GPU-accelerated replica exchange molecular simulation on solid–liquid phase transition study of Lennard-Jones fluids

Determining the solid–liquid phase transition point by conventional molecular dynamics (MD) simulations is difficult because of the tendency of the system to get trapped in local minimum energy states at low temperatures and hysteresis during cooling and heating cycles. The replica exchange method, used in performing many MD simulations of the system at different temperature conditions simultaneously and performs exchanges of these temperatures at certain intervals, has been introduced as a tool to overcome this local-minimum problem. However, around the phase transition temperature, a greater number of different temperatures are required to adequately find the phase transition point. In addition, the number of different temperature values increases when treating larger systems resulting in huge computation times. We propose a computational acceleration of the replica exchange MD simulation on graphics processing units (GPUs) in studying first-order solid–liquid phase transitions of Lennard-Jones (LJ) fluids. The phase transition temperature for a 108-atom LJ fluid has been calculated to validate our new code. The result corresponds with that of a previous study using multicanonical ensemble. The computational speed is measured for various GPU-cluster sizes. A peak performance of 196.3 GFlops with one GPU and 8.13 TFlops with 64 GPUs is achieved.     

On the phase transition in a monolayer adsorbed on graphite at temperatures below the 2D-critical temperature

Monte Carlo simulations in the grand ensemble and meso-canonical ensemble in which the adsorbent is connected to a finite reservoir have been used to study adsorption isotherms for monolayer argon adsorption on graphite at temperatures below the 2D-critical temperature in order to elucidate the microscopic details of the 2D-transitions: vapour–solid, vapour–liquid and liquid–solid. An S-shaped van der Waals (vdW) loop was found when a small square surface was used; however, for large square surfaces and rectangular surfaces the isotherms exhibit a vdW-type loop with a vertical segment which indicates the coexistence of two phases separated by a boundary that changes its shape with the loading. This coexistence occurs at the same chemical potential as determined by the mid-density scheme, developed by Do and co-workers (Z. Liu, L. Herrera, V.T. Nguyen, D.D. Do, and D. Nicholson, A Monte Carlo scheme based on mid-density in a hysteresis loop to determine equilibrium phase transition. Mol Simul. 37(11):932–939, 2011; Z. Liu, D.D. Do, and D. Nicholson, A thermodynamic study of the mid-density scheme to determine the equilibrium phase transition in cylindrical pores. Mol Simul. 38(3):189–199, 2011).     

A restructured framework for modeling oxygen transfer in two-phase partitioning bioreactors

This communication proposes a mechanistic modification to a recently published method for analyzing oxygen mass transfer in two-phase partitioning bioreactors (Nielsen et al., 2003), and corrects an oversight in that paper. The newly proposed modification replaces the earlier empirical approach, which treated the two liquid phases as a single, homogeneous liquid phase, with a two-phase mass transfer model of greater fundamental rigor. Additionally, newly developed empirical models are presented that predict the mass transfer coefficient of oxygen absorption in both aqueous medium and an organic phase (n-hexadecane) as a function of bioreactor operating conditions. Experimental values and theoretical predictions of mass transfer coefficients in two-phase dispersions, k(L)a(TP), are compared. The revised approach more clearly demonstrates the potential for oxygen mass transfer enhancement by organic phase addition, one of the motivations for employing a distinct second phase in a partitioning bioreactor.     

Simultaneous and in situ analysis of thermal and volumetric properties of starch gelatinization over wide pressure and temperature ranges

A method for simultaneous and in situ analysis of thermal and volumetric properties of starch gelatinization from 0.1 to 100 MPa and from 283 to 430 K is described. The temperature of a very sensitive calorimetric detector containing a starch-water emulsion at a selected pressure is programmed to rise at a slow rate; volume variations are performed automatically to keep the selected pressure constant while the heat exchange rate and the volume are recorded. The method is demonstrated with a novel investigation of pressure effects on a sequence of three phase transitions in an aqueous emulsion of wheat starch (56 wt % water). The volume changes during the main endothermic transition (M), associated with melting of the crystalline part of the starch granules and a helix-coil transformation in amylopectin, but also with an important swelling, were separated into a volume increase associated with swelling and a volume decrease associated with the transition itself. Thermodynamic parameters for this transition together with their pressure dependencies have been obtained from four independent experiments at each pressure. The data are thermodynamically consistent, but are poorly described by the Clapeyron equation. The negative volume change of the slow exothermic transition (A) appearing just after the main endothermic transition (M) is small, spread out over a wide temperature interval, and occurs at higher temperatures with increasing pressures. This transition is probably associated with reassociation of the unwound helixes of amylopectin with parts of amylopectin molecules other than their original helix duplex partner. The positive volume change of the high-temperature, endothermic transition (N) with a small enthalpy change is probably associated with a nematic-isotropic transformation ending the formation of a homogeneous SOL phase (in the sense of Flory), and is also pushed to higher temperatures with increasing pressures. Knowledge of the state of wheat starch as a function of pressure and temperature is important in extruder processing. The data also provide a basis for the elliptic phase diagram for starch gelatinization. The method is easily adapted to determine similar data for other macromolecular materials.     

Kinetics of phase separation for polyethylene glycol-phosphate two-phase systems

Phase separation times for polyethylene glycol (PEG)-4000-phosphate aqueous two-phase systems were studied, for small scale (5-g) and large scale (1300-g) systems, as a -function of the stability ratio. Profiles of dispersion height for both large and small scale systems were represented as a fraction of the initial height and were found to be independent of the geometrical dimensions of the separator. Furthermore, by plotting time as a fraction of the initial height the total time of separation can be calculated for a given height of system at a particular stability ratio. This generalization is important for the design of large scale aqueous two-phase separators. Phase separation times were also found to be dependent on which of the phases is continuous. A characteristic change in phase separation time was also observed at the phase inversion point (i.e., where the dispersed phase changes to a continuous phase and vice versa) and this point tends toward higher volume ratios as the tie-line length (TLL) is increased. Furthermore, the phase inversion point at each TLL corresponds to a fixed phosphate concentration. (c) 1995 John Wiley & Sons, Inc.     

Determination of L(alpha)-H(II) phase transition temperature for 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine

The thermodynamic properties of fully-hydrated lipids provide important information about the stability of membranes and the energetic interactions of lipid bilayers with membrane proteins (Nagle and Scott, Physics Today, 2:39, 1978). The lamellar/inverse hexagonal (L(alpha)-H(II)) phase transition of 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine (DOPE) water mixtures is a first-order transition and, therefore, at constant pressure, must have a thermodynamically well-defined equilibrium transition temperature. The observed transition temperature is known to be dependent upon the rate at which the temperature is changed, which accounts for the many different values in the literature. X-ray diffraction was used to study the phase transition of fully-hydrated DOPE to determine the rate-independent transition temperature, T(LH). Samples were heated or cooled for a range of rates, 0.212 < r < 225 degrees C/hr, and the rate-dependent apparent phase transition temperatures, T(A)(r) were determined from the x-ray data. By use of a model-free extrapolation method, the transition temperature was found to be T(LH) = 3.33 +/- 0.16 degrees C. The hysteresis, /T(A)(r) - T(LH)/, was identical for heating and cooling rates, +/-r, and varied as /r/beta for beta approximately 1/4. This unexpected power-law relationship is consistent with a previous study (Tate et al., Biochemistry, 31:1081-1092, 1992) but differs markedly from the exponential behavior of activation barrier kinetics. The methods used in this study are general and provide a simple way to determine the true mesomorphic phase transition temperatures of other lipid and lyotropic systems.     

Lateral organization of mixed, two-phosphatidylcholine liposomes as investigated by GPS, the slope of Laurdan generalized polarization spectra

The effect of the excitation or emission wavelengths on Laurdan generalized polarization (GP) can be evaluated by GPS, a quantitative, simplified determination of the GP spectrum slope, the thermotropic dependence of which allows the assessment of phospholipid lamellar membrane phase, as shown in a recent publication of our laboratory [J.B. Velázquez, M.S. Fernández, Arch. Biochem. Biophys. 455 (2006) 163-174]. In the present work, we applied Laurdan GPS to phase transition studies of mixed, two-phosphatidylcholine liposomes prepared from variable proportions of dimyristoyl- and dipalmitoylphosphatidylcholine (DMPC and DPPC, respectively). We have found that the GPS function reports a clear limit between the gel/liquid-crystalline phase coexistence region and the liquid-crystalline state, not only at a certain temperature T_c for liposomes of constant composition submitted to temperature scans, but also at a defined mole fraction X_c, for two-component liposomes of variable composition at constant temperature. The T_c or the X_c values obtained from GPS vs. temperature or GPS vs. composition plots, respectively, allow the construction of a partial phase diagram for the DMPC-DPPC mixtures, showing the boundary between the two-phase coexisting region and the liquid-crystalline state. Likewise, at the onset of the transition region, i.e., the two-phase coexisting region as detected by GPS, it is possible to determine, although with less precision, a temperature T_o or a mole fraction X_o defining a boundary located below but near the limit between the gel and ripple phase, reported in the literature. These GPS results are consistent with the proposal by several authors that a fraction of L_α phospholipids coexists with gel phospholipids in the rippled phase.     

The effect of increasing membrane curvature on the phase transition and mixing behavior of a dimyristoyl-sn-glycero-3-phosphatidylcholine/ distearoyl-sn-glycero-3-phosphatidylcholine lipid mixture as studied by Fourier transform infrared spectroscopy and differential scanning calorimetry.

The phase transition behavior of a lipid bilayer of dimyristoyl-sn-glycero-3-phosphatidylcholine/distearoyl-sn-glycero-3- phosphatidylcholine (DMPC-d54/DSPC) (1:1) on a solid support with varying curvatures was investigated with differential scanning calorimetry, infrared spectroscopy, and model calculations. With increasing curvature the temperatures of the liquidus and solidus points are shifted to lower values by up to 7 degrees C and 15 degrees C, and the mixing of the two lipid species in the two phase region is altered. With increasing curvature the DSPC dominates the gel phase, whereas the DMPC-d54 is expelled to the fluid phase. Whereas the planar system shows a nearly simultaneous phase transition of DSPC and DMPC-d54, the spherical system with the highest curvature exhibits an almost complete separation of the phase transitions of the two lipids. Model calculations suggest that the shift of the liquidus point can be understood as a reduction of the lateral pressure in the bilayer with increasing curvature. The shift of the solidus line is interpreted as a result of the increased demixing of the two components in the two-phase region with increasing curvature due to lowering of the lateral pressure.     

Molecular Dynamics Simulation of Structural Phase Transition of AlPO4 Induced by Pressure

Abstract

The mechanism of pressure-induced phase transition of AlPO₄ has been investigated by means of a molecular dynamics method of constant temperature and pressure. A new crystalline phase with space group C2, which has not yet been experimentally found, appears by an instantaneous compression of 60, 70 and 80 GPa at 300 K. At high temperature (2500 K) and pressure (58 GPa), another new phase of AlPo₄ (y-phase), which is composed of PO₆ and AlO₆ octahedra, has been observed.     

A low-temperature structural phase transition of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine bilayers in the gel phase

A new thermotropic phase transition, at ?30°C and atmospheric pressure, was found to occur in the gel phase of aqueous DPPC dispersions. The Raman spectral changes at this phase transition are similar to those observed in the gel phase of DMPC dispersions at ?60°C. The thermotropic phase transition at ?30°C is equivalent to the barotropic GII to GIII phase transition observed in DPPC at 1.7 kbar and 30°C. It is shown that the rate of the large angle interchain reorientational fluctuations decreases gradually with decreasing temperature, and that the orientationally disordered acyl chain structure of the GII phase is extended into the GIII phase of DPPC. The interchain interaction, arising from the damping of the reorientational fluctuations, increases with decreasing temperature in the GII gel phase as well as in the GIII gel phase.     

High-pressure Sapphire Cell for Phase Equilibria Measurements of CO2/Organic/Water Systems

The high pressure sapphire cell apparatus was constructed to visually determine the composition of multiphase systems without physical sampling. Specifically, the sapphire cell enables visual data collection from multiple loadings to solve a set of material balances to precisely determine phase composition. Ternary phase diagrams can then be established to determine the proportion of each component in each phase at a given condition. In principle, any ternary system can be studied although ternary systems (gas-liquid-liquid) are the specific examples discussed herein. For instance, the ternary THF-Water-CO₂ system was studied at 25 and 40 °C and is described herein. Of key importance, this technique does not require sampling. Circumventing the possible disturbance of the system equilibrium upon sampling, inherent measurement errors, and technical difficulties of physically sampling under pressure is a significant benefit of this technique. Perhaps as important, the sapphire cell also enables the direct visual observation of the phase behavior. In fact, as the CO₂ pressure is increased, the homogeneous THF-Water solution phase splits at about 2 MPa. With this technique, it was possible to easily and clearly observe the cloud point and determine the composition of the newly formed phases as a function of pressure.The data acquired with the sapphire cell technique can be used for many applications. In our case, we measured swelling and composition for tunable solvents, like gas-expanded liquids, gas-expanded ionic liquids and Organic Aqueous Tunable Systems (OATS)^1-4. For the latest system, OATS, the high-pressure sapphire cell enabled the study of (1) phase behavior as a function of pressure and temperature, (2) composition of each phase (gas-liquid-liquid) as a function of pressure and temperature and (3) catalyst partitioning in the two liquid phases as a function of pressure and composition. Finally, the sapphire cell is an especially effective tool to gather accurate and reproducible measurements in a timely fashion.     

Phase state and surface topography of palmitoyl-ceramide monolayers

In cell biology (and in many biophysical) studies there is a natural tendency to consider ceramide as a highly condensed, solid-type lipid conferring rigidity and close packing to biomembranes. In the present work we advanced the understanding of the phase behavior of palmitoyl-ceramide restricted to a planar interface using Langmuir monolayers under strictly controlled and known surface packing conditions. Surface pressure–molecular area isotherms were complemented with molecular area–temperature isobars and with observations of the surface topography by Brewster Angle Microscopy. The results described herein indicate that palmitoyl-ceramide can exhibit expanded, as well as condensed phase states. Formation of three phases was found, depending on the surface pressure and temperature: a solid (1.80 nm thick), a liquid-condensed (1.73 nm thick, likely tilted) and a liquid-expanded (1.54 nm thick) phase over the temperature range 5–62 °C. A large hysteretic behavior is observed for the S phase monolayer that may indicate high resistance to domain boundary deformation. A second (or higher) order S → LC phase transition is observed at about room temperature while a first order LC → LE transition occurs in a range of temperature encompassing the physiological one (observed above 30 °C at low surface pressure). This phase behavior broadens the view of ceramide as a type of lipid not-always-rigid but able to exhibit polymorphic properties.     

Pressure dependence of pyrene excimer fluorescence in human erythrocyte membranes

The intensity of pyrene excimer fluorescence in human erythrocyte membranes and in sonicated dispersions of the membrane lipid (liposomes) was examined as a function of pressure (1–2080 bar) and temperature (5–40°C). Higher pressure or lower temperature decreased the excimer/monomer intensity ratios. A thermotropic transition was detected in both membranes and liposomes by plots of the logarithm of the excimer/monomer intensity ratio versus 1/K. The transition temperature of the membranes was 19–21°C at 1 bar and 28–31°C at 450 bar, a shift with pressure of approx. 20–22 K per kbar. Corresponding transition temperatures of the liposomes were 21°C at 1 bar and 33°C at 450 bar, a shift of approx. 27 K per kbar. The observed pressure dependence of the thermotropic transition temperature is similar to that reported for phospholipid bilayers and greatly exceeds that of protein conformation changes. In concert with the liposome studies the results provide direct evidence for a lipid transition in the erythrocyte membrane.     

Effect of temperature on the NMR spectra of sonicated dispersions of isomers of dipalmitoylphosphatidylcholine

Sonicated dispersions of 1,2-dipalmitoylsn-glycero-3-phosphorylcholine and of 1,3-dipalmitoylglycero-2-phosphorylcholine were examined by proton nuclear magnetic resonance (NMR) as a function of temperature. The —(CH₂)_n)— peak in the spectrum of the sn-3-isomer of dipalmitoylphosphatidylcholine showed the characteristic dramatic changes in the peak intensity and width associated with the phase transition between the liquid crystalline and gel states of the phospholipid. This occurred over a 2–3°C temperature range with the midpoint of the transition at 38.5°C. With the 2-isomer the change in phase took place over a similar temperature range but the midpoint was at 33.8°C. This lower phase transition temperature is presumably the result of increased acyl chain mobility caused by the increased separation of the two acyl chains by the centre carbon of the glycerol backbone. The effect of sonication of the broadening of the range and lowering of the midpoint temperature of the phase transition from that of the corresponding unsonicated dispersions was similar with each isomer. This suggests that the overall geometry of the sonicated vesicles of the isomers is similar.     

Effects of pressure and temperature on the M412 intermediate of the bacteriorhodopsin photocycle. Implications for the phase transition of the purple membrane

The effects of pressure and temperature on the decay kinetics of the M412 (M) intermediate in the photocycle of bacteriorhodopsin were studied to provide information about the phase transitions of the purple membrane lipids. The activation volume (delta V++) for the decay of M is expected to be different below and above a phase transition. However, no abrupt change in delta V++ was found from 3.5 degrees to 60 degrees C. But a sharp break was observed in a plot of the logarithm of the rate of M decay vs. pressure. Extrapolation of this break point to standard atmospheric pressure gives a temperature of -42 degrees C, which probably corresponds to the phase transition of the purple membrane lipids. This conclusion is supported by studies of the effect of pressure on the M kinetics of bacteriorhodopsin incorporated into dimyristoylphosphatidylcholine vesicles, whose phase transition has previously been characterized.     

Miscibility of phosphatidylcholine binary mixtures in unilamellar vesicles: Phase equilibria

Summary Miscibility among phospholipids with different lipid chain-lengths or with different head groups has attracted a number of research efforts because of its significance in biological membrane structure and function. The general consensus about the miscibility of phosphatidylcholines with varying lipid chainlengths appears to be that binary mixtures of phospholipids with a difference of two carbon atoms in the lipid chain mix well at the main phase transition. Miscibility between phosphatidylcholines with differences of four carbon atoms appears to be inconclusive. Previous reports on the phase transition of binary phospholipid mixtures are concerned mainly with multilamellar vesicles and are mostly limited to the main transition. In the present study, unilamellar vesicles were used and miscibility in binary systems between dimyristoyl-, dipalmitoyl- and distearoyl-phosphatidylcholines at pretransition, as well as main transition temperatures was evaluated by constructing phase diagrams. Two methods were used to monitor the phase transitions: differential scanning microcalorimetry and optical absorbance methods. The optical method has the advantage that unilamellar vesicles of dilute phospholipid concentrations can be used. The liquidus and solidus phase boundaries were determined by the onset temperature of heating and cooling scans, respectively, because the completion temperature of a phase transition has no meaning in binary solutions. Dimyristoyl- and distearoyl-phosphatidylcholines. where the difference in the, lipid chain-length is four carbon atoms, mixed well even at pretransition temperature.     

Prediction of ice content in biological model solutions when frozen under high pressure

High pressure is, at least, as effective as cryoprotective agents (CPAs) and are used for decreasing both homogenous nucleation and freezing temperatures. This fact gives rise to a great variety of possible cryopreservation processes under high pressure. They have not been optimized yet, since they are relatively recent and are mainly based on the pressure–temperature phase diagram of pure water. Very few phase diagrams of biological material are available under pressure. This is owing to the lack of suitable equipment and to the difficulties encountered in carrying out the measurements. Different aqueous solutions of salt and CPAs as biological models are studied in the range of 0°C down to ‐35°C, 0.1 up to 250 MPa, and 0–20% w/w total solute concentration. The phase transition curves of glycerol and of sodium chloride with either glycerol or sucrose in aqueous solutions are determined in a high hydrostatic pressure vessel. The experimental phase diagrams of binary solutions were well described by a third‐degree polynomial equation. It was also shown that Robinson and Stokes' equation at high pressure succeeds in predicting the phase diagrams of both binary and ternary solutions. The solute cryoconcentration and the ice content were calculated as a function of temperature and pressure conditions during the freezing of a binary solution. This information should provide a basis upon which high‐pressure cryopreservation processes may be performed and the damages derived from ice formation evaluated. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Differential scanning calorimetry and 2H NMR studies of the phase behavior of gramicidin-phosphatidylcholine mixtures

The extents of two-phase coexistence in the phase diagrams of mixtures of gramicidin with 1,2-bis(perdeuteriopalmitoyl)-sn-glycero-3-phosphocholine (DPPC-d62) and with 1,2-bis(perdeuteriomyristoyl)-sn-glycero-3-phosphocholine (DMPC-d54) mixtures have been explored with differential scanning calorimetry (DSC) and deuterium nuclear magnetic resonance (2H NMR). For both systems, increased gramicidin content causes a decrease in transition enthalpy and a broadening of the peak in excess heat capacity at the transition. In DMPC-d54-based mixtures, the broadening is roughly symmetric about the pure lipid transition temperature. Addition of gramicidin to DPPC-d62 extends the excess heat capacity peak on the low-temperature side, resulting in a slightly asymmetric scan. Deuterium NMR spectra showing a superposition of gel and liquid-crystalline components, observed for both mixtures, indicate the presence of two-phase coexistence. For the DPPC-d62-based mixtures, two-phase coexistence is restricted to an approximately 2 degrees C temperature range below the pure transition temperature. For DMPC-d54-based mixtures, the region of two-phase coexistence is even narrower. For both mixtures, beyond a gramicidin mole fraction of 2%, distinct gel and liquid-crystal contributions to the spectra cannot be distinguished. Along with the broad featureless nature of the DSC scan in this region, this is taken to indicate that the transition has been replaced by a continuous phase change. These results are consistent with the existence of a closed two-phase region having a critical concentration of gramicidin below 2 mol%.     

Separation of amino acids and peptides by temperature induced phase partitioning. Theoretical model for partitioning and experimental data

There is a strong interest in use of ‘smart polymers’ in separation systems. These are polymers which can react on external influence, such as temperature or pH change. With such polymers it is possible from the outside to affect the properties of a separation system. Amphiphilic copolymers show drastic changes in solubility properties, such as self-association and phase separation, at e.g. temperature increase. The random copolymers of ethylene oxide and propylene oxide units (EOPO-polymers) can form aqueous two-phase systems above the copolymer cloud point temperature. Two phases are formed, one consisting of 40–60% polymer in water and the other of almost 100% water. Amino acids and peptides can be partitioned in the thermoseparating systems. The partitioning strongly depends on the solute hydrophobicity, where aromatic amino acids and peptides are partitioned to the polymer phase and hydrophilic to the water phase. Salt effects can be used to enhance the partitioning of charged molecules. The thermodynamic driving forces which govern the partitioning of molecules in a thermoseparated aqueous phase system is described with use of the Flory-Huggins theory for polymer solutions. Expressions are derived which show the entropic and enthalpic effects on solute partitioning. This revised version was published online in July 2006 with corrections to the Cover Date.