Advancing material property prediction: using physics-informed machine learning models for viscosity.

In materials science, accurately computing properties like viscosity, melting point, and glass transition temperatures solely through physics-based models is challenging. Data-driven machine learning (ML) also poses challenges in constructing ML models, especially in the material science domain where data is limited. To address this, we integrate physics-informed descriptors from molecular dynamics (MD) simulations to enhance the accuracy and interpretability of ML models.

Ligand Lipophilicity Determines Molecular Mechanisms of Nanoparticle Adsorption to Lipid Bilayers.

The interactions of ligand-functionalized nanoparticles with the cell membrane affect cellular uptake, cytotoxicity, and related behaviors, but relating these interactions to ligand properties remains challenging. In this work, we perform coarse-grained molecular dynamics simulations to study how the adsorption of ligand-functionalized cationic gold nanoparticles (NPs) to a single-component lipid bilayer (as a model cell membrane) is influenced by ligand end group lipophilicity. A set of 2 nm diameter NPs, each coated with a monolayer of organic ligands that differ only in their end groups, was simulated to mimic NPs recently studied experimentally.

Topological Analysis of Molecular Dynamics Simulations using the Euler Characteristic.

Molecular dynamics (MD) simulations are used in diverse scientific and engineering fields such as drug discovery, materials design, separations, biological systems, and reaction engineering. These simulations generate highly complex data sets that capture the 3D spatial positions, dynamics, and interactions of thousands of molecules. Analyzing MD data sets is key for understanding and predicting emergent phenomena and in identifying key drivers and tuning design knobs of such phenomena.

Predicting the Physicochemical Properties and Biological Activities of Monolayer-Protected Gold Nanoparticles Using Simulation-Derived Descriptors.

Gold nanoparticles are versatile materials for biological applications because their properties can be modulated by assembling ligands on their surface to form monolayers. However, the physicochemical properties and behaviors of monolayer-protected nanoparticles in biological environments are difficult to anticipate because they emerge from the interplay of ligand-ligand and ligand-solvent interactions that cannot be readily inferred from ligand chemical structure alone. In this work, we demonstrate that quantitative nanostructure-activity relationship (QNAR) models can employ descriptors calculated from molecular dynamics simulations to predict nanoparticle properties and cellular uptake.

Fast predictions of liquid-phase acid-catalyzed reaction rates using molecular dynamics simulations and convolutional neural networks.

The rates of liquid-phase, acid-catalyzed reactions relevant to the upgrading of biomass into high-value chemicals are highly sensitive to solvent composition and identifying suitable solvent mixtures is theoretically and experimentally challenging. We show that the complex atomistic configurations of reactant-solvent environments generated by classical molecular dynamics simulations can be exploited by 3D convolutional neural networks to enable accurate predictions of Brønsted acid-catalyzed reaction rates for model biomass compounds. We develop a 3D convolutional neural network, which we call SolventNet, and train it to predict acid-catalyzed reaction rates using experimental reaction data and corresponding molecular dynamics simulation data for seven biomass-derived oxygenates in water-cosolvent mixtures.

Lipophilicity of Cationic Ligands Promotes Irreversible Adsorption of Nanoparticles to Lipid Bilayers.

A mechanistic understanding of the influence of the surface properties of engineered nanomaterials on their interactions with cells is essential for designing materials for applications such as bioimaging and drug delivery as well as for assessing nanomaterial safety. Ligand-coated gold nanoparticles have been widely investigated because their highly tunable surface properties enable investigations into the effect of ligand functionalization on interactions with biological systems. Lipophilic ligands have been linked to adverse biological outcomes through membrane disruption, but the relationship between ligand lipophilicity and membrane interactions is not well understood.

The Interplay of Ligand Properties and Core Size Dictates the Hydrophobicity of Monolayer-Protected Gold Nanoparticles.

The hydrophobicity of monolayer-protected gold nanoparticles is a crucial design parameter that influences self-assembly, preferential binding to proteins and membranes, and other nano-bio interactions. Predicting the effects of monolayer components on nanoparticle hydrophobicity is challenging due to the nonadditive, cooperative perturbations to interfacial water structure that dictate hydrophobicity at the nanoscale. In this work, we quantify nanoparticle hydrophobicity by using atomistic molecular dynamics simulations to calculate local hydration free energies at the nanoparticle-water interface.

Recycling of multilayer plastic packaging materials by solvent-targeted recovery and precipitation.

Many plastic packaging materials manufactured today are composites made of distinct polymer layers (i.e., multilayer films).

Quantifying the Stability of the Hydronium Ion in Organic Solvents With Molecular Dynamics Simulations.

The solution-phase stability of the hydronium ion catalyst significantly affects the rates of acid-catalyzed reactions, which are ubiquitously utilized to convert biomass to valuable chemicals. In this work, classical molecular dynamics simulations were performed to quantify the stability of hydronium and chloride ions by measuring their solvation free energies in water, 1,4-dioxane (DIOX), tetrahydrofuran (THF), γ-valerolactone (GVL), N-methyl-2-pyrrolidone (NMP), acetone (ACE), and dimethyl sulfoxide (DMSO). By measuring the free energy for transferring a hydronium ion from pure water to pure organic solvent, we found that the hydronium ion is destabilized in DIOX, THF, and GVL and stabilized in NMP, ACE, and DMSO relative to water.

Inherently variable responses to glucocorticoid stress among endogenous retroviruses isolated from 23 mouse strains.

Active participation of endogenous retroviruses (ERVs) in disease processes has been exemplified by the finding that the HERV (human ERV)-W envelope protein is involved in the pathogenesis of multiple sclerosis, an autoimmune disease. We also demonstrated that injury-elicited stressors alter the expression of murine ERVs (MuERVs), both murine leukemia virus-type and mouse mammary tumor virus (MMTV)-type (MMTV-MuERV). In this study, to evaluate MMTV-MuERVs' responses to stress (e.

ERE database: a database of genomic maps and biological properties of endogenous retroviral elements in the C57BL/6J mouse genome.

Endogenous retroviral elements (EREs), a family of transposable elements, constitute a substantial fraction of mammalian genomes. It is expected that profiles of the ERE sequences and their genomic locations are unique for each individual. Comprehensive characterization of the EREs' genomic locations and their biological properties is essential for understanding their roles in the pathophysiology of the host.

Tropism, cytotoxicity, and inflammatory properties of two envelope genes of murine leukemia virus type-endogenous retroviruses of C57BL/6J mice.

Envelope (env) proteins of certain endogenous retroviruses (ERVs) participate in various pathophysiological processes. In this study, we characterized pathophysiologic properties of two murine leukemia virus-type ERV (MuLV-ERV) env genes cloned from the ovary of C57BL/6J mice. The two env genes (named ENV(OV1) and ENV(OV2)), with 1,926 bp coding region, originated from two MuLV-ERV loci on chromosomes 8 and 18, respectively.

Prevalent de novo somatic mutations in superantigen genes of mouse mammary tumor viruses in the genome of C57BL/6J mice and its potential implication in the immune system.

Background: Superantigens (SAgs) of mouse mammary tumor viruses (MMTVs) play a crucial role in T cell selection in the thymus in a T cell receptor (TCR) Vβ-specific manner and SAgs presented by B cells activate T cells in the periphery. The peripheral T cell repertoire is dynamically shaped by the steady induction of T cell tolerance against self antigens throughout the lifespan. We hypothesize that de novo somatic mutation of endogenous MMTV SAgs contributes to the modulation of the peripheral T cell repertoire.

Two-photon luminescence from polar bis-terpyridyl-stilbene derivatives of Ir(III) and Ru(II).

Four structurally related iridium(III) and ruthenium(II) complexes bearing two polar terpyridyl-stilbene derived chromophores 4-(4-{2-[4-(methoxy)phenyl]ethenyl}phenyl)-2,2'-6',2''-terpyridine (ttpyeneanisole) and 4-(4-{2-[phenyl]ethenyl}phenyl)-2,2'-6',2''-terpyridine (tpystilbene) have been synthesised and characterised in the solid state and in solution. In the solid state, the dihedral angle subtending the pyridyl and tolyl groups of 27.1° in the Ir(III) complex [Ir(ttpyeneanisole)(2)]·3PF(6) is more acute than in the Ru(II) derivative [Ru(tpystilbene)(2)]·2PF(6) (35.

Identification of putative endogenous retroviruses actively transcribed in the brain.

Remnant proviral sequences in the genome resulting from the ancient germline infection of exogenous retroviruses are called endogenous retroviruses (ERVs). The transcriptional activation of human ERVs (HERVs) in the brain of patients with some neurologic diseases suggests that ERVs may participate in certain disease processes in the central nervous system. In this study, we identified putative murine ERVs (MuERVs) which are transcriptionally active in the brain and characterized their biological properties to better understand the ERVs' roles in the brain pathophysiology.

Genome-wide expression profiles of endogenous retroviruses in lymphoid tissues and their biological properties.

Endogenous retroviruses (ERVs) constitute approximately 8-10% of the human and mouse genome. Some autoimmune diseases are attributed to the altered expression of ERVs. In this study, we examined the ERV expression profiles in lymphoid tissues and analyzed their biological properties.

Genome-wide changes in expression profile of murine endogenous retroviruses (MuERVs) in distant organs after burn injury.

Background: Previous studies have shown that burn-elicited stress signals alter expression of certain murine endogenous retroviruses (MuERVs) in distant organs of mice. These findings suggest that MuERVs may participate in a network of pathophysiologic events during post-burn systemic response. To gain a better understanding of the biological roles of MuERVs in post-burn systemic response, we examined the genome-wide changes in the MuERV expression profiles in distant organs and the biological properties of the putative-burn related MuERVs were characterized.