mdFoam+: Advanced molecular dynamics in OpenFOAM

This paper introduces mdFoam+, which is an MPI parallelised molecular dynamics (MD) solver implemented entirely within the OpenFOAM software framework. It is open-source and released under the same GNU General Public License (GPL) as OpenFOAM. The source code is released as a publicly open software repository that includes detailed documentation and tutorial cases. Since mdFoam+ is designed entirely within the OpenFOAM C++ object-oriented framework, it inherits a number of key features. The code is designed for extensibility and flexibility, so it is aimed first and foremost as an MD research tool, in which new models and test cases can be developed and tested rapidly. Implementing mdFoam+ in OpenFOAM also enables easier development of hybrid methods that couple MD with continuum-based solvers. Setting up MD cases follows the standard OpenFOAM format, as mdFoam+ also relies upon the OpenFOAM dictionary-based directory structure. This ensures that useful pre- and post-processing capabilities provided by OpenFOAM remain available even though the fully Lagrangian nature of an MD simulation is not typical of most OpenFOAM applications. Results show that mdFoam+ compares well to another well-known MD code (e.g. LAMMPS) in terms of benchmark problems, although it also has additional functionality that does not exist in other open-source MD codes

Efficient construction of free energy profiles of breathing metal–organic frameworks using advanced molecular dynamics simulations

In order to reliably predict and understand the breathing behavior of highly flexible metal–organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials

Exploring new frontiers in modeling complex zeolite-catalyzed reactions using advanced molecular dynamics techniques

We show the potential of advanced molecular dynamics techniques to obtain insight into the complex MTO process by thoroughly studying proton mobility and mapping free energy surfaces of reaction steps at high temperature. The applied methodology can be used to unravel any complex zeolitic process at the nanometer scale level

Effects of hydroxyapatite (0001) Ca2+/Mg2+ substitution on adsorbed D-ribose ring puckering

Advanced Molecular Dynamics (MD) simulation protocols have been used to assess the ring puckering of cyclic D-ribose when the sugar is adsorbed on the most stable (0001) facet of calcium hydroxyapatite (HAp). In addition, sugar¿mineral interactions, which are crucial for transfection processes and prebiotic chemistry, have been studied for systems in which the Ca2+ ions of the above mentioned HAp facet were totally or partially replaced by Mg2+. The latter replacement is spatially and quantitatively limited and has been found to cause important alterations in the conformational behavior of D-ribose that are similar to those suffered in hairpin RNA from A to B helical structures. Accordingly, replacement of Ca2+ by Mg2+ has a dramatic effect on the functionality of the nucleic acid. These changes have been related to both the substitution site on the surface and the amount of ions. Our results show that when replacement by Mg2+ occurs in OH--coordinated Ca2+ ions, Mg2+¿D-ribose interactions are strong enough to prevent the interactions between the hydroxyl groups of the sugar and the remaining Ca2+ ions.Peer ReviewedPostprint (published version

Immunoproteasome and Non-Covalent Inhibition: Exploration by Advanced Molecular Dynamics and Docking Methods

The selective inhibition of immunoproteasome is a valuable strategy to treat autoimmune, inflammatory diseases, and hematologic malignancies. Recently, a new series of amide derivatives as non-covalent inhibitors of the β1i subunit with Ki values in the low/submicromolar ranges have been identified. Here, we investigated the binding mechanism of the most potent and selective inhibitor, N-benzyl-2-(2-oxopyridin-1(2H)-yl)propanamide (1), to elucidate the steps from the ligand entrance into the binding pocket to the ligand-induced conformational changes. We carried out a total of 400 ns of MD-binding analyses, followed by 200 ns of plain MD. The trajectories clustering allowed identifying three representative poses evidencing new key interactions with Phe31 and Lys33 together in a flipped orientation of a representative pose. Further, Binding Pose MetaDynamics (BPMD) studies were performed to evaluate the binding stability, comparing 1 with four other inhibitors of the β1i subunit: N-benzyl-2-(2-oxopyridin-1(2H)-yl)acetamide (2), N-cyclohexyl-3-(2-oxopyridin-1(2H)-yl)propenamide (3), N-butyl-3-(2-oxopyridin-1(2H)-yl)propanamide (4), and (S)-2-(2-oxopyridin-1(2H)-yl)-N,4-diphenylbutanamide (5). The obtained results in terms of free binding energy were consistent with the experimental values of inhibition, confirming 1 as a lead compound of this series. The adopted methods provided a full dynamic description of the binding events, and the information obtained could be exploited for the rational design of new and more active inhibitors

Intrusion and extrusion of water in hydrophobic nanopores

Heterogeneous systems composed of hydrophobic nanoporous materials and water are capable, depending on their characteristics, of efficiently dissipating (dampers) or storing ("molecular springs") energy. However, it is difficult to predict their properties based on macroscopic theories-classical capillarity for intrusion and classical nucleation theory (CNT) for extrusion-because of the peculiar behavior of water in extreme confinement. Here we use advanced molecular dynamics techniques to shed light on these nonclassical effects, which are often difficult to investigate directly via experiments, owing to the reduced dimensions of the pores. The string method in collective variables is used to simulate, without artifacts, the microscopic mechanism of water intrusion and extrusion in the pores, which are thermally activated, rare events. Simulations reveal three important nonclassical effects: the nucleation free-energy barriers are reduced eightfold compared with CNT, the intrusion pressure is increased due to nanoscale confinement, and the intrusion/extrusion hysteresis is practically suppressed for pores with diameters below 1.2 nm. The frequency and size dependence of hysteresis exposed by the present simulations explains several experimental results on nanoporous materials. Understanding physical phenomena peculiar to nanoconfined water paves the way for a better design of nanoporous materials for energy applications; for instance, by decreasing the size of the nanopores alone, it is possible to change their behavior from dampers to molecular springs

Structure Property and Prediction of Novel Materials using Advanced Molecular Dynamics Techniques: Novel Carbons, Germaniums and High-Performance Thermoelectrics

By means of advanced molecular dynamic techniques, we predict the stability of novel materials based on carbon, germanium and PbSe. This topological solutions have been studied and characterised at a DFT/DFTB level of theory and interesting optical, mechanical, electronic and heat transport properties have been pointed out