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In statistical mechanics, the Zimm–Bragg model is a helix-coil transition model that describes helix-coil transitions of macromolecules, usually polymer chains. Most models provide a reasonable approximation of the fractional helicity of a given polypeptide; the Zimm–Bragg model differs by incorporating the ease of propagation (self-replication) with respect to nucleation.
complete, massive, helicity, color, decay chain what is MG5: HA (automatic generation) Output PD: Grace: SM/MSSM 2->n 2->6 complete,massive,helicity,color Manual v2.0: HA Output PD: CompHEP: Model Max FS Tested FS Short description Publication method Output Status CalcHEP: Model Max FS Tested FS Short description Publication: Method Output ...
Synthetic molecular motors are molecular machines capable of continuous directional rotation under an energy input. [2] Although the term "molecular motor" has traditionally referred to a naturally occurring protein that induces motion (via protein dynamics), some groups also use the term when referring to non-biological, non-peptide synthetic motors.
The helicity of a particle is positive (" right-handed") if the direction of its spin is the same as the direction of its motion and negative ("left-handed") if opposite. Helicity is conserved. [1] That is, the helicity commutes with the Hamiltonian, and thus, in the absence of external forces, is time-invariant. It is also rotationally ...
Stochastic thermodynamics is an emergent field of research in statistical mechanics that uses stochastic variables to better understand the non-equilibrium dynamics present in many microscopic systems [1] such as colloidal particles, biopolymers (e.g. DNA, RNA, and proteins), enzymes, and molecular motors. [a] [5] [clarify]
OPLS simulations in aqueous solution typically use the TIP4P or TIP3P water model. A distinctive feature of the OPLS parameters is that they were optimized to fit experimental properties of liquids, such as density and heat of vaporization, in addition to fitting gas-phase torsional profiles.
The two-component helicity eigenstates satisfy ^ (^) = (^) where are the Pauli matrices, ^ is the direction of the fermion momentum, = depending on whether spin is pointing in the same direction as ^ or opposite.
Car–Parrinello molecular dynamics or CPMD refers to either a method used in molecular dynamics (also known as the Car–Parrinello method) or the computational chemistry software package used to implement this method. [1] The CPMD method is one of the major methods for calculating ab-initio molecular dynamics (ab-initio MD or AIMD).