Lorenzo Rovigatti

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By using oxDNA, a coarse-grained nucleotide-level model of DNA, we are able to directly simulate the self-assembly of a small 384-base-pair origami from single-stranded scaffold and staple strands in solution. In general, we see attachment of new staple strands occurring in parallel, but with cooperativity evident for the binding of the second domain of a(More)
We test the relative 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 an "edge-based" approach, where a thread is started per each potentially non-zero interaction. We find that the(More)
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 provide an exact(More)
Microgels are soft colloids that, in virtue of their polymeric nature, can react to external stimuli such as temperature or pH by changing their size. The resulting swelling/deswelling transition can be exploited in fundamental research as well as for many diverse practical applications, ranging from art restoration to medicine. Such an extraordinary(More)
In this Chapter, we present the general statistical-mechanical theory for the derivation of effective Hamiltonians for arbitrary many-body systems in thermodynamic equilibrium. The approach towards a simplified, yet accurate, coarse-grained view of a many-body system has proven to be particularly fruitful in the realm of the Physics of Complex Fluids, a(More)
Microgels are colloidal-scale particles individually made of cross-linked polymer networks that can swell and deswell in response to external stimuli, such as changes to temperature or pH. Despite a large amount of experimental activities on microgels, a proper theoretical description based on individual particle properties is still missing due to the(More)
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(More)
Limited bonding valence, usually accompanied by well-defined directional interactions and selective bonding mechanisms, is nowadays considered among the key ingredients to create complex structures with tailored properties: even though isotropically interacting units already guarantee access to a vast range of functional materials, anisotropic interactions(More)
Polymer brushes are being increasingly used to tailor surface physicochemistry for diverse applications such as wetting, adhesion of biological objects, implantable devices and much more. Here we perform Dissipative Particle Dynamics simulations to study the behaviour of dense polymer brushes under flow in a slit-pore channel. We discover that the system(More)
Heteropolymers are important examples of self-assembling systems. However, in the design of artificial heteropolymers the control over the single chain self-assembling properties does not reach that of the natural bio-polymers, and in particular proteins. Here, we introduce a sufficiency criterion to identify polymers that can be designed to adopt a(More)