Cooperativity in noncovalent interactions

AS Mahadevi, GN Sastry - Chemical reviews, 2016 - ACS Publications
After conquering the atomic structure about a century ago, chemists have been largely
interested in understanding the concept of chemical bond and the formation of a molecule …

Physics of base-pairing dynamics in DNA

M Manghi, N Destainville - Physics Reports, 2016 - Elsevier
As a key molecule of life, Deoxyribo-Nucleic Acid (DNA) is the focus of numbers of
investigations with the help of biological, chemical and physical techniques. From a physical …

Electrostatic interactions in biological DNA-related systems

AG Cherstvy - Physical Chemistry Chemical Physics, 2011 - pubs.rsc.org
In this perspective article, we focus on recent developments in the theory of charge effects in
biological DNA-related systems. The electrostatic effects on different levels of DNA …

Observation of coherent delocalized phonon-like modes in DNA under physiological conditions

M González-Jiménez, G Ramakrishnan… - Nature …, 2016 - nature.com
Underdamped terahertz-frequency delocalized phonon-like modes have long been
suggested to play a role in the biological function of DNA. Such phonon modes involve the …

A predictive model for the thermomechanical melting transition of double stranded DNA

G Florio, G Puglisi - Acta Biomaterialia, 2023 - Elsevier
By extending the classical Peyrard–Bishop model, we are able to obtain a fully analytical
description for the mechanical response of DNA under stretching at variable values of …

Soliton Solution of the Peyrard–Bishop–Dauxois Model of DNA Dynamics with M-Truncated and β-Fractional Derivatives Using Kudryashov's R Function Method

X Wang, G Akram, M Sadaf, H Mariyam, M Abbas - Fractal and Fractional, 2022 - mdpi.com
In this paper, the Peyrard–Bishop–Dauxois model of DNA dynamics is discussed along with
the fractional effects of the M-truncated derivative and β-derivative. The Kudryashov's R …

Compatible solute influence on nucleic acids: many questions but few answers

M Kurz - Saline systems, 2008 - Springer
Compatible solutes are small organic osmolytes including but not limited to sugars, polyols,
amino acids, and their derivatives. They are compatible with cell metabolism even at molar …

Bubbles and denaturation in DNA

TS Van Erp, S Cuesta-Lopez, M Peyrard - The European Physical Journal …, 2006 - Springer
The local opening of DNA is an intriguing phenomenon from a statistical-physics point of
view, but is also essential for its biological function. For instance, the transcription and …

DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation

BS Alexandrov, V Gelev, SW Yoo… - Nucleic acids …, 2010 - academic.oup.com
We assess the role of DNA breathing dynamics as a determinant of promoter strength and
transcription start site (TSS) location. We compare DNA Langevin dynamic profiles of …

A nonlinear dynamic model of DNA with a sequence-dependent stacking term

BS Alexandrov, V Gelev, Y Monisova… - Nucleic Acids …, 2009 - academic.oup.com
No simple model exists that accurately describes the melting behavior and breathing
dynamics of double-stranded DNA as a function of nucleotide sequence. This is especially …