794 citations · 3.6k across the 30 of their papers we have counts for
31 papers
Designing 3D multicomponent self-assembling systems with signal-passing building blocks
Joshua Evans, Petr Šulc
We introduce allostery-mimetic building blocks model for self-assembly of 3D structures. We represent the building blocks as patchy particles, where each binding site (patch) can b…
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…
A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
Aditya Sengar, Thomas E. Ouldridge, Oliver Henrich +2
The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we pre…
Coarse-Grained Nucleic Acid-Protein Model for Hybrid Nanotechnology
Jonah Procyk, Erik Poppleton, Petr Šulc
The emerging field of hybrid DNA - protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with versatil…
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.
Coarse-grained modelling of supercoiled RNA
Christian Matek, Petr Šulc, Ferdinando Randisi +2
We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the m…
Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA
Benedict E. K. Snodin, Ferdinando Randisi, Majid Mosayebi +8
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…
Modelling toehold-mediated RNA strand displacement
Petr Šulc, Thomas E. Ouldridge, Flavio Romano +2
We 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…
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…
A nucleotide-level coarse-grained model of RNA
Petr Šulc, Flavio Romano, Thomas E. Ouldridge +2
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce…
A comparison between parallelization approaches in molecular dynamics simulations on GPUs
Lorenzo Rovigatti, Petr Šulc, István Z. Reguly +1
We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where…
Optimal Distributed Control of Reactive Power via the Alternating Direction Method of Multipliers
Petr Šulc, Scott Backhaus, Michael Chertkov
We formulate the control of reactive power generation by photovoltaic inverters in a power distribution circuit as a constrained optimization that aims to minimize reactive power l…
Coarse-graining DNA for simulations of DNA nanotechnology
Jonathan P. K. Doye, Thomas E. Ouldridge, Ard A. Louis +8
To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coar…
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…
Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
Petr Šulc, Thomas E. Ouldridge, Flavio Romano +2
We 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 consi…