Related papers: The self-assembly and evolution of homomeric prote…
A binary mixture of particles interacting with spherically-symmetric potentials leading to microsegregation is studied by theory and molecular dynamics (MD) simulations. We consider spherical particles with equal diameters and volume…
Self-organization of heterogeneous particle swarms is rich in its dynamics but hard to design in a traditional top-down manner, especially when many types of kinetically distinct particles are involved. In this chapter, we discuss how we…
Fabrication of diamond structures by self-assembly is a fundamental challenge in making three-dimensional photonic crystals. We simulate a system of model hard particles with attractive patches and show that they can self-assemble into a…
A cell dynamics method for domain separation of diblock copolymers (DBCPs) interacting with nanoparticles (NPs) whose diffusion coefficients depend on chain configuration is proposed for self-assembly of DBCP/NP composites. Increasing NP…
Results from molecular dynamics simulations of simple, structured particles capable of self-assembling into polyhedral shells are described. The analysis focuses on the growth histories of individual shells in the presence of an explicit…
Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
We present results from particle simulations with isotropic medium range interactions in two dimensions. At low temperature novel types of aggregated structures appear. We show that these structures can be explained by spontaneous symmetry…
Controlling the topology of structures self-assembled from a set of heterogeneous building blocks is highly desirable for many applications, but is poorly understood theoretically. Here we show that the thermodynamic theory of self-assembly…
The plasticity of amorphous solids undergoing shear is characterized by quasi-localized rearrangements of particles. While many models of plasticity exist, the precise relationship between plastic dynamics and the structure of a particle's…
Complex colloidal cluster morphologies are desirable for the fabrication of advanced materials, such as photonic crystals and meta-materials, and can be formed through evaporation-driven packing. By coupling lattice Boltzmann and discrete…
A lattice model with soft repulsion followed by attraction is developed for a monolayer of hybrid core-shell particles self-assembling at an interface. The model is solved exactly in one dimension. One, two or three periodic structures and…
Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from molecular to mesoscopic level. Herein we report an example of using fully synthetic systems that mimic two levels of…
Random heteropolymers do not display the typical equilibrium properties of globular proteins, but are the starting point to understand the physics of proteins and, in particular, to describe their non-native states. So far, they have been…
We review and further develop an analytical model that describes how thermodynamic constraints on the stability of the native state influence protein evolution in a site-specific manner. To this end, we represent both protein sequences and…
A major goal in nanoscience and nanotechnology is the self-assembly of any desired complex structure with a system of particles interacting through simple potentials. To achieve this objective, intense experimental and theoretical efforts…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
Triply periodic continuous morphologies arising a result of the microphase separation in block copolymer melts have so far never been observed self-assembled in systems of particles with spherically symmetric interaction. We report a…
We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…