Forecasting molecular dynamics energetics of polymers in solution from supervised machine learning.

Machine learning techniques including neural networks are popular tools for chemical, physical and materials applications searching for viable alternative methods in the analysis of structure and energetics of systems ranging from crystals to biomolecules. Efforts are less abundant for prediction of kinetics and dynamics. Here we explore the ability of three well established recurrent neural network architectures for reproducing and forecasting the energetics of a liquid solution of ethyl acetate containing a macromolecular polymer-lipid aggregate at ambient conditions.

Distinctive Formation of PEG-Lipid Nanopatches onto Solid Polymer Surfaces Interfacing Solvents from Atomistic Simulation.

The interface between solid poly(lactic acid--glycolic acid), PLGA, and solvents is described by large-scale atomistic simulations for water, ethyl acetate, and the mixture of them at ambient conditions. Interactions at the interface are dominated by Coulomb forces for water and become overwhelmingly dispersive for the other two solvents. This effect drives a neat liquid-phase separation of the mixed solvent, with ethyl acetate covering the PLGA surface and water being segregated away from it.

Solutions and Condensed Phases of PEG from All-Atom Molecular Dynamics.

Extensive all-atom molecular dynamics studies of polyethylene glycol (PEG) when solvated and in the polymer bulk condensed phases were performed across a wide temperature range. We proposed two modified all-atom force field and observed the fate of the PEG macromolecule when solvated in water, water with 4% ethanol, and ethyl acetate. In aqueous solutions, the macromolecule collapsed into a prolate spheroidal ball-like structure while adopting a rather elongated coiled structure in ethyl acetate.

Modeling oxidised polypyrrole in the condensed phase with a novel force field.

A novel model potential is developed for simulating oxidised oligopyrroles in condensed phases. The force field is a coarse grained model that represents the pyrrole monomers as planar rigid bodies with fixed charge and dipole moment and the chlorine dopants as point atomic charges. The analytic function contains 17 adjustable parameters that are initially fitted on a database of small structures calculated within all-electron density functional theory.

Exploring with Molecular Dynamics the Structural Fate of PLGA Oligomers in Various Solvents.

This study focuses on the solvent effects that promote preferred solvated structures of polylactic--glycolic acid (PLGA) oligomers of molecular weight 278, 668, and 1449 u in ethyl acetate, water, and a mixture of both solvents. Our methodology consists of all-atom, explicit solvent molecular dynamics simulations for inspection of the solvated oligomer structures at ambient conditions. Parameters for the generalized Amber force field are developed in this work for the ethyl acetate liquid and the PLGA oligomers.

Modeling the Tertiary Structure of the Rift Valley Fever Virus L Protein.

A tertiary structure governs, to a great extent, the biological activity of a protein in the living cell and is consequently a central focus of numerous studies aiming to shed light on cellular processes central to human health. Here, we aim to elucidate the structure of the Rift Valley fever virus (RVFV) L protein using a combination of in silico techniques. Due to its large size and multiple domains, elucidation of the tertiary structure of the L protein has so far challenged both dry and wet laboratories.

Simulating the NaK Eutectic Alloy with Monte Carlo and Machine Learning.

Combining atomistic simulations and machine learning techniques can expedite significantly the materials discovery process. We present an application of such methodological combination for the prediction of the melting transition and amorphous-solid behavior of the NaK alloy at the eutectic concentration. We show that efficient prediction of these properties is possible via machine learning methods trained on the topological local structural properties.

Failure of logarithmic oscillators to serve as a thermostat for small atomic clusters.

A logarithmic oscillator has the outstanding property that the expectation value of its kinetic energy is constant for all stationary states. Recently the ansatz that this property can be used to define a Hamiltonian thermostat has been put forward and a suggestion has been made that this logarithmic oscillator weakly coupled to a small system would serve as a thermostat as long as few degrees of freedom are involved as is the case in atomic clusters. We have applied these ideas to a cluster of four Lennard-Jones atoms and inspected two different models of coupling between the cluster and the logarithmic oscillator in three dimensions.

Density functional theory study of neutral and oxidized thiophene oligomers.

The effect of oxidation on the energetics and structure of thiophene (Th) oligomers is studied with density functional theory at the B3PW91∕6-311++G(d,p) level. Neutral n-Th oligomers (2 < n < 13) are gently curved planar chains. Ionization potential and electron affinity results show that n-Th oligomers are easier to be oxidized as their chain length increases.

Theoretical investigation of the photophysics of methyl salicylate isomers.

The photophysics of methyl salicylate (MS) isomers has been studied using time-dependent density functional theory and large basis sets. First electronic singlet and triplet excited states energies, structure, and vibrational analysis were calculated for the ketoB, enol, and ketoA isomers. It is demonstrated that the photochemical pathway involving excited state intramolecular proton transfer (ESIPT) from the ketoB to the enol tautomer agrees well with the dual fluorescence in near-UV (from ketoB) and blue (from enol) wavelengths obtained from experiments.

Monte Carlo study of oligopyrroles in condensed phases.

A classical model potential to simulate pyrrole oligomers in condensed phases is developed in this work. The new potential contains ten parameters that are optimized on a database of energy points calculated within the density functional theory approach. Based on this potential the condensed phase of systems composed of pyrrole oligomers with 4 and 12 monomers is studied as a function of system density.

Energetics and vibrational analysis of methyl salicylate isomers.

Energetics and vibrational analysis study of six isomers of methyl salicylate in their singlet ground state and first excited triple state is put forward in this work at the density functional theory level and large basis sets. The ketoB isomer is the lowest energy isomer, followed by its rotamer ketoA. For both ketoB and ketoA their enolized tautomers are found to be stable as well as their open forms that lack the internal hydrogen bond.

Silicon carbide nanostructures: a tight binding approach.

A tight-binding model Hamiltonian is newly parametrized for silicon carbide based on fits to a database of energy points calculated within the density functional theory approach of the electronic energy surfaces of nanoclusters and the total energy of bulk 3C and 2H polytypes at different densities. This TB model includes s and p angular momentum symmetries with nonorthogonal atomic basis functions. With the aid of the new TB model, minima of silicon carbide cagelike clusters, nanotubes, ring-shaped ribbons, and nanowires are predicted.

Energetics, structure, and charge distribution of reduced and oxidized n-pyrrole oligomers: a density functional approach.

Polypyrrole is a conjugated polymer prototype of conducting polymers. The energetically preferred spatial conformation of n-pyrrole oligomers (n=1-24) in both the reduced and oxidized phases is obtained and analyzed in this paper within the hybrid density functional theory. Binding energies, gap energies, radius of gyration, end-to-end distance, and vibrational frequencies are reported as functions of oligomer length.

Energetics, structure, and electron detachment spectra of calcium and zinc neutral and anion clusters: a density functional theory study.

A hybrid density functional approach with very large basis sets was used for studying Ca2 through Ca19 and Zn3 through Zn11 neutral clusters and their cluster anions. Energetics, structure, and vibrational analysis of all these neutral clusters and cluster anions are reported. The calculated electron affinities are in excellent agreement with experiment displaying a characteristic kink at Ca10 and Zn10.