Related papers: Shape-free theory for the self-assembly kinetics i…
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 grand canonical ensemble lies at the core of quantum and classical statistical mechanics. A small system thermalizes to this ensemble while exchanging heat and particles with a bath. A quantum system may exchange quantities represented…
Self-organization creates new order and shifts sub-boundaries while reorganizing energy and entropy within a control volume. This article examines pathway selection and tests whether maximizing the entropy generation rate can forecast…
The usual formulation of thermodynamics is based on the additivity of macroscopic systems. However, there are numerous examples of macroscopic systems that are not additive, due to the long-range character of the interaction among the…
Understanding thermodynamics in liquids at the atomic level is challenging because of strong atomic interactions and lack of symmetry. Recent prior theoretical works have focused on describing heat capacity of liquids in terms of…
Quantifying energy flows at nanometer scales promises to guide future research in a variety of disciplines, from microscopic control and manipulation, to autonomously operating molecular machines. A general understanding of the…
We consider the problem of recovering the three-dimensional atomic structure of a flexible macromolecule from a heterogeneous cryo-EM dataset. The dataset contains noisy tomographic projections of the electrostatic potential of the…
Molecular building blocks interacting at the nanoscale organize spontaneously into stable mono- layers that display intriguing long-range ordering motifs on the surface of atomic substrates. The patterning process, if appropriately…
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…
There is a growing interest in cylindrical structures of hard and soft particles. A promising new method to assemble such structures has recently been introduced by Lee et al. [T. Lee, K. Gizynski, and B. Grzybowski, Adv. Mater. 29, 1704274…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
Shape formation is a basic distributed problem for systems of computational mobile entities. Intensively studied for systems of autonomous mobile robots, it has recently been investigated in the realm of programmable matter. Namely, it has…
Interactions between the components in many-body systems can give rise to spontaneous formation of complex structures. Usually very little is known about the connection between the interactions and the resulting structure. Here we present a…
We present the phase diagram, in both the microcanonical and the canonical ensemble, of the Self-Gravitating-Ring (SGR) model, which describes the motion of equal point masses constrained on a ring and subject to 3D gravitational…
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.…
The physics of complex systems stands to greatly benefit from the qualitative changes in data availability and advances in data-driven computational methods. Many of these systems can be represented by interacting degrees of freedom on…
For systems that self assemble into finite-sized objects, it is sometimes convenient to compute the thermodynamics for a small system where a single assembly can form. However, we show that in the canonical ensemble the use of small systems…
Equation-free macroscale modelling is a systematic and rigorous computational methodology for efficiently predicting the dynamics of a microscale system at a desired macroscale system level. In this scheme, the given microscale model is…
We use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells.…
Thermodynamic properties of confined systems depend on sizes of the confinement domain due to quantum nature of particles. Here we show that shape also enters as a control parameter on thermodynamic state functions. By considering specially…