Studying the Effects of Dissolved Noble Gases and High Hydrostatic Pressure on the Spherical DOPC Bilayer Using Molecular Dynamic Simulations.

Fine-grained molecular dynamics simulations have been conducted to depict lipid objects enclosed in water and interacting with a series of noble gases dissolved in the medium. The simple point-charge (SPC) water system, featuring a boundary composed of 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) molecules, maintained stability throughout the simulation under standard conditions. This allowed for the accurate modeling of the effects of hydrostatic pressure at an ambient pressure of 25 bar. The chosen pressure references the 240 m depth of seawater: the horizon frequently used by commercial divers, who comprise the primary patient population of the neurological complication of inert gas narcosis and the consequences of high-pressure neurological syndrome. To quantify and validate the neurological effects of noble gases and discriminate them from high hydrostatic pressure, we reduced the dissolved gas molar concentration to 1.5%, three times smaller than what we previously tested for the planar bilayer (3.5%). The nucleation and growth of xenon, argon and neon nanobubbles proved consistent with the data from the planar bilayer simulations. On the other hand, hyperbaric helium induces only a residual distorting effect on the liposome, with no significant condensed gas fraction observed within the hydrophobic core. The bubbles were distributed over a large volume-both in the bulk solvent and in the lipid phase-thereby causing substantial membrane distortion. This finding serves as evidence of the validity of the multisite distortion hypothesis for the neurological effect of inert gases at high pressure.

Full-Atomistic Optimized Potentials for Liquid Simulations and Polymer Consistent Force Field Models for Biocompatible Shape-Memory Poly(ε-caprolactone).

Thermally induced shape memory poly(ε-caprolactone) (PCL)-based polymers are one of the most extensively researched families of biocompatible materials. They are degradable under physiological conditions and have high applicability in general biomedical engineering, with cross-linked PCL networks being particularly useful for tissue engineering. In this study, we used the optimized potentials for liquid simulations (OPLS) force field, which is well suited for describing intermolecular interactions in biomolecules, and the class II polymer consistent force field (PCFF) to investigate the properties of telechelic PCL with diacrylates as reactive functionalities on its end groups. PCFF has been specifically parameterized for simulating synthetic polymeric materials. We compare the findings of all-atom molecular dynamics simulations with known experimental data and theoretical assumptions to verify the applicability of both these force fields. We estimated the melt density, volume, transition temperatures, and mechanical characteristics of two-branched PCL diacrylates with a molecular weight of 2481 Da. Our findings point to the utility of the aforementioned force fields in predicting the properties of PCL-based polymers. It also opens avenues for developing PCL cross-linked polymer models and employing OPLS to investigate the interactions of synthetic polymers with biomolecules.

United-Atom Molecular Dynamics Study of the Mechanical and Thermomechanical Properties of an Industrial Epoxy.

Epoxy resins are the most commonly used adhesives in industry due to their versatility, low cost, low toxicity, low shrinkage, high strength, resistance to moisture, and effective electrical resistance. These diverse properties can be tailored based on the chemical structure of the curing agent and the conditions of the curing process. Molecular simulations of epoxy resins have gained attention in recent years as a means to navigate the vast choice of chemical agents and conditions that will give the required properties of the resin. This work examines the statistical uncertainty in predicting thermodynamic and mechanical properties of an industrial epoxy resin using united atom molecular dynamics simulation. The results are compared with experimental measurements of the elastic modulus, Poisson's ratio, and the glass transition temperature obtained at different temperatures and degrees of curing. The decreasing trend of the elastic modulus with increasing temperature is accurately captured by the simulated model, though the uncertainty in the calculated average is large. The glass transition temperature is expectedly overpredicted due to the high rates accessible to molecular simulations. We find that Poisson's ratio is particularly sensitive to sample anisotropy as well as the method of evaluation, which explains the lack of consistent trends previously observed with molecular simulation at different degrees of crosslinking and temperatures.

The selectivity of protein-imprinted gels and its relation to protein properties: A computer simulation study.

Polymer-based protein recognition systems have enormous potential within clinical and diagnostic fields due to their reusability, biocompatibility, ease of manufacturing, and potential specificity. Imprinted polymer matrices have been extensively studied and applied as a simple technique for creating artificial polymer-based recognition gels for a target molecule. Although this technique has been proven effective when targeting small molecules (such as drugs), imprinting of proteins have so far resulted in materials with limited selectivity due to the large molecular size of the protein and aqueous environment. Using coarse-grained molecular simulation, we investigate the relation between protein makeup, polymer properties, and the selectivity of imprinted gels. Nonspecific binding that results in poor selectivity is shown to be strongly dependent on surface chemistry of the template and competitor proteins as well as on polymer chemistry. Residence time distributions of proteins diffusing within the gels provide a transparent picture of the relation between polymer constitution, protein properties, and the nonspecific interactions with the imprinted gel. The pronounced effect of protein surface chemistry on imprinted gel specificity is demonstrated.