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 …

Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs

L Giorgetti, T Siggers, G Tiana, G Caprara… - Molecular cell, 2010 - cell.com
A paradigm in transcriptional regulation is that graded increases in transcription factor (TF)
concentration are translated into on/off transcriptional responses by cooperative TF binding …

Dependence of DNA persistence length on ionic strength of solutions with monovalent and divalent salts: a joint theory–experiment study

A Brunet, C Tardin, L Salomé, P Rousseau… - Biophysical …, 2016 - cell.com
Chemistry, University of Illinois at Chicago, Chicago, IL, USA. The evaluation of nucleotide
photoionization threshold energies provides useful information for understanding …

Role of temperature in the decohesion of an elastic chain tethered to a substrate by onsite breakable links

G Florio, G Puglisi, S Giordano - Physical Review Research, 2020 - APS
We analyze the role of temperature in the rate-independent cohesion and decohesion
behavior of an elastic film, mimicked by a one-dimensional mass-spring chain, grounded to …

Optimization of the electrodeposition of gold nanoparticles for the application of highly sensitive, label-free biosensor

HC Chiang, Y Wang, Q Zhang, K Levon - Biosensors, 2019 - mdpi.com
A highly sensitive electrochemical biosensor with a signal amplification platform of
electrodeposited gold nanoparticle (AuNP) has been developed and characterized. The …

Thermal control of nucleation and propagation transition stresses in discrete lattices with non-local interactions and non-convex energy

A Cannizzo, L Bellino, G Florio, G Puglisi… - The European Physical …, 2022 - Springer
Non-local and non-convex energies represent fundamental interacting effects regulating the
complex behavior of many systems in biophysics and materials science. We study one …

Temperature controlled decohesion regimes of an elastic chain adhering to a fixed substrate by softening and breakable bonds

A Cannizzo, G Florio, G Puglisi… - Journal of Physics A …, 2021 - iopscience.iop.org
We study the rate-independent decohesion process for a chain linked to a substrate through
a series of breakable elements with a softening mechanism. Such an assumption describes …

Thermodynamics of twisted DNA with solvent interaction

M Zoli - The Journal of chemical physics, 2011 - pubs.aip.org
The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short
fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects …

Stretching multistate flexible chains and loops

G Noh, P Benetatos - Physical Review E, 2024 - APS
Polymer loop structure commonly appears in biological phenomena, such as DNA looping
and DNA denaturation. When a chain forms a loop, its elastic behavior differs from that of an …

Isotensional and isometric force-extension response of chains with bistable units and Ising interactions

M Benedito, S Giordano - Physical Review E, 2018 - APS
The combination of bistability and cooperativity plays a crucial role in several biological and
artificial micro-and nanosystems. In particular, the exhaustive understanding of the …