Quantifying supercoiling-induced denaturation bubbles in DNA
In both eukaryotic and prokaryotic DNA sequences of 30–100 base-pairs rich in AT base-
pairs have been identified at which the double helix preferentially unwinds. Such DNA …
pairs have been identified at which the double helix preferentially unwinds. Such DNA …
Mixed order transition and condensation in an exactly soluble one dimensional spin model
Mixed order phase transitions (MOT), which display discontinuous order parameter and
diverging correlation length, appear in several seemingly unrelated settings ranging from …
diverging correlation length, appear in several seemingly unrelated settings ranging from …
Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) have remarkably similar chemical
structures, but despite this, they play significantly different roles in modern biology. In this …
structures, but despite this, they play significantly different roles in modern biology. In this …
Localization, big-jump regime and the effect of disorder for a class of generalized pinning models
G Giacomin, B Havret - Journal of Statistical Physics, 2020 - Springer
One dimensional pinning models have been widely studied in the physical and
mathematical literature, also in presence of disorder. Roughly speaking, they undergo a …
mathematical literature, also in presence of disorder. Roughly speaking, they undergo a …
Macroscopic loop formation in circular DNA denaturation
The statistical mechanics of DNA denaturation under fixed linking number is qualitatively
different from that of unconstrained DNA. Quantitatively different melting scenarios are …
different from that of unconstrained DNA. Quantitatively different melting scenarios are …
Spatial complexity in nature, science and technology
F Papadimitriou, F Papadimitriou - Spatial complexity: Theory …, 2020 - Springer
Some characteristic domains of science and technology for which spatial complexity is
significant are examined here. In cosmology, spatial complexity relates to the large-scale …
significant are examined here. In cosmology, spatial complexity relates to the large-scale …
Denaturation of circular DNA: supercoils and overtwist
The denaturation transition of circular DNA is studied within a Poland-Scheraga-type
approach, generalized to account for the fact that the total linking number (LK), which …
approach, generalized to account for the fact that the total linking number (LK), which …
The rubber band revisited: Wang–Landau simulation
LS Ferreira, AA Caparica, MA Neto… - Journal of Statistical …, 2012 - iopscience.iop.org
In this work we apply Wang–Landau simulations to a simple model which has exact
solutions both in the microcanonical and canonical formalisms. The simulations were carried …
solutions both in the microcanonical and canonical formalisms. The simulations were carried …
Purification of Recombinant E. Coli Topoisomerase III for Structure-Based Drug Design Using Protein Crystallization
MA Perez Rodriguez… - FIU Undergraduate …, 2024 - digitalcommons.fiu.edu
Type IA Topoisomerases are ubiquitous enzymes found throughout all life forms and
species. These topoisomerases relieve the topographical constrains formed by DNA during …
species. These topoisomerases relieve the topographical constrains formed by DNA during …
Constrained thermal denaturation of DNA under fixed linking number
A DNA molecule with freely fluctuating ends undergoes a sharp thermal denaturation
transition upon heating. However, in circular DNA chains and some experimental setups that …
transition upon heating. However, in circular DNA chains and some experimental setups that …