scholarly journals Publisher's Note: “Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates” [J. Chem. Phys. 140, 034115 (2014)]

2014 ◽  
Vol 140 (6) ◽  
pp. 069902
Author(s):  
Mahmoud Moradi ◽  
Celeste Sagui ◽  
Christopher Roland
Keyword(s):  
Rare Events ◽  
Reaction Rates ◽  
Chem Phys

scholarly journals Achieving Reversible Ligand-Protein Unbinding with Deep Learning and Molecular Dynamics through RAVE

2018 ◽  
Author(s):  
João Marcelo Lamim Ribeiro ◽  
Pratyush Tiwary
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Deep Learning ◽  
Rare Events ◽  
Binding Free Energy ◽  
Piecewise Linear ◽  
Chem Phys ◽  
Enhanced Sampling ◽  
Order Of Magnitude ◽  
Low Dimensional

AbstractIn this work we demonstrate how to leverage our recent iterative deep learning–all atom molecular dynamics (MD) technique “Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)” (Ribeiro, Bravo, Wang, Tiwary, J. Chem. Phys. 149, 072301 (2018)) for sampling protein-ligand unbinding mechanisms and calculating absolute binding affinities when plagued with difficult to sample rare events. RAVE iterates between rounds of MD and deep learning, and unlike other enhanced sampling methods, it stands out in simultaneously learning both a low-dimensional physically interpretable reaction coordinate (RC) and associated free energy. Here, we introduce a simple but powerful extension to RAVE which allows learning a position-dependent RC expressed as a superposition of piecewise linear RCs valid in different metastable states. With this approach, we retain the original physical interpretability of a RAVE-derived RC while making it applicable to a wider range of complex systems. We demonstrate how in its multi-dimensional form introduced here, RAVE can efficiently simulate the unbinding of the tightly bound benzene-lysozyme (L99A variant) complex, in all atom-precision and with minimal use of human intuition except for the choice of a larger dictionary of order parameters. These simulations had a 100 % success rate, and took between 3–50 nanoseconds for a process that takes on an average close to few hundred milliseconds, thereby reflecting a seven order of magnitude acceleration relative to straightforward MD. Furthermore, without any time-dependent biasing, the trajectories display clear back–and– forth movement between various metastable intermediates, demonstrating the reliability of the RC and its probability distribution learnt in RAVE. Our binding free energy is in good agreement with other reported simulation results. We thus believe that RAVE, especially in its multi-dimensional variant introduced here, will be a useful tool for simulating the dissociation process of practical biophysical systems with rare events in an automated manner with minimal use of human intuition.

Investigation of the behavior of tropospheric relevant compounds at the interface gas/organic acid aerosols: An ONIOM QM/MM study

2021 ◽  
Author(s):  
Antoine Roose ◽  
Denis Duflot ◽  
Césaire Fotsing Kwetche ◽  
Céline Toubin
Keyword(s):  
Oleic Acid ◽  
Bulk Diffusion ◽  
Reaction Rates ◽  
Oxidative Capacity ◽  
Chem Phys ◽  
Computational Method ◽  
Strong Impact ◽  
Development Fund ◽  
Wide Range ◽  
Uptake Coefficients

<p>The uptake of atmospheric gaseous oxidant such as O<sub>3</sub> or the ROx (OH, HO<sub>2</sub>, RO<sub>2</sub>) family, have a strong impact on the oxidative capacity of the atmosphere. [1], [2] Last decade, few studies have been carried out on the uptake of such compounds on atmospheric aerosol. However, the large variety of organic compounds provides uptake coefficients with a wide range of order of magnitude. [3], [4] Furthermore, the uptake resulting from the combination of different processes (mass accommodation, bulk diffusion, reactivity), the detailed understanding of such a process is not always accessible through experiments. Theoretical tools such as quantum mechanics (QM) combined with Molecular Mechanics (MM) is one way to investigate separately the different processes.</p><p>The ONIOM hybrid QM/MM method [5] allows to study the reactivity of few molecules in a large system. In our group, a methodology using this computational method have been developed in order to estimate the reactive uptake of gaseous compounds onto organic aerosol particles. In this presentation, reactive uptake of HO<sub>2</sub> and O<sub>3</sub> onto glutaric acid and oleic acid aerosols respectively will be discussed. Comparisons will be addressed with gas phase theoretical reaction rates and with experimental data.</p><p><em>We acknowledge support by the French government through the Program “Investissement d'avenir” through the Labex CaPPA (contract ANR-11-LABX-0005-01) and I-SITE ULNE project OVERSEE (contract ANR-16-IDEX-0004), CPER CLIMIBIO (European Regional Development Fund, Hauts de France council, French Ministry of Higher Education and Research) and French national supercomputing facilities (grants DARI x2016081859 and A0050801859).</em></p><p> </p><p>References</p><p>[1]          H. L. Macintyre and M. J. Evans, “Parameterisation and impact of aerosol uptake of HO2 on a global tropospheric model,” Atmos. Chem. Phys., vol. 11, no. 21, pp. 10965–10974, Nov. 2011, doi: 10.5194/acp-11-10965-2011.</p><p>[2]          M. Zeng and K. R. Wilson, “Efficient Coupling of Reaction Pathways of Criegee Intermediates and Free Radicals in the Heterogeneous Ozonolysis of Alkenes,” The Journal of Physical Chemistry Letters, Jul. 2020, doi: 10.1021/acs.jpclett.0c01823.</p><p>[3]          P. S. J. Lakey, I. J. George, L. K. Whalley, M. T. Baeza-Romero, and D. E. Heard, “Measurements of the HO2 Uptake Coefficients onto Single Component Organic Aerosols,” Environ. Sci. Technol., vol. 49, no. 8, pp. 4878–4885, Apr. 2015, doi: 10.1021/acs.est.5b00948.</p><p>[4]          M. Mendez, N. Visez, S. Gosselin, V. Crenn, V. Riffault, and D. Petitprez, “Reactive and Nonreactive Ozone Uptake during Aging of Oleic Acid Particles,” J. Phys. Chem. A, vol. 118, no. 40, pp. 9471–9481, Oct. 2014, doi: 10.1021/jp503572c.</p><p>[5]          L. W. Chung et al., “The ONIOM Method and Its Applications,” Chem. Rev., vol. 115, no. 12, pp. 5678–5796, Jun. 2015, doi: 10.1021/cr5004419.</p>

Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates

2014 ◽  
Vol 140 (3) ◽  
pp. 034115 ◽  
Author(s):  
Mahmoud Moradi ◽  
Celeste Sagui ◽  
Christopher Roland
Keyword(s):  
Rare Events ◽  
Reaction Rates
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