arXiv subjects

Lorenzo Rovigatti

Publications and source records attributed to Lorenzo Rovigatti.

47 records · Page 3Linked to original sources

arXiv2015

Surface wave excitations and backflow effect over dense polymer brushes

Polymer brushes are increasingly used to tailor surface physicochemistry for various applications such as wetting, adhesion of biological objects, implantable devices, etc. We perform Dissipative Particle Dynamics simulations to study the behavior of dense polymer brushes under flow in a slit-pore channel. We discover that the system displays flow inversion at the brush interface for several disconnected ranges of the imposed flow. We associate such phenomenon to collective polymer dynamics: a wave propagating on the brush surface. The relation between the wavelength, the amplitude and the propagation speed of the flow-generated wave is consistent with the solution of the Stokes equations when an imposed traveling wave is assumed as boundary condition (the famous Taylor's swimmer).

cond-mat.soft↗

arXiv2015

Soft self-assembled nanoparticles with temperature-dependent properties

The fabrication of versatile building blocks that are reliably self-assemble into desired ordered and disordered phases is amongst the hottest topics in contemporary material science. To this end, microscopic units of varying complexity, aimed at assembling the target phases, have been thought, designed, investigated and built. Such a path usually requires laborious fabrication techniques, especially when a specific funcionalisation of the building blocks is required. Telechelic star polymers, i.e., star polymers made of a number $f$ of di-block copolymers consisting of solvophobic and solvophilic monomers grafted on a central anchoring point, spontaneously self-assemble into soft patchy particles featuring attractive spots (patches) on the surface. Here we show that the tunability of such a system can be widely extended by controlling the physical and chemical parameters of the solution. Indeed, at fixed external conditions the self-assembly behaviour depends only on the number of arms and/or on the ratio of solvophobic to solvophilic monomers. However, changes in temperature and/or solvent quality makes it possible to reliably change the number and size of the attractive patches. This allows to steer the mesoscopic self-assembly behaviour without modifying the microscopic constituents. Interestingly, we also demonstrate that diverse combinations of the parameters can generate stars with the same number of patches but different radial and angular stiffness. This mechanism could provide a neat way of further fine-tuning the elastic properties of the supramolecular network without changing its topology.

cond-mat.soft↗

arXiv2014

How soft repulsion enhances the depletion mechanism

We investigate binary mixtures of large colloids interacting through soft potentials with small, ideal depletants. We show that softness has a dramatic effect on the resulting colloid-colloid effective potential when the depletant-to-colloid size ratio $q$ is small, with significant consequences on the colloidal phase behaviour. We also provide an exact relation that allows us to obtain the effective pair potential for {\it any} type of colloid-depletant interactions in the case of ideal depletants, without having to rely on complicated and expensive full-mixture simulations. We also show that soft repulsion among depletants further enhances the tendency of colloids to aggregate. Our theoretical and numerical results demonstrate that --- in the limit of small $q$ --- soft mixtures cannot be mapped onto hard systems and hence soft depletion is not a mere extension of the widely used Asakura-Oosawa potential.

cond-mat.soft↗

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

Accurate phase diagram of tetravalent DNA nanostars

We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA. We find that, as the system is cooled down, tetramers undergo a gas--liquid phase separation in a region of concentrations which, if the difference in salt concentration is taken into account, is comparable with the recently measured experimental phase diagram [S. Biffi \textit{et al}, Proc. Natl. Acad. Sci, \textbf{110}, 15633 (2013)]. We also present a mean-field free energy for modelling the phase diagram based on the bonding contribution, derived by Wertheim in its studies of associating liquids, combined with mass action law expressions appropriate for DNA binding and a numerically evaluated reference free energy. The resulting free energy qualitatively reproduces the numerical data. Finally, we report information on the nanostar structure, e.g. geometry and flexibility of the single tetramer and of the collective behaviour, providing a useful reference for future small angle scattering experiments, for all investigated temperatures and concentrations.

cond-mat.soft↗

arXiv2013

Self-assembly in chains, rings and branches: a single component system with two critical points

We study the interplay between phase separation and self-assembly in chains, rings and branched structures in a model of particles with dissimilar patches. We extend Wertheim's first order perturbation theory to include the effects of ring formation and theoretically investigate the thermodynamics of the model. We find a peculiar shape for the vapor-liquid coexistence, featuring re-entrant behavior in both phases and two critical points, despite the single-component nature of the system. The emergence of the lower critical point is caused by the self-assembly of rings taking place in the vapor, generating a phase with lower energy and lower entropy than the liquid. Monte Carlo simulations of the same model fully support these unconventional theoretical predictions.

cond-mat.soft↗

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 the phase diagram of binary mixtures: a patchy particle case study

We investigate the phase behaviour of 2D mixtures of bi-functional and three-functional patchy particles and 3D mixtures of bi-functional and tetra-functional patchy particles by means of Monte Carlo simulations and Wertheim theory. We start by computing the critical points of the pure systems and then we investigate how the critical parameters change upon lowering the temperature. We extend the Successive Umbrella Sampling method to mixtures to make it possible to extract information about the phase behaviour of the system at a fixed temperature for the whole range of densities and compositions of interest.

cond-mat.soft↗

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

Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link

Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on temperature and duplex length, such chains order into liquid crystal phases. Here, we investigate the self-assembly of such double-helical duplexes with a combined numerical and theoretical approach. We simulate the bulk system employing the coarse-grained DNA model recently proposed by Ouldridge et al. [ J. Chem. Phys. 134, 08501 (2011) ]. Then we evaluate the input quantities for the theoretical framework directly from the DNA model. The resulting parameter-free theoretical predictions provide an accurate description of the simulation results in the isotropic phase. In addition, the theoretical isotropic-nematic phase boundaries are in line with experimental findings, providing a route to estimate the stacking free energy.

cond-mat.soft↗

arXiv2011

The vibrational density of states of a disordered gel model

We investigate the vibrational density of states (vDOS) in harmonic approximation of a binary mixture of colloidal patchy particles with two and three patches for different relative compositions $x_2$. At low temperature, this system forms a thermo-reversible gel, i.e. a fully bonded network of chains of two-patches particles, in which the branching points are provided by three-patches particles. For all the compositions we find in the vDOS a pronounced peak at low frequency whose height grows on increasing the fraction of two-functional particles, or equivalently with the average length of the chains. To identify the various spectral features, we compare the vDOS of the whole system with the one of small representative structures of the network and with the vDOS of a long linear chain of two-patches particles and we find that these structures are indeed able to rationalize the various peaks in the vDOS of the full system. At large $x_2$ the vDOS of the gel and of the long chain show remarkable similarities. Analyzing the dispersion relations and the spectrum of the linear chain we show that the excess of low frequency modes, the analog of the boson peak in glassy disordered systems, arises from the strong coupling between rotations and translations.

cond-mat.soft↗