MassCCS: A High-Performance Collision Cross-Section Software for Large Macromolecular Assemblies.

Ion mobility mass spectrometry (IM-MS) techniques have become highly valued as a tool for structural characterization of biomolecular systems since they yield accurate measurements of the rotationally averaged collision cross-section (CCS) against a buffer gas. Despite its enormous potential, IM-MS data interpretation is often challenging due to the conformational isomerism of metabolites, lipids, proteins, and other biomolecules in the gas phase. Therefore, reliable and fast CCS calculations are needed to help interpret IM-MS data. In this work, we present MassCCS, a parallelized open-source code for computing CCS of molecules ranging from small organic compounds to massive protein assemblies at the trajectory method level of description using atomic and molecular buffer gas particles. The performance of the code is comparable to other available software for small molecules and proteins but is significantly faster for larger macromolecular assemblies. We performed extensive tests regarding accuracy, performance, and scalability with system size and number of CPU cores. MassCCS has proven highly accurate and efficient, with execution times under a few minutes, even for large (84.87 MDa) virus capsid assemblies with very modest computational resources. MassCCS is freely available at https://github.com/cces-cepid/massccs.

Stochastic sampling of the isothermal-isobaric ensemble: Phase diagram of crystalline solids from molecular dynamics simulation.

A methodology to sample the isothermal-isobaric ensemble using Langevin dynamics is proposed, which combines novel features of geometric integrators for the equations of motion. By employing the Trotter expansion, the methodology generates a robust, symmetric, and accurate numerical algorithm. In order to show that the proposed method correctly samples the phase-space, simulations in the isotropic NPT ensemble were carried out for two analytical examples. Also this method lets us study a solid-solid phase transition by conducting a fully flexible-cell molecular dynamics simulation. Additionally, we present an efficient method to determine the Gibbs free energy in a wide interval of pressure along an isothermal path, which allows us to determine the transition pressure in a driven by pressure solid-solid phase transition. Our calculations show that the methodology is highly suitable for the study of the phase diagram of crystalline solids.

Revisiting dynamics near a liquid-liquid phase transition in Si and Ga: the fragile-to-strong transition.

Using molecular dynamics simulations we analyze the dynamics of two atomic liquids that display a liquid-liquid phase transition (LLPT): Si described by the Stillinger-Weber potential and Ga as modeled by the modified embedded-atom model. In particular, our objective is to investigate the extent to which the presence of a dip in the self-intermediate scattering function is a manifestation of an excess of vibrational states at low frequencies and may be associated with a fragile-to-strong transition (FTST) across the LLPT, as suggested recently. Our results suggest a somewhat different picture. First, in the case of Ga we observe the appearance of an excess of vibrational states at low frequencies, even in the absence of the appearance of a dip in the self-intermediate scattering function across the LLPT. Second, studying the behavior of the shear viscosities traversing the LLPTs we find that both substances are fragile in character above and below their respective LLPT temperatures. Instead of a FTST in an absolute sense these findings are more in line with a view in which the LLPTs are accompanied by a transition from a more fragile to a less fragile liquid. Furthermore, we do not find this transition to correlate with the presence of a dip in the intermediate scattering function.

Dynamics near a liquid-liquid phase transition in a non-tetrahedral liquid: the case of gallium.

We use molecular simulation to analyze liquid dynamics in the vicinity of the liquid-liquid phase transition (LLPT) recently discovered in the modified embedded-atom model for elemental gallium. For this purpose we analyze the diffusive behavior in terms of the mean-squared displacement and self-intermediate scattering functions for two systems obtained by cooling the stable liquid through the LLPT at different cooling rates. The results show a pronounced heterogeneity of the dynamics upon the onset of the LLPT. Furthermore, it is found that this heterogeneity is closely correlated to the structural properties of the 9-fold coordinated high-density and 8-fold coordinated low-density liquid forms involved in the transition, showing a mixture of domains with very different diffusion time scales. The dynamics of the low-density liquid is found to be much more sluggish than that of the high-density form. Analysis of the energetics suggests that the origin of this difference is rooted in the fact that the cohesion in the former is significantly stronger than that in the latter.