Publications related to DNA Topology

Crystal Engineering of Polymeric Structures with Dative Boron–Nitrogen Bonds: Design Criteria and Limitations

Rosario Scopelliti, Kay Severin, Kurt Schenk, Farzaneh Fadaei Tirani, Philip Pattison, Euro Solari, Nicolas Luisier, Kevin Bally

The combination of tripyridyl ligands and linear diboronate esters results in the formation of oligomeric or polymeric adducts featuring dative boron−nitrogen bonds. The relative orientation of the two different building blocks in the assemblies can be pre ...

American Chemical Society2016

Generation of supercoils in nicked and gapped DNA drives DNA unknotting and postreplicative decatenation

Julien Dorier, Yannis Burnier, Fabrizio Benedetti, Andrzej Stasiak

Due to the helical structure of DNA the process of DNA replication is topologically complex. Freshly replicated DNA molecules are catenated with each other and are frequently knotted. For proper functioning of DNA it is necessary to remove all of these ent ...

Oxford University Press2015

Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling

Giovanni Dietler, Julien Dorier, Yannis Burnier, Fabrizio Benedetti, Andrzej Stasiak, Aleksandre Japaridze, Robert Sebastian Kwapich

DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from ...

Oxford University Press2015

Influence of DNA Binding Dyes on Bare DNA Structure Studied with Atomic Force Microscopy

Giovanni Dietler, Aleksandr Benke, Aleksandre Japaridze, Sylvain Renevey

Fluorescent dyes are widely used for staining and visualization of DNA in optical microscopy based methods. Even though for some dyes the mechanism of binding is known, how this binding affects DNA remains poorly understood. Here we present a novel experim ...

American Chemical Society2015

Untangling the Mechanics and Topology in the Frictional Response of Long Overhand Elastic Knots

Pedro Miguel Nunes Pereira de Almeida Reis

We combine experiments and theory to study the mechanics of overhand knots in slender elastic rods under tension. The equilibrium shape of the knot is governed by an interplay between topology, friction, and bending. We use precision model experiments to q ...

American Physical Society2015

Constructing reparameterization invariant metrics on spaces of plane curves

Martins Bruveris, Martin Bauer

Metrics on shape spaces are used to describe deformations that take one shape to another, and to define a distance between shapes. We study a family of metrics on the space of curves, which includes several recently proposed metrics, for which the metrics ...

Elsevier2014

Measurement of the Position-Dependent Electrophoretic Force on DNA in a Glass Nanocapillary

Aleksandra Radenovic, Lorenz Jan Steinbock, Roman Bulushev, Sergey Khlybov

The electrophoretic force on a single DNA molecule inside a glass nanocapillary depends on the opening size and varies with the distance along the symmetrical axis of the nanocapillary. Using optical tweezers and DNA-coated beads, we measured the stalling ...

American Chemical Society2014

Threshold phenomenon for the quintic wave equation in three dimensions

Joachim Krieger

For the critical focusing wave equation

\square u=u^5

on

\mathbb{R}^{3+1}

in the radial case, we establish the role of the “center stable” manifold

\Sigma

constructed in [18] near the ground state

(W,0)

as a threshold between blowup and scattering ...

Springer Verlag2014

Phenomenological and physiological approaches in the study of cardiac alternans: Theoretical background, mathematical modeling and numerical simulations

This project presents the theoretical background in electrophysiology that is used as a basis in the development of numerical methods for the simulation of heart’s electrical activity. We discuss the mathematical models currently used in cardiac electrophy ...

2013

Comment une situation d’investigation policière fait évoluer les conceptions d’élèves de troisième sur l’ADN

The work presented focuses on the analysis of a police investigation implemented in the computing environment SCY-Lab. The prime objective is to check if the implementation of the situation helps pupils change their conceptions concerning the DNA molecule ...

2013

DNA Topology

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Crystal Engineering of Polymeric Structures with Dative Boron–Nitrogen Bonds: Design Criteria and Limitations

Generation of supercoils in nicked and gapped DNA drives DNA unknotting and postreplicative decatenation

Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling

Influence of DNA Binding Dyes on Bare DNA Structure Studied with Atomic Force Microscopy

Untangling the Mechanics and Topology in the Frictional Response of Long Overhand Elastic Knots

Constructing reparameterization invariant metrics on spaces of plane curves

Measurement of the Position-Dependent Electrophoretic Force on DNA in a Glass Nanocapillary

Threshold phenomenon for the quintic wave equation in three dimensions

Phenomenological and physiological approaches in the study of cardiac alternans: Theoretical background, mathematical modeling and numerical simulations

Comment une situation d’investigation policière fait évoluer les conceptions d’élèves de troisième sur l’ADN

Measurement of the Position-Dependent Electrophoretic Force on DNA in a Glass Nanocapillary

Phenomenological and physiological approaches in the study of cardiac alternans: Theoretical background, mathematical modeling and numerical simulations

Untangling the Mechanics and Topology in the Frictional Response of Long Overhand Elastic Knots

Comment une situation d’investigation policière fait évoluer les conceptions d’élèves de troisième sur l’ADN

Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling

Threshold phenomenon for the quintic wave equation in three dimensions

Crystal Engineering of Polymeric Structures with Dative Boron–Nitrogen Bonds: Design Criteria and Limitations

Influence of DNA Binding Dyes on Bare DNA Structure Studied with Atomic Force Microscopy

Constructing reparameterization invariant metrics on spaces of plane curves

Generation of supercoils in nicked and gapped DNA drives DNA unknotting and postreplicative decatenation