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Flavio Romano

Publications and source records attributed to Flavio Romano.

34 records · Page 2Linked to original sources
arXiv2014

Modelling toehold-mediated RNA strand displacement

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 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.

physics.bio-ph↗
arXiv2014

The role of loop stacking in the dynamics of DNA hairpin formation

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 and non-native base pairing on the hairpin closing times. We find a non-monotonic variation of the hairpin closing time with temperature, in agreement with the experimental work of Wallace et al. [Proc. Nat. Acad. Sci. USA 2001, 98, 5584-5589]. The hairpin closing process involves the formation of an initial nucleus of one or two bonds between the stems followed by a rapid zippering of the stem. At high temperatures, typically above the hairpin melting temperature, an effective negative activation enthalpy is observed because the nucleus has a lower enthalpy than the open state. By contrast, at low temperatures, the activation enthalpy becomes positive mainly due to the increasing energetic cost of bending a loop that becomes increasingly highly stacked as the temperature decreases. We show that stacking must be very strong to induce this experimentally observed behavior, and that the existence of just a few weak stacking points along the loop can substantially suppress it. Non-native base pairs are observed to have only a small effect, slightly accelerating hairpin formation.

physics.bio-ph↗
arXiv2014

A comparison between parallelization approaches in molecular dynamics simulations on GPUs

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 a computing thread is started per particle, is compared to a newly proposed "edge-based" approach, where a thread is started per each potentially non-zero interaction. We find that the former is more efficient for systems with many simple interactions per particle, while the latter is more efficient if the system has more complicated interactions or fewer of them. By comparing computation times on more and less recent GPU technology, we predict that, if the current trend of increasing the number of processing cores - as opposed to their computing power - remains, the "edge-based" approach will gradually become the most efficient choice in an increasing number of cases.

physics.comp-ph↗
arXiv2014

DNA hairpins primarily promote duplex melting rather than inhibiting hybridization

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 hybridization rates by factors of 2 and 10 respectively, in good agreement with experiment. By contrast, melting rates are accelerated by factors of ~100 and ~2000. This surprisingly large speed-up occurs because hairpins form during the melting process, stabilizing partially melted states, and facilitating dissociation. These results may help guide the design of DNA devices that use hairpins to modulate hybridization and dissociation pathways and rates.

cond-mat.soft↗
arXiv2014

A nucleotide-level coarse-grained model of RNA

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 structural, mechanical and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.

physics.bio-ph↗
arXiv2013

Coarse-graining DNA for simulations of DNA nanotechnology

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 coarse graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.

q-bio.BM↗
arXiv2013

Computing phase diagrams for a quasicrystal-forming patchy-particle system

We 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 stabilised over its crystalline approximants.

cond-mat.stat-mech↗
arXiv2013

DNA hybridization kinetics: zippering, internal displacement and sequence dependence

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 urgency because DNA nanotechnology often depends critically on binding rates. Here we use a coarse-grained model to explore the hybridization kinetics of DNA oligomers, finding that strand association proceeds through a complex set of intermediate states. Successful binding events start with the formation of a few metastable base-pairing interactions, followed by zippering of the remaining bonds. However, despite reasonably strong interstrand interactions, initial contacts frequently fail to lead to zippering because the typical configurations in which they form differ from typical states of similar enthalpy in the double-stranded equilibrium ensemble. Therefore, if the association process is analyzed on the base-pair (secondary structure) level, it shows non-Markovian behavior. 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 is observed as the number of base pairs in the effective transition state increases with temperature. In addition, we find that alternative pathways involving misbonds can increase association rates. For repetitive sequences, misaligned duplexes frequently rearrange to form fully paired duplexes by two distinct processes which we label `pseudoknot' and `inchworm' internal displacement. We show how the above processes can explain why experimentally observed association rates of GC-rich oligomers are higher than rates of AT-rich equivalents. More generally, we argue that association rates can be modulated by sequence choice.

cond-mat.soft↗
arXiv2013

Coarse-grained simulations of DNA overstretching

We use a recently developed coarse-grained model to simulate the overstretching of duplex DNA. Overstretching at 23C occurs at 74 pN in the model, about 6-7 pN higher than the experimental value at equivalent salt conditions. Furthermore, the model reproduces the temperature dependence of the overstretching force well. The mechanism of overstretching is always force-induced melting by unpeeling from the free ends. That we never see S-DNA (overstretched duplex DNA), even though there is clear experimental evidence for this mode of overstretching under certain conditions, suggests that S-DNA is not simply an unstacked but hydrogen-bonded duplex, but instead probably has a more exotic structure.

q-bio.BM↗
arXiv2012

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model

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 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.

physics.bio-ph↗
arXiv2012

Sequence-dependent thermodynamics of a coarse-grained DNA model

We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes. By developing a histogram reweighting technique, we are able to fit our parameters to the melting temperatures of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its melting point, (c) the effects of stacking strength in the loop on the melting temperature of hairpins, (d) the force-extension properties of single strands and (e) the structure of a kissing-loop complex. Where possible we compare our results with experimental data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as free software.

physics.bio-ph↗
arXiv2012

The effect of topology on the structure and free energy landscape of DNA kissing complexes

We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain constant. By studying systems with linking numbers -1, 0 or 1 we show that the average number of interstrand base pairs is larger when the topology is more favourable for the right-handed wrapping of strands around each other. The thermodynamic stability of the kissing complex also decreases when the linking number changes from -1 to 0 to 1. The structures of the kissing complexes typically involve two intermolecular helices that coaxially stack with the hairpin stems at a parallel four-way junction.

cond-mat.soft↗
arXiv2012

Fluid-Fluid and Fluid-Solid transitions in the Kern-Frenkel model from Barker-Henderson thermodynamic perturbation theory

We study the Kern-Frenkel model for patchy colloids using Barker-Henderson second-order thermodynamic perturbation theory. The model describes a fluid where hard sphere particles are decorated with one patch, so that they interact via a square-well (SW) potential if they are sufficiently close one another, and if patches on each particle are properly aligned. Both the gas-liquid and fluid-solid phase coexistences are computed and contrasted against corresponding Monte-Carlo simulations results. We find that the perturbation theory describes rather accurately numerical simulations all the way from a fully covered square-well potential down to the Janus limit (half coverage). In the region where numerical data are not available (from Janus to hard-spheres), the method provides estimates of the location of the critical lines that could serve as a guideline for further efficient numerical work at these low coverages. A comparison with other techniques, such as integral equation theory, highlights the important aspect of this methodology in the present context.

cond-mat.soft↗
arXiv2011

Nucleation barriers in tetrahedral liquids spanning glassy and crystallizing regimes

Crystallization and vitrification of tetrahedral liquids are important both from a fundamental and a technological point of view. Here, we study via extensive umbrella sampling Monte Carlo computer simulations the nucleation barriers for a simple model for tetrahedral patchy particles in the regime where open tetrahedral crystal structures (namely cubic and hexagonal diamond and their stacking hybrids) are thermodynamically stable. We show that by changing the angular bond width, it is possible to move from a glass-forming model to a readily crystallizing model. From the shape of the barrier we infer the role of surface tension in the formation of the crystalline clusters. Studying the trends of the nucleation barriers with the temperature and the patch width, we are able to identify an optimal value of the patch size that leads to easy nucleation. Finally, we find that the nucleation barrier is the same, within our numerical precision, for both diamond crystals and for their stacking forms.

cond-mat.soft↗
arXiv2011

Crystal phases of two dimensional assembly of triblock Janus particles

Recent experimental work on spherical colloidal particles decorated with two hydrophobic poles separated by an electrically-charged middle band (triblock Janus particles) has documented self-assembly into a Kagome two-dimensional lattice, when particles are confined by gravity at the bottom of the sample holder [Q. Chen {\em et. al.}, Nature, in press]. Here we assess the ability of a previously proposed simple two-patch effective potential to reproduce the experimental findings. We show that the effective potential is able to reproduce the observed crystallization pathway in the Kagome structure. Based on free energy calculations, we also show that the Kagome lattice is stable at low temperatures and low pressure, but that it transforms into a hexagonal lattice with alternating attractive and repulsive bands on increasing pressure.

cond-mat.soft↗