Simulation of fluid/gel phase equilibrium in lipid vesicles

Freezing of water and melting of ice: theoretical modeling at the nanoscale

Freezing of water and melting of ice at the nanoscale play critical roles in science and technology fields, including aviation systems, infrastructures, and other broad spectrum of technologies. To cope with the icing challenge, nanoscale anti-icing surface technology has been developed. The freezing and melting temperatures can be tailored by manipulating the size (the radius of water or ice); however, it lacks systemic research. In this work, the size effect on the melting temperature of ice nanocrystals was first established, which considered the variation of bond energy and equivalent heat energy from the perspective of the force-heat equivalence energy density principle. Based on the heterogeneous nucleation mode and by further considering the size and temperature effects on the interface energy involved solid-liquid energy and liquid-vapor energy as well as the above developed melting temperature model, another model is established to accurately predict the freezing temperature of water nanodroplets. The parameters required by the two models established in this paper have a clear physical meaning and establish the quantitative relationships among freezing temperature, melting temperature, surface stress, interface energy, and other thermodynamic parameters. The agreement between model prediction and experimental simulation data confirms the validity and universality of the established models. The higher prediction accuracy of this work compared to the other theoretical models, due to the more detailed consideration and the reference point, captures the errors introduced by the experiment or simulation. This study contributes to a deeper understanding of the underlying mechanism of freezing of water and melting of ice nanocrystals and provides theoretical guidance for the design of cryopreservation systems and anti-icing systems for aviation.

Effects of lipid saturation on bicelle to vesicle transition of a binary phospholipid mixture: a molecular dynamics simulation study

Controlling the transition from lipid bicelles to vesicles is essential for producing engineered vesicles. We perform coarse-grained molecular dynamics (CGMD) simulations of unsaturated/saturated lipid mixtures to clarify the effects of lipid unsaturation on vesiculation at the molecular scale. The results demonstrate that vesiculation depends on the concentration of unsaturated lipids and the degree of unsaturation. The probability of vesiculation increases linearly with the apparent unsaturated lipid concentration at a low degree of unsaturation. Higher degrees of unsaturation lead to phase segregation within the binary bicelles, reducing the probability of vesiculation. A comparison between CGMD simulations and the conventional theory of vesiculation shows that the theoretical predictions of binary lipid systems must explicitly include phase segregation effects. Furthermore, simulations with biased lipid distributions reveal that vesiculation is facilitated by the preconcentration of unsaturated lipids in the core region of the bicelle but is then temporally limited as the unsaturated lipids move to the bicelle edges. These findings advance theoretical and experimental studies on binary lipid systems and promote the development of tailor-made vesicles.

Stimuli-responsive vesicles as distributed artificial organelles for bacterial activation

Intercellular communication is a hallmark of living systems. As such, engineering artificial cells that possess this behavior has been at the heart of activities in bottom-up synthetic biology. Communication between artificial and living cells has potential to confer novel capabilities to living organisms that could be exploited in biomedicine and biotechnology. However, most current approaches rely on the exchange of chemical signals that cannot be externally controlled. Here, we report two types of remote-controlled vesicle-based artificial organelles that translate physical inputs into chemical messages that lead to bacterial activation. Upon light or temperature stimulation, artificial cell membranes are activated, releasing signaling molecules that induce protein expression in Escherichia coli. This distributed approach differs from established methods for engineering stimuli-responsive bacteria. Here, artificial cells (as opposed to bacterial cells themselves) are the design unit. Having stimuli-responsive elements compartmentalized in artificial cells has potential applications in therapeutics, tissue engineering, and bioremediation. It will underpin the design of hybrid living/nonliving systems where temporal control over population interactions can be exerted.

Cholesterol Distribution in Small Unilamellar Vesicles

The plasma membrane has heterogeneity, where the constituents are not only asymmetrically distributed between the inner leaflet and the outer leaflet but also laterally organized within each leaflet. There is still an ongoing controversy over the cholesterol distribution between the two leaflets, and it is also significant to explore the lateral flow and localization of cholesterol. The unilamellar vesicle is extensively employed as a simplified model of the plasma membrane in research studies. In this work, we study the spontaneous spatial distribution of cholesterol in the small unilamellar vesicles with a single type of phospholipid as the bilayer backbone through coarse-grained molecular dynamics simulations. The results show that in a spherical vesicle under ambient pressure, cholesterol is more abundant in the inner leaflet than in the outer leaflet. As the vesicle is deformed under pressurization, the net lateral flow of cholesterol in the two leaflets is in the exactly opposite directions, finally leading to a distribution strongly associated with the monolayer curvature. One of the possible explanations for our results is from the point of view of curvature elastic energy. Another possibility is from the point of view of stress: according to the correlation between the cholesterol distribution and the tail angles of lipids, it is suggested that the possible governing mechanism for the distribution of cholesterol in a membrane is to alleviate the mismatch of stress between the two leaflets. Additionally, we obtain the effect of cholesterol infiltration on the bending modulus and the spontaneous curvature of the vesicles.

MLLPA: A Machine Learning-assisted Python module to study phase-specific events in lipid membranes

Machine Learning-assisted Lipid Phase Analysis (MLLPA) is a new Python 3 module developed to analyze phase domains in a lipid membrane based on lipid molecular states. Reading standard simulation coordinate and trajectory files, the software first analyze the phase composition of the lipid membrane by using machine learning tools to label each individual molecules with respect to their state, and then decompose the simulation box using Voronoi tessellations to analyze the local environment of all the molecules of interest. MLLPA is versatile as it can read from multiple format (e.g., GROMACS, LAMMPS) and from either all-atom (e.g., CHARMM36) or coarse-grain models (e.g., Martini). It can also analyze multiple geometries of membranes (e.g., bilayers, vesicles). Finally, the software allows for training with more than two phases, allowing for multiple phase coexistence analysis.

Revealing Thermodynamics and Kinetics of Lipid Self-Assembly by Markov State Model Analysis

Self-assembly is ubiquitous in the realm of biology and has become an elegant bottom-up approach to fabricate new materials. Although molecular dynamics (MD) simulations can complement experiments by providing the missing atomic details, it still remains a grand challenge to reveal the thermodynamic and kinetic information on a self-assembly system. In this work, we demonstrate for the first time that the Markov state model analysis can be used to delineate the variation of free energy during the self-assembly process of a typical amphiphilic lipid dipalmitoyl-phosphatidylcholine (DPPC). Free energy profiles against the solvent-accessible surface area and the root-mean-square deviation have been derived from extensive MD results of more than five hundred trajectories, which identified a metastable crossing-cylinder (CC) state and a transition state of the distorted bilayer with a free energy barrier of ∼0.02 kJ mol^-1 per DPPC lipid, clarifying a long-standing speculation for 20 years that there exists a free energy barrier during lipid self-assembly. Our simulations also unearth two mesophase structures at the early stage of self-assembly, discovering two assembling pathways to the CC state that have never been reported before. Further thermodynamic analysis derives the contributions from the enthalpy and the entropy terms to the free energy, demonstrating the critical role played by the enthalpy-entropy compensation. Our strategy opens the door to quantitatively understand the self-assembly processes in general and provides new opportunities for identifying common thermodynamic and kinetic patterns in different self-assembly systems and inspiring new ideas for experiments. It may also contribute to the refinement of force field parameters of various self-assembly systems.

Loading of lutein in egg-sphingomyelin vesicles as lipid carriers: Thermotropic phase behaviour, structure of sphingosome membranes and lutein crystals

Lutein is a xanthophyll carotenoid provided exclusively by the diet, that has protective functions and beneficial effects on human health. Supplementation in lutein is necessary to reach the recommended daily dietary intake. However, the introduction of lutein into foods and beverages is a real challenge since this lipophilic nutrient has a poor aqueous solubility and a low bioavailability. In this study, we investigated the capacity of egg-sphingomyelin (ESM) vesicles called sphingosomes to solubilise lutein into the bilayers. The thermal and structural properties of ESM bilayers were examined in presence of various amounts of lutein by differential scanning calorimetry (DSC) and temperature-controlled X-ray diffraction (XRD), the structures of sphingosomes and lutein crystals were observed by microscopic techniques. ESM bilayers were in the fluid L_α phase above the phase transition temperature T_m = 39.6 °C and in the lamellar ripple P_β' phase below T_m where ESM sphingosomes exhibited ondulations and were facetted. Lutein molecules were successfully incorporated into the ESM bilayers where they induced a structural disorganisation. For ESM/lutein 90/10 %mol (91.8/8.2 %wt; 89 mg lutein / g ESM), lutein partitioning occured with the formation of lutein crystals in the aqueous phase together with lutein-loaded ESM vesicles. This study highlighted the capacity of new lipid carriers such as egg-sphingosomes to solubilise lutein and opens perspectives for the formulation of effective lutein-fortified functionnal foods and beverages providing health benefits.