arXiv subjects

L. Rovigatti

Publications and source records attributed to L. Rovigatti.

4 recordsLinked to original sources

arXiv2024

ANNaMo: Coarse-grained modelling for folding and assembly of RNA and DNA systems

The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales and system sizes involved. In this article, we present a new coarse-grained model for investigating the folding dynamics of nucleic acids. Our model represents 3 nucleotides with a patchy particle and is parametrized using well-established nearest-neighbor models. Thanks to the reduction of degrees of freedom and to a bond-swapping mechanism, our model allows for simulations at timescales and length scales that are currently inaccessible to more detailed models. To validate the performance of our model, we conducted extensive simulations of various systems: We examined the thermodynamics of DNA hairpins, capturing their stability and structural transitions, the folding of an MMTV pseudoknot, a complex RNA structure involved in viral replication, and also explored the folding of an RNA tile containing a k-type pseudoknot. Finally, we evaluated the performance of the new model in reproducing the melting temperatures of oligomers and the dependence on the toehold length of the displacement rate in toehold-mediated displacement processes, a key reaction used in molecular computing. All in all, the successful reproduction of experimental data and favorable comparisons with existing coarse-grained models validate the effectiveness of the new model.

cond-mat.soft↗

arXiv2021

A Systematic Analysis of the Memory term in Coarse-Grained models: the case of the Markovian Approximation

The systematic development of Coarse-Grained (CG) models via the Mori-Zwanzig projector operator formalism requires the explicit description of several terms, including a deterministic drift term, a dissipative memory term and a random fluctuation term. In many applications, the memory and fluctuation terms are related by the fluctuation-dissipation relation and are, in general, more challenging to derive than the drift term. In this work we analyse an approximation of the memory term and propose a rational basis for a data-driven approach to an approximation of the memory and fluctuating terms which can be considered included in the class of the Markovian ones.

cond-mat.stat-mech↗

arXiv2021

Charge affinity and solvent effects in numerical simulations of ionic microgels

Ionic microgel particles are intriguing systems in which the properties of thermo-responsive polymeric colloids are enriched by the presence of charged groups. In order to rationalize their properties and predict the behaviour of microgel suspensions, it is necessary to develop a coarse-graining strategy that starts from the accurate modelling of single particles. Here, we provide a numerical advancement of a recently-introduced model for charged co-polymerized microgels by improving the treatment of ionic groups in the polymer network. We investigate the thermoresponsive properties of the particles, in particular their swelling behaviour and structure, finding that, when charged groups are considered to be hydrophilic at all temperatures, highly charged microgels do not achieve a fully collapsed state, in favorable comparison to experiments. In addition, we explicitly include the solvent in the description and put forward a mapping between the solvophobic potential in the absence of the solvent and the monomer-solvent interactions in its presence, which is found to work very accurately for any charge fraction of the microgel. Our work paves the way for comparing single-particle properties and swelling behaviour of ionic microgels to experiments and to tackle the study of these charged soft particles at a liquid-liquid interface.

cond-mat.soft↗

arXiv2019

Numerical modelling of non-ionic microgels: an overview

Microgels are complex macromolecules. These colloid-sized polymer networks possess internal degrees of freedom and, depending on the polymer(s) they are made of, can acquire a responsiveness to variations of the environment (temperature, pH, salt concentration, etc.). Besides being valuable for many practical applications, microgels are also extremely important to tackle fundamental physics problems. As a result, these last years have seen a rapid development of protocols for the synthesis of microgels, and more and more research has been devoted to the investigation of their bulk properties. However, from a numerical standpoint the picture is more fragmented, as the inherently multi-scale nature of microgels, whose bulk behaviour crucially depends on the microscopic details, cannot be handled at a single level of coarse-graining. Here we present an overview of the methods and models that have been proposed to describe non-ionic microgels at different length-scales, from the atomistic to the single-particle level. We especially focus on monomer-resolved models, as these have the right level of details to capture the most important properties of microgels, responsiveness and softness. We suggest that these microscopic descriptions, if realistic enough, can be employed as starting points to develop the more coarse-grained representations required to investigate the behaviour of bulk suspensions.

cond-mat.soft↗