Repeatability of material parameter extraction of liquids from transmission terahertz time-domain measurements.

Recently, many research groups worldwide have reported on the THz properties of liquids. Often these parameters, i.e., refractive index and absorption coefficient, are determined using liquids in cuvettes and terahertz time-domain spectroscopy. Here, we discuss the measurement process and determine how repeatable such measurements and the data extraction are using rapeseed oil as a sample. We address system stability, cuvette positioning, cuvette cleaning and cuvette assembly as sources affecting the repeatability. The results show that system stability and cuvette assembly are the most prominent factors limiting the repeatability of the THz measurements. These findings suggest that a single cuvette with precise positioning and thorough cleaning of the cuvette delivers the best discrimination among different liquid samples. Furthermore, when using a single cuvette and measurement systems of similar stability, the repeatability calculated based on several consecutive measurements is a good estimate to tell whether samples can be discriminated.

Periodic sampling errors in terahertz time-domain measurements.

An extensive investigation of the origin and the impact of periodic sampling errors of terahertz time-domain spectroscopy systems is given. We present experimental findings and compare them to a theoretical model which is developed in this work. Special attention is given to the influence on the extraction of the refractive index from measurements. It can be shown that even distortions of the spectrum at frequencies higher than the used bandwidth can have a significant impact on the extracted refractive index.

Glass polymorphism in glycerol-water mixtures: I. A computer simulation study.

We perform out-of-equilibrium molecular dynamics (MD) simulations of water-glycerol mixtures in the glass state. Specifically, we study the transformations between low-density (LDA) and high-density amorphous (HDA) forms of these mixtures induced by compression/decompression at constant temperature. Our MD simulations reproduce qualitatively the density changes observed in experiments. Specifically, the LDA-HDA transformation becomes (i) smoother and (ii) the hysteresis in a compression/decompression cycle decreases as T and/or glycerol content increase. This is surprising given the fast compression/decompression rates (relative to experiments) accessible in MD simulations. We study mixtures with glycerol molar concentration χ(g) = 0-13% and find that, for the present mixture models and rates, the LDA-HDA transformation is detectable up to χ(g) ≈ 5%. As the concentration increases, the density of the starting glass (i.e., LDA at approximately χ(g) ≤ 5%) rapidly increases while, instead, the density of HDA remains practically constant. Accordingly, the LDA state and hence glass polymorphism become inaccessible for glassy mixtures with approximately χ(g) > 5%. We present an analysis of the molecular-level changes underlying the LDA-HDA transformation. As observed in pure glassy water, during the LDA-to-HDA transformation, water molecules within the mixture approach each other, moving from the second to the first hydration shell and filling the first interstitial shell of water molecules. Interestingly, similar changes also occur around glycerol OH groups. It follows that glycerol OH groups contribute to the density increase during the LDA-HDA transformation. An analysis of the hydrogen bond (HB)-network of the mixtures shows that the LDA-HDA transformation is accompanied by minor changes in the number of HBs of water and glycerol. Instead, large changes in glycerol and water coordination numbers occur. We also perform a detailed analysis of the effects that the glycerol force field (FF) has on our results. By comparing MD simulations using two different glycerol models, we find that glycerol conformations indeed depend on the FF employed. Yet, the thermodynamic and microscopic mechanisms accompanying the LDA-HDA transformation and hence, our main results, do not. This work is accompanied by an experimental report where we study the glass polymorphism in glycerol-water mixtures prepared by isobaric cooling at 1 bar.

Glass polymorphism in glycerol-water mixtures: II. Experimental studies.

We report a detailed experimental study of (i) pressure-induced transformations in glycerol-water mixtures at T = 77 K and P = 0-1.8 GPa, and (ii) heating-induced transformations of glycerol-water mixtures recovered at 1 atm and T = 77 K. Our samples are prepared by cooling the solutions at ambient pressure at various cooling rates (100 K s(-1)-10 K h(-1)) and for the whole range of glycerol mole fractions, χ(g). Depending on concentration and cooling rates, cooling leads to samples containing amorphous ice (χg ≥ 0.20), ice (χ(g) ≤ 0.32), and/or "distorted ice" (0 < χ(g) ≤ 0.38). Upon compression, we find that (a) fully vitrified samples at χ(g) ≥ 0.20 do not show glass polymorphism, in agreement with previous works; (b) samples containing ice show pressure-induced amorphization (PIA) leading to the formation of high-density amorphous ice (HDA). PIA of ice domains within the glycerol-water mixtures is shown to be possible only up to χ(g) ≈ 0.32 (T = 77 K). This is rather surprising since it has been known that at χ(g) < 0.38, cooling leads to phase-separated samples with ice and maximally freeze-concentrated solution of χ(g) ≈ 0.38. Accordingly, in the range 0.32 < χ(g) < 0.38, we suggest that the water domains freeze into an interfacial ice, i.e., a highly-distorted form of layered ice, which is unable to transform to HDA upon compression. Upon heating samples recovered at 1 atm, we observe a rich phase behavior. Differential scanning calorimetry indicates that only at χ(g) ≤ 0.15, the water domains within the sample exhibit polyamorphism, i.e., the HDA-to-LDA (low-density amorphous ice) transformation. At 0.15 < χ(g) ≤ 0.38, samples contain ice, interfacial ice, and/or HDA domains. All samples (χ(g) ≤ 0.38) show: the crystallization of amorphous ice domains, followed by the glass transition of the vitrified glycerol-water domains and, finally, the melting of ice at high temperatures. Our work exemplifies the complex "phase" behavior of glassy binary mixtures due to phase-separation (ice formation) and polyamorphism, and the relevance of sample preparation, concentration as well as cooling rates. The presence of the distorted ice (called "interphase" by us) also explains the debated "drift anomaly" upon melting. These results are compatible with the high-pressure study by Suzuki and Mishima indicating disappearance of polyamorphism at P ≈ 0.03-0.05 GPa at χ(g) ≈ 0.12-0.15 [J. Chem. Phys., 2014, 141, 094505].

Pressure-induced transformations in glassy water: A computer simulation study using the TIP4P/2005 model.

We study the pressure-induced transformations between low-density amorphous (LDA) and high-density amorphous (HDA) ice by performing out-of-equilibrium molecular dynamics (MD) simulations. We employ the TIP4P/2005 water model and show that this model reproduces qualitatively the LDA-HDA transformations observed experimentally. Specifically, the TIP4P/2005 model reproduces remarkably well the (i) structure (OO, OH, and HH radial distribution functions) and (ii) densities of LDA and HDA at P = 0.1 MPa and T = 80 K, as well as (iii) the qualitative behavior of ρ(P) during compression-induced LDA-to-HDA and decompression-induced HDA-to-LDA transformations. At the rates explored, the HDA-to-LDA transformation is less pronounced than in experiments. By studying the LDA-HDA transformations for a broad range of compression/decompression temperatures, we construct a "P-T phase diagram" for glassy water that is consistent with experiments and remarkably similar to that reported previously for ST2 water. This phase diagram is not inconsistent with the possibility of TIP4P/2005 water exhibiting a liquid-liquid phase transition at low temperatures. A comparison with previous MD simulation studies of SPC/E and ST2 water as well as experiments indicates that, overall, the TIP4P/2005 model performs better than the SPC/E and ST2 models. The effects of cooling and compression rates as well as aging on our MD simulations results are also discussed. The MD results are qualitatively robust under variations of cooling/compression rates (accessible in simulations) and are not affected by aging the hyperquenched glass for at least 1 µs. A byproduct of this work is the calculation of TIP4P/2005 water's diffusion coefficient D(T) at P = 0.1 MPa. It is found that, for T ≥ 210 K, D(T) ≈ (T - T(MCT))(-γ) as predicted by mode coupling theory and in agreement with experiments. For TIP4P/2005 water, T(MCT) = 209 K and γ = 2.14, very close to the corresponding experimental values T(MCT) = 221 K and γ = 2.2.

Effects of temperature on the thermodynamic and dynamical properties of glycerol-water mixtures: a computer simulation study of three different force fields.

Glycerol-water solutions are relevant in technological and scientific applications, such as in the preservation of biomolecules and tissues at low temperatures. We perform molecular dynamics simulations of glycerol-water mixtures with glycerol molar fractions of χg = 0-100% at P = 0.1 MPa and T = 210-460 K. We focus on the effects of temperature and concentration on the thermodynamic (density ρ, thermal expansion coefficient αP, isobaric specific heat cP, compressibility κT) and dynamical (glycerol and water diffusion coefficients, Dg and Dw) properties of the mixtures. In particular, we test the sensitivity of computer simulation results to the glycerol force field and water model (TIP3P and TIP4P/2005) employed. All mixture models underestimate ρ at high T and tend to overestimate ρ at low T; only the mixture model based on TIP4P/2005 water exhibits a density maximum at low χg, as expected. All models overestimate αP, cP, and κT; they are able to reproduce qualitatively the T dependence of αP and κT but fail in the case of cP. In all cases, Dg and Dw follow the Vogel-Tamman-Fulcher equation and decouple at low T, with Dw/Dg increasing upon cooling. Overall, the mixture based on TIP4P/2005 water provides better thermodynamic and dynamical properties than the mixtures based on TIP3P water, even at χg = 20%.

Specialization and bet hedging in heterogeneous populations.

Phenotypic heterogeneity is a strategy commonly used by bacteria to rapidly adapt to changing environmental conditions. Here, we study the interplay between phenotypic heterogeneity and genetic diversity in spatially extended populations. By analyzing the spatiotemporal dynamics, we show that the level of mobility and the type of competition qualitatively influence the persistence of phenotypic heterogeneity. While direct competition generally promotes persistence of phenotypic heterogeneity, specialization dominates in models with indirect competition irrespective of the degree of mobility.

Effects of temperature on the properties of glycerol: a computer simulation study of five different force fields.

We perform molecular dynamics simulations of glycerol (propane-1,2,3-triol) at normal pressure and a wide range of temperatures (300-460 K) and study the sensitivity of simulation results to the force field (FF) considered. We employ five commonly used FFs: (i) AMBER, (ii) CHARMM22, and (iii) three versions of the OPLS-AA FF (OPLS1, OPLS2, and OPLS3). We study thermodynamic (density ρ(T), thermal expansion coefficient αP(T), isobaric specific heat cP(T)), dynamic (diffusion coefficient D(T)), as well as structural properties (molecular conformations and hydrogen-bond statistics). In comparison with experiments, FFs i and iii provide reasonable estimations of ρ(T) with deviations of ≤4.5%; for FF ii, deviations in density are more pronounced, ≤9%. Values of αP(T) vary considerably among the FFs; e.g., deviations are ≤9% for OPLS1-FF and ≤60% for FF ii. For all models studied, values of cP(T) are approximately twice the corresponding experimental values. Diffusion coefficients are very sensitive to the FFs considered. Specifically, for FFs i and ii and OPLS3, the values of D(T) are remarkably close to the experimental values over the whole range of temperatures studied. Instead, in the cases of OPLS1 and OPLS2-FFs, D(T) is underestimated by approximately 2 orders of magnitude. Interestingly, in all cases, D(T) can be well described by a Vogel-Tamman-Fulcher equation, as observed in experiments. We present a detailed characterization of glycerol backbone conformation based on the traditional classification introduced by Bastiansen, defined in terms of glycerol's OCCC dihedral angles. All FFs indicate that the conformer population varies smoothly with temperature. However, the FFs provide very different conformer distributions. This implies that, from the microscopic point of view, these glycerol models may provide very different liquid environments for, for example, guest biomolecules and hence may play a relevant role in interpreting simulation results involving glycerol-based solutions. We also discuss the statistics of inter- and intramolecular hydrogen bonds (HBs). The FFs are qualitatively comparable regarding HB statistics; however, quantitative differences remain. For example, molecules form a total of 5.5-7 HBs at T = 350 K, depending on the FF considered, including at least one intramolecular HB.