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Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated…
An ideal nanofabrication method should allow the organization of nanoparticles and molecules with nanometric positional precision, stoichiometric control and well-defined orientation. The DNA origami technique has evolved into a highly…
We design a system with a binary suspension of colloids and a surface that triggers the self-assembly of crystallites with a finite thickness. The proposed design allows controlling the number of layers forming the aggregate and constrains…
We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can…
DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in presence of an…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
Nanopore sensing is a key technology for single-molecule detection and analysis. Solid-state nanopores have emerged as a versatile platform, since their fabrication allows to engineer their properties by controlling size, shape, and…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…
Block copolymer melts self-assemble in the bulk into a variety of nanostructures, making them perfect candidates to template the position of nanoparticles. The morphological changes of block copolymers are studied in the presence of a…
Weak multivalent interactions govern a large variety of biological processes like cell-cell adhesion and virus-host interactions. These systems distinguish sharply between surfaces based on receptor density, known as superselectivity.…
It is increasingly being realized that liquid-crystalline features can play an important role in the properties and dynamics of cell monolayers. Here, we present a cell-based model of cell layers, based on the phase-field formulation, that…
Polymer-coated pores play a crucial role in nucleo-cytoplasmic transport and in a number of biomimetic and nanotechnological applications. Here we present Monte Carlo and Density Functional Theory approaches to identify different collective…
Cytoskeletal active nematics exhibit striking non-equilibrium dynamics that are powered by energy-consuming molecular motors. To gain insight into the structure and mechanics of these materials, we design programmable clusters in which…
The combination of soft responsive particles, such as microgels, with nanoparticles (NPs) yields highly versatile complexes of great potential for applications, from ad-hoc plasmonic sensors to controlled protocols for loading and release.…
In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to…
Motivated by the relevance of higher-order interactions in quantum physics and materials science at the nanoscale, recently a model has been introduced for new classes of networks that grow by the geometrically constrained aggregation of…
DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface,…
We present a theoretical discussion of a self-assembly scheme which makes it possible to use DNA to uniquely encode the composition and structure of micro- and nanoparticle clusters. These anisotropic DNA-decorated clusters can be further…
Synthetic molecular motors are an appealing means to control motion at the nanoscale, but understanding their behaviour as single-molecule actuators and integrating them into larger, functional systems remain technical challenges.…