Brownian motion friction model

Inspired by Christiansen s treatment of a chemical reaction as a diffu-sional problem, Kramers studied the model of a particle in Brownian motion in a one-dimensional force field and predicted the existence of three fundamental kinetic regimes, depending on the magnitude of the friction. The basic hypothesis and results of this work will be summarized below, as many of the results most recently obtained using more sophisticated models are still best described by reference to Kramers original model and reduce to Kramers models when the appropriate limits are taken. 

The general principle of BD is based on Brownian motion, which is the random movement of solute molecules in dilute solution that result from repeated collisions of the solute with solvent molecules. In BD, solute molecules diffuse under the influence of systematic intermolecular and intramolecular forces, which are subject to frictional damping by the solvent, and the stochastic effects of the solvent, which is modeled as a continuum. The BD technique allows the generation of trajectories on much longer temporal and spatial scales than is feasible with molecular dynamics simulations, which are currently limited to a time of about 10 ns for medium-sized proteins. 

A third requirement is less absolute but still provide a useful consistency check for models that reduce to simple Brownian motion in the absence of external potentials The dissipation should be invariant to translation (e.g. the resulting friction coefficient should not depend on position). Although it can be validated only in representations that depend explicitly on the position coordinate, it can be shown that Redfield-type time evolution described in such (position or phase space) representations indeed satisfies this requirement under the required conditions. 

The construction of Cooper and Mann (7) for the surface viscosity includes the substrate effect by a model that represents the result of very frequent molecular collisions between the small substrate molecules and the larger molecules of the monolayer. This was done by adding a term to the Boltzmann equation for the 2D singlet distribution function that is equivalent to the friction coefficient term of the Fokker-Planck equation from which Equations 24 and 25 can be constructed. Thus a Brownian motion aspect was introduced into the kinetic theory of surface viscosity. It would be interesting to derive the collision frequency of Equation 19 using the better model (7) and observe how the T/rj variable of Equation 26 emerges. 

The first requirement is the definition of a low-dimensional space of reaction coordinates that still captures the essential dynamics of the processes we consider. Motions in the perpendicular null space should have irrelevant detail and equilibrate fast, preferably on a time scale that is separated from the time scale of the essential motions. Motions in the two spaces are separated much like is done in the Born-Oppenheimer approximation. The average influence of the fast motions on the essential degrees of freedom must be taken into account this concerns (i) correlations with positions expressed in a potential of mean force, (ii) correlations with velocities expressed in frictional terms, and iit) an uncorrelated remainder that can be modeled by stochastic terms. Of course, this scheme is the general idea behind the well-known Langevin and Brownian dynamics. 

In contrast to D, the prediction of other viscoelastic properties, such as the friction coefficient f or the zero-shear rate viscosity i/o, requires that the atomistic MD data be mapped upon a mesoscopic theoretical model. For unentangled polymer melts, such a model is the Rouse model, wherein a chain is envisioned as a set of Brownian particles connected by harmonic springs [25,28]. For entangled polymer melts, a better model that describes more accurately their dynamics is the tube or reptation model [26]. According to this model, the motion of an individual chain is restricted by the surrounding chains within a tube defined by the overall chain contour or primitive path. During the lifetime of this tube, any lateral motion of the chain is quenched. 

The Zimm model rests upon the Langevin equation for over-damped motion of the monomers, i.e., it applies for times larger than the Brownian time scale Tb 2> OTm/where is Stokes friction coefficient [12]. On such time scales, velocity correlation functions have decayed to zero and the monomer momenta are in equilibrium with the solvent Moreover, hydrodynamic interactions between the various parts of the polymer are assumed to propagate instantaneously. This is not the case in our simulations. First of all, the monomer inertia term is taken into account, which implies non-zero velocity autocorrelation functions. Secondly, the hydrodynamic interactions build up gradually. The center-of-mass velocity autocorrelation function displayed in Fig. 9 reflects these aspects. The correlation function exhibits a long-time tail, which decays as (vcm(t)vcm(O)) on larger time scales. The... 

So far we concentrated on the single particle crossing the barrier, but for a set of coupled equations of motion, as discussed in Section 9.8, the formalism is equally valid. The results of this chapter so far can be summarized using Eq. (9.33) as follows if the friction f = 0, we get classical TST if the friction acts on the reaction coordinate directly, we get Kramers s theory and if we let the friction act on a coordinate coupled to the, itself frictionless barrier transition coordinate, we get the Brownian oscillator model described in Section 9.8. 

---