Related papers: Shape-free theory for the self-assembly kinetics i…
A simple phenomenological model for describing the conformational dynamics of biological macromolecules via the nonlinearity-induced instabilities is proposed. It is shown that the interaction between charges and bending degrees of freedom…
For classical system under constant composition, macroscopic structure in thermodynamically equilibrium state can be determined through the so-called canonical average, including sum over possible microscopic states on phase space. Although…
Microcanonical thermodynamics studies the operations that can be performed on systems with well-defined energy. So far, this approach has been applied to classical and quantum systems. Here we extend it to arbitrary physical theories,…
We consider an important class of self-assembly problems and using the formalism of stochastic thermodynamics, we derive a set of design principles for growing controlled assemblies far from equilibrium. The design principles constrain the…
Self-propulsion allows living systems to display unusual collective behavior. Unlike passive systems in thermal equilibrium, active matter systems are not constrained by conventional thermodynamic laws. A question arises however as to what…
In this study, a variational method for the inverse problem of self-assembly, i.e., a reconstruction of the interparticle interaction potential of a given structure, is applied to three-dimensional crystals. According to the method, the…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…
We have performed multicanonical computer simulations of a small system of short protein-like heteropolymers and found that their aggregation transition possesses similarities to first-order phase separation processes. Not being a phase…
The maximally-decoupled method has been considered as a theory to apply an basic idea of an integrability condition to certain multiple parametrized symmetries. The method is regarded as a mathematical tool to describe a symmetry of a…
A system of a metastable phase with a pseudo continuous set of the heterogeneous centers is considered. An analytical theory for kinetics of decay of the metastable phase in such a system is constructed. The free energy of formation of a…
In this work, we use a minimal model to introduce a framework for controlling self-assembly under the influence of time-dependent driving forces. We develop a mean-field thermodynamic framework that predicts the conditions required to…
We derive a dynamical field theory for self-propelled particles subjected to generic torques and forces by explicitly coarse-graining their microscopic dynamics, described by a many-body Fokker-Planck equation. The model includes both…
Predictions of relative stabilities of (competing) molecular crystals are of great technological relevance, most notably for the pharmaceutical industry. However, they present a long-standing challenge for modeling, as often minuscule free…
Self-assembly is a phenomenon observed in nature at all scales where autonomous entities build complex structures, without external influences nor centralised master plan. Modelling such entities and programming correct interactions among…
We review a recently developed micellization theory, which is based on a free-energy approach and offers several advantages over the conventional one, based on mass action and rate equations. As all the results are derived from a single…
Complexity Theory is highly interdisciplinary, therefore any regularities must hold on all levels of organization, independent on the nature of the system. An open question in science is how complex systems self-organize to produce emergent…
We show how any system with morphological degrees of freedom and locally limited free energy will, under the constraints of the free energy principle, evolve toward a neuromorphic morphology that supports hierarchical computations in which…
The phase field crystal (PFC) method has emerged as a promising technique for modeling materials with atomistic resolution on mesoscopic time scales. The approach is numerically much more efficient than classical density functional theory…
A geometrically nonlinear continuum mechanical theory is formulated for deformation and failure behaviors of amorphous polymers. The model seeks to capture material response over a range of loading rates, temperatures, and stress states…
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…