Publications by John Maddocks | EPFL Graph Search

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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 ...

The most classic approach to the dynamics of an n-dimensional mechanical system constrained by d independent holonomic constraints is to pick explicitly a new set of (n - d) curvilinear coordinatesparametrizingthe manifold of configurations satisfying the constraints, and to compute the Lagrangian generating the unconstrained dynamics in these (n - d) configuration coordinates. Starting from this Lagrangian an unconstrained Hamiltonian H(q,p) on 2(n-d) dimensional phase space can then typically be defined i

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 ...

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 ...

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 ...

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 ...

We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algori ...

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 ...

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 ...

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 ...

The recently developed cgNA+ model of double-stranded DNA (dsDNA) accurately predicts equilibrium distributions (in solution) of linear dsDNA fragments of arbitrary sequence, expressed in enhanced Curves+ internal coordinates. This article introduces cgNA+min, a computational framework built on the cgNA+ energy to compute sequence-dependent energy-minimizing configurations of topologically closed dsDNA minicircles with a range of linking numbers. We employ a chain rule to re-express the cgNA+ energy in abso

We present a tour de force of atomistic molecular dynamics simulations involving the coordinated effort of 14 research groups of the Ascona B-DNA Consortium (ABC). This initiative provides a complete characterization of the 2080 DNA hexamers embedded in 190 carefully selected 20-mer duplexes, each simulated in replicate for at least 10 microseconds in explicit solvent. The consortium generates 0.25 petabytes of data, capturing millisecond-scale ensembles at the oligomer level and dynamics up to 10−1 seconds

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

John Maddocks

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Looping probabilities of elastic chains: A path integral approach

Ambient space formulations and statistical mechanics of holonomically constrained Langevin systems

A sequence-dependent rigid-base model of DNA

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

Mechanics of two filaments in tight orthogonal contact

Navigation of Concentric Tube Continuum Robots using Optimal Control

Conformational analysis of nucleic acids revisited: Curves

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

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

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

cgNA+min: computation of sequence-dependent dsDNA energy-minimizing minicircles

hexABC seeking the physical code of DNA

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

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

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

The shapes of physical trefoil knots

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

Analyzing ion distributions around DNA

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

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