Related papers: Lattice model for self-folding at the microscale
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
We describe a 3D percolation-type approach to modeling of the processes of aging and certain other properties of tissues analyzed as systems consisting of interacting cells. Lattice sites are designated as regular (healthy) cells, senescent…
We review models of random geometries based on the dynamical lattice approach. We discuss one dimensional model of simplicial complexes (branched polymers), two dimensional model of dynamical triangulations and four dimensional model of…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
To go beyond the simple model for the fold as two flexible surfaces or faces linked by a crease that behaves as an elastic hinge, we carefully shape and anneal a crease within a polymer sheet and study its mechanical response. First, we…
Triangular lattice models for pattern formation by hard-core soft-shell particles at interfaces are introduced and studied in order to determine the effect of the shell thickness and structure. In model I, we consider particles with…
The triangular lattice model with nearest-neighbor attraction and third-neighbor repulsion, introduced in [J. Pekalski, A. Ciach and N. G. Almarza, arXiv:1401.0801 [cond-mat.soft]] is studied by Monte Carlo simulation. Introduction of…
Macromolecules can form regular structures on inert surfaces. We have developed a combined empirical and modeling approach to derive the bonding. From experimental scanning tunneling microscopy (STM) images of structures formed on Au(111)…
Modeling folding surfaces with nonzero thickness is of practical interest for mechanical engineering. There are many existing approaches that account for material thickness in folding applications. We propose a new systematic and broadly…
A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical…
We present a Lattice-Boltzmann method for simulating self-propelling (active) colloidal particles in two-dimensions. Active particles with symmetric and asymmetric force distribution on its surface are considered. The velocity field…
We develop a mesoscopic lattice model to study the morphology formation in interacting ternary mixtures with evaporation of one component. As concrete application of our model, we wish to capture morphologies as they are typically arising…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
We present a three-dimensional lattice-gas model with trivial thermodynamics, but nontrivial dynamics. The model is characterized by each particle having its own random energy landscape. The equilibrium dynamics of the model were…
The folding kinetics of three-dimensional lattice Go models with side chains is studied using two different Monte Carlo move sets. A flexible move set based on single, double and triple backbone moves is found to be far superior compared to…
We show that chiral symmetry can be broken spontaneously in one-component systems with isotropic interactions, i.e. many-particle systems having maximal a priori symmetry. This is achieved by designing isotropic potentials that lead to…
In order to elucidate the process underpinning the apparently counterintuitive phenomena observed in the freefall experiments conducted by E. Hamm and J. G\'eminard [Amer. J. Phys. 78, 828 (2010)], we construct a simple dynamical model of a…
We study the problem of folding of the regular triangular lattice in the presence of a quenched random bending rigidity + or - K and a magnetic field h (conjugate to the local normal vectors to the triangles). The randomness in the bending…
We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…
Fitting two different materials is a versatile methodology in manufacturing complex structures. One of the canonical models for fitting is the snap-fit model, in which flexible materials and rigid structures are assembled by pushing their…