Related papers: Two-dimensional structure in a generic model of tr…
We employ extensive NPT molecular dynamics simulations to explore the thermal transitions of two-dimensional colloidal crystals interacting via a core-softened potential with competing length scales. The system stabilizes three distinct…
The existence of normal deterministic diffusion in dynamical systems with a two-dimensional phase space tiled by regular triangles (or their unions into regular hexagons) is proven.
Two-dimensional transition metal dichalcogenides (TMDs) can adopt one of several possible structures, with the most common being the trigonal prismatic and octahedral symmetry phases. Since the structure determines the electronic…
Positional ordering of a two-dimensional fluid of hard disks is examined in such narrow tubes where only the nearest-neighbor interactions take place. Using the exact transfer-matrix method the transverse and longitudinal pressure…
We study the temperature dependence of static and dynamic responses of Coulomb interacting particles in two-dimensional traps across the thermal crossover from an amorphous solid- to liquid-like behaviors. While static correlations, that…
We present a scaled particle density functional study of two-dimensional binary mixtures of hard convex particles with one or both species being ellipses. In particular, we divide our study into two parts. The first part is devoted to the…
Using molecular dynamics simulation, we study structural and dynamical heterogeneities at melting in two-dimensional one-component systems with 36000 particles. Between crystal and liquid we find intermediate hexatic states, where the…
Determining protein structures at an atomic level remains a significant challenge in structural biology. We introduce $\texttt{RecCrysFormer}$, a hybrid model that exploits the strengths of transformers with the aim of integrating…
The phase-field-crystal model is used to access the structure and thermodynamics of interfaces between two coexisting liquid crystalline phases in two spatial dimensions. Depending on the model parameters there is a variety of possible…
We investigate a behavior of a core-softened system in a thin slit pore (the width of the pore is equil to three diameters of the particles). In previous studies it was shown that strongly confined systems form crystalline phases which…
Layered, hexagonal crystal structures, like zeta and eta phases, play an important role in ultra-high temperature ceramics, often significantly increasing toughness of carbide composites. Despite their importance open questions remain about…
In this research, formation of finite two-dimensional (2D) plasma crystals was numerically simulated. The structure was investigated for systems with various Debye length and it was found there is a transition from a complete hexagonal…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
Collagen fibrils, cable-like assemblies of long biological molecules, are dominant components of connective tissues. Their determinant morphological and functional roles motivated a large number of studies concerning their formation and…
In continuation of our work in [A.P. Gantapara et al., Phys. Rev. Lett. 111, 015501 (2013)], we investigate here the thermodynamic phase behavior of a family of truncated hard cubes, for which the shape evolves smoothly from a cube via a…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
We study the statistical mechanics of double-stranded semi-flexible polymers using both analytical techniques and simulation. We find a transition at some finite temperature, from a type of short range order to a fundamentally different…
Multi-step assembly of individual protein building blocks is key to the formation of essential higher-order structures inside and outside of cells. Optical tweezers is a technique well suited to investigate the mechanics and dynamics of…
Quasicrystals have been observed in a variety of materials ranging from metal alloys to block copolymers. However, their structural and dynamical properties cannot be readily described in terms of conventional solid-state models of liquids…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…