Ultrametric diffusion, rugged energy landscapes and transition networks (Q2133082): Difference between revisions

Since Igor Volovich in 1987 postulated that space beyond the Planck scale must be non-archimedean, \(p\)-adic analysis was adopted within mathematical physics in order to study systems having a hierarchical nature, precisely because the \(p\)-adic numbers exhibit a hierarchical nature of their own. This adoption was strengthend by the fact that also in the 1980s, Giorgio Parisi discovered the ultrametric nature of physical systems called ``spin glasses''. In general, complex systems in which the states are organised hierarchically have a hierarchically structured energy landscape, and thus are examples of ultrametric spaces, and these are susceptible for p-adic analyis for studying them. In this context, also protein folding was discovered as exhibiting such an ultrametric structure. This is where Wilson Zúñiga-Galindo's article under review is situated. The aim of this article is to introduce and study \(p\)-adic transition networks for modelling Markov processes on hierarchical energy landscapes, together with a master equation. The idea behind this is that the nodes of the network are represented by balls within the p-adic number field, and to define a bounded linear operators on spaces of real-valued \(p\)-adic functions supported on the union of these balls, i.e.\ on a compact subspace \(Z\). Under certain assumptions, these operators are shown to define a strong Markov process on \(Z\) whose paths are right continuous and have no discontinuities other than jumps, and the Cauchy problem for the corresponding heat equation has a unique solution determined by the transition functions of this Markov process. In the case that the Markov process attached to the network is conservative, i.e.\ the set of allowed states \(Z\) is not exited from, then the long term response of the network is controlled by a Markov chain. Otherwise, there are absorbing states. Terms in the solution to the Cauchy problem are identified, which are responsible for fast transitions to absorbing states, and are called ``fast transition modes''. Their existence is shown to be because of the ultrametric structure of the energy landscape. In the end, the developped theory is applied to a toy model for protein folding using certain binary networks, and to show that it is possible for a ``protein'' to get trapped in a basin. This exemplarily models the so-called ``Levinthal paradox'', which says that, although in certain temperature ranges, a protein will fold from states of higher entropy to states of lower entropy, it does happen that it can be trapped in a state in which the entropy is not minimal.