Relationship between Capillary Wettability, Mass, and Momentum Transfer in Nanoconfined Water: The Case of Water in Nanoslits of Graphite and Hexagonal Boron Nitride.

The flow of water confined in nanosize capillaries is subject of intense research due to its relevance in the fabrication of nanofluidic devices and in the development of theories for fluid transport in porous media. Here, using molecular dynamics simulations carried out on 2D capillaries made up of graphite, hexagonal boron nitride (hBN) and a mix of the two, and of sizes from subnanometer to few nanometers, we investigate the relationship between the wettability of the wall capillary, the water diffusion, and its flow rate. We find that the water diffusion is decoupled from its flow properties as the former is not affected either by the height or chemistry of the capillary (except for the subnanometer slits), while the latter is dependent on both.

Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units.

The generalized Born with molecular volume and solvent accessible surface area (GBMV2/SA) implicit solvent model provides an accurate description of molecular volume and has the potential to accurately describe the conformational equilibria of structured and disordered proteins. However, its broader application has been limited by the computational cost and poor scaling in parallel computing. Here, we report an efficient implementation of both the electrostatic and nonpolar components of GBMV2/SA on graphics processing unit (GPU) within the CHARMM/OpenMM module.

Multiscale Aggregation of the Amyloid Aβ Peptide: From Disordered Coagulation and Lateral Branching to Amorphous Prefibrils.

In this work we investigate the multiscale dynamics of the aggregation process of an amyloid peptide, Aβ. By performing massive coarse-grained simulations at the quasi-atomistic resolution and including hydrodynamic effects, we followed the formation and growth of a large elongated aggregate and its slow structuring. The elongation proceeds via a two-step nucleation mechanism with disordered aggregates formed initially and subsequently fusing to elongate the amorphous prefibril.

Multiscale simulation of molecular processes in cellular environments.

We describe the recent advances in studying biological systems via multiscale simulations. Our scheme is based on a coarse-grained representation of the macromolecules and a mesoscopic description of the solvent. The dual technique handles particles, the aqueous solvent and their mutual exchange of forces resulting in a stable and accurate methodology allowing biosystems of unprecedented size to be simulated.

Hydrodynamic effects on β-amyloid (16-22) peptide aggregation.

Computer simulations based on simplified representations are routinely used to explore the early steps of amyloid aggregation. However, when protein models with implicit solvent are employed, these simulations miss the effect of solvent induced correlations on the aggregation kinetics and lifetimes of metastable states. In this work, we apply the multi-scale Lattice Boltzmann Molecular Dynamics technique (LBMD) to investigate the initial aggregation phases of the amyloid Aβ16-22 peptide.

Structural, energetic, and electronic properties of La(III)-dimethyl sulfoxide clusters.

By using accurate density functional theory calculations, we have studied the cluster complexes of a La(3+) ion interacting with a small number of dimethyl sulfoxide (DMSO) molecules of growing size (from 1 to 12). Extended structural, energetic, and electronic structure analyses have been performed to provide a complete picture of the physical properties that are the basis of the interaction of La(III) with DMSO. Recent experimental data in the solid and liquid phase have suggested a coordination number of 8 DMSO molecules with a square antiprism geometry arranged similarly in the liquid and crystalline phases.