Publications by 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, Alessandro Samuele Patelli, Lennart de Bruin, Rahul Sharma

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, Paolo Carloni, Marco Pasi, Rahul Sharma

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

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

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

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

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

cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA

John Maddocks, Daiva Petkeviciute, Marco Pasi

cgDNA is a package for the prediction of sequence-dependent configuration-space free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any given length and sequence, cgDNA calculates the configuration of the associated fre ...

Oxford Univ Press2014

mu ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

John Maddocks, Daiva Petkeviciute, Jonathan Mitchell, Marco Pasi

We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have ex ...

Oxford Univ Press2014

A sequence-dependent rigid-base model of DNA

John Maddocks, Daiva Petkeviciute

A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A signi ...

Amer Inst Physics2013

Twist and Stretch of Helices Explained via the Kirchhoff-Love Rod Model of Elastic Filaments

John Maddocks

In various single-molecule experiments, a chiral polymer, such as DNA, is simultaneously pulled and twisted. We address an elementary but fundamental question raised by various authors: does the molecule overwind or unwind under tension? We show that withi ...

Amer Physical Soc2013

Second-Order Comparison of Gaussian Random Functions and the Geometry of DNA Minicircles

John Maddocks, Victor Panaretos, David Kraus

Given two samples of continuous zero-mean iid Gaussian processes on [0,1], we consider the problem of testing whether they share the same covariance structure. Our study is motivated by the problem of determining whether the mechanical properties of short ...

2010

Looping probabilities of elastic chains: A path integral approach

John Maddocks, Ludovica Cotta-Ramusino

We consider an elastic chain at thermodynamic equilibrium with a heat bath, and derive an approximation to the probability density function, or pdf, governing the relative location and orientation of the two ends of the chain. Our motivation is to exploit ...

2010

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

John Maddocks

It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays a significant role in protein-DNA interactions vital for cellular processes. Understanding and predicting base sequence effects requires an extensive ...

2010

On The Stochastic Modeling Of Rigid Body Systems With Application To Polymer Dynamics

John Maddocks

The stochastic equations of motion for a system of interacting rigid bodies in a solvent are formulated and studied. Three-dimensional bodies of arbitrary shape, with arbitrary couplings between translational and rotational degrees of freedom, as arise in ...

2010

Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

John Maddocks, Jacques Dubochet, Andrzej Stasiak, Arnaud Amzallag, Davide Demurtas

We use cryo-electron microscopy (cryo-EM) to study the 3D shapes of 94-bp-long DNA minicircles and address the question of whether cyclization of such short DNA molecules necessitates the formation of sharp, localized kinks in DNA or whether the necessary ...

Oxford University Press2009

On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations

John Maddocks, Leesa Maree Heffler

A method is described to extract a complete set of sequence-dependent material parameters for rigid base and basepair models of DNA in solution from atomistic molecular dynamics simulations. The method is properly consistent with equilibrium statistical me ...

2009