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The semiring of discrete dynamical systems is a simple algebraic model for modularity in deterministic systems. The objects of the semiring are finite transformations (viewed as directed graphs and regarded up to isomorphism), the sum of…
We numerically investigate nucleation processes in the transient dynamics of the two-dimensional complex Ginzburg-Landau equation towards its "frozen" state with quasi-stationary spiral structures. We study the transition kinetics from…
Soft matter systems are common in nature and make up nearly all the essential components necessary for life, from cells to the organelles within those cells. The ability of these soft materials to deform is crucial for the proper…
In this work we describe the thermodynamics and mechanism of CO$_2$ polymorphic transitions under pressure from form I to form III combining standard molecular dynamics, well-tempered metadynamics and committor analysis. We find that the…
We re-examine the physical origin of the polymer glass transition from the point of view of marginal rigidity, which is achieved above a certain number of intermolecular contacts. In the case of polymer chains in a melt / poor solvent, each…
Iron-sulfur clusters conduct a wide variety of biochemical reactions that are conserved across all domains of life. The hyperfine structure of reactive ligands of these clusters can be studied experimentally and theoretically by means of…
We use a semi-supervised, neural-network based machine learning technique, the confusion method, to investigate structural transitions in magnetic polymers, which we model as chains of magnetic colloidal nanoparticles characterized by…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…
A growing body of experiments display indirect evidence of icosahedral structures in supercooled liquid metals. Computer simulations provide more direct evidence but generally rely on approximate interatomic potentials of unproven accuracy.…
We report a numerical study of the diffusiophoresis of short polymers using non-equilibrium molecular dynamics simulations. More precisely, we consider polymer chains in a fluid containing a solute which has a concentration gradient, and…
Three fundamental segregation and pattern formation processes are known in granular mixtures in a rotating cylindrical drum: radial segregation, axial banding, and coarsening of the band pattern. While the mechanism for the first effect is…
Rigid particles pack into structures, such as sand dunes on the beach, whose overall stability is determined by the average number of contacts between particles. However, when packing spatially extended objects with flexible shapes,…
This paper presents results of a theoretical investigation of transport in a numerical model of a two-dimensional Kolmogorov flow. We investigate the changes in its mixing properties associated with transition from laminar regime to…
The relationship between polymer topology and bulk rheology remains a key question in soft matter physics. Architecture-specific constraints (or threadings) are thought to control the dynamics of ring polymers in ring-linear blends, which…
Localised turbulent structures such as puffs or oblique stripes are building blocks of the intermittency regimes in subcritical wall-bounded shear flows. These turbulent structures are investigated in incompressible pressure-driven annular…
We consider the dynamics of a translocation process of a flexible linear polymer through a nanopore into an environment of active rods in the {\it trans} side. Using Langevin dynamics simulations we find that the rods facilitate…
A cubic structure of polymer colloid complexes is studied. The technique of the research includes i) an analysis of well-known literature SAXS data; on this base, at some assumptions, ii) constructing a simple model to estimate geometric…
We consider a two-dimensional, tangentially active, semi-flexible, self-avoiding polymer to find a dynamical re-entrant transition between motile open chains and spinning achiral spirals with increasing activity. Utilizing probability…
A simple model of a polymer with long rigid segments which interact via excluded volume repulsions and short ranged attractions is proposed. The coil-globule transition of this model polymer is strongly first order, the globule is…
We use lattice-Boltzmann molecular dynamics (LBMD) simulations to study the compression of a confined polymer immersed in a fluid and pushed by a large spherical colloid with a diameter comparable to the channel width. We examined the…