Related papers: Pathways for virus assembly around nucleic acids
Curved structures in soft matter and biological systems commonly emerge as a result of self-assembly processes where building blocks aggregate in a controlled manner, giving rise to specific system structure and properties. Learning how to…
We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
We simulate the assembly dynamics of icosahedral capsids from subunits that interconvert between different conformations (or quasi-equivalent states). The simulations identify mechanisms by which subunits form empty capsids with only one…
Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex or the actin cytoskeleton is strongly determined by their spatial structure. Moreover it is becoming increasingly clear that the reversible nature of…
The majority of viruses are organised according to the structural blueprints of the seminal Caspar-Klug theory. However, there are a number of notable exceptions to this geometric design principle. Prominent examples are the cancer-causing…
Living cells dynamically modulate the local morphologies of their actin cytoskeletons to perform biological functions, including force transduction, intracellular transport, and cell division. A major challenge is to understand how diverse…
Most genome assemblers construct point estimates, choosing a genome sequence from among many alternative hypotheses that are supported by the data. We present a Markov Chain Monte Carlo approach to sequence assembly that instead generates…
We performed "weighted ensemble" path-sampling simulations of adenylate kinase, using several semi-atomistic protein models. Our study investigated both the biophysics of conformational transitions as well as the possibility of increasing…
Capillarity-driven self-assembly at fluidic interfaces offers a scalable route to large, reconfigurable materials. Microscale particles with high horizontal-to-vertical aspect ratios become attractive building blocks for shape-directed…
We model the spontaneous assembly of a capsid (a virus's closed outer shell) from many copies of identical units, using entirely irreversible steps and only information local to the growing edge. Our model is formulated in terms of (i) an…
The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…
One of the challenges of self-assembling finite-sized colloidal aggregates with a sought morphology is the necessity of precisely sorting the position of the colloids at the microscopic scale to avoid the formation of off-target structures.…
Computational methods for discovering patterns of local correlations in sequences are important in computational biology. Here we show how to determine the optimal partitioning of aligned sequences into non-overlapping segments such that…
The field of complex self-assembly is moving toward the design of multi-particle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such `addressable complexity,' we need to…
The kinetics of the self-assembly of nanocomponents into a virus, nanocapsule, or other composite structure is analyzed via a multiscale approach. The objective is to achieve predictability and to preserve key atomic-scale features that…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the…
Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a…