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In this paper, a simple case of Bayesian mechanics under the free energy principle is formulated in axiomatic terms. We argue that any dynamical system with constraints on its dynamics necessarily looks as though it is performing inference…
It can be fruitful to view two-component physical systems of attractive monomers, A and B, ``chemically'' in terms of a reaction A + B <-> C, where C = AB is an associated pair or complex. We show how to construct free energies in the…
The decomposition kinetics of a solid-solution into separate phases are analyzed with an equation of motion initially developed to account for dissipative processes in quantum systems. This equation and the steepest-entropy-ascent quantum…
Although pathway-specific kinetic theories are fundamentally important to describe and understand reversible polymerisation kinetics, they come in principle at a cost of having a large number of system-specific parameters. Here, we…
We present a simple mesoscale field theory inspired by rate-independent plasticity that reflects the symmetry of the deformation process. We parameterize the plastic deformation by a scalar field which evolves with loading. The evolution…
Construction of the microscopic theory of large-amplitude collective motion, capable of describing a wide variety of quantum collective phenomena in nuclei, is a long-standing and fundamental subject in the study of nuclear many-body…
Alternative approach for description of the non-equilibrium phenomena arising in solids at a severe external loading is analyzed. The approach is based on the new form of kinetic equations in terms of the internal and modified free energy.…
We present the first simulations of the self-assembly kinetics of the gyroid cubic mesophase using a Boltzmann transport method. No macroscopic parameters are included in the model and three-dimensional hydrodynamics is emergent from the…
We discuss general thermodynamic properties of molecular structure formation processes like protein folding by means of simplified, coarse-grained models. The conformational transitions accompanying these processes exhibit similarities to…
For classical discrete systems under constant composition, a set of microscopic state dominantly contributing to thermodynamically equilibrium structure should depend on temperature and energy through Boltzmann factor, exp(-bE). Despite…
Inspired by the Turing mechanism for pattern formation, we propose a simple self-propelled particle model with short-ranged alignment and anti-alignment at larger distances. It is able to produce orientationally ordered states, periodic…
Equilibrium phase transitions usually emerge from the microscopic behavior of many-body systems and are associated to interesting phenomena such as the generation of long-range order and spontaneous symmetry breaking. They can be defined…
It is believed that thermodynamic laws are associated with random processes occurring in the system and, therefore, deterministic mechanical systems cannot be described within the framework of the thermodynamic approach. In this paper, we…
Simulations of charge transport in amorphous semiconductors are often performed in microscopically sized systems. As a result, charge carrier mobilities become system-size dependent. We propose a simple method for extrapolating a…
Although coarse-grained models have been widely used to explain exotic phenomena in complex fluids, such as droplet formation in living cells, these conventional approaches often fail to capture the intricate microscopic degrees of freedom…
Descriptions of molecular systems usually refer to two distinct theoretical frameworks. On the one hand the quantum pure state, i.e. the wavefunction, of an isolated system which is determined to calculate molecular properties and to…
A force-free granular gas is considered with impact-velocity dependent coefficient of restitution as it follows from the model of viscoelastic particles. We analyze structure formation in this system by means of three independent methods:…
The kinetics of aggregation in a monolayer of magnetic particles are studied using stochastic dynamics computer simulations. At low densities (<8% coverage) the equilibrium structure is made up of chains and rings; the primary mechanisms by…
Investigations of the phase transitions and self-organization in the magnetic aggregates are of the fundamental and applied interest. The long-range ordering structures described in the Tom\'anek's systematization (M. Yoon, and D.…
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…