Related papers: Self-assembly of a dimer system
Computational modeling of assembly is challenging for many systems because their timescales vastly exceed those accessible to simulations. This article describes the MultiMSM, which is a general framework that uses Markov state models…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
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…
An active system consisting of many self-spinning dimers is simulated, and a distinct local rotational jamming transition is observed as the density increases. In the low density regime, the system stays in an absorbing state, in which each…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…
We introduce and numerically study a model designed to mimic the bulk behavior of a system composed of single-stranded DNA dendrimers. Complementarity of the base sequences of different strands results in the formation of strong cooperative…
We present a quantitative measure of physical complexity, based on the amount of information required to build a given physical structure through self-assembly. Our procedure can be adapted to any given geometry, and thus to any given type…
The assembly of filamentous bundles with controlled diameters is common in biological systems and desirable for the development of nanomaterials. We discuss dynamical simulations and free energy calculations on patchy spheres with chiral…
We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RNA molecule inside. The proteins are flexible and described…
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.…
Self-assembly at submicroscopic scales is an important but little understood phenomenon. A prominent example is virus capsid growth, whose underlying behavior can be modeled using simple particles that assemble into polyhedral shells.…
Geometric frustration offers a pathway to soft matter self-assembly with controllable finite sizes. While the understanding of frustration in soft matter assembly derives almost exclusively from continuum elastic descriptions, a current…
A coarse-grained computational model is used to investigate the effect of a fluctuating fluid membrane on the dynamics of patchy-particle assembly into virus capsid-like cores. Results from simulations for a broad range of parameters are…
We present a theoretical model for predicting the phase behavior of polymer solutions in which phase separation competes with oligomerization. Specifically, we consider scenarios in which the assembly of polymer chains into stoichiometric…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Cyanobacteria sequester photosynthetic enzymes into microcompartments which facilitate the conversion of carbon dioxide into sugars. Geometric similarities between these structures and self-assembling viral capsids have inspired models that…
Proteinaceous aggregation occurs through self-assembly-- a process not entirely understood. In a recent article [1], an analytical theory for amyloid fibril growth via secondary rather than primary nucleation was presented. Remarkably, with…
We use neuroevolutionary learning to identify time-dependent protocols for low-dissipation self-assembly in a model of generic active particles with interactions. When the time allotted for assembly is sufficiently long, low-dissipation…
Understanding how highly symmetric, robust, monodisperse protein cages self-assemble can have major applications in various areas of bio-nanotechnology, such as drug delivery, biomedical imaging and gene therapy. We develop a model to…