794 citations · 3.6k across the 30 of their papers we have counts for
13 papers · 1 filter
Coarse-grained modelling of DNA-RNA hybrids
Eryk J. Ratajczyk, Petr Šulc, Andrew J. Turberfield +2
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models$\unicode{x2014}$oxDNA and oxRNA. The model nat…
Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments
Hao Liu, Michael Matthies, John Russo +10
Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility to self-assemble complex lattices or finite size constructs, but have mostly on…
Inverse design of self-folding 3D shells
Diogo E. P. Pinto, Nuno A. M. Araújo, Petr Šulc +1
Self-folding is an emerging paradigm for the inverse design of three-dimensional structures. While most efforts have concentrated on the shape of the net, our approach introduces a…
Design strategies for the self-assembly of polyhedral shells
Diogo E. P. Pinto, Petr Sulc, Francesco Sciortino +1
The control over the self-assembly of complex structures is a long-standing challenge of material science, especially at the colloidal scale, as the desired assembly pathway is oft…
Two-step nucleation in a binary mixture of Patchy Particles
Camilla Beneduce, Diogo E. P. Pinto, Petr Sulc +2
Nucleation in systems with a metastable liquid-gas critical point is the prototypical example of a two-step nucleation process, in which the appearance of the critical nucleus is p…
Engineering azeotropy to optimize the self-assembly of colloidal mixtures
Camilla Beneduce, Francesco Sciortino, Petr Sulc +1
The goal of inverse self-assembly is to design inter-particle interactions capable of assembling the units into a desired target structure. The effective assembly of complex struct…
Designing the self-assembly of arbitrary shapes using minimal complexity building blocks
Joakim Bohlin, Andrew J. Turberfield, Ard A. Louis +1
The design space for a self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building bloc…
A simple solution to the problem of self-assembling cubic diamond crystals
Lorenzo Rovigatti, John Russo, Flavio Romano +3
The self-assembly of colloidal diamond (CD) crystals is considered as one of the most coveted goals of nanotechnology, both from the technological and fundamental points of view. F…
SAT-assembly: A new approach for designing self-assembling systems
John Russo, Flavio Romano, Lukas Kroc +3
We propose a general framework for solving inverse self-assembly problems, i.e. designing interactions between elementary units such that they assemble spontaneously into a predete…
Designing patchy interactions to self-assemble arbitrary structures
Flavio Romano, John Russo, Lukáš Kroc +1
One of the fundamental goals of nanotechnology is to exploit selective and directional interactions between molecules to design particles that self-assemble into desired structures…
The oxDNA coarse-grained model as a tool to simulate DNA origami
Jonathan P. K. Doye, Hannah Fowler, Domen Prešern +12
This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.
DNA hairpins primarily promote duplex melting rather than inhibiting hybridization
John S. Schreck, Thomas E. Ouldridge, Flavio Romano +4
The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybrid…
DNA hybridization kinetics: zippering, internal displacement and sequence dependence
Thomas E. Ouldridge, Petr Šulc, Flavio Romano +2
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgenc…