The goal of this work is to investigate self-organization processes in molecular chains. Computer simulation has been performed by means of a molecular dynamics method. Morse potential was chosen as the potential of atomic interaction. Molecular chains were exposed to low-energy ion impact by two means: mono beam and plasma treatment. The amount of the energy transferred to molecules of the chain was varied in wide range but it must be less than the energy needed to break the chain. Chains with water molecules that were cut from microcrystal of ice (homogeneous chains) as well as net of hydrogen bonds (heterogeneous chains) were under our investigations. In last case areas with periodical structure symbolize embedded crystal nanoclusters in the whole disordered medium.

We showed that nonlinear oscillations become excited in the chains after low-energy ion impact and as a result of them molecules become stabilized in new positions, which results in the formation and development of new metastable molecular groups (nanoclusters). In homogenous chains formed nanoclusters correspond to elements of “molecular memory”. We showed that in homogeneous molecular chains critical energy needed for self-organization processes development is less than for nonlinear molecular chains with already embedded clusters. In this case nanocluster becomes an active zone which determines further self-organization processes. It is clusters that provide new complexes of physical and chemical properties. This computer model can be also used for simulation of low-energy ion impact on polymers and biological objects.