Related papers: Nucleation rates from small scale atomistic simula…
Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of the system is altered by the bias. With infrequent…
We present a simulation technique to evaluate the most important quantity for nucleation processes: the nucleation barrier, i.e. the free energy of formation of the critical cluster. The method is based on stabilizing a small cluster by…
Computational studies of crystal nucleation can be impacted by finite size effects, primarily due to unphysical interactions between crystalline nuclei and their periodic images. It is, however, not always feasible to systematically…
Semiclassical instanton theory is a form of quantum transition-state theory which can be applied to computing thermal reaction rates for complex molecular systems including quantum tunneling effects. There have been a number of attempts to…
A nonperturbative correction to the thermal nucleation rate of critical bubbles in a first order phase transition is estimated. The correction originates from large-amplitude fluctuations which may be present before the transition occurs.…
A new combination of first principle molecular dynamics (MD) simulations with a rate equation model presented in the preceding paper (paper I) is applied to analyze in detail the scattering of argon atoms from a platinum (111) surface. The…
We apply quantum rate theory to calculate the transition rates as hydrogen or deuterium atoms escape from a vacancy trap in iron into a neighbouring metastable site. We determine transition rates and corresponding activation energies over a…
We investigated the nucleation process at the molecular level. Controlled sticking of individual atoms onto mass selected clusters over a wide mass range has been carried out for the first time. We measured the absolute unimolecular…
We present the statistical method as a direct extension of the mean first-passage time concept to the analysis of molecular dynamics simulation data of a phase transformation. According to the method, the mean first-passage time…
A practical method for finding free energy barriers for transitions in high-dimensional classical and quantum systems is presented and used to calculate the dissociative sticking probability of H2 on a metal surface within transition state…
We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach -- based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a…
Using the entropy $S$ as a reaction coordinate, we determine the free energy barrier associated with the formation of a liquid droplet from a supersaturated vapor for atomic and molecular fluids. For this purpose, we develop the $\mu VT-S$…
We study the dynamics of cosmological phase transitions in the case of small velocities of bubble walls, $v_w<0.1$. We discuss the conditions in which this scenario arises in a physical model, and we compute the development of the phase…
The evaluation of the sub-saturation nuclear equation of state at finite temperature requires a proper state counting of the internal partition sum of nuclei which are immersed in the background of their continuum states. This classical…
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…
The time evolution of the thermally activated decay rates is considered. This evolution is of particular importance for the recent nanoscale experiments discussed in the literature, where the potential barrier is relatively low (or the…
We estimate bubble-nucleation rates for cosmological phase transitions. We concentrate on the evaluation of the pre-exponential factor, for which we give approximate analytical expressions. Our approach relies on the use of a real…
The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
A description in terms of transition rates among cells is used to analyze self-diffusion of hard spheres in the fluid phase. Cell size is assumed much larger than the mean free path. Transition state theory is used to obtain an equation…