Modeling oceanic sedimentary methane hydrate growth through molecular dynamics simulation.

The crystallization process of methane hydrates in a confined geometry resembling seabed porous silica sedimentary conditions has been studied using molecular dynamics simulations. With this objective in mind, a fully atomistic quartz silica slit pore has been designed, and the temperature stability of a methane hydrate crystalline seed in the presence of water and guest molecule methane has been analyzed. NaCl ion pairs have been added in different concentrations, simulating salinity conditions up to values higher than average oceanic conditions.

Location and Concentration of Aromatic-Rich Segments Dictates the Percolating Inter-Molecular Network and Viscoelastic Properties of Ageing Condensates.

Maturation of functional liquid-like biomolecular condensates into solid-like aggregates has been linked to the onset of several neurodegenerative disorders. Low-complexity aromatic-rich kinked segments (LARKS) contained in numerous RNA-binding proteins can promote aggregation by forming inter-protein β-sheet fibrils that accumulate over time and ultimately drive the liquid-to-solid transition of the condensates. Here, atomistic molecular dynamics simulations are combined with sequence-dependent coarse-grained models of various resolutions to investigate the role of LARKS abundance and position within the amino acid sequence in the maturation of condensates.

Homogeneous ice nucleation rates for mW and TIP4P/ICE models through Lattice Mold calculations.

Freezing of water is the most common liquid-to-crystal phase transition on Earth; however, despite its critical implications on climate change and cryopreservation among other disciplines, its characterization through experimental and computational techniques remains elusive. In this work, we make use of computer simulations to measure the nucleation rate (J) of water at normal pressure under different supercooling conditions, ranging from 215 to 240 K. We employ two different water models: mW, a coarse-grained potential for water, and TIP4P/ICE, an atomistic nonpolarizable water model that provides one of the most accurate representations of the different ice phases.

Competition between ices Ih and Ic in homogeneous water freezing.

The role of cubic ice, ice Ic, in the nucleation of ice from supercooled water has been widely debated in the past decade. Computer simulations can provide insightful information about the mechanism of ice nucleation at a molecular scale. In this work, we use molecular dynamics to study the competition between ice Ic and hexagonal ice, ice Ih, in the process of ice nucleation.

The phase diagram of water from quantum simulations.

The phase diagram of water has been calculated from the TIP4PQ/2005 model, an empirical rigid non-polarisable model. The path integral Monte Carlo technique was used, permitting the incorporation of nuclear quantum effects. The coexistence lines were traced out using the Gibbs-Duhem integration method, once having calculated the free energies of the liquid and solid phases in the quantum limit, which were obtained via thermodynamic integration from the classical value by scaling the mass of the water molecule.

Can gas hydrate structures be described using classical simulations?

Quantum path-integral simulations of the hydrate solid structures have been performed using the recently proposed TIP4PQ/2005 model. By also performing classical simulations using this model, the impact of the nuclear quantum effects on the hydrates is highlighted; nuclear quantum effects significantly modify the structure, densities, and energies of the hydrates, leading to the conclusion that nuclear quantum effects are important not only when studying the solid phases of water but also when studying the hydrates. To analyze the validity of a classical description of hydrates, a comparison of the results of the TIP4P/2005 model (optimized for classical simulations) with those of TIP4PQ/2005 (optimized for path-integral simulations) was undertaken.