423 citations · 2.3k across the 33 of their papers we have counts for
34 papers
A Falsifiability Test for Classical Nucleation Theory
Camilla Beneduce, Diogo E. P. Pinto, Lorenzo Rovigatti +4
Classical nucleation theory (CNT) is built upon the capillarity approximation, i.e., the assumption that the nucleation properties can be inferred from the bulk properties of the m…
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…
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…
Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling
Jonathan P. K. Doye, Ard A. Louis, John S. Schreck +5
This chapter will provide an overview of how characterizing free-energy landscapes can provide insights into the biophysical properties of DNA, as well as into the behaviour of the…
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…
Phase behaviour of hard cylinders
Joyce T. Lopes, Flavio Romano, Eric Grelet +2
Using isobaric Monte Carlo simulations, we map out the entire phase diagram of a system of hard cylindrical particles of length and diameter , using an improved algorithm to…
Measuring internal forces in single-stranded DNA: Application to a DNA force clamp
Megan C. Engel, Flavio Romano, Ard A. Louis +1
We present a new method for calculating internal forces in DNA structures using coarse-grained models and demonstrate its utility with the oxDNA model. The instantaneous forces on…
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 the structural properties of DNA origami
Benedict E. K. Snodin, John S. Schreck, Flavio Romano +2
We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origamis, focussing on archetypal 2D and 3D origamis. T…
How to Simulate Patchy Particles
Lorenzo Rovigatti, John Russo, Flavio Romano
Patchy particles is the name given to a large class of systems of mesoscopic particles characterized by a repulsive core and a discrete number of short-range and highly directional…
Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly
Pedro Fonseca, Flavio Romano, John S. Schreck +3
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculat…
Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal
Aleks Reinhardt, John S. Schreck, Flavio Romano +1
We use Monte Carlo simulations and free-energy techniques to show that binary solutions of penta- and hexavalent two-dimensional patchy particles can form thermodynamically stable…
Coarse-grained modelling of strong DNA bending II: Cyclization
Ryan M. Harrison, Flavio Romano, Thomas E. Ouldridge +2
DNA cyclization is a powerful technique to gain insight into the nature of DNA bending. The worm-like chain model provides a good description of small to moderate bending fluctuati…
Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"
Ryan M. Harrison, Flavio Romano, Thomas E. Ouldridge +2
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than i…
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…
Characterizing the bending and flexibility induced by bulges in DNA duplexes
John S. Schreck, Thomas E. Ouldridge, Flavio Romano +2
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used ex…
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…
The role of loop stacking in the dynamics of DNA hairpin formation
Majid Mosayebi, Flavio Romano, Thomas E. Ouldridge +2
We study the dynamics of DNA hairpin formation using oxDNA, a nucleotide-level coarse-grained model of DNA. In particular, we explore the effects of the loop stacking interactions…
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…
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…