The intrinsic rate constants in diffusion-influenced reactions

Intrinsic rate constants play a dominant role in the theory of diffusion-influenced reactions, but usually as abstract quantities that are implicitly assumed to be known. However, recently it has become clear that modeling complex processes requires explicit knowledge of these intrinsic rates. In this paper we provide microscopic expressions for the intrinsic rate constants for association and dissociation processes of isotropically interacting particles and illustrate how these rates can be computed efficiently using rare event simulations techniques. In addition, we address the role of the orientational dynamics, for particles interacting via anisotropic potentials.

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Equilibrium and Rate Constants, and Reaction Mechanism of the HF Dissociation in the HF(H2O)7 Cluster by ab Initio Rare Event Simulations

The Journal of Physical Chemistry A ◽

10.1021/jp406982h ◽

2013 ◽

Vol 117 (49) ◽

pp. 13039-13050 ◽

Cited By ~ 7

Author(s):

Alin Marin Elena ◽

Simone Meloni ◽

Giovanni Ciccotti

Keyword(s):

Reaction Mechanism ◽

Ab Initio ◽

Rate Constants ◽

Rare Event ◽

Rare Event Simulations ◽

Event Simulations

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Phosphate has dual roles in cross-bridge kinetics in rabbit psoas single myofibrils

The Journal of General Physiology ◽

10.1085/jgp.202012755 ◽

2021 ◽

Vol 153 (3) ◽

Cited By ~ 1

Author(s):

Masataka Kawai ◽

Robert Stehle ◽

Gabriele Pfitzer ◽

Bogdan Iorga

Keyword(s):

Rate Constants ◽

Striated Muscle ◽

Intrinsic Rate ◽

Isometric Tension ◽

Force Generation ◽

Skinned Fibers ◽

Sinusoidal Analysis ◽

Rabbit Psoas ◽

Cross Bridge

In this study, we aimed to study the role of inorganic phosphate (Pi) in the production of oscillatory work and cross-bridge (CB) kinetics of striated muscle. We applied small-amplitude sinusoidal length oscillations to rabbit psoas single myofibrils and muscle fibers, and the resulting force responses were analyzed during maximal Ca2+ activation (pCa 4.65) at 15°C. Three exponential processes, A, B, and C, were identified from the tension transients, which were studied as functions of Pi concentration ([Pi]). In myofibrils, we found that process C, corresponding to phase 2 of step analysis during isometric contraction, is almost a perfect single exponential function compared with skinned fibers, which exhibit distributed rate constants, as described previously. The [Pi] dependence of the apparent rate constants 2πb and 2πc, and that of isometric tension, was studied to characterize the force generation and Pi release steps in the CB cycle, as well as the inhibitory effect of Pi. In contrast to skinned fibers, Pi does not accumulate in the core of myofibrils, allowing sinusoidal analysis to be performed nearly at [Pi] = 0. Process B disappeared as [Pi] approached 0 mM in myofibrils, indicating the significance of the role of Pi rebinding to CBs in the production of oscillatory work (process B). Our results also suggest that Pi competitively inhibits ATP binding to CBs, with an inhibitory dissociation constant of ∼2.6 mM. Finally, we found that the sinusoidal waveform of tension is mostly distorted by second harmonics and that this distortion is closely correlated with production of oscillatory work, indicating that the mechanism of generating force is intrinsically nonlinear. A nonlinear force generation mechanism suggests that the length-dependent intrinsic rate constant is asymmetric upon stretch and release and that there may be a ratchet mechanism involved in the CB cycle.

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