Related papers: A simulation that recapitulates the dynamics of PE…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…
Multiple dissipative self-assembly protocols designed to create novel structures or to reduce kinetic traps have recently emerged. Specifically, temporal oscillations of particle interactions have been shown effective at both aims, but…
Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well…
Extreme deformation of soft matter is central to our understanding of the effects of shock, fracture, and phase change in a variety of systems. Yet, despite, the increasing interest in this area, far-from-equilibrium behaviours of soft…
Programmable self-assembly has recently enabled the creation of complex structures through precise control of the interparticle interactions and the particle geometries. Targeting ever more structurally complex, dynamic, and functional…
We propose a synthesis method for the design of digital twins applicable to various systems (pneumatic, hydraulic, electrical/electronic circuits). The methodology allows representing the operation of these systems through an active digital…
Spontaneous self-assembly in molecular systems is a fundamental route to both biological and engineered soft matter. Simple micellisation, emulsion formation, and polymer mixing principles are well understood. However, the principles behind…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
Self-assembly is the autonomous organization of components into patterns or structures: an essential ingredient of biology and a desired route to complex organization. At equilibrium, the structure is encoded through specific interactions,…
This dissertation explores how deep generative models can advance the analysis of challenging biological problems by integrating domain knowledge with deep learning. It focuses on two areas: DNA reaction kinetics and cryogenic electron…
Within simulations of molecules deposited on a surface we show that neuroevolutionary learning can design particles and time-dependent protocols to promote self-assembly, without input from physical concepts such as thermal equilibrium or…
Locally (re)structuring colloidal gels $\unicode{x2013}$ micron-sized particles forming a connected network with arrested dynamics $\unicode{x2013}$ enables precise tuning of the micromechanical and -rheological properties of the system. A…
We present the Brownian dynamics simulation of active colloidal suspension in two dimensions, where the self-propulsion speed of a colloid is regulated according to the local density sensed by it. The role of concentration-dependent…
Directed assembly of block polymers is rapidly becoming a viable strategy for lithographic patterning of nanoscopic features. One of the key attributes of directed assembly is that an underlying chemical or topographic substrate pattern…
Colloidal particles with mobile binding molecules constitute a powerful platform for probing the physics of self-assembly. Binding molecules are free to diffuse and rearrange on the surface, giving rise to spontaneous control over the…
An efficient numerical algorithm is presented for massively parallel simulations of dispersion-managed wavelength-division-multiplexed optical fiber systems. The algorithm is based on a weak nonlinearity approximation and independent…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
We present modeling approaches to explain mechanisms of control of uniformity (narrow distribution) of sizes and shapes in synthesis of nanosize crystals and micron-size colloids. We consider those situations when the nanocrystals are…