Related papers: Shape-free theory for the self-assembly kinetics i…
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…
The algorithmic self-assembly of shapes has been considered in several models of self-assembly. For the problem of \emph{shape construction}, we consider an extended version of the Two-Handed Tile Assembly Model (2HAM), which contains…
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…
The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing…
We use density functional theory to describe the phase behaviors of rigid molecules. The construction of kernel function G(x, P, x, P) is discussed. Excluded-volume potential is calculated for two types of molecules with C_{2v} symmetry.…
In this paper we present a self-contained macroscopic description of diffusive systems interacting with boundary reservoirs and under the action of external fields. The approach is based on simple postulates which are suggested by a wide…
This paper is concerned with the analysis of polyatomic gases within the framework of kinetic theory. Internal degrees of freedom are modeled using a single continuous variable corresponding to the molecular internal energy. Non-equilibrium…
We use computational modeling to investigate the assembly thermodynamics of a particle-based model for geometrically frustrated assembly, in which the local packing geometry of subunits is incompatible with uniform, strain-free large-scale…
We derive a hydrodynamic description of metric-free active matter: starting from self-propelled particles aligning with neighbors defined by "topological" rules, not metric zones, -a situation advocated recently to be relevant for bird…
The eigenstate thermalization hypothesis provides a framework for understanding thermalization in isolated quantum many-body systems by characterizing statistical properties of local observables in energy eigenstates. Here we demonstrate…
We investigate the cooperative effects of a single finite chain of monomers near an attractive substrate by first constructing a conformational pseudo-phase diagram based on the thermal fluctuations of energetic and structural quantities.…
This paper concerns the self-assembly of scaled-up versions of arbitrary finite shapes. We work in the multiple temperature model that was introduced by Aggarwal, Cheng, Goldwasser, Kao, and Schweller (Complexities for Generalized Models of…
We examine the dependence of a thermodynamic potential of a fluid on the geometry of its container. If motion invariance, continuity, and additivity of the potential are fulfilled, only four morphometric measures are needed to describe…
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…
We describe some of the important physical characteristics of the `pathways', i.e. dynamical processes, by which molecular, nanoscale and micron-scale self-assembly occurs. We highlight the fact that there exist features of self-assembly…
In this paper we develop a field-theoretic description for run and tumble chemotaxis, based on a density functional description of crystalline materials modified to capture orientational ordering. We show that this framework, with its…
The kinetics of ordering and concurrent ordering and clustering is analyzed with an equation of motion initially developed to account for dissipative processes in quantum systems. A simplified energy eigenstructure, or…
We study a generic model of self-assembling chains which can branch and form networks with branching points (junctions) of arbitrary functionality. The physical realizations include physical gels, wormlike micells, dipolar fluids and…
The kinetics and microstructure of solid-phase crystallization under continuous heating conditions and random distribution of nuclei are analyzed. An Arrhenius temperature dependence is assumed for both nucleation and growth rates. Under…
Based on statistical mechanics, a macroscopically homogeneous system, i.e., a single phase in the present context, is composed of many independent configurations that the system embraces. The macroscopical properties of the system are…