Related papers: Molecular dynamics simulations of a single strande…

We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…

Single molecule force spectroscopy of DNA strands adsorbed at surfaces is a powerful technique used in air or liquid environments to quantify their mechanical properties. Although the force responses are limited to unfolding events so far,…

Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…

Synthetic molecular dynamics (synMD) trajectories from learned generative models have been proposed as a useful addition to the biomolecular simulation toolbox. The computational expense of explicitly integrating the equations of motion in…

We suggest that the thermodynamic stability parameters (nearest neighbor stacking and hydrogen bonding free energies) of double-stranded DNA molecules can be inferred reliably from time series of the size fluctuations (breathing) of local…

We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…

The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever…

We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…

This paper presents a molecular mechanics study for new nanorobotic structures using molecular dynamics (MD) simulations coupled to virtual reality (VR) techniques. The operator can design and characterize through molecular dynamics…

The oxidative damage of DNA is a compelling issue in molecular biophysics as it plays a vital role in the epigenetic control of gene expression and is believed to be associated with mutagenesis, carcinogenesis, and ageing. To understand the…

We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…

During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation…

In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to…

The thermodynamic binding networks (TBN) model is a tool for studying engineered molecular systems. The TBN model allows one to reason about their behavior through a simplified abstraction that ignores details about molecular composition,…

Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA…

A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…

We introduce and numerically study a model designed to mimic the bulk behavior of a system composed of single-stranded DNA dendrimers. Complementarity of the base sequences of different strands results in the formation of strong cooperative…

Single-cell sequencing is revolutionizing biology by enabling detailed investigations of cell-state transitions. Many biological processes unfold along continuous trajectories, yet it remains challenging to extract smooth, low-dimensional…

The thermal conductivity of B-form double-stranded DNA (dsDNA) of the Drew-Dickerson sequence d(CGCGAATTCGCG) is computed using classical Molecular Dynamics (MD) simulations. In contrast to previous studies, which focus on a simplified 1D…

We introduce an extended version of oxDNA, a coarse-grained model of DNA designed to capture the thermodynamic, structural and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves, and by…