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Lattice models in biophysics represent a class of statistical-mechanical models which consider a biological macromacromolecule (such as DNA, protein, actin, etc.) as a lattice of units, each unit being in different states or conformations.
The crystal lattice parameters a, b, and c have the dimension of length. The three numbers represent the size of the unit cell , that is, the distance from a given atom to an identical atom in the same position and orientation in a neighboring cell (except for very simple crystal structures, this will not necessarily be distance to the nearest ...
Lattice proteins are highly simplified models of protein-like heteropolymer chains on lattice conformational space which are used to investigate protein folding. [1] Simplification in lattice proteins is twofold: each whole residue ( amino acid ) is modeled as a single "bead" or "point" of a finite set of types (usually only two), and each ...
A primitive cell is a unit cell that contains exactly one lattice point. For unit cells generally, lattice points that are shared by n cells are counted as 1 / n of the lattice points contained in each of those cells; so for example a primitive unit cell in three dimensions which has lattice points only at its eight vertices is considered to contain 1 / 8 of each of them. [3]
The geometry of the unit cell is defined as a parallelepiped, providing six lattice parameters taken as the lengths of the cell edges (a, b, c) and the angles between them (α, β, γ). The positions of particles inside the unit cell are described by the fractional coordinates ( x i , y i , z i ) along the cell edges, measured from a reference ...
In applied mathematics, a weighted planar stochastic lattice (WPSL) is a structure that has properties in common with those of lattices and those of graphs. In general, space-filling planar cellular structures can be useful in a wide variety of seemingly disparate physical and biological systems.
Cell-based models are mathematical models that represent biological cells as discrete entities. Within the field of computational biology they are often simply called agent-based models [1] of which they are a specific application and they are used for simulating the biomechanics of multicellular structures such as tissues. to study the influence of these behaviors on how tissues are organised ...
In either case, one needs to choose the three lattice vectors a 1, a 2, and a 3 that define the unit cell (note that the conventional unit cell may be larger than the primitive cell of the Bravais lattice, as the examples below illustrate). Given these, the three primitive reciprocal lattice vectors are also determined (denoted b 1, b 2, and b 3).