Coupling Bulk Phase Separation of Disordered Proteins to Membrane Domain Formation in Molecular Simulations on a Bespoke Compute Fabric

Phospholipid membranes surround the cell and its internal organelles, and their multicomponent nature allows the formation of domains that are important in cellular signalling, the immune system, and bacterial infection. Cytoplasmic compartments are also created by the phase separation of intrinsically disordered proteins into biomolecular condensates. The ubiquity of lipid membranes and protein condensates raises the question of how three-dimensional droplets might interact with two-dimensional domains, and whether this coupling has physiological or pathological importance. Here, we explore the equilibrium morphologies of a dilute phase of a model disordered protein interacting with an ideal-mixing, two-component lipid membrane using coarse-grained molecular simulations. We find that the proteins can wet the membrane with and without domain formation, and form phase separated droplets bound to membrane domains. Results from much larger simulations performed on a novel non-von-Neumann compute architecture called POETS, which greatly accelerates their execution compared to conventional hardware, confirm the observations. Reducing the wall clock time for such simulations requires new architectures and computational techniques. We demonstrate here an inter-disciplinary approach that uses real-world biophysical questions to drive the development of new computing hardware and simulation algorithms.

Revisiting pure component wax esters as basis of wax-based oleogels

Current research on wax-based oleogels indicates wax esters to be the key component in many natural waxes. This necessitates understanding the properties of pure wax esters to unravel the gelling mechanism in wax-based oleogels. Therefore, wax esters with different carbon numbers and symmetries were studied and characterized regarding their thermal (DSC) and viscoelastic (oscillatory rheology) behavior. Pure wax esters and binary mixtures of wax esters were studied as such and in oleogels formed in combination with medium chained triglyceride oil at WE-inclusion levels of 10 % (w/w). Interpretation of the observations was based on detailed analysis of pre-existing data on crystallographic (SAXS) and thermal properties. It is found that all observations concerning single pure WE’s obey a systematic framework linking molecular make up, crystal structure and behavior. The study on the gelling of four different binary mixtures of wax esters revealed that substantial chain length differences do have the expected consequence of separate crystallization. Mixtures of wax esters with only limited chain length difference reconfirmed earlier speculations on mixing and crystal structure. Applying mixtures of wax esters only differing in their position of the ester bond indicated ideal mixing behavior in the solid phase of the gels. Actually, the data revealed that despite these expected observations in both systems, additional thermal events occur at specific mixing ratios. Their supposed relation to compound formation certainly needs further confirmation. Rheological analysis confirmed that sequential crystallization results in highest firmness values for the systems studied.

Molecular-scale description of interfacial mass transfer in phase-separated aqueous secondary organic aerosol

Liquid–liquid phase-separated (LLPS) aerosol particles are known to exhibit increased cloud condensation nuclei (CCN) activity compared to well-mixed ones due to a complex effect of low surface tension and non-ideal mixing. The relation between the two contributions as well as the molecular-scale mechanism of water uptake in the presence of an internal interface within the particle is to date not fully understood. Here we attempt to gain understanding in these aspects through steered molecular dynamics simulation studies of water uptake by a vapor–hydroxy-cis-pinonic acid–water double interfacial system at 200 and 300 K. Simulated free-energy profiles are used to map the water uptake mechanism and are separated into energetic and entropic contributions to highlight its main thermodynamic driving forces. Atmospheric implications are discussed in terms of gas–particle partitioning, intraparticle water redistribution timescales and water vapor equilibrium saturation ratios. Our simulations reveal a strongly temperature-dependent water uptake mechanism, whose most prominent features are determined by local extrema in conformational and orientational entropies near the organic–water interface. This results in a low core uptake coefficient (ko/w=0.03) and a concentration gradient of water in the organic shell at the higher temperature, while entropic effects are negligible at 200 K due to the association-entropic-term reduction in the free-energy profiles. The concentration gradient, which results from non-ideal mixing – and is a major factor in increasing LLPS CCN activity – is responsible for maintaining liquid–liquid phase separation and low surface tension even at very high relative humidities, thus reducing critical supersaturations. Thermodynamic driving forces are rationalized to be generalizable across different compositions. The conditions under which single uptake coefficients can be used to describe growth kinetics as a function of temperature in LLPS particles are described.

Detailed Calorimetric Analysis of Mixed Micelle Formation from Aqueous Binary Surfactants for Design of Nanoscale Drug Carriers

While numerous papers have been published according to the binary surfactant mixtures, only a few articles provide deeper information on the composition dependence of the micellization, and even less work attempts to apply the enhanced feature of the mixed micelles. The most important parameter of the self-assembled surfactants is the critical micelle concentration (cmc), which quantifies the tendency to associate, and provides the Gibbs energy of micellization. Several techniques are known for determining the cmc, but the isothermal titration calorimetry (ITC) can be used to measure both cmc and enthalpy change (ΔmicH) accompanying micelle formation. Outcomes of our calorimetric investigations were evaluated using a self-developed routine for handling ITC data and the thermodynamic parameters of mixed micelle formation were obtained from the nonlinear modelling of temperature- and composition- dependent enthalpograms. In the investigated temperature and micelle mole fractions interval, we observed some intervals where the cmc is lower than the ideal mixing model predicted value. These equimolar binary surfactant mixtures showed higher solubilization ability for poorly water-soluble model drugs than their individual compounds. Thus, the rapid and fairly accurate calorimetric analysis of mixed micelles can lead to the successful design of a nanoscale drug carrier.

Computer simulation of block polymerization of 1,6-Hexanediol Diacrylate

In this paper, a computer model of the block three-dimensional free-radical polymerization of 1,6-Hexanediol Diacrylate (HDDA) is proposed. The model of the reaction system is based on an ideal mixing reactor. The reaction process is modeled by the Monte Carlo method. Accounting for the diffusion inhibition of the reaction is described using the free volume model. An adequate description of the experimental data of the calculated conversion rate curve is obtained. The nature of the change in the rate constant of the growth reaction with increasing conversion is shown.

Numerical Analysis of the Influence of the Modification of the Ladle Shroud on Fluid Flow Behavior in a One-strand Tundish during Continuous Steel Casting

A tundish is a device from which liquid steel is pour into a mold. Therefore tundish hydrodynamic conditions have a significant impact on solidification during continuous steel casting (CSC) process. Modification of ladle shroud workspace, allows for the modification of liquid steel movement in the tundish. In the following work, numerical simulations were performed which allowed the impact of the modification of the ladle shroud workspace on the liquid steel flow structure in a one-strand tundish to be determined. In order to assess the impact of the modification of the ladle shroud on the behavior of the liquid steel in the tundish, simulations were performed, on the basis of which the percentage share of stagnant, ideal mixing and plug flow zones were determined. In addition, the mixing parameters were determined, allowing the estimation of casting duration during sequential casting. The flow fields of liquid steel for each modification of the ladle shroud were performed. The average velocity of liquid steel flowing through the tundish, the Reynolds number and turbulent intensity were also described. The obtained results showed, among others, that the application of three cylinders with a diameter of 0.041 m into the ladle shroud with a diameter of 0.11 m increases the share of active flow in the tundish in relation to the tundish with Conventional Ladle Shroud. At the same time, applying a ladle shroud with a diameter of 0.11 m during casting is the most favorable in relation to the hydrodynamics of the tundish.

Thermodynamic and Structural Modelling of Non-Stoichiometric Ln-Doped UO2 Solid Solutions,Ln = {La, Pr, Nd, Gd}

Available data on the dependence of the equilibrium chemical potential of oxygen on degrees of doping, z, and non-stoichiometry, x, y, in U1-zLnzO2+0.5(x-y) fluorite solid solutions and data on the dependence of the lattice parameter, a, on the same variables are combined within a unified structural-thermodynamic model. The thermodynamic model fits experimental isotherms of the oxygen potential under the assumptions of a non-ideal mixing of the endmembers, UO2, UO2.5, UO1.5, LnO1.5, and Ln0.5U0.5O2, and of a significant reduction in the configurational entropy arising from short-range ordering (SRO) within cation-anion distributions. The structural model further investigates the SRO in terms of constraints on admissible values of cation coordination numbers and, building on these constraints, fits the lattice parameter as a function of z, y, and x. Linking together the thermodynamic and structural models allows predicting the lattice parameter as a function of z, T and the oxygen partial pressure. The model elucidates contrasting structural and thermodynamic changes due to the doping with LaO1.5, on the one hand, and with NdO1.5 and GdO1.5, on the other hand. An increased oxidation resistance in the case of Gd and Nd is attributed to strain effects caused by the lattice contraction due to the doping and to an increased thermodynamic cost of a further contraction required by the oxidation.

Excess heat capacity and entropy of mixing along the hydroxyapatite-chlorapatite and hydroxyapatite-fluorapatite binaries

The heat capacity, Cp, of synthetic hydroxyapatite [Ca5(PO4)3OH–OH-Ap], as well as of ten compositions along the OH-Ap-chlorapatite (Cl-Ap) join and 12 compositions along the OH-Ap-fluorapatite (F-Ap) join have been measured using relaxation calorimetry (heat capacity option of the Physical Properties Measurement System—PPMS) and differential scanning calorimetry (DSC) in the temperature range of 5–764 K. Apatites along the Cl-OH and F-OH joins were synthesized at 1100 °C and 300 MPa in an internally heated gas pressure vessel via an exchange process between synthetic fluorapatite or chlorapatite crystals (200–500 μm size) and a series of Ca(OH)2-H2O solutions with specific compositions and amounts relative to the starting apatite. The standard third-law entropy of OH-Ap, derived from the low-temperature heat capacity measurements, is S° = 386.3 ± 2.5 J mol−1 K−1, which is ~ 1% lower than that resulting from low-temperature adiabatic calorimetry data on OH-Ap from the 1950’s. The heat capacity of OH-Ap above 298.15 K shows a hump-shaped anomaly centred around 442 K. Based on published structural and calorimetric work, this feature is interpreted to result from a monoclinic to hexagonal phase transition. Super ambient Cp up to this transition can be represented by the polynomial: $$C_{p}^{{\text{OH - Ap}}} {}_{{298K - 442K}}\left( {{\text{J mol}}^{ - 1} {\text{K}}^{- 1}} \right) = {1013.7-13735.5T^{{ - 0.5}}} + 2.616718\,10^{7} T^{{ - 2}} - 3.551381\,10^{9} T^{{ - 3}} .$$ C p OH - Ap 298 K - 442 K J mol - 1 K - 1 = 1013.7 - 13735.5 T - 0.5 + 2.616718 10 7 T - 2 - 3.551381 10 9 T - 3 . . The DSC data above this transition were combined with heat capacities computed using density functional theory and can be given by the Cp polynomial: $$C_{p}^{{\text{OH - Ap}}} {}_{{ >\,442K}}\left( {{\text{J mol}}^{ - 1} {\text{K}}^{- 1}} \right) = {877.2-11393.7 T^{ - 0.5}} + {5.452030\,10^{7}} \,T^{- {2}} - {1.394125\,10^{10}} \,T^{- {3}}$$ C p OH - Ap > 442 K J mol - 1 K - 1 = 877.2 - 11393.7 T - 0.5 + 5.452030 10 7 T - 2 - 1.394125 10 10 T - 3 . Positive excess heat capacities of mixing, ∆Cpex, in the order of 1–2 J mol−1 K−1, occur in both solid solutions at around 70 K. They are significant at these conditions exceeding the 2σ-uncertainty of the data. This positive ∆Cpex is compensated by a negative ∆Cpex of the same order at around 250 K in both binaries. At higher temperatures (up to 1200 K), ∆Cpex is zero within error for all solid solution members. As a consequence, the calorimetric entropies, Scal, show no deviation from ideal mixing behaviour within a 2σ-uncertainty for both joins. Excess entropies of mixing, ∆Sex, are thus zero for the OH-Ap–F-Ap, as well as for the OH-Ap–Cl-Ap join. The Cp–T behaviour of the OH-Ap endmember is discussed in relation to that of the F- and Cl-endmembers.