Coarse-grained simulations of DNA overstretching

Two-phase stretching of molecular chains

(2013) A. V. Savin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mesoscopic models for DNA stretching under force: New results and comparison with experiments

(2012) Manoel Manghi et al.   EUROPEAN PHYSICAL JOURNAL E

The effect of topology on the structure and free energy landscape of DNA kissing complexes

(2012) Flavio Romano et al.   JOURNAL OF CHEMICAL PHYSICS

Sequence-dependent thermodynamics of a coarse-grained DNA model

(2012) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

Ab initio determination of coarse-grained interactions in double-stranded DNA

(2012) Chia Wei Hsu et al.   JOURNAL OF CHEMICAL PHYSICS

DNA Cruciform Arms Nucleate through a Correlated but Asynchronous Cooperative Mechanism

(2012) Christian Matek et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamical model for the full stretching curve of DNA

(2012) Alessandro Fiasconaro et al.   PHYSICAL REVIEW E

Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements

(2012) X. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tension induces a base-paired overstretched DNA conformation

(2012) N. Bosaeus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link

(2012) Cristiano De Michele et al.   Soft Matter

Coarse-Grained Simulations of Macromolecules: From DNA to Nanocomposites

(2011) Juan J. de Pablo   Annual Review of Physical Chemistry

PicoNewton-Millisecond Force Steps Reveal the Transition Kinetics and Mechanism of the Double-Stranded DNA Elongation

(2011) Pasquale Bianco et al.   BIOPHYSICAL JOURNAL

Structural Rigidity of Paranemic Crossover and Juxtapose DNA Nanostructures

(2011) Mogurampelly Santosh et al.   BIOPHYSICAL JOURNAL

DNA stretching modeled at the base pair level: Overtwisting and shear instability in elastic linkages

(2011) Attila Kocsis et al.   INTERNATIONAL JOURNAL OF NON-LINEAR MECHANICS

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

(2011) Thomas E. Ouldridge et al.   JOURNAL OF CHEMICAL PHYSICS

On the Structure and Stretching of Microhydrated DNA

(2011) Mario Wolter et al.   JOURNAL OF PHYSICAL CHEMISTRY A

B-DNA to Zip-DNA: Simulating a DNA Transition to a Novel Structure with Enhanced Charge-Transport Characteristics

(2011) Alexander Balaeff et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Overstretching DNA at 65 pN Does Not Require Peeling from Free Ends or Nicks

(2011) D. Hern Paik et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DNA stretching by bacterial initiators promotes replication origin opening

(2011) Karl E. Duderstadt et al.   NATURE

Quantifying how DNA stretches, melts and changes twist under tension

(2011) Peter Gross et al.   Nature Physics

Secondary structure of double-stranded DNA under stretching: Elucidation of the stretched form

(2011) M. Maaloum et al.   PHYSICAL REVIEW E

Thermomechanics of DNA: Theory of Thermal Stability under Load

(2011) Cristiano Nisoli et al.   PHYSICAL REVIEW LETTERS

A Three-State Model with Loop Entropy for the Overstretching Transition of DNA

(2010) Thomas R. Einert et al.   BIOPHYSICAL JOURNAL

Stretched DNA Investigated Using Molecular-Dynamics and Quantum-Mechanical Calculations

(2010) Jan Řezáč et al.   BIOPHYSICAL JOURNAL

Force induced melting of the constrained DNA

(2010) Amit Raj Singh et al.   JOURNAL OF CHEMICAL PHYSICS

Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching

(2010) Hongxia Fu et al.   NUCLEIC ACIDS RESEARCH

Two distinct overstretched DNA states

(2010) Hongxia Fu et al.   NUCLEIC ACIDS RESEARCH

Force spectroscopy and fluorescence microscopy of dsDNA-YOYO-1 complexes: implications for the structure of dsDNA in the overstretching region

(2010) C. U. Murade et al.   NUCLEIC ACIDS RESEARCH

Different pulling modes in DNA overstretching: A theoretical analysis

(2010) D. Marenduzzo et al.   PHYSICAL REVIEW E

Microscopic implications of S-DNA

(2010) Stephen Whitelam et al.   PHYSICAL REVIEW E

DNA Nanotweezers Studied with a Coarse-Grained Model of DNA

(2010) Thomas E. Ouldridge et al.   PHYSICAL REVIEW LETTERS

Biophysical characterization of DNA binding from single molecule force measurements

(2010) Kathy R. Chaurasiya et al.   Physics of Life Reviews

Microscopic implications of competing pictures of DNA overstretching

(2010) Stephen Whitelam   Physics of Life Reviews

DNA overstretched state: S-DNA form or force-induced melting?

(2010) Oleg Krichevsky   Physics of Life Reviews

Single-molecule derivation of salt dependent base-pair free energies in DNA

(2010) J. M. Huguet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA curvature and flexibility in vitro and in vivo

(2010) Justin P. Peters et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Overstretching of a 30 bp DNA duplex studied with steered molecular dynamics simulation: Effects of structural defects on structure and force-extension relation

(2009) H. Li et al.   EUROPEAN PHYSICAL JOURNAL E

Reversible gels of patchy particles: Role of the valence

(2009) John Russo et al.   JOURNAL OF CHEMICAL PHYSICS

Shear Unzipping of DNA†

(2009) Buddhapriya Chakrabarti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Stretching and twisting of the DNA duplexes in coarse-grained dynamical models

(2009) Szymon Niewieczerzał et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Phase diagrams for DNA denaturation under stretching forces

(2009) D Marenduzzo et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

The structure of DNA overstretched from the 5'5' ends differs from the structure of DNA overstretched from the 3'3' ends

(2009) C. Danilowicz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Peeling back the mystery of DNA overstretching

(2009) M. C. Williams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging

(2009) J. van Mameren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stretching chimeric DNA: A test for the putative S-form

(2008) Stephen Whitelam et al.   JOURNAL OF CHEMICAL PHYSICS

Quantifying DNA melting transitions using single-molecule force spectroscopy

(2008) Christopher P Calderon et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Force induced DNA melting

(2008) Mogurampelly Santosh et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Melting of persistent double-stranded polymers

(2008) Sahand Jamal Rahi et al.   PHYSICAL REVIEW E

Strain Softening in Stretched DNA

(2008) Binquan Luan et al.   PHYSICAL REVIEW LETTERS

Denaturation Transition of Stretched DNA

(2008) Andreas Hanke et al.   PHYSICAL REVIEW LETTERS

There and (Slowly) Back Again: Entropy-Driven Hysteresis in a Model of DNA Overstretching

(2007) Stephen Whitelam et al.   BIOPHYSICAL JOURNAL