Publications de John Maddocks | EPFL Graph Search

Special issue: Multiscale simulations of DNA from electrons to nucleosomes

This editorial for Volume 16, Issue 3 of Biophysical Reviews highlights the three-dimensional structural and dynamic information encoded in DNA sequences and introduces the topics covered in this special issue of the journal on Multiscale Simulations of DN ...

2024

cgNA plus web : A Visual Interface to the cgNA plus Sequence-dependent Statistical Mechanics Model of Double-stranded Nucleic Acids

John Maddocks, Rahul Sharma, Alessandro Samuele Patelli, Lennart de Bruin

The sequence-dependent statistical mechanics of double-stranded nucleic acid, or dsNA, is believed to be essential in its biological functions. In turn, the equilibrium statistical mechanics behaviour of dsNA depends strongly both on sequence-dependent per ...

Elsevier2023

Navigation of Concentric Tube Continuum Robots using Optimal Control

John Maddocks, Siva Prasad Chakri Dhanakoti

Recently developed Concentric Tube Continuum Robots (CTCRs) are widely exploited in, for example in minimally invasive surgeries which involve navigating inside narrow body cavities close to sensitive regions. These CTCRs can be controlled by extending and ...

SCITEPRESS2022

Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?

John Maddocks, Daiva Petkeviciute, Rahul Sharma, Marco Pasi, Paolo Carloni

The structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational ch ...

Springernature2021

Mechanics of two filaments in tight orthogonal contact

Pedro Miguel Nunes Pereira de Almeida Reis, John Maddocks, Tomohiko Sano, Paul Johanns, Harmeet Singh, Paul Grandgeorge

Networks of flexible filaments often involve regions of tight contact. Predictively understanding the equilibrium configurations of these systems is challenging due to intricate couplings between topology, geometry, large nonlinear deformations, and fricti ...

National Academy of Sciences2021

The shapes of physical trefoil knots

Pedro Miguel Nunes Pereira de Almeida Reis, John Maddocks, Tomohiko Sano, Paul Johanns, Changyeob Baek, Paul Grandgeorge

We perform a compare-and-contrast investigation between the equilibrium shapes of physical and ideal trefoil knots, both in closed and open configurations. Ideal knots are purely geometric abstractions for the tightest configuration tied in a perfectly fle ...

2021

The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules

John Maddocks, Daiva Petkeviciute, Alessandro Samuele Patelli, Marco Pasi

We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structura ...

Oxford University Press (OUP)2019

cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA

John Maddocks, Lennart de Bruin

Oxford University Press2018

Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics

John Maddocks, Marco Pasi

Microsecond molecular dynamics simulations of B-DNA oligomers carried out in an aqueous environment with a physiological salt concentration enable us to perform a detailed analysis of how potassium ions interact with the double helix. The oligomers studied ...

Oxford University Press2015

Analyzing ion distributions around DNA

John Maddocks, Marco Pasi

We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordin ...

Oxford University Press2014