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PubMed2001

Fluctuation dissipation theorems and irreversible thermodynamics.

We investigate the statistics of fluctuations in macroscopic systems described by thermodynamics. We begin by reviewing fluctuations in the context of linear irreversible thermodynamics and show that a more direct characterization of the fluctuations is possible, if velocity fluctuations are explicitly included in the second variation of the entropy, delta2S, about the equilibrium state. A similar procedure is then applied to what is the main goal of this paper: elucidating the nature of fluctuations in hyperbolic macroscopic systems, where signals have a finite transmission velocity. We find that, once again, velocity fluctuations have to be explicitly included, which takes us outside of extended irreversible thermodynamics as it is often defined. We find the explicit form of the fluctuation-dissipation theorem in this case, and determine the statistics of the stochastic variables in terms of the quantities appearing in the deterministic dynamics. The fluctuating theory is then reformulated in order to elucidate the relationship between the extended theory and linear irreversible thermodynamics. This has the effect of bringing out the general structure more clearly: the real, frequency-independent transport coefficients of linear irreversible thermodynamics are replaced by their complex, frequency-dependent counterparts in the extended theory.

Journal Article↗
PubMed2002

Schrödinger link between nonequilibrium thermodynamics and Fisher information.

It is known that equilibrium thermodynamics can be deduced from a constrained Fisher information extemizing process. We show here that, more generally, both nonequilibrium and equilibrium thermodynamics can be obtained from such a Fisher treatment. Equilibrium thermodynamics corresponds to the ground-state solution, and nonequilibrium thermodynamics corresponds to excited-state solutions, of a Schrödinger wave equation (SWE). That equation appears as an output of the constrained variational process that extremizes Fisher information. Both equilibrium and nonequilibrium situations can thereby be tackled by one formalism that clearly exhibits the fact that thermodynamics and quantum mechanics can both be expressed in terms of a formal SWE, out of a common informational basis. As an application, we discuss viscosity in dilute gases.

Journal Article↗
PubMed2002

Thermodynamics and effective temperatures in sheared granular matter and emulsions.

Recent theories postulate that the non-equilibrium behavior of systems experiencing jamming or structural arrest could be described by equilibrium thermodynamic concepts. If a thermodynamic framework can describe the behavior of systems far from equilibrium, then an effective temperature with a true thermodynamic meaning exists as a key parameter in characterizing the material's properties. In order to examine the validity of the thermodynamics for jammed systems, we perform a numerical experiment with a realistic granular matter model specially conceived to be reproducible in the laboratory. The results strongly support the thermodynamic picture.

Journal Article↗
PubMed2004

"A calorie is a calorie" violates the second law of thermodynamics.

The principle of "a calorie is a calorie," that weight change in hypocaloric diets is independent of macronutrient composition, is widely held in the popular and technical literature, and is frequently justified by appeal to the laws of thermodynamics. We review here some aspects of thermodynamics that bear on weight loss and the effect of macronutrient composition. The focus is the so-called metabolic advantage in low-carbohydrate diets--greater weight loss compared to isocaloric diets of different composition. Two laws of thermodynamics are relevant to the systems considered in nutrition and, whereas the first law is a conservation (of energy) law, the second is a dissipation law: something (negative entropy) is lost and therefore balance is not to be expected in diet interventions. Here, we propose that a misunderstanding of the second law accounts for the controversy about the role of macronutrient effect on weight loss and we review some aspects of elementary thermodynamics. We use data in the literature to show that thermogenesis is sufficient to predict metabolic advantage. Whereas homeostasis ensures balance under many conditions, as a general principle, "a calorie is a calorie" violates the second law of thermodynamics.

Journal Article↗
PubMed1999

Melting studies of short DNA hairpins: influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability.

Spectroscopic and calorimetric melting studies of 28 DNA hairpins were performed. These hairpins form by intramolecular folding of 16 base self-complementary DNA oligomer sequences. Sequence design dictated that the hairpin structures have a six base pair duplex linked by a four base loop and that the first five base pairs in the stem are the same in every molecule. Only loop sequence and identity of the duplex base pair closing the loop vary for the set of hairpins. For these DNA samples, melting studies were carried out to investigate effects of the variables on hairpin stability. Stability of the 28 oligomers was ascertained from their temperature-induced melting transitions in buffered 115 mM Na(+) solvent, monitored by ultraviolet absorbance and differential scanning calorimetry (DSC). Experiments revealed the melting temperatures of these molecules range from 32.4 to 60.5 degrees C and are concentration independent over strand concentrations of 0.5 to 260 microM; thus, as expected for hairpins, the melting transitions are apparently unimolecular. Model independent thermodynamic transition parameters, DeltaH(cal), DeltaS(cal), and DeltaG(cal), were determined from DSC measurements. Model dependent transition parameters, DeltaH(vH), DeltaS(vH), and DeltaG(vH) were estimated from a van't Hoff (two-state) analysis of optical melting transitions. Results of these studies reveal a significant sequence dependence to DNA hairpin stability. Thermodynamic parameters evaluated by either procedure reveal the transition enthalpy, DeltaH(cal) (DeltaH(vH)) can differ by as much as 20 kcal/mol depending on sequence. Similarly, values of the transition entropy DeltaS(cal) (DeltaS(vH)) can differ by as much as 60 cal/Kmol (eu) for different molecules. Differences in free energies DeltaG(cal) (DeltaG(vH)) are as large as 4 kcal/mol for hairpins with different sequences. Comparisons between the model independent calorimetric values and the thermodynamic parameters evaluated assuming a two-state model reveal that 10 of the 28 hairpins display non-two-state melting behavior. The database of sequence-dependent melting free energies obtained for the hairpins was employed to extract a set of n-n (nearest-neighbor) sequence dependent loop parameters that were able to reproduce the input data within error (with only two exceptions). Surprisingly, this suggests that the thermodynamic stability of the DNA hairpins can in large part be reasonably represented in terms of sums of appropriate nearest-neighbor loop sequence parameters.

Base Sequence↗
PubMed2000

Structural thermodynamics of a random coil protein in guanidine hydrochloride.

An important problem in protein folding is to understand the relationship between the structure of a denatured ensemble and its thermodynamics. Using 0 - 6M GdnHCl at fixed pH, we evaluated dimensional changes of an extensively denatured ensemble along with a thermodynamic parameter (Deltaupsilon) that monitors the proton inventory of the ensemble. Reduced and carboxyamidated ribonuclease A (RCAM) is a member of a class of disulfide-free RNase A molecules believed to be random coils (extensively denatured) in aqueous solution. Because GdnHCl interacts more favorably with the protein than water does, this denaturant is observed to increase the Stokes radius of the random coil, with the greatest Stokes radius change occurring in the 0 - 1.5M GdnHCl range. Measurement of the degree of protonation (proton inventory) of the ensemble as a function of GdnHCl at the fixed pH shows that the thermodynamic character of the ensemble also changes markedly in the 0 - 1.5M GdnHCl range, but with little or no change beyond 1.5M GdnHCl. To obtain denaturant-independent DeltaG degrees (N-D) values, the linear extrapolation method (LEM) requires the thermodynamic character of the native and denatured ensembles to be invariant in the transition zone. The results reported here indicate that proteins with a transition midpoint in the 0 - 1.5M GdnHCl range will not give denaturant-concentration independent DeltaG degrees (N-D) values. Such LEM-derived DeltaG degrees (N-D) quantities are a property of the protein and the denaturant, a condition that considerably limits their value in understanding structural energetics.

Guanidine↗
PubMed1975

The role of surface thermodynamics in thromboresistance of biomaterials.

A thermodynamic approach to the problem of platelet adsorption out of a suspension on to a smooth and homogeneous solid surface is developed. The interfacial tension values required may be estimated from contact angle data by means of an equation of state relation. According to the thermodynamic approach the functional dependence of platelet adsorption on surface tension of the solid differs according to whether the surface tension of the platelets is smaller or larger than the surface tension of the liquid in which they are suspended. The implications of this thermodynamic approach in situations where plasma proteins are present and the biomaterials surfaces may be heterogeneous and rough are discussed. Previous analyses using the critical surface tension of wetting and other surface-related parameters are compared with the thermodynamic analysis given here.

Biocompatible Materials↗
PubMed1979

[Thermodynamics of microbial processes].

The unique description of the dependences of the specific consumption coefficients on the process state known from the literature is an important prerequisite to the further increase of the intensity and efficiency of the process for the industrial protein synthesis. Suitable measuring quantities for it are entropy production, an important quantity of thermodynamics of irreversible processes, and differential heat flow which can be measured by microcalorimetry. The description of the dependences of consumption coefficients by thermodynamics of irreversible processes allows an ingenious statement of calorimetric measurements of the fermentation process to confirm and to make precise the knowledge deduced from thermodynamics. Thermodynamical considerations and calorimetric measurements are used to describe the dependences of consumption coefficients on substrate concentration, nature of limitation, and periodical perturbations of the process.

Aerobiosis↗
PubMed2002

Physical stability of amorphous pharmaceuticals: Importance of configurational thermodynamic quantities and molecular mobility.

This work relates the thermodynamic quantities (Gc, Hc, and Sc) and the molecular mobility values (1/tau) of five structurally diverse amorphous compounds to their crystallization behavior. The model compounds included: ritonavir, ABT-229, fenofibrate, sucrose, and acetaminophen. Modulated temperature DSC was used to measure the heat capacities as a function of temperature for the amorphous and crystalline phases of each compound. Knowledge of the heat capacities and fusion data allowed calculation of the configurational thermodynamic quantities and the Kauzmann temperatures (T(K)) using established relationships. The molecular relaxation time constants (tau) were then calculated from the Vogel-Tammann-Fulcher representation of the Adam-Gibbs model. Amorphous samples were heated at 1 K/min and a reduced crystallization temperature, defined as (Tc - Tg)/(Tm-Tg), was used to compare crystallization tendencies. Crystallization was observed for all compounds except ritonavir. The configurational free energy values (Gc) show that thermodynamic driving forces for crystallization follow the order: ritonavir > acetaminophen approximately fenofibrate > sucrose > ABT-229. The entropic barrier to crystallization, which is inversely related to the probability that the molecules are in the proper orientation, followed the order: ritonavir > fenofibrate > ABT-229 > acetaminophen approximately sucrose. Molecular mobility values, which are proportional to molecular collision rates, followed the order: acetaminophen > fenofibrate > sucrose > ABT-229 approximately ritonavir. Crystallization studies under nonisothermal conditions revealed that compounds with the highest entropic barriers and lowest mobilities were most difficult to crystallize, regardless of the thermodynamic driving forces. This investigation demonstrates the importance of both configurational entropy and molecular mobility to understanding the physical stability of amorphous pharmaceuticals.

Algorithms↗
PubMed2004

Analysis of solution nonideality of a pseudomorphic drug system through a comprehensive thermodynamic framework for the design of a crystallization process.

Solutions of a semipolar drug belonging to the alpha(V) beta(iii) integrin antagonist class of compounds were studied in a comprehensive thermodynamic framework. The solubility of two pseudomorphic forms (an anhydrate and a monohydrate) was measured at several temperatures and various solvent mixtures of acetonitrile and water. Both forms displayed a "bell"-shaped solubility behavior as a function of cosolvent composition. Thermodynamic framework used to analyze the data comprised van't Hoff and enthalpy-entropy compensation analyses. The two pseudomorphs exhibited linear temperature dependence from 25 to 65 degrees C at all solvent compositions (i.e., ideal behavior with temperature for fixed solvent composition). Plots of enthalpy of solublization and Gibbs free energy showed two distinct regions with contrasting thermodynamic, and consequently, underlying structural properties (indicating non-deal behavior with solvent composition for a fixed temperature). Solubility increased due to entropy effects in the acetonitrile rich region, whereas enthalpy effects dominated solublization in the water-rich region. Quantification of this phenomenon by plotting DeltaH versus DeltaG showed considerable nonlinearity, and that the two regions were separated by a significant discontinuity-a trend rarely seen before in the literature. The reason behind this behavior is believed to be due to the complex interactions in the solution of the drug in water acetonitrile solvent system. A very significant aspect of the comprehensive thermodynamic analysis is that it helped explain the puzzling feature of the data, which showed that the free energy of phase transformation between the two pseudomorphic forms for a given temperature was not independent of the solvent composition. The resulting explanation has major consequences for crystallization process development.

Algorithms↗
PubMed1996

Prediction of alpha-helices in proteins based on thermodynamic parameters from solution chemistry.

Current studies on the protein folding problem are chiefly pursued by two approaches; one statistically investigates the three-dimensional structures of proteins and the other focuses on their thermodynamic properties in solution. It remains to be demonstrated that information from these two sources are consistent and complementary. Using two sets of thermodynamic parameters experimentally obtained from solution studies, namely the helix propensities derived from small model peptides and hydrophobicity based on solvent transfer free energies for amino acids, we predict alpha-helices in native proteins. The correlation coefficient of our predictions on 98 non-homologous proteins is 0.26, a value comparable to that of the statistical prediction of Chou & Fasman but less than that from the state of the art prediction (0.39) based on neural network methodology. Helix propensities derived from different experimental systems in aqueous solutions are highly consistent for predicting alpha-helices in proteins. The helix propensities and amphiphilicity in primary sequences make independent contributions to the occurrence of alpha-helices. We also show that, with appropriate models, statistical analyses of known three-dimensional structures can provide thermodynamically relevant quantities. These findings indicate that for practical helix prediction, various sets of propensities have reached reasonable consensus. The report also suggests integrating solution thermodynamic studies with protein structural analyses, and the role of supersecondary structures on helices in proteins.

Databases, Factual↗
PubMed2002

Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: how applicable is the transition state picture to folding and unfolding?

To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplified protein chain model that embodies a cooperative interplay between local conformational preferences and hydrophobic burial. The present four-helix-bundle 55mer model exhibits protein-like calorimetric two-state cooperativity. It rationalizes native-state hydrogen exchange observations. Our analysis indicates that a coherent, self-consistent physical account of both the thermodynamic and kinetic properties of the model leads naturally to the concept of a native state ensemble that encompasses considerable conformational fluctuations. Such a multiple-conformation native state is seen to involve conformational states similar to those revealed by native-state hydrogen exchange. Many of these conformational states are predicted to lie below native baselines commonly used in interpreting calorimetric data. Folding and unfolding kinetics are studied under a range of intrachain interaction strengths as in experimental chevron plots. Kinetically determined transition midpoints match well with their thermodynamic counterparts. Kinetic relaxations are found to be essentially single-exponential over an extended range of model interaction strengths. This includes the entire unfolding regime and a significant part of a folding regime with a chevron rollover, as has been observed for real proteins that fold with non-two-state kinetics. The transition state picture of protein folding and unfolding is evaluated by comparing thermodynamic free energy profiles with actual kinetic rates. These analyses suggest that some chevron rollovers may arise from an internal frictional effect that increasingly impedes chain motions with more native conditions, rather than being caused by discrete deadtime folding intermediates or shifts of the transition state peak as previously posited.

Calorimetry↗
PubMed2002

Thermodynamics of E. coli cytidine repressor interactions with DNA: distinct modes of binding to different operators suggests a role in differential gene regulation.

Interactions between the Escherichia coli cytidine repressor protein (CytR) and its operator sites at the different promoters that comprise the CytR regulon, play an important role in the regulation of these promoters. The natural operators are palindromes separated by variable length central spacers (0-9 bp). We have suggested that this variability affects the flexibility of CytR-DNA contacts, thereby affecting the critical protein-protein interactions between CytR and the cAMP receptor protein (CRP) that underlie differential repression and activation of CytR-regulated genes. To assess this hypothesis, we investigated the thermodynamics of CytR binding to the natural operator sequences found in udpP and deoP2. To separate effects due to spacing from effects due to the differing sequences of the recognition half-sites of these two operators, we also investigated CytR binding to artificial hybrid operators, in which the half-site sequences of udpP and deoP2 were exchanged. Thermodynamic parameters, DeltaS(o), DeltaH(o) and DeltaC(o)(p), were determined by van't Hoff analysis of CytR binding, monitored by changes in the steady-state fluorescence anisotropy of dye-conjugated, operator-containing oligonucleotides. Large differences in thermodynamics were observed that depend primarily on the central spacer rather than the sequences of the recognition half-sites. Binding to operators with deoP2 spacing results in a very large, negative DeltaC(o)(p). Association is strongly favored enthalpically and strongly disfavored entropically at ambient temperature. By contrast, binding to operators with udpP spacing results in a small, negative DeltaC(o)(p). Association is weakly favored both enthalpically and entropically at ambient temperature. A difference of such magnitude in DeltaDeltaC(o)(p) has not been reported previously for specific binding of a transcription factor to different sites. The identical salt dependence of CytR binding to deoP2 and udpP operators indicates that ion-dependent processes do not contribute significantly to this difference. Thus, the different thermodynamic effects appear to reflect distinctly different modes of site-specific DNA binding. We discuss similarities to operator binding by CytR homologs among LacI family repressors, and we consider how different CytR binding modes might affect interactions with other components of the gene regulatory machinery that contribute to differential gene regulation.

Base Sequence↗
PubMed1995

Comments on "Let there be life; thermodynamic reflections on biogenesis and evolution" by Avshalom C. Elitzur.

This comment is in response to a paper previously published in the Journal entitled "Let there be life", by A. C. Elitzur. Elitzur ascribes to Eigen the proposal that life began with the appearance of an autocatalytic (self-replicating) molecule. This was discussed by biologists and philosophers in the nineteenth century. Eigen's proposal is moot: there never was a primeval soup. The absence of evidence is evidence of absence. Elitzur also confuses thermodynamics with statistical mechanics. The statistical equation of Boltzmann and Planck for entropy appears in discussions of statistical mechanics, not in discussions of classical thermodynamics. Elitzur calls the Second Law of Thermodynamics an explanation of evolution. On the contrary, his mentor Eigen wrote: "In physics we know of principles which cannot be reduced to any more fundamental laws. As axioms, they are abstracted from experience, their predictions being consistent with the consequences that can be subjected to experimental test. "Typical examples are the first and second law of thermodynamics. Darwin's principle of natural selection does not fall into the category of first principles." The reader is invited to compare the material in Elitzur's paper with the discussion in Yockey's (1992) book, Information Theory and Molecular Biology, Cambridge, Cambridge University Press.

Animals↗
PubMed2003

Back to basics: thermodynamics in biochemical engineering.

Rational and efficient process development in chemical technology always makes heavy use of process analysis in terms of balances, kinetics, and thermodynamics. While the first two of these concepts have been extensively used in biotechnology, it appears that thermodynamics has received relatively little attention from biotechnologists. This state of affairs is one among several reasons why development and design of biotechnological processes is today mostly carried out in an essentially empirical fashion and why bioprocesses are often not as thoroughly optimized as many chemical processes. Since quite a large body of knowledge in the area of bio thermodynamics already existed in the early nineties, the Steering Committee of a European Science Foundation program on Process Integration in Biochemical Engineering identified a need to stimulate a more systematic use of thermodynamics in the area. To this effect, a bianual course for advanced graduate students and researchers was developed. The present contribution uses the course structure to provide an outline of the area and to characterize very briefly the achievements, the challenges, and the research needs in the various sub-topics.

Animals↗
PubMed1996

On the relationship of thermodynamic parameters with the buried surface area in protein-ligand complex formation.

Prediction of thermodynamic parameters of protein-protein and antigen-antibody complex formation from high resolution structural parameters has recently received much attention, since an understanding of the contributions of different fundamental processes like hydrophobic interactions, hydrogen bonding, salt bridge formation, solvent reorganization etc. to the overall thermodynamic parameters and their relations with the structural parameters would lead to rational drug design. Using the results of the dissolution of hydrocarbons and other model compounds the changes in heat capacity (delta C(p)), enthalpy (delta H) and entropy (delta S) have been empirically correlated with the polar and apolar surface areas buried during the process of protein folding/unfolding and protein-ligand complex formation. In this regard, the polar and apolar surfaces removed from the solvent in a protein-ligand complex have been calculated from the experimentally observed values of changes in heat capacity (delta C(p)) and enthalpy (delta H) for protein-ligand complexes for which accurate thermodynamic and high resolution structural data are available, and the results have been compared with the x-ray crystallographic observations. Analyses of the available results show poor correlation between the thermodynamic and structural parameters. Probable reasons for this discrepancy are mostly related with the reorganization of water accompanying the reaction which is indeed proven by the analyses of the energetics of the binding of the wheat germ agglutinin to oligosaccharides.

Animals↗
PubMed1975

[Thermodynamic aspects of phagocytosis and thrombosis (author's transl)].

In this paper, thermodynamic considerations are applied to two biological processes, phagocytosis and platelet adhesion, the latter being an important step in thrombosis formation. Simple thermodynamic models in terms of changes of the Helmholtz free energy are presented for the engulfment of bacteria by phagocystic cells, as well as for the attachment of platelets to biomaterial surfaces. The interfacial tensions contained in the expressions for the Helmholtz free energy may be obtained from contact angles, by means of an equation of state approach. The in vitro phagocytosis tests show that hydrophobic bacteria are more readily phagocytized than hydrophilic ones, and the thermodynamic model elucidates the reason for this pattern of behaviour. Preliminary results for two types of platelet adhesion tests are presented. Although there is, in terms of simple thermodynamic considerations, a strong similarity between platelet adhesion and the early stages of phagocytosis, we anticipate that specific interactions will play a larger role in platelet adhesion than in phagocytosis.

Bacteria↗
PubMed1985

Thermodynamic reversibility of phase transitions. Specific effects of alcohols on phosphatidylcholines.

The gel-to-fluid phase transitions of several phosphatidylethanolamines (PE's) and phosphatidylcholines (PC's) have been investigated in the presence of three short-chain alcohols. The effects of the alcohols on the thermodynamic reversibility of these transitions was studied and it was found that the transitions for PC's are not thermodynamically reversible at relatively high alcohol concentrations. The PE transitions are thermodynamically reversible for all alcohol concentrations, and the PE's do not exhibit the biphasic effects of alcohol on the transition temperature previously reported for the PC's (Rowe, E.S. (1983) Biochemistry 22, 3299-3305). The biphasic transition temperature effects and the thermodynamic irreversibility of PC transitions at high alcohol concentrations appear to be correlated with the induction of a fully interdigitated gel phase recently reported in the literature (Simon, S.A. and McIntosh, T.J. (1984) Biochim. Biophys. Acta 773, 169-172). The biological significance of these findings is discussed.

1-Propanol↗