Kramers turnover: From energy diffusion to spatial diffusion using metadynamics

Tiwary, Pratyush; Berne, B. J.

doi:10.1063/1.4944577

Cited by 19 publications

(17 citation statements)

References 24 publications

(59 reference statements)

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“…This approach is expected to work best in the diffusion controlled regime. 40 The infrequent metadynamics method requires a good and small set of slow collective variables demarcating all relevant stable states of interest. Whether this is the case or not can be verified a posteriori by checking if the cumulative distribution function for the transition times out of each stable state is Poissonian 30 .…”

Section: B Dynamics From Infrequent Metadynamicsmentioning

confidence: 99%

How wet should be the reaction coordinate for ligand unbinding?

Tiwary

Berne

2016

The Journal of Chemical Physics

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We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) [P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. U. S. A. 113, 2839 (2016)], to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Using SGOOP with under-sampled biased simulations, we predict that water plays a distinct role in the reaction coordinate for unbinding in the case when the ligand is sterically constrained to move along an axis of symmetry. This prediction is validated through extensive calculations of the unbinding times through metadynamics and by comparison through detailed balance with unbiased molecular dynamics estimate of the binding time. However when the steric constraint is removed, we find that the role of water in the reaction coordinate diminishes. Here instead SGOOP identifies a good one-dimensional RC involving various motional degrees of freedom.

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Section: B Dynamics From Infrequent Metadynamicsmentioning

confidence: 99%

How wet should be the reaction coordinate for ligand unbinding?

Tiwary

Berne

2016

The Journal of Chemical Physics

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“…Corresponding to δ = 0.1, 1 and 10, we took (γ x , γ y ) = (2,20), (5,5) and (20,2) respectively in inverse time units. All of these simulations correspond to the overdamped friction regime 31 .…”

Section: Resultsmentioning

confidence: 99%

“…The potential is detailed in Ref. 31. Here we perform Langevin dynamics at inverse temperature β = 5.…”

Section: B Deleon-berne (Db) Potentialmentioning

confidence: 99%

Predicting reaction coordinates in energy landscapes with diffusion anisotropy

Tiwary

Berne

2017

The Journal of Chemical Physics

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We consider a range of model potentials with metastable states undergoing molecular dynamics coupled to a thermal bath in the high friction regime and consider how the optimal reaction coordinate depends on the diffusion anisotropy. For this we use our recently proposed method "spectral gap optimization of order parameters (SGOOP)" [P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. U. S. A. 113, 2839 (2016)]. We show how available information about dynamical observables in addition to static information can be incorporated into SGOOP, which can then be used to accurately determine the "best" reaction coordinate for arbitrary anisotropies. We compare our results with transmission coefficient calculations and published benchmarks wherever applicable or available, respectively.

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“…These are examples of the Kramers' problem [22][23][24][25][26][27]. Still active research is going on this issue [7][8][9][10][11][12][28][29][30][31][32][33][34][35]. Ion moves to the neighboring site along the direction of transport through hopping.…”

Section: The Modelmentioning

confidence: 99%

Mechanism of barrier crossing dynamics in the presence of both time dependent and independent magnetic fields

Mondal,

Biswas,

Bag

2021

Preprint

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In this paper we have presented the mechanism of the barrier crossing dynamics of a Brownian particle which is coupled to a thermal bath in the presence of both time independent and fluctuating magnetic fields. Here the following three aspects are important in addition to the role of the thermal bath on the barrier crossing dynamics. Magnetic field induced coupling may introduce a resonance like effect. Another role of the field is that enhancement of its strength reduces the frequency factor of the barrier crossing rate constant. Finally, the fluctuating magnetic field introduces an induced electric field which activates the Brownian particle to cross the energy barrier. As a result of interplay among these aspects versatile non-monotonic behavior may appear in the variation of the rate constant as a function of the strength of the time independent magnetic field.

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Kramers turnover: From energy diffusion to spatial diffusion using metadynamics

Cited by 19 publications

References 24 publications

How wet should be the reaction coordinate for ligand unbinding?

How wet should be the reaction coordinate for ligand unbinding?

Predicting reaction coordinates in energy landscapes with diffusion anisotropy

Mechanism of barrier crossing dynamics in the presence of both time dependent and independent magnetic fields

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