Classical and quantum pictures of reaction dynamics in condensed matter: resonances, dephasing, and all that

Onuchic, José N.; Wolynes, Peter G.

doi:10.1021/j100334a007

Cited by 222 publications

(112 citation statements)

References 4 publications

(4 reference statements)

Supporting

Mentioning

102

Contrasting

Unclassified

Order By: Relevance

“…However, by the time Q ‡ = 25 is chosen there would be virtually no trajectories that cross back without first reaching the folded state. We have also previously used a 2 dimensional analysis of the trajectories and free energy surfaces and again we find the transition region to be between [16][17][18][19][20][21][22] and not at 25. 3 Since we know that the transition state is somewhere between 16 and 22 we define a specific transition point, for use in calculating the barrier for the Kramer's rate equation, as the value of Q that is a maximum in this region.…”

Section: Details Of Simulations and Comparison With Bw Analysismentioning

confidence: 84%

Diffusive dynamics of the reaction coordinate for protein folding funnels

Socci

Onuchic

Wolynes

1996

The Journal of Chemical Physics

480

525

View full text Add to dashboard Cite

The quantitative description of model protein folding kinetics using a diffusive collective reaction coordinate is examined. Direct folding kinetics, diffusional coefficients and free energy profiles are determined from Monte Carlo simulations of a 27-mer, 3 letter code lattice model, which corresponds roughly to a small helical protein. Analytic folding calculations, using simple diffusive rate theory, agree extremely well with the full simulation results. Folding in this system is best seen as a diffusive, funnel-like process. I IntroductionProtein folding is a collective self-organization process, conventionally described as a chemical reaction. However, this process generally does not occur by an obligate series of discrete intermediates, a "pathway," but by a multiplicity of routes down a folding funnel. 1-7 Dynamics within a folding funnel involves the progressive formation of an ensemble of partially ordered structures, which is transiently impeded in its flow toward the folded structure by trapping in local minima on the energy landscape. As one proceeds down the folding funnel, the different ensembles of partially ordered structures can be conveniently described by one or more collective reaction coordinates or order parameters. Thermodynamically this funnel is characterized by a free energy that is a function of the reaction coordinate which is determined by the competition between the energy and entropy. A crucial feature of the funnel description is the concerted change in both the energy and the entropy as one moves along the reaction coordinate. As the entropy decreases so does the energy. The gradient of the free energy determines the average drift up or down the funnel. Superimposed on this drift is a stochastic motion whose statistics depends on the jumps between local minima. To first approximation this process can be described as diffusion. Folding rates are determined both by the free energy profile of the funnel and the stochastic dynamics of the reaction coordinates. In this paper we study the dynamics of a reaction coordinate describing the folding funnel of a lattice model with thermodynamic parameters which theoretical arguments suggest realistically correspond with fast folding small helical proteins. 3 We determine from simulation both the free energy profiles and effective configurational diffusion coefficients for a folding reaction coordinate as a function of temperature. Folding times, also determined by simulations, are compared to analytical calculations based on these quantities.The kinetic analysis of a single folding funnel is most appropriate for the fast folding proteins that mainly flow downhill progressively in energy to the folded state. During folding, even for this case, trapping in local minima will occur for times very short compared the overall folding time. Alternatively, when the residence time in these traps becomes too long leading to a substantial slow down of the folding time, the traps can be thought of as creating additional funnels. This occurs near ...

show abstract

Section: Details Of Simulations and Comparison With Bw Analysismentioning

confidence: 84%

Diffusive dynamics of the reaction coordinate for protein folding funnels

Socci

Onuchic

Wolynes

1996

The Journal of Chemical Physics

480

525

View full text Add to dashboard Cite

show abstract

“…Many barrier recrossings occur in the nonadiabatic case, which are important and contribute to the kinetics through the prefactor or transmission coefficient, and cannot be ignored. 23 Our FPT kinetics analysis emphasizes the exponential part of the barrier regarding the height. Since our FPT analysis is more connected with the barrier height, for nonadiabatic studies where recrossings often occur, full kinetics information, such as survival probability, is needed.…”

Section: Kinetics and High-order Statistical Fluctuationsmentioning

confidence: 99%

Statistics and kinetics of single-molecule electron transfer dynamics in complex environments: A simulation model study

Paula

Wang

Leite

2008

The Journal of Chemical Physics

View full text Add to dashboard Cite

Dynamics of the environments of complex systems such as biomolecules, polar solvents, and glass plays an important role in controlling electron transfer reactions. The kinetics is determined by the nature of a complex multidimensional landscape. By quantifying the mean and high-order statistics of the first-passage time and the associated ratios, the dynamics in electron transfer reactions controlled by the environments can be revealed. We consider real experimental conditions with finite observation time windows. At high temperatures, exponential kinetics is observed and there are multiple kinetic paths leading to the product state. At and below an intermediate temperature, nonexponential kinetics starts to appear, revealing the nature of the distribution of local traps on the landscape. Discrete kinetic paths emerge. At very low temperatures, nonexponential kinetics continues to be observed. We point out that the size of the observational time window is crucial in revealing the intrinsic nature of the real kinetics. The mean first-passage time is defined as a characteristic time. Only when the observational time window is significantly larger than this characteristic time does one have the opportunity to collect enough statistics to capture rare statistical fluctuations and characterize the kinetics accurately.

show abstract

“…Theoretical approaches to this problem have included the use of integral equation methods, such as the mean spherical approximation (MSA), and generalized continuum tactics which attempt to account for the wavevector (k)-as well as frequency-dependence of the solvent dielectric permittivity [3,4,18,19]. The former, however, suffer from an inadequate account of solvent-solvent interactions, while the latter face the difficulty of deducing suitable k-dependent dielectric parameters.…”

mentioning

confidence: 99%