Quantitative Theories Research Articles

Numerical evaluation of overestimation of the interface thickness around ellipsoidal particle

When interfacial layers are viewed as a separate phase, the interface thickness plays an essential role in assessing physico-mechanical properties of particulate materials. However, the interface thickness from sectional analysis is often overestimated, due to the irregularity of surface textures of grains in opaque materials that gives rise to the normal of a cross-sectional plane non-perpendicular to the surface of grains. Hence, the determination of the overestimation degree is very critical to precisely obtain the interface thickness. This article develops a numerical model for the overestimation degree of the interface thickness around an ellipsoidal grain with an arbitrary aspect ratio, by applying an accurate sectional analysis algorithm, and quantitative stereology and geometrical probability theories. Furthermore, on the basis of the developed numerical model, the influence of ellipsoidal particle shape on the overestimation degree is quantitatively characterized.

Using height association studies to gain insights into human idiopathic short and syndromic stature phenotypes

Variation in adult height is not the most clinically relevant human quantitative trait, yet its study provides the foundation of many quantitative genetics theories and important statistical concepts (e.g. regression). Even today, the analysis of adult height by genome-wide association studies (GWAS) continues to significantly impact human genetics: these studies have led to the discovery of >200 loci associated with variation in adult height and have highlighted the very polygenic nature of human continuous traits. In this brief review, I discuss and provide examples on how such genetic associations, identified in individuals of normal height, could help understand the complex genetics behind such phenotypes as idiopathic short stature (ISS) or extreme/syndromic height phenotypes of unknown cause.

Investment Decision Support for Engineering Projects Based on Risk Correlation Analysis

Investment decisions are usually made on the basis of the subjective judgments of experts subjected to the information gap during the preliminary stages of a project. As a consequence, a series of errors in risk prediction and/or decision‐making will be generated leading to out of control investment and project failure. In this paper, the variable fuzzy set theory and intelligent algorithms integrated with case‐based reasoning are presented. The proposed algorithm manages the numerous fuzzy concepts and variable factors of a project and also sets up the decision‐making process in accordance with past cases and experiences. Furthermore, it decreases the calculation difficulty and reduces the decision‐making reaction time. Three types of risk correlations combined with different characteristics of engineering projects are summarized, and each of these correlations is expounded at the project investment decision‐making stage. Quantitative and qualitative change theories of variable fuzzy sets are also addressed for investment risk warning. The approach presented in this paper enables the risk analysis in a simple and intuitive manner and realizes the integration of objective and subjective risk assessments within the decision‐makers′ risk expectation.

Optimal and Non-optimal Behavior Across Species

We take a behavioral approach to decision-making and, apply it across species. First we review quantitative theories that provide good accounts of both non-human and human choice, as, for example, in operant analogues to foraging (including the optimal diet model and delay-reduction theory). Second we show that for all species studied, organisms will acquire observing responses, whose only function is to produce stimuli correlated with the schedule of reinforcement in effect. Observing responses are maintained only by “good news”: “no news” is preferred to “bad news”. We then review two areas of decision-making in which human participants (but not necessarily non-humans) tend to make robust errors of judgment or to approach decisions non-optimally. The first area is the sunk-cost effect in which participants persist in a losing course of action, ignoring the currently operative marginal utilities. The second area is base-rate neglect in which participants overweight case cues (such as witness testimony or medical diagnostic tests) and underweight information about the base rates or probabilities of the events in question. In both cases we argue that the poor decisions we make are affected by the misapplication of previously learned rules and strategies that have utility in other situations. These conclusions are strengthened both by the behavioral approach taken and by the data revealed in cross-species comparisons.

MODELING AND ANALYTICAL/NUMERICAL ANALYSIS OF WEAR PROCESSES IN A MECHANICAL FRICTION CLUTCH

This work is devoted to modeling and the analytical/numerical analysis of tribological processes occurring on the contact surface of shields of a mechanical friction clutch. Although the considered problems have been already studied earlier, however, simplified mathematical models have been used and applied. Unlike previous works, our work takes into account elasticity and wear properties of material of shields rubbing themselves. A general nonlinear differential model of wear is considered, as well as a wear model in the integral form taking into account gradual decrease of speed of wear of shields as a result of abrasive adapting to each other in the process of the exploitation. Equations modeling contact pressure on the contact surface of shields are derived and they yield the contact pressure and the wear of the shields. An analytical/numerical analysis is carried out with the qualitative and quantitative theories of differential and integral equations, including Laplace transformation. Many interesting results are obtained, illustrated and discussed. The presented results can be widened and used in other disciplines of the science, for instance, in physics of solids or biomechanics of various human joints.

Globalization as a Driver or Bottleneck for Sustainable Development: General Tendencies and European Implications

This article looks at the long-term, structural determinants of environmental performance in the world system. In multiple standard OLS regression models, we test the effects of 26 standard predictor variables, including the ‘four freedoms’ of goods, capital, labour and services, on the following indicators of sustainable development • avoiding net trade of ecological footprint gha per person • Carbon emissions per million US dollars GDP • CO2 per capita • Environmental Performance Index (EPI) • Global footprint per capita • Happy Life Years • Happy Planet Index • ln (number of people per mill inhabitants 1980-2000 killed by natural disasters per year+1) Our research shows that the apprehensions of quantitative globalization critical research are fully vindicated by the significant negative environmental effects of the foreign savings rate. High foreign savings are indeed a driver of global footprint, and are a blockade against a satisfactory Happy Planet Index performance. The New International Division of Labour (NIDL)-model (Froebel et al., 1980) is one of the prime drivers of high CO2 per capita emissions. MNC penetration, the master variable of most quantitative dependency theories, blocks environmental performance (EPI-Index) and several other socially important processes. Worker remittances have a significant positive effect on the Happy Planet Index, and Happy Life Years.

Animal dynamics based approach for modeling pedestrian crowd egress under panic conditions

Collective movement is important during emergencies such as natural disasters or terrorist attacks, when rapid egress is essential for escape. The development of quantitative theories and models to explain and predict the collective dynamics of pedestrians has been hindered by the lack of complementary data under emergency conditions. Collective patterns are not restricted to humans, but have been observed in other non-human biological systems. In this study, a mathematical model for crowd panic is derived from collective animal dynamics. The development and validation of the model is supported by data from experiments with panicking Argentine ants ( Linepithema humile). A first attempt is also made to scale the model parameters for collective pedestrian traffic from those for ant traffic, by employing a scaling concept approach commonly used in biology.

Animal dynamics based approach for modeling pedestrian crowd egress under panic conditions

Collective movement is important during emergencies such as natural disasters or terrorist attacks, when rapid egress is essential for escape. The development of quantitative theories and models to explain and predict the collective dynamics of pedestrians has been hindered by the lack of complementary data under emergency conditions. Collective patterns are not restricted to humans, but have been observed in other non-human biological systems. In this study, a mathematical model for crowd panic is derived from collective animal dynamics. The development and validation of the model is supported by data from experiments with panicking Argentine ants (Linepithema humile). A first attempt is also made to scale the model parameters for collective pedestrian traffic from those for ant traffic, by employing a scaling concept approach commonly used in biology.

From Boolean to Quantitative Theories of Reactive Systems

From Boolean to Quantitative Theories of Reactive Systems

Conditioned reinforcement and response strength.

Stimuli associated with primary reinforcers appear themselves to acquire the capacity to strengthen behavior. This paper reviews research on the strengthening effects of conditioned reinforcers within the context of contemporary quantitative choice theories and behavioral momentum theory. Based partially on the finding that variations in parameters of conditioned reinforcement appear not to affect response strength as measured by resistance to change, long-standing assertions that conditioned reinforcers do not strengthen behavior in a reinforcement-like fashion are considered. A signposts or means-to-an-end account is explored and appears to provide a plausible alternative interpretation of the effects of stimuli associated with primary reinforcers. Related suggestions that primary reinforcers also might not have their effects via a strengthening process are explored and found to be worthy of serious consideration.

Are psychological quantities and measurement relevant in the 21st century?

Osborne (2010, p. 1) argues that as quantitative psychologists we must “keep challenging ourselves…and…continue questioning and examining our tacit assumptions”. Whilst I wholeheartedly endorse the critical and optimistic spirit of his article, I find it alarming that he only implicitly directs quantitative psychologists to question and examine their most fundamental tacit assumption. This is the claim, or rather, inadequately tested hypothesis that continuous, psychological quantities exist. Unless we “shrug off the shackles of 20th century methodology and thinking” (Osborne, 2010, p. 3) and seriously address this hypothesis, the relevance of quantitative psychology, and the “measurements” it provides will remain obscure in this century and beyond. The desire to replicate the physical sciences model in psychology has a long history, as do criticisms of this desire, which I cannot do justice in the present commentary (see Michell, 1999). The culmination of this history took place when Stevens (1946)proposed a new definition of measurement, as numerical application according to rule, which would have a profound effect upon the practice of Psychology, including the “explosive progress” that Osborne (2010, p. 2) refers to. But, at what cost has this “progress” come? The fact that Stevens’ definition endures in the mainstream even today is testament to the schism between quantitative psychology and quantitative science more generally. There is only one rule for measurement in quantitative science. This is, the estimation of a magnitude of a quantity by its ratio to a unit of the same quantity (Michell, 1999). This is not a trivial matter, as even Stevens (1946) acknowledged that everything from the calculation of the humble mean and t-test through to the sophisticated multivariate analyses that Osborne (2010) refers to are contingent upon this “kind of” measurement1. Thus, even though our data may be “hard-earned” (p. 3), if they are not derived from defensible measurement practices, then our toil simply leads to questionable inferences and continued scepticism from outside the discipline (Cliff, 1996). Thankfully, a number of quantitative psychologists have eschewed Stevens’ definition and proposed ways to measure psychological attributes in a manner that is consistent with the physical sciences (Luce and Tukey, 1964; Rasch, 1980; Michell, 1990). Axiomatic Conjoint Measurement theory and the class of Rasch models stand out from the crowd as potential tools to be used by psychologists to test their quantitative assumptions, establish standard units of measurement, and bring about defensible methodological practices (see Humphry and Andrich, 2008; Kyngdon, 2008). However, the minimal impact that these approaches have had on mainstream psychology over the past half-century does raise the question of whether they are sufficient or even necessary for addressing the question of psychological quantities. A more fundamental cognitive shift seems to be required whereby the application of such mathematical models is not seen as an end unto itself, as measurement never takes place in a theoretical vacuum. One only needs to take a cursory look at measurement practices in the physical sciences to realize that they are intrinsically linked to what has been described as a “body of workable, quantitative theories and laws” (Michell, 1999, p. 217). This means a body of substantive, quantitative theories and laws and not algebraic ideals. Thus, before we may defensibly apply such models, the burden is upon us as quantitative psychologists to delve into the applied literature to establish and experimentally investigate strong, quantitative psychological theories (Borsboom, 2006). Michell (2009) and Trendler (2009) provide examples of the necessary theoretical analysis and their conclusions are alarming. Firstly, Michell argues that many psychological attributes are necessarily not quantitative, as unlike established physical quantities, the differences between levels of these attributes are not mutually homogeneous. Furthermore, Trendler argues that quantification and measurement will never be possible in psychology, as we will never possess the necessary control over our subject matter. Whilst their arguments are compelling, it is pertinent to note that the systems of measurement in the physical sciences were developed over centuries and necessarily required a large amount of qualitative work to substantiate them (Kuhn, 1961). Thus, it seems premature to conclude that quantification and measurement are, in principle, not possible in psychology. However, this possibility can only be realized (or not) if we stop begging the quantity and measurement questions. So I accept Osborne's (2010) challenges and I add my own (on behalf of the authors cited from whom this commentary is derived). If it is to be shown that Quantitative Psychology is relevant to the 21st century and beyond, then we must provide empirical evidence for the existence of psychological quantities and then establish units by which they can be measured. Hopefully, given Osborne's editorial directive, some of the pages of this new and exciting journal will be dedicated to this most fundamental challenge.

Discovering Associative Long-term Synaptic Modification and Timing Dependence of Plasticity – a Very Brief and Personal History

My long-term career goal was, and is, to construct credible quantitative theories of the biological basis of cognitive function. My approach is severely reductive which was a problem early on. We knew nothing about associative synaptic modification, the heart and soul of such cognitive theories. So motivated, I went to Virginia to work with my good friend Oswald Steward. In particular, I wanted to improve upon the observations of McNaughton (1977). His primary result was a demonstration of the intensity-dependence of long-term potentiation (LTP; a result that Bliss et al., 1973 looked for and somehow missed). Before arriving in Virginia, I knew a two-stimulating-electrode experiment (using provably independent and non-overlapping inputs) was necessary to produce an unequivocal demonstration of associative LTP. Unfortunately, I had no specific idea of how to do the experiment. When Ossie explained his discovery of the crossed entorhinal cortex to dentate gyrus pathway and showed me the baseline physiology ongoing in his lab, I seized on the opportunity presented by two independent monosynaptic pathways suitable for associative studies. A small number of layer II cells project monosynaptically to the ipsilateral and contralateral dentate gyrus. Using a one stimulating electrode in the left dentate gyrus and a second stimulating electrode in the right dentate gyrus yielded the necessary independent monosynaptic excitatory pathways converging on the same postsynaptic neurons. Although we began with just the intention of studying LTP, we quickly discovered a postsynaptic-dependent, synaptic long-term depression. This discovery was essentially unavoidable due to all the controls built into studying the bilateral path on both sides of the brain and studying the effect of brief high frequency stimulation of just one entorhinal cortex while recording from both the left and right dentate gyri. In essence, we were running two experiments at once, one by recording from the left dentate gyrus and one by recording from the right dentate gyrus. As we were finishing up the manuscript for this work (Levy and Steward, 1983), I began thinking about the next study, and these thoughts must have been influenced by my earlier training. As background, there were my undergraduate studies in psychology and an awareness that stimuli used for conditioning worked best if they preceded a shock in negative reinforcement or a reactivated pressable lever for positive reinforcement. I also knew the Pavlovian paradigms (see discussion in Levy and Steward, 1983) and was aware of associative timing experiments in this behavioral context. Once again, by recording on both sides of the brain while performing an associative timing experiment, we automatically examined a pre-then-post as well as a post-then-pre activity paradigm. That is, if the left stimulating electrode was active before the right stimulating electrode, then recording from the left dentate gyrus was a depression paradigm while recording from the right dentate gyrus was a potentiation paradigm. Thus the spike-timing effect was discovered. The published experiments themselves were completed before the end of 1980 and were reported at a wonderful little gathering in 1981 at Brown University (hosted by Leon Cooper and eventually published in 1985; Levy, 1985). Shortly after our publication, in which postsynaptic cell firing in the dentate gyrus was controlled by each ipsilateral pathway, Gustafsson et al. (1987) published a timing study in CA1. They used intracellular control of postsynaptic excitation. However, their temporal resolution was lower than our work. With later studies came higher temporal resolution (Bi and Poo, 1998). Our later work showed that the accuracy of timing was better than 20 ms and – by using large, multiple TTX injections – that we really were in complete control of the EC inputs (Lopez et al., 1990). Another pretty set of studies by Ossie's student Geoff White show that STDP could be localized within a dendritic region (White et al., 1988, 1990). Later in the decade, Holmes and Levy (1990) worked out the biophysics of the potentiation portion of the spike timing rule. My major experimental regret is the drug experiments that I shunned early on (but see Desmond et al., 1991). My undergraduate and graduate experience with neuropharmacology left me with skepticism concerning drug specificity, and I was mistaken not to accept and use the rapidly developing glutamate receptor pharmacology of the early 1980s. Nevertheless, the two original Levy and Steward (1979, 1983) studies were enough to embark on my goal of quantitative modeling with half of the STDP playing a major role in later theoretical work (Levy and Desmond, 1985; Levy, 1989; Levy et al., 1990).

Quantifying the evolutionary divergence of protein structures: The role of function change and function conservation

The molecular clock hypothesis, stating that protein sequences diverge in evolution by accumulating amino acid substitutions at an almost constant rate, played a major role in the development of molecular evolution and boosted quantitative theories of evolutionary change. These studies were extended to protein structures by the seminal paper by Chothia and Lesk, which established the approximate proportionality between structure and sequence divergence. Here we analyse how function influences the relationship between sequence and structure divergence, studying four large superfamilies of evolutionarily related proteins: globins, aldolases, P-loop and NADP-binding. We introduce the contact divergence, which is more consistent with sequence divergence than previously used structure divergence measures. Our main findings are: (1) Small structure and sequence divergences are proportional, consistent with the molecular clock. Approximate validity of the clock is also supported by the analysis of the clustering coefficient of structure similarity networks. (2) Functional constraints strongly limit the structure divergence of proteins performing the same function and may allow to identify incomplete or wrong functional annotations. (3) The rate of structure versus sequence divergence is larger for proteins performing different functions than for proteins performing the same function. We conjecture that this acceleration is due to positive selection for new functions. Accelerations in structure divergence are also suggested by the analysis of the clustering coefficient. (4) For low sequence identity, structural diversity explodes. We conjecture that this explosion is related to functional diversification. (5) Large indels are almost always associated with function changes.

Quantitative Notions of Leakage for One-try Attacks

Recent research in quantitative theories for information-hiding topics, such as Anonymity and Secure Information Flow, tend to converge towards the idea of modeling the system as a noisy channel in the information-theoretic sense. The notion of information leakage, or vulnerability of the system, has been related in some approaches to the concept of mutual information of the channel. A recent work of Smith has shown, however, that if the attack consists in one single try, then the mutual information and other concepts based on Shannon entropy are not suitable, and he has proposed to use Rényi's min-entropy instead. In this paper, we consider and compare two different possibilities of defining the leakage, based on the Bayes risk, a concept related to Rényi min-entropy.

Questioning the universe: concepts in physics

UNITS AND POWERS OF TEN PHYSICS AND ITS METHODOLOGY What Is Physics? Methodology The First Scientist Why Do You Believe? Back to the Questions How Do We Answer the Questions? The Need to Be Quantitative Theories Models Aesthetic Judgments MOTION Relating the Variables of Motion Graphs of One-Dimensional Motion Constant Speed Constant Acceleration Two-Dimensional Motion FORCES The Fundamental Forces A Specific Force Law: Newtonian Gravity Weight How Does Force Affect Motion? Newton's Second Law Newton, the Apple, and the Moon Combining Two Laws The Mass of the Earth Newton's First Law What and Where Is the Force? Newton's Third Law How Does a Horse Pull a Wagon? How Can We Walk? ELECTROMAGNETISM The Electric Force Law Unifying Electricity and Magnetism Ampere's Law Faraday's Law The Lorentz Force Back to Ampere's Law Where Are the Moving Charges? THE FIELD CONCEPT What Is the Connection? Action at a Distance Is This a Legitimate Explanation? The Field Concept How Does This Help Explain Noncontact Forces? Thinking Like a Physicist Is There a Way to Tell the Difference? Understanding the Time Delay The Speed and Identity of the Kink Back to Contact Forces THE CHARACTER OF NATURAL LAWS Causality The Prime Directive Symmetry Symmetry and the Laws of Nature Space Translation Symmetry Time Translation Symmetry Time Reversal (Reflection) Symmetry Matter-Antimatter Symmetry (Matter Reflection) Space Reflection Symmetry (Parity) CONSERVATION LAWS Conservation of Momentum Conservation of Energy The Different Forms of Energy Conversion of Energy A Specific Example: The Roller Coaster A Nonconservation Law: The Second Law of Thermodynamics THE HISTORY OF THE ATOM The Greek Model Thomson's Plum Pudding Model The Rutherford Experiment The Planetary Model What Do We Do Now? The Atom Today The Electron Volt: A Useful Energy Unit THE NUCLEUS Nuclear Properties Why Neutrons? Nuclear Decays Alpha Decay Beta Decay Gamma Decay Half-Life and Carbon Dating The Full Beta Decay Story The Prediction The Experimental Results What Do We Do Now? Look Closely at the Theory Look Closely at the Experimental Results A Possible Explanation THE NATURE OF LIGHT Properties of Particles Properties of Waves Wave Vocabulary Is Light Made Up of Waves or Particles? Back to Diffraction Why the Sky Is Blue THE THEORY OF RELATIVITY Frames of Reference and Relative Speeds Galilean Relativity Maxwell and the Ether The Speed of Waves The Ether The Michelson Morley Experiment An Analogy: Boats in a River The Real Experiment The Lorentz Contraction Another Crazy Idea Assumptions We Take for Granted The Postulates of Special Relativity Some Interesting Facts about Einstein and the Birth of Relativity Consequences of the Postulates of Relativity The Relativity of Simultaneity Time Dilation The Light Clock Useful Definitions Length Contraction Length and Lorentz Contraction E = mc2 and All That Back to Addition of Speeds The Car in the Garage Paradox The Twin Paradox and Space Travel Relativity and You QUANTUM MECHANICS Max Planck and the Beginnings of Quantum Theory The Photoelectric Effect The Bohr Atom de Broglie Waves Time to Stop and Catch Our Breath The Heisenberg Uncertainty Principle The Schrodinger Equation: An Equation for the Waves Does God Play Dice? THE STANDARD MODEL OF ELEMENTARY PARTICLE PHYSICS The Basic Ideas of the Standard Model The Unification of Forces Bosons: The Particles Associated with Forces Electroweak Unification The Unification of Matter Two Classes of Matter Particles Similarities Differences More about Quarks More about Leptons A Mystery Particle Flowchart COSMOLOGY The Expansion of the Universe Measuring Speeds Using the Doppler Effect Measuring Distances Nearby Stars More Distant Stars: Standard Candles Light from the Big Bang: CMB Radiation The Evolution of the Universe The Planck Time The GUT Time The Disappearance of Antimatter Two Sticky Problems and a Solution The Solution: Inflation The Electroweak Time The Formation of Particles The Formation of Nuclei The Formation of Atoms The Formation of Stars and Galaxies Dark Matter Dark Energy EPILOGUE SUGGESTED FURTHER READINGS INDEX Each chapter ends with a Guide to Key Ideas and Questions/Problems

Theories of hearing.

One of the more compelling and important aspects of auditory science has been the ability to relate perception to physiology and physics. This challenging endeavor has attracted fine minds from various disciplines and has provided theoretical frameworks for rigorously studying and describing at various levels many basic aspects of hearing. An example is the application of “signal detection theory” and its collection of tools for empirical and theoretical investigation of certain aspects of audition. But what of the future? Do we have comparable tools to construct quantitative theories that enable prediction of complex aspects of audition? Do we need new tools? Definitive answers may or may not be provided during this session.

THE ONTOGENETIC TRAJECTORY OF THE PHENOTYPIC COVARIANCE MATRIX, WITH EXAMPLES FROM CRANIOFACIAL SHAPE IN RATS AND HUMANS

Many classic quantitative genetic theories assume the covariance structure among adult phenotypic traits to be relatively static during evolution. But the cross-sectional covariance matrix arises from the joint variation of a large range of developmental processes and hence is not constant over the period during which a population of developing organisms is actually exposed to selection. To examine how development shapes the phenotypic covariance structure, we ordinate the age-specific covariance matrices of shape coordinates for craniofacial growth in rats and humans. The metric that we use for this purpose is given by the square root of the summed squared log relative eigenvalues. This is the natural metric on the space of positive-definite symmetric matrices, which we introduce and justify in a biometric context. In both species, the covariance matrices appear to change continually throughout the full period of postnatal development. The resulting ontogenetic trajectories alter their direction at major changes of the developmental programs whereas they are fairly straight in between. Consequently, phenotypic covariance matrices--and thus also response to selection--should be expected to vary both over ontogenetic and phylogenetic time scales as different phenotypes are necessarily produced by different developmental pathways.

Redox entropy of plastocyanin: Developing a microscopic view of mesoscopic polar solvation

We report applications of analytical formalisms and molecular dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of the theory required to describe polar solvation at the mesoscopic scale. The analytical techniques include a microscopic formalism based on structure factors of the solvent dipolar orientations and density and continuum dielectric theories. The microscopic theory employs the atomistic structure of the protein with force-field atomic charges and solvent structure factors obtained from separate MD simulations of the homogeneous solvent. The MD simulations provide linear response solvation free energies and reorganization energies of electron transfer in the temperature range of 280-310 K. We found that continuum models universally underestimate solvation entropies, and a more favorable agreement is reported between the microscopic calculations and MD simulations. The analysis of simulations also suggests that difficulties of extending standard formalisms to protein solvation are related to the inhomogeneous structure of the solvation shell at the protein-water interface combining islands of highly structured water around ionized residues along with partial dewetting of hydrophobic patches. Quantitative theories of electrostatic protein hydration need to incorporate realistic density profile of water at the protein-water interface.

Prevalence of Temperature-Dependent Heat Capacity Changes in Protein-DNA Interactions

A large, negative ΔCp of DNA binding is a thermodynamic property of the majority of sequence-specific DNA-protein interactions, and a common, but not universal property of non-sequence-specific DNA binding. In a recent study of the binding of Taq polymerase to DNA, we showed that both the full-length polymerase and its “Klentaq” large fragment bind to primed-template DNA with significant negative heat capacities. Herein, we have extended this analysis by analyzing this data for temperature-variable heat capacity effects (ΔΔCp), and have similarly analyzed an additional 47 protein-DNA binding pairs from the scientific literature. Over half of the systems examined can be easily fit to a function that includes a ΔΔCp parameter. Of these, 90% display negative ΔΔCp values, with the result that the ΔCp of DNA binding will become more negative with rising temperature. The results of this collective analysis have potentially significant consequences for current quantitative theories relating ΔCp values to changes in accessible surface area, which rely on the assumption of temperature invariance of the ΔCp of binding. Solution structural data for Klentaq polymerase demonstrate that the observed heat capacity effects are not the result of a coupled folding event.

Formation mechanisms for ice‐stream lateral shear margin moraines

AbstractThe lateral shear margins of palaeo‐ice stream beds are occasionally marked by large curvilinear moraines, but little work has addressed how they might form. In this paper we review the characteristics of ‘lateral shear margin moraines’ and present two quantitative models for their formation: (i) differential erosion rates related to lateral variations in the stream velocity and (ii) lateral incursion from inter‐stream ridges after the thinner stream retreats, where the shear margin moraine is consequently just a terminal moraine of the inter‐stream ridge. Other possible mechanisms of formation are addressed qualitatively. Both of our quantitative theories are, in principle, feasible, but the incursion model is less plausible and inconsistent with observations. The differential erosion model can predict moraines tens of metres thick and several kilometres wide, which can be formed in a thousand years. The width of the moraine depends on the competition between a term that varies across the ice stream because it is dependent on ice velocity and that always causes erosion, and a term related to the local accumulation rate, which causes erosion if is positive and deposition if negative. These terms combine to create the possibility of deposition at the shear margins of ice streams in ablation areas. The width of the moraine has a tendency to increase with the width of the stream. The conditions that permit shear margin moraines to form are quite constrained: too much ablation and deposition occurs everywhere rather than just near the lateral margins of the ice streams; too little ablation and there is erosion everywhere. This is consistent with the infrequent observations of lateral shear margin moraines. Copyright © 2008 John Wiley & Sons, Ltd.