Related papers: Exploring Programmable Self-Assembly in Non-DNA ba…
Nanoparticles with "sticky patches" have long been proposed as building blocks for the self-assembly of complex structures. The synthetic realizability of such patchy particles, however, greatly lags behind predictions of patterns they…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…
Materials with bespoke properties have long been identified by computational searches, and their experimental realisation is now coming within reach through autonomous laboratories. Scattering experiments are central to verifying the atomic…
Self-assembly of granular particles is of great interest in both applied and basic research. It is commonly observed that when randomly packed into a container, granular particles form disordered structures like glass. As the particles are…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
Understanding chromatin dynamics across multiple spatiotemporal scales requires models that reconcile biological specificity with physics-based interactions and computational tractability. We present a modular, recognition-enabled…
Molecule generation is central to a variety of applications. Current attention has been paid to approaching the generation task as subgraph prediction and assembling. Nevertheless, these methods usually rely on hand-crafted or external…
Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…
Computational studies of chemical reactions in complex environments such as proteins, nanostructures, or on surfaces require accurate and efficient atomistic models applicable to the nanometer scale. In general, an accurate parametrization…
The Self-Assembly of Nano-Objects (SANO) code we implemented demonstrates the ability to predict the molecular self-assembly of different structural motifs by tuning the molecular building blocks as well as the metallic substrate. It…
Inspired by biology and implemented using nanotechnology, the self-assembly of patchy particles has emerged as a pivotal mechanism for constructing complex structures that mimic natural systems with diverse functionalities. Here, we explore…
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…
Component-Based Development (CBD) is a popular approach to mitigating the costs of creating software systems. However, it is not clear to what extent the core component selection and adaptation activities of CBD can be implemented to…
Unlike molecular crystals, soft self-assembled fibres, micelles, vesicles, etc., exhibit a certain order in the arrangement of their constitutive monomers, but also high structural dynamicity and variability. Defects and disordered local…
A proof-of-concept framework for identifying molecules of unknown elemental composition and structure using experimental rotational data and probabilistic deep learning is presented. Using a minimal set of input data determined…
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,…
We report canonical and grand-canonical lattice Monte Carlo simulations of the self-assembly of addressable structures comprising hundreds of distinct component types. The nucleation behaviour, in the form of free-energy barriers to…
In many virus families, tens to thousands of proteins assemble spontaneously into a capsid (protein shell) while packaging the genomic nucleic acid. This review summarizes recent advances in computational modeling of these dynamical…
Colloidal particles can self-assemble into various ordered structures in fluid flows that have potential applications in biomedicine, materials synthesis and encryption. These dynamic processes are also of fundamental interest for probing…
Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…