ABSTRACT Modeling and simulation are transforming all fields of biology. Tools like AlphaFold have revolutionized structural biology, while molecular dynamics simulations provide invaluable insights into the behavior macromolecules in solution or on membranes. In contrast, we lack effective tools to represent dynamic endomembrane system. Static diagrams that connect organelles with arrows used depict transport across space time but fail specify underlying mechanisms. This static...

In this paper, the percolation of (a) linear segments size k and (b) k-mers different structures forms deposited on a square lattice contaminated with previously adsorbed impurities have been studied. The or diluted is built by randomly selecting fraction elements (either bonds sites) which are considered forbidden for deposition. Results obtained extensive use finite scaling theory. Thus, in order to test universality phase transition occurring system, numerical values critical exponents...

A two-dimensional lattice-gas model with square symmetry is investigated by using the real-space renormalization group (RSRG) approach blocks of different size and symmetries. It has been shown that precision method depends strongly not only on number sites in block but also its symmetry. In general, accuracy increases block. The most accurate results have obtained for largest cluster containing 34 sites. minimal relative error determining critical values interaction parameter equal to...

A two-dimensional lattice-gas model with triangular symmetry is investigated by using the real-space renormalization group (RSRG) approach blocks of different size and symmetries. It has been shown that precision this method depends strongly not only on number sites in block but also its symmetry. In general, accuracy increases block. Using RSRG method, we have explored phase diagrams a Ising spin lattice gas pair lateral repulsive interactions. We calculated: (i) adsorption isotherms...

In the Edwards-Anderson model of spin glasses with a bimodal distribution bonds, degeneracy ground state allows one to define structure called backbone, which can be characterized by rigid lattice (RL), consisting bonds that retain their frustration (or lack it) in all states. this work we have performed detailed numerical study properties RL, both two-dimensional (2D) and three-dimensional (3D) lattices. Whereas 3D find strong evidence for percolation thermodynamic limit, 2D our results...

A generalization of the classical monomer site-bond percolation problem is studied in which linear k-uples nearest neighbor sites (site k-mers) and bonds (bond are independently occupied at random on a square lattice. We called this model polyatomic species or k-mer percolation. Motivated by considerations cluster connectivity, we have used two distinct schemes (denoted as S intersection B union B) for In B(S B), points said to be connected if sequence (or) joins them. By using Monte Carlo...

We study the phase stability of Edwards-Anderson spin glass model by analyzing domain-wall energy. For a bimodal $\ifmmode\pm\else\textpm\fi{}J$ distribution bonds, topological analysis ground state allows us to separate system into two regions: backbone and its environment. find that distributions energies are very different in these regions for three-dimensional (3D) case. Although turns out have high stability, combined effect excitations correlations produces low global displayed as...

The chemical diffusion coefficient D for noninteracting particles on heterogeneous surfaces with different energetic topographies is studied by Monte Carlo simulation. Two kinds of are considered: strongly correlated patches and weakly amorphous surfaces. Topography effects clearly identified due to the fact that no adsorbate−adsorbate interactions competing. These strong depend trap−barrier feature spatial correlation length adsorptive energy. dependence temperature T does not follow, in...

The adsorption of binary mixtures with non-additive lateral interactions has been studied through grand canonical Monte Carlo simulations in the framework lattice-gas model. traditional assumption additive is replaced a more general one including non-pairwise interactions. It assumed that energy linking certain atom any its nearest neighbors strongly depends on state occupancy first coordination sphere such an adatom. process monitored isotherms and differential heats adsorption. Different...

In this paper the percolation of monomers on a square lattice is studied as particles interact with either repulsive or attractive energies. By means finite-size scaling analysis, critical exponents and collapsing fraction percolating are found. A phase diagram separating from non-percolating region determined. The main features discussed in terms simple considerations related to interactions present problem. influence transitions occurring system reflected by diagram. addition, treatment...

In the present paper, connection between surface order-disorder phase transitions and percolating properties of adsorbed has been studied. For this purpose, four lattice-gas models in presence repulsive interactions have considered. Namely, monomers on honeycomb, square, triangular lattices, dimers (particles occupying two adjacent adsorption sites) square substrates. By using Monte Carlo simulation finite-size scaling analysis, we obtain percolation threshold θc adlayer, which presents an...