Effects Of Compositional Heterogeneity Research Articles

Effects of compositional heterogeneity and spatial autocorrelation on richness and diversity in simulated landscapes

AbstractLandscape structure plays a key role in mediating a variety of ecological processes affecting biodiversity patterns; however, its precise effects and the mechanisms underpinning them remain unclear. While the effects of landscape structure have been extensively investigated both empirically and theoretically from a metapopulation perspective, the effects of spatial structure at the landscape scale remain poorly explored from a metacommunity perspective. Here, we attempt to address this gap using a spatially explicit, individual‐based metacommunity model to explore the effects of landscape compositional heterogeneity and per se spatial configuration on diversity at the landscape and patch levels via their influence on long‐term community assembly processes. Our model simulates communities composed of species of annual, asexual organisms living, reproducing, dispersing, and competing within grid‐based, fractal landscapes that vary in their magnitude of spatial environmental heterogeneity and in their degree of spatial environmental autocorrelation. Communities are additionally subject to temporal environmental fluctuations and external immigration, allowing for turnover in community composition. We found that compositional heterogeneity and spatial autocorrelation had differing effects on richness, diversity, and the landscape and patch scales. Landscape‐level diversity was driven by community dissimilarity at the patch level and increased with greater heterogeneity, while landscape richness was largely the result of the short‐term accumulation of immigrants and decreased with greater compositional heterogeneity. Both richness and diversity decreased in variance with greater compositional heterogeneity, indicating a reduction in community turnover over time. Patch‐level richness and diversity patterns appeared to be driven by overall landscape richness and local mass effects, resulting in maximum patch‐level richness and diversity at moderate levels of compositional heterogeneity and high spatial autocorrelation.

Effect of compositional heterogeneity on the mechanical properties of a single-phase Cu-9Al alloy with different grain sizes

Recent investigations have indicated that compositional heterogeneity, which is compositional undulation of alloying elements in single-phase solid solutions, can enhance the strength without sacrificing ductility, similar to cluster strengthening, of single-crystal nano-pillars and bulk nanocrystalline metallic materials. However, the impact of compositional heterogeneity on the mechanical properties of coarse-grained metallic materials is not yet fully understood. In this study, we examine the influence of compositional heterogeneity on the tensile mechanical properties of a Cu-9Al (at.%) alloy with a coarse-grained structure fabricated using wire arc additive manufacturing and with an ultrafine-grained structure after further processing. Our results demonstrate that the effects of compositional heterogeneity depend significantly on the grain size. Specifically, in ultrafine-grained samples, there is a remarkable improvement in strength with only a slight reduction in ductility. However, as grain size increases, the strengthening effect of compositional heterogeneity diminishes, resulting in softening with a significant loss of ductility. These phenomena can be attributed to the behaviour of dislocations in the materials. Overall, this study highlights the importance of understanding the relationship between compositional heterogeneity, grain size, and mechanical properties in metallic materials, which can inform the design of new materials with improved strength and ductility.

The Effect of Compositional Heterogeneity on the Martensite Start Temperature of a High Strength Steel During Rapid Austenitisation and Cooling

Many low alloy steels are compositionally heterogeneous due to the preferential segregation of alloying elements to the dendritic or interdendritic regions when the steel is first solidified (microsegregation). This segregation is often ignored when using CCT diagrams to predict the phase transformation behaviour of steels, but may be of importance in some industrially-relevant cases. This work focuses on the martensite start temperature (Ms ) of Super CMV, a high strength aerospace steel, after rapid austenitisation treatment to various peak temperatures from 900 °C to 1300 °C. It was found that the average Ms temperature increased with increasing peak temperature (and prior austenite grain size) at peak temperatures of 1100°C and above, which is to be expected conventionally. However, at peak temperatures of below 1100°C, the Ms temperature increased with decreasing prior-austenite grain size. It is proposed that this was due to the presence of non-dissolved carbides in these conditions, particularly in enriched bands of material, which deplete the matrix and hence raise Ms .

Analytical pyrolysis of bagasse and groundnut shell briquettes: Kinetics and pyrolysate composition studies

Biomass briquettes are expanding its reach from domestic stoves to giant power plants. This study aims to evaluate the effect of compositional heterogeneity of bagasse and groundnut shell briquettes on slow pyrolysis kinetics, fast pyrolysis product distribution and time evolution of pyrolysates. The average apparent activation energy of pyrolysis was low for 0.71–1.4 mm particles of bagasse (175.5 kJ mol−1) and 1.4–2 mm particles of groundnut shell (169.3 kJ mol−1). The production of phenolics, furan derivatives, monoaromatics and condensed ring aromatics exhibited marked changes with respect to particle size of biomass and temperature. The phenolic selectivity was more from large biomass particles. The production of aromatic hydrocarbons is correlated with the particle size of biomass, and the extent of secondary reactions is shown to be coupled with heat and mass transport of pyrolysates within the confined pores of the sample. The evolution rate of pyrolysis vapors increased with increasing temperature.

Six-State Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses.

Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of six-state recoding approaches by comparing the performance of analyses on recoded and non-recoded data sets that have been simulated under gradients of compositional heterogeneity or saturation. In our simulation analyses, non-recoding approaches consistently outperform six-state recoding approaches. Our results suggest that six-state recoding strategies are not effective in the face of high saturation. Furthermore, while recoding strategies do buffer the effects of compositional heterogeneity, the loss of information that accompanies six-state recoding outweighs its benefits. In addition, we evaluate recoding schemes with 9, 12, 15, and 18 states and show that these consistently outperform six-state recoding. Our analyses of other recoding schemes suggest that under conditions of very high compositional heterogeneity, it may be advantageous to apply recoding using more than six states, but we caution that applying any recoding should include sufficient justification. Our results have important implications for the more than 90 published papers that have incorporated six-state recoding, many of which have significant bearing on relationships across the tree of life. [Compositional heterogeneity; Dayhoff 6-state recoding; S&R 6-state recoding; six-state amino acid recoding; substitution saturation.]

Examining the Role of Atomic Scale Heterogeneity on the Thermal Conductivity of Transparent, Thermally Insulating, Mesoporous Silica–Titania Thin Films

This paper examines the effect of compositional heterogeneity on the thermal conductivity of transparent, mesoporous silica–titania composites that contain either 10 or 20 mol % titania. The relative hydrolysis rates of the silica and titania precursors were modified to control their compositional heterogeneity, while the ratio of polymer to inorganic precursors (silica + titania) was varied to control the porosity of the films. All films were optically transparent at thicknesses up to 1 μm with transmittance above 90% and haze below 5% at visible wavelengths. It was found that the heterogeneity of the titania species in the 10 mol % titania samples could be easily tailored from highly dispersed titania to a composition with heterogeneous silica-rich and titania-rich domains. By contrast, samples with 20 mol % titania always showed a heterogeneous titania distribution. The results show that mesoporous films with more homogeneously distributed titania had a lower thermal conductivity at all porosities, likely due to increases in propagon and diffuson scattering as a result of the increased number density of titania heteroatom scattering centers. These results increase our understanding of heat carrier propagation in amorphous materials and add to the design rules for creating amorphous, optically clear, low thermal conductivity materials.

Most Cephalaspidea have a shell, but transcriptomes can provide them with a backbone (Gastropoda: Heterobranchia)

Cephalaspidea is an order of marine gastropods found worldwide, often in sandy or muddy habitats, which has a convoluted taxonomic history based on convergent or ill-defined morphological characters. The cephalaspidean shell—which can be external and robust, internal, or altogether absent in the adult—is of particular interest in this group, and a well-resolved phylogeny can give us greater insight into the evolution of this character. Molecular data have clarified many relationships within Cephalaspidea, but studies involving few Sanger sequenced phylogenetic markers remain limited in the resolution they provide. Here we take a phylogenomic approach, the first to address internal cephalaspidean relationships, sequencing and assembling transcriptomes de novo from 22 ingroup taxa—representing the five currently accepted superfamilies, 10 of the 21 currently recognized families, and 21 genera—and analyzing these along with publicly available data. We generated two main datasets varying by a minimum taxon occupancy threshold (50% and 75%), and analyzed these using maximum likelihood, Bayesian inference and a coalescence-based method. We find a consistent, well-supported topology, with full support across most nodes including at the family and genus level, which also appears to be robust to the effect of compositional heterogeneity among amino acids in the dataset. Our analyses find Newnesioidea as the sister group to the rest of Cephalaspidea. Within the rest of the order, Philinoidea is the sister group to a clade that comprises (Bulloidea (Haminoeoidea, Cylichnoidea)). There is strong support for several previously suggested, but tenuously supported relationships such as the genus Odontoglaja nesting within the family Aglajidae, and a sister group relationship between Gastropteridae and Colpodaspididae, with Philinoglossidae as their sister group. We discuss these results and their implications in the context of current cephalaspidean taxonomy and evolution. Genomic-scale data give a backbone to this group of snails and slugs, and hold promise for a completely resolved Cephalaspidea.

Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae, Bignoniaceae)

AbstractThe accurate analyses of massive amounts of data obtained through next‐generation sequencing depend on the selection of appropriate evolutionary models. Many plastid phylogenomic studies typically analyze plastome data as a single partition, or divided by a region, using a concatenate “supergene” approach. The effects of molecular evolutionary models and character partition strategies on plastome‐based phylogenies have generally been evaluated at higher taxonomic levels in green plants. Using plastome data from 32 species of Amphilophium, a genus of Neotropical lianas, we explored potential sources of topological incongruence with different plastid genome datasets and approaches. Specifically, we evaluated the effects of compositional heterogeneity, codon usage bias, positive selection, and incomplete lineage sorting as sources of systematic error (i.e., the recovery of well‐supported conflicting topologies). We compared different datasets (e.g., non‐coding regions, exons, and codon‐aligned and translated amino acids) using concatenated approaches under site‐heterogeneous and site‐homogeneous models, as well as multispecies coalescent (MSC) methods. We found incongruences in recovered phylogenetic relationships, which were mainly located in short internodes. The MSC and concatenated approaches recovered similar topologies. The analysis of GC content and codon usage bias indicated higher substitution rates and AT excess at the third codon positions, and we found evidence of positive selection in 3% of amino acid sites. There were no significant differences among species in site biochemical profiles. We argue that the selection of appropriate partition strategies and evolutionary models is important to increase accuracy in phylogenetic relationships, even when using plastome datasets, which is still the primarily used genome in plant phylogenetics.

Insights into the phylogeny of Hemiptera from increased mitogenomic taxon sampling

Although reconstruction of the phylogeny of Hemiptera has progressed tremendously over the past two decades, some higher-level relationships remain poorly resolved. Here, we investigated the Hemiptera higher-level relationships using full mitochondrial genome data from 357 ingroup species, representing the most comprehensive sampling yet undertaken for reconstructing the phylogeny of this group. In this study, 92 mitochondrial genomes were newly determined. Various data treatment methods and substitution models were applied to tree reconstructions. Effects of compositional heterogeneity, rate heterogeneity, model adequacy and taxon sampling on support values and topological stability were explored. Phylogenetic analyses (1) confirmed the monophyly of Hemiptera under site-heterogeneous model, (2) placed Sternorrhyncha as sister to all other Hemiptera, (3) recovered Coccoidea as the sister taxon of Aphidoidea, followed successively by Aleyrodoidea and Psylloidea, and (4) indicated that the grouping of Coleorrhyncha and Fulgoromorpha was the result of long-branch attraction effect.

Sequencing of complete mitochondrial genomes confirms synonymization of Hyalomma asiaticum asiaticum and kozlovi, and advances phylogenetic hypotheses for the Ixodidae.

Phylogeny of hard ticks (Ixodidae) remains unresolved. Mitochondrial genomes (mitogenomes) are increasingly used to resolve phylogenetic controversies, but remain unavailable for the entire large Hyalomma genus. Hyalomma asiaticum is a parasitic tick distributed throughout the Asia. As a result of great morphological variability, two subspecies have been recognised historically; until a morphological data-based synonymization was proposed. However, this hypothesis was never tested using molecular data. Therefore, objectives of this study were to: 1. sequence the first Hyalomma mitogenome; 2. scrutinise the proposed synonymization using molecular data, i.e. complete mitogenomes of both subspecies: H. a. asiaticum and kozlovi; 3. conduct phylogenomic and comparative analyses of all available Ixodidae mitogenomes. Results corroborate the proposed synonymization: the two mitogenomes are almost identical (99.6%). Genomic features of both mitogenomes are standard for Metastriata; which includes the presence of two control regions and all three "Tick-Box" motifs. Gene order and strand distribution are perfectly conserved for the entire Metastriata group. Suspecting compositional biases, we conducted phylogenetic analyses (29 almost complete mitogenomes) using homogeneous and heterogeneous (CAT) models of substitution. The results were congruent, apart from the deep-level topology of prostriate ticks (Ixodes): the homogeneous model produced a monophyletic Ixodes, but the CAT model produced a paraphyletic Ixodes (and thereby Prostriata), divided into Australasian and non-Australasian clades. This topology implies that all metastriate ticks have evolved from the ancestor of the non-Australian branch of prostriate ticks. Metastriata was divided into three clades: 1. Amblyomminae and Rhipicephalinae (Rhipicephalus, Hyalomma, Dermacentor); 2. Haemaphysalinae and Bothriocrotoninae, plus Amblyomma sphenodonti; 3. Amblyomma elaphense, basal to all Metastriata. We conclude that mitogenomes have the potential to resolve the long-standing debate about the evolutionary history of ticks, but heterogeneous evolutionary models should be used to alleviate the effects of compositional heterogeneity on deep-level relationships.

Regulating kinetics of deformation-induced phase transformation in amorphous alloy composite via tuning nano-scale compositional heterogeneity in crystalline phase

Nano-scale compositional heterogeneity of crystalline phase in Ti-based amorphous alloy composites (AACs) has been successfully tuned by tuning cooling rate in solidification process. And the effect of compositional heterogeneity on the kinetics of the deformation-induced phase transformation was investigated by in-situ synchrotron-based high-energy X-ray diffraction (HE-XRD) and ex-situ transmission electron microscopy. In-situ HEXRD experiments provide obvious evidence that with the decrease of the cooling rate during solidification, the critical stress of the deformation-induced phase transformation becomes lower, and the phase transformation rate becomes higher. Further high angle annular dark field-scanning electron microscopy investigation shows that the occurrence of the nano-scale Zr-lean compositional heterogeneity, which can favor the nucleation of the martensite, is the reason for the variation of the phase transformation kinetics.

Double layering of a thermochemical plume in the upper mantle beneath Hawaii

According to classical plume theory, purely thermal upwellings rise through the mantle, pond in a thin layer beneath the lithosphere, and generate hotspot volcanism. Neglected by this theory, however, are the dynamical effects of compositional heterogeneity carried by mantle plumes even though this heterogeneity has been commonly identified in sources of hotspot magmas. Numerical models predict that a hot, compositionally heterogeneous mantle plume containing a denser eclogite component tends to pool at ∼300–410 km depth before rising to feed a shallower sublithospheric layer. This double-layered structure of a thermochemical plume is more consistent with seismic tomographic images at Hawaii than the classical plume model. The thermochemical structure as well as time dependence of plume material rising from the deeper into the shallower layer can further account for long-term fluctuations in volcanic activity and asymmetry in bathymetry, seismic structure, and magma chemistry across the hotspot track, as are observed.

Encrustation and trace element composition of <i>Neogloboquadrina dutertrei</i> assessed from single chamber analyses – implications for paleotemperature estimates

Abstract. Crust formation is a common phenomenon in planktonic foraminifera. Because of their different formation mechanism and hence composition, crusts affect the overall test composition and therefore complicate the use of crust-bearing foraminifera in paleoceanography. Such species are often used to estimate subsurface paleotemperatures, and although the influence of encrustation on the trace element/Ca ratio is recognised, it has not been systematically explored between and within tests. Here we use laser ablation ICP-MS to assess the variability in trace element composition of the crust of Neogloboquadrina dutertrei within individual chambers, as well as the effect of compositional heterogeneity of the crust on whole test chemistry. Compositionally, the outer crust differs from inner layer by lower Mg/Ca and Mn/Ca, but is indistinguishable in Sr/Ca. Crust thickness decreases towards the younger chambers, and it may be entirely absent from the last chamber. In contrast to Mn/Ca and Sr/Ca, crustal Mg/Ca ratios show a tendency towards higher values on the younger chambers. These patterns in crust thickness and in crust Mg/Ca indicate that temperature is not the dominant factor controlling crust composition. Temperature estimates based on N. dutertrei, and presumably other crust-forming species too, are therefore biased towards too low values. Through comparison of modern and glacial tests, we show that this bias is not constant and that changes in crust thickness and/or in Mg/Ca values can spuriously suggest temperature changes.

Effects of hydrophilic unit and its distribution on interfacial binding between single-walled carbon nanotubes, vinyl pyrrolidone and vinyl acetate copolymers

In this work, a molecular dynamic (MD) simulation method was employed to study the interfacial binding between the single-walled carbon nanotubes (SWCNTs) and some polymers and copolymers. The polymers studied include poly(vinyl pyrrolidone) as hydrophilic and poly(vinyl acetate) as hydrophobic polymers and also copolymers consisting of a series of vinyl pyrrolidone and vinyl acetate copolymers with different homogeneities in the backbone. The copolymers investigated have different structures and include alternative, diblock and triblock copolymers. This study has computed the intermolecular interaction energies between SWCNTs and polymers/copolymers in order to assess the effects of compositional heterogeneity on the interfacial binding between SWCNTs and polymers/copolymers. Also, the morphology of polymers/copolymers adsorbed to the surface of nanotubes has been studied. The obtained results showed that the intermolecular interactions in the simulated systems are strongly influenced by the monomer sequence distribution of hydrophilic and hydrophobic monomers in copolymers. The different values of intermolecular interaction energy for copolymers with identical numbers of hydrophilic and hydrophobic monomers but with different distributions suggest that an efficient load transfer through the interface between nanotube and copolymers is highly dependent on compositional heterogeneity of copolymers. Furthermore, we obtained the plots of the radial distribution function and the radius of gyration in order to study the effects of compositional heterogeneity on behavior of the studied nanocomposites. The results of the radial distribution function and the radius of gyration are in agreement with the findings of interfacial binding between SWCNTs and polymers/copolymers.

Effects of compositional heterogeneity and nanoporosity of raw and treated biomass-generated soot on adsorption and absorption of organic contaminants

A biomass-generated soot was sequentially treated by HCl-HF solution, organic solvent, and oxidative acid to remove ash, extractable native organic matter (EOM), and amorphous carbon. The compositional heterogeneity and nano-structure of the untreated and treated soot samples were characterized by elemental analysis, thermal gravimetric analysis, BET-N2 surface area, and electron microscopic analysis. Sorption properties of polar and nonpolar organic pollutants onto the soot samples were compared, and individual contributions of adsorption and absorption were quantified. The sorption isotherms for raw sample were practically linear, while were nonlinear for the pretreated-soot. The removal of EOM enhanced adsorption and reduced absorption, indicating that EOM served as a partitioning phase and simultaneously masked the adsorptive sites. By drastic-oxidation, the outer amorphous carbon and the inner disordered core of the soot particles were completely removed, and a fullerene-like nanoporous structure (aromatic shell) was created, which promoted additional π–π interaction between phenanthrene and the soot.

Numerical study of scattering from chains composed of two nonsegregated labeled blocks in an athermal solvent: Effects of compositional heterogeneity

Numerical calculations and Monte Carlo simulations have been performed to explore the dynamic scattering behavior of solutions of copolymer chains composed by two nonsegregated blocks in an athermal solvent. The experimental investigation of this property for real copolymers has shown the presence of a variety of modes, with a complex variation of their locations and intensities, which we try to partially understand with the present simulation work. For this purpose, we use chain samples with a small amount of polydispersity in the block lengths. We have introduced opposite scattering contrast factors for the A and B units. In this way, zero-averaged contrast conditions have been set for the overall scattering, avoiding the presence of the collective mode that otherwise would manifest for any nondilute system of polymer chains. Static and dynamic scattering functions have been obtained for the different samples. For the dynamic scattering functions, three modes are observed in agreement with existing experiments. The first two modes, predominant for low values of the scattering variable, q, are assigned to correspond to the compositional heterogeneity and the first internal relaxation of the chains, as predicted by the theory. The variation of the mode intensities and positions with polymer concentration is analyzed. It semiquantitatively agrees with the existing experimental data.

Phase Behavior of Ordered Diblock Copolymer Blends: Effect of Compositional Heterogeneity

Diblock copolymers order into a variety of periodic morphologies when the constituent blocks are sufficiently incompatible. Previous studies have demonstrated that classical dispersion (spherical and cylindrical) and lamellar morphologies, as well as complex morphologies (e.g., gyroid*, lamellar catenoid, and hexagonally perforated lamellae), can be selectively accessed through either tailored molecular synthesis or copolymer/homopolymer blends. In the present work, control over ultimate morphology is achieved through the use of binary copolymer blends composed of two strongly-segregated poly(styrene-b-isoprene) (SI) diblock copolymers of equal molecular weights but different compositions (one 50 wt % S and the other 85 wt % S). Blend morphologies are examined by electron microscopy (including three-dimensional imaging) and small-angle X-ray scattering, and a theoretical framework is proposed to describe strongly-segregated copolymer blends exhibiting the lamellar morphology. Results obtained here indicate that diblock copolymer blends of a given bulk composition may exhibit coexisting morphologies but in general behave as single-phase diblock copolymers of equal molecular composition, suggesting that such blends offer an alternative, and attractive, route by which to generate a desired morphology.

Geochemical constraints on initial and final depths of melting beneath mid‐ocean ridges

The comparison of the composition and volume of mid‐ocean ridge basalts to predicted values inferred from experimental and theoretical studies is one of the primary tools for mapping thermal structure and the geometry of melting beneath mid‐ocean ridges. Several indicators of either the pressure or degree of melting are commonly employed: Na2O concentration in melts is roughly inversely proportional to the extent of melting; (Srn/Yb)N is affected by the proportion of melt that is generated in the garnet stability field (deeper than 60 km); and FeO content increases with increasing pressure of melting. Crustal thickness also depends on the geometry and extent of melting. K2O/TiO2 is used as an indicator of the enrichment of the mantle source. For normal ridges, we find that regional averages of Fe(8) (FeO normalized to 8 wt % MgO to correct for fractionation) are strongly dependent on enrichment. Thus if Fe(8) is used to infer to the pressure of melting, correction for the effects of compositional heterogeneity of the source is needed. Even with the correction for heterogeneity, however, it is difficult to correct for all fractionation effects accurately enough to use FeO as a depth indicator except in the most extreme cases. Mantle heterogeneity also affects Na(8) and (Sm/Yb)N, but the correction for enrichment by linear regression of the Na(8) and (Sm/Yb)N to a common reference value of K2O/TiO2 does not change the relationship between (Sm/Yb)N and Na(8) that is used to estimate depth and degree of melting. In simple melting models, the composition and crustal thickness depend on the rate of pressure release melting per kilometer of uplift; the initial depth of onset of melting; the final depth of termination of melting; the nature of melt equilibration, i.e., batch or fractional melting; and the geometry of upwelling, i.e., passive or dynamic flow. We find that melting beneath normal ridges commences in a narrow depth range in the spinel‐garnet transition zone (about 60–70 km in depth), suggesting a much smaller variation in potential temperature beneath normal ridges (<60°K) than previously suggested (250°K, Klein and Langmuir, 1987; Langmuir et al., 1992). The difference is due primarily to the component of Fe(8) variation caused by mantle heterogeneity in the global data set and to difficulties in correcting FeO for fractionation. The initial depth of melting beneath hotspots is greater than beneath normal ridges, indicating significantly higher temperatures. Instead of melting continuing to the base of the crust beneath normal ridges, it ceases at a variety of depths beneath the crust. Variations in final depth of melting may be due to cooling to the surface, effects of transform faults, and the local, relative importance of dynamic upwelling.

Helix-coil transitions of compositionally heterogeneous DNA.

AbstractFragmented and mitomycin C cross‐linked E. coli DNA was fractionated according to base composition by means of hydroxylapatite chromatography and density‐gradient centrifugation in order to determine the effect of compositional heterogeneity on the breadth of the helix–coil transition. The transitions of some of the fractions are broader than that of the unfractionated DNA, due, presumably, to nonrandom sequences in molecules of 5 × 105 daltons. Analysis of the transition breadths in terms of the known heterogeneity leads to reconsideration of current DNA helix–coil transition theory. We propose that partially denatured states include those for which the chains do not remain in strict register. Denaturation profiles are comprehensible only if this multitude of entropically favorable, degenerate states is included in the theory.