Direct Observation of Single Ostwald Ripening Processes by Molecular Dynamics Simulation

GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems

Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to investigate slow biological processes that involve multiple proteins, nucleic acids, and their complexes. Biomolecules in a large simulation system are distributed non-uniformly, limiting computational efficiency with conventional methods. Here, we develop a hierarchical domain decomposition scheme with dynamic load balancing for heterogeneous biomolecular systems to keep computational efficiency even after drastic changes in particle distribution. These schemes are applied to the dynamics of intrinsically disordered protein (IDP) droplets. During the fusion of two droplets, we find that the changes in droplet shape correlate with the mixing of IDP chains. Additionally, we simulate large systems with multiple IDP droplets, achieving simulation sizes comparable to those observed in microscopy. In our MD simulations, we directly observe Ostwald ripening, a phenomenon where small droplets dissolve and their molecules redeposit into larger droplets. These methods have been implemented in CGDYN of the GENESIS software, offering a tool for investigating mesoscopic biological processes using the residue-level CG models.

Inulin Can Improve Red Blood Cell Cryopreservation by Promoting Vitrification, Stabilizing Cell Membranes, and Inhibiting Ice Recrystallization

In transfusion medicine, the cryopreservation of red blood cells (RBCs) is of major importance. The organic solvent glycerol (Gly) is considered the current gold-standard cryoprotectant (CPA) for RBC cryopreservation, but the deglycerolization procedure is complex and time-consuming, resulting in severe hemolysis. Therefore, it remains a research hotspot to find biocompatible and effective novel CPAs. Herein, the natural and biocompatible inulin, a polysaccharide, was first employed as a CPA for RBC cryopreservation. The presence of inulin could improve the thawed RBC recovery from 11.83 ± 1.40 to 81.86 ± 0.37%. It was found that inulin could promote vitrification because of its relatively high viscosity and glass transition temperature (Tg'), thus reducing the damage during cryopreservation. Inulin possessed membrane stability, which also had beneficial effects on RBC recovery. Moreover, inulin could inhibit the mechanical damage induced by ice recrystallization during thawing. After cryopreservation, the RBC properties were maintained normally. Mathematical modeling analysis was adopted to compare the performance of inulin, Gly, and hydroxyethyl starch (HES) in cryopreservation, and inulin presented the best efficiency. This work provides a promising CPA for RBC cryopreservation and may be beneficial for transfusion therapy in the clinic.

Nanomaterial accumulation in boiling brines enhances epithermal bonanzas

Epithermal bonanza-type ores, characterized by weight-percent contents of e.g., gold and silver in a few mm to cm, are generated by mixtures of magmatic-derived hydrothermal brines and external fluids (e.g., meteoric) that transport a variety of metals to the site of deposition. However, the low solubilities of precious metals in hydrothermal fluids cannot justify the high concentrations necessary to produce such type of hyper-enriched metal ore. Here we show that boiling metal-bearing brines can produce, aggregate, and accumulate metal nanomaterials, ultimately leading to focused gold + silver ± copper over-enrichments. We found direct nano-scale evidence of nanoparticulate gold- and/or silver-bearing ores formed via nonclassical growth (i.e., nanomaterial attachment) during boiling in an intermediate-sulfidation epithermal bonanza. The documented processes may explain the generation of bonanzas in metal-rich brines from a range of mineral deposit types.

Quantification of Ostwald Ripening in Emulsions via Coarse-Grained Simulations

Ostwald ripening is a diffusional mass transfer process that occurs in polydisperse emulsions, often with the result of threatening the emulsion stability. In this work, we design a simulation protocol that is capable of quantifying the process of Ostwald ripening at the molecular level. To achieve experimentally relevant time scales, the dissipative particle dynamics (DPD) simulation protocol is implemented. The simulation parameters are tuned to represent two benzene droplets dispersed in water. The coalescence between the two droplets is prevented via the introduction of membranes, which allow diffusion of benzene from one droplet to the other. The simulation results are quantified in terms of the changes in the droplet volume as a function of time. The results are in qualitative agreement with experiments. The agreement with the Lifshitz-Slyozov-Wagner theory becomes quantitative when the simulated solubility and diffusion coefficient of benzene-in-water are considered. The effect of two different surfactants was also investigated. In agreement with both experimental observations and theory, the addition of surfactants at moderate concentrations decreased the Ostwald ripening rate because of the reduction in the interfacial tension between benzene and water; as the surfactant film becomes dense, other phenomena are likely to further delay the Ostwald ripening. In fact, the results suggest that the surfactant that yields higher density at the benzene-water interface delayed more effectively Ostwald ripening. The formation of micelles can also affect the ripening rate, in qualitative agreement with experiments, although our simulations are not conclusive on such effects. Our simulations show that the coarse-grained DPD formalism is able to capture the molecular phenomena related to Ostwald ripening and reveal molecular level features that could help to understand experimental observations. The results could be useful for predicting and eventually controlling the long-term stability of emulsions.

Effect of polyvinyl alcohol on survival and function of angora buck spermatozoa following cryopreservation

The aim of this study was to examine effects of polyvinyl alcohol (PVA) on buck semen quality. Seventy-five ejaculates were collected and diluted in Tris-egg yolk extender containing one of three PVA co-polymers of 9, 18 and 100 kDa. Five different concentrations 0.001, 0.01, 0.1, 1 and 2% of the PVA co-polymers were added to the extender with respected to the decreasing glycerol concentrations of 5, 4, 3, 3, 2% respectively. Following freeze-thaw, sperm motility, viability, acrosome-intact spermatozoa and mitochondrial membrane potentials were analysed. During freezing, sperm seeding temperature were recorded with a cryo-thermometer. PVA 2% glycerol group gained 8.2 ± 1 °C latent heat plateau difference comparing to control. Highest motility was found in PVA 18 kDa with regardless of the dosage (P < 0.001). All PVA copolymers gained higher motility independently in all other dosage groups (except PVA 2%) comparing to control (P < 0.001). Live spermatozoa rate between treatment groups were statistically insignificant (P = 0.953), however, when moribund sperm were gated out PVA 9 induced better protection with respect to other groups (P < 0.05). Intact acrosome rate was statically higher in PVA groups (P < 0.002) and subgroups (P < 0.001). Mitochondrial membrane potential was higher in all experimental groups comparing to control group (P < 0.001). PVA co-polymer concentrations of 0.01, 0.1, 1 and 2% v/v (PBS: PVA) decreased the concentration of glycerol required for freezing in a 100 ml volume by 0, 1, 2, 2, and 3% v/v from the control dose (5%), respectively. In conclusion, synthetic PVA-derived ice blocking agents offer new opportunities for improving the post-thaw buck sperm quality.

Solid-to-Solid Crystallization of Organic Thin Films: Classical and Nonclassical Pathways

The solid-to-solid crystallization processes of organic molecules have been poorly understood in view of the complexity and the instability of organic crystals. Here, we studied the crystallization of a π-conjugated small molecular semiconductor, bis-(8-hydroxyquinoline) copper (CuQ₂), by annealing the thin films at different temperatures. We observed a classical film-to-nanorods crystallization at 80 °C, a coexistence of classical and nonclassical nucleation and particle growth at 120 °C, and a nonclassical crystal growth at 150 °C. We found that the growth of the crystals followed the following processes: particle nucleation, particle growth, particle migration, nondirectional particle attachment, and structure reconstruction. We notice that the growth of CuQ₂ particles follows an outside-to-inside process. More interestingly, our experiments suggest that the submicron CuQ₂ particles are able to migrate dozens of micrometers at 150 °C.

Droplet formation and growth inside a polymer network: A molecular dynamics simulation study

We present a molecular dynamics simulation study that focuses on the formation and growth of nanoscale droplets inside polymer networks. Droplet formation and growth are investigated by the liquid-vapor phase separation of a dilute Lennard-Jones (LJ) fluid inside regularly crosslinked, polymer networks with varying mesh sizes. In a polymer network with small mesh sizes, droplet formation can be suppressed, the extent of which is dependent on the attraction strength between the LJ particles. When droplets form in a polymer network with intermediate mesh sizes, subsequent growth is significantly slower when compared with that in bulk without a polymer network. Interestingly, droplet growth beyond the initial nucleation stage occurs by different mechanisms depending on the mesh size: droplets grow mainly by diffusion and coalescence inside polymer networks with large mesh sizes (as observed in bulk), whereas Ostwald ripening becomes a more dominant mechanism for droplet growth for small mesh sizes. The analysis of droplet trajectories clearly reveals the obstruction effect of the polymer network on the movement of growing droplets, which leads to Ostwald ripening of droplets. This study suggests how polymer networks can be used to control the growth of nanoscale droplets.