Accelerating Solvent Dynamics with Replica Exchange for Improved Free Energy Sampling

Molecular reactions in solution typically involve solvent exchange; for example, a surface must partly desolvate for a molecule to adsorb onto it. When these reactions are simulated, slow solvent dynamics can limit the sampling of configurations and reduce the accuracy of free energy estimates. Here, we combine Hamiltonian replica exchange (HREX) with well-tempered metadynamics (WTMD) to accelerate the sampling of solvent configurations orthogonal to the collective variable space. We compute the formation free energy of a carbonate vacancy in the calcite–water interface and find that the combination of WTMD with HREX significantly improves the sampling relative to WTMD without HREX

Nonequilibrium capture of impurities that completely block kinks during crystal growth

Some impurities cannot integrate into isolated kinks because they completely block the growth of the kinks to which they adsorb. For this class of impurity, we derive an equation for the amount that incorporates into a crystal during growth of the elementary step by assuming that such an impurity incorporates if and only if it gets captured between a kink and an antikink. We show that the impurity concentration in the crystal increases monotonically with the impurity concentration in the mother phase, but that it can vary non-monotonically with both the supersaturation of the mother phase and the kink density of the step. In contrast to other capture mechanisms, we find that weakly adsorbed impurities incorporate to an extent that is independent of the supersaturation when the supersaturation is high. Irrespective of the growth conditions, the amount of impurity that can incorporate into a crystal is limited by an upper bound determined by the kink density

Calcite Kinks Grow via a Multistep Mechanism

The classical model of crystal growth assumes that kinks grow via a sequence of independent adsorption events where each solute transitions from the solution directly to the crystal lattice site. Here, we challenge this view by showing that some calcite kinks grow via a multistep mechanism where the solute adsorbs to an intermediate site and only transitions to the lattice site upon the adsorption of a second solute. We compute the free energy curves for Ca and CO3 ions adsorbing to a large selection of kink types, and we identify kinks terminated both by Ca ions and by CO3 ions that grow in this multistep way

Electronic effects in high-energy radiation damage in iron

Electronic effects are believed to be important in high--energy radiation damage processes where high electronic temperature is expected, yet their effects are not currently understood. Here, we perform molecular dynamics simulations of high-energy collision cascades in $\alpha$-iron using the coupled two-temperature molecular dynamics (2T-MD) model that incorporates both effects of electronic stopping and electron-ion interaction. We subsequently compare it with the model employing the electronic stopping only, and find several interesting novel insights. The 2T-MD results in both decreased damage production in the thermal spike and faster relaxation of the damage at short times. Notably, the 2T-MD model gives a similar amount of the final damage at longer times, which we interpret to be the result of two competing effects: smaller amount of short-time damage and shorter time available for damage recovery.Comment: 8 pages, 6 figure

Electronic effects in high-energy radiation damage in tungsten

Although the effects of the electronic excitations during high-energy radiation damage processes are not currently understood, it is shown that their role in the interaction of radiation with matter is important. We perform molecular dynamics simulations of high-energy collision cascades in bcc-tungsten using the coupled two-temperature molecular dynamics (2T-MD) model that incorporates both the effects of electronic stopping and electron-phonon interaction. We compare the combination of these effects on the induced damage with only the effect of electronic stopping, and conclude in several novel insights. In the 2T-MD model, the electron-phonon coupling results in less damage production in the molten region and in faster relaxation of the damage at short times. These two effects lead to significantly smaller amount of the final damage at longer times.Comment: 7 pages, 7 figure

Calcite Kinetics for Spiral Growth and Two-Dimensional Nucleation

Calcite crystals grow by means of molecular steps that develop on {10.4} faces. These steps can arise stochastically via two-dimensional (2D) nucleation or emerge steadily from dislocations to form spiral hillocks. Here, we determine the kinetics of these two growth mechanisms as a function of supersaturation. We show that calcite crystals larger than ∼1 μm favor spiral growth over 2D nucleation, irrespective of the supersaturation. Spirals prevail beyond this length scale because slow boundary layer diffusion creates a low surface supersaturation that favors the spiral mechanism. Sub-micron crystals favor 2D nucleation at high supersaturations, although diffusion can still limit the growth of nanoscopic crystals. Additives can change the dominant mechanism by impeding spiral growth or by directly promoting 2D nucleation

Dynamical simulations of an electronically induced solid-solid phase transformation in tungsten

The rearrangement of a material's electron density during laser irradiation leads to modified nonthermal forces on the atoms that may lead to coherent atomic motions and structural phase transformation on very short time scales. We present ab initio molecular dynamics simulations of a martensitic solid-solid phase transformation in tungsten under conditions of strong electronic excitation. The transformation is ultrafast, taking just over a picosecond, and follows the tetragonal Bain path. To examine whether a solid-solid bcc-fcc phase transformation could occur during laser irradiation, we use two-temperature molecular dynamics (2T-MD) simulations with a specially developed potential dependent on the electronic temperature. Our simulations show that the occurrence of the solid-solid phase transformation is in competition with ultrafast nonthermally assisted melting with the strength of the electron-phonon coupling determining the lifetime of the new solid phase. In tungsten the melting transition is predicted to occur too rapidly for the fcc phase to be detectable during laser irradiation