DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling

I Junier, E Ghobadpour, O Espeli… - Frontiers in …, 2023 - frontiersin.org
DNA supercoiling is central to many fundamental processes of living organisms. Its average
level along the chromosome and over time reflects the dynamic equilibrium of opposite …

Local Molecular Field Theory for Coulomb Interactions in Aqueous Solutions

A Gao, RC Remsing, JD Weeks - The Journal of Physical …, 2023 - ACS Publications
Coulomb interactions play a crucial role in a wide array of processes in aqueous solutions
but present conceptual and computational challenges to both theory and simulations. We …

Abnormal open states patterns in the ATXN2 DNA sequence depends on the CAG repeats length

MI Drobotenko, OM Lyasota… - International Journal of …, 2024 - Elsevier
Hereditary ataxias are one of the «anticipation diseases» types. Spinocerebral ataxia type 2
occurs when the number of CAG repeats in the coding region of the ATXN2 gene exceeds …

Multiplexable and biocomputational virus detection by CRISPR-cas9-mediated strand displacement

R Márquez-Costa, R Montagud-Martínez… - Analytical …, 2023 - ACS Publications
Recurrent disease outbreaks caused by different viruses, including the novel respiratory
virus SARS-CoV-2, are challenging our society at a global scale; so versatile virus detection …

Inequality in the Frequency of the Open States Occurrence Depends on Single 2H/1H Replacement in DNA

A Basov, M Drobotenko, A Svidlov, E Gerasimenko… - Molecules, 2020 - mdpi.com
In the present study, the effect of 2H/1H isotopic exchange in hydrogen bonds between
nitrogenous base pairs on occurrence and open states zones dynamics is investigated …

Elucidation of leak-resistance DNA hybridization chain reaction with universality and extensibility

S Li, P Li, M Ge, H Wang, Y Cheng, G Li… - Nucleic Acids …, 2020 - academic.oup.com
Hybridization chain reaction (HCR) was a significant discovery for the development of
nanoscale materials and devices. One key challenge for HCR is the vulnerability to …

DNA dynamics under periodic force effects

A Svidlov, M Drobotenko, A Basov… - International Journal of …, 2021 - mdpi.com
The sensitivity of DNA to electromagnetic radiation in different ranges differs depending on
various factors. The aim of this study was to examine the molecular dynamics of DNA under …

[图书][B] Gibbs measures in biology and physics: The Potts model

UA Rozikov - 2022 - World Scientific
In this chapter we give main definitions and useful facts of the theory of Gibbs measures of
lattice spin systems. In the first section we give general definitions. This chapter also …

Genesis of open states zones in a DNA molecule depends on the localization and value of the torque

S Dzhimak, A Svidlov, A Elkina, E Gerasimenko… - International Journal of …, 2022 - mdpi.com
The formation and dynamics of the open states in a double-stranded DNA molecule are
largely determined by its mechanical parameters. The main one is the torque. However, the …

Influence of Environmental Parameters on the Stability of the DNA Molecule

A Svidlov, M Drobotenko, A Basov, E Gerasimenko… - Entropy, 2021 - mdpi.com
Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule
passes from the region of high viscosity values to the region of low values, open states …