On a model of energy and information transfer from the “donor” molecular structure to the molecular chain

It is thought that molecular chains (such as protein chains with alpha-helical secondary structure, DNA and RNA molecules) can play the role of "bridges" for the highly efficient transfer of vibron excitations or electrons over very long distances (comparable to the length of the molecular chain itself). Due to the interaction with the thermal oscillations of the structure, these excitations can be captured and can form a stable self-trapped (polaron-like) state, which can move through the structure with minimal energy loss. However, the properties of the possibly formed polaron must also be influenced by the presence of the donor molecule. In the presented work, we discussed the mechanism of excitation transfer from one molecular structure (donor molecule) to the molecular chain. The presence of the donor structure and temperature influence on the energy of self-trapped excitation was considered, in the dependence of the basic energy parameters of the molecular bridge. The obtained results indicate the possibility of the formation of two types of self-trapped states: a quasi-free excitation that can easily move through the molecular bridge and a localized, practically immobile excitation, similar to a non-adiabatic polaron quasiparticle.DYNALIFE : 80, 70, 20 Conference Towards Excellence and Convergence Research in Theoretical Biology : COST action CA21169 : Dynalife, Venice 2-4 May 2023

Energy and information exchange between “donor” and “molecular bridge” structures: non adiabatic polaron model

Molecular chains (such as protein chains with alpha-helical secondary structure, DNA and RNA molecules) can play the role of “bridges” for the highly efficient transfer of various types of submolecular excitations (vibron excitations or electrons) over very long distances (comparable to the length of the molecular chain itself). In the case when this process takes place in living cells, the biomolecule is placed in an environment where it is usually in thermodynamic equilibrium with the “heat bath”. As a result, the structural elements of the molecular chain perform mechanical oscillations. In the general case, such mechanical oscillations disrupt the ability of the molecular bridge to transfer the excitation over a longer distance. On the other side, by interacting with the thermal oscillations of the structure, excitations injected into the molecule may be trapped and can form a stable self-trapped (polaronlike) state. Such quasiparticles can move through the structure with minimal energy loss. In this way, the high efficiency of energy and charge transport in living cells can be explained. However, the properties of the possibly formed polaron quasiparticle must also be affected by the presence of the donor molecule. Here, we have discussed the mechanism of excitation transfer from a molecular structure (donor molecule) to the molecular chain. The presence of the donor structure and the temperature influence on the energy of the self-trapped excitation were considered in the dependence of the basic energy parameters of the molecular bridge. The obtained results indicate the possibility of the formation of two types of self-trapped states: a quasi-free excitation, which can easily move through the molecular bridge, and a localized, practically immobile excitation, which is similar to a non-adiabatic polaron quasiparticleBelBi2023 : 4th Belgrade Bioinformatics Conference : 19-23 June, 2023

Energy and information exchange between “donor” and “molecular bridge” structures: non adiabatic polaron model

Molecular chains (such as protein chains with alpha-helical secondary structure, DNA and RNA molecules) can play the role of “bridges” for the highly efficient transfer of various types of submolecular excitations (vibron excitations or electrons) over very long distances (comparable to the length of the molecular chain itself). In the case when this process takes place in living cells, the biomolecule is placed in an environment where it is usually in thermodynamic equilibrium with the “heat bath”. As a result, the structural elements of the molecular chain perform mechanical oscillations. In the general case, such mechanical oscillations disrupt the ability of the molecular bridge to transfer the excitation over a longer distance. On the other side, by interacting with the thermal oscillations of the structure, excitations injected into the molecule may be trapped and can form a stable self-trapped (polaronlike) state. Such quasiparticles can move through the structure with minimal energy loss. In this way, the high efficiency of energy and charge transport in living cells can be explained. However, the properties of the possibly formed polaron quasiparticle must also be affected by the presence of the donor molecule. Here, we have discussed the mechanism of excitation transfer from a molecular structure (donor molecule) to the molecular chain. The presence of the donor structure and the temperature influence on the energy of the self-trapped excitation were considered in the dependence of the basic energy parameters of the molecular bridge. The obtained results indicate the possibility of the formation of two types of self-trapped states: a quasi-free excitation, which can easily move through the molecular bridge, and a localized, practically immobile excitation, which is similar to a non-adiabatic polaron quasiparticle.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202

Influence of donor or acceptor presence on excitation states in molecular chains: Nonadiabatic polaron approach

In this paper, we considered a molecular structure that consists of a molecular chain and an additional molecule (donor or acceptor) that can inject (or remove) single excitation (vibron, electron, etc.) onto the molecular chain. We assumed that the excitation forms a self-trapped state due to the interaction with mechanical oscillations of the chain structure elements. We analyzed the energy spectra of the excitation and showed that its state (when it migrates to the molecular chain) has the properties of the nonadiabatic polaron state. The conditions under which the excitation can migrate from one subsystem to another one were considered. It was shown that the presence of a “donor” molecule cannot significantly change the properties of the excitation located on the molecular chain. At the same time, the molecular chain can affect the position of the energy level of the excitation localized on the donor subsystem. Indirectly, this can influence the process of excitation migration from one subsystem to another one. The influence of the basic energy parameters of the system and the environment temperature on this process are discussed. The entire system was assumed to be in thermal equilibrium with the environment