Related papers: Lattice model for self-folding at the microscale
Scaling of folding properties of proteins is studied in a toy system -- the lattice Go model with various two- and three- dimensional geometries of the maximally compact native states. Characteristic folding times grow as power laws with…
In the paper a self-consistent theoretical description of the lattice and magnetic properties of a model system with magnetoelastic interaction is presented. The dependence of magnetic exchange integrals on the distance between interacting…
We use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells.…
A recently introduced model describing the folding of the triangular lattice is generalized allowing for defects in the lattice and written as an Ising model with nearest-neighbor and plaquette interactions on the honeycomb lattice. Its…
An elastic surface model is investigated by using the canonical Monte Carlo simulation technique on triangulated spherical meshes. The model undergoes a first-order collapsing transition and a continuous surface fluctuation transition. The…
Rectangular standard Young tableaux with 2 or 3 rows are in bijection with $U_q(\mathfrak{sl}_2)$-webs and $U_q(\mathfrak{sl}_3)$-webs respectively. When $W$ is a web with a reflection symmetry, the corresponding tableau $T_W$ has a…
The nature of glassy states in realistic finite dimensions is still under fierce debate. Lattice models can offer valuable insights and facilitate deeper theoretical understanding. Recently, a disordered-interacting lattice model with…
We numerically elucidate the microscopic mechanisms controlling the relaxation dynamics of a three-dimensional lattice glass model that has static properties compatible with the approach to a random first-order transition. At low…
We use a three dimensional cubic lattice model of proteins to study their properties that determine folding to the native state. The protein chain is modeled as a sequence of $N$ beads. The interactions between beads are taken from a…
We investigate the iterative construction of discrete Laplacians on 2D square lattices, revealing emergent fractal-like patterns shaped by modular arithmetic. While classical 2222-style iterations reproduce known structures such as the…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…
We investigate a lattice-fluid model defined on a two-dimensional triangular lattice, with the aim of reproducing qualitatively some anomalous properties of water. Model molecules are of the "Mercedes Benz" type, i.e., they possess a D3…
We introduce a simple geometric model which describes the kinetics of fragmentation of d-dimensional objects. In one dimension our model coincides with the random scission model and show a simple scaling behavior in the long-time limit. For…
Self-assembly is a process which is ubiquitous in natural, especially biological systems. It occurs when groups of relatively simple components spontaneously combine to form more complex structures. While such systems have inspired a large…
Based on symmetry consideration of migration and shape deformations, we formulate phenomenologically the dynamics of cell crawling in two dimensions. Forces are introduced to change the cell shape. The shape deformations induce migration of…
Kirigami-inspired designs can enable self-folding three-dimensional materials from flat, two-dimensional sheets. Hierarchical designs of connected levels increase the diversity of possible target structures, yet they can lead to longer…
We present a generic framework for modelling three-dimensional deformable shells of active matter that captures the orientational dynamics of the active particles and hydrodynamic interactions on the shell and with the surrounding…
Developments in dynamical systems theory provides new support for the macroscale modelling of pdes and other microscale systems such as Lattice Boltzmann, Monte Carlo or Molecular Dynamics simulators. By systematically resolving subgrid…
Spin spirals form inside the magnetic layers of antiferromagnetic and noncollinearly-coupled magnetic multilayers in the presence of an external magnetic field. This spin structure can be modeled to extract the direct exchange stiffness of…