Chemical Reactions Using a Non-Equilibrium Wigner Function Approach
Abstract
:1. Introduction
- The two macromolecular chains were described, from the outset, by a classical (non-negative) probability distribution, depending on all spatial positions of all atoms and on time and evolving through an irreversible Kramers-like master equation (stochasticity being thereby taken care of). Neither Planck’s constant ℏ nor thermal wavelengths were included. However, the formulation did include an important length scale, namely the bond length yielding the average distance between two successive atoms along each chain.
- The overall center of mass (CM) motion was factored out off-equilibrium from the remaining spatial variables (the set of all positions of the atoms along the two chains and the relative position y of the two centers of mass of the chains). The interest focused then on the non-equilibrium reduced probability distribution depending on , y and time t. The inclusion of attractive potentials between the two chains in the corresponding Kramers-like master equation seemed to be, to the best of our knowledge, a novel feature.
- Upon integrating over all (leaving y unintegrated), the classical reduced Boltzmann equilibrium distribution for the two interacting chains was used as the generating function for an infinite family of orthogonal polynomials in (depending on y, parametrically). That generating function was not a Gaussian one, due to the various potentials.
- The orthogonal polynomials were used to define non-equilibrium moments (y- and t-dependent) for the non-equilibrium reduced probability distribution.
- The Kramers-like equation yielded a hierarchy for the non-equilibrium moments.
- At temperatures below, but close to, the melting one (i.e., DNA denaturation), the long-time dynamics was approximated by a Smoluchowski-like equation (containing a y-dependent effective potential) for the lowest non-equilibrium moment.
- The application of the mean first passage time formalism [16,17,35] to the Smoluchowski-like equation in step 6 enabled us to study approximately the time duration of non-equilibrium thermal denaturation of the two strands, initially bound to each other, towards configurations of two separate single strands.
2. Two Particles: Towards Non-Equilibrium Toy Chemical Reactions
2.1. General Features
2.2. Non-Equilibrium Statistical Formulation and Equilibrium Distributions
2.3. Assumptions on , the Spectrum of and Application to
- is repulsive () for (“hard core”, with adequately small ), attractive () in the interval and vanishes fast as .
- is finite everywhere, and its magnitude is appreciable in . a is understood to be the range of V.
- and all , for , are continuous for all .
- does give rise to only one bound state (bound spectrum). Thus, the relevance of the region where is larger than that of the hard core.
2.4. as a Quasi-Definite Functional of Momenta
2.5. Orthogonal Polynomials Generated by
2.6. Moments: Off-Equilibrium and at Equilibrium
3. Hierarchy for the Non-Equilibrium Moments and Approximations
3.1. Non-Equilibrium Hierarchy
3.2. Order of Magnitude Estimates
3.3. Approximations: Small Thermal Wavelength and Long Time
4. Towards Kinetic Equations
5. Thermal and Chemical Equilibria
6. Transitions among a Bound and Continuous Spectrum: Mean First Passage Time
7. Estimating Effective Evolution Times
8. Comparison with Other Approaches: Recombination and Possible Extensions
9. Conclusions and Discussions
Acknowledgments
Author Contributions
Conflicts of Interest
Appendix A. Behavior of Wre,eq for Large q
Appendix B. Various Quantities Related to Wre,eq
Appendix C. One-Dimensional Non-Equilibrium Hierarchy (1)
Appendix D. One-Dimensional Non-Equilibrium Hierarchy (2): Small Thermal Wavelength
Appendix E. One-Dimensional Non-Equilibrium Hierarchy (3): Long-Time Approximation
Appendix F. One-Dimensional Non-Equilibrium Hierarchy (4): Remarks
Appendix G. Alternative Starting Point: A Master Equation with Ab Initio Dissipation
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Álvarez-Estrada, R.F.; Calvo, G.F. Chemical Reactions Using a Non-Equilibrium Wigner Function Approach. Entropy 2016, 18, 369. https://doi.org/10.3390/e18100369
Álvarez-Estrada RF, Calvo GF. Chemical Reactions Using a Non-Equilibrium Wigner Function Approach. Entropy. 2016; 18(10):369. https://doi.org/10.3390/e18100369
Chicago/Turabian StyleÁlvarez-Estrada, Ramón F., and Gabriel F. Calvo. 2016. "Chemical Reactions Using a Non-Equilibrium Wigner Function Approach" Entropy 18, no. 10: 369. https://doi.org/10.3390/e18100369
APA StyleÁlvarez-Estrada, R. F., & Calvo, G. F. (2016). Chemical Reactions Using a Non-Equilibrium Wigner Function Approach. Entropy, 18(10), 369. https://doi.org/10.3390/e18100369