2014/11/20 by Mykola Lavrskyi, M. Lavrskyi, H. Zapolsky +4
Computer Science · Engineering · Physics and Astronomy · #FOS: Physical sciences #Force Microscopy Techniques and Applications #Nonlinear Dynamics and Pattern Formation #Other Condensed Matter (cond-mat.other) #Slime Mold and Myxomycetes Research #cond-mat.other
paper · pdf · doi:10.48550/arxiv.1411.5587
openalex publication_date 2014/11/20 · arxiv created 2014/11/22 · arxiv updated 2014/11/25 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
A self-organization is an universal phenomenon in nature and, in particular, is highly important in materials systems and biology. We proposed a new theory that allowed us to model the most challenging cases of atomic self-assembling whose complexity prevented their modeling before. For example, the most challenging and biologically relevant case of formation of double-stranded helix polymers from a solution of monomers is successfully simulated. The self-organization is in the atomic scale resolution while a time resolution is commensurate with the typical diffusion time. These advancements are achieved due to introduction of two novel concepts, atomic fragments (fraton) regarded as interacting pseudo-particles and structural clusters that are central for the proposed construction of the model Hamiltonian as a bilinear expansion in structural clusters. Both novelties provide a self-organization of even disordered atomic distribution to a desired atomic structure of practically any complexity. Several other examples including a crystallization of the diamond and zinc-blende structures are presented.