Patterns of shrub expansion in Alaskan arctic river corridors suggest phase transition

Recent increases in deciduous shrub cover are a primary focus of terrestrial Arctic research. This study examined the historic spatial patterns of shrub expansion on the North Slope of Alaska to determine the potential for a phase transition from tundra to shrubland. We examined the historic variability of landscape‐scale tall shrub expansion patterns on nine sites within river valleys in the Brooks Range and North Slope uplands (BRNS) between the 1950s and circa 2010 by calculating percent cover (PCTCOV), patch density (PADENS), patch size variability (CVSIZE), mean nearest neighbor distance (MEDIST) and the multi‐scale information fractal dimension (d_I) to assess spatial homogeneity for shrub cover. We also devised conceptual models for trends in these metrics before, during, and after a phase transition, and compared these to our results. By developing a regression equation between PCTCOV and d_I and using universal critical d_I values, we derived the PCTCOV required for a phase transition to occur. All nine sites exhibited increases in PCTCOV. Five of the nine sites exhibited an increase in PADENS, seven exhibited an increase in CVSIZE, and five exhibited a decrease in MEDIST. The d_I values for each site exceeded the requirements necessary for a phase transition. Although fine‐scale heterogeneity is still present, landscape‐scale patterns suggest our study areas are either currently in a state of phase transition from tundra to shrubland or are progressing towards spatial homogeneity for shrubland. Our results indicate that the shrub tundra in the river valleys of the north slope of Alaska has reached a tipping point. If climate trends observed in recent decades continue, the shrub tundra will continue towards homogeneity with regard to the cover of tall shrubs.     

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.     

Infrared characterization of conformational differences in the lamellar phases of 1,3-dipalmitoyl-sn-glycero-2-phosphocholine

Fourier transform infrared spectroscopy was used to characterize the lamellar phases of 1,3-dipalmitoyl-sn-glycero-2-phosphocholine (1,3-DPPC), a positional isomer of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (1,2-DPPC). The molecule exists in three distinct phases over the temperature interval 0–70°C. In the low-temperature (L_c) phase, the spectra are indicative of acyl chains packed in an orthorhombic subcell, while the carbonyl groups and phosphate ester at the head group show evidence of only partial hydration. The transition from the low-temperature (L_c) phase to the intermediate-temperature (Lβ) phase at 25°C corresponds to a temperature-induced head-group hydration in which the hydration of the phosphate and carbonyl ester groups results in the reorganization of the hydrocarbon chain-packing subcell from orthorhombic to hexagonal. The transition from the intermediate (L_β) to the high-temperature (L_α) phase at 37°C is a gel-to-liquid-crystalline phase transition analogous to the 41.5°C transition of 1,2-DPPC. The spectra of the acyl-chain carbonyl groups show evidence of significant differences in molecular conformation at the carbonyl esters in the L_c phase. In the L_β and L_α phases, the carbonyl band contour becomes much more symmetric. However, two components are clearly present in the spectra indicating that the sn-1 and sn-3 carbonyls experience slightly different environments. The observed differences are likely due to a preferred conformation of the phosphocholine group relative to the glycerol backbone. Indications from the infrared spectra of differences in the structure of the C=O groups provide a possible explanation for the selection of the sn-1 chain of 1,3-DPPC by phospholipase A₂ on the basis of a preferred head group conformation.     

CHARACTERIZATION OF THE MAIN PHASE TRANSITION IN 1,2-DIPALMITOYL-PHOSPHATIDYLCHOLINE LUVS BY 1H NMR*

ABSTRACT

The main phase transition (Tm) of 100 nm large unilamellar vesicles (LUVs) of 1,2-dipalmitoylphosphatidylcholine (DPPC) was investigated using ¹H NMR (proton magnetic resonance) in deuterium oxide, and both DSC (differential scanning calorimetry) and IR (infrared) spectroscopy in water and deuterium oxide. The ability of ¹H NMR to determine Tm was demonstrated and the values obtained were in general agreement with those observed with DSC and IR. However, the temperature range of the transition observed by NMR was significantly broader than that observed with either DSC or IR. The effect of deuterium oxide on Tm was studied by comparing results obtained in water and deuterium oxide with DSC and IR. The results showed no significant difference in Tm or temperature range of transition determined in these solvents.     

Percolation Transition in the Parallel Hard-cube Model Fluid

Abstract

Pressure and self-diffusion calculations for a model fluid system of parallel hard cubes are reported. When viewed alongside equations of state incorporating the known coefficients in the virial expansion (b ₂ to b ₇), a weak phase change is postulated around 1/4 close-packing. Changes in behaviour are also seen at the same density for the self-diffusion coefficient and an associated single-particle free volume. It is conjectured that a transition may be identifiable with the low-density percolation transition that occurs in all hard-core fluids when the single particle configurational volume becomes extensive. If the hard-sphere model were to behave similarly, the observations may have implications for the general development of liquid-state theory.     

Fine-tuned spatiotemporal dynamics of sporophylls in movement-assisted dichogamy: A study on Clerodendrum infortunatum

Hermaphroditism is cost-effective because a common investment in reward and attractive structures yields benefits through both male and female reproductive success. However, the advantage is accompanied by an increased risk of self-pollen deposition, which is generally disadvantageous. Hermaphroditic plants reduce self-pollen deposition by separating sporophylls (a term applied to the stamens and carpels) either spatially (herkogamy) or temporally (dichogamy). In movement-assisted dichogamy, both sporophylls show coordinated motion in opposite directions. However, the effectiveness of this movement in reducing self-pollen deposition may be compromised at the point when the sporophylls cross each other and are close enough to interfere, resulting in a transition phase problem. The solution to this problem lies in the details of the spatiotemporal dynamics of the sporophylls in relation to their reproductive maturity. We studied these details across the floral lifetime of a protandrous shrub, Clerodendrum infortunatum (Lamiaceae), in rainforest fragments of the Western Ghats, India. We took photos of flowers at regular time intervals and measured sporophyll angles from the images. We also carried out a field experiment to determine stigma receptivity. We found that the stigma lobes remained narrowly opened at transition, and the stigma surfaces remained non-receptive. Our findings suggest that the effectiveness of dichogamy is maximized through two properties of the transition phase: physical resistance to self-pollen deposition by narrow stigma lobe opening and chemical non-receptivity of the stigma during this phase. This study emphasizes the importance of accessory adaptations in movement-assisted dichogamy to tackle the transition phase problem.     

Succinate production in dual-phase Escherichia coli fermentations depends on the time of transition from aerobic to anaerobic conditions

We examined succinic acid production in Escherichia coli AFP111 using dual-phase fermentations, which comprise an initial aerobic growth phase followed by an anaerobic production phase. AFP111 has mutations in the pfl, ldhA, and ptsG genes, and we additionally transformed this strain with the pyc gene (AFP111/pTrc99A-pyc) to provide metabolic flexibility at the pyruvate node. Aerobic fermentations with these two strains were completed to catalog physiological states during aerobic growth that might influence succinate generation in the anaerobic phase. Activities of six key enzymes were also determined for these aerobic fermentations. From these results, six transition times based on physiological states were selected for studying dual-phase fermentations. The final succinate yield and productivity depend greatly on the physiological state of the cells at the time of transition. Using the best transition time, fermentations achieved a final succinic acid concentration of 99.2 g/l with an overall yield of 110% and productivity of 1.3 g/l h. Journal of Industrial Microbiology & Biotechnology (2002) 28, 325–332 DOI: 10.1038/sj/jim/7000250 Received 01 October 2001/ Accepted in revised form 12 March 2002     

State and Phase Transition Behaviors ofQuercus rubraSeed Axes and Cotyledonary Tissues: Relevance to the Desiccation Sensitivity and Cryopreservation of Recalcitrant Seeds

Freezing and melting transitions of cellular water in embryonic axes and cotyledonary tissues of recalcitrantQuercus rubra(red oak) seeds were compared under slow and rapid cooling conditions. The relevance of desiccation sensitivity (critical water content) and state/phase transition behaviors to cryopreservation was examined. Under a slow to intermediate cooling condition (≤10°C min⁻¹), unfrozen water content in the tissues decreased to less than the critical water content, resulting in a dehydration damage. Under a rapid cooling condition (>100°C min⁻¹) using liquid nitrogen (LN₂), freeze-induced dehydration damage could be avoided if the initial water content was >0.50 g g⁻¹dry wt. However, at water content >0.50 g g⁻¹dry wt, the vitrified cellular matrix was highly unstable upon warming at 10°C min⁻¹. These results offered a theoretical explanation on the difficulty for successful cryopreservation of recalcitrant red oak embryonic axes. A complete state/phase transition diagram for red oak axes was constructed, and a vitrification-based cryopreservation protocol that employed predehydration and rapid cooling was examined. State/phase transition behaviors of cellular water are important parameters for cryopreservation; however, vitrification alone was not sufficient for seed tissues to survive the cryopreservation condition.     

Studies on the Critical Micellar Concentration and Phase Transitions of Stearoylcarnitine

The critical micellar concentration (CMC) of stearoylcarnitine was determined at different pH values at room temperature by fluorescence spectroscopy, monitoring the spectral changes of 8-anilinonaphthalene-1-sulfonate (ANS). The CMC was found to vary with pH, increasing from about 10 μM at pH 3.0 to ca. 25 μM at pH 7.0, but decreasing slightly with further increase in pH to approximately 19 μM at pH 10.0. Differential scanning calorimetry (DSC) shows that stearoylcarnitine dispersed in water at low concentration undergoes a broad thermotropic phase transition at 44.5°C, with a transition enthalpy of 15.0 kcal/mol. The transition temperature (T _t) shifts to ca. 50.5°C in the presence of 1 mM EDTA or when the concentration is increased significantly. The turbidity of aqueous dispersions of stearoylcarnitine was found to be considerably high at low temperatures, which decreases quite abruptly over a short temperature range, indicating that a transition occurs from a phase of large aggregates to one of much smaller aggregates, most likely micelles. The phase transition temperature was determined as 29.1°C at pH 3.0, which increased with increasing pH up to a value of 55.3°C at pH 8.6 and remains nearly constant thereafter up to pH 11.2. The pH dependence of CMC and T _t suggest that the pK _a of the carboxyl group of long chain acylcarnitines shifts to higher temperatures upon aggregation (micelles or bilayer membranes).     

Glass Transition Temperatures Studied by MD Simulation of Some Alkali Metasilicates

Abstract

Molecular dynamics simulation of some alkali metasilicates (M₂SiO₃, M = Li, Na, K) was performed to compare glass transition temperatures, T_g , defined in various ways. The potential parameters derived from ab initio MO calculations were used and found to reproduce the inflection of V-T relation on cooling the system. The T_g defined by the inflection point corresponds well to that defined by geometrical changes of coordination polyhedra found in previous work. The self-diffusion coefficients of the alkali ions in higher temperature regions were shown to be related to the amount of free volume in these systems.     

Three-State Diagram for DNA

Abstract

Experimental phase diagrams (A form, B form, Coil) were built in the coordinates (a, alcohol fraction: T, temperature) for the natural DNAs and poly d(A-T). The main parameter of the B-A transition,—cooperativity length, v _o, was estimated by the slopes of the branches A-B, A-Coil, B-Coil in the vicinity of the triple point: v _o +AD0- 10-20 base pairs, which corresponds to the energy for the B/A junction of 1.2–1.8 kcal/mol.

We discovered two new effects which are due to the coexistence of the three different conformations in one polymeric molecule: an increase in the melting temperature above that for the ‘ideal’ triple point (i.e. for the case of the ideal phase transitions); a widening of the melting curve within the B-A transition range.

The physics of these phenomena is discussed.     

Dimyristoylphosphatidic acid/cholesterol bilayers

Lipid bilayers and monolayers composed of dimyristoylphosphatidic acid (DMPA) and cholesterol were characterized by differential scanning calorimetry and film balance measurements. Increasing cholesterol content decreases the bilayer phase transition temperature and enthalpy in a manner similar to that observed before for other lipid/cholesterol systems. In monomolecular films at the air-water interface cholesterol exhibits the well known condensing effect in the liquid-expanded phase, while the liquid-condensed phase is less affected. As with the bilayer phase transition, the transition temperature and change in area at the liquid-condensed to liquid-expanded phase transition, as measured from isobars at 25 dynes/cm, decreases with increasing cholesterol content. The kinetics of the phase transition of DMPA/cholesterol bilayers were measured using the pressure jump relaxation technique with optical detection. Three relaxation times were observed. The relaxation times and amplitudes pass through maximum values at the transition midpoint. With increasing cholesterol content the maximum values of the relaxation times decrease but not in a linear fashion. The time constants display an intermediate maximum at ca. 10% to 12 mol% cholesterol. This observation is discussed in terms of a possible change in the nature of the phase transition from first-order with phase separation to a continuous second-order transition. The dependence of the relaxation amplitudes on cholesterol content gave evidence for nucleation being the rate limiting step for the transition in this particular system.Abbreviations DMPA dimyristoylphosphatidic acid - DMPC dimyristoylphosphatidylcholine - DMPE dimyristoylphosphatidylethanolamine - DPPC dipalmitoylphosphatidylcholine - DSC differential scanning calorimetry Part of this research has been presented at the VIII. Discussion Group Meeting Fast Reactions in Solution of the Royal Society of Chemistry and the Max-Planck-Gesellschaft, Berlin, 26th–29th August 1984     

Molecular Dynamics Simulation of Model Lipid Membranes: Structural Effects of Impurities

Abstract

The gel to fluid phase transition or ordered to disordered phase transition observed in biological membranes are simulated by using constant energy Molecular Dynamics. The surface part of the membrane is modelled as a two-dimensional matrix formed by the head groups of the phospholipid molecules. Head molecules which are modelled as three spheres fused with three force centers, interact with each other via van der Waals and Coulomb type interactions. The -so called- impurity or foreign molecule embedded in the surface represents the protein type molecule which is present in biological membranes and control its activity. It is modelled as a pentagon having one force centers in each corner. It also interacts with the surface molecules again via van der Waals and Coulomb type interactions. The surface density is kept constant in the simulations of the systems with or without impurity. Structural and orientational changes due to impurity were observed and proved by monitoring two-dimensional order parameter. It has been shown that melting of the surface or breakage of the ordering of the surface molecules becomes easier and ordered to disordered phase transition temperature was lowered by 100 K if the impurity is present.     

Computer Simulation of the Liquid-Vapor Interface in Two Dimensions

Abstract

Constant-temperature and constant-volume molecular dynamics computer simulation results are reported for the structure of the liquid-vapor interface of two-dimensional fluids. Particles interact via a Lennard-Jones pair potential in the absence of external fields. The effects of temperature and system size on the density profile and the interfacial thickness are investigated, and the exponent describing the divergence of the interfacial thickness at the critical point is determined. The results are used to test the predictions of phenomenological theories and support the view that, in a system of small interfacial area, long-wavelength capillary waves are suppressed and the interfacial thickness is of the form predicted by the nonclassical van der Waals theory.     

A novel method to predict the glass transition of 70% glycerol aqueous solution

Vitrification has been used to successfully cryopreserve cells and tissues for over 60 years. Glass transition temperature (T _g) of the vitrification is a critical parameter, which has been investigated experimentally. In this study, an isothermal–isobaric molecular simulation (NPT-MD) is proposed to investigate the glass transition and T _g of such vitrification solution. The cohesive energy density, solubility parameter (δ) and bulk modulus of the solution during the process of the glass transition are investigated as well. The results indicate that these properties as functions of temperature can give a definite inflexion; thus, these properties can be used to predict T _g more accurately than the heat capacity (C _p ), density (ρ), volume (V) and radial distribution function (rdf). At the same time, the predicted values of T _g agree well with the experimental results. Therefore, molecular dynamics simulation is a potential method for investigating the glass transition and T _g of the vitrification solutions.     

A Monte Carlo Simulation Study of Orientational Domain Clusters in the Planar Quadrupole Model

Abstract

We have carried out a series of Monte Carlo simulations of the planar quadrupole model, using the Distributed Array Processor. A very large system size, 16 384 molecules, was employed, and special attention was given to orientational domain clustering near the order—disorder transition. Very slow fluctuations of the orientational order parameter, possibly associated with switching from one orientational domain to another, are observed. Close to the phase transition, domain clusters become extremely ramified, with highly irregular borders. On heating through the transition, the low-temperature dominant domain disappears, essentially by becoming a fractal object. The associated Hausdorff dimension decreases from D = 2 to D = 1.6 as this occurs. Although our results are consistent with a continuous, rather than a first-order, phase transition, effects of finite system size and long time scales prevent us from drawing a definite conclusion on this point.     

The Sleep Cycle Modelled as a Cortical Phase Transition

We present a mean-field model of the cortex that attempts to describe the gross changes in brain electrical activity for the cycles of natural sleep. We incorporate within the model two major sleep modulatory effects: slow changes in both synaptic efficiency and in neuron resting voltage caused by the ∼90-min cycling in acetylcholine, together with even slower changes in resting voltage caused by gradual elimination during sleep of somnogens (fatigue agents) such as adenosine. We argue that the change from slow-wave sleep (SWS) to rapid-eye-movement (REM) sleep can be understood as a first-order phase transition from a low-firing, coherent state to a high-firing, desychronized cortical state. We show that the model predictions for changes in EEG power, spectral distribution, and correlation time at the SWS-to-REM transition are consistent not only with those observed in clinical recordings of a sleeping human subject, but also with the on-cortex EEG patterns recently reported by Destexhe et al. [J. Neurosci. 19(11), (1999) 4595–4608] for the sleeping cat.     

Intermolecular Interaction of Fluoro Propanes

Abstract

Intermolecular interaction is investigated for an isomeric pair of fluoro propane, CH₃CF₂CF₃ (HFC–245cb, CB) and CH₂FCF₂CHF₂ (HFC–245ca, CA). CB has a larger dipole moment than CA. This may suggest that CB has a larger intermolecular attractive interaction than CA; the reverse is, however, found from the experimental data: normal boiling point, critical temperature, and heat of vaporization. Systematic ab initio calculations have been done for both CB dimer and CA dimer, and confirmed that the former has a smaller attractive interaction than the latter.

On the basis of these calculations, analytic functions have been constructed as the pair potential models for the two isomers. Each of these models has 11 Lennard-Jones and Coulomb interaction sites in the molecule. The present models can explain why CB dimer has a smaller attractive interaction than CA dimer, and they will easily be extended to a series of fluoro propanes, and make it possible to perform the systematic molecular simulation studies.     

Understanding bursting oscillations as periodic slow passages through bifurcation and limit points

We consider a biochemical system consisting of two allosteric enzyme reactions coupled in series. The system has been modeled by Decroly and Goldbeter (J. Theor. Biol. 124, 219 (1987)) and is described by three coupled, first-order, nonlinear, differential equations. Bursting oscillations correspond to a succession of alternating active and silent phases. The active phase is characterized by rapid oscillations while the silent phase is a period of quiescence. We propose an asymptotic analysis of the differential equations which is based on the limit of large allosteric constants. This analysis allows us to construct a time-periodic bursting solution. This solution is jumping periodically between a slowly varying steady state and a slowly varying oscillatory state. Each jump follows a slow passage through a bifurcation or limit point which we analyze in detail. Of particular interest is the slow passage through a supercritical Hopf bifurcation. The transition is from an oscillatory solution to a steady state solution. We show that the transition is delayed considerably and characterize this delay by estimating the amplitude of the oscillations at the Hopf bifurcation point.     

A Chemical Approach to Raise Cell Voltage and Suppress Phase Transition in O3 Sodium Layered Oxide Electrodes

Sodium ion batteries (NIBs) are one of the versatile technologies for low‐cost rechargeable batteries. O3‐type layered sodium transition metal oxides (NaMO₂, M = transition metal ions) are one of the most promising positive electrode materials considering their capacity. However, the use of O3 phases is limited due to their low redox voltage and associated multiple phase transitions which are detrimental for long cycling. Herein, a simple strategy is proposed to successfully combat these issues. It consists of the introduction of a larger, nontransition metal ion Sn⁴⁺ in NaMO₂ to prepare a series of NaNi_0.5Mn_{0.5? y} Sn _y O₂ (y = 0–0.5) compositions with attractive electrochemical performances, namely for y = 0.5, which shows a single‐phase transition from O3 ? P3 at the very end of the oxidation process. Na‐ion NaNi_0.5Sn_0.5O₂/C coin cells are shown to deliver an average cell voltage of 3.1 V with an excellent capacity retention as compared to an average stepwise voltage of ≈2.8 V and limited capacity retention for the pure NaNi_0.5Mn_0.5O₂ phase_. This study potentially shows the way to manipulate the O3 NaMO₂ for facilitating their practical use in NIBs.