John Maddocks

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Publications associées (23)

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, Marco Pasi, Jonathan Mitchell

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

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

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

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

John Maddocks

2010