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Flavio Romano

Publications and source records attributed to Flavio Romano.

At least 19 recordsLinked to original sources

A Falsifiability Test for Classical Nucleation Theory

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 melt and the crystal. Although CNT's simplicity and usefulness cannot be overstated, experiments and simulations regularly uncover significant deviations from its predictions, which are often reconciled through phenomenological extensions of the CNT, fueling the debate over the general validity of the theory. In this study, we present a falsifiability test for any nucleation theory grounded in the capillarity approximation. We focus on cases where the theory predicts no differences in nucleation rates between different crystal polymorphs. We then introduce a system in which all polymorphs have the same free energy (both bulk and interfacial) across all state points. Through extensive molecular simulations, we show that the polymorphs exhibit remarkably different nucleation properties, directly contradicting CNT's predictions. We argue that CNT's primary limitation lies in its neglect of structural fluctuations within the liquid phase.

cond-mat.soft

Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments

Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility to self-assemble complex lattices or finite size constructs, but have mostly only been successful in silico. The proposed strategies quite often fail in experiment due to unpredicted traps associated to kinetic slowing down (gelation, glass transition), as well as to competing ordered structures. An additional challenge that theoretical predictions face is the difficulty to encode the desired inter-particle interaction potential with the currently available library of nano- and micron-sized particles. To overcome these issues, we conjugate here SAT-assembly -- a patchy-particle interaction design algorithm based on constrained optimization solvers -- with coarse-grained simulations of DNA nanotechnology to experimentally realize trap-free self-assembly pathways. As a proof of concept we investigate the assembly of the pyrochlore (also known as tetrastack) lattice, a highly coveted 3D crystal lattice due to its promise in construction of optical metamaterials. We confirm the successful assembly with two different patchy DNA origami designs via SAXS as well as SEM visualization of the silica-coated lattice. Our approach offers a versatile modeling pipeline that starts from patchy particles designed in silico and ends with wireframe DNA origami that self-assemble into the desired structure.

cond-mat.soft

Janus helices: From fully attractive to hard helices

The phase diagram of hard helices differs from its hard rods counterpart by the presence of chiral "screw" phases stemming from the characteristic helical shape, in addition to the conventional liquid crystal phases also found for rod-like particles. Using extensive Monte Carlo and Molecular Dynamics simulations, we study the effect of the addition of a short-range attractive tail representing solvent-induced interactions to a fraction of the sites forming the hard helices, ranging from a single-site attraction to fully attractive helices for a specific helical shape. Different temperature regimes exist for different fractions of the attractive sites, as assessed in terms of the relative Boyle temperatures, that are found to be rather insensitive to the specific shape of the helical particle. The temperature range probed by the present study is well above the corresponding Boyle temperatures, with the phase behaviour still mainly entropically dominated and with the existence and location of the various liquid crystal phases only marginally affected. The pressure in the equation of state is found to decrease upon increasing the fraction of attractive beads and/or on lowering the temperature at fixed volume fraction, as expected on physical grounds. All screw phases are found to be stable within the considered range of temperatures with the smectic phase becoming more stable on lowering the temperature. By contrast, the location of the transition lines do not display a simple dependence on the fraction of attractive beads in the considered range of temperatures.

cond-mat.soft

A simple solution to the problem of self-assembling cubic diamond crystals

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. For applications, colloidal diamond is a photonic crystal which can open new possibilities of manipulating light for information processing. From a fundamental point of view, its unique symmetry exacerbates a series of problems that are commonly faced during the self-assembly of target structures, such as the presence of kinetic traps and the formation of crystalline defects and alternative structures (polymorphs). Here we demonstrate that all these problems can be systematically addressed via SAT-assembly, a design framework that converts self-assembly into a satisfiability problem. Contrary to previous solutions (requiring four or more components), we prove that the assembly of the CD crystal only requires a binary mixture. Moreover, we use molecular dynamics simulations of a system composed by nearly a million nucleotides to test a DNA nanotechnology design that constitutes a promising candidate for experimental realization.

cond-mat.soft

SAT-assembly: A new approach for designing self-assembling systems

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 predetermined structure. Our approach uses patchy particles as building blocks, where the different units bind at specific interaction sites (the patches), and we exploit the possibility of having mixtures with several components. The interaction rules between the patches is determined by transforming the combinatorial problem into a Boolean satisfiability problem (SAT) which searches for solutions where all bonds are formed in the target structure. Additional conditions, such as the non-satisfiability of competing structures (e.g. metastable states) can be imposed, allowing to effectively design the assembly path in order to avoid kinetic traps. We demonstrate this approach by designing and numerically simulating a cubic diamond structure from four particle species that assembles without competition from other polymorphs, including the hexagonal structure.

cond-mat.soft

Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling

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 DNA assemblies used in the field of DNA nanotechnology. The landscapes for these complex systems are accessible through the use of accurate coarse-grained descriptions of DNA. Particular foci will be the landscapes associated with DNA self-assembly and mechanical deformation, where the latter can arise from either externally imposed forces or internal stresses.

cond-mat.soft

Phase behaviour of hard cylinders

Using isobaric Monte Carlo simulations, we map out the entire phase diagram of a system of hard cylindrical particles of length $L$ and diameter $D$, using an improved algorithm to identify the overlap condition between two cylinders. Both the prolate $L/D>1$ and the oblate $L/D<1$ phase diagrams are reported with no solution of continuity. In the prolate $L/D>1$ case, we find intermediate nematic \textrm{N} and smectic \textrm{SmA} phases in addition to a low density isotropic \textrm{I} and a high density crystal \textrm{X} phase, with \textrm{I-N-SmA} and \textrm{I-SmA-X} triple points. An apparent columnar phase \textrm{C} is shown to be metastable as in the case of spherocylinders. In the oblate $L/D<1$ case, we find stable intermediate cubatic \textrm{Cub}, nematic \textrm{N}, and columnar \textrm{C} phases with \textrm{I-N-Cub}, \textrm{N-Cub-C}, and \textrm{I-Cub-C} triple points. Comparison with previous numerical and analytical studies is discussed. The present study, accounting for the explicit cylindrical shape, paves the way to more sophisticated models with important biological applications, such as viruses and nucleosomes.

cond-mat.soft

Designing patchy interactions to self-assemble arbitrary structures

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, from capsids, to nano-clusters, to fully formed crystals with target properties (e.g. optical, mechanical, etc.). Here we provide a general framework which transforms the inverse problem of self-assembly of colloidal crystals into a Boolean satisfiability problem for which solutions can be found numerically. Given a reference structure and the desired number of components, our approach produces designs for which the target structure is an energy minimum, and also allows to exclude solutions that correspond to competing structures. We demonstrate the effectiveness of our approach by designing model particles that spontaneously nucleate milestone structures such as the cubic diamond, the pyrochlore and the clathrate lattices.

cond-mat.soft

Measuring internal forces in single-stranded DNA: Application to a DNA force clamp

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 individual nucleotides are explored and related to model potentials, and using our framework, internal forces are calculated for two simple DNA systems and for a recently-published nanoscopic force clamp. Our results highlight some pitfalls associated with conventional methods for estimating internal forces, which are based on elastic polymer models, and emphasise the importance of carefully considering secondary structure and ionic conditions when modelling the elastic behaviour of single-stranded DNA. Beyond its relevance to the DNA nanotechnological community, we expect our approach to be broadly applicable to calculations of internal force in a variety of structures -- from DNA to protein -- and across other coarse-grained simulation models.

cond-mat.soft

Coarse-grained modelling of the structural properties of DNA origami

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. The model reproduces well the characteristic pattern of helix bending in a 2D origami, showing that it stems from the intrinsic tendency of anti-parallel four-way junctions to splay apart, a tendency that is enhanced both by less screened electrostatic interactions and by increased thermal motion. We also compare to the structure of a 3D origami whose structure has been determined by cryo-electron microscopy. The oxDNA average structure has a root-mean-square deviation from the experimental structure of 8.4 Angstrom, which is of the order of the experimental resolution. These results illustrate that the oxDNA model is capable of providing detailed and accurate insights into the structure of DNA origamis, and has the potential to be used to routinely pre-screen putative origami designs.

cond-mat.soft

How to Simulate Patchy Particles

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 interaction sites. Numerical simulations have contributed significantly to our understanding of the behaviour of patchy particles, but, although simple in principle, advanced simulation techniques are often required to sample the low temperatures and long time scales associated with their self-assembly behaviour. In this work we review the most popular simulation techniques that have been used to study patchy particles, with a special focus on Monte Carlo methods. We cover many of the tools required to simulate patchy systems, from interaction potentials to biased moves, cluster moves, and free energy methods. The review is complemented by an educationally-oriented Monte Carlo computer code that implements all the techniques described in the text to simulate a well-known tetrahedral patchy particle model.

cond-mat.soft

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly

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 calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so) and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.

cond-mat.soft

Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal

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 quasicrystals even at very narrow patch widths, provided their patch interactions are chosen in an appropriate way. Such patchy particles can be thought of as a coarse-grained representation of DNA multi-arm `star' motifs, which can be chosen to bond with one another very specifically by tuning the DNA sequences of the protruding arms. We explore several possible design strategies and conclude that DNA star tiles that are designed to interact with one another in a specific but not overly constrained way could potentially be used to construct soft quasicrystals in experiment. We verify that such star tiles can form stable dodecagonal motifs using oxDNA, a realistic coarse-grained model of DNA.

cond-mat.soft

Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"

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 implied by the widely-used worm-like chain model; many of these studies, however, remain controversial. We use a coarse-grained model, previously fitted to DNA's basic thermodynamic and mechanical properties, to explore strongly bent systems. We find that as the end-to-end distance is decreased sufficiently short duplexes undergo a transition to a state in which the bending strain is localized at a flexible kink that involves disruption of base-pairing and stacking. This kinked state, which is not well-described by the worm-like chain model, allows the duplex to more easily be sharply bent. It is not completely flexible, however, due to constraints arising from the connectivity of both DNA backbones. We also perform a detailed comparison to recent experiments on a "molecular vice" that probes highly bent DNA. Close agreement between simulations and experiments strengthens the hypothesis that localised bending via kinking occurs in the molecular vice and causes enhanced flexibility of duplex DNA. Our calculations therefore suggests that the cost of kinking implied by this experiment is consistent with the known thermodynamic and mechanical properties of DNA.

q-bio.BM

Coarse-grained modelling of strong DNA bending II: Cyclization

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 fluctuations, but some experiments on strongly-bent shorter molecules suggest enhanced flexibility over and above that expected from the worm-like chain. Here, we use a coarse-grained model of DNA to investigate the thermodynamics of DNA cyclization for molecules with less than 210 base pairs. As the molecules get shorter we find increasing deviations between our computed equilibrium j-factor and the worm-like chain predictions of Shimada and Yamakawa. These deviations are due to sharp kinking, first at nicks, and only subsequently in the body of the duplex. At the shortest lengths, substantial fraying at the ends of duplex domains is the dominant method of relaxation. We also estimate the dynamic j-factor measured in recent FRET experiments. We find that the dynamic j-factor is systematically larger than its equilibrium counterpart, with the deviation larger for shorter molecules, because not all the stress present in the fully cyclized state is present in the transition state. These observations are important for the interpretation of recent experiments, as only kinking within the body of the duplex is genuinely indicative of non-worm-like chain behaviour.

q-bio.BM

Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA

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 DNA. By including explicit major and minor grooves, and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures such as DNA origami which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na$^+$]=0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

q-bio.BM

Characterizing the bending and flexibility induced by bulges in DNA duplexes

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 extensively in structures such as polyhedral cages, two-dimensional arrays, and ribbons, is a bulged duplex, that is two helical segments that connect at a bulge loop. We use a coarse-grained model of DNA to characterize such bulged duplexes. We find that this motif can adopt structures belonging to two main classes: one where the stacking of the helices at the center of the system is preserved, the geometry is roughly straight and the bulge is on one side of the duplex, and the other where the stacking at the center is broken, thus allowing this junction to act as a hinge and increasing flexibility. Small loops favor states where stacking at the center of the duplex is preserved, with loop bases either flipped out or incorporated into the duplex. Duplexes with longer loops show more of a tendency to unstack at the bulge and adopt an open structure. The unstacking probability, however, is highest for loops of intermediate lengths, when the rigidity of single-stranded DNA is significant and the loop resists compression. The properties of this basic structural motif clearly correlate with the structural behavior of certain nano-scale objects, where the enhanced flexibility associated with larger bulges has been used to tune the self-assembly product as well as the detailed geometry of the resulting nanostructures.

cond-mat.soft