We illuminate the influence of transition mutations and disorder on charge localization and transfer along B-DNA sequences. Homopolymers are the best for charge transfer (cf. Refs.~ \cite{LVBMS:2018, MLTS:2019}). Hence, we consider as flawless a homopolymer sequence and then disturb it, introducing transition mutations and disorder. We exclude the possibility of charge transfer via the backbone that will be addressed soon in another work. We employ the Tight Binding (TB) Wire model to study the influence of transition mutations and the TB Fishbone Wire model to evaluate the influence of disorder emanating either from the $π$ path or from the backbone. For the TB Wire parameters, we employ the parametrization created in Ref.~\cite{MLS:2023}, where another TB at atomic level was used, considering all valence orbitals of all atoms. We calculate the HOMO and LUMO regime eigenenergies and eigenvectors, the participation ratio (a measure of the localization of each eigenstate), the time-dependent probability to find the carrier at each site, the mean over time probability at each site, and the mean transfer rate from site to site. Transition mutations increase localization in terms of participation ratio and impede charge transfer in terms of mean probability and transfer rates, provided the TB parameters involving mutated sites are significantly modified relative to the original. Disorder leads to severe modifications of participation ratios, i.e., increase of localization. Relevant changes occur on eigenenergies, mean probabilities at each site, and transfer rates.
Mechanical response of a simple DNA nanostar hydrogel: symptoms of disorder and glassy emergence of solidity
Institut Néel-CNRS/UGA-Grenoble INP（内尔研究所）；LIMMS-CNRS/Institute of Industrial Science-The University of Tokyo（理化学研究所-东京大学工业科学研究所）；LIP-CNRS/ENS Lyon（里昂高等师范学校）；Universite Claude Bernard Lyon 1, CNRS, Institut Lumière Matière（里昂第一大学）
Reply to Comment on "Why is the DNA Transition First Order?" and "Griffiths Singularities in Unbinding of Strongly Disordered Polymers" by M. Ya. Azbel
它表明，在评论中提出的各种索赔M。Ya. Azbel（物理学/0403106）在两个出版物物理。91，055502（2003）和Phys. Rev. Lett. 85，4988（2000）无效。这是对这两份文件要点的误解造成的。
