors. Journal of Physics A: Mathematical and Theoretical,
DOI  http://dx.doi.org/10.1088/1751-8121/ab8b75

Katsanikas M, García-Garrido VJ, Agaoglou M, Wiggins S. (2020). Phase space analysis of the dynamics on a potential energy surface with an entrance channel and two potential wells.. Physical review. E, 102 (1-1), pp. 012215
PubMed DOI  http://dx.doi.org/10.1103/PhysRevE.102.012215

García-Garrido V, Agaoglou M, Wiggins S. (2020). Exploring isomerization dynamics on a potential energy surface with an index-2 saddle using lagrangian descriptors. Communications in Nonlinear Science and Numerical Simulation,
DOI  http://dx.doi.org/10.1016/j.cnsns.2020.105331

Deeks HM, Walters RK, Hare SR, O’Connor MB, Mulholland AJ, Glowacki DR. (2020). Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking.. PloS one, 15 (3), pp. e0228461
PubMed DOI  http://dx.doi.org/10.1371/journal.pone.0228461

García-Garrido V, (2020). An Extension of Discrete Lagrangian Descriptors for Unbounded Maps. International Journal of Bifurcation and Chaos,
DOI  http://dx.doi.org/10.1142/S0218127420300128

Freixas VM, Tretiak S, Makhov DV, Shalashilin DV, Fernandez-Alberti S. (2020). Vibronic Quantum Beating between Electronic Excited States in a Heterodimer.. The journal of physical chemistry. B, 124 (19), pp. 3992-4001
PubMed DOI  http://dx.doi.org/10.1021/acs.jpcb.0c01685

Krajňák V, Ezra G, Wiggins S. (2020). Using Lagrangian Descriptors to Uncover Invariant Structures in Chesnavich’s Isokinetic Model with Application to Roaming. International Journal of Bifurcation and Chaos,
DOI  http://dx.doi.org/10.1142/S0218127420500765

Chen L, Gelin MF, Shalashilin DV. (2019). Dynamics of a one-dimensional Holstein polaron: The multiconfigurational Ehrenfest method.. The Journal of chemical physics, 151 (24), pp. 244116
PubMed DOI  http://dx.doi.org/10.1063/1.5132341

Gerrard W, Bratholm LA, Packer MJ, Mulholland AJ, Glowacki DR, Butts CP. (2020). IMPRESSION – prediction of NMR parameters for 3-dimensional chemical structures using machine learning with near quantum chemical accuracy.. Chemical science, 11 (2), pp. 508-515
PubMed DOI http://dx.doi.org/10.1039/c9sc03854j

Naik S, Wiggins S. (2019). Finding normally hyperbolic invariant manifolds in two and three degrees of freedom with Hénon-Heiles-type potential.. Physical review. E, 100 (2-1), pp. 022204
PubMed DOI http://dx.doi.org/10.1103/PhysRevE.100.022204

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,
DOI  http://dx.doi.org/10.1142/S0218127419501578

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

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,

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