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- Richard Lavery, John H. Maddocks, Marco Pasi, Krystyna Zakrzewska
- Nucleic acids research
- 2014

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 coordinates and leads to highly localized ion densities compared to those obtained by simply superposing… (More)

- O Gonzalez, J H Maddocks
- Proceedings of the National Academy of Sciences…
- 1999

The global radius of curvature of a space curve is introduced. This function is related to, but distinct from, the standard local radius of curvature and is connected to various physically appealing properties of a curve. In particular, the global radius of curvature function provides a concise characterization of the thickness of a curve, and of certain… (More)

- F Lankas, O Gonzalez, L M Heffler, G Stoll, M Moakher, J H Maddocks
- Physical chemistry chemical physics : PCCP
- 2009

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 mechanics, leads to effective shape, stiffness and mass parameters, and employs special procedures for… (More)

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 strands of DNA are significantly affected by their base-pair sequence; though expected to be true, had… (More)

- Richard Lavery, Krystyna Zakrzewska, +15 authors Jiri Sponer
- Nucleic acids research
- 2010

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 structural and dynamic dataset which is currently unavailable from experiment. A consortium of… (More)

A conjugate point test determining an index of the constrained second variation in one-dimensional isoperimetric calculus of variations problems is described. The test is then implemented numerically to determine stability properties of equilibria within a continuum mechanics model of DNA minicircles.

Many different physical systems, e.g. super-coiled DNA molecules, have been successfully modelled as elastic curves, ribbons or rods. We will describe all such systems as framed curves, and will consider problems in which a three dimensional framed curve has an associated energy that is to be minimized subject to the constraint of there being no… (More)

- P B Furrer, R S Manning, J H Maddocks
- Biophysical journal
- 2000

Within the context of DNA rings, we analyze the relationship between intrinsic shape and the existence of multiple stable equilibria, either nicked or cyclized with the same link. A simple test, based on a perturbation expansion of symmetry breaking within a continuum elastic rod model, provides good predictions of the occurrence of such multiple… (More)

- Surjit B Dixit, David L Beveridge, +9 authors Péter Varnai
- Biophysical journal
- 2005

Molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide basepair steps are reported. The objective is to obtain the calculated dynamical structure for at least two copies of each case, use the results to examine issues with regard to convergence and dynamical stability of MD on DNA,… (More)

- Filip Lankas, Richard Lavery, John H Maddocks
- Structure
- 2006

Recent experiments on minicircle formation suggest that a conformational mechanism other than smooth deformation may be playing a role in enhancing DNA flexibility. Both local base unpairing and kink formation have been suggested as possible explanations. Although kinks within isolated DNA were proposed 30 years ago, they have, until now, only been observed… (More)