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Disputation Laura Lavacchi

13.05.2024 | 16:30
Thema der Dissertation:
Non-Markovian barrier-crossing dynamics at equilibrium and non-equilibrium
Abstract: The concept of barrier crossing can describe many biological systems. Rare events, such as protein folding or chemical reactions, can be modeled as systems that must cross a barrier potential to change their states, e.g., folded or unfolded states. These systems do not occur in isolation but are rather coupled with their environment. Typically, we choose a reaction co- ordinate and project out all the other orthogonal degrees of freedom. If the orthogonal degrees of freedom relax as rapidly as the reaction coordi- nates, non-Markovian memory effects must be taken into account in order to describe the dynamics accurately.
This thesis uses the generalized Langevin equation to study the mean first-passage time τMFfor various non-Markovian systems. We begin by considering a multi-exponential memory kernel exhibiting various memory times and friction coefficients. We then propose a heuristic formula that shows that the τMFis dominated by the single memory exponential with short memory time as well as large amplitude.
Following this, we relax the condition of equilibrium, and therefore we take into consideration a generalized Langevin equation out of equilibrium. Also, in this case, we suggest a formula that takes into account the effect of non equilibrium, showing non-Arrhenius behavior.
Since many chemical and biological systems exhibit asymmetric free- energy profiles, we next consider an asymmetric potential. From simulation data, we gather evidence that the dynamics in one well is independent of the other. Therefore, we describe the dynamics via the times τ L,R  that are needed to reach the barrier from left and right, respectively.
In the final section, we focus on another important factor that charac- terizes the process of barrier crossing, the mean transition path time τMTP. Again, we concentrate on a non-Markovian system, and, with the help of simulations, derive a heuristic formula. Contrary to the mean first-passage time τMFP, the mean transition path time τMTPreaches its maximum in the Markovian case; for intermediate memory time it decreases, particularly for smaller mass, and settles on a constant value for large memory times.

Zeit & Ort

13.05.2024 | 16:30

Hörsaal A (1.3.14)
Fachbereich Physik, Arnimallee 14, 14195 Berlin