MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC.

MoSDeF-GOMC is a python interface for the Monte Carlo software GOMC to the Molecular Simulation Design Framework (MoSDeF) ecosystem. MoSDeF-GOMC automates the process of generating initial coordinates, assigning force field parameters, and writing coordinate (PDB), connectivity (PSF), force field parameter, and simulation control files. The software lowers entry barriers for novice users while allowing advanced users to create complex workflows that encapsulate simulation setup, execution, and data analysis in a single script. All relevant simulation parameters are encoded within the workflow, ensuring reproducible simulations. MoSDeF-GOMC's capabilities are illustrated through a number of examples, including prediction of the adsorption isotherm for CO2 in IRMOF-1, free energies of hydration for neon and radon over a broad temperature range, and the vapor-liquid coexistence curve of a four-component surrogate for the jet fuel S-8. The MoSDeF-GOMC software is available on GitHub at https://github.com/GOMC-WSU/MoSDeF-GOMC.

py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD.

py-MCMD, an open-source Python software, provides a robust workflow layer that manages communication of relevant system information between the simulation engines NAMD and GOMC and generates coherent thermodynamic properties and trajectories for analysis. To validate the workflow and highlight its capabilities, hybrid Monte Carlo/molecular dynamics (MC/MD) simulations are performed for SPC/E water in the isobaric-isothermal (NPT) and grand canonical (GC) ensembles as well as with Gibbs ensemble Monte Carlo (GEMC). The hybrid MC/MD approach shows close agreement with reference MC simulations and has a computational efficiency that is 2 to 136 times greater than traditional Monte Carlo simulations. MC/MD simulations performed for water in a graphene slit pore illustrate significant gains in sampling efficiency when the coupled-decoupled configurational-bias MC (CD-CBMC) algorithm is used compared with simulations using a single unbiased random trial position. Simulations using CD-CBMC reach equilibrium with 25 times fewer cycles than simulations using a single unbiased random trial position, with a small increase in computational cost. In a more challenging application, hybrid grand canonical Monte Carlo/molecular dynamics (GCMC/MD) simulations are used to hydrate a buried binding pocket in bovine pancreatic trypsin inhibitor. Water occupancies produced by GCMC/MD simulations are in close agreement with crystallographically identified positions, and GCMC/MD simulations have a computational efficiency that is 5 times better than MD simulations. py-MCMD is available on GitHub at https://github.com/GOMC-WSU/py-MCMD.

Accurate determination of solvation free energies of neutral organic compounds from first principles.

The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools' computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation.

Erratum: Thermodynamic and Transport Properties of Tetrabutylphosphonium Hydroxide and Tetrabutylphosphonium Chloride-Water Mixtures via Molecular Dynamics Simulation.

The authors wish to make the following changes to the published paper as listed below [...].

Insight into Cellulose Dissolution with the Tetrabutylphosphonium Chloride-Water Mixture using Molecular Dynamics Simulations.

All-atom molecular dynamics simulations are utilized to determine the properties and mechanisms of cellulose dissolution using the ionic liquid tetrabutylphosphonium chloride (TBPCl)-water mixture, from 63.1 to 100 mol % water. The hydrogen bonding between small and large cellulose bundles with 18 and 88 strands, respectively, is compared for all concentrations. The Cl, TBP, and water enable cellulose dissolution by working together to form a cooperative mechanism capable of separating the cellulose strands from the bundle. The chloride anions initiate the cellulose breakup, and water assists in delaying the cellulose strand reformation; the TBP cation then more permanently separates the cellulose strands from the bundle. The chloride anion provides a net negative pairwise energy, offsetting the net positive pairwise energy of the peeling cellulose strand. The TBP-peeling cellulose strand has a uniquely favorable and potentially net negative pairwise energy contribution in the TBPCl-water solution, which may partially explain why it is capable of dissolving cellulose at moderate temperatures and high water concentrations. The cellulose dissolution declines rapidly with increasing water concentration as hydrogen bond lifetimes of the chloride-cellulose hydroxyl hydrogens fall below the cellulose's largest intra-strand hydrogen bonding lifetime.

Thermodynamic and Transport Properties of Tetrabutylphosphonium Hydroxide and Tetrabutylphosphonium Chloride-Water Mixtures via Molecular Dynamics Simulation.

Thermodynamic, structural, and transport properties of tetrabutylphosphonium hydroxide (TBPH) and tetrabutylphosphonium chloride (TBPCl)-water mixtures have been investigated using all-atom molecular dynamics simulations in response to recent experimental work showing the TBPH-water mixtures capability as a cellulose solvent. Multiple transitional states exist for the water-ionic liquid (IL) mixture between 70 and 100 mol% water, which corresponds to a significant increase in water hydrogen bonds. The key transitional region, from 85 to 92.5 mol% water, which coincides with the mixture's maximum cellulose solubility, reveals small and distinct water veins with cage structures formed by the TBP+ ions, while the hydroxide and chloride ions have moved away from the P atom of TBP+ and are strongly hydrogen bonded to the water. The maximum cellulose solubility of the TBPH-water solution at approximately 91.1 mol% water, appears correlated with the destruction of the TBP's interlocking structure in the simulations, allowing the formation of water veins and channeling structures throughout the system, as well as changing from a subdiffusive to a near-normal diffusive regime, increasing the probability of the IL's interaction with the cellulose polymer. A comparison is made between the solution properties of TBPH and TBPCl with those of alkylimidazolium-based ILs, for which water appears to act as anti-solvent rather than a co-solvent.

Correction of severe hypotension by oral pseudoephedrine in a patient with idiopathic autonomic dysfunction.

The purpose of this case study was to review the use of an oral alpha-adrenergic agent to correct severe vasopressor-dependent hypotension in a patient with idiopathic autonomic dysfunction. Autonomic dysfunction resulting in severe hypotension that requires intravenous vasopressors can present challenges in the treatment of critically ill patients. Most patients are weaned from intravenous vasopressor agents once severe sepsis has resolved. Because of worsening idiopathic autonomic dysfunction during recovery from sepsis, this 76-year-old woman required prolonged care in the intensive care unit. Oral alpha-adrenergic agonist therapy in the form of pseudoephedrine proved to be a valuable treatment option to wean this patient off the vasopressor dependence and allow for placement in a long-term care facility.

Improving biocatalytic activity of enzyme-loaded nanofibers by dispersing entangled nanofiber structure.

A simple and efficient way of dispersing hydrophobic nanofibers in aqueous solution was devised, and its utility in production and application of enzyme-loaded nanofibers was demonstrated. Polystyrene-based nanofibers were produced via an electro-spinning process. A small amount of maleic anhydride group in the polystyrene fiber was used for covalent attachment of lipase onto the fiber surface. The pristine polystyrene nanofibers are hydrophobic and aggregate in water, forming a tightly collapsed clump. These nanofibers can be dispersed in a surfactant-free aqueous solution via a simple alcohol pretreatment. The tightly aggregated electro-spun polystyrene nanofibers can be dispersed into a loosely entangled structure in aqueous alcohol solution. Once treated with aqueous alcohol solution, the polystyrene nanofibers remain dispersed even in DI water as long as the nanofibers are not dried during the washing step. The dispersion of polystyrene nanofibers increases the enzyme loading up to approximately 8 times and augments the steady-state conversion of a continuous flow reactor filled with enzyme-loaded nanofibers.