1,721,159 research outputs found
Final configuration files for umbrella sampling in "Characterizing the free-energy landscapes of DNA origamis"
No full textFinal configuration and topology files in oxDNA format for each umbrella sampling window of the three DNA nanotube systems investigated
Input files for example oxDNA simulations of DNA origami
No full textThe zip file contains cadnano .json files for three example DNA origami and oxDNA input files to first relax and then simulate these DNA origami using molecular dynamics for the oxDNA coarse-grained model. The native oxDNA simulation code is available at https://sourceforge.net/projects/oxdna/. The zip file contains cadnano files for three example DNA origami and oxDNA input files to first relax and then simulate these DNA origami using molecular dynamics for the oxDNA coarse-grained model. These files are to accompany a tutorial on simulating DNA origami with oxDN
Data associated with "How to design an icosahedral quasicrystal through directional bonding"
No full textFinal configurations associated with simulations of patchy particles that form icosahedral quasicrystals. The configurations are in .xyz format and can be viewed using a molecular viewer. Example .tcl files are included that allow the configurations to be viewed using vmd
Simulation data for "The Free-Energy Landscape of a Mechanically Bistable DNA Origami"
No full textSimulation data containing the cadnano design files for the systems simulated, the raw data for the free energy landscapes and the final configurations for each umbrella sampling window for each system
Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
Get PDFWe apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a 'burnt-bridges' DNA motor consisting of a single-stranded cargo that steps processively along a track of single-stranded stators. We demonstrate that the model is able to simulate such a system, and investigate the sensitivity of the stepping process to the spatial separation of stators, finding that an increased distance can suppress successful steps due to the build up of unfavourable tension. The mechanism of suppression suggests that varying the distance between stators could be used as a method for improving signal-to-noise ratios for motors that are required to make a decision at a junction of stators
Modelling toehold-mediated RNA strand displacement
Get PDFWe study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5′ end of the substrate; and that the displacement slows down with increasing temperature for longer toeholds
Computing phase diagrams for a quasicrystal-forming patchy-particle system.
Get PDFWe introduce an approach to computing the free energy of quasicrystals, which we use to calculate phase diagrams for systems of two-dimensional patchy particles with five regularly arranged patches that have previously been shown to form dodecagonal quasicrystals. We find that the quasicrystal is a thermodynamically stable phase for a wide range of conditions and remains a robust feature of the system as the potential's parameters are varied. We also demonstrate that the quasicrystal is entropically stabilized over its crystalline approximants
Coarse-Grained Modeling of RNA for Biology and Nanotechnology
No full textWe present a recently developed nucleotide-level model for RNA, oxRNA. The model is\ud
designed to reproduce structural, mechanical and thermodynamic properties of RNA, and\ud
the coarse-graining level aims to retain the relevant physics for RNA hybridization and the\ud
structure of single-and double-stranded RNA
DNA hybridization kinetics: zippering, internal displacement and sequence dependence.
Get PDFAlthough the thermodynamics of DNA hybridization is generally well established, the kinetics of this classic transition is less well understood. Providing such understanding has new urgency because DNA nanotechnology often depends critically on binding rates. Here, we explore DNA oligomer hybridization kinetics using a coarse-grained model. Strand association proceeds through a complex set of intermediate states, with successful binding events initiated by a few metastable base-pairing interactions, followed by zippering of the remaining bonds. But despite reasonably strong interstrand interactions, initial contacts frequently dissociate because typical configurations in which they form differ from typical states of similar enthalpy in the double-stranded equilibrium ensemble. Initial contacts must be stabilized by two or three base pairs before full zippering is likely, resulting in negative effective activation enthalpies. Non-Arrhenius behavior arises because the number of base pairs required for nucleation increases with temperature. In addition, we observe two alternative pathways-pseudoknot and inchworm internal displacement-through which misaligned duplexes can rearrange to form duplexes. These pathways accelerate hybridization. Our results explain why experimentally observed association rates of GC-rich oligomers are higher than rates of AT- rich equivalents, and more generally demonstrate how association rates can be modulated by sequence choice
- …
