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Sample records for level unfolding thermodynamics

  1. Thermodynamics of the temperature-induced unfolding of globular proteins.

    OpenAIRE

    Khechinashvili, N. N.; Janin, J.; Rodier, F.

    1995-01-01

    The heat capacity, enthalpy, entropy, and Gibbs energy changes for the temperature-induced unfolding of 11 globular proteins of known three-dimensional structure have been obtained by microcalorimetric measurements. Their experimental values are compared to those we calculate from the change in solvent-accessible surface area between the native proteins and the extended polypeptide chain. We use proportionality coefficients for the transfer (hydration) of aliphatic, aromatic, and polar groups...

  2. Site-specific unfolding thermodynamics of a helix-turn-helix protein.

    Science.gov (United States)

    Amunson, Krista E; Ackels, Loren; Kubelka, Jan

    2008-07-01

    The thermal unfolding of a 40-residue helix-turn-helix subdomain of the P22 viral coat protein was investigated using circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR) with site-specific 13C isotopic labeling. Helix-turn-helix is the simplest alpha-helical structural motif that combines both secondary and tertiary structural elements. The CD of individual helical fragments reveals that the P22 subdomain is stabilized by tertiary interhelical interactions. Overall the temperature-dependent CD and FTIR data can be described by a three-state process with a partially folded intermediate. However, the analysis of the site-specific 13C IR signals reveals distinct unfolding thermodynamics for each of the labeled sites. The thermodynamic parameters of the thermal unfolding of each of the labeled segments were obtained using singular value decomposition in combination with target transformation and global fitting. The P22 subdomain unfolds from the N-terminus toward the helical segments near the turn. Our results show that as few as two 13C labeled residues can be detected in a 40 residue protein and provide local, site-specific structural information about protein unfolding, which is not resolved by standard, nonsite-specific spectroscopic probes.

  3. Urea-temperature phase diagrams capture the thermodynamics of denatured state expansion that accompany protein unfolding.

    Science.gov (United States)

    Tischer, Alexander; Auton, Matthew

    2013-09-01

    We have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea-induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea-temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two-state character. Global analysis of the urea-temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of ΔH0 and ΔCP0 that define a complex temperature dependence of the m-value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea-denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions.

  4. Unfolding thermodynamics of intramolecular G-quadruplexes: base sequence contributions of the loops.

    Science.gov (United States)

    Olsen, Chris M; Lee, Hui-Ting; Marky, Luis A

    2009-03-05

    G-quadruplexes are a highly studied DNA motif with a potential role in a variety of cellular processes and more recently are considered novel targets for drug therapy in aging and anticancer research. In this work, we have investigated the thermodynamic contributions of the loops on the stable formation of G-quadruplexes. Specifically, we use a combination of UV, circular dichroism (CD) and fluorescence spectroscopies, and differential scanning calorimetry (DSC) to determine thermodynamic profiles, including the differential binding of ions and water, for the unfolding of the thrombin aptamer: d(GGT2GGTGTGGT2GG) that is referred to as G2. The sequences in italics, TGT and T2, are known to form loops. Other sequences examined contained base substitutions in the TGT loop (TAT, TCT, TTT, TAPT, and UUU), in the T2 loops (T4, U2), or in both loops (UGU and U2, UUU and U2). The CD spectra of all molecules show a positive band centered at 292 nm, which corresponds to the "chair" conformation. The UV and DSC melting curves of each G-quadruplex show monophasic transitions with transition temperatures (T(M)s) that remained constant with increasing strand concentration, confirming their intramolecular formation. These G-quadruplexes unfold with T(M)s in the range from 43.2 to 56.5 degrees C and endothermic enthalpies from 22.9 to 37.2 kcal/mol. Subtracting the contribution of a G-quartet stack from each experimental profile indicated that the presence of the loops stabilize each G-quadruplex by favorable enthalpy contributions, larger differential binding of K+ ions (0.1-0.6 mol K+/ mol), and a variable uptake/release of water molecules (-6 to 8 mol H2O/mol). The thermodynamic contributions for these specific base substitutions are discussed in terms of loop stacking (base-base stacking within the loops) and their hydration effects.

  5. A fluorescence approach to the unfolding thermodynamics of horseradish peroxidase based on heme degradation by hydrogen peroxide

    Science.gov (United States)

    Ke, Zhigang; Ma, Shanshan; Li, Lamei; Huang, Qing

    2016-07-01

    Horseradish peroxidase (HRP) is a classical heme-containing protein which has been applied in many fields. The prosthetic group heme in HRP, especially in unfolded state, can react with hydrogen peroxide (H2O2) to produce a fluorescent product with the maximum emission wavelength at 450 nm. Utilizing this emission band as a fluorescence probe, the unfolding process of HRP in urea can be assessed quantitatively, and the calculated thermodynamic parameters are consistent with those determined by circular dichroism (CD) at 222 nm and steady-state tryptophan (Trp) fluorescence methods.

  6. Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics.

    Science.gov (United States)

    Dupuis, Nicholas F; Holmstrom, Erik D; Nesbitt, David J

    2014-06-10

    The effects of "molecular crowding" on elementary biochemical processes due to high solute concentrations are poorly understood and yet clearly essential to the folding of nucleic acids and proteins into correct, native structures. The present work presents, to our knowledge, first results on the single-molecule kinetics of solute molecular crowding, specifically focusing on GAAA tetraloop-receptor folding to isolate a single RNA tertiary interaction using time-correlated single-photon counting and confocal single-molecule FRET microscopy. The impact of crowding by high-molecular-weight polyethylene glycol on the RNA folding thermodynamics is dramatic, with up to ΔΔG° ∼ -2.5 kcal/mol changes in free energy and thus >60-fold increase in the folding equilibrium constant (Keq) for excluded volume fractions of 15%. Most importantly, time-correlated single-molecule methods permit crowding effects on the kinetics of RNA folding/unfolding to be explored for the first time (to our knowledge), which reveal that this large jump in Keq is dominated by a 35-fold increase in tetraloop-receptor folding rate, with only a modest decrease in the corresponding unfolding rate. This is further explored with temperature-dependent single-molecule RNA folding measurements, which identify that crowding effects are dominated by entropic rather than enthalpic contributions to the overall free energy change. Finally, a simple "hard-sphere" treatment of the solute excluded volume is invoked to model the observed kinetic trends, and which predict ΔΔG° ∼ -5 kcal/mol free-energy stabilization at excluded volume fractions of 30%.

  7. Evolution and thermodynamics of the slow unfolding of hyperstable monomeric proteins

    Directory of Open Access Journals (Sweden)

    Koga Yuichi

    2010-07-01

    Full Text Available Abstract Background The unfolding speed of some hyperthermophilic proteins is dramatically lower than that of their mesostable homologs. Ribonuclease HII from the hyperthermophilic archaeon Thermococcus kodakaraensis (Tk-RNase HII is stabilized by its remarkably slow unfolding rate, whereas RNase HI from the thermophilic bacterium Thermus thermophilus (Tt-RNase HI unfolds rapidly, comparable with to that of RNase HI from Escherichia coli (Ec-RNase HI. Results To clarify whether the difference in the unfolding rate is due to differences in the types of RNase H or differences in proteins from archaea and bacteria, we examined the equilibrium stability and unfolding reaction of RNases HII from the hyperthermophilic bacteria Thermotoga maritima (Tm-RNase HII and Aquifex aeolicus (Aa-RNase HII and RNase HI from the hyperthermophilic archaeon Sulfolobus tokodaii (Sto-RNase HI. These proteins from hyperthermophiles are more stable than Ec-RNase HI over all the temperature ranges examined. The observed unfolding speeds of all hyperstable proteins at the different denaturant concentrations studied are much lower than those of Ec-RNase HI, which is in accordance with the familiar slow unfolding of hyperstable proteins. However, the unfolding rate constants of these RNases H in water are dispersed, and the unfolding rate constant of thermophilic archaeal proteins is lower than that of thermophilic bacterial proteins. Conclusions These results suggest that the nature of slow unfolding of thermophilic proteins is determined by the evolutionary history of the organisms involved. The unfolding rate constants in water are related to the amount of buried hydrophobic residues in the tertiary structure.

  8. Human defensins facilitate local unfolding of thermodynamically unstable regions of bacterial protein toxins

    National Research Council Canada - National Science Library

    Kudryashova, Elena; Quintyn, Royston; Seveau, Stephanie; Lu, Wuyuan; Wysocki, Vicki H; Kudryashov, Dmitri S

    2014-01-01

    .... In this study, we showed that binding of neutrophil ?-defensin HNP1 to affected bacterial toxins caused their local unfolding, potentiated their thermal melting and precipitation, exposed new regions for proteolysis, and increased susceptibility...

  9. Unfolding Thermodynamics of Cysteine-Rich Proteins and Molecular Thermal-Adaptation of Marine Ciliates

    Directory of Open Access Journals (Sweden)

    Giorgia Cazzolli

    2013-11-01

    Full Text Available Euplotes nobilii and Euplotes raikovi are phylogenetically closely allied species of marine ciliates, living in polar and temperate waters, respectively. Their evolutional relation and the sharply different temperatures of their natural environments make them ideal organisms to investigate thermal-adaptation. We perform a comparative study of the thermal unfolding of disulfide-rich protein pheromones produced by these ciliates. Recent circular dichroism (CD measurements have shown that the two psychrophilic (E. nobilii and mesophilic (E. raikovi protein families are characterized by very different melting temperatures, despite their close structural homology. The enhanced thermal stability of the E. raikovi pheromones is realized notwithstanding the fact that these proteins form, as a rule, a smaller number of disulfide bonds. We perform Monte Carlo (MC simulations in a structure-based coarse-grained (CG model to show that the higher stability of the E. raikovi pheromones is due to the lower locality of the disulfide bonds, which yields a lower entropy increase in the unfolding process. Our study suggests that the higher stability of the mesophilic E. raikovi phermones is not mainly due to the presence of a strongly hydrophobic core, as it was proposed in the literature. In addition, we argue that the molecular adaptation of these ciliates may have occurred from cold to warm, and not from warm to cold. To provide a testable prediction, we identify a point-mutation of an E. nobilii pheromone that should lead to an unfolding temperature typical of that of E. raikovi pheromones.

  10. Determining Students' Conceptual Understanding Level of Thermodynamics

    Science.gov (United States)

    Saricayir, Hakan; Ay, Selahattin; Comek, Arif; Cansiz, Gokhan; Uce, Musa

    2016-01-01

    Science students find heat, temperature, enthalpy and energy in chemical reactions to be some of the most difficult subjects. It is crucial to define their conceptual understanding level in these subjects so that educators can build upon this knowledge and introduce new thermodynamics concepts. This paper reports conceptual understanding levels of…

  11. Estimation of neutron spectrum in the low-level gamma spectroscopy system using unfolding procedure

    Science.gov (United States)

    Knežević, D.; Jovančević, N.; Krmar, M.

    2016-03-01

    The radiation resulting from neutron interactions with Ge nuclei in active volume of HPGe detectors is one of the main concerns in low-level gamma spectroscopy measurements [1,2]. It is usually not possible to measure directly spectrum of neutrons which strike detector. This paper explore the possibility of estimation of neutron spectrum using measured activities of certain Ge(n,γ) and Ge(n,n') reactions (obtained from low-level gamma measurements), available ENDF cross section data and unfolding procedures. In this work HPGe detector with passive shield made from commercial low background lead was used for the measurement. The most important objective of this study was to reconstruct muon induced neutron spectrum created in the shield of the HPGe detector. MAXED [3] and GRAVEL [4] algorithms for neutron spectra unfolding were used. The results of those two algorithms were compared and we analyzed the sensitivity of the unfolding procedure to the various input parameters.

  12. Using circular dichroism collected as a function of temperature to determine the thermodynamics of protein unfolding and binding interactions

    Science.gov (United States)

    Greenfield, Norma J.

    2009-01-01

    Circular dichroism (CD) is an excellent spectroscopic technique for following the unfolding and folding of proteins as a function of temperature. One of its principal applications is to determine the effects of mutations and ligands on protein and polypeptide stability If the change in CD as a function of temperature is reversible, analysis of the data may be used to determined the van't Hoff enthalpy (ΔH) and entropy (ΔS) of unfolding, the midpoint of the unfolding transition (TM) and the free energy (ΔG) of unfolding. Binding constants of protein-protein and protein-ligand interactions may also be estimated from the unfolding curves. Analysis of CD spectra obtained as a function of temperature is also useful to determine whether a protein has unfolding intermediates. Measurement of the spectra of five folded proteins and their unfolding curves at a single wavelength takes approximately eight hours. PMID:17406506

  13. Simulation of the thermodynamics of folding and unfolding of the Trp-cage mini-protein TC5b using different combinations of force fields and solvation models

    Institute of Scientific and Technical Information of China (English)

    ZHANG; John; ZengHui

    2010-01-01

    Molecular dynamics simulations based on AMBER force fields(ff96 and ff03) and generalized Born models(igb1 and igb5) have been carried out in order to study folding/unfolding of the Trp-cage mini-protein TC5b.The thermodynamic properties of TC5b were found to be sensitive to the specific version of the solvation model and force field employed.When the ff96/igb5 combination was used,the predicted melting temperature from unfolding simulations was in good agreement with the experimental value of 315 K,but the folding simulation did not converge.The most stable thermodynamic profile in both folding and unfolding simulations was obtained when the ff03/igb5 combination was employed,and the predicted melting temperature was about 345 K,showing over-stabilization of the protein.Simulations using the igb1 version in combination with ff96 or ff03 were difficult to converge within the simulation time limit(50 ns).

  14. Efficiencies of thermodynamics when temperature-dependent energy levels exist.

    Science.gov (United States)

    Yamano, Takuya

    2016-03-14

    Based on a generalized form of the second law of thermodynamics, in which the temperature-dependent energy levels of a system are appropriately included in entropy generation, we show that the effect reasonably appears in efficiencies of thermodynamic processes.

  15. Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins

    Directory of Open Access Journals (Sweden)

    J. M. Dick

    2006-01-01

    Full Text Available Thermodynamic calculations can be used to quantify environmental constraints on the speciation of proteins, such as the pH and temperature dependence of ionization state, and the relative chemical stabilities of proteins in different biogeochemical settings. These calculations depend in part on values of the standard molal Gibbs energies of proteins and their ionization reactions as a function of temperature and pressure. Because these values are not generally available, we calculated values of the standard molal thermodynamic properties at 25°C and 1 bar as well as the revised Helgeson-Kirkham-Flowers equations of state parameters of neutral and charged zwitterionic reference model compounds including aqueous amino acids, polypeptides, and unfolded proteins. The experimental calorimetric and volumetric data for these species taken from the literature were combined with group additivity algorithms to calculate the properties and parameters of neutral and ionized sidechain and backbone groups in unfolded proteins. The resulting set of group contributions enables the calculation of the standard molal Gibbs energy, enthalpy, entropy, isobaric heat capacity, volume, and isothermal compressibility of unfolded proteins in a range of proton ionization states to temperatures and pressures exceeding 100°C and 1000 bar. This approach provides a useful frame of reference for thermodynamic studies of protein folding and complexation reactions. It can also be used to assign provisional values of the net charge and Gibbs energy of ionized proteins as a function of temperature and pH. Using these values, an Eh-pH diagram for a reaction representing the speciation of extracellular proteins from Pyrococcus furiosus and Bacillus subtilis was generated. The predicted predominance limits of these proteins correspond with the different electrochemical conditions of hydrothermal vents and soils. More comprehensive calculations of this kind may reveal pervasive

  16. Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins

    Science.gov (United States)

    Dick, J. M.; Larowe, D. E.; Helgeson, H. C.

    2006-07-01

    Thermodynamic calculations can be used to quantify environmental constraints on the speciation of proteins, such as the pH and temperature dependence of ionization state, and the relative chemical stabilities of proteins in different biogeochemical settings. These calculations depend in part on values of the standard molal Gibbs energies of proteins and their ionization reactions as a function of temperature and pressure. Because these values are not generally available, we calculated values of the standard molal thermodynamic properties at 25°C and 1 bar as well as the revised Helgeson-Kirkham-Flowers equations of state parameters of neutral and charged zwitterionic reference model compounds including aqueous amino acids, polypeptides, and unfolded proteins. The experimental calorimetric and volumetric data for these species taken from the literature were combined with group additivity algorithms to calculate the properties and parameters of neutral and ionized sidechain and backbone groups in unfolded proteins. The resulting set of group contributions enables the calculation of the standard molal Gibbs energy, enthalpy, entropy, isobaric heat capacity, volume, and isothermal compressibility of unfolded proteins in a range of proton ionization states to temperatures and pressures exceeding 100°C and 1000 bar. This approach provides a useful frame of reference for thermodynamic studies of protein folding and complexation reactions. It can also be used to assign provisional values of the net charge and Gibbs energy of ionized proteins as a function of temperature and pH. Using these values, an Eh-pH diagram for a reaction representing the speciation of extracellular proteins from Pyrococcus furiosus and Bacillus subtilis was generated. The predicted predominance limits of these proteins correspond with the different electrochemical conditions of hydrothermal vents and soils. More comprehensive calculations of this kind may reveal pervasive chemical potential

  17. Group additivity calculation of the standard molal thermodynamic properties of aqueous amino acids, polypeptides and unfolded proteins as a function of temperature, pressure and ionization state

    Directory of Open Access Journals (Sweden)

    J. M. Dick

    2005-10-01

    Full Text Available Thermodynamic calculation of the chemical speciation of proteins and the limits of protein metastability affords a quantitative understanding of the biogeochemical constraints on the distribution of proteins within and among different organisms and chemical environments. These calculations depend on accurate determination of the ionization states and standard molal Gibbs free energies of proteins as a function of temperature and pressure, which are not generally available. Hence, to aid predictions of the standard molal thermodynamic properties of ionized proteins as a function of temperature and pressure, calculated values are given below of the standard molal thermodynamic properties at 25°C and 1 bar and the revised Helgeson-Kirkham-Flowers equations of state parameters of the structural groups comprising amino acids, polypeptides and unfolded proteins. Group additivity and correlation algorithms were used to calculate contributions by ionized and neutral sidechain and backbone groups to the standard molal Gibbs free energy (Δ G°, enthalpy (Δ H°, entropy (S°, isobaric heat capacity (C°P, volume (V° and isothermal compressibility (κ°T of multiple reference model compounds. Experimental values of C°P, V° and κ°T at high temperature were taken from the recent literature, which ensures an internally consistent revision of the thermodynamic properties and equations of state parameters of the sidechain and backbone groups of proteins, as well as organic groups. As a result, Δ G°, Δ H°, S° C°P, V° and κ°T of unfolded proteins in any ionization state can be calculated up to T~-300°C and P~-5000 bars. In addition, the ionization states of unfolded proteins as a function of not only pH, but also temperature and pressure can be calculated by taking account of the degree of ionization of the sidechain and backbone groups present in the sequence. Calculations of this

  18. Group additivity calculation of the standard molal thermodynamic properties of aqueous amino acids, polypeptides and unfolded proteins as a function of temperature, pressure and ionization state

    Science.gov (United States)

    Dick, J. M.; Larowe, D. E.; Helgeson, H. C.

    2005-10-01

    Thermodynamic calculation of the chemical speciation of proteins and the limits of protein metastability affords a quantitative understanding of the biogeochemical constraints on the distribution of proteins within and among different organisms and chemical environments. These calculations depend on accurate determination of the ionization states and standard molal Gibbs free energies of proteins as a function of temperature and pressure, which are not generally available. Hence, to aid predictions of the standard molal thermodynamic properties of ionized proteins as a function of temperature and pressure, calculated values are given below of the standard molal thermodynamic properties at 25°C and 1 bar and the revised Helgeson-Kirkham-Flowers equations of state parameters of the structural groups comprising amino acids, polypeptides and unfolded proteins. Group additivity and correlation algorithms were used to calculate contributions by ionized and neutral sidechain and backbone groups to the standard molal Gibbs free energy (Δ G°), enthalpy (Δ H°), entropy (S°), isobaric heat capacity (C°P), volume (V°) and isothermal compressibility (κ°T) of multiple reference model compounds. Experimental values of C°P, V° and κ°T at high temperature were taken from the recent literature, which ensures an internally consistent revision of the thermodynamic properties and equations of state parameters of the sidechain and backbone groups of proteins, as well as organic groups. As a result, Δ G°, Δ H°, S° C°P, V° and κ°T of unfolded proteins in any ionization state can be calculated up to T~-300°C and P~-5000 bars. In addition, the ionization states of unfolded proteins as a function of not only pH, but also temperature and pressure can be calculated by taking account of the degree of ionization of the sidechain and backbone groups present in the sequence. Calculations of this kind represent a first step in the prediction of chemical affinities of many

  19. pH and solvent H/D isotope effects on the thermodynamics and kinetics of electron transfer for electrode-immobilized native and urea-unfolded stellacyanin.

    Science.gov (United States)

    Ranieri, Antonio; Battistuzzi, Gianantonio; Borsari, Marco; Bortolotti, Carlo Augusto; Di Rocco, Giulia; Sola, Marco

    2012-10-23

    The thermodynamics of Cu(II) to Cu(I) reduction and the kinetics of the electron transfer (ET) process for Rhus vernicifera stellacyanin (STC) immobilized on a decane-1-thiol coated gold electrode have been measured through cyclic voltammetry at varying pH and temperature, in the presence of urea and in D(2)O. Immobilized STC undergoes a limited conformational change that mainly results in an enhanced exposure of one or both copper binding histidines to solvent which slightly stabilizes the cupric state and increases histidine basicity. The large immobilization-induced increase in the pK(a) for the acid transition (from 4.5 to 6.3) makes this electrode-SAM-protein construct an attractive candidate as a biomolecular ET switch operating near neutral pH in molecular electronics. Such a potential interest is increased by the robustness of this interface against chemical unfolding as it undergoes only moderate changes in the reduction thermodynamics and in the ET rate in the presence of up to 8 M urea. The sensitivity of these parameters to solvent H/D isotope effects testifies to the role of protein solvation as effector of the thermodynamics and kinetics of ET.

  20. Glucosylation of β-lactoglobulin lowers the heat capacity change of unfolding; a unique way to affect protein thermodynamics

    NARCIS (Netherlands)

    Teeffelen, A.M.M. van; Broersen, K.; Jongh, H.H.J. de

    2005-01-01

    Chemical glycosylation of proteins occurs in vivo spontaneously, especially under stress conditions, and has been linked in a number of cases to diseases related to protein denaturation and aggregation. It is the aim of this work to study the origin of the change in thermodynamic properties due to

  1. Glucosylation of beta-lactoglobulin lowers the heat capacity change of unfolding; a unique way to affect protein thermodynamics

    NARCIS (Netherlands)

    Teeffelen, Van A.M.M.; Broersen, K.; Jongh, de H.H.J.

    2005-01-01

    Chemical glycosylation of proteins occurs in vivo spontaneously, especially under stress conditions, and has been linked in a number of cases to diseases related to protein denaturation and aggregation. It is the aim of this work to study the origin of the change in thermodynamic properties due to

  2. Glycosylation and thermodynamic versus kinetic stability of horseradish peroxidase

    DEFF Research Database (Denmark)

    Tams, J.W.; Welinder, Karen G.

    1998-01-01

    Glycoprotein stability, glycoprotein unfolding, horseradish peroxidase, thermodynamic stability, kinetik stability......Glycoprotein stability, glycoprotein unfolding, horseradish peroxidase, thermodynamic stability, kinetik stability...

  3. Unfolding Participation

    DEFF Research Database (Denmark)

    Saad-Sulonen, Joanna; Halskov, Kim; Eriksson, Eva

    2015-01-01

    The aim of the Unfolding Participation workshop is to outline an agenda for the next 10 years of participatory design (PD) and participatory human computer interaction (HCI) research. We will do that through a double strategy: 1) by critically interrogating the concept of participation (unfolding......, urban planning, participatory arts, business, science and technology studies) to bring a plurality of perspectives and expertise related to participation.......The aim of the Unfolding Participation workshop is to outline an agenda for the next 10 years of participatory design (PD) and participatory human computer interaction (HCI) research. We will do that through a double strategy: 1) by critically interrogating the concept of participation (unfolding...... the concept itself), while at the same time, 2) reflecting on the way that participation unfolds across different participatory configurations. We invite researchers and practitioners from PD and HCI and fields in which information technology mediated participation is embedded (e.g. in political studies...

  4. Unfolding Participation

    DEFF Research Database (Denmark)

    Saad-Sulonen, Joanna; Halskov, Kim; Eriksson, Eva

    2015-01-01

    The aim of the Unfolding Participation workshop is to outline an agenda for the next 10 years of participatory design (PD) and participatory human computer interaction (HCI) research. We will do that through a double strategy: 1) by critically interrogating the concept of participation (unfolding...... the concept itself), while at the same time, 2) reflecting on the way that participation unfolds across different participatory configurations. We invite researchers and practitioners from PD and HCI and fields in which information technology mediated participation is embedded (e.g. in political studies......, urban planning, participatory arts, business, science and technology studies) to bring a plurality of perspectives and expertise related to participation....

  5. Distinct levels in the nanoscale organization of DNA-histone complex revealed by its mechanical unfolding

    Science.gov (United States)

    Soni, G. V.; Brar, Loveleen; Hameed, Feroz M.; Raychaudhuri, A. K.; Shivashankar, G. V.

    2007-04-01

    Mechanical unfolding of nanoscale DNA-histone complex, using an atomic force microscope, shows a stepwise disassembly of histones from the nucleosome. A quantitative analysis of the rupture jump statistics and the length released per jump reveals insights into the possible histone contacts within the octamer complex. The measured ruptures correlate with the breakage of multiple contacts that stabilize the histone octamer. These results provide a mechanistic basis by which stepwise disassembly of histone proteins may result from an external force exerted by the adenosinetriphosphate (ATP) dependent chromatin remodeling machines to access regulatory sites on DNA.

  6. Thermodynamics

    CERN Document Server

    Fermi, Enrico

    1956-01-01

    Indisputably, this is a modern classic of science. Based on a course of lectures delivered by the author at Columbia University, the text is elementary in treatment and remarkable for its clarity and organization. Although it is assumed that the reader is familiar with the fundamental facts of thermometry and calorimetry, no advanced mathematics beyond calculus is assumed.Partial contents: thermodynamic systems, the first law of thermodynamics (application, adiabatic transformations), the second law of thermodynamics (Carnot cycle, absolute thermodynamic temperature, thermal engines), the entr

  7. Natural osmolytes alleviate GRP78 and ATF-4 levels: Corroboration for potential modulators of unfolded protein response.

    Science.gov (United States)

    Hazari, Younis Mohammad; Habib, Mudasir; Bashir, Samirul; Bashir, Arif; Hilal, Nazia; Irfan, Sheikh; Ul Haq, Ehtisham; Fazili, Khalid Majid

    2016-02-01

    Osmolytes are small organic molecules which play a significant role in maintaining functional homeostasis of proteins under extreme hostile stresses. Any imbalance to cell homeostasis leads to Endoplasmic Reticulum stress (ER-stress) to which a set of cellular responses both at transcriptional and translational level are initialed for restoration of cellular homeostasis called Unfolded Protein Response (UPR). In the present study we evaluated the role of Sarcosine, Betaine, Hydroxyectoine and Ectoine as potential modulators of UPR. ER-stress was induced by Tunicamycin, a prototypic experimental ER-stress inducer. The endogenous cellular levels of UPR markers Glucose-Regulated Protein 78 (GRP78) and Activating Transcription Factor-4 (ATF-4) were evaluated in presence and absence of these osmolytes after inducing UPR with tunicamycin. As a prelude to this, IC50 values of these osmolytes were determined by using cell viability assays like MTT and Trypan Blue exclusion assay. We found that these osmolytes in a dose-dependent manner increased the rate of restoration of homeostasis as was evident by the decreased endogenous levels of GRP78 and ATF-4. These natural osmolytes can thus be useful in therapeutic intervention to mitigate the pathophysiological state resulting from ER-stress. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Transient violations of the second law of thermodynamics in protein unfolding examined using synthetic atomic force microscopy and the fluctuation theorem.

    Science.gov (United States)

    Paramore, Sterling; Ayton, Gary S; Voth, Gregory A

    2007-09-14

    The synthetic atomic force microscopy (AFM) method is developed to simulate a periodically replicated atomistic system subject to force and length fluctuations characteristic of an AFM experiment. This new method is used to examine the forced-extension and subsequent rupture of the alpha-helical linker connecting periodic images of a spectrin protein repeat unit. A two-dimensional potential of mean force (PMF) along the length and a reaction coordinate describing the state of the linker was calculated. This PMF reveals that the basic material properties of the spectrin repeat unit are sensitive to the state of linker, an important feature that cannot be accounted for in a one-dimensional PMF. Furthermore, nonequilibrium simulations were generated to examine the rupture event in the context of the fluctuation theorem. These atomistic simulations demonstrate that trajectories which are in apparent violation of the second law can overcome unfolding barriers at significantly reduced rupture forces.

  9. Site-specific thermodynamic stability and unfolding of a de novo designed protein structural motif mapped by 13C isotopically edited IR spectroscopy.

    Science.gov (United States)

    Kubelka, Ginka S; Kubelka, Jan

    2014-04-23

    The mechanism of protein folding remains poorly understood, in part due to limited experimental information available about partially folded states. Isotopically edited infrared (IR) spectroscopy has emerged as a promising method for studying protein structural changes with site-specific resolution, but its full potential to systematically probe folding at multiple protein sites has not yet been realized. We have used (13)C isotopically edited IR spectroscopy to investigate the site-specific thermal unfolding at seven different locations in the de novo designed helix-turn-helix protein αtα. As one of the few stable helix-turn-helix motifs, αtα is an excellent model for studying the roles of secondary and tertiary interactions in folding. Circular dichroism (CD) experiments on the full αtα motif and its two peptide fragments show that interhelical tertiary contacts are critical for stabilization of the secondary structure. The site-specific thermal unfolding probed by (13)C isotopically edited IR is likewise consistent with primarily tertiary stabilization of the local structure. The least thermally stable part of the αtα motif is near the turn where the interhelical contacts are rather loose, while the motif's center with best established core packing has the highest stability. Similar correlation between the local thermal stability and tertiary contacts was found previously for a naturally occurring helix-turn-helix motif. These results underline the importance of native-like tertiary stabilizing interactions in folding, in agreement with recent state-of-the art folding simulations as well as simplified, native-centric models.

  10. Assessing the Conceptual Understanding about Heat and Thermodynamics at Undergraduate Level

    Science.gov (United States)

    Kulkarni, Vasudeo Digambar; Tambade, Popat Savaleram

    2013-01-01

    In this study, a Thermodynamic Concept Test (TCT) was designed to assess student's conceptual understanding heat and thermodynamics at undergraduate level. The different statistical tests such as item difficulty index, item discrimination index, point biserial coefficient were used for assessing TCT. For each item of the test these indices were…

  11. Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.

    Science.gov (United States)

    Baron, Riccardo; Trzesniak, Daniel; de Vries, Alex H; Elsener, Andreas; Marrink, Siewert J; van Gunsteren, Wilfred F

    2007-02-19

    Thermodynamic data are often used to calibrate or test amomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently, a CG force field for lipids, hydrocarbons, ions, and water, in which approximately four non-hydrogen atoms are mapped onto one interaction site, has been proposed and applied to study various aspects of lipid systems. To date, no extensive investigation of its capability to describe salvation thermodynamics has been undertaken. In the present study, a detailed picture of vaporization, solvation, and phase-partitioning thermodynamics for liquid hydrocarbons and water was obtained at CG and AL resolutions, in order to compare the two types or models and evaluate their ability to describe thermodynamic properties in the temperature range between 263 and 343 K. Both CG and AL models capture the experimental dependence of the thermodynamic properties on the temperature, albeit a systematically weaker dependence is found for the CG model. Moreover, deviations are found for solvation thermodynamics and for the corresponding enthalpy-entropy compensation for the CG model. Particularly water/oil repulsion seems to be overestimated. However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties.

  12. Protein Unfolding Coupled to Ligand Binding: Differential Scanning Calorimetry Simulation Approach

    Science.gov (United States)

    Celej, Maria Soledad; Fidelio, Gerardo Daniel; Dassie, Sergio Alberto

    2005-01-01

    A comprehensive theoretical description of thermal protein unfolding coupled to ligand binding is presented. The thermodynamic concepts are independent of the method used to monitor protein unfolding but a differential scanning calorimetry is being used as a tool for examining the unfolding process.

  13. Evaluation of the thermodynamics of a four level system using canonical density matrix method

    Directory of Open Access Journals (Sweden)

    Awoga Oladunjoye A.

    2013-02-01

    Full Text Available We consider a four-level system with two subsystems coupled by weak interaction. The system is in thermal equilibrium. The thermodynamics of the system, namely internal energy, free energy, entropy and heat capacity, are evaluated using the canonical density matrix by two methods. First by Kronecker product method and later by treating the subsystems separately and then adding the evaluated thermodynamic properties of each subsystem. It is discovered that both methods yield the same result, the results obey the laws of thermodynamics and are the same as earlier obtained results. The results also show that each level of the subsystems introduces a new degree of freedom and increases the entropy of the entire system. We also found that the four-level system predicts a linear relationship between heat capacity and temperature at very low temperatures just as in metals. Our numerical results show the same trend.

  14. Mass-Elastic Band Thermodynamics: A Visual Teaching Aid at the Introductory Level

    Science.gov (United States)

    Galley, William C.

    2007-01-01

    The analysis a recently developed mass-elastic band process that will help in providing a better understanding of various aspects of chemical thermodynamics. These processes also include the use of a visual teaching aid at the introductory level, which helps students to think better.

  15. Improving Students' Chemical Literacy Levels on Thermochemical and Thermodynamics Concepts through a Context-Based Approach

    Science.gov (United States)

    Cigdemoglu, Ceyhan; Geban, Omer

    2015-01-01

    The aim of this study was to delve into the effect of context-based approach (CBA) over traditional instruction (TI) on students' chemical literacy level related to thermochemical and thermodynamics concepts. Four eleventh-grade classes with 118 students in total taught by two teachers from a public high school in 2012 fall semester were enrolled…

  16. Improving Students' Chemical Literacy Levels on Thermochemical and Thermodynamics Concepts through a Context-Based Approach

    Science.gov (United States)

    Cigdemoglu, Ceyhan; Geban, Omer

    2015-01-01

    The aim of this study was to delve into the effect of context-based approach (CBA) over traditional instruction (TI) on students' chemical literacy level related to thermochemical and thermodynamics concepts. Four eleventh-grade classes with 118 students in total taught by two teachers from a public high school in 2012 fall semester were enrolled…

  17. Protein Unfolding and Alzheimer's

    Science.gov (United States)

    Cheng, Kelvin

    2012-10-01

    Early interaction events of beta-amyloid (Aβ) proteins with neurons have been associated with the pathogenesis of Alzheimer's disease. Knowledge pertaining to the role of lipid molecules, particularly cholesterol, in modulating the single Aβ interactions with neurons at the atomic length and picosecond time resolutions, remains unclear. In our research, we have used atomistic molecular dynamics simulations to explore early molecular events including protein insertion kinetics, protein unfolding, and protein-induced membrane disruption of Aβ in lipid domains that mimic the nanoscopic raft and non-raft regions of the neural membrane. In this talk, I will summarize our current work on investigating the role of cholesterol in regulating the Aβ interaction events with membranes at the molecular level. I will also explain how our results will provide new insights into understanding the pathogenesis of Alzheimer's disease associated with the Aβ proteins.

  18. Disposal of high level nuclear wastes: Thermodynamic equilibrium and environment ethics

    Institute of Scientific and Technical Information of China (English)

    RANA Mukhtar Ahmed

    2009-01-01

    Contamination of soil, water or air, due to a failure of containment or disposal of high level nuclear wastes, can potentially cause serious hazards to the environment or human health. Essential elements of the environment and radioactivity dangers to it are illustrated. Issues of high level nuclear waste disposal are discussed with a focus on thermodynamic equilibrium and environment ethics. Major aspects of the issues are analyzed and described briefly to build a perception of risks involved and ethical implications. Nuclear waste containment repository should be as close as possible to thermodynamic equilibrium. A clear demonstration about safety aspects of nuclear waste management is required in gaining public and political confidence in any possible scheme of permanent disposal. Disposal of high level nuclear waste offers a spectrum of environment connected challenges and a long term future of nuclear power depends on the environment friendly solution of the problem of nuclear wastes.

  19. Three-level systems as amplifiers and attenuators: a thermodynamic analysis.

    Science.gov (United States)

    Boukobza, E; Tannor, D J

    2007-06-15

    Thermodynamics of a three-level maser was studied in the pioneering work of Scovil-Schulz-DuBois [Phys. Rev. Lett. 2, 262 (1959)10.1103/PhysRevLett.2.262]. In this Letter we consider the same three-level model, but we give a full thermodynamic analysis based on Hamiltonian and dissipative Lindblad superoperators. The first law of thermodynamics is obtained using a recently developed alternative [Phys. Rev. A 74, 063823 (2006)10.1103/PhysRevA.74.063823] to Alicki's definitions for heat flux and power [J. Phys. A 12, L103 (1979)10.1088/0305-4470/12/5/007]. Using a novel variation on Spohn's entropy production function [J. Math. Phys. (N.Y.) 19, 1227 (1978)10.1063/1.523789], we obtain Carnot's efficiency inequality and the Scovil-Schulz-DuBois maser efficiency formula when the three-level system is operated as a heat engine (amplifier). Finally, we show that the three-level system has two other modes of operation--a refrigerator mode and a squanderer mode--both of which attenuate the electric field.

  20. Discrete Thermodynamics of 2-level Laser - Why Not and When Yes

    CERN Document Server

    Zilbergleyt, B

    2006-01-01

    The paper explores a possible application of the discrete thermodynamics to a 2-level laser. The model accounts for the laser openness to incoming pumping power and coming out energy with the emitted light. As an open system, a laser should be in open equilibrium with thermodynamic forces, related to both energy flows. Conditions of equilibria are expressed by a logistic map with specially developed dynamic inverse pitchfork bifurcation diagrams for graphical presentation of the solutions. The graphs explicitly confirm the triggering nature of a laser where bistability is manifested by pitchfork ground and laser branches, with the relative population equilibrium values close to 1 and 0 correspondingly. Simulation was run for a 2-level laser emitting light from far infrared to short wave UV. A newly discovered feature of such a laser is the line spectrum of up and down transitions of the laser excitable dwellers, occurring between the laser and the ground pitchfork branches beyond bifurcation point. The densit...

  1. Mechanics of collective unfolding

    CERN Document Server

    Caruel, M; Truskinovsky, L

    2015-01-01

    Mechanically induced unfolding of passive crosslinkers is a fundamental biological phenomenon encountered across the scales from individual macro-molecules to cytoskeletal actin networks. In this paper we study a conceptual model of athermal load-induced unfolding and use a minimalistic setting allowing one to emphasize the role of long-range interactions while maintaining full analytical transparency. Our model can be viewed as a description of a parallel bundle of N bistable units confined between two shared rigid backbones that are loaded through a series spring. We show that the ground states in this model correspond to synchronized, single phase configurations where all individual units are either folded or unfolded. We then study the fine structure of the wiggly energy landscape along the reaction coordinate linking the two coherent states and describing the optimal mechanism of cooperative unfolding. Quite remarkably, our study shows the fundamental difference in the size and structure of the folding-u...

  2. Unfolding features of bovine testicular hyaluronidase studied by fluorescence spectroscopy and fourier transformed infrared spectroscopy.

    Science.gov (United States)

    Pan, Nina; Cai, Xiaoqiang; Tang, Kai; Zou, Guolin

    2005-11-01

    Chemical unfolding of bovine testicular hyaluronidase (HAase) has been studied by fluorescence spectroscopy and Fourier transformed infrared spectroscopy (FTIR). Thermodynamic parameters were determined for unfolding HAase from changes in the intrinsic fluorescence emission intensity and the formations of several possible unfolding intermediates have been identified. This was further confirmed by representation of fluorescence data in terms of 'phase diagram'. The secondary structures of HAase have been assigned and semiquantitatively estimated from the FTIR. The occurrence of conformational change during chemical unfolding as judged by fluorescence and FTIR spectroscopy indicated that the unfolding of HAase may not follow the typical two-state model.

  3. JNC thermodynamic database for performance assessment of high-level radioactive waste disposal system

    Energy Technology Data Exchange (ETDEWEB)

    Yui, Mikazu; Azuma, Jiro; Shibata, Masahiro [Japan Nuclear Cycle Development Inst., Tokai Works, Waste Isolation Research Division, Tokai, Ibaraki (Japan)

    1999-11-01

    This report is a summary of status, frozen datasets, and future tasks of the JNC (Japan Nuclear Cycle Development Institute) thermodynamic database (JNC-TDB) for assessing performance of high-level radioactive waste in geological environments. The JNC-TDB development was carried out after the first progress report on geological disposal research in Japan (H-3). In the development, thermodynamic data (equilibrium constants at 25degC, I=0) for important radioactive elements were selected/determined based on original experimental data using different models (e.g., SIT, Pitzer). As a result, the reliability and traceability of the data for most of the important elements were improved over those of the PNC-TDB used in H-3 report. For detailed information of data analysis and selections for each element, see the JNC technical reports listed in this document. (author)

  4. Unfolding single- and multilayers

    Science.gov (United States)

    Llorens, Maria-Gema; Bons, Paul D.; Griera, Albert; Gomez-Rivas, Enrique

    2014-05-01

    When planar structures (e.g. sedimentary layers, veins, dykes, cleavages, etc.) are subjected to deformation, they have about equal chances to be shortened or stretched. The most common shortening and stretching structures are folds and boudinage, respectively. However, boudinage requires additional deformation mechanisms apart from viscous flow, like formation of fractures or strain localization. When folded layers are subjected to extension, they could potentially unfold back to straight layers. Although probably not uncommon, this would be difficult to recognize. Open questions are whether folded layers can unfold, what determines their mechanical behaviour and how we can recognize them in the field. In order to approach these questions, we present a series of numerical experiments that simulate stretching of previously folded single- and multi-layers in simple shear, using the two dimensional numerical modelling platform ELLE, including the finite element module BASIL that calculates viscous deformation. We investigate the parameters that affect a fold train once it rotates into the extensional field. The results show that the unfolding process strongly depends on the viscosity contrast between the layer and matrix (Llorens et al., 2013). Layers do not completely unfold when they experience softening before or during the stretching process or when other neighbouring competent layers prevent them from unfolding. The foliation refraction patterns are the main indicators of unfolded folds. Additionally, intrafolial folds and cusp-like folds adjacent to straight layers, as well as variations in fold amplitudes and limb lengths of irregular folds can also be used as indicators of stretching of a layer after shortening and folding. References: Llorens, M-.G., Bons, P.D., Griera, A. and Gomez-Rivas, E. 2013. When do folds unfold during progressive shear?. Geology, 41, 563-566.

  5. Level densities and thermodynamical quantities of heated $^{93-98}$Mo isotopes

    CERN Document Server

    Chankova, R; Agvaanluvsan, U; Algin, E; Bernstein, L A; Guttormsen, M; Ingebretsen, F; Lönnroth, T; Messelt, S; Mitchell, G E; Rekstad, J; Siem, S; Sunde, A C; Voinov, A

    2006-01-01

    Level densities for $^{93-98}$Mo have been extracted using the ($^3$He,$\\alpha \\gamma$) and ($^3$He,$^3$He'$\\gamma$) reactions. From the level densities thermodynamical quantities such as temperature and heat capacity can be deduced. Data have been analyzed by utilizing both the microcanonical and the canonical ensemble. Structures in the microcanonical temperature are due to the breaking of Cooper pairs. The S-shape of the heat capacity curves found within the canonical ensemble indicates the pairing phase transition and critical temperatures for the quenching of pairing correlation are found at $T_c\\sim 0.7 -1.0$ MeV.

  6. Quantum Thermodynamics: Non-equilibrium 3D Description of an Unbounded System at an Atomistic Level

    Directory of Open Access Journals (Sweden)

    Vittorio Verda

    2010-03-01

    Full Text Available Quantum thermodynamics (QT provides a general framework for the description of non-equilibrium phenomena at any level, particularly the atomistic one. This theory and its dynamical postulate are used here to extend the work reported in previous papers of modeling the storage of hydrogen in an isolated system, by extending the modeling to 3D. The system is prepared in a state with the hydrogen molecules initially far from stable equilibrium after which the system is allowed to relax (evolve to a state of stable equilibrium. The so-called energy eigenvalue problem, which entails a many-body problem that for dilute and moderately dense gases can be solved using virial expansion theory, is used to determine the energy eigenvalues and eigenstates of the system. This information is then used in the nonlinear Beretta equation of motion of QT to determine the evolution of the thermodynamic state of the system as well as the spatial distributions of the hydrogen molecules in time. The results of our simulations provide a quantification of the entropy generated due to irreversibilities at an atomistic level and show in detail the trajectory of the state of the system as the hydrogen molecules, which are initially arranged to be far from the carbon nanotube, spread out in the system and eventually become more concentrated near the carbon atoms which make up the nanotube.

  7. The deconvolution of differential scanning calorimetry unfolding transitions.

    Science.gov (United States)

    Spink, Charles H

    2015-04-01

    This paper is a review of a process for deconvolution of unfolding thermal transitions measured by differential scanning calorimetry. The mathematical background is presented along with illustrations of how the unfolding data is processed to resolve the number of sequential transitions needed to describe an unfolding mechanism and to determine thermodynamic properties of the intermediate states. Examples of data obtained for a simple two-state unfolding of a G-quadruplex DNA structure derived from the basic human telomere sequence, (TTAGGG)4TT are used to present some of the basic issues in treating the DSC data. A more complex unfolding mechanism is also presented that requires deconvolution of a multistate transition, the unfolding of a related human telomere structure, (TTAGGG)12 TT. The intent of the discussion is to show the steps in deconvolution, and to present the data at each step to help clarify how the information is derived from the various mathematical manipulations. Copyright © 2014. Published by Elsevier Inc.

  8. Teaching Thermodynamics and Kinetics to Advanced General Chemistry Students and to Upper-Level Undergraduate Students Using PV Diagrams

    Science.gov (United States)

    Iyengar, Srinivasan S.; deSouza, Romualdo T.

    2014-01-01

    We describe how complex concepts in macroscopic chemistry, namely, thermodynamics and kinetics, can be taught at considerable depth both at the first-year undergraduate as well as upper levels. We begin with a careful treatment of PV diagrams, and by pictorially integrating the appropriate area in a PV diagram, we introduce work. This starting…

  9. Teaching Thermodynamics and Kinetics to Advanced General Chemistry Students and to Upper-Level Undergraduate Students Using PV Diagrams

    Science.gov (United States)

    Iyengar, Srinivasan S.; deSouza, Romualdo T.

    2014-01-01

    We describe how complex concepts in macroscopic chemistry, namely, thermodynamics and kinetics, can be taught at considerable depth both at the first-year undergraduate as well as upper levels. We begin with a careful treatment of PV diagrams, and by pictorially integrating the appropriate area in a PV diagram, we introduce work. This starting…

  10. Thermodynamics of Radiation Modes

    Science.gov (United States)

    Pina, Eduardo; de la Selva, Sara Maria Teresa

    2010-01-01

    We study the equilibrium thermodynamics of the electromagnetic radiation in a cavity of a given volume and temperature. We found three levels of description, the thermodynamics of one mode, the thermodynamics of the distribution of frequencies in a band by summing over the frequencies in it and the global thermodynamics by summing over all the…

  11. Unfolding the Sulcus

    Science.gov (United States)

    Hohlfeld, Evan; Mahadevan, L.

    2011-03-01

    Sulci are localized furrows on the surface of soft materials that form by a compression-induced instability. We unfold this instability by breaking its natural scale and translation invariance, and compute a limiting bifurcation diagram for sulcfication showing that it is a scale-free, subcritical nonlinear instability. In contrast with classical nucleation, sulcification is continuous, occurs in purely elastic continua and is structurally stable in the limit of vanishing surface energy. During loading, a sulcus nucleates at a point with an upper critical strain and an essential singularity in the linearized spectrum. On unloading, it quasistatically shrinks to a point with a lower critical strain, explained by breaking of scale symmetry. At intermediate strains the system is linearly stable but nonlinearly unstable with no energy barrier. Simple experiments confirm the existence of these two critical strains.

  12. Determination of heat capacity of unfolding for marginally stable proteins from a single temperature induced protein unfolding profile

    Energy Technology Data Exchange (ETDEWEB)

    Saini, Komal; Ahluwalia, Unnati [Department of Chemistry, Indian Institute of Technology, Delhi 110016 (India); Deep, Shashank, E-mail: sdeep@chemistry.iitd.ac.in [Department of Chemistry, Indian Institute of Technology, Delhi 110016 (India)

    2010-07-10

    A reliable estimation of heat capacity of denaturation ({Delta}C{sub p}) is necessary to calculate the free energy of unfolding of proteins. For marginally stable proteins, such as mutants of a protein or proteins at low pH or under denaturating conditions, the pre-transition region is not fully populated by the native state. Analysis of differential scanning calorimeter (DSC) data under such conditions may not yield a reliable value of {Delta}C{sub p} and other associated thermodynamic parameters of unfolding. Analysis of denaturation profiles of (a) cytochrome c at pH 2.5, 3 and 8 and (b) myoglobin at pH 4, show that an accurate value of {Delta}C{sub p} can be extracted from a single unfolding profile obtained spectroscopically by including low temperature data.

  13. Slow Unfolding of Monomeric Proteins from Hyperthermophiles with Reversible Unfolding

    Directory of Open Access Journals (Sweden)

    Atsushi Mukaiyama

    2009-03-01

    Full Text Available Based on the differences in their optimal growth temperatures microorganisms can be classified into psychrophiles, mesophiles, thermophiles, and hyperthermophiles. Proteins from hyperthermophiles generally exhibit greater stability than those from other organisms. In this review, we collect data about the stability and folding of monomeric proteins from hyperthermophilies with reversible unfolding, from the equilibrium and kinetic aspects. The results indicate that slow unfolding is a general strategy by which proteins from hyperthermophiles adapt to higher temperatures. Hydrophobic interaction is one of the factors in the molecular mechanism of the slow unfolding of proteins from hyperthermophiles.

  14. Resolution of the unfolded state.

    Science.gov (United States)

    Beaucage, Gregory

    2008-03-01

    The unfolded states in proteins and nucleic acids remain weakly understood despite their importance to protein folding; misfolding diseases (Parkinson's & Alzheimer's); natively unfolded proteins (˜ 30% of eukaryotic proteins); and to understanding ribozymes. Research has been hindered by the inability to quantify the residual (native) structure present in an unfolded protein or nucleic acid. Here, a scaling model is proposed to quantify the degree of folding and the unfolded state (Beaucage, 2004, 2007). The model takes a global view of protein structure and can be applied to a number of analytic methods and to simulations. Three examples are given of application to small-angle scattering from pressure induced unfolding of SNase (Panick, 1998), from acid unfolded Cyt c (Kataoka, 1993) and from folding of Azoarcus ribozyme (Perez-Salas, 2004). These examples quantitatively show 3 characteristic unfolded states for proteins, the statistical nature of a folding pathway and the relationship between extent of folding and chain size during folding for charge driven folding in RNA. Beaucage, G., Biophys. J., in press (2007). Beaucage, G., Phys. Rev. E. 70, 031401 (2004). Kataoka, M., Y. Hagihara, K. Mihara, Y. Goto J. Mol. Biol. 229, 591 (1993). Panick, G., R. Malessa, R. Winter, G. Rapp, K. J. Frye, C. A. Royer J. Mol. Biol. 275, 389 (1998). Perez-Salas U. A., P. Rangan, S. Krueger, R. M. Briber, D. Thirumalai, S. A. Woodson, Biochemistry 43 1746 (2004).

  15. Unfolding of the spectrum for chaotic and mixed systems

    Science.gov (United States)

    Abul-Magd, Ashraf A.; Abul-Magd, Adel Y.

    2014-02-01

    Random Matrix Theory (RMT) is capable of making predictions for the spectral fluctuations of a physical system only after removing the influence of the level density by unfolding the spectra. When the level density is known, unfolding is done by using the integrated level density to transform the eigenvalues into dimensionless variables with unit mean spacing. When it is not known, as in most practical cases, one usually approximates the level staircase function by a polynomial. We here study the effect of unfolding procedure on the spectral fluctuation of two systems for which the level density is known asymptotically. The first is a time-reversal-invariant chaotic system, which is modeled in RMT by a Gaussian Orthogonal Ensemble (GOE). The second is the case of chaotic systems in which m quantum numbers remain almost undistorted in the early stage of the stochastic transition. The Hamiltonian of a system may be represented by a block diagonal matrix with m blocks of the same size, in which each block is a GOE. Unfolding is done once by using the asymptotic level densities for the eigenvalues of the m blocks and once by representing the integrated level density in terms of polynomials of different orders. We find that the spacing distribution of the eigenvalues shows a little sensitivity to the unfolding method. On the other hand, the variance of level number Σ2(L) is sensitive to the choice of the unfolding function. Unfolding that utilizes low order polynomials enhances Σ2(L) relative to the theoretical value, while the use of high order polynomial reduces it. The optimal value of the order of the unfolding polynomial depends on the dimension of the corresponding ensemble.

  16. Exploring early stages of the chemical unfolding of proteins at the proteome scale.

    Directory of Open Access Journals (Sweden)

    Michela Candotti

    Full Text Available After decades of using urea as denaturant, the kinetic role of this molecule in the unfolding process is still undefined: does urea actively induce protein unfolding or passively stabilize the unfolded state? By analyzing a set of 30 proteins (representative of all native folds through extensive molecular dynamics simulations in denaturant (using a range of force-fields, we derived robust rules for urea unfolding that are valid at the proteome level. Irrespective of the protein fold, presence or absence of disulphide bridges, and secondary structure composition, urea concentrates in the first solvation shell of quasi-native proteins, but with a density lower than that of the fully unfolded state. The presence of urea does not alter the spontaneous vibration pattern of proteins. In fact, it reduces the magnitude of such vibrations, leading to a counterintuitive slow down of the atomic-motions that opposes unfolding. Urea stickiness and slow diffusion is, however, crucial for unfolding. Long residence urea molecules placed around the hydrophobic core are crucial to stabilize partially open structures generated by thermal fluctuations. Our simulations indicate that although urea does not favor the formation of partially open microstates, it is not a mere spectator of unfolding that simply displaces to the right of the folded ←→ unfolded equilibrium. On the contrary, urea actively favors unfolding: it selects and stabilizes partially unfolded microstates, slowly driving the protein conformational ensemble far from the native one and also from the conformations sampled during thermal unfolding.

  17. Isoentropic and Isoenthalpic Temperatures of Protein Unfolding in Hydrophobic Interaction Chromatography

    Institute of Scientific and Technical Information of China (English)

    Yan YAN; Rui Xian LIU; Yin Mao WEI; Ye Hua SHEN; Xin Du GENG

    2006-01-01

    The thermal behaviors of five proteins in hydrophobic interaction chromatography (HIC) were investigated in the temperature range from 0 to 50℃. The thermodynamic parameters (△H°,△S°, △Cp°and △G°) of these proteins in the process of retention and unfolding were determined.The existence of enthalpy and entropy convergence with temperature was confirmed. The differences of the isoentropic and isoenthalpic temperatures for protein unfolding in HIC system from the traditional solution were elucidated.

  18. Protein co-translocational unfolding depends on the direction of pulling

    Science.gov (United States)

    Rodriguez-Larrea, David; Bayley, Hagan

    2014-09-01

    Protein unfolding and translocation through pores occurs during trafficking between organelles, protein degradation and bacterial toxin delivery. In vivo, co-translocational unfolding can be affected by the end of the polypeptide that is threaded into the pore first. Recently, we have shown that co-translocational unfolding can be followed in a model system at the single-molecule level, thereby unravelling molecular steps and their kinetics. Here, we show that the unfolding kinetics of the model substrate thioredoxin, when pulled through an α-haemolysin pore, differ markedly depending on whether the process is initiated from the C terminus or the N terminus. Further, when thioredoxin is pulled from the N terminus, the unfolding pathway bifurcates: some molecules finish unfolding quickly, while others finish ~100 times slower. Our findings have important implications for the understanding of biological unfolding mechanisms and in the application of nanopore technology for the detection of proteins and their modifications.

  19. Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model

    Science.gov (United States)

    Li, Chunhua; Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin; Su, Jiguo; Zhang, Yang

    2016-07-01

    Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.

  20. Steepest-entropy-ascent nonequilibrium quantum thermodynamic framework to model chemical reaction rates at an atomistic level

    Science.gov (United States)

    Beretta, G. P.; Al-Abbasi, Omar; von Spakovsky, M. R.

    2017-04-01

    The steepest entropy ascent (SEA) dynamical principle provides a general framework for modeling the dynamics of nonequilibrium (NE) phenomena at any level of description, including the atomistic one. It has recently been shown to provide a precise implementation and meaning to the maximum entropy production principle and to encompass many well-established theories of nonequilibrium thermodynamics into a single unifying geometrical framework. Its original formulation in the framework of quantum thermodynamics (QT) assumes the simplest and most natural Fisher-Rao metric to geometrize from a dynamical standpoint the manifold of density operators, which represent the thermodynamic NE states of the system. This simplest SEAQT formulation is used here to develop a general mathematical framework for modeling the NE time evolution of the quantum state of a chemically reactive mixture at an atomistic level. The method is illustrated for a simple two-reaction kinetic scheme of the overall reaction F +H2⇔HF +F in an isolated tank of fixed volume. However, the general formalism is developed for a reactive system subject to multiple reaction mechanisms. To explicitly implement the SEAQT nonlinear law of evolution for the density operator, both the energy and the particle number eigenvalue problems are set up and solved analytically under the dilute gas approximation. The system-level energy and particle number eigenvalues and eigenstates are used in the SEAQT equation of motion to determine the time evolution of the density operator, thus effectively describing the overall kinetics of the reacting system as it relaxes toward stable chemical equilibrium. The predicted time evolution in the near-equilibrium limit is compared to the reaction rates given by a standard detailed kinetic model so as to extract the single time constant needed by the present SEA model.

  1. Steepest-entropy-ascent nonequilibrium quantum thermodynamic framework to model chemical reaction rates at an atomistic level.

    Science.gov (United States)

    Beretta, G P; Al-Abbasi, Omar; von Spakovsky, M R

    2017-04-01

    The steepest entropy ascent (SEA) dynamical principle provides a general framework for modeling the dynamics of nonequilibrium (NE) phenomena at any level of description, including the atomistic one. It has recently been shown to provide a precise implementation and meaning to the maximum entropy production principle and to encompass many well-established theories of nonequilibrium thermodynamics into a single unifying geometrical framework. Its original formulation in the framework of quantum thermodynamics (QT) assumes the simplest and most natural Fisher-Rao metric to geometrize from a dynamical standpoint the manifold of density operators, which represent the thermodynamic NE states of the system. This simplest SEAQT formulation is used here to develop a general mathematical framework for modeling the NE time evolution of the quantum state of a chemically reactive mixture at an atomistic level. The method is illustrated for a simple two-reaction kinetic scheme of the overall reaction F+H_{2}⇔HF+F in an isolated tank of fixed volume. However, the general formalism is developed for a reactive system subject to multiple reaction mechanisms. To explicitly implement the SEAQT nonlinear law of evolution for the density operator, both the energy and the particle number eigenvalue problems are set up and solved analytically under the dilute gas approximation. The system-level energy and particle number eigenvalues and eigenstates are used in the SEAQT equation of motion to determine the time evolution of the density operator, thus effectively describing the overall kinetics of the reacting system as it relaxes toward stable chemical equilibrium. The predicted time evolution in the near-equilibrium limit is compared to the reaction rates given by a standard detailed kinetic model so as to extract the single time constant needed by the present SEA model.

  2. Stochastic thermodynamics

    Science.gov (United States)

    Eichhorn, Ralf; Aurell, Erik

    2014-04-01

    theory for small deviations from equilibrium, in which a general framework is constructed from the analysis of non-equilibrium states close to equilibrium. In a next step, Prigogine and others developed linear irreversible thermodynamics, which establishes relations between transport coefficients and entropy production on a phenomenological level in terms of thermodynamic forces and fluxes. However, beyond the realm of linear response no general theoretical results were available for quite a long time. This situation has changed drastically over the last 20 years with the development of stochastic thermodynamics, revealing that the range of validity of thermodynamic statements can indeed be extended deep into the non-equilibrium regime. Early developments in that direction trace back to the observations of symmetry relations between the probabilities for entropy production and entropy annihilation in non-equilibrium steady states [5-8] (nowadays categorized in the class of so-called detailed fluctuation theorems), and the derivations of the Bochkov-Kuzovlev [9, 10] and Jarzynski relations [11] (which are now classified as so-called integral fluctuation theorems). Apart from its fundamental theoretical interest, the developments in stochastic thermodynamics have experienced an additional boost from the recent experimental progress in fabricating, manipulating, controlling and observing systems on the micro- and nano-scale. These advances are not only of formidable use for probing and monitoring biological processes on the cellular, sub-cellular and molecular level, but even include the realization of a microscopic thermodynamic heat engine [12] or the experimental verification of Landauer's principle in a colloidal system [13]. The scientific program Stochastic Thermodynamics held between 4 and 15 March 2013, and hosted by The Nordic Institute for Theoretical Physics (Nordita), was attended by more than 50 scientists from the Nordic countries and elsewhere, amongst them

  3. Level Densities, Thermodynamics and gamma -Ray Strength Functions in 163,164Dy

    Science.gov (United States)

    Nyhus, H. T.; Siem, S.; Guttormsen, M.; Larsen, A. C.; Bürger, A.; Syed, N. U. H.; Toft, H. K.; Tveten, G. M.; Voinov, A.

    2009-03-01

    The nuclei 163,164Dy have been investigated by use of the Oslo method on data from the pick-up reaction {(3He,alpha )} and the inelastic scattering {(3He,3He')}, respectively. The experiment was conducted at the Oslo cyclotron laboratory (OCL). The gamma -decay and ejectiles were measured with the CACTUS multidetector array, which consists of 28 NaI gamma -detectores and 8 Delta E - E Si particle telescopes. Thermodynamic quantities have been extracted within the micro-canonical ensemble theory. The pygmy resonance found around 3 MeV in the gamma -ray strength function, also referred to as the scissors mode, was studied. The question whether the width of the pygmy resonance is reaction dependent is addressed.

  4. Neutron spectrum unfolding: Pt. 1; Theoretical

    Energy Technology Data Exchange (ETDEWEB)

    Matiullah (Centre for Nuclear Studies, Nilore, Islamabad (Pakistan)); Wiyaja, D.S. (PPTN - BATAN, Bandung (Indonesia)); Berzonis, M.A.; Bondars, H.; Lapenas, A.A. (Latvijskij Gosudarstvennyj Univ., Riga (USSR)); Kudo, K. (Electrotechnical Lab., Tsukuba, Ibaraki (Japan)); Majeed, A.; Durrani, S.A. (Birimingham Univ. (United Kingdom). School of Physics and Space Research)

    1991-01-01

    The use of the latest PC version of the computer code SAIPS in neutron spectrum unfolding is described. Guidelines for extending the use of SAIPS to unfold the spectrum from a CR-39-based spectrometer are presented. (author).

  5. Ising Model Reprogramming of a Repeat Protein's Equilibrium Unfolding Pathway.

    Science.gov (United States)

    Millership, C; Phillips, J J; Main, E R G

    2016-05-08

    Repeat proteins are formed from units of 20-40 aa that stack together into quasi one-dimensional non-globular structures. This modular repetitive construction means that, unlike globular proteins, a repeat protein's equilibrium folding and thus thermodynamic stability can be analysed using linear Ising models. Typically, homozipper Ising models have been used. These treat the repeat protein as a series of identical interacting subunits (the repeated motifs) that couple together to form the folded protein. However, they cannot describe subunits of differing stabilities. Here we show that a more sophisticated heteropolymer Ising model can be constructed and fitted to two new helix deletion series of consensus tetratricopeptide repeat proteins (CTPRs). This analysis, showing an asymmetric spread of stability between helices within CTPR ensembles, coupled with the Ising model's predictive qualities was then used to guide reprogramming of the unfolding pathway of a variant CTPR protein. The designed behaviour was engineered by introducing destabilising mutations that increased the thermodynamic asymmetry within a CTPR ensemble. The asymmetry caused the terminal α-helix to thermodynamically uncouple from the rest of the protein and preferentially unfold. This produced a specific, highly populated stable intermediate with a putative dimerisation interface. As such it is the first step in designing repeat proteins with function regulated by a conformational switch. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  6. Enthalpy-entropy compensation in protein unfolding

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Enthalpy-entropy compensation was found to be a universal law in protein unfolding based on over 3 000 experimental data. Water molecular reorganization accompanying the protein unfolding was suggested as the origin of the enthalpy-entropy compensation in protein unfolding. It is indicated that the enthalpy-entropy compensation constitutes the physical foundation that satisfies the biological need of the small free energy changes in protein unfolding, without the sacrifice of the bio-diversity of proteins. The enthalpy-entropy compensation theory proposed herein also provides valuable insights into the Privalov's puzzle of enthalpy and entropy convergence in protein unfolding.

  7. Nanomechanics of Protein Unfolding outside Protease Nanopores

    Science.gov (United States)

    Luan, Binquan; Zhou, Ruhong

    Protein folding and unfolding have been the subject of active research for decades. Most of previous studies in protein unfolding were focused on temperature, chemical and/or force (such as in AFM) induced denaturations. Recent studies on the functional roles of proteasomes (such as ClpXP) revealed a novel unfolding process in cell, during which a target protein is mechanically unfolded and pulled into a confined, pore-like geometry for degradation. While the proteasome nanomachine has been extensively studied, the mechanism for unfolding proteins with the proteasome pore is still poorly understood. Here, we investigate the mechanical unfolding process of ubiquitin with (or really outside) an idealized proteasome pore, and compare such process with that in the AFM pulling experiment. Unexpectedly, the required force by a proteosome can be much smaller than that by the AFM. Simulation results also unveiled different nanomechanics, tearing fracture vs. shearing friction, in these two distinct types of mechanical unfoldings.

  8. Chemical thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Rock, P.A.

    1983-01-01

    This book, suitable as an introductory text for undergraduates, presents temperature, internal energy, and entropy with a minimum of mathematics. The basic mathematical models of classical chemical thermodynamics are developed later in the text. Includes numerous problems at the end of each chapter, an appendix giving thermodynamic data for common substances, a short list of references, answers to selected problems, and a subject index. Contents, abridged: Energy and the first law of thermodynamics. Thermodynamic functions. The third law of thermodynamics and absolute entropies. Thermodynamics of chemical reactions. Phase equilibria: the activity function. Thermodynamics of ions in solution. Statistical thermodynamics. Appendices. Index.

  9. BUMS--Bonner sphere Unfolding Made Simple an HTML based multisphere neutron spectrometer unfolding package

    CERN Document Server

    Sweezy, J; Veinot, K

    2002-01-01

    A new multisphere neutron spectrometer unfolding package, Bonner sphere Unfolding Made Simple (BUMS) has been developed that uses an HTML interface to simplify data input and code execution for the novice and the advanced user. This new unfolding package combines the unfolding algorithms contained in other popular unfolding codes under one easy to use interface. The interface makes use of web browsing software to provide a graphical user interface to the unfolding algorithms. BUMS integrates the SPUNIT, BON, MAXIET, and SAND-II unfolding algorithms into a single package. This package also includes a library of 14 response matrices, 58 starting spectra, and 24 dose and detector responses. BUMS has several improvements beyond the addition of unfolding algorithms. It has the ability to search for the most appropriate starting spectra. Also, plots of the unfolded neutron spectra are automatically generated. The BUMS package runs via a web server and may be accessed by any computer with access to the Internet at h...

  10. The Ca(2+ influence on calmodulin unfolding pathway: a steered molecular dynamics simulation study.

    Directory of Open Access Journals (Sweden)

    Yong Zhang

    Full Text Available The force-induced unfolding of calmodulin (CaM was investigated at atomistic details with steered molecular dynamics. The two isolated CaM domains as well as the full-length CaM were simulated in N-C-terminal pulling scheme, and the isolated N-lobe of CaM was studied specially in two other pulling schemes to test the effect of pulling direction and compare with relevant experiments. Both Ca(2+-loaded CaM and Ca(2+-free CaM were considered in order to define the Ca(2+ influence to the CaM unfolding. The results reveal that the Ca(2+ significantly affects the stability and unfolding behaviors of both the isolated CaM domains and the full-length CaM. In Ca(2+-loaded CaM, N-terminal domain unfolds in priori to the C-terminal domain. But in Ca(2+-free CaM, the unfolding order changes, and C-terminal domain unfolds first. The force-extension curves of CaM unfolding indicate that the major unfolding barrier comes from conquering the interaction of two EF-hand motifs in both N- and C- terminal domains. Our results provide the atomistic-level insights in the force-induced CaM unfolding and explain the observation in recent AFM experiments.

  11. Different thermal unfolding pathways of catalase in the presence of cationic surfactants.

    Science.gov (United States)

    Blanco, Elena; Ruso, Juan M; Prieto, Gerardo; Sarmiento, Félix

    2007-03-01

    In this paper we have corroborated the usefulness of spectroscopic techniques, such as UV-visible, in the study and thermodynamic characterization of the thermal unfolding of catalase as a function of the concentration and alkyl chain length of n-alkyltrimethylammonium bromides (CnTAB, n = 8, 10, and 12). For this reason, a thermodynamic model was used which included experimental data corresponding to the pre- and posttransition into the observable transition. It has been found that n-alkyltrimethylammonium bromides play two opposite roles in the folding and stability of catalase. They act as a structure stabilizer at a low molar concentration and as a destabilizer at a higher concentration. The maximum of the unfolding temperature has been found to decrease with the alkyl chain. The reason for this difference has been suggested to be the side chains involved. In the presence of C8TAB and C10TAB, Gibbs energies of unfolding (DeltaG(T)) decrease with concentration, whereas for C12TAB an increase has been observed. These findings can be explained by the fact that when differences in the hydrophobic nature of the surfactants exist, different pathways of unfolding may occur. Also, the presence of surfactants has been observed to affect the cold denaturation of catalase. Thermodynamic results suggest that the thermal denaturation of catalase in the presence of n-alkyltrimethylammonium bromides is a perfect transition between two states.

  12. Varying Use of Conceptual Metaphors across Levels of Expertise in Thermodynamics

    Science.gov (United States)

    Jeppsson, Fredrik; Haglund, Jesper; Amin, Tamer G.

    2015-01-01

    Many studies have previously focused on how people with different levels of expertise solve physics problems. In early work, focus was on characterising differences between experts and novices and a key finding was the central role that propositionally expressed principles and laws play in expert, but not novice, problem-solving. A more recent…

  13. Nuclear Level Density and Thermodynamic Functions for Nuclei with Static Deformation

    Institute of Scientific and Technical Information of China (English)

    A.N.Behkami; M.N.Nasrabadi

    2002-01-01

    The level densities of even-odd and even-even isotopes 161,162Dy,166 Er and 171,172yb were calculated using microscopic theory of interacting fermions and compared with experiments.It is found that the data can be well reproduced with level density formalism for nuclei with static deformation.Thc nuclear temperature as well as the entropy of nuclear system as a function of excitation energy has been extracted from the BCS theory.It is shown that the entropy exhibits an S-formed shape as a function of excitation energy.This is interpreted as a phase transition.Procedure of treating the even-odd and even-even nuclear systems has been presented and discussed.

  14. Varying Use of Conceptual Metaphors across Levels of Expertise in Thermodynamics

    Science.gov (United States)

    Jeppsson, Fredrik; Haglund, Jesper; Amin, Tamer G.

    2015-04-01

    Many studies have previously focused on how people with different levels of expertise solve physics problems. In early work, focus was on characterising differences between experts and novices and a key finding was the central role that propositionally expressed principles and laws play in expert, but not novice, problem-solving. A more recent line of research has focused on characterising continuity between experts and novices at the level of non-propositional knowledge structures and processes such as image-schemas, imagistic simulation and analogical reasoning. This study contributes to an emerging literature addressing the coordination of both propositional and non-propositional knowledge structures and processes in the development of expertise. Specifically, in this paper, we compare problem-solving across two levels of expertise-undergraduate students of chemistry and Ph.D. students in physical chemistry-identifying differences in how conceptual metaphors (CMs) are used (or not) to coordinate propositional and non-propositional knowledge structures in the context of solving problems on entropy. It is hypothesised that the acquisition of expertise involves learning to coordinate the use of CMs to interpret propositional (linguistic and mathematical) knowledge and apply it to specific problem situations. Moreover, we suggest that with increasing expertise, the use of CMs involves a greater degree of subjective engagement with physical entities and processes. Implications for research on learning and instructional practice are discussed. Third contribution to special issue entitled: Conceptual metaphor and embodied cognition in science learning

  15. Application of arrangement theory to unfolding models

    CERN Document Server

    Kamiya, Hidehiko; Tokushige, Norihide

    2010-01-01

    Arrangement theory plays an essential role in the study of the unfolding model used in many fields. This paper describes how arrangement theory can be usefully employed in solving the problems of counting (i) the number of admissible rankings in an unfolding model and (ii) the number of ranking patterns generated by unfolding models. The paper is mostly expository but also contains some new results such as simple upper and lower bounds for the number of ranking patterns in the unidimensional case.

  16. The temperature dependence of the Hofmeister series: thermodynamic fingerprints of cosolute-protein interactions.

    Science.gov (United States)

    Senske, Michael; Constantinescu-Aruxandei, Diana; Havenith, Martina; Herrmann, Christian; Weingärtner, Hermann; Ebbinghaus, Simon

    2016-11-02

    The Hofmeister series is a universal homologous series to rank ion-specific effects on biomolecular properties such as protein stability or aggregation propensity. Although this ranking is widely used, outliers and exceptions are discussed controversially and a molecular level understanding is still lacking. Studying the thermal unfolding equilibrium of RNase A, we here show that this ambiguity arises from the oversimplified approach to determine the ion rankings. Instead of measuring salt effects on a single point of the protein folding stability curve (e.g. the melting point Tm), we here consider the salt induced shifts of the entire protein 'stability curve' (the temperature dependence of the unfolding free energy change, ΔGu(T)). We found multiple intersections of these curves, pinpointing a widely ignored fact: the Hofmeister cation and anion rankings are temperature dependent. We further developed a novel classification scheme of cosolute effects based on their thermodynamic fingerprints, reaching beyond salt effects to non-electrolytes.

  17. Thermodynamics of radiation modes

    Energy Technology Data Exchange (ETDEWEB)

    Pina, Eduardo; De la Selva, Sara Maria Teresa [Departamento de Fisica, Universidad Autonoma Metropolitana - Iztapalapa, PO Box 55 534, Mexico, D F, 09340 (Mexico)], E-mail: pge@xanum.uam.mx, E-mail: tere@xanum.uam.mx

    2010-03-15

    We study the equilibrium thermodynamics of the electromagnetic radiation in a cavity of a given volume and temperature. We found three levels of description, the thermodynamics of one mode, the thermodynamics of the distribution of frequencies in a band by summing over the frequencies in it and the global thermodynamics by summing over all the frequencies. One equation relating frequency and volume is used to define the thermodynamics of one mode, and to explain the mystery of the frequency-dependent quantities having a similar behaviour to the non-frequency-dependent quantities for some thermodynamic equations and different behaviour for others. Besides, this frequency-volume relation is used to count the number of modes in a band of frequency.

  18. SVD-based unfolding: implementation and experience

    CERN Document Server

    AUTHOR|(CDS)2072546

    2011-01-01

    With the first year of data taking at the LHC by the experiments, unfolding methods for measured spectra are reconsidered with much interest. Here, we present a novel ROOT-based implementation of the Singular Value Decomposition approach to data unfolding, and discuss concrete analysis experience with this algorithm.

  19. A Linear Iterative Unfolding Method

    CERN Document Server

    Laszlo, Andras

    2011-01-01

    A frequently faced task in experimental physics is to measure the probability distribution of some quantity. Often this quantity to be measured is smeared by a non-ideal detector response or by some physical process. The procedure of removing this smearing effect from the measured distribution is called unfolding, and is a delicate problem in signal processing. Due to the numerical ill-posedness of this task, various methods were invented which, given some assumptions on the initial probability distribution, try to regularize the problem. Most of these methods definitely introduce bias on the estimate of the initial probability distribution. We propose a linear iterative method (motivated by the Neumann series / Landweber iteration known in functional analysis), which has the advantage that no assumptions on the initial probability distribution is needed, and the only regularization parameter is the stopping order of the iteration. Convergence is proved under certain quite general conditions, which hold for p...

  20. The thermodynamics of protein folding: a critique of widely used quasi-thermodynamic interpretations and a restatement based on the Gibbs-Duhem relation and consistent with the Phase Rule.

    Science.gov (United States)

    Pethica, Brian A

    2010-07-21

    Interpretations of data in the extensive literature on the unfolding of proteins in aqueous solution follow a variety of methods involving assumptions leading to estimates of thermodynamic quantities associated with the unfolding transition. Inconsistencies and thermodynamic errors in these methods are identified. Estimates of standard molar free energies and enthalpies of unfolding using incompletely defined equilibrium constants and the van't Hoff relation are unsound, and typically contradict model-free interpretation of the data. A widely used routine for estimating the change in heat capacity associated with unfolding based on changes in the unfolding temperature and enthalpy co-induced by addition of denaturant or protective additives is thermodynamically incorrect by neglect of the Phase Rule. Many models and simulations predicting thermodynamic measures of unfolding are presently making comparisons with insecure quantities derived by incorrect thermodynamic analyses of experimental data. Analysis of unfolding via the Gibbs-Duhem equation with the correct Phase Rule constraints avoids the assumptions associated with incomplete equilibrium constants and misuse of the van't Hoff relation, and applies equally to positive, negative, sitewise or diffuse solute binding to the protein. The method gives the necessary relations between the thermodynamic parameters for thermal and isothermal unfolding and is developed for the case of two-state unfolding. The differences in binding of denaturants or stabilizers to the folded and unfolded forms of the protein are identified as major determinants of the unfolding process. The Phase Rule requires the temperature and enthalpy of unfolding to depend generally on the protein concentration. The available evidence bears out this expectation for thermal unfolding, indicating that protein-protein interactions influence folding. A parallel dependence of the denaturant concentrations for isothermal unfolding on the protein

  1. Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding.

    Science.gov (United States)

    Meuzelaar, Heleen; Tros, Martijn; Huerta-Viga, Adriana; van Dijk, Chris N; Vreede, Jocelyne; Woutersen, Sander

    2014-03-06

    Salt bridges are known to play an essential role in the thermodynamic stability of the folded conformation of many proteins, but their influence on the kinetics of folding remains largely unknown. Here, we investigate the effect of Glu-Arg salt bridges on the kinetics of α-helix folding using temperature-jump transient-infrared spectroscopy and steady-state UV circular dichroism. We find that geometrically optimized salt bridges (Glu(-) and Arg(+) are spaced four peptide units apart, and the Glu/Arg order is such that the side-chain rotameric preferences favor salt-bridge formation) significantly speed up folding and slow down unfolding, whereas salt bridges with unfavorable geometry slow down folding and slightly speed up unfolding. Our observations suggest a possible explanation for the surprising fact that many biologically active proteins contain salt bridges that do not stabilize the native conformation: these salt bridges might have a kinetic rather than a thermodynamic function.

  2. Quantum chemical analysis of the unfolding of a penta-glycyl 310-helix initiated by HO•, HO2•, and O2-•

    Science.gov (United States)

    Owen, Michael C.; Viskolcz, Bela; Csizmadia, Imre G.

    2011-07-01

    In this study, the thermodynamic functions of hydrogen abstraction from the Cα and amide nitrogen of Gly3 in a homo-pentapeptide (N-Ac-GGGGG-NH2; G5) by HO•, HO2•, and O2-• were computed using the Becke three-parameter Lee-Yang-Parr (B3LYP) density functional. The thermodynamic functions, standard enthalpy (ΔH°), Gibbs free energy (ΔG°), and entropy (ΔS°), of these reactions were computed with G5 in the 310-helical (G5Hel) and fully-extended (G5Ext) conformations at the B3LYP/6-31G(d) and B3LYP/6-311+G(d,p) levels of theory, both in the gas phase and using the conductor-like polarizable continuum model implicit water model. H abstraction is more favorable at the Cα than at the amide nitrogen. The secondary structure of G5 affects the bond dissociation energy of the H-Cα, but has a negligible effect on the dissociation energy of the H-N bond. The HO• radical is the strongest hydrogen abstractor, followed by HO2•, and finally O2-•. The secondary structure elements, such as H-bonds in the 310-helix, protect the peptide from radical attack by disabling the potential electron delocalization at the Cα, which is possible when G5 is in the extended conformation. The unfolding of the peptide radicals is more favorable than the unfolding of G5Hel; however, only the HO• can initiate the unfolding of G5Hel and the formation of G5Ext•. These results are relevant to peptides that are prone to undergoing transitions from helical structures to β-sheets in the cellular condition known as "oxidative stress" and the results are discussed in this context.

  3. Conformational dynamics of a protein in the folded and the unfolded state

    Energy Technology Data Exchange (ETDEWEB)

    Fitter, Joerg

    2003-08-01

    In a quasielastic neutron scattering experiment, the picosecond dynamics of {alpha}-amylase was investigated for the folded and the unfolded state of the protein. In order to ensure a reasonable interpretation of the internal protein dynamics, the protein was measured in D{sub 2}O-buffer solution. The much higher structural flexibility of the pH induced unfolded state as compared to the native folded state was quantified using a simple analytical model, describing a local diffusion inside a sphere. In terms of this model the conformational volume, which is explored mainly by confined protein side-chain movements, is parameterized by the radius of a sphere (folded state, r=1.2 A; unfolded state, 1.8 A). Differences in conformational dynamics between the folded and the unfolded state of a protein are of fundamental interest in the field of protein science, because they are assumed to play an important role for the thermodynamics of folding/unfolding transition and for protein stability.

  4. Residual structures in the unfolded state of starch-binding domain of glucoamylase revealed by near-UV circular dichroism and protein engineering techniques.

    Science.gov (United States)

    Ota, Chiaki; Ikeguchi, Masamichi; Tanaka, Akiyoshi; Hamada, Daizo

    2016-10-01

    Protein folding is a thermodynamic process driven by energy gaps between the native and unfolded states. Although a wealth of information is available on the structure of folded species, there is a paucity of data on unfolded species. Here, we analyzed the structural properties of the unfolded state of the starch-binding domain of glucoamylase from Aspergillus niger (SBD) formed in the presence of guanidinium hydrochloride (GuHCl). Although far-UV CD and intrinsic tryptophan fluorescence spectra as well as small angle X-ray scattering suggested that SBD assumes highly unfolded structures in the presence of GuHCl, near-UV circular dichroism of wild-type SBD suggested the presence of residual structures in the unfolded state. Analyses of the unfolded states of tryptophan mutants (W543L, W563A, W590A and W615L) using Similarity Parameter, a modified version of root mean square deviation as a measure of similarity between two spectra, suggested that W543 and W563 have preferences to form native-like residual structures in the GuHCl-unfolded state. In contrast, W615 was entirely unstructured, while W590 tended to form non-native ordered structures in the unfolded state. These data and the amino acid sequence of SBD suggest that local structural propensities in the unfolded state can be determined by the probability of the presence of hydrophobic or charged residues nearby tryptophan residues. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Retrocyclins neutralize bacterial toxins by potentiating their unfolding.

    Science.gov (United States)

    Kudryashova, Elena; Seveau, Stephanie; Lu, Wuyuan; Kudryashov, Dmitri S

    2015-04-15

    Defensins are a class of immune peptides with a broad range of activities against bacterial, fungal and viral pathogens. Besides exerting direct anti-microbial activity via dis-organization of bacterial membranes, defensins are also able to neutralize various unrelated bacterial toxins. Recently, we have demonstrated that in the case of human α- and β-defensins, this later ability is achieved through exploiting toxins' marginal thermodynamic stability, i.e. defensins act as molecular anti-chaperones unfolding toxin molecules and exposing their hydrophobic regions and thus promoting toxin precipitation and inactivation [Kudryashova et al. (2014) Immunity 41, 709-721]. Retrocyclins (RCs) are humanized synthetic θ-defensin peptides that possess unique cyclic structure, differentiating them from α- and β-defensins. Importantly, RCs are more potent against some bacterial and viral pathogens and more stable than their linear counterparts. However, the mechanism of bacterial toxin inactivation by RCs is not known. In the present study, we demonstrate that RCs facilitate unfolding of bacterial toxins. Using differential scanning fluorimetry (DSF), limited proteolysis and collisional quenching of internal tryptophan fluorescence, we show that hydrophobic regions of toxins normally buried in the molecule interior become more exposed to solvents and accessible to proteolytic cleavage in the presence of RCs. The RC-induced unfolding of toxins led to their precipitation and abrogated activity. Toxin inactivation by RCs was strongly diminished under reducing conditions, but preserved at physiological salt and serum concentrations. Therefore, despite significant structural diversity, α-, β- and θ-defensins employ similar mechanisms of toxin inactivation, which may be shared by anti-microbial peptides from other families.

  6. Experience with using unfolding procedures in ATLAS

    CERN Document Server

    Biondi, Silvia; The ATLAS collaboration

    2016-01-01

    In ATLAS, several unfolding methods are used to correct experimental measurements for detector effects, like acceptance and resolution. These methods use as input the raw experimental distributions, as well as Monte Carlo simulation for the description of the detector effects. The systematic uncertainties associated to the various unfolding methods are evaluated. The statistical and systematic uncertainties affecting the raw measurements and/or the simulation are propagated through the unfolding procedure. The resulting corrected measurements with their uncertainties can be directly compared with the corresponding theoretical predictions.

  7. Extended thermodynamics

    CERN Document Server

    Müller, Ingo

    1993-01-01

    Physicists firmly believe that the differential equations of nature should be hyperbolic so as to exclude action at a distance; yet the equations of irreversible thermodynamics - those of Navier-Stokes and Fourier - are parabolic. This incompatibility between the expectation of physicists and the classical laws of thermodynamics has prompted the formulation of extended thermodynamics. After describing the motifs and early evolution of this new branch of irreversible thermodynamics, the authors apply the theory to mon-atomic gases, mixtures of gases, relativistic gases, and "gases" of phonons and photons. The discussion brings into perspective the various phenomena called second sound, such as heat propagation, propagation of shear stress and concentration, and the second sound in liquid helium. The formal mathematical structure of extended thermodynamics is exposed and the theory is shown to be fully compatible with the kinetic theory of gases. The study closes with the testing of extended thermodynamics thro...

  8. Pressure perturbation calorimetry of unfolded proteins.

    Science.gov (United States)

    Tsamaloukas, Alekos D; Pyzocha, Neena K; Makhatadze, George I

    2010-12-16

    We report the application of pressure perturbation calorimetry (PPC) to study unfolded proteins. Using PPC we have measured the temperature dependence of the thermal expansion coefficient, α(T), in the unfolded state of apocytochrome C and reduced BPTI. We have shown that α(T) is a nonlinear function and decreases with increasing temperature. The decrease is most significant in the low (2-55 °C) temperature range. We have also tested an empirical additivity approach to predict α(T) of unfolded state from the amino acid sequence using α(T) values for individual amino acids. A comparison of the experimental and calculated functions shows a very good agreement, both in absolute values of α(T) and in its temperature dependence. Such an agreement suggests the applicability of using empirical calculations to predict α(T) of any unfolded protein.

  9. Thermal dissociation and unfolding of insulin

    DEFF Research Database (Denmark)

    Huus, Kasper; Havelund, Svend; Olsen, Helle B

    2005-01-01

    The thermal stability of human insulin was studied by differential scanning microcalorimetry and near-UV circular dichroism as a function of zinc/protein ratio, to elucidate the dissociation and unfolding processes of insulin in different association states. Zinc-free insulin, which is primarily...... dimeric at room temperature, unfolded at approximately 70 degrees C. The two monomeric insulin mutants Asp(B28) and Asp(B9),Glu(B27) unfolded at higher temperatures, but with enthalpies of unfolding that were approximately 30% smaller. Small amounts of zinc caused a biphasic thermal denaturation pattern...... of insulin. The biphasic denaturation is caused by a redistribution of zinc ions during the heating process and results in two distinct transitions with T(m)'s of approximately 70 and approximately 87 degrees C corresponding to monomer/dimer and hexamer, respectively. At high zinc concentrations (>or=5 Zn(2...

  10. Data Unfolding Methods in High Energy Physics

    CERN Document Server

    Schmitt, Stefan

    2016-01-01

    A selection of unfolding methods commonly used in High Energy Physics is compared. The methods discussed here are: bin-by-bin correction factors, matrix inversion, template fit, Tikhonov regularisation and two examples of iterative methods. Two procedures to choose the strength of the regularisation are tested, namely the L-curve scan and a scan of global correlation coefficients. The advantages and disadvantages of the unfolding methods and choices of the regularisation strength are discussed using a toy example.

  11. Reversible projection technique for colon unfolding.

    Science.gov (United States)

    Yao, Jianhua; Chowdhury, Ananda S; Aman, Javed; Summers, Ronald M

    2010-12-01

    Colon unfolding provides an efficient way to navigate the colon in computed tomographic colonography (CTC). Most existing unfolding techniques only compute forward projections. When radiologists find abnormalities or conduct measurements on the unfolded view (which is often quicker and easier), it is difficult to locate the corresponding region on the 3-D view for further examination (which is more accurate and reliable). To address this, we propose a reversible projection technique for colon unfolding. The method makes use of advanced algorithms including rotation-minimizing frames, recursive ring sets, mesh skinning, and cylindrical projection. Both forward and reverse mapping can be computed for points on the colon surface. Therefore, it allows for detecting and measuring polyps on the unfolded view and mapping them back to the 3-D surface. We generated realistic colon simulation data incorporating most colon characteristics, such as curved centerline, variable distention, haustral folds, teniae coli, and colonic polyps. Our method was tested on both simulated data and data from 110 clinical CTC studies. The results showed submillimeter accuracy in simulated data and -0.23 ± 1.67 mm in the polyp measurement using clinical CTC data. The major contributions of our technique are: 1) the use of a recursive ring set method to solve the centerline and surface correspondence problem; 2) reverse transformation from the unfolded view to the 3-D view; and 3) quantitative validation using a realistic colon simulation and clinical CTC polyp measurement.

  12. General thermodynamics

    CERN Document Server

    Olander, Donald

    2007-01-01

    The book’s methodology is unified, concise, and multidisciplinary, allowing students to understand how the principles of thermodynamics apply to all technical fields that touch upon this most fundamental of scientific theories. It also offers a rigorous approach to the quantitative aspects of thermodynamics, accompanied by clear explanations to help students transition smoothly from the physical concepts to their mathematical representations

  13. Fibronectin unfolding revisited: modeling cell traction-mediated unfolding of the tenth type-III repeat.

    Directory of Open Access Journals (Sweden)

    Elaine P S Gee

    Full Text Available Fibronectin polymerization is essential for the development and repair of the extracellular matrix. Consequently, deciphering the mechanism of fibronectin fibril formation is of immense interest. Fibronectin fibrillogenesis is driven by cell-traction forces that mechanically unfold particular modules within fibronectin. Previously, mechanical unfolding of fibronectin has been modeled by applying tensile forces at the N- and C-termini of fibronectin domains; however, physiological loading is likely focused on the solvent-exposed RGD loop in the 10(th type-III repeat of fibronectin (10FNIII, which mediates binding to cell-surface integrin receptors. In this work we used steered molecular dynamics to study the mechanical unfolding of 10FNIII under tensile force applied at this RGD site. We demonstrate that mechanically unfolding 10FNIII by pulling at the RGD site requires less work than unfolding by pulling at the N- and C- termini. Moreover, pulling at the N- and C-termini leads to 10FNIII unfolding along several pathways while pulling on the RGD site leads to a single exclusive unfolding pathway that includes a partially unfolded intermediate with exposed hydrophobic N-terminal beta-strands - residues that may facilitate fibronectin self-association. Additional mechanical unfolding triggers an essential arginine residue, which is required for high affinity binding to integrins, to move to a position far from the integrin binding site. This cell traction-induced conformational change may promote cell detachment after important partially unfolded kinetic intermediates are formed. These data suggest a novel mechanism that explains how cell-mediated forces promote fibronectin fibrillogenesis and how cell surface integrins detach from newly forming fibrils. This process enables cells to bind and unfold additional fibronectin modules - a method that propagates matrix assembly.

  14. Thermal, chemical and pH induced denaturation of a multimeric β-galactosidase reveals multiple unfolding pathways.

    Directory of Open Access Journals (Sweden)

    Devesh Kishore

    Full Text Available BACKGROUND: In this case study, we analysed the properties of unfolded states and pathways leading to complete denaturation of a multimeric chick pea β-galactosidase (CpGAL, as obtained from treatment with guanidium hydrochloride, urea, elevated temperature and extreme pH. METHODOLOGY/PRINCIPAL FINDINGS: CpGAL, a heterodimeric protein with native molecular mass of 85 kDa, belongs to α+β class of protein. The conformational stability and thermodynamic parameters of CpGAL unfolding in different states were estimated and interpreted using circular dichroism and fluorescence spectroscopic measurements. The enzyme was found to be structurally and functionally stable in the entire pH range and upto 50 °C temperature. Further increase in temperature induces unfolding followed by aggregation. Chemical induced denaturation was found to be cooperative and transitions were irreversible, non-coincidental and sigmoidal. Free energy of protein unfolding (ΔG(0 and unfolding constant (K(obs were also calculated for chemically denatured CpGAL. SIGNIFICANCE: The protein seems to use different pathways for unfolding in different environments and is a classical example of how the environment dictates the path a protein might take to fold while its amino acid sequence only defines its final three-dimensional conformation. The knowledge accumulated could be of immense biotechnological significance as well.

  15. Mechanics of forced unfolding of proteins.

    Science.gov (United States)

    Su, Tianxiang; Purohit, Prashant K

    2009-07-01

    We describe and solve a two-state kinetic model for the forced unfolding of proteins. The protein oligomer is modeled as a heterogeneous, freely jointed chain with two possible values of Kuhn length and contour length representing its folded and unfolded configurations. We obtain analytical solutions for the force-extension response of the protein oligomer for different types of loading conditions. We fit the analytical solutions for constant-velocity pulling to the force-extension data for ubiquitin and fibrinogen and obtain model parameters, such as Kuhn lengths and kinetic coefficients, for both proteins. We then predict their response under a linearly increasing force and find that our solutions for ubiquitin are consistent with a different set of experiments. Our calculations suggest that the refolding rate of proteins at low forces is several orders larger than the unfolding rate, and neglecting it can lead to lower predictions for the unfolding force, especially at high stretching velocities. By accounting for the refolding of proteins we obtain a critical force below which equilibrium is biased in favor of the folded state. Our calculations also suggest new methods to determine the distance of the transition state from the energy wells representing the folded and unfolded states of a protein.

  16. Workshop on Teaching Thermodynamics

    CERN Document Server

    1985-01-01

    It seemed appropriate to arrange a meeting of teachers of thermodynamics in the United Kingdom, a meeting held in the pleasant surroundings of Emmanuel College, Cambridge, in Sept~mber, 1984. This volume records the ideas put forward by authors, the discussion generated and an account of the action that discussion has initiated. Emphasis was placed on the Teaching of Thermodynamics to degree-level students in their first and second years. The meeting, a workshop for practitioners in which all were expected to take part, was remarkably well supported. This was notable in the representation of essentially every UK university and polytechnic engaged in teaching engineering thermodynamics and has led to a stimulating spread of ideas. By intention, the emphasis for attendance was put on teachers of engineering concerned with thermodynamics, both mechanical and chemical engineering disciplines. Attendance from others was encouraged but limited as follows: non-engineering acad­ emics, 10%, industrialists, 10%. The ...

  17. Temperature induced structural transitions from native to unfolded aggregated states of tobacco etch virus protease

    Science.gov (United States)

    Zhu, Guo-Fei; Ren, Si-Yan; Xi, Lei; Du, Lin-Fang; Zhu, Xiao-Feng

    2015-02-01

    Tobacco etch virus protease (TEVp) is widely used to remove fusion tags from recombinant proteins because of its high and unique specificity. This work describes the conformational and the thermodynamic properties in the unfolding/refolding process of TEVp3M (three-point mutant: L56V/S135G/S219V) induced by temperature. With temperature increasing from 20 to 100 °C, the CD spectra showed a transition trend from α-helix to β-sheet, and the fluorescence emission, synchronous fluorescence, ANS and RLS spectroscopy consistently revealed that the temperature-induced unfolding process behaved in a three-state manner, for there was a relatively stable intermediate state observed around 50 °C. The reversibility of thermal unfolding of TEVp3M further showed that the transition from the native to the intermediate state was reversible (below 50 °C), however the transition from the intermediate to the unfolded state was irreversible (above 60 °C). Moreover, aggregates were observed above 60 °C as revealed by SDS-PAGE, Thioflavin-T fluorescence and Congo red absorbance.

  18. Statistical coil model of the unfolded state: resolving the reconciliation problem.

    Science.gov (United States)

    Jha, Abhishek K; Colubri, Andrés; Freed, Karl F; Sosnick, Tobin R

    2005-09-13

    An unfolded state ensemble is generated by using a self-avoiding statistical coil model that is based on backbone conformational frequencies in a coil library, a subset of the Protein Data Bank. The model reproduces two apparently contradicting behaviors observed in the chemically denatured state for a variety of proteins, random coil scaling of the radius of gyration and the presence of significant amounts of local backbone structure (NMR residual dipolar couplings). The most stretched members of our unfolded ensemble dominate the residual dipolar coupling signal, whereas the uniformity of the sign of the couplings follows from the preponderance of polyproline II and beta conformers in the coil library. Agreement with the NMR data substantially improves when the backbone conformational preferences include correlations arising from the chemical and conformational identity of neighboring residues. Although the unfolded ensembles match the experimental observables, they do not display evidence of native-like topology. By providing an accurate representation of the unfolded state, our statistical coil model can be used to improve thermodynamic and kinetic modeling of protein folding.

  19. Green thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Cengel, Y.A. [Nevada Univ., Reno, NV (United States). Dept. of Mechanical Engineering

    2006-07-01

    Green components of thermodynamics were identified and general aspects of green practices associated with thermodynamics were assessed. Energy uses associated with fossil fuels were reviewed. Green energy sources such as solar, wind, geothermal and hydropower were discussed, as well as biomass plantations. Ethanol production practices were reviewed. Conservation practices in the United States were outlined. Energy efficiency and exergy analyses were discussed. Energy intensity measurements and insulation products for houses were also reviewed. Five case studies were presented to illustrate aspects of green thermodynamics: (1) light in a classroom; (2) fuel saved by low-resistance tires; and (3) savings with high-efficiency motors; (4) renewable energy; and (5) replacing a valve with a turbine at a cryogenic manufacturing facility. It was concluded that the main principles of green thermodynamics are to ensure that all material and energy inputs minimize the depletion of energy resources; prevent waste; and improve or innovate technologies that achieve sustainability. 17 refs., 2 tabs., 9 figs.

  20. Atmospheric thermodynamics

    CERN Document Server

    Iribarne, J V

    1973-01-01

    The thermodynamics of the atmosphere is the subject of several chapters in most textbooks on dynamic meteorology, but there is no work in English to give the subject a specific and more extensive treatment. In writing the present textbook, we have tried to fill this rather remarkable gap in the literature related to atmospheric sciences. Our aim has been to provide students of meteorology with a book that can playa role similar to the textbooks on chemical thermodynamics for the chemists. This implies a previous knowledge of general thermodynamics, such as students acquire in general physics courses; therefore, although the basic principles are reviewed (in the first four chapters), they are only briefly discussed, and emphasis is laid on those topics that will be useful in later chapters, through their application to atmospheric problems. No attempt has been made to introduce the thermodynamics of irreversible processes; on the other hand, consideration of heterogeneous and open homogeneous systems permits a...

  1. Introductory statistical thermodynamics

    CERN Document Server

    Dalarsson, Nils; Golubovic, Leonardo

    2011-01-01

    Introductory Statistical Thermodynamics is a text for an introductory one-semester course in statistical thermodynamics for upper-level undergraduate and graduate students in physics and engineering. The book offers a high level of detail in derivations of all equations and results. This information is necessary for students to grasp difficult concepts in physics that are needed to move on to higher level courses. The text is elementary, self contained, and mathematically well-founded, containing a number of problems with detailed solutions to help students to grasp the more difficult

  2. Neutron spectrum unfolding: Pt. 2; Experimental

    Energy Technology Data Exchange (ETDEWEB)

    Matiullah (Centre for Nuclear Studies, Nilore, Islamabad (Pakistan)); Wiyaja, D.S. (PPTN - BATAN, Bandung (Indonesia)); Berzonis, M.A.; Bondars, H.; Lapenas, A.A. (Latvijskij Gosudarstvennyj Univ., Riga (USSR)); Kudo, K. (Electrotechnical Lab., Tsukuba, Ibaraki (Japan)); Majeed, A.; Durrani, S.A. (Birimingham Univ. (United Kingdom). School of Physics and Space Research)

    1991-01-01

    In Part I of this paper, we described the use of the computer code SAIPS in neutron spectrum unfolding. Here in Part II, we present our experimental work carried out to study the shape of the neutron spectrum in different experimental channels of a 5 MW light-water cooled and moderated research reactor. The spectral neutron flux was determined using various fission foils (placed in close contact with mica track detectors) and activation detectors. From the measured activities, the neutron spectrum was unfolded by SAIPS. (author).

  3. Regularization and error assignment to unfolded distributions

    CERN Document Server

    Zech, Gunter

    2011-01-01

    The commonly used approach to present unfolded data only in graphical formwith the diagonal error depending on the regularization strength is unsatisfac-tory. It does not permit the adjustment of parameters of theories, the exclusionof theories that are admitted by the observed data and does not allow the com-bination of data from different experiments. We propose fixing the regulariza-tion strength by a p-value criterion, indicating the experimental uncertaintiesindependent of the regularization and publishing the unfolded data in additionwithout regularization. These considerations are illustrated with three differentunfolding and smoothing approaches applied to a toy example.

  4. Chemical and thermal unfolding of calreticulin

    DEFF Research Database (Denmark)

    Duus, K.; Larsen, N.; Tran, T. A. T.;

    2013-01-01

    was found to obtain a molten structure in urea concentrations between 1-1.5 M urea, and to unfold/aggregate at high and low pH values. The results demonstrated that the fluorescent dye binding assay could measure the thermal stability of calreticulin in aqueous buffers with results comparable to melting...... assay, we have investigated the chemical and thermal stability of calreticulin. When the chemical stability of calreticulin was assessed, a midpoint for calreticulin unfolding was calculated to 3.0M urea using CD data at 222 nm. Using the fluorescent dye binding thermal shift assay, calreticulin...

  5. Zinc induces unfolding and aggregation of dimeric arginine kinase by trapping reversible unfolding intermediate.

    Science.gov (United States)

    Liu, Taotao; Wang, Xicheng

    2010-11-01

    Arginine kinase plays an important role in the cellular energy metabolism of invertebrates. Dimeric arginine kinase (dAK) is unique in some marine invertebrates. The effects of Zn²(+) on the unfolding and aggregation of dAK from the sea cucumber Stichopus japonicus were investigated. Our results indicated that Zn²(+) caused dAK inactivation accompanied by conformational unfolding, the exposure of hydrophobic surface, and aggregation. Kinetic studies showed the inactivation and unfolding of dAK followed biphasic kinetic courses. Zn²(+) can affect unfolding and refolding of dAK by trapping the reversible intermediate. Our study provides important information regarding the effect of Zn²(+) on metabolic enzymes in marine invertebrates.

  6. Modern thermodynamics

    CERN Document Server

    Ben-Naim, Arieh

    2017-01-01

    This textbook introduces thermodynamics with a modern approach, starting from four fundamental physical facts (the atomic nature of matter, the indistinguishability of atoms and molecules of the same species, the uncertainty principle, and the existence of equilibrium states) and analyzing the behavior of complex systems with the tools of information theory, in particular with Shannon's measure of information (or SMI), which can be defined on any probability distribution. SMI is defined and its properties and time evolution are illustrated, and it is shown that the entropy is a particular type of SMI, i.e. the SMI related to the phase-space distribution for a macroscopic system at equilibrium. The connection to SMI allows the reader to understand what entropy is and why isolated systems follow the Second Law of Thermodynamics. The Second Llaw is also formulated for other systems, not thermally isolated and even open with respect to the transfer of particles. All the fundamental aspects of thermodynamics are d...

  7. Discrete Thermodynamics of Lasers

    CERN Document Server

    Zilbergleyt, B

    2007-01-01

    The paper offers a discrete thermodynamic model of lasers. Laser is an open system; its equilibrium is based on a balance of two thermodynamic forces, one related to the incoming pumping power and another to the emitted light. The basic expression for such equilibrium is a logistic map, graphical solutions to which are pitchfork bifurcation diagrams. As pumping force increases, the relative populations on the ground and lasing branches tend to zero and unity correspondingly. An interesting feature of this model is the line spectrum of the up and down transitions between the branches beyond bifurcation point. Even in a simple case of 2-level laser with only 2 possible transition types (up and down), the spectra look like sets of the line packets, starting well before the population inversion. This effect is an independent confirmation of the Einstein's prohibition on practical realization of 2-level laser. Multilevel lasers may be approached by employing the idea of thermodynamic activity for the emitting atom...

  8. Populated intermediates in the thermal unfolding of the human telomeric quadruplex.

    Science.gov (United States)

    Gray, Robert D; Buscaglia, Robert; Chaires, Jonathan B

    2012-10-10

    Thermal denaturation profiles of several model oligonucleotides of the human telomere DNA sequence including d[A(GGGTTA)(3)GGG] (Tel22) were determined using circular dichroism (CD), fluorescence of adenine → 2-aminopurine analogs, and fluorescence resonance energy transfer (FRET) to monitor the unfolding process at specific locations within the quadruplex. The resulting optical spectra vs temperature data matrices were analyzed by singular value decomposition (SVD) to ascertain the minimum number of species required to reproduce the unfolding spectral profiles. Global nonlinear least-squares fitting of the SVD amplitude vectors was used to estimate thermodynamic parameters and optical spectra of all species for a series of unfolding mechanisms that included one-, two-, and three-step sequential pathways F ⇌ I(n) ⇌ U, n = 0, 1, or 2) as well as two mechanisms with spectroscopically distinct starting structures (F(1) and F(2)). The CD and FRET data for Tel22 unfolding between 4 and 94 °C in 25 mM KCl were best described by a sequential unfolding model with two intermediates, while the 2-aminopurine analogs required one intermediate. The higher melting intermediate I(2) had a transition midpoint temperature (T(m)) of 61 °C and a CD spectrum with a maximum and minimum at ~265 and ~245 nm, respectively. The fluorescence emission spectra of the 2-aminopurine and FRET derivatives suggest greater solvent exposure of the 5'-AGGGTTA- segment in the intermediate compared to the folded state. The spectroscopic properties of the 61 °C intermediate suggest that it may be a triple helical structure.

  9. Precursory signatures of protein folding/unfolding: From time series correlation analysis to atomistic mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Hsu, P. J.; Lai, S. K., E-mail: sklai@coll.phy.ncu.edu.tw [Complex Liquids Laboratory, Department of Physics, National Central University, Chungli 320 Taiwan (China); Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan (China); Cheong, S. A. [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore)

    2014-05-28

    Folded conformations of proteins in thermodynamically stable states have long lifetimes. Before it folds into a stable conformation, or after unfolding from a stable conformation, the protein will generally stray from one random conformation to another leading thus to rapid fluctuations. Brief structural changes therefore occur before folding and unfolding events. These short-lived movements are easily overlooked in studies of folding/unfolding for they represent momentary excursions of the protein to explore conformations in the neighborhood of the stable conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid fluctuations through a combination of three techniques: (1) ultrafast shape recognition, (2) time series segmentation, and (3) time series correlation analysis. The first procedure measures the differences between statistical distance distributions of atoms in different conformations by calculating shape similarity indices from molecular dynamics simulation trajectories. The second procedure is used to discover the times at which the protein makes transitions from one conformation to another. Finally, we employ the third technique to exploit spatial fingerprints of the stable conformations; this procedure is to map out the sequences of changes preceding the actual folding and unfolding events, since strongly correlated atoms in different conformations are different due to bond and steric constraints. The aforementioned high-frequency fluctuations are therefore characterized by distinct correlational and structural changes that are associated with rate-limiting precursors that translate into brief segments. Guided by these technical procedures, we choose a model system, a fragment of the protein transthyretin, for identifying in this system not only the precursory signatures of transitions associated with α helix and β hairpin, but also the important role played by weaker correlations in such protein

  10. Unfolding the phenomenon of inter-rater agreement

    DEFF Research Database (Denmark)

    Slaug, Bjørn; Schilling, Oliver; Helle, Tina

    2011-01-01

    Objective: The overall objective was to unfold the phenomenon of inter-rater agreement: to identify potential sources of variation in agreement data and to explore how they can be statistically accounted for. The ultimate aim was to propose recommendations for in-depth examination of agreement...... of in-depth examination of agreement variation, as a strategy for increasing the level of inter-rater agreement. By identifying and limiting the most important sources of disagreement, ultimately instrument reliability can be improved. Keywords: inter-rater, reliability, sources of disagreement, kappa...

  11. Time-resolved Fourier transform infrared spectroscopy, gravimetry, and thermodynamic modeling for a molecular level description of water sorption in poly(ε-caprolactone).

    Science.gov (United States)

    Musto, Pellegrino; Galizia, Michele; Pannico, Marianna; Scherillo, Giuseppe; Mensitieri, Giuseppe

    2014-07-03

    Sorption of water in poly(ε-caprolactone) (PCL), with specific focus on the hydrogen-bonding interactions, has been analyzed by combining ab initio calculations, macroscopic thermodynamics modeling, and relevant features emerging from spectroscopic and gravimetric measurements. Fourier transform infrared (FTIR) data, analyzed by difference spectroscopy, two-dimensional correlation spectroscopy, and least-squares curve-fitting analysis associated with gravimetric determination of water sorption isotherm provided information on the system's behavior and on the molecular interactions established between the polymer and the penetrant. A consistent physical picture emerged pointing to the presence of two spectroscopically discernible water species (first-shell and second-shell layers) that have been quantified. Water molecules are present in the form of dimers within the polymer equilibrated with water vapor up to a relative humidity of 0.65. At higher humidities, clustering of water sorbed molecules starts to take place. The multicomponent ν(OH) band representative of absorbed water has been interpreted with the aid of ab initio calculations performed on suitably chosen model systems. The outcomes of spectroscopic analyses were interpreted at a macroscopic level by modeling the thermodynamics of water sorption in PCL based on a nonrandom compressible lattice theory accounting for hydrogen-bonding (HB) interactions. Starting from the fitting of the gravimetric sorption isotherm, the model provided quantitative estimates for the amount of self- and cross-HBs which compare favorably with the FTIR results.

  12. The Evolutionary Unfolding of Complexity

    CERN Document Server

    Crutchfield, J P; Crutchfield, James P.; Nimwegen, Erik van

    1999-01-01

    We analyze the population dynamics of a broad class of fitness functions that exhibit epochal evolution---a dynamical behavior, commonly observed in both natural and artificial evolutionary processes, in which long periods of stasis in an evolving population are punctuated by sudden bursts of change. Our approach---statistical dynamics---combines methods from both statistical mechanics and dynamical systems theory in a way that offers an alternative to current ``landscape'' models of evolutionary optimization. We describe the population dynamics on the macroscopic level of fitness classes or phenotype subbasins, while averaging out the genotypic variation that is consistent with a macroscopic state. Metastability in epochal evolution occurs solely at the macroscopic level of the fitness distribution. While a balance between selection and mutation maintains a quasistationary distribution of fitness, individuals diffuse randomly through selectively neutral subbasins in genotype space. Sudden innovations occur w...

  13. Thermodynamics and statistical mechanics

    CERN Document Server

    Landsberg, Peter T

    1990-01-01

    Exceptionally articulate treatment combines precise mathematical style with strong physical intuition. Wide range of applications includes negative temperatures, negative heat capacities, special and general relativistic effects, black hole thermodynamics, gravitational collapse, more. Over 100 problems with worked solutions. Advanced undergraduate, graduate level. Table of applications. Useful formulas and other data.

  14. Quantum thermodynamic cooling cycle

    CERN Document Server

    Palao, J P; Gordon, J M; Palao, Jose P.; Kosloff, Ronnie; Gordon, Jeffrey M.

    2001-01-01

    The quantum-mechanical and thermodynamic properties of a 3-level molecular cooling cycle are derived. An inadequacy of earlier models is rectified in accounting for the spontaneous emission and absorption associated with the coupling to the coherent driving field via an environmental reservoir. This additional coupling need not be dissipative, and can provide a thermal driving force - the quantum analog of classical absorption chillers. The dependence of the maximum attainable cooling rate on temperature, at ultra-low temperatures, is determined and shown to respect the recently-established fundamental bound based on the second and third laws of thermodynamics.

  15. Chemical and thermal unfolding of calreticulin.

    Science.gov (United States)

    Duus, K; Larsen, N; Tran, T A T; Güven, E; Skov, L K; Jespersgaard, C; Gajhede, M; Houen, G

    2013-05-01

    Calreticulin is a soluble endoplasmic reticulum chaperone, which has a relatively low melting point due to its remarkable structure with a relatively high content of flexible structural elements. Using far ultraviolet circular dichroism (CD) spectroscopy and a fluorescent dye binding thermal shift assay, we have investigated the chemical and thermal stability of calreticulin. When the chemical stability of calreticulin was assessed, a midpoint for calreticulin unfolding was calculated to 3.0M urea using CD data at 222 nm. Using the fluorescent dye binding thermal shift assay, calreticulin was found to obtain a molten structure in urea concentrations between 1-1.5 M urea, and to unfold/aggregate at high and low pH values. The results demonstrated that the fluorescent dye binding assay could measure the thermal stability of calreticulin in aqueous buffers with results comparable to melting points obtained by other techniques.

  16. Spectral unfolding of fast neutron energy distributions

    Science.gov (United States)

    Mosby, Michelle; Jackman, Kevin; Engle, Jonathan

    2015-10-01

    The characterization of the energy distribution of a neutron flux is difficult in experiments with constrained geometry where techniques such as time of flight cannot be used to resolve the distribution. The measurement of neutron fluxes in reactors, which often present similar challenges, has been accomplished using radioactivation foils as an indirect probe. Spectral unfolding codes use statistical methods to adjust MCNP predictions of neutron energy distributions using quantified radioactive residuals produced in these foils. We have applied a modification of this established neutron flux characterization technique to experimentally characterize the neutron flux in the critical assemblies at the Nevada National Security Site (NNSS) and the spallation neutron flux at the Isotope Production Facility (IPF) at Los Alamos National Laboratory (LANL). Results of the unfolding procedure are presented and compared with a priori MCNP predictions, and the implications for measurements using the neutron fluxes at these facilities are discussed.

  17. Transition-Systems, Event Structures, and Unfoldings

    DEFF Research Database (Denmark)

    Nielsen, Mogens; Rozenberg, Grzegorz; Thiagarajan, P.S.

    1995-01-01

    A subclass of transition systems called elementary transition systems can be identified with the help of axioms based on a structural notion called regions. Elementary transition systems have been shown to be the transition system model of a basic system model of net theory called elementary net ...... event structures. We then propose an operation of unfolding elementary transition systems into occurrence transition systems, We prove that it is "correct" in a strong categorical sense....

  18. A Constrained Unfolding Methodology for Product Positioning

    OpenAIRE

    Wayne DeSarbo; Rao, Vithala R

    1986-01-01

    This paper presents a recently developed unfolding methodology for analyzing preferential/dominance data that addresses the product positioning/repositioning decision problem of product (re)design and targeting by relating brand and consumer characteristics explicitly to perceptual brand locations and ideal points respectively. The methodology and associated algorithm are applied to a set of preference data for twelve models of residential communication devices. Various managerial implication...

  19. Natively unfolded proteins: a point where biology waits for physics.

    Science.gov (United States)

    Uversky, Vladimir N

    2002-04-01

    The experimental material accumulated in the literature on the conformational behavior of intrinsically unstructured (natively unfolded) proteins was analyzed. Results of this analysis showed that these proteins do not possess uniform structural properties, as expected for members of a single thermodynamic entity. Rather, these proteins may be divided into two structurally different groups: intrinsic coils, and premolten globules. Proteins from the first group have hydrodynamic dimensions typical of random coils in poor solvent and do not possess any (or almost any) ordered secondary structure. Proteins from the second group are essentially more compact, exhibiting some amount of residual secondary structure, although they are still less dense than native or molten globule proteins. An important feature of the intrinsically unstructured proteins is that they undergo disorder-order transition during or prior to their biological function. In this respect, the Protein Quartet model, with function arising from four specific conformations (ordered forms, molten globules, premolten globules, and random coils) and transitions between any two of the states, is discussed.

  20. Thermal unfolding and aggregation of actin.

    Science.gov (United States)

    Levitsky, Dmitrii I; Pivovarova, Anastasiya V; Mikhailova, Valeria V; Nikolaeva, Olga P

    2008-09-01

    Actin is one of the most abundant proteins in nature. It is found in all eukaryotes and plays a fundamental role in many diverse and dynamic cellular processes. Also, actin is one of the most ubiquitous proteins because actin-like proteins have recently been identified in bacteria. Actin filament (F-actin) is a highly dynamic structure that can exist in different conformational states, and transitions between these states may be important in cytoskeletal dynamics and cell motility. These transitions can be modulated by various factors causing the stabilization or destabilization of actin filaments. In this review, we look at actin stabilization and destabilization as expressed by changes in the thermal stability of actin; specifically, we summarize and analyze the existing data on the thermal unfolding of actin as measured by differential scanning calorimetry. We also analyze in vitro data on the heat-induced aggregation of actin, the process that normally accompanies actin thermal denaturation. In this respect, we focus on the effects of small heat shock proteins, which can prevent the aggregation of thermally denatured actin with no effect on actin thermal unfolding. As a result, we have proposed a mechanism describing the thermal denaturation and aggregation of F-actin. This mechanism explains some of the special features of the thermal unfolding of actin filaments, including the effects of their stabilization and destabilization; it can also explain how small heat shock proteins protect the actin cytoskeleton from damage caused by the accumulation of large insoluble aggregates under heat shock conditions.

  1. The unfolded protein response and translation attenuation: a modelling approach.

    Science.gov (United States)

    Trusina, A; Tang, C

    2010-10-01

    Unfolded protein response (UPR) is a stress response to increased levels of unfolded proteins in the endoplasmic reticulum (ER). To deal with this stress, all eukaryotic cells share a well-conserved strategy--the upregulation of chaperons and proteases to facilitate protein folding and to degrade the misfolded proteins. For metazoans, however, an additional and seemingly redundant strategy has been evolved--translation attenuation (TA) of proteins targeted to the ER via the protein kinase PERK pathway. PERK is essential in secretory cells, such as the pancreatic β-cells, but not in non-secretory cell types. We have recently developed a mathematical model of UPR, focusing on the interplay and synergy between the TA arm and the conserved Ire1 arm of the UPR. The model showed that the TA mechanism is beneficial in highly fluctuating environment, for example, in the case where the ER stress changes frequently. Under highly variable levels of ER stress, tight regulation of the ER load by TA avoids excess amount of chaperons and proteases being produced. The model also showed that TA is of greater importance when there is a large flux of proteins through the ER. In this study, we further expand our model to investigate different types of ER stress and different temporal profiles of the stress. We found that TA is more desirable in dealing with the translation stress, for example, prolonged stimulation of proinsulin biosynthesis, than the chemical stress.

  2. (Chemical thermodynamics)

    Energy Technology Data Exchange (ETDEWEB)

    Mesmer, R.E.

    1990-09-12

    The purpose of this travel was for the traveler to participate in the 11th IUPAC International Conference on Chemical Thermodynamics and to present a paper of which he is co-author entitled The Transition from Strong-to-Weak Electrolyte Behavior Near the Critical Point of Water'' in the session on Solutions. The conference brought together nearly 500 scientists from around the world to discuss broad aspects of experimental thermodynamics and theoretical modeling. The traveler also visited the University of Karlsruhe to discuss current research with E.U. Franck and his collaborators. This institution has been for many years one of the leading centers for experimental studies on phase equilibrium and physical chemical studies especially on pure substances under the direction of Franck.

  3. Solvation thermodynamics

    CERN Document Server

    Ben-Naim, Arieh

    1987-01-01

    This book deals with a subject that has been studied since the beginning of physical chemistry. Despite the thousands of articles and scores of books devoted to solvation thermodynamics, I feel that some fundamen­ tal and well-established concepts underlying the traditional approach to this subject are not satisfactory and need revision. The main reason for this need is that solvation thermodynamics has traditionally been treated in the context of classical (macroscopic) ther­ modynamics alone. However, solvation is inherently a molecular pro­ cess, dependent upon local rather than macroscopic properties of the system. Therefore, the starting point should be based on statistical mechanical methods. For many years it has been believed that certain thermodynamic quantities, such as the standard free energy (or enthalpy or entropy) of solution, may be used as measures of the corresponding functions of solvation of a given solute in a given solvent. I first challenged this notion in a paper published in 1978 b...

  4. Crystal structures of highly simplified BPTIs provide insights into hydration-driven increase of unfolding enthalpy.

    Science.gov (United States)

    Islam, Mohammad Monirul; Yohda, Masafumi; Kidokoro, Shun-Ichi; Kuroda, Yutaka

    2017-03-07

    We report a thermodynamic and structural analysis of six extensively simplified bovine pancreatic trypsin inhibitor (BPTI) variants containing 19-24 alanines out of 58 residues. Differential scanning calorimetry indicated a two-state thermal unfolding, typical of a native protein with densely packed interior. Surprisingly, increasing the number of alanines induced enthalpy stabilization, which was however over-compensated by entropy destabilization. X-ray crystallography indicated that the alanine substitutions caused the recruitment of novel water molecules facilitating the formation of protein-water hydrogen bonds and improving the hydration shells around the alanine's methyl groups, both of which presumably contributed to enthalpy stabilization. There was a strong correlation between the number of water molecules and the thermodynamic parameters. Overall, our results demonstrate that, in contrast to our initial expectation, a protein sequence in which over 40% of the residues are alanines can retain a densely packed structure and undergo thermal denaturation with a large enthalpy change, mainly contributed by hydration.

  5. Unfolding DNA condensates produced by DNA-like charged depletants: A force spectroscopy study

    Science.gov (United States)

    Lima, C. H. M.; Rocha, M. S.; Ramos, E. B.

    2017-02-01

    In this work, we have measured, by means of optical tweezers, forces acting on depletion-induced DNA condensates due to the presence of the DNA-like charged protein bovine serum albumin (BSA). The stretching and unfolding measurements performed on the semi-flexible DNA chain reveal (1) the softening of the uncondensed DNA contour length and (2) a mechanical behavior strikingly different from those previously observed: the force-extension curves of BSA-induced DNA condensates lack the "saw-tooth" pattern and applied external forces as high as ≈80 pN are unable to fully unfold the condensed DNA contour length. This last mechanical experimental finding is in agreement with force-induced "unpacking" detailed Langevin dynamics simulations recently performed by Cortini et al. on model rod-like shaped condensates. Furthermore, a simple thermodynamics analysis of the unfolding process has enabled us to estimate the free energy involved in the DNA condensation: the estimated depletion-induced interactions vary linearly with both the condensed DNA contour length and the BSA concentration, in agreement with the analytical and numerical analysis performed on model DNA condensates. We hope that future additional experiments can decide whether the rod-like morphology is the actual one we are dealing with (e.g. pulling experiments coupled with super-resolution fluorescence microscopy).

  6. Unfolding-based corrector estimates for a reaction-diffusion system predicting concrete corrosion

    CERN Document Server

    Fatima, Tasnim; Ptashnyk, Mariya

    2011-01-01

    We use the periodic unfolding technique to derive corrector estimates for a reaction-diffusion system describing concrete corrosion penetration in the sewer pipes. The system, defined in a periodically-perforated domain, is semi-linear, partially dissipative, and coupled via a non-linear ordinary differential equation posed on the solid-water interface at the pore level. After discussing the solvability of the pore scale model, we apply the periodic unfolding techniques (adapted to treat the presence of perforations) not only to get upscaled model equations, but also to prepare a proper framework for getting a convergence rate (corrector estimates) of the averaging procedure.

  7. Steepest-entropy-ascent quantum thermodynamic framework for describing the non-equilibrium behavior of a chemically reactive system at an atomistic level

    CERN Document Server

    Beretta, Gian Paolo

    2015-01-01

    Steepest-Entropy-Ascent Quantum Thermodynamics (SEAQT) provides a general framework for the description of non-equilibrium phenomena at any level, particularly the atomistic one. This theory and its dynamical postulate are used here to develop a general mathematical framework, which at an atomistic level, in particular, can be used to predict the non-equilibrium evolution in state of a closed, chemically reactive mixture such as the one examined here, i.e., a mixture of hydrogen (H2) and flourine (F) contained in an isolated tank of fixed volume. The general framework provided, however, is written for a reactive system subject to multiple reaction mechanisms. To predict this evolution in state, both the energy and particle number eigenvalue problems for a dilute gas are set up and solved analytically. Wall and non-ideal-gas behavior effects are neglected, although the extension to dense gases is straightforward but left for a future paper. The system-level energy and particle number eigenvalues and eigenstate...

  8. Using an amino acid fluorescence resonance energy transfer pair to probe protein unfolding: application to the villin headpiece subdomain and the LysM domain.

    Science.gov (United States)

    Glasscock, Julie M; Zhu, Yongjin; Chowdhury, Pramit; Tang, Jia; Gai, Feng

    2008-10-21

    Previously, we have shown that p-cyanophenylalanine (Phe CN) and tryptophan (Trp) constitute an efficient fluorescence resonance energy transfer (FRET) pair that has several advantages over commonly used dye pairs. Here, we aim to examine the general applicability of this FRET pair in protein folding-unfolding studies by applying it to the urea-induced unfolding transitions of two small proteins, the villin headpiece subdomain (HP35) and the lysin motif (LysM) domain. Depending on whether Phe CN is exposed to solvent, we are able to extract either qualitative information about the folding pathway, as demonstrated by HP35, which has been suggested to unfold in a stepwise manner, or quantitative thermodynamic and structural information, as demonstrated by LysM, which has been shown to be an ideal two-state folder. Our results show that the unfolding transition of HP35 reported by FRET occurs at a denaturant concentration lower than that measured by circular dichroism (CD) and that the loop linking helix 2 and helix 3 remains compact in the denatured state, which are consistent with the notion that HP35 unfolds in discrete steps and that its unfolded state contains residual structures. On the other hand, our FRET results on the LysM domain allow us to develop a model for extracting structural and thermodynamic parameters about its unfolding, and we find that our results are in agreement with those obtained by other methods. Given the fact that Phe CN is a non-natural amino acid and, thus, amenable to incorporation into peptides and proteins via existing peptide synthesis and protein expression methods, we believe that the FRET method demonstrated here is widely applicable to protein conformational studies, especially to the study of relatively small proteins.

  9. Heat, Acid and Chemically Induced Unfolding Pathways, Conformational Stability and Structure-Function Relationship in Wheat α-Amylase.

    Directory of Open Access Journals (Sweden)

    Kritika Singh

    Full Text Available Wheat α-amylase, a multi-domain protein with immense industrial applications, belongs to α+β class of proteins with native molecular mass of 32 kDa. In the present study, the pathways leading to denaturation and the relevant unfolded states of this multi-domain, robust enzyme from wheat were discerned under the influence of temperature, pH and chemical denaturants. The structural and functional aspects along with thermodynamic parameters for α-amylase unfolding were probed and analyzed using fluorescence, circular dichroism and enzyme assay methods. The enzyme exhibited remarkable stability up to 70°C with tendency to aggregate at higher temperature. Acid induced unfolding was also incomplete with respect to the structural content of the enzyme. Strong ANS binding at pH 2.0 suggested the existence of a partially unfolded intermediate state. The enzyme was structurally and functionally stable in the pH range 4.0-9.0 with 88% recovery of hydrolytic activity. Careful examination of biophysical properties of intermediate states populated in urea and GdHCl induced denaturation suggests that α-amylase unfolding undergoes irreversible and non-coincidental cooperative transitions, as opposed to previous reports of two-state unfolding. Our investigation highlights several structural features of the enzyme in relation to its catalytic activity. Since, α-amylase has been comprehensively exploited for use in a range of starch-based industries, in addition to its physiological significance in plants and animals, knowledge regarding its stability and folding aspects will promote its biotechnological applications.

  10. Near-exact enthalpy-entropy compensation governs the thermal unfolding of protonation states of oxidized cytochrome c.

    Science.gov (United States)

    Soffer, Jonathan B; Schweitzer-Stenner, Reinhard

    2014-10-01

    This paper reports the first quantitative analysis of the thermal transitions of all protonation states of oxidized horse heart cytochrome c at low anion concentration. Changes of secondary and tertiary structure were probed by ultraviolet (UV) as well as visible circular dichroism and absorption spectroscopy, respectively. The temperature dependence of spectra were recorded at pH values assignable to a set of different protonation states which encompass the canonical Theorell-Åkesson states and the recently discovered III* state. Our experimental data suggest a two-step process of thermal unfolding for all protonation states. The respective thermodynamic parameters were obtained from a global analysis of the temperature dependence of corresponding visible circular dichroism (CD) and absorption spectra. The results of this analysis revealed a statistically significant enthalpy-entropy compensation with different apparent compensation temperatures for the two consecutive thermal transitions (319 and 357 K). This reflects the narrow distribution of the respective folding temperatures. UVCD spectra suggest that even the thermal transitions of protonation states occupied at acidic and alkaline pH cause only a very modest unfolding of the protein's helical structure. Our data indicate the protonation-induced unfolding at room temperatures predominantly affects the Ω-loops of the protein. The two thermal transitions involve changes of two foldons, i.e. the unfolding of two short β-strand segments (associated with the yellow foldon) followed by the unfolding of the 60' helix (green foldon) that connects the two Ω-loops of the protein. Apparently, intra-backbone hydrogen bonding is strong enough to mostly protect the terminal N- and C-helices from unfolding even at rather extreme conditions.

  11. Heat, Acid and Chemically Induced Unfolding Pathways, Conformational Stability and Structure-Function Relationship in Wheat α-Amylase.

    Science.gov (United States)

    Singh, Kritika; Shandilya, Manish; Kundu, Suman; Kayastha, Arvind M

    2015-01-01

    Wheat α-amylase, a multi-domain protein with immense industrial applications, belongs to α+β class of proteins with native molecular mass of 32 kDa. In the present study, the pathways leading to denaturation and the relevant unfolded states of this multi-domain, robust enzyme from wheat were discerned under the influence of temperature, pH and chemical denaturants. The structural and functional aspects along with thermodynamic parameters for α-amylase unfolding were probed and analyzed using fluorescence, circular dichroism and enzyme assay methods. The enzyme exhibited remarkable stability up to 70°C with tendency to aggregate at higher temperature. Acid induced unfolding was also incomplete with respect to the structural content of the enzyme. Strong ANS binding at pH 2.0 suggested the existence of a partially unfolded intermediate state. The enzyme was structurally and functionally stable in the pH range 4.0-9.0 with 88% recovery of hydrolytic activity. Careful examination of biophysical properties of intermediate states populated in urea and GdHCl induced denaturation suggests that α-amylase unfolding undergoes irreversible and non-coincidental cooperative transitions, as opposed to previous reports of two-state unfolding. Our investigation highlights several structural features of the enzyme in relation to its catalytic activity. Since, α-amylase has been comprehensively exploited for use in a range of starch-based industries, in addition to its physiological significance in plants and animals, knowledge regarding its stability and folding aspects will promote its biotechnological applications.

  12. Nanoscopic Thermodynamics.

    Science.gov (United States)

    Qi, Weihong

    2016-09-20

    Conventional thermodynamics for bulk substances encounters challenges when one considers materials on the nanometer scale. Quantities such as entropy, enthalpy, free energy, melting temperature, ordering temperature, Debye temperature, and specific heat no longer remain constant but change with the crystal dimension, size, and morphology. Often, one phenomenon is associated with a variety of theories from different perspectives. Still, a model that can reconcile the size and shape dependence of the thermal properties of the nanoscaled substances remains one of the goals of nanoscience and nanotechnology. This Account highlights the nanoscopic thermodynamics for nanoparticles, nanowires, and nanofilms, with particular emphasis on the bond energy model. The central idea is that the atomic cohesive energy determines the thermodynamic performance of a substance and the cohesive energy varies with the atomic coordination environment. It is the cohesive energy difference between the core and the shell that dictates the nanoscopic thermodynamics. This bond energy model rationalizes the following: (i) how the surface dangling bonds depress the melting temperature, entropy, and enthalpy; (ii) how the order-disorder transition of the nanoparticles depends on particle size and how their stability may vary when they are embedded in an appropriate matrix; (iii) predictions of the existence of face-centered cubic structures of Ti, Zr, and Hf at small size; (iv) how two elements that are immiscible in the bulk can form an alloy on the nanoscale, where the critical size can be predicted. The model has enabled us to reproduce the size and shape dependence of a number of physical properties, such as melting temperature, melting entropy, melting enthalpy, ordering temperature, Gibbs free energy, and formation heat, among others, for materials such as Pd, Au, Ag, Cu, Ni, Sn, Pb, In, Bi, Al, Ti, Zr, Hf, In-Al, Ag-Ni, Co-Pt, Cu-Ag, Cu-Ni, Au-Ni, Ag-Pt, and Au-Pt on the nanometer scale

  13. Quantitative evaluation of myoglobin unfolding in the presence of guanidinium hydrochloride and ionic liquids in solution.

    Science.gov (United States)

    Fiebig, Olivia C; Mancini, Emily; Caputo, Gregory; Vaden, Timothy D

    2014-01-16

    The use of ionic liquids in biochemical and biophysical applications has increased dramatically in recent years due to their interesting properties. We report results of a thermodynamic characterization of the chaotrope-induced denaturation of equine myoglobin in two different ionic liquid aqueous environments using a combined absorption/fluorescence spectroscopic approach. Denaturation by guanidinium hydrochloride was monitored by loss of heme absorptivity and limited unfolding structural information was obtained from Förster resonance energy transfer experiments. Results show that myoglobin unfolding is generally unchanged in the presence of ethylmethylimidazolium acetate (EMIAc) in aqueous solution up to 150 mM concentration but is facilitated by butylmethylimidazolium boron tetrafluoride (BMIBF4) in solution. The presence of 150 mM BMIBF4 alone does not induce unfolding but destabilizes the structure as observed by a decrease in threshold denaturant concentration for unfolding and an 80% decrease in the magnitude of ΔGunfolding from 44 kJ/mol in the absence of BMIBF4 to 8 kJ/mol in the presence of 150 mM BMIBF4. Thus, the BMIBF4 significantly destabilizes the myoglobin structure while the EMIAc does not, likely due to differences in anion interaction capabilities. This is confirmed with control studies using NaAc and LiBF4 solutions. EMIAc may be chosen as cosolvent additive with minimal effects on protein structure while BMIBF4 may be used as a supplement in protein folding experiments, potentially allowing access to proteins which have been traditionally difficult to denature as well as designing ionic liquids to match protein characteristics.

  14. Universal convergence of the specific volume changes of globular proteins upon unfolding.

    Science.gov (United States)

    Schweiker, Katrina L; Fitz, Victoria W; Makhatadze, George I

    2009-11-24

    Both pressure and temperature are important environmental variables, and to obtain a complete understanding of the mechanisms of protein folding, it is necessary to determine how protein stability is dependent on these fundamental thermodynamic parameters. Although the temperature dependence of protein stability has been widely explored, the dependence of protein stability on pressure is not as well studied. In this paper, we report the results of the direct thermodynamic determination of the change in specific volume (DeltaV/V) upon protein unfolding, which defines the pressure dependence of protein stability, for five model proteins (ubiquitin, eglin c, ribonuclease A, lysozyme, and cytochrome c). We have shown that the specific volumetric changes upon unfolding for four of the proteins (ubiquitin, eglin c, ribonuclease A, and lysozyme) appear to converge to a common value at high temperatures. Analysis of various contributions to the change in volume upon protein unfolding allowed us to put forth the hypothesis that the change in volume due to hydration is very close to zero at this temperature, such that DeltaV/V is defined largely by the total volume of cavities and voids within a protein, and that this is a universal property of all small globular proteins without prosthetic groups. To test this hypothesis, additional experiments were performed with variants of eglin c that had site-directed substitutions at two buried positions, to create an additional cavity in the protein core. The results of these experiments, coupled with the structural analysis of cytochrome c showing a lower packing density compared to those of the other four proteins, provided further support for the hypothesis. Finally, we have shown that the deviation of the high-temperature DeltaV value of a given protein from the convergence value can be used to determine the size of the excess cavities in globular proteins.

  15. Band electron spectrum and thermodynamic properties of the pseudospin-electron model with tunneling splitting of levels

    Directory of Open Access Journals (Sweden)

    O.Ya.Farenyuk

    2006-01-01

    Full Text Available The pseudospin-electron model with tunneling splitting of levels is considered. Generalization of dynamic mean-field method for systems with correlated hopping was applied to the investigation of the model. Electron spectra, electron concentrations, average values of pseudospins and grand canonical potential were calculated within the alloy-analogy approximation. Electron spectrum and dependencies of the electron concentrations on chemical potential were obtained. It was shown that in the alloy-analogy approximation, the model possesses the first order phase transition to ferromagnetic state with the change of chemical potential and the second order phase transition with the change of temperature.

  16. Neutron spectrum unfolding using radial basis function neural networks.

    Science.gov (United States)

    Alvar, Amin Asgharzadeh; Deevband, Mohammad Reza; Ashtiyani, Meghdad

    2017-07-26

    Neutron energy spectrum unfolding has been the subject of research for several years. The Bayesian theory, Monte Carlo simulation, and iterative methods are some of the methods that have been used for neutron spectrum unfolding. In this study, the radial basis function (RBF), multilayer perceptron, and artificial neural networks (ANNs) were used for the unfolding of neutron spectrum, and a comparison was made between the networks' results. Both neural network architectures were trained and tested using the same data set for neutron spectrum unfolding from the response of LiI detectors with Eu impurity. Advantages of each ANN method in the unfolding of neutron energy spectrum were investigated, and the performance of the networks was compared. The results obtained showed that RBF neural network can be applied as an effective method for unfolding neutron spectrum, especially when the main target is the neutron dosimetry. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. An introduction to the theory of unidimensional unfolding.

    Science.gov (United States)

    Kyngdon, Andrew

    2006-01-01

    Despite its 55 year presence in the field of mathematical psychology, the theory of unidimensional unfolding remains an enigma for many psychometricians and applied practitioners. This paper is the first of a three part series; and it aims to introduce unidimensional unfolding theory. The paper begins with a simple hypothetical example presenting an idealised distinction between responses to cumulative and unfolding dichotomous items. This followed by an accessible presentation of the theory of unidimensional unfolding as first articulated by Clyde H. Coombs (1950, 1964). The concept of the single peaked preference function (Coombs and Avrunin, 1977) which underpins unfolding theory is then presented. The article then progresses to the class of Rasch (1960) based IRT models developed by Andrich (1995) and Luo (2001). It was shown these models propose arguments not inconsistent with Coombs's (1964) original theory. The presumption of additive structure in psychological attributes was concluded to be the key weakness of the theories of unidimensional unfolding discussed.

  18. Protein unfolding pathways explored through molecular dynamics simulations.

    Science.gov (United States)

    Daggett, V; Levitt, M

    1993-07-20

    Herein we describe the results of molecular dynamics simulations of the bovine pancreatic trypsin inhibitor (BPTI) in solution at a variety of temperatures both with and without disulfide bonds. The reduced form of the protein unfolded at high temperature to an ensemble of conformations with all the properties of the molten globule state. In this account we outline the structural details of the actual unfolding process between the native and molten globule states. The first steps of unfolding involved expansion of the protein, which disrupted packing interactions. The solvent-accessible surface area also quickly increased. The unfolding was localized mostly to the turn and loop regions of the molecule, while leaving the secondary structure intact. Then, there was more gradual unfolding of the secondary structure and non-native turns became prevalent. This same trajectory was continued and more drastic unfolding occurred that resulted in a relatively compact state devoid of stable secondary structure.

  19. Parameterization of the Non-Local Thermodynamic Equilibrium Source Function with Chemical Production by an Equivalent Two-Level Model

    Institute of Scientific and Technical Information of China (English)

    Xun ZHU

    2003-01-01

    The classic two-level or equivalent two-level model that includes only the statistical equilibriumof radiative and thermal processes of excitation and quenching between two vibrational energy levelsis extended by adding chemical production to the rate equations. The modifications to the non-localthermodynamic equilibrium source function and cooling rate are parameterized by φc, which characterizesthe ratio of chemical production to collisional quenching. For applications of broadband emission of O3 at9.6 μm, the non-LTE effect of chemical production on the cooling rate and limb emission is proportionalto the ratio of O to O3. For a typical [O]/[O3], the maximum enhancements of limb radiance and coolingrate are about 15%-30% and 0.03-0.05 K day-1, respectively, both occurring near the mesopause regions.This suggests that the broadband limb radiance above ~80 km is sensitive to O3 density but not sensitiveto the direct cooling rate along the line-of-sight, which makes O3 retrieval feasible but the direct coolingrate retrieval difficult by using the O3 9.6 μm band limb emission.

  20. Unfolding Implementation in Industrial Market Segmentation

    DEFF Research Database (Denmark)

    Bøjgaard, John; Ellegaard, Chris

    2011-01-01

    of implementing industrial market segmentation is discussed and unfolded in this article. Extant literature has identified segmentation implementation as a core challenge for marketers, but also one, which has received limited empirical attention. Future research opportunities are formulated in this article......Market segmentation is an important method of strategic marketing and constitutes a cornerstone of the marketing literature. It has undergone extensive scientific inquiry during the past 50 years. Reporting on an extensive review of the market segmentation literature, the challenging task...... for marketing management. Three key elements and challenges connected to execution of market segmentation are identified — organization, motivation, and adaptation....

  1. Unfolding of differential energy spectra in the MAGIC experiment

    CERN Document Server

    Albert, J; Anderhub, H; Antoranz, P; Armada, A; Asensio, M; Baixeras, C; Barrio, J A; Bartko, H; Bastieri, D; Becker, J; Bednarek, W; Berger, K; Bigongiari, C; Biland, A; Böck, R K; Bordas, P; Bosch-Ramon, V; Bretz, T; Britvitch, I; Camara, M; Carmona, E; Chilingarian, A; Ciprini, S; Coarasa, J A; Commichau, S; Contreras, J L; Cortina, J; Costado, M T; Curtef, V; Danielyan, V; Dazzi, F; De Angelis, A; Delgado, C; De los Reyes, R; De Lotto, B; Domingo-Santamaria, E; Dorner, D; Doro, M; Errando, M; Fagiolini, M; Ferenc, D; Fernández, E; Firpo, R; Flix, J; Fonseca, M V; Font, L; Fuchs, M; Galante, N; Garcia-Lopez, R J; Garczarczyk, M; Gaug, M; Giller, M; Göbel, F; Hakobyan, D; Hayashida, M; Hengstebeck, T; Herrero, A; Höhne, D; Hose, J; Hsu, C C; Jacon, P; Jogler, T; Kosyra, R; Kranich, D; Kritzer, R; Laille, A; Lindfors, E; Lombardi, S; Longo, F; López, J; López, M; Lorenz, E; Majumdar, P; Maneva, G; Mannheim, K; Mansutti, O; Mariotti, M; Martínez, M; Mazin, D; Merck, C; Meucci, M; Meyer, M; Miranda, J M; Mirzoyan, R; Mizobuchi, S; Moralejo, A; Nieto, D; Nilsson, K; Ninkovic, J; Ona-Wilhelmi, E; Otte, N; Oya, I; Panniello, M; Paoletti, R; Paredes, J M; Pasanen, M; Pascoli, D; Pauss, F; Pegna, R; Persic, M; Peruzzo, L; Piccioli, A; Puchades, N; Prandini, E; Raymers, A; Rhode, W; Ribó, M; Rico, J; Rissi, M; Robert, A; Rugamer, S; Saggion, A; Saitô, T; Sánchez, A; Sartori, P; Scalzotto, V; Scapin, V; Schmitt, R; Schweizer, T; Shayduk, M; Shinozaki, K; Shore, S N; Sidro, N; Sillanpää, A; Sobczynska, D; Stamerra, A; Stark, L S; Takalo, L; Temnikov, P; Tescaro, D; Teshima, M; Torres, D F; Turini, N; Vankov, H; Vitale, V; Wagner, R M; Wibig, T; Wittek, W; Zandanel, F; Zanin, R; Zapatero, J

    2007-01-01

    The paper describes the different methods, used in the MAGIC experiment, to unfold experimental energy distributions of cosmic ray particles (gamma-rays). Questions and problems related to the unfolding are discussed. Various procedures are proposed which can help to make the unfolding robust and reliable. The different methods and procedures are implemented in the MAGIC software and are used in most of the analyses.

  2. Unfolding spinor wave functions and expectation values of general operators: Introducing the unfolding-density operator

    Science.gov (United States)

    Medeiros, Paulo V. C.; Tsirkin, Stepan S.; Stafström, Sven; Björk, Jonas

    2015-01-01

    We show that the spectral weights Wm K ⃗(k ⃗) used for the unfolding of two-component spinor eigenstates | ψmK ⃗ SC>=|α >| ψmK ⃗ SC,α >+|β >| ψmK ⃗ SC,β > can be decomposed as the sum of the partial spectral weights WmK ⃗ μ(k ⃗) calculated for each component μ =α ,β independently, effortlessly turning a possibly complicated problem involving two coupled quantities into two independent problems of easy solution. Furthermore, we define the unfolding-density operator ρ̂K ⃗(k ⃗;ɛ ) , which unfolds the primitive cell expectation values φpc(k ⃗;ɛ ) of any arbitrary operator φ ̂ according to φpc(k ⃗;ɛ ) =Tr( ρ̂K ⃗(k ⃗;ɛ ) φ ̂) . As a proof of concept, we apply the method to obtain the unfolded band structures, as well as the expectation values of the Pauli spin matrices, for prototypical physical systems described by two-component spinor eigenfunctions.

  3. Mechanically unfolding proteins: The effect of unfolding history and the supramolecular scaffold

    Science.gov (United States)

    Zinober, Rebecca C.; Brockwell, David J.; Beddard, Godfrey S.; Blake, Anthony W.; Olmsted, Peter D.; Radford, Sheena E.; Smith, D. Alastair

    2002-01-01

    The mechanical resistance of a folded domain in a polyprotein of five mutant I27 domains (C47S, C63S I27)5is shown to depend on the unfolding history of the protein. This observation can be understood on the basis of competition between two effects, that of the changing number of domains attempting to unfold, and the progressive increase in the compliance of the polyprotein as domains unfold. We present Monte Carlo simulations that show the effect and experimental data that verify these observations. The results are confirmed using an analytical model based on transition state theory. The model and simulations also predict that the mechanical resistance of a domain depends on the stiffness of the surrounding scaffold that holds the domain in vivo, and on the length of the unfolded domain. Together, these additional factors that influence the mechanical resistance of proteins have important consequences for our understanding of natural proteins that have evolved to withstand force. PMID:12441375

  4. Thermal unfolding of barstar and the properties of interfacial water around the unfolded forms

    Energy Technology Data Exchange (ETDEWEB)

    Pal, Somedatta; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302 (India)

    2013-12-21

    Identification of the intermediates along the folding-unfolding pathways and probing their interactions with surrounding solvent are two important but relatively unexplored issues in protein folding. In this work, we have carried out atomistic molecular dynamics simulations to study the thermal unfolding of barstar in aqueous solution from its folded native form at two different temperatures (400 K and 450 K). The calculations at 400 K reveal partial unfolding of two α-helices (helix-1 and helix-2) and their interconnecting loop. At 450 K, on the other hand, the entire protein attains an expanded flexible conformation due to disruption of a large fraction of tertiary contacts and breaking of almost all the secondary structures. These two disordered structures obtained at such high temperatures are then studied around room temperature to probe their influence on the properties of surrounding solvent. It is found that though the unfolding of the protein in general leads to increasingly hydrated interface, but new structural motifs with locally dehydrated interface may also form during the structural transition. Additionally, independent of the conformational state of the protein, its influence on surrounding solvent has been found to be restricted to the first hydration layer.

  5. ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble

    Directory of Open Access Journals (Sweden)

    Blackledge Martin

    2009-04-01

    Full Text Available Abstract Background The stability of proteins is governed by the heat capacity, enthalpy and entropy changes of folding, which are strongly correlated to the change in solvent accessible surface area experienced by the polypeptide. While the surface exposed in the folded state can be easily determined, accessibilities for the unfolded state at the atomic level cannot be obtained experimentally and are typically estimated using simplistic models of the unfolded ensemble. A web application providing realistic accessibilities of the unfolded ensemble of a given protein at the atomic level will prove useful. Results ProtSA, a web application that calculates sequence-specific solvent accessibilities of the unfolded state ensembles of proteins has been developed and made freely available to the scientific community. The input is the amino acid sequence of the protein of interest. ProtSA follows a previously published calculation protocol which uses the Flexible-Meccano algorithm to generate unfolded conformations representative of the unfolded ensemble of the protein, and uses the exact analytical software ALPHASURF to calculate atom solvent accessibilities, which are averaged on the ensemble. Conclusion ProtSA is a novel tool for the researcher investigating protein folding energetics. The sequence specific atom accessibilities provided by ProtSA will allow obtaining better estimates of the contribution of the hydrophobic effect to the free energy of folding, will help to refine existing parameterizations of protein folding energetics, and will be useful to understand the influence of point mutations on protein stability.

  6. The unfolded protein response protects from tau neurotoxicity in vivo.

    Directory of Open Access Journals (Sweden)

    Carin A Loewen

    Full Text Available The unfolded protein response is a critical system by which the cell handles excess misfolded protein in the secretory pathway. The role of the system in modulating the effects of aggregation prone cytosolic proteins has received less attention. We use genetic reporters to demonstrate activation of the unfolded protein response in a transgenic Drosophila model of Alzheimer's disease and related tauopathies. We then use loss of function genetic reagents to support a role for the unfolded protein response in protecting from tau neurotoxicity. Our findings suggest that the unfolded protein response can ameliorate the toxicity of tau in vivo.

  7. A Statistician’s View on Deconvolution and Unfolding

    CERN Document Server

    Panaretos, Victor M

    2011-01-01

    We briefly review some of the basic features of unfolding problems from the point of view of the statistician. To illustrate these, we mostly concentrate on the particular instance of unfolding called deconvolution. We discuss the issue of ill-posedness, the bias-variance trade-off, and regularisation tuning, placing emphasis on the important class of kernel density estimators. We also briefly consider basic aspects of the more general unfolding problem and men- tion some of the points that where raised during the discussion session of the unfolding workshop.

  8. The rectified second law of thermodynamics.

    Science.gov (United States)

    Ben-Amotz, Dor; Honig, J M

    2006-10-12

    Equilibrium thermodynamics is combined with Jarzynski's irreversible work theorem to quantify the excess entropy produced by irreversible processes. The resulting rectified form of the second law parallels the first law, in the sense that it facilitates the experimental measurement of excess entropy changes resulting from irreversible work and heat exchanges, just as the first law quantifies energy changes produced by either reversible or irreversible work and heat exchanges. The general form of the rectified second law is further applied to a broad class of quasi-static irreverisble (QSI) processes, for which all of the thermodynamic functions of both the system and surroundings remain continuously well-defined, thus facilitating excess entropy measurements by integrating exact differential functions along QSI paths. The results are illustrated by calculating the mechanical and thermal excess entropy produced by the irreversible unfolding of an RNA molecule.

  9. Equilibrium thermodynamics

    CERN Document Server

    de Oliveira, Mário J

    2017-01-01

    This textbook provides an exposition of equilibrium thermodynamics and its applications to several areas of physics with particular attention to phase transitions and critical phenomena. The applications include several areas of condensed matter physics and include also a chapter on thermochemistry. Phase transitions and critical phenomena are treated according to the modern development of the field, based on the ideas of universality and on the Widom scaling theory. For each topic, a mean-field or Landau theory is presented to describe qualitatively the phase transitions. These theories include the van der Waals theory of the liquid-vapor transition, the Hildebrand-Heitler theory of regular mixtures, the Griffiths-Landau theory for multicritical points in multicomponent systems, the Bragg-Williams theory of order-disorder in alloys, the Weiss theory of ferromagnetism, the Néel theory of antiferromagnetism, the Devonshire theory for ferroelectrics and Landau-de Gennes theory of liquid crystals. This new edit...

  10. Equilibrium thermodynamics

    CERN Document Server

    Oliveira, Mário J

    2013-01-01

    This textbook provides an exposition of equilibrium thermodynamics and its applications to several areas of physics with particular attention to phase transitions and critical phenomena. The applications include several areas of condensed matter physics and include also a chapter on thermochemistry. Phase transitions and critical phenomena are treated according to the modern development of the field, based on the ideas of universality and on the Widom scaling theory. For each topic, a mean-field or Landau theory is presented to describe qualitatively the phase transitions.  These theories include the van der Waals theory of the liquid-vapor transition, the Hildebrand-Heitler theory of regular mixtures, the Griffiths-Landau theory for multicritical points in multicomponent systems, the Bragg-Williams theory of order-disorder in alloys, the Weiss theory of ferromagnetism, the Néel theory of antiferromagnetism, the Devonshire theory for ferroelectrics and Landau-de Gennes theory of liquid crystals. This textbo...

  11. ANDI-03: a genetic algorithm tool for the analysis of activation detector data to unfold high-energy neutron spectra.

    Science.gov (United States)

    Mukherjee, Bhaskar

    2004-01-01

    The thresholds of (n,xn) reactions in various activation detectors are commonly used to unfold the neutron spectra covering a broad energy span, i.e. from thermal to several hundreds of MeV. The saturation activities of the daughter nuclides (i.e. reaction products) serve as the input data of specific spectra unfolding codes, such as SAND-II and LOUHI-83. However, most spectra unfolding codes, including the above, require an a priori (guess) spectrum to starting up the unfolding procedure of an unknown spectrum. The accuracy and exactness of the resulting spectrum primarily depends on the subjectively chosen guess spectrum. On the other hand, the Genetic Algorithm (GA)-based spectra unfolding technique ANDI-03 (Activation-detector Neutron DIfferentiation) presented in this report does not require a specific starting parameter. The GA is a robust problem-solving tool, which emulates the Darwinian Theory of Evolution prevailing in the realm of biological world and is ideally suited to optimise complex objective functions globally in a large multidimensional solution space. The activation data of the 27Al(n,alpha)24Na, 116In(n,gamma)116mIn, 12C(n,2n)11C and 209Bi(n,xn)(210-x)Bi reactions recorded at the high-energy neutron field of the ISIS Spallation source (Rutherford Appleton Laboratory, UK) was obtained from literature and by applying the ANDI-03 GA tool, these data were used to unfold the neutron spectra. The total neutron fluence derived from the neutron spectrum unfolded using GA technique (ANDI-03) agreed within +/-6.9% (at shield top level) and +/-27.2% (behind a 60 cm thick concrete shield) with the same unfolded with the SAND-II code.

  12. Unfolded protein response in hepatitis C virus infection

    Directory of Open Access Journals (Sweden)

    Shiu-Wan eChan

    2014-05-01

    Full Text Available Hepatitis C virus (HCV is a single-stranded, positive-sense RNA virus of clinical importance. The virus establishes a chronic infection and can progress from chronic hepatitis, steatosis to fibrosis, cirrhosis and hepatocellular carcinoma. The mechanisms of viral persistence and pathogenesis are poorly understood. Recently the unfolded protein response (UPR, a cellular homeostatic response to endoplasmic reticulum (ER stress, has emerged to be a major contributing factor in many human diseases. It is also evident that viruses interact with the host UPR in many different ways and the outcome could be pro-viral, anti-viral or pathogenic, depending on the particular type of infection. Here we present evidence for the elicitation of chronic ER stress in HCV infection. We analyze the UPR signaling pathways involved in HCV infection, the various levels of UPR regulation by different viral proteins and finally, we propose several mechanisms by which the virus provokes the UPR.

  13. Thermodynamics of weight loss diets.

    Science.gov (United States)

    Fine, Eugene J; Feinman, Richard D

    2004-12-08

    BACKGROUND: It is commonly held that "a calorie is a calorie", i.e. that diets of equal caloric content will result in identical weight change independent of macronutrient composition, and appeal is frequently made to the laws of thermodynamics. We have previously shown that thermodynamics does not support such a view and that diets of different macronutrient content may be expected to induce different changes in body mass. Low carbohydrate diets in particular have claimed a "metabolic advantage" meaning more weight loss than in isocaloric diets of higher carbohydrate content. In this review, for pedagogic clarity, we reframe the theoretical discussion to directly link thermodynamic inefficiency to weight change. The problem in outline: Is metabolic advantage theoretically possible? If so, what biochemical mechanisms might plausibly explain it? Finally, what experimental evidence exists to determine whether it does or does not occur? RESULTS: Reduced thermodynamic efficiency will result in increased weight loss. The laws of thermodynamics are silent on the existence of variable thermodynamic efficiency in metabolic processes. Therefore such variability is permitted and can be related to differences in weight lost. The existence of variable efficiency and metabolic advantage is therefore an empiric question rather than a theoretical one, confirmed by many experimental isocaloric studies, pending a properly performed meta-analysis. Mechanisms are as yet unknown, but plausible mechanisms at the metabolic level are proposed. CONCLUSIONS: Variable thermodynamic efficiency due to dietary manipulation is permitted by physical laws, is supported by much experimental data, and may be reasonably explained by plausible mechanisms.

  14. Correction of tuberous breasts using the unfolded subareolar gland flap.

    Science.gov (United States)

    Oroz-Torres, Javier; Pelay-Ruata, María-Josefa; Escolán-Gonzalvo, Nieves; Jordán-Palomar, Elena

    2014-08-01

    In this retrospective study, the authors present 12 years of experience using a modified Puckett's technique with a double unfolded strictly subareolar glandular flap for surgical correction of the deformity known as "tuberous breast." In 1976, Rees and Aston documented this congenital malformation of the mammary glands in women. Its cause is unknown, and it affects adolescent girls with varying severity uni- or bilaterally. The condition is characterized by a lack of development, primarily in the lower quadrants of the breast plus a rising of the inframammary fold, together with herniation and increased diameter of the areola. Many varied surgical techniques for correction of this malformation in its different degrees of severity have been documented in the available literature. This study examined the treatment of 42 breasts in 26 patients with a high percentage of full correction of the deformity. The advantages and achievements of the double unfolded strictly subareolar glandular flap include restructuring of the breast's lower pole in volume, length, and shape; reduction and even removal of the double-bubble effect as the flap covers the implant fitted; lowering of inframammary fold height; and correction of areola size and herniation. The procedure is performed through a hemi- or periareolar incision. The technique is versatile for managing the different variations of tuberous breasts, making it another interesting option for correction of the deformity. Level of Evidence IV This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

  15. Glucose and Fructose to Platform Chemicals: Understanding the Thermodynamic Landscapes of Acid-Catalysed Reactions Using High-Level ab Initio Methods

    Energy Technology Data Exchange (ETDEWEB)

    Assary, Rajeev S.; Kim, Taijin; Low, John; Greeley, Jeffrey P.; Curtiss, Larry A.

    2012-12-28

    Molecular level understanding of acid-catalysed conversion of sugar molecules to platform chemicals such as hydroxy-methyl furfural (HMF), furfuryl alcohol (FAL), and levulinic acid (LA) is essential for efficient biomass conversion. In this paper, the high-level G4MP2 method along with the SMD solvation model is employed to understand detailed reaction energetics of the acid-catalysed decomposition of glucose and fructose to HMF. Based on protonation free energies of various hydroxyl groups of the sugar molecule, the relative reactivity of gluco-pyranose, fructo-pyranose and fructo-furanose are predicted. Calculations suggest that, in addition to the protonated intermediates, a solvent assisted dehydration of one of the fructo-furanosyl intermediates is a competing mechanism, indicating the possibility of multiple reaction pathways for fructose to HMF conversion in aqueous acidic medium. Two reaction pathways were explored to understand the thermodynamics of glucose to HMF; the first one is initiated by the protonation of a C2–OH group and the second one through an enolate intermediate involving acyclic intermediates. Additionally, a pathway is proposed for the formation of furfuryl alcohol from glucose initiated by the protonation of a C2–OH position, which includes a C–C bond cleavage, and the formation of formic acid. The detailed free energy landscapes predicted in this study can be used as benchmarks for further exploring the sugar decomposition reactions, prediction of possible intermediates, and finally designing improved catalysts for biomass conversion chemistry in the future.

  16. Unfolding in particle physics: a window on solving inverse problems

    Directory of Open Access Journals (Sweden)

    Spanò Francesco

    2013-07-01

    Full Text Available Unfolding is the ensemble of techniques aimed at resolving inverse, ill-posed problems. A pedagogical introduction to the origin and main problems related to unfolding is presented and used as the the stepping stone towards the illustration of some of the most common techniques that are currently used in particle physics experiments.

  17. THE UNFOLDING OF EQUIVARIANT BIFURCATION PROBLEMS WITH PARAMETERS SYMMETRY

    Institute of Scientific and Technical Information of China (English)

    高守平; 李养成

    2004-01-01

    In this paper versal unfolding theorem of multiparameter equivariant bifurcation problem with parameter symmetry is given. The necessary and sufficient condition that unfolding of multiparameter equivariant bifurcation problem with parameter symmetry factors through another is given. The corresponding results in [1]-[6] are generalized.

  18. Chemical thermodynamics of americium

    Energy Technology Data Exchange (ETDEWEB)

    Silva, R.J. [California Univ., Livermore, CA (United States). Lawrence Livermore National Lab.; Bidoglio, G. [Commission of the European Communities, Ispra (Italy). Environment Inst.; Rand, M.H. [Wintershill Consultancy, Dry Sandford, Abingdon (United Kingdom); Robouch, P.B. [Commission of the European Communities, Geel (Belgium). Inst. for Reference Materials and Measurements; Wanner, H. [MBT Environmental Engineering, Zurich (Switzerland); Puigdomenech, I. [OECD Nuclear Energy Agency, Issy-les-Moulineaux (France)

    1995-09-01

    This is the second volume in a series of critical reviews of the chemical thermodynamic data of those elements of particular importance in the safety assessment modeling of high-level radioactive waste storage and disposal facilities. The objective of these reviews is to provide a set of reliable thermodynamic data that can be used to describe the behaviour of these elements under conditions relevant for radioactive waste disposal systems and the geochemical environments. The present volume is a review of experimental data reported in the literature for americium. On a few occasions, where no data existed, comparisons and estimates were made based on experimental data on analog lanthanide elements. The basic philosophy was to develop a minimum set of solid phases and solution species of americium that would fit all experimental data being reviewed. 15 figs., 32 tabs., 485 refs., 4 appendices

  19. Neutron spectrum unfolding using computer code SAIPS

    CERN Document Server

    Karim, S

    1999-01-01

    The main objective of this project was to study the neutron energy spectrum at rabbit station-1 in Pakistan Research Reactor (PARR-I). To do so, multiple foils activation method was used to get the saturated activities. The computer code SAIPS was used to unfold the neutron spectra from the measured reaction rates. Of the three built in codes in SAIPS, only SANDI and WINDOWS were used. Contribution of thermal part of the spectra was observed to be higher than the fast one. It was found that the WINDOWS gave smooth spectra while SANDII spectra have violet oscillations in the resonance region. The uncertainties in the WINDOWS results are higher than those of SANDII. The results show reasonable agreement with the published results.

  20. Mimicking unfolding motion of a beetle hind wing

    Institute of Scientific and Technical Information of China (English)

    MUHAMMAD Azhar; PARK Hoon C; HWANG Do Y; BYUN Doyoung; GOO Nam S

    2009-01-01

    This paper presents an experimental research aiming to realize an artificial hind wing that can mimic the wing unfolding motion of Allomyrina dichotoma, an insect in coleopteran order. Based on the understanding of working principles of beetle wing folding/unfolding mechanisms, the hind wing unfolding motion is mimicked by a combination of creative ideas and state-of-art artificial muscle actuator. In this work, we devise two types of artificial wings and the successfully demonstrate that they can be unfolded by actuation of shape memory alloy wires to provide actuation force at the wing base and along the leading edge vein. The folding/unfolding mechanisms may provide an insight for portable nano/micro air vehicles with morphing wings.

  1. Should unfolded histograms be used to test hypotheses?

    CERN Document Server

    Cousins, Robert D; Sun, Yipeng

    2016-01-01

    In many analyses in high energy physics, attempts are made to remove the effects of detector smearing in data by techniques referred to as "unfolding" histograms, thus obtaining estimates of the true values of histogram bin contents. Such unfolded histograms are then compared to theoretical predictions, either to judge the goodness of fit of a theory, or to compare the abilities of two or more theories to describe the data. When doing this, even informally, one is testing hypotheses. However, a more fundamentally sound way to test hypotheses is to smear the theoretical predictions by simulating detector response and then comparing to the data without unfolding; this is also frequently done in high energy physics, particularly in searches for new physics. One can thus ask: to what extent does hypothesis testing after unfolding data materially reproduce the results obtained from testing by smearing theoretical predictions? We argue that this "bottom-line-test" of unfolding methods should be studied more commonl...

  2. On Inductive and Coinductive Proofs via Unfold/Fold Transformations

    Science.gov (United States)

    Seki, Hirohisa

    We consider a new application condition of negative unfolding, which guarantees its safe use in unfold/fold transformation of stratified logic programs. The new condition of negative unfolding is a natural one, since it is considered as a special case of replacement rule. The correctness of our unfold/fold transformation system in the sense of the perfect model semantics is proved. We then consider the coinductive proof rules proposed by Jaffar et al. We show that our unfold/fold transformation system, when used together with Lloyd-Topor transformation, can prove a proof problem which is provable by the coinductive proof rules by Jaffar et al. To this end, we propose a new replacement rule, called sound replacement, which is not necessarily equivalence-preserving, but is essential to perform a reasoning step corresponding to coinduction.

  3. Lysozyme Thermal Denaturation and Self-Interaction: Four Integrated Thermodynamic Experiments for the Physical Chemistry Laboratory

    Science.gov (United States)

    Schwinefus, Jeffrey J.; Schaefle, Nathaniel J.; Muth, Gregory W.; Miessler, Gary L.; Clark, Christopher A.

    2008-01-01

    As part of an effort to infuse our physical chemistry laboratory with biologically relevant, investigative experiments, we detail four integrated thermodynamic experiments that characterize the denaturation (or unfolding) and self-interaction of hen egg white lysozyme as a function of pH and ionic strength. Students first use Protein Explorer to…

  4. Ethanol Effects Involve Non-canonical Unfolded Protein Response Activation in Yeast Cells

    Science.gov (United States)

    Navarro-Tapia, Elisabet; Pérez-Torrado, Roberto; Querol, Amparo

    2017-01-01

    The unfolded protein response (UPR) is a conserved intracellular signaling pathway that controls transcription of endoplasmic reticulum (ER) homeostasis related genes. Ethanol stress has been recently described as an activator of the UPR response in yeast Saccharomyces cerevisiae, but very little is known about the causes of this activation. Although some authors ensure that the UPR is triggered by the unfolded proteins generated by ethanol in the cell, there are studies which demonstrate that protein denaturation occurs at higher ethanol concentrations than those used to trigger the UPR. Here, we studied UPR after ethanol stress by three different approaches and we concluded that unfolded proteins do not accumulate in the ER under. We also ruled out inositol depletion as an alternative mechanism to activate the UPR under ethanol stress discarding that ethanol effects on the cell decreased inositol levels by different methods. All these data suggest that ethanol, at relatively low concentrations, does not cause unfolded proteins in the yeasts and UPR activation is likely due to other unknown mechanism related with a restructuring of ER membrane due to the effect of ethanol. PMID:28326077

  5. Thermodynamic interpolation

    Energy Technology Data Exchange (ETDEWEB)

    Maiden, D E

    1998-10-01

    A method for constructing bicubic interpolation polynomials for the pressure P and internal energy E that are thermodynamically consistent at the mesh ponts and continuous across mesh boundaries is presented. The slope boundary conditions for the pressure and energy are derived from finite differences of the data and from Maxwell's consistency relation. Monotonicity of the sound speed and the specific heat is obtained by a bilinear interpolation of the slopes of the tabulated data. Monotonicity of the functions near steep gradients may be achieved by mesh refinement or by using a non-consistent bilinear to the data. Mesh refinement is very efficient for uniform-linear or uniform-logarithmic spaced data because a direct table lookup can be used. The direct method was compared to binary search and was 37 percent faster for logarithmic-spaced data and 106 percent faster for linear-spaced data. This improvement in speed is very important in the radiation-transport opacity-lookup part of the calculation. Interpolation in P-E space, with mesh refinement, can be made simple, robust, and conserve energy. In the final analysis the interpolation of the free energy and entropy (Maiden and Cook) remains a competitor.

  6. Holostar thermodynamics

    CERN Document Server

    Petri, M

    2003-01-01

    A simple thermodynamic model for the final state of a collapsed, spherically symmetric star is presented. It is assumed, that the star's interior at the endpoint of the collapse consists of an ideal gas of ultra-relativistic fermions and bosons in thermal equilibrium and that the metric approaches the static metric of the so called holostar-solution of general relativity. The final configuration has a radius slightly exceeding the gravitational radius of the star. The radial coordinate difference between gravitational and actual radius is of order of the Planck length. The total number of ultra-relativistic particles within the star is proportional its proper surface-area, measured in units of the Planck-area. This is first direct evidence for the microscopic-statistical nature of the Hawking entropy and indicates, that the holographic principle is valid for compact self gravitating objects of any size. A "Stephan-Boltzmann-type" relation between the surface temperature and the surface area of the star is der...

  7. Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level.

    Science.gov (United States)

    Jayaram, B; McConnell, K; Dixit, S B; Das, A; Beveridge, D L

    2002-01-15

    Noncovalent association of proteins to specific target sites on DNA--a process central to gene expression and regulation--has thus far proven to be idiosyncratic and elusive to generalizations on the nature of the driving forces. The spate of structural information on protein--DNA complexes sets the stage for theoretical investigations on the molecular thermodynamics of binding aimed at identifying forces responsible for specific macromolecular recognition. Computation of absolute binding free energies for systems of this complexity transiting from structural information is a stupendous task. Adopting some recent progresses in treating atomic level interactions in proteins and nucleic acids including solvent and salt effects, we have put together an energy component methodology cast in a phenomenological mode and amenable to systematic improvements and developed a computational first atlas of the free energy contributors to binding in approximately 40 protein-DNA complexes representing a variety of structural motifs and functions. Illustrating vividly the compensatory nature of the free energy components contributing to the energetics of recognition for attaining optimal binding, our results highlight unambiguously the roles played by packing, electrostatics including hydrogen bonds, ion and water release (cavitation) in protein-DNA binding. Cavitation and van der Waals contributions without exception favor complexation. The electrostatics is marginally unfavorable in a consensus view. Basic residues on the protein contribute favorably to binding despite the desolvation expense. The electrostatics arising from the acidic and neutral residues proves unfavorable to binding. An enveloping mode of binding to short stretches of DNA makes for a strong unfavorable net electrostatics but a highly favorable van der Waals and cavitation contribution. Thus, noncovalent protein-DNA association is a system-specific fine balancing act of these diverse competing forces. With the

  8. The secondary structure and the thermal unfolding parameters of the S-layer protein from Lactobacillus salivarius.

    Science.gov (United States)

    Lighezan, Liliana; Georgieva, Ralitsa; Neagu, Adrian

    2016-09-01

    Surface layer (S-layer) proteins have been identified in the cell envelope of many organisms, such as bacteria and archaea. They self-assemble, forming monomolecular crystalline arrays. Isolated S-layer proteins are able to recrystallize into regular lattices, which proved useful in biotechnology. Here we investigate the structure and thermal unfolding of the S-layer protein isolated from Lactobacillus salivarius 16 strain of human origin. Using circular dichroism (CD) spectroscopy, and the software CDSSTR from DICHROWEB, CONTINLL from CDPro, as well as CDNN, we assess the fractions of the protein's secondary structural elements at temperatures ranging between 10 and 90 °C, and predict the tertiary class of the protein. To study the thermal unfolding of the protein, we analyze the temperature dependence of the CD signal in the far- and near-UV domains. Fitting the experimental data by two- and three-state models of thermal unfolding, we infer the midpoint temperatures, the temperature dependence of the changes in Gibbs free energy, enthalpy, and entropy of the unfolding transitions in standard conditions, and the temperature dependence of the equilibrium constant. We also estimate the changes in heat capacity at constant pressure in standard conditions. The results indicate that the thermal unfolding of the S-layer protein from L. salivarius is highly cooperative, since changes in the secondary and tertiary structures occur simultaneously. The thermodynamic analysis predicts a "cold" transition, at about -3 °C, of both the secondary and tertiary structures. Our findings may be important for the use of S-layer proteins in biotechnology and in biomedical applications.

  9. Mathematical foundations of thermodynamics

    CERN Document Server

    Giles, R; Stark, M; Ulam, S

    2013-01-01

    Mathematical Foundations of Thermodynamics details the core concepts of the mathematical principles employed in thermodynamics. The book discusses the topics in a way that physical meanings are assigned to the theoretical terms. The coverage of the text includes the mechanical systems and adiabatic processes; topological considerations; and equilibrium states and potentials. The book also covers Galilean thermodynamics; symmetry in thermodynamics; and special relativistic thermodynamics. The book will be of great interest to practitioners and researchers of disciplines that deal with thermodyn

  10. Toward resolution of ambiguity for the unfolded state.

    Science.gov (United States)

    Beaucage, Gregory

    2008-07-01

    The unfolded states in proteins and nucleic acids remain weakly understood despite their importance in folding processes; misfolding diseases (Parkinson's and Alzheimer's); natively unfolded proteins (as many as 30% of eukaryotic proteins, according to Fink); and the study of ribozymes. Research has been hindered by the inability to quantify the residual (native) structure present in an unfolded protein or nucleic acid. Here, a scaling model is proposed to quantify the molar degree of folding and the unfolded state. The model takes a global view of protein structure and can be applied to a number of analytic methods and to simulations. Three examples are given of application to small-angle scattering from pressure-induced unfolding of SNase, from acid-unfolded cytochrome c, and from folding of Azoarcus ribozyme. These examples quantitatively show three characteristic unfolded states for proteins, the statistical nature of a protein folding pathway, and the relationship between extent of folding and chain size during folding for charge-driven folding in RNA.

  11. Comparative study of the folding/unfolding dynamics of poly(glutamic acid) in light and heavy water.

    Science.gov (United States)

    Mendonça, Lucille; Steinbacher, Andreas; Bouganne, Raphaël; Hache, François

    2014-05-22

    The folding/unfolding equilibrium is investigated in poly(glutamic acid) (PGA) by two complementary sets of experiments: temperature-dependent steady-state circular dichroism spectra on the one hand and time-resolved circular dichroism measurements coupled with a T-jump experiment on the other hand. The experiments are performed for PGA dissolved in water for various pH values, as well as in heavy water. The kinetic and thermodynamic parameters extracted from these measurements are shown to be markedly different between light and heavy water, which is assigned to the difference in hydrogen bond energies in both solvents.

  12. Iron corrosion in concentrated saline solutions at elevated T in high-level radioactive waste salt rock repositories. A thermodynamic study

    Energy Technology Data Exchange (ETDEWEB)

    Munoz, Andres G.; Moog, Helge C. [Gesellschaft fuer Anlagen und Reaktorsicherheit mbH (GRS), Braunschweig (Germany)

    2015-07-01

    Predictions of the evolution of the interfacial chemistry of corroding iron in high salinary milieus at temperatures of 25 C to 100 C based on an extended thermodynamic data basis for the system Fe(II)-Fe(III)-Na-K-Cl-Mg-Ca-SO{sub 4}-S-CO{sub 3}-H{sub 2} are presented. Future research directions are discussed.

  13. Thermodynamics of downhill folding: multi-probe analysis of PDD, a protein that folds over a marginal free energy barrier.

    Science.gov (United States)

    Naganathan, Athi N; Muñoz, Victor

    2014-07-31

    Downhill folding proteins fold in microseconds by crossing a very low or no free energy barrier (<3 RT), and exhibit a complex unfolding behavior in equilibrium. Such unfolding complexity is due to the weak thermodynamic coupling that exists between the various structural segments of these proteins, and it is manifested in unfolding curves that differ depending on the structural probe employed to monitor the process. Probe-dependent unfolding has important practical implications because it permits one to investigate the folding energy landscape in detail using multiprobe thermodynamic experiments. This type of thermodynamic behavior has been investigated in depth on the protein BBL, an example of extreme (one-state) downhill folding in which there is no free energy barrier at any condition, including the denaturation midpoint. However, an open question is, to what extent is such thermodynamic behavior observed on less extreme downhill folders? Here we perform a multiprobe spectroscopic characterization of the microsecond folder PDD, a structural and functional homologue of BBL that folds within the downhill regime, but is not an example of one-state downhill folding; rather at the denaturation midpoint PDD folds by crossing an incipient free energy barrier. Model-free analysis of the unfolding curves from four different spectroscopic probes together with differential scanning calorimetry reveals a dispersion of ∼9 K in the apparent melting temperature and also marked differences in unfolding broadness (from ∼50 to ∼130 kJ mol(-1) when analyzed with a two-state model), confirming that such properties are also observed on less extreme downhill folders. We subsequently perform a global quantitative analysis of the unfolding data of PDD using the same ME statistical mechanical model that was used before for the BBL domain. The analysis shows that this simple model captures all of the features observed on the unfolding of PDD (i.e., the intensity and temperature

  14. Thermodynamic tables to accompany Modern engineering thermodynamics

    CERN Document Server

    Balmer, Robert T

    2011-01-01

    This booklet is provided at no extra charge with new copies of Balmer's Modern Engineering Thermodynamics. It contains two appendices. Appendix C contains 40 thermodynamic tables, and Appendix D consists of 6 thermodynamic charts. These charts and tables are provided in a separate booklet to give instructors the flexibility of allowing students to bring the tables into exams. The booklet may be purchased separately if needed.

  15. Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding.

    Science.gov (United States)

    Nagpal, Suhani; Tiwari, Satyam; Mapa, Koyeli; Thukral, Lipi

    2015-01-01

    Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central "hubs". Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates.

  16. Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding.

    Directory of Open Access Journals (Sweden)

    Suhani Nagpal

    Full Text Available Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD, 1-anilinonaphthalene-8-sulfonic acid (ANS binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS. Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central "hubs". Overall, our results implicate that genomic variations (or mutations in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates.

  17. Classical and statistical thermodynamics

    CERN Document Server

    Rizk, Hanna A

    2016-01-01

    This is a text book of thermodynamics for the student who seeks thorough training in science or engineering. Systematic and thorough treatment of the fundamental principles rather than presenting the large mass of facts has been stressed. The book includes some of the historical and humanistic background of thermodynamics, but without affecting the continuity of the analytical treatment. For a clearer and more profound understanding of thermodynamics this book is highly recommended. In this respect, the author believes that a sound grounding in classical thermodynamics is an essential prerequisite for the understanding of statistical thermodynamics. Such a book comprising the two wide branches of thermodynamics is in fact unprecedented. Being a written work dealing systematically with the two main branches of thermodynamics, namely classical thermodynamics and statistical thermodynamics, together with some important indexes under only one cover, this treatise is so eminently useful.

  18. Unfolding Visual Lexical Decision in Time

    Science.gov (United States)

    Barca, Laura; Pezzulo, Giovanni

    2012-01-01

    Visual lexical decision is a classical paradigm in psycholinguistics, and numerous studies have assessed the so-called “lexicality effect" (i.e., better performance with lexical than non-lexical stimuli). Far less is known about the dynamics of choice, because many studies measured overall reaction times, which are not informative about underlying processes. To unfold visual lexical decision in (over) time, we measured participants' hand movements toward one of two item alternatives by recording the streaming x,y coordinates of the computer mouse. Participants categorized four kinds of stimuli as “lexical" or “non-lexical:" high and low frequency words, pseudowords, and letter strings. Spatial attraction toward the opposite category was present for low frequency words and pseudowords. Increasing the ambiguity of the stimuli led to greater movement complexity and trajectory attraction to competitors, whereas no such effect was present for high frequency words and letter strings. Results fit well with dynamic models of perceptual decision-making, which describe the process as a competition between alternatives guided by the continuous accumulation of evidence. More broadly, our results point to a key role of statistical decision theory in studying linguistic processing in terms of dynamic and non-modular mechanisms. PMID:22563419

  19. The identification of unfolding facial expressions.

    Science.gov (United States)

    Fiorentini, Chiara; Schmidt, Susanna; Viviani, Paolo

    2012-01-01

    We asked whether the identification of emotional facial expressions (FEs) involves the simultaneous perception of the facial configuration or the detection of emotion-specific diagnostic cues. We recorded at high speed (500 frames s-1) the unfolding of the FE in five actors, each expressing six emotions (anger, surprise, happiness, disgust, fear, sadness). Recordings were coded every 10 frames (20 ms of real time) with the Facial Action Coding System (FACS, Ekman et al 2002, Salt Lake City, UT: Research Nexus eBook) to identify the facial actions contributing to each expression, and their intensity changes over time. Recordings were shown in slow motion (1/20 of recording speed) to one hundred observers in a forced-choice identification task. Participants were asked to identify the emotion during the presentation as soon as they felt confident to do so. Responses were recorded along with the associated response times (RTs). The RT probability density functions for both correct and incorrect responses were correlated with the facial activity during the presentation. There were systematic correlations between facial activities, response probabilities, and RT peaks, and significant differences in RT distributions for correct and incorrect answers. The results show that a reliable response is possible long before the full FE configuration is reached. This suggests that identification is reached by integrating in time individual diagnostic facial actions, and does not require perceiving the full apex configuration.

  20. Neutron spectrum unfolding using neural networks

    Energy Technology Data Exchange (ETDEWEB)

    Vega C, H.R.; Hernandez D, V.M.; Manzanares A, E. [Universidad Autonoma de Zacatecas, A.P. 336, 98000 Zacatecas (Mexico)]. E-mail: rvega@cantera.reduaz.mx

    2004-07-01

    An artificial neural network has been designed to obtain the neutron spectra from the Bonner spheres spectrometer's count rates. The neural network was trained using a large set of neutron spectra compiled by the International Atomic Energy Agency. These include spectra from iso- topic neutron sources, reference and operational neutron spectra obtained from accelerators and nuclear reactors. The spectra were transformed from lethargy to energy distribution and were re-binned to 31 energy groups using the MCNP 4C code. Re-binned spectra and UTA4 matrix were used to calculate the expected count rates in Bonner spheres spectrometer. These count rates were used as input and correspondent spectrum was used as output during neural network training. The network has 7 input nodes, 56 neurons as hidden layer and 31 neurons in the output layer. After training the network was tested with the Bonner spheres count rates produced by twelve neutron spectra. The network allows unfolding the neutron spectrum from count rates measured with Bonner spheres. Good results are obtained when testing count rates belong to neutron spectra used during training, acceptable results are obtained for count rates obtained from actual neutron fields; however the network fails when count rates belong to monoenergetic neutron sources. (Author)

  1. Measuring Thermodynamic Length

    Energy Technology Data Exchange (ETDEWEB)

    Crooks, Gavin E

    2007-09-07

    Thermodynamic length is a metric distance between equilibrium thermodynamic states. Among other interesting properties, this metric asymptotically bounds the dissipation induced by a finite time transformation of a thermodynamic system. It is also connected to the Jensen-Shannon divergence, Fisher information, and Rao's entropy differential metric. Therefore, thermodynamic length is of central interestin understanding matter out of equilibrium. In this Letter, we will consider how to denethermodynamic length for a small system described by equilibrium statistical mechanics and how to measure thermodynamic length within a computer simulation. Surprisingly, Bennett's classic acceptance ratio method for measuring free energy differences also measures thermodynamic length.

  2. Slow proton transfer coupled to unfolding explains the puzzling results of single-molecule experiments on BBL, a paradigmatic downhill folding protein.

    Directory of Open Access Journals (Sweden)

    Michele Cerminara

    Full Text Available A battery of thermodynamic, kinetic, and structural approaches has indicated that the small α-helical protein BBL folds-unfolds via the one-state downhill scenario. Yet, single-molecule fluorescence spectroscopy offers a more conflicting view. Single-molecule experiments at pH 6 show a unique half-unfolded conformational ensemble at mid denaturation, whereas other experiments performed at higher pH show a bimodal distribution, as expected for two-state folding. Here we use thermodynamic and laser T-jump kinetic experiments combined with theoretical modeling to investigate the pH dependence of BBL stability, folding kinetics and mechanism within the pH 6-11 range. We find that BBL unfolding is tightly coupled to the protonation of one of its residues with an apparent pKa of ~ 7. Therefore, in chemical denaturation experiments around neutral pH BBL unfolds gradually, and also converts in binary fashion to the protonated species. Moreover, under the single-molecule experimental conditions (denaturant midpoint and 279 K, we observe that proton transfer is much slower than the ~ 15 microseconds folding-unfolding kinetics of BBL. The relaxation kinetics is distinctly biphasic, and the overall relaxation time (i.e. 0.2-0.5 ms becomes controlled by the proton transfer step. We then show that a simple theoretical model of protein folding coupled to proton transfer explains quantitatively all these results as well as the two sets of single-molecule experiments, including their more puzzling features. Interestingly, this analysis suggests that BBL unfolds following a one-state downhill folding mechanism at all conditions. Accordingly, the source of the bimodal distributions observed during denaturation at pH 7-8 is the splitting of the unique conformational ensemble of BBL onto two slowly inter-converting protonation species. Both, the unprotonated and protonated species unfold gradually (one-state downhill, but they exhibit different degree of unfolding

  3. Analysis of distorted measurements -- parameter estimation and unfolding

    CERN Document Server

    Zech, Guenter

    2016-01-01

    1. Parameter inference from distorted measurements is discussed. 2. Smeared measurements are unfolded without explicit regularization. The corresponding results are unbiased and permit to fit parameters and to apply quantitative goodness-of-fit tests. 3. Common unfolding methods (iterative EM with early stopping, truncated SVD, ML fits with curvature, entropy and norm penalties) are tested and compared to each other with the regularization parameter adjusted to minimize the integrated square error (ISE) in all cases. Apart from histogram representations, spline approximations are considered. All simulations indicate that the EM method leads to smaller ISEs than the competing approaches. Especially promising is the EM unfolding to spline approximations. The studies are based on different distributions, event numbers, resolutions and enough independent simulations to obtain conclusive results. It is proposed to unfold data with the EM method to b-spline approximations and to supplement the results with histogra...

  4. Catalogue to select the initial guess spectrum during unfolding

    CERN Document Server

    Vega-Carrillo, H R

    2002-01-01

    A new method to select the initial guess spectrum is presented. Neutron spectra unfolded from Bonner sphere data are dependent on the initial guess spectrum used in the unfolding code. The method is based on a catalogue of detector count rates calculated from a set of reported neutron spectra. The spectra of three isotopic neutron sources sup 2 sup 5 sup 2 Cf, sup 2 sup 3 sup 9 PuBe and sup 2 sup 5 sup 2 Cf/D sub 2 O, were measured to test the method. The unfolding was carried out using the three initial guess options included in the BUNKIUT code. Neutron spectra were also calculated using MCNP code. Unfolded spectra were compared with those calculated; in all the cases our method gives the best results.

  5. First Passage Times, Lifetimes, and Relaxation Times of Unfolded Proteins

    Science.gov (United States)

    Dai, Wei; Sengupta, Anirvan M.; Levy, Ronald M.

    2015-01-01

    The dynamics of proteins in the unfolded state can be quantified in computer simulations by calculating a spectrum of relaxation times which describes the time scales over which the population fluctuations decay to equilibrium. If the unfolded state space is discretized we can evaluate the relaxation time of each state. We derive a simple relation that shows the mean first passage time to any state is equal to the relaxation time of that state divided by the equilibrium population. This explains why mean first passage times from state to state within the unfolded ensemble can be very long but the energy landscape can still be smooth (minimally frustrated). In fact, when the folding kinetics is two-state, all of the unfolded state relaxation times within the unfolded free energy basin are faster than the folding time. This result supports the well-established funnel energy landscape picture and resolves an apparent contradiction between this model and the recently proposed kinetic hub model of protein folding. We validate these concepts by analyzing a Markov State Model of the kinetics in the unfolded state and folding of the mini-protein NTL9 constructed from a 2.9 millisecond simulation provided by D. E. Shaw Research. PMID:26252709

  6. OPERATOR NORM INEQUALITIES BETWEEN TENSOR UNFOLDINGS ON THE PARTITION LATTICE.

    Science.gov (United States)

    Wang, Miaoyan; Duc, Khanh Dao; Fischer, Jonathan; Song, Yun S

    2017-05-01

    Interest in higher-order tensors has recently surged in data-intensive fields, with a wide range of applications including image processing, blind source separation, community detection, and feature extraction. A common paradigm in tensor-related algorithms advocates unfolding (or flattening) the tensor into a matrix and applying classical methods developed for matrices. Despite the popularity of such techniques, how the functional properties of a tensor changes upon unfolding is currently not well understood. In contrast to the body of existing work which has focused almost exclusively on matricizations, we here consider all possible unfoldings of an order-k tensor, which are in one-to-one correspondence with the set of partitions of {1, …, k}. We derive general inequalities between the l(p) -norms of arbitrary unfoldings defined on the partition lattice. In particular, we demonstrate how the spectral norm (p = 2) of a tensor is bounded by that of its unfoldings, and obtain an improved upper bound on the ratio of the Frobenius norm to the spectral norm of an arbitrary tensor. For specially-structured tensors satisfying a generalized definition of orthogonal decomposability, we prove that the spectral norm remains invariant under specific subsets of unfolding operations.

  7. Order Statistics Theory of Unfolding of Multimeric Proteins

    Science.gov (United States)

    Zhmurov, A.; Dima, R.I.; Barsegov, V.

    2010-01-01

    Dynamic force spectroscopy has become indispensable for the exploration of the mechanical properties of proteins. In force-ramp experiments, performed by utilizing a time-dependent pulling force, the peak forces for unfolding transitions in a multimeric protein (D)N are used to map the free energy landscape for unfolding for a protein domain D. We show that theoretical modeling of unfolding transitions based on combining the observed first (f1), second (f2), …, Nth (fN) unfolding forces for a protein tandem of fixed length N, and pooling the force data for tandems of different length, n1 molecular characteristics that determine the unfolding micromechanics. We present a simple method of estimation of the parent distribution, ψD(f), based on analyzing the force data for a tandem (D)n of arbitrary length n. Order statistics theory is exemplified through a detailed analysis and modeling of the unfolding forces obtained from pulling simulations of the monomer and oligomers of the all-β-sheet WW domain. PMID:20858442

  8. Unfolded protein response activation in cataracts.

    Science.gov (United States)

    Torres-Bernal, Beatriz E; Torres-Bernal, Luis Fernando; Gutiérrez-Campos, Rafael R; Kershenobich Stalnikowitz, David D; Barba-Gallardo, Luis Fernando; Chayet, Arturo A; Ventura-Juárez, Javier

    2014-10-01

    To analyze the expression of 78 kDa glucose-regulated protein (GRP78) and activating transcription factor 6 (ATF6), 2 factors in the unfolded protein response (UPR), in age-related and diabetes-associated cataract. Universidad Autónoma de Aguascalientes, Aguascalientes, México. Experimental study. The qualitative and quantitative expression of GRP78 and ATF6 were measured in surgical samples from 11 senile cataracts, 9 diabetic-associated cataracts, and 3 normal lenses. Both proteins were detected by immunofluorescence and immunogold-conjugated antibodies. Quantitative morphometry was used to analyze the differences in GRP78 and ATF6 between samples. The Mann-Whitney test was used for statistical analysis. Scanning electron microscopy showed the characteristic organization of fibers in normal lenses with regular alignment and interdigitation between them. On the other hand, lenses from eyes with senile or diabetic cataract showed the same pattern of misalignment and disorganization of the fibers. Both proteins were detected through immunofluorescence in senile and diabetic cataracts, but not in normal lenses. Immunogold-conjugated antibodies and transmission electron microscopy showed that GRP78 and ATF6 grains were 30% higher and 35% higher, respectively, in diabetic cataracts than in senile cataracts (P<.05). These data show for the first time in humans that GRP78 and ATF6 are present in lens fibers of senile cataracts and diabetic cataracts, establishing that the UPR may be important in the process of cataractogenesis. No author has a financial or proprietary interest in any material or method mentioned. Copyright © 2014 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  9. Chemical thermodynamics: plenary review.

    Science.gov (United States)

    Fegley, B., Jr.

    1990-05-01

    The invited and contributed papers dealing with the applications of chemical thermodynamics to planetary atmospheres research are briefly reviewed. The key areas for future applications of chemical thermodynamics research to planetary atmospheres are also described.

  10. Unfolding Simulations of Holomyoglobin from Four Mammals: Identification of Intermediates and β-Sheet Formation from Partially Unfolded States

    DEFF Research Database (Denmark)

    Dasmeh, Pouria; Kepp, Kasper Planeta

    2013-01-01

    simulations of holoMb and the first comparative study of unfolding of protein orthologs from different species (sperm whale, pig, horse, and harbor seal). We also provide new interpretations of experimental mean molecular ellipticities of myoglobin intermediates, notably correcting for random coil and number......Myoglobin (Mb) is a centrally important, widely studied mammalian protein. While much work has investigated multi-step unfolding of apoMb using acid or denaturant, holomyoglobin unfolding is poorly understood despite its biological relevance. We present here the first systematic unfolding...... of helices in intermediates. The simulated holoproteins at 310 K displayed structures and dynamics in agreement with crystal structures (Rg ,1.48–1.51 nm, helicity ,75%). At 400 K, heme was not lost, but some helix loss was observed in pig and horse, suggesting that these helices are less stable...

  11. Thermodynamics of weight loss diets

    Directory of Open Access Journals (Sweden)

    Fine Eugene J

    2004-12-01

    Full Text Available Abstract Background It is commonly held that "a calorie is a calorie", i.e. that diets of equal caloric content will result in identical weight change independent of macronutrient composition, and appeal is frequently made to the laws of thermodynamics. We have previously shown that thermodynamics does not support such a view and that diets of different macronutrient content may be expected to induce different changes in body mass. Low carbohydrate diets in particular have claimed a "metabolic advantage" meaning more weight loss than in isocaloric diets of higher carbohydrate content. In this review, for pedagogic clarity, we reframe the theoretical discussion to directly link thermodynamic inefficiency to weight change. The problem in outline: Is metabolic advantage theoretically possible? If so, what biochemical mechanisms might plausibly explain it? Finally, what experimental evidence exists to determine whether it does or does not occur? Results Reduced thermodynamic efficiency will result in increased weight loss. The laws of thermodynamics are silent on the existence of variable thermodynamic efficiency in metabolic processes. Therefore such variability is permitted and can be related to differences in weight lost. The existence of variable efficiency and metabolic advantage is therefore an empiric question rather than a theoretical one, confirmed by many experimental isocaloric studies, pending a properly performed meta-analysis. Mechanisms are as yet unknown, but plausible mechanisms at the metabolic level are proposed. Conclusions Variable thermodynamic efficiency due to dietary manipulation is permitted by physical laws, is supported by much experimental data, and may be reasonably explained by plausible mechanisms.

  12. Heat and thermodynamics

    CERN Document Server

    Saxena, A K

    2014-01-01

    Heat and thermodynamics aims to serve as a textbook for Physics, Chemistry and Engineering students. The book covers basic ideas of Heat and Thermodynamics, Kinetic Theory and Transport Phenomena, Real Gases, Liquafaction and Production and Measurement of very Low Temperatures, The First Law of Thermodynamics, The Second and Third Laws of Thermodynamics and Heat Engines and Black Body Radiation. KEY FEATURES Emphasis on concepts Contains 145 illustrations (drawings), 9 Tables and 48 solved examples At the end of chapter exercises and objective questions

  13. Shape-constrained uncertainty quantification in unfolding steeply falling elementary particle spectra

    CERN Document Server

    Kuusela, Mikael

    2015-01-01

    The high energy physics unfolding problem is an important statistical inverse problem arising in data analysis at the Large Hadron Collider at CERN. The problem arises in making nonparametric inferences about a particle spectrum from measurements smeared by the finite resolution of the particle detectors. Existing unfolding methodology has major practical limitations stemming from ad hoc discretization and regularization of the problem. As a result, confidence intervals derived using the current methods can have significantly lower coverage than expected. In this work, we regularize the problem by imposing physically justified shape constraints. We quantify the uncertainty by constructing a nonparametric confidence set for the true spectrum consisting of all spectra that satisfy the shape constraints and that predict observations within an appropriately calibrated level of fit to the data. Projecting that set produces simultaneous confidence intervals for all functionals of the spectrum, including averages wi...

  14. RNA Thermodynamic Structural Entropy.

    Science.gov (United States)

    Garcia-Martin, Juan Antonio; Clote, Peter

    2015-01-01

    Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http

  15. RNA Thermodynamic Structural Entropy.

    Directory of Open Access Journals (Sweden)

    Juan Antonio Garcia-Martin

    Full Text Available Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs. However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http

  16. Sequential protein unfolding through a carbon nanotube pore

    Science.gov (United States)

    Xu, Zhonghe; Zhang, Shuang; Weber, Jeffrey K.; Luan, Binquan; Zhou, Ruhong; Li, Jingyuan

    2016-06-01

    An assortment of biological processes, like protein degradation and the transport of proteins across membranes, depend on protein unfolding events mediated by nanopore interfaces. In this work, we exploit fully atomistic simulations of an artificial, CNT-based nanopore to investigate the nature of ubiquitin unfolding. With one end of the protein subjected to an external force, we observe non-canonical unfolding behaviour as ubiquitin is pulled through the pore opening. Secondary structural elements are sequentially detached from the protein and threaded into the nanotube, interestingly, the remaining part maintains native-like characteristics. The constraints of the nanopore interface thus facilitate the formation of stable ``unfoldon'' motifs above the nanotube aperture that can exist in the absence of specific native contacts with the other secondary structure. Destruction of these unfoldons gives rise to distinct force peaks in our simulations, providing us with a sensitive probe for studying the kinetics of serial unfolding events. Our detailed analysis of nanopore-mediated protein unfolding events not only provides insight into how related processes might proceed in the cell, but also serves to deepen our understanding of structural arrangements which form the basis for protein conformational stability.An assortment of biological processes, like protein degradation and the transport of proteins across membranes, depend on protein unfolding events mediated by nanopore interfaces. In this work, we exploit fully atomistic simulations of an artificial, CNT-based nanopore to investigate the nature of ubiquitin unfolding. With one end of the protein subjected to an external force, we observe non-canonical unfolding behaviour as ubiquitin is pulled through the pore opening. Secondary structural elements are sequentially detached from the protein and threaded into the nanotube, interestingly, the remaining part maintains native-like characteristics. The constraints of

  17. Protein unfolding under isometric tension-what force can integrins generate, and can it unfold FNIII domains?

    Science.gov (United States)

    Erickson, Harold P

    2017-02-01

    Extracellular matrix fibrils of fibronectin (FN) are highly elastic, and are typically stretched three to four times their relaxed length. The mechanism of stretching has been controversial, in particular whether it involves tension-induced unfolding of FNIII domains. Recent studies have found that ∼5pN is the threshold isometric force for unfolding various protein domains. FNIII domains should therefore not be unfolded until the tension approaches 5pN. Integrins have been reported to generate forces ranging from 1 to >50pN, but I argue that studies reporting 1-2pN are the most convincing. This is not enough to unfold FNIII domains. Even if domains were unfolded, 2pN would only extend the worm-like-chain to about twice the length of the folded domain. Overall I conclude that stretching FN matrix fibrils involves primarily the compact to extended conformational change of FN dimers, with minimal contribution from unfolding FNIII domains. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Some Considerations about Thermodynamic Cycles

    Science.gov (United States)

    da Silva, M. F. Ferreira

    2012-01-01

    After completing their introductory studies on thermodynamics at the university level, typically in a second-year university course, most students show a number of misconceptions. In this work, we identify some of those erroneous ideas and try to explain their origins. We also give a suggestion to attack the problem through a systematic and…

  19. Structural Studies of Phycobiliproteins from Spirulina: Combining Spectroscopy, Thermodynamics, and Molecular Modeling in an Undergraduate Biochemistry Experiment

    Science.gov (United States)

    Taylor, Ann T. S.; Feller, Scott E.

    2002-12-01

    Molecular modeling provides a powerful mechanism for students to connect molecular-level structural changes with macroscopically observable properties. We describe an experiment that integrates spectroscopy, thermodynamics, and molecular modeling into a single activity examining structural changes in phycobiliproteins upon denaturation with urea. Phycobiliproteins contain a covalently attached chromophore, phycocyanobilin, which is constrained in a planar conformation by the folded protein. Upon denaturation of the protein, the chromophore undergoes a conformational change, leading to a significant alteration of the absorption spectrum. By measuring the absorbance at 625 nm as a function of urea concentration, the free energy of unfolding can be determined. Students determine the dihedral angles in the chromophore and map the contacts between protein and chromophore using Protein Explorer, a structure visualization program freely available on the Internet. The change in absorption wavelength can be related to the difference between the LUMO and HOMO energies, obtained using PC Spartan Pro, for the chromophore in the folded and unfolded phycobiliprotein. This experiment could be used in a physical chemistry class in a curriculum that integrates biochemistry throughout the course work as well as in a traditional biochemistry course. Featured on the Cover

  20. The Thermodynamic Machinery of Life

    CERN Document Server

    Kurzynski, Michal

    2006-01-01

    Living organisms are open thermodynamic systems whose functional structure has developed and been kinetically frozen during the historical process of biological evolution. A thermodynamics of both nonequilibrium and complex systems is needed for their description. In this book, the foundations of such a thermodynamics are presented. Biological processes at the cellular level are considered as coupled chemical reactions and transport processes across internal and the cytoplasmic membrane. All these processes are catalyzed by specific enzymes hence the kinetics of enzymatic catalysis and its control are described here in detail. The coupling of several processes through a common enzyme is considered in the context of free energy or signal transduction. Special attention is paid to evidence for a rich stochastic internal dynamics of native proteins and its possible role in the control of enzyme activity and in the action of biological molecular machines.

  1. Thermodynamics a complete undergraduate course

    CERN Document Server

    Steane, Andrew M

    2016-01-01

    This is an undergraduate textbook in thermodynamics—the science of heat, work, temperature, and entropy. The text presents thermodynamics in and of itself, as an elegant and powerful set of ideas and methods. These methods open the way to understanding a very wide range of phenomena in physics, chemistry, engineering, and biology. Starting out from an introduction of concepts at first year undergraduate level, the roles of temperature, internal energy, and entropy are explained via the laws of thermodynamics. The text employs a combination of examples, exercises, and careful discussion, with a view to conveying the feel of the subject as well as avoiding common misunderstandings. The Feynman–Smuluchowski ratchet, Szilard’s engine, and Maxwell’s daemon are used to elucidate entropy and the second law. Free energy and thermodynamic potentials are discussed at length, with applications to solids as well as fluids and flow processes. Thermal radiation is discussed, and the main ideas significant to global...

  2. Thermodynamics for dummies

    CERN Document Server

    Pauken, Mike

    2011-01-01

    Take some heat off the complexity of thermodynamics Does the mere thought of thermodynamics make you sweat? It doesn't have to! This hands-on guide helps you score your highest in a thermodynamics course by offering easily understood, plain-English explanations of how energy is used in things like automobiles, airplanes, air conditioners, and electric power plants. Thermodynamics 101 - take a look at some examples of both natural and man-made thermodynamic systems and get a handle on how energy can be used to perform work Turn up the heat - discover how to use the firs

  3. Introduction to applied thermodynamics

    CERN Document Server

    Helsdon, R M; Walker, G E

    1965-01-01

    Introduction to Applied Thermodynamics is an introductory text on applied thermodynamics and covers topics ranging from energy and temperature to reversibility and entropy, the first and second laws of thermodynamics, and the properties of ideal gases. Standard air cycles and the thermodynamic properties of pure substances are also discussed, together with gas compressors, combustion, and psychrometry. This volume is comprised of 16 chapters and begins with an overview of the concept of energy as well as the macroscopic and molecular approaches to thermodynamics. The following chapters focus o

  4. Twenty lectures on thermodynamics

    CERN Document Server

    Buchdahl, H A

    2013-01-01

    Twenty Lectures on Thermodynamics is a course of lectures, parts of which the author has given various times over the last few years. The book gives the readers a bird's eye view of phenomenological and statistical thermodynamics. The book covers many areas in thermodynamics such as states and transition; adiabatic isolation; irreversibility; the first, second, third and Zeroth laws of thermodynamics; entropy and entropy law; the idea of the application of thermodynamics; pseudo-states; the quantum-static al canonical and grand canonical ensembles; and semi-classical gaseous systems. The text

  5. The unfolding/denaturation of immunogammaglobulin of isotype 2b and its F-ab and F-c fragments

    NARCIS (Netherlands)

    Vermeer, AWP; Norde, W; van Amerongen, A

    2000-01-01

    The unfolding and further denaturation of IgG and its F-ab and F-c fragments were studied both on a macroscopic and molecular level, using differential scanning calorimetry and circular dichroism spectroscopy, respectively. It was shown that the structural integrity of the F-ab and F-c units was ret

  6. The angiopoietin-like protein ANGPTL4 catalyzes unfolding of the hydrolase domain in lipoprotein lipase and the endothelial membrane protein GPIHBP1 counteracts this unfolding

    DEFF Research Database (Denmark)

    Mysling, Simon; Kristensen, Kristian Kølby; Larsson, Mikael

    2016-01-01

    Lipoprotein lipase (LPL) undergoes spontaneous inactivation via global unfolding and this unfolding is prevented by GPIHBP1 (Mysling et al., 2016). We now show: (1) that ANGPTL4 inactivates LPL by catalyzing the unfolding of its hydrolase domain; (2) that binding to GPIHBP1 renders LPL largely...

  7. Thermodynamic study of yeast phosphoglycerate kinase.

    Science.gov (United States)

    Hu, C Q; Sturtevant, J M

    1987-01-13

    Enthalpies of binding of MgADP, MgATP, and 3-phosphoglycerate to yeast phosphoglycerate kinase have been determined by flow calorimetry at 9.95-32.00 degrees C. Combination of these data with published dissociation constants [Scopes, R.K. (1978) Eur. J. Biochem. 91, 119-129] yielded the following thermodynamic parameters for the binding of 3-phosphoglycerate at 25 degrees C: delta Go = -6.76 +/- 0.11 kcal mol-1, delta H = 3.74 +/- 0.08 kcal mol-1, delta So = 35.2 +/- 0.6 cal K-1 mol-1, and delta Cp = 0.12 +/- 0.32 kcal K-1 mol-1. The thermal unfolding of phosphoglycerate kinase in the absence and presence of the ligands listed above was studied by differential scanning calorimetry. The temperature of half-completion, t 1/2, of the denaturation and the denaturational enthalpy are increased by the binding of the ligands, the increase in t 1/2 being a manifestation of Le Chatelier's principle and that in enthalpy reflecting the enthalpy of dissociation of the ligand. Only one denaturational peak was observed under all conditions, and in contrast with the case of yeast hexokinase [Takahashi, K., Casey, J.L., & Sturtevant, J.M. (1981) Biochemistry 20, 4693-4697], no definitive evidence for the unfolding of more than one domain was obtained.

  8. Rational extended thermodynamics

    CERN Document Server

    Müller, Ingo

    1998-01-01

    Ordinary thermodynamics provides reliable results when the thermodynamic fields are smooth, in the sense that there are no steep gradients and no rapid changes. In fluids and gases this is the domain of the equations of Navier-Stokes and Fourier. Extended thermodynamics becomes relevant for rapidly varying and strongly inhomogeneous processes. Thus the propagation of high­ frequency waves, and the shape of shock waves, and the regression of small-scale fluctuation are governed by extended thermodynamics. The field equations of ordinary thermodynamics are parabolic while extended thermodynamics is governed by hyperbolic systems. The main ingredients of extended thermodynamics are • field equations of balance type, • constitutive quantities depending on the present local state and • entropy as a concave function of the state variables. This set of assumptions leads to first order quasi-linear symmetric hyperbolic systems of field equations; it guarantees the well-posedness of initial value problems and f...

  9. Crystal structures of highly simplified BPTIs provide insights into hydration-driven increase of unfolding enthalpy

    Science.gov (United States)

    Islam, Mohammad Monirul; Yohda, Masafumi; Kidokoro, Shun-ichi; Kuroda, Yutaka

    2017-01-01

    We report a thermodynamic and structural analysis of six extensively simplified bovine pancreatic trypsin inhibitor (BPTI) variants containing 19–24 alanines out of 58 residues. Differential scanning calorimetry indicated a two-state thermal unfolding, typical of a native protein with densely packed interior. Surprisingly, increasing the number of alanines induced enthalpy stabilization, which was however over-compensated by entropy destabilization. X-ray crystallography indicated that the alanine substitutions caused the recruitment of novel water molecules facilitating the formation of protein–water hydrogen bonds and improving the hydration shells around the alanine’s methyl groups, both of which presumably contributed to enthalpy stabilization. There was a strong correlation between the number of water molecules and the thermodynamic parameters. Overall, our results demonstrate that, in contrast to our initial expectation, a protein sequence in which over 40% of the residues are alanines can retain a densely packed structure and undergo thermal denaturation with a large enthalpy change, mainly contributed by hydration. PMID:28266637

  10. Unfolding simulations of holomyoglobin from four mammals: identification of intermediates and β-sheet formation from partially unfolded states.

    Directory of Open Access Journals (Sweden)

    Pouria Dasmeh

    Full Text Available Myoglobin (Mb is a centrally important, widely studied mammalian protein. While much work has investigated multi-step unfolding of apoMb using acid or denaturant, holomyoglobin unfolding is poorly understood despite its biological relevance. We present here the first systematic unfolding simulations of holoMb and the first comparative study of unfolding of protein orthologs from different species (sperm whale, pig, horse, and harbor seal. We also provide new interpretations of experimental mean molecular ellipticities of myoglobin intermediates, notably correcting for random coil and number of helices in intermediates. The simulated holoproteins at 310 K displayed structures and dynamics in agreement with crystal structures (R g ~1.48-1.51 nm, helicity ~75%. At 400 K, heme was not lost, but some helix loss was observed in pig and horse, suggesting that these helices are less stable in terrestrial species. At 500 K, heme was lost within 1.0-3.7 ns. All four proteins displayed exponentially decaying helix structure within 20 ns. The C- and F-helices were lost quickly in all cases. Heme delayed helix loss, and sperm whale myoglobin exhibited highest retention of heme and D/E helices. Persistence of conformation (RMSD, secondary structure, and ellipticity between 2-11 ns was interpreted as intermediates of holoMb unfolding in all four species. The intermediates resemble those of apoMb notably in A and H helices, but differ substantially in the D-, E- and F-helices, which interact with heme. The identified mechanisms cast light on the role of metal/cofactor in poorly understood holoMb unfolding. We also observed β-sheet formation of several myoglobins at 500 K as seen experimentally, occurring after disruption of helices to a partially unfolded, globally disordered state; heme reduced this tendency and sperm-whale did not display any sheet propensity during the simulations.

  11. Unfolding code for neutron spectrometry based on neural nets technology

    Energy Technology Data Exchange (ETDEWEB)

    Ortiz R, J. M.; Vega C, H. R., E-mail: morvymm@yahoo.com.mx [Universidad Autonoma de Zacatecas, Unidad Academica de Ingenieria Electrica, Apdo. Postal 336, 98000 Zacatecas (Mexico)

    2012-10-15

    The most delicate part of neutron spectrometry, is the unfolding process. The derivation of the spectral information is not simple because the unknown is not given directly as a result of the measurements. The drawbacks associated with traditional unfolding procedures have motivated the need of complementary approaches. Novel methods based on Artificial Neural Networks have been widely investigated. In this work, a neutron spectrum unfolding code based on neural nets technology is presented. This unfolding code called Neutron Spectrometry and Dosimetry by means of Artificial Neural Networks was designed in a graphical interface under LabVIEW programming environment. The core of the code is an embedded neural network architecture, previously optimized by the {sup R}obust Design of Artificial Neural Networks Methodology{sup .} The main features of the code are: is easy to use, friendly and intuitive to the user. This code was designed for a Bonner Sphere System based on a {sup 6}Lil(Eu) neutron detector and a response matrix expressed in 60 energy bins taken from an International Atomic Energy Agency compilation. The main feature of the code is that as entrance data, only seven rate counts measurement with a Bonner spheres spectrometer are required for simultaneously unfold the 60 energy bins of the neutron spectrum and to calculate 15 dosimetric quantities, for radiation protection porpoises. This code generates a full report in html format with all relevant information. (Author)

  12. A simple conductometric method for trace level determination of brilliant green in water based on β-cyclodextrin and silver nitrate and determination of their thermodynamic parameters

    Directory of Open Access Journals (Sweden)

    Roya Mohammad Zadeh Kakhki

    2014-12-01

    Full Text Available A gravimetric and complexometric titration method based on conductometric technique is presented for the quantitative determination of brilliant green (BG in water. The equilibrium constants and the thermodynamic parameters for the complex formation of β-cyclodextrin (β-CD with brilliant green (BG and precipitation of silver nitrate with BG have been determined by conductivity measurements in water. The results suggest that stable 1:1 complex is formed between BG and β-cyclodextrin and the thermodynamic parameters (ΔHc°,ΔSc° for this complexation reaction have been determined from temperature dependence of the stability constant using the van’t Hoff plots. Based on the obtained results, the conductometric method for the determination of BG in the presence of β-CD at 25 °C was developed in the range of 10−8–10−3 molL−1 and with AgNO3 is 10−3–10−5 molL−1.

  13. Characterization of ionizing radiation-induced unfolded protein response in human vascular endothelial cells

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Eun Ju; Lee, Yoon Jin; Kang, Seong Man [Laboratory of Radiation Effect, Korea Institute of Radiological and Medical Sciences, Seoul (Korea, Republic of)

    2013-04-15

    Misfolded or unfolded proteins within the endoplasmic reticulum (ER stress), viral infection, or amino acid deprivation induce eukaryotic translation initiation factor 2α phosphorylation (eIF2α) in eukaryotic cells, repressing global protein synthesis coincident with preferential translation of activating transcription factor 4 (ATF4). ATF4 is a transcriptional activator of genes involved in amino acid metabolism, cellular redox homeostasis, and regulation of apoptosis. When the eIF2α/ATF4 pathway is initiated by ER stress, the pathway is referred toas the unfolded protein response (UPR). In addition to DNA, proteins may be initial and important targets of ionizing radiation (IR), and the damaged protein can trigger ER stress pathway. Recent investigations suggested that IR induces ER stress followed by UPR in various cell types including intestinal epithelial cells. We conducted this study to determine whether IR can activate UPR in human vascular endothelial cells. Our data have shown that IR increased PERK-dependent eIF2α phosphorylation accompanied by induction in ATF4 protein levels in human vascular endothelial cells without alterations in expressions of XBP-1s and GRP78. Based on these data, we suggest that IR selectively activates PERK branch of unfolded protein response in human vascular endothelial cells.

  14. Single-molecule force spectroscopy reveals the individual mechanical unfolding pathways of a surface layer protein.

    Science.gov (United States)

    Horejs, Christine; Ristl, Robin; Tscheliessnig, Rupert; Sleytr, Uwe B; Pum, Dietmar

    2011-08-05

    Surface layers (S-layers) represent an almost universal feature of archaeal cell envelopes and are probably the most abundant bacterial cell proteins. S-layers are monomolecular crystalline structures of single protein or glycoprotein monomers that completely cover the cell surface during all stages of the cell growth cycle, thereby performing their intrinsic function under a constant intra- and intermolecular mechanical stress. In gram-positive bacteria, the individual S-layer proteins are anchored by a specific binding mechanism to polysaccharides (secondary cell wall polymers) that are linked to the underlying peptidoglycan layer. In this work, atomic force microscopy-based single-molecule force spectroscopy and a polyprotein approach are used to study the individual mechanical unfolding pathways of an S-layer protein. We uncover complex unfolding pathways involving the consecutive unfolding of structural intermediates, where a mechanical stability of 87 pN is revealed. Different initial extensibilities allow the hypothesis that S-layer proteins adapt highly stable, mechanically resilient conformations that are not extensible under the presence of a pulling force. Interestingly, a change of the unfolding pathway is observed when individual S-layer proteins interact with secondary cell wall polymers, which is a direct signature of a conformational change induced by the ligand. Moreover, the mechanical stability increases up to 110 pN. This work demonstrates that single-molecule force spectroscopy offers a powerful tool to detect subtle changes in the structure of an individual protein upon binding of a ligand and constitutes the first conformational study of surface layer proteins at the single-molecule level.

  15. Dewetting-induced globule-coil transitions of model polymers and possible implications high-temperature and low-pressure unfolding of proteins.

    Science.gov (United States)

    Sumi, Tomonari; Imazaki, Nobuyuki; Sekino, Hideo

    2010-04-28

    A thermodynamic analysis of high-temperature and low-pressure unfolding of proteins using a coarse-grained multiscale simulation combined with a liquid-state density-functional theory is presented. In this study, a hydrophobic polymer chain is employed as a probe molecule for investigating qualitative changes in a hydration free energy surface acting on proteins with changes in temperature and pressure. When water is heated so that its vapor pressure is equal to the atmospheric pressure, it boils. Long-ranged dewetting or drying caused by a hydrophobic planar wall and a large hydrophobic solute surface is significantly enhanced as it approaches the liquid-vapor coexistence curve of water. In this study, we demonstrate that high-temperature and low-pressure unfolding of the polymer chain is interpreted as dewetting-induced unfolding that occurs as it approaches the liquid-vapor coexistence. The unfolding of proteins due to high-temperature and low-pressure denaturation enhances the long-ranged dewetting or drying around them. The long-ranged dewetting phenomenon is considered to be originating from positive changes in both volume and entropy due to the high-temperature and low-pressure denaturation of the proteins.

  16. Large negative numbers in number theory, thermodynamics, information theory, and human thermodynamics

    Science.gov (United States)

    Maslov, V. P.

    2016-10-01

    We show how the abstract analytic number theory of Maier, Postnikov, and others can be extended to include negative numbers and apply this to thermodynamics, information theory, and human thermodynamics. In particular, we introduce a certain large number N 0 on the "zero level" with a high multiplicity number q i ≫ 1 related to the physical concept of gap in the spectrum. We introduce a general notion of "hole," similar to the Dirac hole in physics, in the theory. We also consider analogs of thermodynamical notions in human thermodynamics, in particular, in connection with the role of the individual in history.

  17. Human pescadillo induces large-scale chromatin unfolding

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hao; FANG Yan; HUANG Cuifen; YANG Xiao; YE Qinong

    2005-01-01

    The human pescadillo gene encodes a protein with a BRCT domain. Pescadillo plays an important role in DNA synthesis, cell proliferation and transformation. Since BRCT domains have been shown to induce chromatin large-scale unfolding, we tested the role of Pescadillo in regulation of large-scale chromatin unfolding. To this end, we isolated the coding region of Pescadillo from human mammary MCF10A cells. Compared with the reported sequence, the isolated Pescadillo contains in-frame deletion from amino acid 580 to 582. Targeting the Pescadillo to an amplified, lac operator-containing chromosome region in the mammalian genome results in large-scale chromatin decondensation. This unfolding activity maps to the BRCT domain of Pescadillo. These data provide a new clue to understanding the vital role of Pescadillo.

  18. An empirical study into the theory of unidimensional unfolding.

    Science.gov (United States)

    Kyngdon, Andrew

    2006-01-01

    This article is the second in the series on unidimensional unfolding. Its aim was to test the quantitative component of Coombs's (1964) theory via an empirical application to subjective control in gambling behavior (Dickerson and Baron, 2000). It was found that approximately 96% of judgments upon bilateral stimulus pairs were as predicted by the theory of unidimensional unfolding. The double cancellation axiom of the theory of axiomatic conjoint measurement (ACM) (Krantz, Luce, Suppes and Tversky, 1971) was satisfied by the interstimulus midpoint order obtained from these judgments. These results supported previous unfolding studies on attitudes (Johnson, 2001; Michell, 1994). Exponential and linear relationships were found between the transformed scaling solutions of Coombs's (1964) theory and the SHCMpp (Andrich, 1995). The implications of these results were discussed. Additionally, the article presented both a formal theory of item construction (Michell, 1994) and an accessible demonstration of the Goode's algorithm scaling procedure.

  19. [Unfolding item response model using best-worst scaling].

    Science.gov (United States)

    Ikehara, Kazuya

    2015-02-01

    In attitude measurement and sensory tests, the unfolding model is typically used. In this model, response probability is formulated by the distance between the person and the stimulus. In this study, we proposed an unfolding item response model using best-worst scaling (BWU model), in which a person chooses the best and worst stimulus among repeatedly presented subsets of stimuli. We also formulated an unfolding model using best scaling (BU model), and compared the accuracy of estimates between the BU and BWU models. A simulation experiment showed that the BWU modell performed much better than the BU model in terms of bias and root mean square errors of estimates. With reference to Usami (2011), the proposed models were apllied to actual data to measure attitudes toward tardiness. Results indicated high similarity between stimuli estimates generated with the proposed models and those of Usami (2011).

  20. Protein unfolding under force: crack propagation in a network.

    Science.gov (United States)

    de Graff, Adam M R; Shannon, Gareth; Farrell, Daniel W; Williams, Philip M; Thorpe, M F

    2011-08-03

    The mechanical unfolding of a set of 12 proteins with diverse topologies is investigated using an all-atom constraint-based model. Proteins are represented as polypeptides cross-linked by hydrogen bonds, salt bridges, and hydrophobic contacts, each modeled as a harmonic inequality constraint capable of supporting a finite load before breaking. Stereochemically acceptable unfolding pathways are generated by minimally overloading the network in an iterative fashion, analogous to crack propagation in solids. By comparing the pathways to those from molecular dynamics simulations and intermediates identified from experiment, it is demonstrated that the dominant unfolding pathways for 9 of the 12 proteins studied are well described by crack propagation in a network. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  1. An introduction to equilibrium thermodynamics

    CERN Document Server

    Morrill, Bernard; Hartnett, James P; Hughes, William F

    1973-01-01

    An Introduction to Equilibrium Thermodynamics discusses classical thermodynamics and irreversible thermodynamics. It introduces the laws of thermodynamics and the connection between statistical concepts and observable macroscopic properties of a thermodynamic system. Chapter 1 discusses the first law of thermodynamics while Chapters 2 through 4 deal with statistical concepts. The succeeding chapters describe the link between entropy and the reversible heat process concept of entropy; the second law of thermodynamics; Legendre transformations and Jacobian algebra. Finally, Chapter 10 provides a

  2. Using the unfolding case study in midwifery education.

    Science.gov (United States)

    Carr, Katherine Camacho

    2015-01-01

    One of the challenges in teaching clinicians is helping health care provider students, including midwives, develop the critical thinking and clinical decision-making skills needed for various situations encountered in practice. Health care provider students need to master the required core knowledge and skills but also need to assess, analyze, judge, decide on action, act, and evaluate their actions. Lecture-heavy classroom teaching, which is usually delivered separately from clinical experiences in health care education, focuses on knowledge acquisition, often leaving knowledge application to trial and error. Case studies are commonly used by faculty with a problem-based learning approach, which is more analytic but sometimes static. The unfolding case study presents students with a patient scenario that changes over time and allows for discussion; lecture points as needed; and decision making as the situation or condition changes, reflecting what happens in real-life clinical practice. The use of the unfolding case study moves health care provider education from fact-based lecturing to situation-based discussion and decision making as a person's condition or situation changes. Use of the unfolding case facilitates collaborative learning, covers necessary content, and assists students to think beyond the facts and use their clinical imagination. Unfolding case studies require students to begin to grasp the nature of a clinical situation and adjust interventions as the clinical situation unfolds. Steps in developing and using an unfolding case study for midwifery students are presented, including 2 examples. This article is part of a special series of articles that address midwifery innovations in clinical practice, education, interprofessional collaboration, health policy, and global health.

  3. Ethanol cellular defense induce unfolded protein response in yeast

    Directory of Open Access Journals (Sweden)

    Elisabet eNavarro-Tapia

    2016-02-01

    Full Text Available Ethanol is a valuable industrial product and a common metabolite used by many cell types. However, this molecule produces high levels of cytotoxicity affecting cellular performance at several levels. In the presence of ethanol, cells must adjust some of their components, such as the membrane lipids to maintain homeostasis. In the case of microorganism as Saccharomyces cerevisiae, ethanol is one of the principal products of their metabolism and is the main stress factor during fermentation. Although many efforts have been made, mechanisms of ethanol tolerance are not fully understood and very little evidence is available to date for specific signaling by ethanol in the cell. This work studied two Saccharomyces cerevisiae strains, CECT10094 and Temohaya-MI26, isolated from flor wine and agave fermentation (a traditional fermentation from Mexico respectively, which differ in ethanol tolerance, in order to understand the molecular mechanisms underlying the ethanol stress response and the reasons for different ethanol tolerance. The transcriptome was analyzed after ethanol stress and, among others, an increased activation of genes related with the unfolded protein response (UPR and its transcription factor, Hac1p, was observed in the tolerant strain CECT10094. We observed that this strain also resist more UPR agents than Temohaya-MI26 and the UPR-ethanol stress correlation was corroborated observing growth of 15 more strains and discarding UPR correlation with other stresses as thermal or oxidative stress. Furthermore, higher activation of UPR pathway in the tolerant strain CECT10094 was observed using a UPR mCherry reporter. Finally, we observed UPR activation in response to ethanol stress in other S. cerevisiae ethanol tolerant strains as the wine strains T73 and EC1118. This work demonstrates that the UPR pathway is activated under ethanol stress occurring in a standard fermentation and links this response to an enhanced ethanol tolerance. Thus

  4. Flat Zipper-Unfolding Pairs for Platonic Solids

    CERN Document Server

    O'Rourke, Joseph

    2010-01-01

    We show that four of the five Platonic solids' surfaces may be cut open with a Hamiltonian path along edges and unfolded to a polygonal net each of which can "zipper-refold" to a flat doubly covered parallelogram, forming a rather compact representation of the surface. Thus these regular polyhedra have particular flat "zipper pairs." No such zipper pair exists for a dodecahedron, whose Hamiltonian unfoldings are "zip-rigid." This report is primarily an inventory of the possibilities, and raises more questions than it answers.

  5. The laws of thermodynamics a very short introduction

    CERN Document Server

    Atkins, Peter

    2010-01-01

    From the sudden expansion of a cloud of gas or the cooling of a hot metal, to the unfolding of a thought in our minds and even the course of life itself, everything is governed by the four Laws of Thermodynamics. These laws specify the nature of 'energy' and 'temperature', and are soon revealed to reach out and define the arrow of time itself: why things change and why death must come. In this Very Short Introduction Peter Atkins explains the basis and deeper implications of each law, highlighting their relevance in everyday examples. Using the minimum of mathematics, he introduces concepts su

  6. Thermodynamic Stability of Wormholes

    CERN Document Server

    Sajadi, S N

    2016-01-01

    In the context of GR, we study the thermodynamic stability of evolving Lorentzian wormholes at the apparent horizon. The average pressure of the anisotrropic components is considered as the pressure of the wormhole. According to the requirements of stable equilibrium in conventional thermodynamics, we calculate the heat capacity at constant pressure and Gibbs free energy and analyze the local and global thermodynamic stability of the wormhole.

  7. Stochastic Thermodynamics of Learning

    Science.gov (United States)

    Goldt, Sebastian; Seifert, Udo

    2017-01-01

    Virtually every organism gathers information about its noisy environment and builds models from those data, mostly using neural networks. Here, we use stochastic thermodynamics to analyze the learning of a classification rule by a neural network. We show that the information acquired by the network is bounded by the thermodynamic cost of learning and introduce a learning efficiency η ≤1 . We discuss the conditions for optimal learning and analyze Hebbian learning in the thermodynamic limit.

  8. Stochastic Thermodynamics of Learning

    CERN Document Server

    Goldt, Sebastian

    2016-01-01

    Virtually every organism gathers information about its noisy environment and builds models from that data, mostly using neural networks. Here, we use stochastic thermodynamics to analyse the learning of a classification rule by a neural network. We show that the information acquired by the network is bounded by the thermodynamic cost of learning and introduce a learning efficiency $\\eta\\le1$. We discuss the conditions for optimal learning and analyse Hebbian learning in the thermodynamic limit.

  9. Methods of thermodynamics

    CERN Document Server

    Reiss, Howard

    1997-01-01

    Since there is no shortage of excellent general books on elementary thermodynamics, this book takes a different approach, focusing attention on the problem areas of understanding of concept and especially on the overwhelming but usually hidden role of ""constraints"" in thermodynamics, as well as on the lucid exposition of the significance, construction, and use (in the case of arbitrary systems) of the thermodynamic potential. It will be especially useful as an auxiliary text to be used along with any standard treatment.Unlike some texts, Methods of Thermodynamics does not use statistical m

  10. Simulating metabolism with statistical thermodynamics.

    Directory of Open Access Journals (Sweden)

    William R Cannon

    Full Text Available New methods are needed for large scale modeling of metabolism that predict metabolite levels and characterize the thermodynamics of individual reactions and pathways. Current approaches use either kinetic simulations, which are difficult to extend to large networks of reactions because of the need for rate constants, or flux-based methods, which have a large number of feasible solutions because they are unconstrained by the law of mass action. This report presents an alternative modeling approach based on statistical thermodynamics. The principles of this approach are demonstrated using a simple set of coupled reactions, and then the system is characterized with respect to the changes in energy, entropy, free energy, and entropy production. Finally, the physical and biochemical insights that this approach can provide for metabolism are demonstrated by application to the tricarboxylic acid (TCA cycle of Escherichia coli. The reaction and pathway thermodynamics are evaluated and predictions are made regarding changes in concentration of TCA cycle intermediates due to 10- and 100-fold changes in the ratio of NAD+:NADH concentrations. Finally, the assumptions and caveats regarding the use of statistical thermodynamics to model non-equilibrium reactions are discussed.

  11. Simulating metabolism with statistical thermodynamics.

    Science.gov (United States)

    Cannon, William R

    2014-01-01

    New methods are needed for large scale modeling of metabolism that predict metabolite levels and characterize the thermodynamics of individual reactions and pathways. Current approaches use either kinetic simulations, which are difficult to extend to large networks of reactions because of the need for rate constants, or flux-based methods, which have a large number of feasible solutions because they are unconstrained by the law of mass action. This report presents an alternative modeling approach based on statistical thermodynamics. The principles of this approach are demonstrated using a simple set of coupled reactions, and then the system is characterized with respect to the changes in energy, entropy, free energy, and entropy production. Finally, the physical and biochemical insights that this approach can provide for metabolism are demonstrated by application to the tricarboxylic acid (TCA) cycle of Escherichia coli. The reaction and pathway thermodynamics are evaluated and predictions are made regarding changes in concentration of TCA cycle intermediates due to 10- and 100-fold changes in the ratio of NAD+:NADH concentrations. Finally, the assumptions and caveats regarding the use of statistical thermodynamics to model non-equilibrium reactions are discussed.

  12. Entropy reduction in unfolded peptides (and proteins) due to conformational preferences of amino acid residues.

    Science.gov (United States)

    Schweitzer-Stenner, Reinhard; Toal, Siobhan E

    2014-11-07

    As established by several groups over the last 20 years, amino acid residues in unfolded peptides and proteins do not exhibit the unspecific random distribution as assumed by the classical random coil model. Individual amino acid residues in small peptides were found to exhibit different conformational preferences. Here, we utilize recently obtained conformational distributions of guest amino acid residues in GxG peptides to estimate their conformational entropy, which we find to be significantly lower than the entropy of an assumed random coil like distribution. Only at high temperature do backbone entropies approach random coil like values. We utilized the obtained backbone entropies of the investigated amino acid residues to estimate the loss of conformational entropy caused by a coil → helix transition and identified two subsets of amino acid residues for which the thus calculated entropy losses correlate well with the respective Gibbs energy of helix formation obtained for alanine based host-guest systems. Calculated and experimentally derived entropic losses were found to be in good agreement. For most of the amino acid residues investigated entropic losses derived from our GxG distributions correlate very well with corresponding values recently obtained from MD simulations biased by conformational propensities derived from truncated coil libraries. Both, conformational entropy and the entropy of solvation exhibit a strong, residue specific temperature dependence, which can be expected to substantially affect the stability of unfolded states. Altogether, our results provide strong evidence for the notion that conformational preferences of amino acid residues matter with regard to the thermodynamics of peptide and protein folding.

  13. Thermodynamic and Quantum Thermodynamic Analyses of Brownian Movement

    OpenAIRE

    Gyftopoulos, Elias P.

    2006-01-01

    Thermodynamic and quantum thermodynamic analyses of Brownian movement of a solvent and a colloid passing through neutral thermodynamic equilibrium states only. It is shown that Brownian motors and E. coli do not represent Brownian movement.

  14. Thermal stability of pepsin: A predictive thermodynamic model of a multi-domain protein

    Directory of Open Access Journals (Sweden)

    Ali Asghar Rastegari

    2017-03-01

    Full Text Available Pepsin is generally used in the preparation of F(ab2 fragments from antibodies. The antibodies that are one of the largest and fastest growing categories of bio- pharmaceutical candidates. Differential scanning calorimetric is principally suitable method to follow the energetics of a multi-domain, fragment to perform a more exhaustive description of the thermodynamics in an associating system. The thermodynamical models of analysis include the construction of a simultaneous fitting of a theoretical expression. The expression depending on the equilibrium unfolding data from multimeric proteins that have a two-state monomer. The aim of the present study is considering the DSC data in connection with pepsin going through reversible thermal denaturation. Afterwards, we calculate the homology modeling identification of pepsin in complex multi-domain families with varied domain architectures. In order to analyze the DSC data, the thermal denaturation of multimer proteins were considered, the “two independent two-state sequential transitions with domains dissociation model” was introduced by using of the effective ΔG concept. The reversible unfolding of the protein description was followed by the two-state transition quantities which is a slower irreversible process of aggregation. The protein unfolding is best described by two non-ideal transitions, suggesting the presence of unfolding intermediates. These evaluations are also applicable for high throughput investigation of protein stability.

  15. Conformational unfolding in the N-terminal region of ribonuclease A detected by nonradiative energy transfer.

    Science.gov (United States)

    McWherter, C A; Haas, E; Leed, A R; Scheraga, H A

    1986-04-22

    Unfolding in the N-terminal region of RNase A was studied by the nonradiative energy-transfer technique. RNase A was labeled with a nonfluorescent acceptor (2,4-dinitrophenyl) on the alpha-amino group and a fluorescent donor (ethylenediamine monoamide of 2-naphthoxyacetic acid) on a carboxyl group in the vicinity of residue 50 (75% at Glu-49 and 25% at Asp-53). The distribution of donor labeling sites does not affect the results of this study since they are close in both the sequence and the three-dimensional structure. The sites of labeling were determined by peptide mapping. The derivatives possessed full enzymatic activity and underwent reversible thermal transitions. However, there were some quantitative differences in the thermodynamic parameters. When the carboxyl groups were masked, there was a 5 degrees C lowering of the melting temperature at pH 2 and 4, and no significant change in delta H(Tm). Labeling of the alpha-amino group had no effect on the melting temperature or delta H(Tm) at pH 2 but did result in a dramatic decrease in delta H(Tm) of the unfolding reaction at pH 4. The melting temperature did not change appreciably at pH 4, indicating that an enthalpy/entropy compensation had occurred. The efficiencies of energy transfer determined with both fluorescence intensity and lifetime measurements were in reasonably good agreement. The transfer efficiency dropped from about 60% under folding conditions to roughly 20% when the derivatives were unfolded with disulfide bonds intact and was further reduced to 5% when the disulfide bonds were reduced. The interprobe separation distance was estimated to be 35 +/- 2 A under folding conditions. The contribution to the interprobe distance resulting from the finite size of the probes was treated by using simple geometric considerations and a rotational isomeric state model of the donor probe linkage. With this model, the estimated average interprobe distance of 36 A is in excellent agreement with the

  16. Computerized Classification Testing under the Generalized Graded Unfolding Model

    Science.gov (United States)

    Wang, Wen-Chung; Liu, Chen-Wei

    2011-01-01

    The generalized graded unfolding model (GGUM) has been recently developed to describe item responses to Likert items (agree-disagree) in attitude measurement. In this study, the authors (a) developed two item selection methods in computerized classification testing under the GGUM, the current estimate/ability confidence interval method and the cut…

  17. Perceived Helpfulness and Unfolding Processes in Body-Oriented ...

    African Journals Online (AJOL)

    Christopher R Stones

    Research specific to this approach is being conducted by. Price .... the therapy as well as the unfolding of the therapeutic process (Elliott et al., ... benefits of increased emotional awareness, a more ..... described this as gaining the appreciation that it was ..... The tears I felt welling up-in gratitude toward a connection with.

  18. An Analysis of Lexical Cohesion in"How Empathy Unfolds"

    Institute of Scientific and Technical Information of China (English)

    朱玲霞

    2016-01-01

    This thesis aims to analyze the lexical cohesion in the text"How Empathy Unfolds" in the new standard college English textbook. This paper focuses on four kinds of lexical cohesive devices: repetition, synonymy, hyponymy and collocation. It is expected that these analyses can help readers gain a better and deeper comprehension of the structure and content of the text.

  19. Light-triggered β-hairpin folding and unfolding

    NARCIS (Netherlands)

    Schrader, Tobias E.; Schreier, Wolfgang J.; Cordes, Thorben; Koller, Florian O.; Babitzki, Galina; Denschlag, Robert; Renner, Christian; Löweneck, Markus; Dong, Shou-Liang; Moroder, Luis; Tavan, Paul; Zinth, Wolfgang

    2007-01-01

    A light-switchable peptide is transformed with ultrashort pulses from a β-hairpin to an unfolded hydrophobic cluster and vice versa. The structural changes are monitored by mid-IR probing. Instantaneous normal mode analysis with a Hamiltonian combining density functional theory with molecular

  20. High-pressure SANS and fluorescence unfolding study of calmodulin.

    Science.gov (United States)

    Gibrat, Gabriel; Hoa, Gaston Hui Bon; Craescu, Constantin T; Assairi, Liliane; Blouquit, Yves; Annighöfer, Burkhard; May, Roland P; Bellissent-Funel, Marie-Claire

    2014-09-01

    Apo-calmodulin, a small soluble mainly α protein, is a calcium-dependent protein activator. Calcium binding affects the calmodulin conformation but also its stability. Calcium free form unfolds between 40 and 80°C, whereas the calcium-saturated form is stable up to temperatures as high as 100°C, forbidding comparison of the thermal unfolding pathways of the two forms. Thus, this paper focuses especially on the conformation of pressure-induced unfolding states of both forms of calmodulin, by combining small-angle neutron scattering (SANS) with biophysical techniques such as tyrosines and ANS fluorescence. In contrast to heat denaturation (Gibrat et al., BBA, 2012), the pressure denaturation of calmodulin is reversible up to pressures of 3000bar (300MPa). A pressure-induced compact intermediate state has been found for the two calmodulin forms, but their unfolding pathways are different. A domain compaction and an increase of the ANS fluorescence of holo form have been evidenced. On the contrary, a domain dilatation and an ANS fluorescence decrease have been found for the apo form. The pressure induced an increase of the interdomain distance for both calmodulin forms, suggesting that the central linker of calmodulin is flexible in solution.

  1. Mathematical Knowledge for Teaching and Task Unfolding: An Exploratory Study

    Science.gov (United States)

    Charalambous, Charalambos Y.

    2010-01-01

    Although teachers' knowledge is thought to contribute to the selection and implementation of mathematical tasks, empirical evidence supporting this claim is scarce. To investigate this relationship and understand its nature, this exploratory study examines the unfolding of tasks in a series of lessons led by 2 elementary school teachers who…

  2. Effect of antimicrobial preservatives on partial protein unfolding and aggregation.

    Science.gov (United States)

    Hutchings, Regina L; Singh, Surinder M; Cabello-Villegas, Javier; Mallela, Krishna M G

    2013-02-01

    One-third of protein formulations are multi-dose. These require antimicrobial preservatives (APs); however, some APs have been shown to cause protein aggregation. Our previous work on a model protein cytochrome c indicated that partial protein unfolding, rather than complete unfolding, triggers aggregation. Here, we examined the relative strength of five commonly used APs on such unfolding and aggregation, and explored whether stabilizing the aggregation 'hot-spot' reduces such aggregation. All APs induced protein aggregation in the order m-cresol > phenol > benzyl alcohol > phenoxyethanol > chlorobutanol. All these enhanced the partial protein unfolding that includes a local region which was predicted to be the aggregation 'hot-spot'. The extent of destabilization correlated with the extent of aggregation. Further, we show that stabilizing the 'hot-spot' reduces aggregation induced by all five APs. These results indicate that m-cresol causes the most protein aggregation, whereas chlorobutanol causes the least protein aggregation. The same protein region acts as the 'hot-spot' for aggregation induced by different APs, implying that developing strategies to prevent protein aggregation induced by one AP will also work for others.

  3. Lactoperoxidase folding and catalysis relies on the stabilization of the alpha-helix rich core domain: a thermal unfolding study.

    Science.gov (United States)

    Boscolo, Barbara; Leal, Sónia S; Ghibaudi, Elena M; Gomes, Cláudio M

    2007-09-01

    Lactoperoxidase (LPO) belongs to the mammalian peroxidase family and catalyzes the oxidation of halides, pseudo-halides and a number of aromatic substrates at the expense of hydrogen peroxide. Despite the complex physiological role of LPO and its potential involvement in carcinogenic mechanisms, cystic fibrosis and inflammatory processes, little is known on the folding and structural stability of this protein. We have undertaken an investigation of the conformational dynamics and catalytic properties of LPO during thermal unfolding, using complementary biophysical techniques (differential scanning calorimetry, electron spin resonance, optical absorption, fluorescence and circular dichroism spectroscopies) together with biological activity assays. LPO is a particularly stable protein, capable of maintaining catalysis and structural integrity up to a high temperature, undergoing irreversible unfolding at 70 degrees C. We have observed that the first stages of the thermal denaturation involve a minor conformational change occurring at 40 degrees C, possibly at the level of the protein beta-sheets, which nevertheless does not result in an unfolding transition. Only at higher temperature, the protein hydrophobic core, which is rich in alpha-helices, unfolds with concomitant disruption of the catalytic heme pocket and activity loss. Evidences concerning the stabilizing role of the disulfide bridges and the covalently bound heme cofactor are shown and discussed in the context of understanding the structural stability determinants in a relatively large protein.

  4. Heat and thermodynamics

    CERN Document Server

    Brewster, Hilary D

    2009-01-01

    Thermodynamics is an exciting and fascinating subject that deals with energy, which is essential for sustenance of life, and Thermodynamics has long been an essential part of Engineering Curricula all over the world. It has a broad application area ranging from Microscopic Organisms to common Household Appliances, Transportation Vehicles, and Power Generation Systems.

  5. Thermodynamic system drift in protein evolution.

    Directory of Open Access Journals (Sweden)

    Kathryn M Hart

    2014-11-01

    Full Text Available Proteins from thermophiles are generally more thermostable than their mesophilic homologs, but little is known about the evolutionary process driving these differences. Here we attempt to understand how the diverse thermostabilities of bacterial ribonuclease H1 (RNH proteins evolved. RNH proteins from Thermus thermophilus (ttRNH and Escherichia coli (ecRNH share similar structures but differ in melting temperature (T(m by 20 °C. ttRNH's greater stability is caused in part by the presence of residual structure in the unfolded state, which results in a low heat capacity of unfolding (ΔCp relative to ecRNH. We first characterized RNH proteins from a variety of extant bacteria and found that Tm correlates with the species' growth temperatures, consistent with environmental selection for stability. We then used ancestral sequence reconstruction to statistically infer evolutionary intermediates along lineages leading to ecRNH and ttRNH from their common ancestor, which existed approximately 3 billion years ago. Finally, we synthesized and experimentally characterized these intermediates. The shared ancestor has a melting temperature between those of ttRNH and ecRNH; the T(ms of intermediate ancestors along the ttRNH lineage increased gradually over time, while the ecRNH lineage exhibited an abrupt drop in Tm followed by relatively little change. To determine whether the underlying mechanisms for thermostability correlate with the changes in T(m, we measured the thermodynamic basis for stabilization--ΔCp and other thermodynamic parameters--for each of the ancestors. We observed that, while the T(m changes smoothly, the mechanistic basis for stability fluctuates over evolutionary time. Thus, even while overall stability appears to be strongly driven by selection, the proteins explored a wide variety of mechanisms of stabilization, a phenomenon we call "thermodynamic system drift." This suggests that even on lineages with strong selection to increase

  6. Optimization of Cr(VI biosorption onto Aspergillus niger using 3-level Box-Behnken design: Equilibrium, kinetic, thermodynamic and regeneration studies

    Directory of Open Access Journals (Sweden)

    Naba Kumar Mondal

    2017-06-01

    Full Text Available Heavy metal biosorption is an efficient technology for the decontamination of metal from industrial waste water. The present study focused on exploration of Aspergillus niger towards removal of Cr(VI from aqueous solution. The influence of different experimental parameters—initial pH, adsorbent dose, initial concentration, contact time, shaking speed, temperature, and their combined effect during Cr(VI adsorption—was investigated by means of response surface methodology based on four factorial Box–Behnken experimental design. Optimized values of initial Cr(VI concentration, pH, adsorbent dose, and contact time were found as 33.33 mg/L, 4.6, 1.0 g/L, and 48.45 min, respectively. A. niger showed the highest adsorption capacity 11.792 mg/g at initial pH 2.0. Equilibrium data fitted well to the Temkin and Freundlich isotherms. Cr(VI biosorption showed Pseudo-second order rate kinetics. The activation energy of the adsorption was estimated as 2.9 × 10−3 kJ/mol. Thermodynamics properties of the Cr(VI biosorption was spontaneous in nature. Desorption study showed that nearly 94% of the Cr(VI adsorbed on A. niger could be desorbed using 0.5 M EDTA.

  7. Applied chemical engineering thermodynamics

    CERN Document Server

    Tassios, Dimitrios P

    1993-01-01

    Applied Chemical Engineering Thermodynamics provides the undergraduate and graduate student of chemical engineering with the basic knowledge, the methodology and the references he needs to apply it in industrial practice. Thus, in addition to the classical topics of the laws of thermodynamics,pure component and mixture thermodynamic properties as well as phase and chemical equilibria the reader will find: - history of thermodynamics - energy conservation - internmolecular forces and molecular thermodynamics - cubic equations of state - statistical mechanics. A great number of calculated problems with solutions and an appendix with numerous tables of numbers of practical importance are extremely helpful for applied calculations. The computer programs on the included disk help the student to become familiar with the typical methods used in industry for volumetric and vapor-liquid equilibria calculations.

  8. Thermodynamics an engineering approach

    CERN Document Server

    Cengel, Yunus A

    2014-01-01

    Thermodynamics, An Engineering Approach, eighth edition, covers the basic principles of thermodynamics while presenting a wealth of real-world engineering examples so students get a feel for how thermodynamics is applied in engineering practice. This text helps students develop an intuitive understanding by emphasizing the physics and physical arguments. Cengel and Boles explore the various facets of thermodynamics through careful explanations of concepts and use of numerous practical examples and figures, having students develop necessary skills to bridge the gap between knowledge and the confidence to properly apply their knowledge. McGraw-Hill is proud to offer Connect with the eighth edition of Cengel/Boles, Thermodynamics, An Engineering Approach. This innovative and powerful new system helps your students learn more efficiently and gives you the ability to assign homework problems simply and easily. Problems are graded automatically, and the results are recorded immediately. Track individual stude...

  9. Thermodynamic matchers for the construction of the cuckoo RNA family.

    Science.gov (United States)

    Reinkensmeier, Jan; Giegerich, Robert

    2015-01-01

    RNA family models describe classes of functionally related, non-coding RNAs based on sequence and structure conservation. The most important method for modeling RNA families is the use of covariance models, which are stochastic models that serve in the discovery of yet unknown, homologous RNAs. However, the performance of covariance models in finding remote homologs is poor for RNA families with high sequence conservation, while for families with high structure but low sequence conservation, these models are difficult to built in the first place. A complementary approach to RNA family modeling involves the use of thermodynamic matchers. Thermodynamic matchers are RNA folding programs, based on the established thermodynamic model, but tailored to a specific structural motif. As thermodynamic matchers focus on structure and folding energy, they unfold their potential in discovering homologs, when high structure conservation is paired with low sequence conservation. In contrast to covariance models, construction of thermodynamic matchers does not require an input alignment, but requires human design decisions and experimentation, and hence, model construction is more laborious. Here we report a case study on an RNA family that was constructed by means of thermodynamic matchers. It starts from a set of known but structurally different members of the same RNA family. The consensus secondary structure of this family consists of 2 to 4 adjacent hairpins. Each hairpin loop carries the same motif, CCUCCUCCC, while the stems show high variability in their nucleotide content. The present study describes (1) a novel approach for the integration of the structurally varying family into a single RNA family model by means of the thermodynamic matcher methodology, and (2) provides the results of homology searches that were conducted with this model in a wide spectrum of bacterial species.

  10. Thermodynamic Model of Spatial Memory

    Science.gov (United States)

    Kaufman, Miron; Allen, P.

    1998-03-01

    We develop and test a thermodynamic model of spatial memory. Our model is an application of statistical thermodynamics to cognitive science. It is related to applications of the statistical mechanics framework in parallel distributed processes research. Our macroscopic model allows us to evaluate an entropy associated with spatial memory tasks. We find that older adults exhibit higher levels of entropy than younger adults. Thurstone's Law of Categorical Judgment, according to which the discriminal processes along the psychological continuum produced by presentations of a single stimulus are normally distributed, is explained by using a Hooke spring model of spatial memory. We have also analyzed a nonlinear modification of the ideal spring model of spatial memory. This work is supported by NIH/NIA grant AG09282-06.

  11. Gravity and/is Thermodynamics

    CERN Document Server

    Padmanabhan, T

    2015-01-01

    The equations of motion describing all physical systems, except gravity, remain invariant if a constant is added to the Lagrangian. In the conventional approach, gravitational theories break this symmetry exhibited by all other physical systems. Restoring this symmetry to gravity and demanding that gravitational field equations should also remain invariant under the addition of a constant to a Lagrangian, leads to the interpretation of gravity as the thermodynamic limit of the kinetic theory of atoms of space. This approach selects, in a very natural fashion, Einstein's general relativity in $d=4$. Developing this paradigm at a deeper level, one can obtain the distribution function for the atoms of space and connect it up with the thermodynamic description of spacetime. This extension relies on a curious fact that the quantum spacetime endows each event with a finite area but zero volume. This approach allows us determine the numerical value of the cosmological constant and suggests a new perspective on cosmo...

  12. Non-equilibrium thermodynamics

    CERN Document Server

    De Groot, Sybren Ruurds

    1984-01-01

    The study of thermodynamics is especially timely today, as its concepts are being applied to problems in biology, biochemistry, electrochemistry, and engineering. This book treats irreversible processes and phenomena - non-equilibrium thermodynamics.S. R. de Groot and P. Mazur, Professors of Theoretical Physics, present a comprehensive and insightful survey of the foundations of the field, providing the only complete discussion of the fluctuating linear theory of irreversible thermodynamics. The application covers a wide range of topics: the theory of diffusion and heat conduction, fluid dyn

  13. Advanced thermodynamics engineering

    CERN Document Server

    Annamalai, Kalyan; Jog, Milind A

    2011-01-01

    Thermolab Excel-Based Software for Thermodynamic Properties and Flame Temperatures of Fuels IntroductionImportance, Significance and LimitationsReview of ThermodynamicsMathematical BackgroundOverview of Microscopic/NanothermodynamicsSummaryAppendix: Stokes and Gauss Theorems First Law of ThermodynamicsZeroth LawFirst Law for a Closed SystemQuasi Equilibrium (QE) and Nonquasi-equilibrium (NQE) ProcessesEnthalpy and First LawAdiabatic Reversible Process for Ideal Gas with Constant Specific HeatsFirst Law for an Open SystemApplications of First Law for an Open SystemIntegral and Differential Form

  14. Thermodynamics I essentials

    CERN Document Server

    REA, The Editors of

    2012-01-01

    REA's Essentials provide quick and easy access to critical information in a variety of different fields, ranging from the most basic to the most advanced. As its name implies, these concise, comprehensive study guides summarize the essentials of the field covered. Essentials are helpful when preparing for exams, doing homework and will remain a lasting reference source for students, teachers, and professionals. Thermodynamics I includes review of properties and states of a pure substance, work and heat, energy and the first law of thermodynamics, entropy and the second law of thermodynamics

  15. Modern engineering thermodynamics

    CERN Document Server

    Balmer, Robert T

    2010-01-01

    Designed for use in a standard two-semester engineering thermodynamics course sequence. The first half of the text contains material suitable for a basic Thermodynamics course taken by engineers from all majors. The second half of the text is suitable for an Applied Thermodynamics course in mechanical engineering programs. The text has numerous features that are unique among engineering textbooks, including historical vignettes, critical thinking boxes, and case studies. All are designed to bring real engineering applications into a subject that can be somewhat abstract and mathematica

  16. High-irradiance reactors with unfolded aplanatic optics.

    Science.gov (United States)

    Feuermann, Daniel; Gordon, Jeffrey M

    2008-11-01

    Reconstituting the intense irradiance of short-arc discharge lamps at a remote target, at high radiative efficiency, represents a central challenge in the design of high-temperature chemical reactors, heightened by the need for high numerical aperture at both the target and the source. Separating the optical system from both the source and the reactor allows pragmatic operation, monitoring, and control. We explore near-field unfolded aplanats as feasible solutions and report measurements for a prototype that constitutes a double-ellipsoid mirror. We also propose compound unfolded aplanats that collect lamp emission over all angles (in lieu of light recycling optics) and irradiate the reactor over nearly its full circumference.

  17. Unfolding large-scale online collaborative human dynamics

    CERN Document Server

    Zha, Yilong; Zhou, Changsong

    2015-01-01

    Large-scale interacting human activities underlie all social and economic phenomena, but quantitative understanding of regular patterns and mechanism is very challenging and still rare. Self-organized online collaborative activities with precise record of event timing provide unprecedented opportunity. Our empirical analysis of the history of millions of updates in Wikipedia shows a universal double power-law distribution of time intervals between consecutive updates of an article. We then propose a generic model to unfold collaborative human activities into three modules: (i) individual behavior characterized by Poissonian initiation of an action, (ii) human interaction captured by a cascading response to others with a power-law waiting time, and (iii) population growth due to increasing number of interacting individuals. This unfolding allows us to obtain analytical formula that is fully supported by the universal patterns in empirical data. Our modeling approaches reveal "simplicity" beyond complex interac...

  18. An efficient method for unfolding kinetic pressure driven VISAR data

    Institute of Scientific and Technical Information of China (English)

    M.Hess; K.Peterson; A.Harvey-Thompson

    2015-01-01

    Velocity Interferometer System for Any Reflector(VISAR) [Barker and Hollenbach, J. Appl. Phys. 43, 4669(1972)]is a well-known diagnostic that is employed on many shock physics and pulsed-power experiments. With the VISAR diagnostic, the velocity on the surface of any metal flyer can be found. For most experiments employing VISAR, either a kinetic pressure [Grady, Mech. Mater. 29, 181(1998)] or a magnetic pressure [Lemke et al., Intl J. Impact Eng. 38,480(2011)] drives the motion of the flyer. Moreover, reliable prediction of the time-dependent pressure is often a critical component to understanding the physics of these experiments. Although VISAR can provide a precise measurement of a flyer’s surface velocity, the real challenge of this diagnostic implementation is using this velocity to unfold the timedependent pressure. The purpose of this paper is to elucidate a new method for quickly and reliably unfolding VISAR data.

  19. Plant transducers of the endoplasmic reticulum unfolded protein response

    KAUST Repository

    Iwata, Yuji

    2012-12-01

    The unfolded protein response (UPR) activates a set of genes to overcome accumulation of unfolded proteins in the endoplasmic reticulum (ER), a condition termed ER stress, and constitutes an essential part of ER protein quality control that ensures efficient maturation of secretory and membrane proteins in eukaryotes. Recent studies on Arabidopsis and rice identified the signaling pathway in which the ER membrane-localized ribonuclease IRE1 (inositol-requiring enzyme 1) catalyzes unconventional cytoplasmic splicing of mRNA, thereby producing the active transcription factor Arabidopsis bZIP60 (basic leucine zipper 60) and its ortholog in rice. Here we review recent findings identifying the molecular components of the plant UPR, including IRE1/bZIP60 and the membrane-bound transcription factors bZIP17 and bZIP28, and implicating its importance in several physiological phenomena such as pathogen response. © 2012 Elsevier Ltd.

  20. Unfolding the band structure of GaAsBi

    Science.gov (United States)

    Maspero, R.; Sweeney, S. J.; Florescu, Marian

    2017-02-01

    Typical supercell approaches used to investigate the electronic properties of GaAs(1-x)Bi(x) produce highly accurate, but folded, band structures. Using a highly optimized algorithm, we unfold the band structure to an approximate E≤ft(\\mathbf{k}\\right) relation associated with an effective Brillouin zone. The dispersion relations we generate correlate strongly with experimental results, confirming that a regime of band gap energy greater than the spin-orbit-splitting energy is reached at around 10% bismuth fraction. We also demonstrate the effectiveness of the unfolding algorithm throughout the Brillouin zone (BZ), which is key to enabling transition rate calculations, such as Auger recombination rates. Finally, we show the effect of disorder on the effective masses and identify approximate values for the effective mass of the conduction band and valence bands for bismuth concentrations from 0-12%.

  1. Amyloid protein unfolding and insertion kinetics on neuronal membrane mimics

    Science.gov (United States)

    Qiu, Liming; Buie, Creighton; Vaughn, Mark; Cheng, Kwan

    2010-03-01

    Atomistic details of beta-amyloid (Aβ ) protein unfolding and lipid interaction kinetics mediated by the neuronal membrane surface are important for developing new therapeutic strategies to prevent and cure Alzheimer's disease. Using all-atom MD simulations, we explored the early unfolding and insertion kinetics of 40 and 42 residue long Aβ in binary lipid mixtures with and without cholesterol that mimic the cholesterol-depleted and cholesterol-enriched lipid nanodomains of neurons. The protein conformational transition kinetics was evaluated from the secondary structure profile versus simulation time plot. The extent of membrane disruption was examined by the calculated order parameters of lipid acyl chains and cholesterol fused rings as well as the density profiles of water and lipid headgroups at defined regions across the lipid bilayer from our simulations. Our results revealed that both the cholesterol content and the length of the protein affect the protein-insertion and membrane stability in our model lipid bilayer systems.

  2. Clinical Application of the Sapphire Unfolder Lens Injection System

    Institute of Scientific and Technical Information of China (English)

    Weiai Guo; Danying Zheng; Zhenyu Li; Yiyong Qian; Zhenping Zhang

    2002-01-01

    Purpose: To summarize the clinical experience of 300 cases using the Sapphire unfloder intraocular lens (IOL) injection system.Methods: After the standard phacoemulsification, an AR40e IOL was implanted using the Sapphire Unfolder. The involved problems during and after the operation were observed and analyzed.Results:The complications occurred during the operation including the crack at the haptic-optic junction in 2 cases, slight kink in the haptic in 5 cases, IOL clamp into the cartridge in 2 cases, posterior capsular rupture in 2 cases and endothelium damage in the central small area in 4 cases. All the patients recovered successfully with IOLs in good position.Conclusion: IOL implantation with the Sapphire Unfolder led to no serious complications and got the satisfactory results.

  3. Folding/Unfolding Properties of Metal Foils in Transformable Structure

    Science.gov (United States)

    Daming, Nie; Zhen, Lu; Kaifeng, Zhang

    2017-01-01

    Transformable structures are widely applied in the aerospace, temporary facilities, etc. Compared to the structures made of polyester materials, the metal foil ones occupy many special advantages while have been rarely investigated. In this study, a series of transformable structures made of four different metal materials, 6065 Al, copper, TA1 and SUS 304 stainless steel, with thickness of 0.1 mm were prepared. Moreover, the folding (i.e., compressing the structure to the lowest height with external force) and unfolding (i.e., extending the structure to the largest height with external force) behaviors of these structures were exhibited and explained by experiments. Besides, the differences and corresponding mechanisms of various materials on the folding/unfolding properties of the structures were examined and discussed.

  4. Multiple unfolding pathways of leucine binding protein (LBP) probed by single-molecule force spectroscopy (SMFS).

    Science.gov (United States)

    Kotamarthi, Hema Chandra; Sharma, Riddhi; Narayan, Satya; Ray, Sayoni; Ainavarapu, Sri Rama Koti

    2013-10-02

    Experimental studies on the folding and unfolding of large multi-domain proteins are challenging, given the proteins' complex energy landscapes with multiple intermediates. Here, we report a mechanical unfolding study of a 346-residue, two-domain leucine binding protein (LBP) from the bacterial periplasm. Forced unfolding of LBP is a prerequisite for its translocation across the cytoplasmic membrane into the bacterial periplasm. During the mechanical stretching of LBP, we observe that 38% of the unfolding flux followed a two-state pathway, giving rise to a single unfolding force peak at ~70 pN with an unfolding contour length of 120 nm in constant-velocity single-molecule pulling experiments. The remaining 62% of the unfolding flux followed multiple three-state pathways, with intermediates having unfolding contour lengths in the range ~20-85 nm. These results suggest that the energy landscape of LBP is complex, with multiple intermediate states, and a large fraction of molecules go through intermediate states during the unfolding process. Furthermore, the presence of the ligand leucine increased the unfolding flux through the two-state pathway from 38% to 65%, indicating the influence of ligand binding on the energy landscape. This study suggests that unfolding through parallel pathways might be a general mechanism for the large two-domain proteins that are translocated to the bacterial periplasmic space.

  5. An introduction to statistical thermodynamics

    CERN Document Server

    Hill, Terrell L

    1987-01-01

    ""A large number of exercises of a broad range of difficulty make this book even more useful…a good addition to the literature on thermodynamics at the undergraduate level."" - Philosophical MagazineAlthough written on an introductory level, this wide-ranging text provides extensive coverage of topics of current interest in equilibrium statistical mechanics. Indeed, certain traditional topics are given somewhat condensed treatment to allow room for a survey of more recent advances.The book is divided into four major sections. Part I deals with the principles of quantum statistical mechanics a

  6. Elements of statistical thermodynamics

    CERN Document Server

    Nash, Leonard K

    2006-01-01

    Encompassing essentially all aspects of statistical mechanics that appear in undergraduate texts, this concise, elementary treatment shows how an atomic-molecular perspective yields new insights into macroscopic thermodynamics. 1974 edition.

  7. Theoretical physics 5 thermodynamics

    CERN Document Server

    Nolting, Wolfgang

    2017-01-01

    This concise textbook offers a clear and comprehensive introduction to thermodynamics, one of the core components of undergraduate physics courses. It follows on naturally from the previous volumes in this series, defining macroscopic variables, such as internal energy, entropy and pressure,together with thermodynamic principles. The first part of the book introduces the laws of thermodynamics and thermodynamic potentials. More complex themes are covered in the second part of the book, which describes phases and phase transitions in depth. Ideally suited to undergraduate students with some grounding in classical mechanics, the book is enhanced throughout with learning features such as boxed inserts and chapter summaries, with key mathematical derivations highlighted to aid understanding. The text is supported by numerous worked examples and end of chapter problem sets. About the Theoretical Physics series Translated from the renowned and highly successful German editions, the eight volumes of this series cove...

  8. Polyelectrolytes thermodynamics and rheology

    CERN Document Server

    P M, Visakh; Picó, Guillermo Alfredo

    2014-01-01

    This book discusses current development of theoretical models and experimental findings on the thermodynamics of polyelectrolytes. Particular emphasis is placed on the rheological description of polyelectrolyte solutions and hydrogels.

  9. Thermodynamics and Frozen Foods.

    Science.gov (United States)

    Kerr, William L.; Reid, David S.

    1993-01-01

    The heat content of a food at a given temperature can be described by the thermodynamic property of enthalpy. Presents a method to construct a simple calorimeter for measuring the enthalpy changes of different foods during freezing. (MDH)

  10. Constructor Theory of Thermodynamics

    CERN Document Server

    Marletto, Chiara

    2016-01-01

    The laws of thermodynamics, powerful for countless purposes, are not exact: both their phenomenological and their statistical-mechanical versions are valid only at 'macroscopic scales', which are never defined. Here I propose a new, exact and scale-independent formulation of the first and second laws of thermodynamics, using the principles and tools of the recently proposed constructor theory. Specifically, I improve upon the axiomatic formulations of thermodynamics (Carath\\'eodory, 1909; Lieb and Yngvason, 1999) by proposing an exact and more general formulation of 'adiabatic accessibility'. This work provides an exact distinction between work and heat; it reveals an unexpected connection between information theory and the first law of thermodynamics (not just the second); it resolves the clash between the irreversibility of the 'cycle'-based second law and time-reversal symmetric dynamical laws. It also achieves the long-sought unification of the axiomatic version of the second law with Kelvin's.

  11. Thermodynamics of primary photosynthesis.

    Science.gov (United States)

    Mauzerall, D

    2013-10-01

    The thermodynamics of photosynthesis has been much discussed, but recent articles have pointed to some confusion on the subject. The aim of this review is to clarify a limited part of this state of affairs.

  12. Thermodynamics of complexity

    DEFF Research Database (Denmark)

    Westerhoff, Hans V.; Jensen, Peter Ruhdal; Snoep, Jacky L.

    1998-01-01

    Thermodynamics has always been a remarkable science in that it studies macroscopic properties that are only partially determined by the properties of individual molecules. Entropy and free energy only exist in constellations of more than a single molecule (degree of freedom). They are the so......-called emergent properties. Tendency towards increased entropy is an essential determinant for the behaviour of ideal gas mixtures, showing that even in the simplest physical/chemical systems, (dys)organisation of components is crucial for the behaviour of systems. This presentation aims at illustrating...... understanding of this BioComplexity, modem thermodynamic concepts and methods (nonequilibrium thermodynamics, metabolic and hierarchical control analysis) will be needed. We shall propose to redefine nonequilibrium thermodynamics as: The science that aims at understanding the behaviour of nonequilibrium systems...

  13. Electrochemical thermodynamic measurement system

    Science.gov (United States)

    Reynier, Yvan; Yazami, Rachid; Fultz, Brent T.

    2009-09-29

    The present invention provides systems and methods for accurately characterizing thermodynamic and materials properties of electrodes and electrochemical energy storage and conversion systems. Systems and methods of the present invention are configured for simultaneously collecting a suite of measurements characterizing a plurality of interconnected electrochemical and thermodynamic parameters relating to the electrode reaction state of advancement, voltage and temperature. Enhanced sensitivity provided by the present methods and systems combined with measurement conditions that reflect thermodynamically stabilized electrode conditions allow very accurate measurement of thermodynamic parameters, including state functions such as the Gibbs free energy, enthalpy and entropy of electrode/electrochemical cell reactions, that enable prediction of important performance attributes of electrode materials and electrochemical systems, such as the energy, power density, current rate and the cycle life of an electrochemical cell.

  14. Elements of chemical thermodynamics

    CERN Document Server

    Nash, Leonard K

    2005-01-01

    This survey of purely thermal data in calculating the position of equilibrium in a chemical reaction highlights the physical content of thermodynamics, as distinct from purely mathematical aspects. 1970 edition.

  15. Elementary chemical thermodynamics

    CERN Document Server

    Mahan, Bruce H

    1963-01-01

    This text introduces thermodynamic principles in a straightforward manner. Suitable for advanced undergraduates and graduate students, it emphasizes chemical applications and physical interpretations and simplifies mathematical development. 1964 edition.

  16. Unfolding Ubiquitin by force: water mediated H-bond destabilization

    Directory of Open Access Journals (Sweden)

    Germán Pabón

    2012-12-01

    Full Text Available Using the “pull and wait” (PNW simulation protocol at 300 K, we studied the unfolding by force of an ubiquitin molecule. PNW was implemented in the CHARMM program using an integration time step of 1 fs and a uniform dielectric constant of 1. The ubiquitin molecule, initially solvated, was put under mechanical stress, exerting forces from different directions. The rupture of five hydrogen bonds between parallel strands β1 and β5 takes place during the extension from 13 to 15 Å, defines a mechanical barrier for unfolding and dominates the point of maximum unfolding force. The simulations described here show that given adequate time, a small applied force can destabilize those five H-bonds relative to the bonds that can be created to water molecules; allowing the formation of stable H-bonds between a single water molecule and the donor and acceptor groups of the interstrand H-bonds. Thus, simulations run with PNW show that the force is not responsible for “ripping apart” the backbone H-bonds; it merely destabilizes them making them less stable than the H-bonds they can make with water. Additional simulations show that the force necessary to destabilize the H-bonds and allow them to be replaced by H-bonds to water molecules depends strongly on the pulling direction. By using a simulation protocol that allows equilibration at each extension we have been able to observe the details of the events leading to the unfolding of ubiquitin by mechanical force.

  17. Unfolding education for sustainable development as didactic thinking and practice

    DEFF Research Database (Denmark)

    Madsen, Katrine Dahl

    2013-01-01

    This article’s primary objective is to unfold how teachers translate education for sustainable development (ESD) in a school context. The article argues that exploring tensions, ruptures and openings apparent in this meeting is crucial for the development of existing teaching practices in relatio...... the analytical foundation; thus it is the practices as seen from the ‘inside’. Furthermore, ESD practices are considered in a broader societal perspective, pointing to the critical power of the practice lens....

  18. Simulating protein unfolding under pressure with a coarse-grained model.

    Science.gov (United States)

    Perezzan, Ramiro; Rey, Antonio

    2012-11-14

    We describe and test a coarse-grained molecular model for the simulation of the effects of pressure on the folding/unfolding transition of proteins. The model is a structure-based one, which takes into account the desolvation barrier for the formation of the native contacts. The pressure is taken into account in a qualitative, mean field approach, acting on the parameters describing the native stabilizing interactions. The model has been tested by simulating the thermodynamic and structural behavior of protein GB1 with a parallel tempering Monte Carlo algorithm. At low effective pressures, the model reproduces the standard two-state thermal transition between the native and denatured states. However, at large pressures a new state appears. Its structural characteristics have been analyzed, showing that it corresponds to a swollen version of the native structure. This swollen state is at equilibrium with the native state at low temperatures, but gradually transforms into the thermally denatured state as temperature is increased. Therefore, our model predicts a downhill transition between the swollen and the denatured states. The analysis of the model permits us to obtain a phase diagram for the pressure-temperature behavior of the simulated system, which is compatible with the known elliptical shape of this diagram for real proteins.

  19. Probing the Folding-Unfolding Transition of a Thermophilic Protein, MTH1880.

    Directory of Open Access Journals (Sweden)

    Heeyoun Kim

    Full Text Available The folding mechanism of typical proteins has been studied widely, while our understanding of the origin of the high stability of thermophilic proteins is still elusive. Of particular interest is how an atypical thermophilic protein with a novel fold maintains its structure and stability under extreme conditions. Folding-unfolding transitions of MTH1880, a thermophilic protein from Methanobacterium thermoautotrophicum, induced by heat, urea, and GdnHCl, were investigated using spectroscopic techniques including circular dichorism, fluorescence, NMR combined with molecular dynamics (MD simulations. Our results suggest that MTH1880 undergoes a two-state N to D transition and it is extremely stable against temperature and denaturants. The reversibility of refolding was confirmed by spectroscopic methods and size exclusion chromatography. We found that the hyper-stability of the thermophilic MTH1880 protein originates from an extensive network of both electrostatic and hydrophobic interactions coordinated by the central β-sheet. Spectroscopic measurements, in combination with computational simulations, have helped to clarify the thermodynamic and structural basis for hyper-stability of the novel thermophilic protein MTH1880.

  20. Differential geometry and thermodynamics

    CERN Document Server

    Quevedo, H

    2003-01-01

    In this work we present the first steps of a new approach to the study of thermodynamics in the context of differential geometry. We introduce a fundamental differential 1-form and a metric on a pseudo-Euclidean manifold coordinatized by means of the extensive thermodynamic variables. The study of the connection and the curvature of these objects is initialized in this work by using Cartan structure equations. (Author)

  1. Information theory and Thermodynamics

    OpenAIRE

    Kafri, Oded

    2006-01-01

    A communication theory for a transmitter broadcasting to many receivers is presented. In this case energetic considerations cannot be neglected as in Shannon theory. It is shown that, when energy is assigned to the information bit, information theory complies with classical thermodynamic and is part of it. To provide a thermodynamic theory of communication it is necessary to define equilibrium for informatics systems that are not in thermal equilibrium and to calculate temperature, heat, and ...

  2. Thermodynamics - basic conception

    Energy Technology Data Exchange (ETDEWEB)

    Wee, Eul Bok

    1979-08-15

    This book tells of basic conception of thermodynamics, condition and property of matter, work and power, thermal efficiency, the principle of the conservation of energy, relationship between work and heat, enthalpy, Jouel's law, complete gasification, the second low of thermodynamics such as thermal efficiency and quality factor, carnot cycle, and entropy, condensation of gas like press of internal combustion engine, vapor, steam power plant and structure, internal combustion cycle, freeze cycle, flow of fluid, combustion and heat transfer.

  3. Fundamentals of engineering thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Moran, M.J.; Shapiro, H.N.

    1988-01-01

    This book provides a thorough development of the second law of thermodynamics (featuring the entropy-production concept), an up-to-date discussion of availability analysis (including an introduction to chemical availability), and a sound description of the application areas. Topics covered include control volume energy analysis, vapor power systems, gas power systems, thermodynamic relations for simple compressible substances, nonreacting ideal gas mixtures and psycrometrics, reacting mixtures and combustion, and chemical and phase equilibrium.

  4. Chemical thermodynamics of technetium

    Energy Technology Data Exchange (ETDEWEB)

    Amaia Sandino, M.C.; Oesthols, E. [eds.] [OECD Nuclear Energy Agency NEA, Issy-les-Moulineaux (France)

    1999-07-01

    This volume on technetium is the third volume in a series of critical reviews of the chemical thermodynamic properties of elements of special importance to modelling efforts for the safety assessment of radioactive waste disposal systems, and is the only one concerned with a fission product element. The first two volumes were reviews of the chemical thermodynamics of uranium and americium. Thermochemical data for neptunium and plutonium are being reviewed for a later volume. refs.

  5. Measurement of the unfolded protein response (UPR) in monocytes.

    LENUS (Irish Health Repository)

    Carroll, Tomas P

    2012-02-01

    In mammalian cells, the primary function of the endoplasmic reticulum (ER) is to synthesize and assemble membrane and secreted proteins. As the main site of protein folding and posttranslational modification in the cell, the ER operates a highly conserved quality control system to ensure only correctly assembled proteins exit the ER and misfolded and unfolded proteins are retained for disposal. Any disruption in the equilibrium of the ER engages a multifaceted intracellular signaling pathway termed the unfolded protein response (UPR) to restore normal conditions in the cell. A variety of pathological conditions can induce activation of the UPR, including neurodegenerative disorders such as Parkinson\\'s disease, metabolic disorders such as atherosclerosis, and conformational disorders such as cystic fibrosis. Conformational disorders are characterized by mutations that modify the final structure of a protein and any cells that express abnormal protein risk functional impairment. The monocyte is an important and long-lived immune cell and acts as a key immunological orchestrator, dictating the intensity and duration of the host immune response. Monocytes expressing misfolded or unfolded protein may exhibit UPR activation and this can compromise the host immune system. Here, we describe in detail methods and protocols for the examination of UPR activation in peripheral blood monocytes. This guide should provide new investigators to the field with a broad understanding of the tools required to investigate the UPR in the monocyte.

  6. Measurement of the unfolded protein response (UPR) in monocytes.

    LENUS (Irish Health Repository)

    Carroll, Tomás P

    2011-01-01

    In mammalian cells, the primary function of the endoplasmic reticulum (ER) is to synthesize and assemble membrane and secreted proteins. As the main site of protein folding and posttranslational modification in the cell, the ER operates a highly conserved quality control system to ensure only correctly assembled proteins exit the ER and misfolded and unfolded proteins are retained for disposal. Any disruption in the equilibrium of the ER engages a multifaceted intracellular signaling pathway termed the unfolded protein response (UPR) to restore normal conditions in the cell. A variety of pathological conditions can induce activation of the UPR, including neurodegenerative disorders such as Parkinson\\'s disease, metabolic disorders such as atherosclerosis, and conformational disorders such as cystic fibrosis. Conformational disorders are characterized by mutations that modify the final structure of a protein and any cells that express abnormal protein risk functional impairment. The monocyte is an important and long-lived immune cell and acts as a key immunological orchestrator, dictating the intensity and duration of the host immune response. Monocytes expressing misfolded or unfolded protein may exhibit UPR activation and this can compromise the host immune system. Here, we describe in detail methods and protocols for the examination of UPR activation in peripheral blood monocytes. This guide should provide new investigators to the field with a broad understanding of the tools required to investigate the UPR in the monocyte.

  7. Assessing Mitochondrial Unfolded Protein Response in Mammalian Cells.

    Science.gov (United States)

    Durand, Fiona; Hoogenraad, Nicholas

    2017-01-01

    Mitochondria serve a key role in the supply of energy to cells in the form of ATP, the supply of essential cellular components such as phospholipids and heme, in apoptosis and as a mediator of cellular signaling pathways. Mitochondria have their own DNA, consisting of a small number of genes, but the majority of the total protein complement is encoded in the nucleus, synthesized in the cytosol, and is imported into the mitochondria in a largely, if not completely unfolded form. These proteins need to be folded into their functional form within the organelle with the concomitant requirement that the organelle has its own suite of molecular chaperones and complexes to degrade damaged proteins to avoid stress arising from accumulation of unfolded proteins. This mitochondrial unfolded protein response can also be induced in cells and protein regulation can be determined using western blot, luciferase reporter assay, and sensitive mass spectrometry techniques. In this chapter, we describe a method to induce mtUPR in mammalian cells and the three methods to analyze components involved in it.

  8. Numerical Simulation of Folding and Unfolding of Proteins

    CERN Document Server

    Kouza, Maksim

    2013-01-01

    The thesis examines in detail the folding and unfolding processes of a number of proteins including hbSBD, DDLNF4, single and multi Ubiquitin. Using simplified coarse-grained off-lattice Go model and CD experiments we have shown the two-state behavior of hbSBD protein. It was shown that refolding pathways of single Ubiquitin depend on what end is anchored to the surface. Namely, the fixation of the N-terminal changes refolding pathways but anchoring the C-terminal leaves them unchanged. Interestingly, the end fixation has no effect on multi-domain Ubiquitin. Using the Go modeling and all-atom models with explicit water, we have studied the mechanical unfolding mechanism of DDFLN4 in detail. We predict that, contrary to the AFM experiments, an additional unfolding peak would occur at the end-to-end $\\Delta R \\approx 1.5 $nm in the force-extension curve. Our study reveals the important role of non-native interactions which are responsible for a peak located at $\\Delta R \\approx 22 $nm. This peak can not be enco...

  9. Differential stability of the bovine prion protein upon urea unfolding

    Science.gov (United States)

    Julien, Olivier; Chatterjee, Subhrangsu; Thiessen, Angela; Graether, Steffen P; Sykes, Brian D

    2009-01-01

    Prion diseases, or transmissible spongiform encephalopathies, are a group of infectious neurological diseases associated with the structural conversion of an endogenous protein (PrP) in the central nervous system. There are two major forms of this protein: the native and noninfectious cellular form, PrPC; and the misfolded, infectious, and proteinase K-resistant form, PrPSc. The C-terminal domain of PrPC is mainly α-helical in structure, whereas PrPSc in known to aggregate into an assembly of β-sheets, forming amyloid fibrils. To identify the regions of PrPC potentially involved in the initial steps of the conversion to the infectious conformation, we have used high-resolution NMR spectroscopy to characterize the stability and structure of bovine recombinant PrPC (residues 121 to 230) during unfolding with the denaturant urea. Analysis of the 800 MHz 1H NMR spectra reveals region-specific information about the structural changes occurring upon unfolding. Our data suggest that the dissociation of the native β-sheet of PrPC is a primary step in the urea-induced unfolding process, while strong hydrophobic interactions between helices α1 and α3, and between α2 and α3, stabilize these regions even at very high concentrations of urea. PMID:19693935

  10. A New Perspective on Thermodynamics

    CERN Document Server

    Lavenda, Bernard H

    2010-01-01

    Dr. Bernard H. Lavenda has written A New Perspective on Thermodynamics to combine an old look at thermodynamics with a new foundation. The book presents a historical perspective, which unravels the current presentation of thermodynamics found in standard texts, and which emphasizes the fundamental role that Carnot played in the development of thermodynamics. A New Perspective on Thermodynamics will: Chronologically unravel the development of the principles of thermodynamics and how they were conceived by their discoverers Bring the theory of thermodynamics up to the present time and indicate areas of further development with the union of information theory and the theory of means and their inequalities. New areas include nonextensive thermodynamics, the thermodynamics of coding theory, multifractals, and strange attractors. Reintroduce important, yet nearly forgotten, teachings of N.L. Sardi Carnot Highlight conceptual flaws in timely topics such as endoreversible engines, finite-time thermodynamics, geometri...

  11. Gravity as a thermodynamic phenomenon

    OpenAIRE

    Moustos, Dimitris

    2017-01-01

    The analogy between the laws of black hole mechanics and the laws of thermodynamics led Bekenstein and Hawking to argue that black holes should be considered as real thermodynamic systems that are characterised by entropy and temperature. Black hole thermodynamics indicates a deeper connection between thermodynamics and gravity. We review and examine in detail the arguments that suggest an interpretation of gravity itself as a thermodynamic theory.

  12. Unfolding pathway of CotA-laccase and the role of copper on the prevention of refolding through aggregation of the unfolded state

    Energy Technology Data Exchange (ETDEWEB)

    Fernandes, Andre T. [Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Av. da Republica, 2780-157 Oeiras (Portugal); Lopes, Carlos [Centre for Molecular and Structural Biomedicine, Institute for Biotechnology and Bioengineering, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Martins, Ligia O. [Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Av. da Republica, 2780-157 Oeiras (Portugal); Melo, Eduardo Pinho, E-mail: emelo@ualg.pt [Centre for Molecular and Structural Biomedicine, Institute for Biotechnology and Bioengineering, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro (Portugal)

    2012-06-08

    Highlights: Black-Right-Pointing-Pointer CotA-laccase unfolds with an intermediate state. Black-Right-Pointing-Pointer Copper stabilizes the native and the intermediate state. Black-Right-Pointing-Pointer Copper binding to the unfolded state prevents refolding through protein aggregation. Black-Right-Pointing-Pointer Copper incorporation in CotA-laccase occurs as a later step during folding. -- Abstract: Copper is a redox-active metal and the main player in electron transfer reactions occurring in multicopper oxidases. The role of copper in the unfolding pathway and refolding of the multicopper oxidase CotA laccase in vitro was solved using double-jump stopped-flow experiments. Unfolding of apo- and holo-CotA was described as a three-state process with accumulation of an intermediate in between the native and unfolded state. Copper stabilizes the native holo-CotA but also the intermediate state showing that copper is still bound to this state. Also, copper binds to unfolded holo-CotA in a non-native coordination promoting CotA aggregation and preventing refolding to the native structure. These results gather information on unfolding/folding pathways of multicopper oxidases and show that copper incorporation in vivo should be a tight controlled process as copper binding to the unfolded state under native conditions promotes protein aggregation.

  13. Systematic vibration thermodynamic properties of bromine

    Science.gov (United States)

    Liu, G. Y.; Sun, W. G.; Liao, B. T.

    2015-11-01

    Based on the analysis of the maturity and finiteness of vibrational levels of bromine molecule in ground state and evaluating the effect on statistical computation, according to the elementary principles of quantum statistical theorem, using the full set of bromine molecular vibrational levels determined with algebra method, the statistical contribution for bromine systematical macroscopic thermodynamic properties is discussed. Thermodynamic state functions Helmholtz free energy, entropy and observable vibration heat capacity are calculated. The results show that the determination of full set of vibrational levels and maximum vibrational quantum number is the key in the correct statistical analysis of bromine systematical thermodynamic property. Algebra method results are clearly different from data of simple harmonic oscillator and the related algebra method results are no longer analytical but numerical and are superior to simple harmonic oscillator results. Compared with simple harmonic oscillator's heat capacities, the algebra method's heat capacities are more consistent with the experimental data in the given temperature range of 600-2100 K.

  14. Thermodynamics for separation-process technology

    Energy Technology Data Exchange (ETDEWEB)

    Prausnitz, J.M.

    1995-10-01

    When contemplating or designing a separation process, every chemical engineer at once recognizes the thermodynamic boundary conditions that must be satisfied: when a mixture is continuously processed to yield at least partially purified products, energy and mass must be conserved and work must be done. In his daily tasks, a chemical engineer uses thermodynamic concepts as tacit, almost subconscious, knowledge. Thus, qualitative thermodynamics significantly informs process conception at its most fundamental level. However, quantitative design requires detailed knowledge of thermodynamic relations and physical chemistry. Most process engineers, concerned with flow sheets and economics, cannot easily command that detailed knowledge and therefore it is advantageous for them to maintain close contact with those specialists who do. Quantitative chemical thermodynamics provides an opportunity to evaluate possible separation processes not only because it may give support to the process engineer`s bold imagination but also because, when coupled with molecular models, it can significantly reduce the experimental effort required to determine an optimum choice of process alternatives. Six examples are presented to indicate the application of thermodynamics for conventional and possible future separation processes.

  15. Predictive thermodynamics for ionic solids and liquids.

    Science.gov (United States)

    Glasser, Leslie; Jenkins, H Donald Brooke

    2016-08-21

    The application of thermodynamics is simple, even if the theory may appear intimidating. We describe tools, developed over recent years, which make it easy to estimate often elusive thermodynamic parameter values, generally (but not exclusively) for ionic materials, both solid and liquid, as well as for their solid hydrates and solvates. The tools are termed volume-based thermodynamics (VBT) and thermodynamic difference rules (TDR), supplemented by the simple salt approximation (SSA) and single-ion values for volume, Vm, heat capacity, , entropy, , formation enthalpy, ΔfH°, and Gibbs formation energy, ΔfG°. These tools can be applied to provide values of thermodynamic and thermomechanical properties such as standard enthalpy of formation, ΔfH°, standard entropy, , heat capacity, Cp, Gibbs function of formation, ΔfG°, lattice potential energy, UPOT, isothermal expansion coefficient, α, and isothermal compressibility, β, and used to suggest the thermodynamic feasibility of reactions among condensed ionic phases. Because many of these methods yield results largely independent of crystal structure, they have been successfully extended to the important and developing class of ionic liquids as well as to new and hypothesised materials. Finally, these predictive methods are illustrated by application to K2SnCl6, for which known experimental results are available for comparison. A selection of applications of VBT and TDR is presented which have enabled input, usually in the form of thermodynamics, to be brought to bear on a range of topical problems. Perhaps the most significant advantage of VBT and TDR methods is their inherent simplicity in that they do not require a high level of computational expertise nor expensive high-performance computation tools - a spreadsheet will usually suffice - yet the techniques are extremely powerful and accessible to non-experts. The connection between formula unit volume, Vm, and standard thermodynamic parameters represents a

  16. Direct observation of markovian behavior of the mechanical unfolding of individual proteins.

    Science.gov (United States)

    Cao, Yi; Kuske, Rachel; Li, Hongbin

    2008-07-01

    Single-molecule force-clamp spectroscopy is a valuable tool to analyze unfolding kinetics of proteins. Previous force-clamp spectroscopy experiments have demonstrated that the mechanical unfolding of ubiquitin deviates from the generally assumed Markovian behavior and involves the features of glassy dynamics. Here we use single molecule force-clamp spectroscopy to study the unfolding kinetics of a computationally designed fast-folding mutant of the small protein GB1, which shares a similar beta-grasp fold as ubiquitin. By treating the mechanical unfolding of polyproteins as the superposition of multiple identical Poisson processes, we developed a simple stochastic analysis approach to analyze the dwell time distribution of individual unfolding events in polyprotein unfolding trajectories. Our results unambiguously demonstrate that the mechanical unfolding of NuG2 fulfills all criteria of a memoryless Markovian process. This result, in contrast with the complex mechanical unfolding behaviors observed for ubiquitin, serves as a direct experimental demonstration of the Markovian behavior for the mechanical unfolding of a protein and reveals the complexity of the unfolding dynamics among structurally similar proteins. Furthermore, we extended our method into a robust and efficient pseudo-dwell-time analysis method, which allows one to make full use of all the unfolding events obtained in force-clamp experiments without categorizing the unfolding events. This method enabled us to measure the key parameters characterizing the mechanical unfolding energy landscape of NuG2 with improved precision. We anticipate that the methods demonstrated here will find broad applications in single-molecule force-clamp spectroscopy studies for a wide range of proteins.

  17. The effect of citric acid on the activity, thermodynamics and conformation of mushroom polyphenoloxidase.

    Science.gov (United States)

    Liu, Wei; Zou, Li-qiang; Liu, Jun-ping; Zhang, Zhao-qin; Liu, Cheng-mei; Liang, Rui-hong

    2013-09-01

    Few reports have focused on the effect of citric acid on thermodynamics and conformation of polyphenoloxidase (PPO). In this study, variations on activity, thermodynamics and conformation of mushroom PPO induced by citric acid (1-60mM) and relationships among these were investigated. It showed that with the increasing concentration of citric acid, the activity of PPO decreased gradually to an inactivity condition; inactivation rate constant (k) of PPO increased and the activation energy (Ea) as well as thermodynamic parameters (ΔG, ΔH, ΔS) decreased, which indicated that the thermosensitivity, stability and number of non-covalent bonds of PPO decreased. The conformation was gradually unfolded, which was reflected in the decrease of α-helix contents, increase of β-sheet and exposure of aromatic amino acid residuals. Moreover, two linear relationships of relative activities, enthalpies (ΔH) against α-helix contents were obtained. It indicated that changes of activity and thermodynamics might correlate to the unfolding of conformation.

  18. The structural basis of urea-induced protein unfolding in β-catenin.

    Science.gov (United States)

    Wang, Chao; Chen, Zhongzhou; Hong, Xia; Ning, Fangkun; Liu, Haolin; Zang, Jianye; Yan, Xiaoxue; Kemp, Jennifer; Musselman, Catherine A; Kutateladze, Tatinna G; Zhao, Rui; Jiang, Chengyu; Zhang, Gongyi

    2014-11-01

    Although urea and guanidine hydrochloride are commonly used to denature proteins, the molecular underpinnings of this process have remained unclear for a century. To address this question, crystal structures of β-catenin were determined at various urea concentrations. These structures contained at least 105 unique positions that were occupied by urea molecules, each of which interacted with the protein primarily via hydrogen bonds. Hydrogen-bond competition experiments showed that the denaturing effects of urea were neutralized when polyethylene glycol was added to the solution. These data suggest that urea primarily causes proteins to unfold by competing and disrupting hydrogen bonds in proteins. Moreover, circular-dichroism spectra and nuclear magnetic resonance (NMR) analysis revealed that a similar mechanism caused protein denaturation in the absence of urea at pH levels greater than 12. Taken together, the results led to the conclusion that the disruption of hydrogen bonds is a general mechanism of unfolding induced by urea, high pH and potentially other denaturing agents such as guanidine hydrochloride. Traditionally, the disruption of hydrophobic interactions instead of hydrogen bonds has been thought to be the most important cause of protein denaturation.

  19. Evolution in thermodynamics

    Science.gov (United States)

    Bejan, Adrian

    2017-03-01

    This review covers two aspects of "evolution" in thermodynamics. First, with the constructal law, thermodynamics is becoming the domain of physics that accounts for the phenomenon of evolution in nature, in general. Second, thermodynamics (and science generally) is the evolving add-on that empowers humans to predict the future and move more easily on earth, farther and longer in time. The part of nature that thermodynamics represents is this: nothing moves by itself unless it is driven by power, which is then destroyed (dissipated) during movement. Nothing evolves unless it flows and has the freedom to change its architecture such that it provides greater and easier access to the available space. Thermodynamics is the modern science of heat and work and their usefulness, which comes from converting the work (power) into movement (life) in flow architectures that evolve over time to facilitate movement. I also review the rich history of the science, and I clarify misconceptions regarding the second law, entropy, disorder, and the arrow of time, and the supposed analogy between heat and work.

  20. Thermodynamics of Fractal Universe

    CERN Document Server

    Sheykhi, Ahmad; Wang, Bin

    2012-01-01

    We investigate the thermodynamical properties of the apparent horizon in a fractal universe. We find that one can always rewrite the Friedmann equation of the fractal universe in the form of the entropy balance relation $ \\delta Q=TdS+Td\\tilde{S}$, where $ \\delta Q $ and $ T $ are the energy flux and Unruh temperature seen by an accelerated observer just inside the apparent horizon, and $d\\tilde{S}$ is the entropy production term due to nonequilibrium thermodynamics of fractal universe. This shows that in a fractal universe, a treatment with nonequilibrium thermodynamics of spacetime may be needed. We also study the generalized second law of thermodynamics in the framework of fractal universe. When the temperature of the apparent horizon and the matter fields inside the horizon are equal, i.e. $T=T_h$, the generalized second law of thermodynamics can be fulfilled provided the deceleration and the equation of state parameters ranges either as $-1 \\leq q < 0 $, $- 1 \\leq w < - 1/3$ or as $q<-1$, $w<...

  1. Thermodynamics of Biological Processes

    Science.gov (United States)

    Garcia, Hernan G.; Kondev, Jane; Orme, Nigel; Theriot, Julie A.; Phillips, Rob

    2012-01-01

    There is a long and rich tradition of using ideas from both equilibrium thermodynamics and its microscopic partner theory of equilibrium statistical mechanics. In this chapter, we provide some background on the origins of the seemingly unreasonable effectiveness of ideas from both thermodynamics and statistical mechanics in biology. After making a description of these foundational issues, we turn to a series of case studies primarily focused on binding that are intended to illustrate the broad biological reach of equilibrium thinking in biology. These case studies include ligand-gated ion channels, thermodynamic models of transcription, and recent applications to the problem of bacterial chemotaxis. As part of the description of these case studies, we explore a number of different uses of the famed Monod–Wyman–Changeux (MWC) model as a generic tool for providing a mathematical characterization of two-state systems. These case studies should provide a template for tailoring equilibrium ideas to other problems of biological interest. PMID:21333788

  2. Thermodynamics "beyond" local equilibrium

    Science.gov (United States)

    Vilar, Jose; Rubi, Miguel

    2002-03-01

    Nonequilibrium thermodynamics has shown its applicability in a wide variety of different situations pertaining to fields such as physics, chemistry, biology, and engineering. As successful as it is, however, its current formulation considers only systems close to equilibrium, those satisfying the so-called local equilibrium hypothesis. Here we show that diffusion processes that occur far away from equilibrium can be viewed as at local equilibrium in a space that includes all the relevant variables in addition to the spatial coordinate. In this way, nonequilibrium thermodynamics can be used and the difficulties and ambiguities associated with the lack of a thermodynamic description disappear. We analyze explicitly the inertial effects in diffusion and outline how the main ideas can be applied to other situations. [J.M.G. Vilar and J.M. Rubi, Proc. Natl. Acad. Sci. USA 98, 11081-11084 (2001)].

  3. Statistical thermodynamics of alloys

    CERN Document Server

    Gokcen, N A

    1986-01-01

    This book is intended for scientists, researchers, and graduate students interested in solutions in general, and solutions of metals in particular. Readers are assumed to have a good background in thermodynamics, presented in such books as those cited at the end of Chapter 1, "Thermo­ dynamic Background." The contents of the book are limited to the solutions of metals + metals, and metals + metalloids, but the results are also appli­ cable to numerous other types of solutions encountered by metallurgists, materials scientists, geologists, ceramists, and chemists. Attempts have been made to cover each topic in depth with numerical examples whenever necessary. Chapter 2 presents phase equilibria and phase diagrams as related to the thermodynamics of solutions. The emphasis is on the binary diagrams since the ternary diagrams can be understood in terms of the binary diagrams coupled with the phase rule, and the Gibbs energies of mixing. The cal­ culation of thermodynamic properties from the phase diagrams is ...

  4. Extended Irreversible Thermodynamics

    CERN Document Server

    Jou, David

    2010-01-01

    This is the 4th edition of the highly acclaimed monograph on Extended Irreversible Thermodynamics, a theory that goes beyond the classical theory of irreversible processes. In contrast to the classical approach, the basic variables describing the system are complemented by non-equilibrium quantities. The claims made for extended thermodynamics are confirmed by the kinetic theory of gases and statistical mechanics. The book covers a wide spectrum of applications, and also contains a thorough discussion of the foundations and the scope of the current theories on non-equilibrium thermodynamics. For this new edition, the authors critically revised existing material while taking into account the most recent developments in fast moving fields such as heat transport in micro- and nanosystems or fast solidification fronts in materials sciences. Several fundamental chapters have been revisited emphasizing physics and applications over mathematical derivations. Also, fundamental questions on the definition of non-equil...

  5. Thermodynamics and Thermoeconomics

    Directory of Open Access Journals (Sweden)

    Yehia M. El-Sayed

    1999-03-01

    Full Text Available Raising the efficiency of an energy system is within the domain of thermodynamics. Raising the efficiency cost-effectively (Thermoeconomics is a multi-disciplinary problem in which thermodynamics interfaces other disciplines of knowledge which in this particular case are design, manufacture and economics. This paper deals with a communication/optimization strategy, via the concept of costing equations, whereby the system can be analyzed and optimized for minimum cost within the domain of thermodynamics. The communication/optimization strategy is explained. The generation of costing equations is demonstrated. A gas turbine power system and seawater distillation process system are used as examples for improved design point and improved configuration. The results of their optimized design points for configurations in order of increasing complexity are displayed on cost-efficiency coordinates.

  6. Thermodynamics of Nonadditive Systems.

    Science.gov (United States)

    Latella, Ivan; Pérez-Madrid, Agustín; Campa, Alessandro; Casetti, Lapo; Ruffo, Stefano

    2015-06-12

    The usual formulation of thermodynamics is based on the additivity of macroscopic systems. However, there are numerous examples of macroscopic systems that are not additive, due to the long-range character of the interaction among the constituents. We present here an approach in which nonadditive systems can be described within a purely thermodynamics formalism. The basic concept is to consider a large ensemble of replicas of the system where the standard formulation of thermodynamics can be naturally applied and the properties of a single system can be consequently inferred. After presenting the approach, we show its implementation in systems where the interaction decays as 1/r(α) in the interparticle distance r, with α smaller than the embedding dimension d, and in the Thirring model for gravitational systems.

  7. Thermodynamics of Crystalline States

    CERN Document Server

    Fujimoto, Minoru

    2010-01-01

    Thermodynamics is a well-established discipline of physics for properties of matter in thermal equilibrium surroundings. Applying to crystals, however, the laws encounter undefined properties of crystal lattices, which therefore need to be determined for a clear and well-defined description of crystalline states. Thermodynamics of Crystalline States explores the roles played by order variables and dynamic lattices in crystals in a wholly new way. This book is divided into three parts. The book begins by clarifying basic concepts for stable crystals. Next, binary phase transitions are discussed to study collective motion of order variables, as described mostly as classical phenomena. In the third part, the multi-electron system is discussed theoretically, as a quantum-mechanical example, for the superconducting state in metallic crystals. Throughout the book, the role played by the lattice is emphasized and examined in-depth. Thermodynamics of Crystalline States is an introductory treatise and textbook on meso...

  8. The physical basis of thermodynamics with applications to chemistry

    CERN Document Server

    Richet, Pascal

    2001-01-01

    Given that thermodynamics books are not a rarity on the market, why would an additional one be useful? The answer is simple: at any level, thermodynamics is usually taught as a somewhat abstruse discipline where many students get lost in a maze of difficult concepts. However, thermodynamics is not as intricate a subject as most people feel. This book fills a niche between elementary textbooks and mathematically oriented treatises, and provides readers with a distinct approach to the subject. As indicated by the title, this book explains thermodynamic phenomena and concepts in physical terms before proceeding to focus on the requisite mathematical aspects. It focuses on the effects of pressure, temperature and chemical composition on thermodynamic properties and places emphasis on rapidly evolving fields such as amorphous materials, metastable phases, numerical simulations of microsystems and high-pressure thermodynamics. Topics like redox reactions are dealt with in less depth, due to the fact that there is a...

  9. Thermodynamics of graphene

    Science.gov (United States)

    Rusanov, A. I.

    2014-12-01

    The 21st century has brought a lot of new results related to graphene. Apparently, graphene has been characterized from all points of view except surface science and, especially, surface thermodynamics. This report aims to close this gap. Since graphene is the first real two-dimensional solid, a general formulation of the thermodynamics of two-dimensional solid bodies is given. The two-dimensional chemical potential tensor coupled with stress tensor is introduced, and fundamental equations are derived for energy, free energy, grand thermodynamic potential (in the classical and hybrid forms), enthalpy, and Gibbs energy. The fundamentals of linear boundary phenomena are formulated with explaining the concept of a dividing line, the mechanical and thermodynamic line tensions, line energy and other linear properties with necessary thermodynamic equations. The one-dimensional analogs of the Gibbs adsorption equation and Shuttleworth-Herring relation are presented. The general thermodynamic relationships are illustrated with calculations based on molecular theory. To make the reader sensible of the harmony of chemical and van der Waals forces in graphene, the remake of the classical graphite theory is presented with additional variable combinations of graphene sheets. The calculation of the line energy of graphene is exhibited including contributions both from chemical bonds and van der Waals forces (expectedly, the latter are considerably smaller than the former). The problem of graphene holes originating from migrating vacancies is discussed on the basis of the Gibbs-Curie principle. An important aspect of line tension is the planar sheet/nanotube transition where line tension acts as a driving force. Using the bending stiffness of graphene, the possible radius range is estimated for achiral (zigzag and armchair) nanotubes.

  10. Concise chemical thermodynamics

    CERN Document Server

    Peters, APH

    2010-01-01

    EnergyThe Realm of ThermodynamicsEnergy BookkeepingNature's Driving ForcesSetting the Scene: Basic IdeasSystem and SurroundingsFunctions of StateMechanical Work and Expanding GasesThe Absolute Temperature Scale Forms of Energy and Their Interconversion Forms of Renewable Energy Solar Energy Wind Energy Hydroelectric Power Geothermal Energy Biomass Energy References ProblemsThe First Law of Thermodynamics Statement of the First Law Reversible Expansion of an Ideal GasConstant-Volume ProcessesConstant-Pressure ProcessesA New Function: EnthalpyRelationship between ?H and ?UUses and Conventions of

  11. Thermodynamics II essentials

    CERN Document Server

    REA, The Editors of

    2013-01-01

    REA's Essentials provide quick and easy access to critical information in a variety of different fields, ranging from the most basic to the most advanced. As its name implies, these concise, comprehensive study guides summarize the essentials of the field covered. Essentials are helpful when preparing for exams, doing homework and will remain a lasting reference source for students, teachers, and professionals. Thermodynamics II includes review of thermodynamic relations, power and refrigeration cycles, mixtures and solutions, chemical reactions, chemical equilibrium, and flow through nozzl

  12. Thermodynamics of ABC transporters.

    Science.gov (United States)

    Zhang, Xuejun C; Han, Lei; Zhao, Yan

    2016-01-01

    ABC transporters form the largest of all transporter families, and their structural study has made tremendous progress over recent years. However, despite such advances, the precise mechanisms that determine the energy-coupling between ATP hydrolysis and the conformational changes following substrate binding remain to be elucidated. Here, we present our thermodynamic analysis for both ABC importers and exporters, and introduce the two new concepts of differential-binding energy and elastic conformational energy into the discussion. We hope that the structural analysis of ABC transporters will henceforth take thermodynamic aspects of transport mechanisms into account as well.

  13. Mechanics, Waves and Thermodynamics

    Science.gov (United States)

    Ranjan Jain, Sudhir

    2016-05-01

    Figures; Preface; Acknowledgement; 1. Energy, mass, momentum; 2. Kinematics, Newton's laws of motion; 3. Circular motion; 4. The principle of least action; 5. Work and energy; 6. Mechanics of a system of particles; 7. Friction; 8. Impulse and collisions; 9. Central forces; 10. Dimensional analysis; 11. Oscillations; 12. Waves; 13. Sound of music; 14. Fluid mechanics; 15. Water waves; 16. The kinetic theory of gases; 17. Concepts and laws of thermodynamics; 18. Some applications of thermodynamics; 19. Basic ideas of statistical mechanics; Bibliography; Index.

  14. Components in Chemical Thermodynamics

    Science.gov (United States)

    Alberty, Robert A.

    1995-09-01

    Chemical equations are actually matrix equations, and this has important implications for their thermodynamic treatment. The fundamental equation for chemical thermodynamics for a chemical reaction system can be written in terms of species, but at chemical equilibrium, it has to be written in terms of components. The number of components is equal to the number of species minus the number of independent chemical reactions. The fundamental equation for the Gibbs energy of a system containing ethylene, methane, ethane, and propane is discussed. At chemical equilibrium there are two components, which can be taken to be carbon and hydrogen or ethylene and methane. There are advantages in using matrix notation.

  15. Black Hole Thermodynamics

    CERN Document Server

    Carlip, S

    2014-01-01

    The discovery in the early 1970s that black holes radiate as black bodies has radically affected our understanding of general relativity, and offered us some early hints about the nature of quantum gravity. In this chapter I will review the discovery of black hole thermodynamics and summarize the many independent ways of obtaining the thermodynamic and (perhaps) statistical mechanical properties of black holes. I will then describe some of the remaining puzzles, including the nature of the quantum microstates, the problem of universality, and the information loss paradox.

  16. Investigating different analytical procedures to unfold neutron energy spectra, using HEPRO software to compare existing algorithms

    CERN Document Server

    Moghimzadeh Mohebi, A

    1999-01-01

    A system of programs is described which can be used for unfolding particle spectra from measured pulse height distribution, provided the corresponding response functions are known. There are two reasons for re-opening the question of unfolding: to discuss the properties of several unfolding algorithms and to describe a system of programs developed in the past to unfold neutron spectra. In the first part, least squares algorithms known from literature are described and discussed together with the MIEKE Monte Carlo unfolding code. The second part contains a detailed description of the codes, which are available on a diskette. In the discussion of examples it is shown that the MIEKE Monte Carlo code is well suited for unfolding neutron and photon induced pulse height distributions. For the resulting particle spectra a consistent uncertainty analysis can be performed.

  17. Molecular simulation of the reversible mechanical unfolding of proteins.

    Science.gov (United States)

    Rathore, Nitin; Yan, Qiliang; de Pablo, Juan J

    2004-03-22

    In this work we have combined a Wang-Landau sampling scheme [F. Wang and D. Landau, Phys. Rev. Lett. 86, 2050 (2001)] with an expanded ensemble formalism to yield a simple and powerful method for computing potentials of mean force. The new method is implemented to investigate the mechanical deformation of proteins. Comparisons are made with analytical results for simple model systems such as harmonic springs and Rouse chains. The method is then illustrated on a model 15-residue alanine molecule in an implicit solvent. Results for mechanical unfolding of this oligopeptide are compared to those of steered molecular dynamics calculations.

  18. Unfolding multicourse case study: developing students' administrative competencies.

    Science.gov (United States)

    Porter-Wenzlaffs, Linda J

    2013-01-01

    Providing students with learning opportunities that integrate disparate data into meaningful constructs can be a challenge for faculty. The author discusses an unfolding case study that provided simulated learning opportunities related to administrative student competencies, staged to increase in complexity and scope over time while affording multiple student evaluation opportunities. A hybrid delivery format was used, including Blackboard Learn e-technology, to support individual student assignments and small group collaboration, cloud technology for shared student document development, Excel budget manipulation, and face-to-face classroom interactions.

  19. Cluster algebras of finite mutation type via unfoldings

    CERN Document Server

    Felikson, Anna; Tumarkin, Pavel

    2010-01-01

    We complete classification of mutation-finite cluster algebras by extending the technique derived by Fomin, Shapiro, and Thurston to skew-symmetrizable case. We show that every mutation-finite skew-symmetrizable matrix admits an unfolding which embeds the mutation class of mutation-finite skew-symmetrizable matrix to the mutation class of some mutation-finite skew-symmetric matrix. In particular, this establishes a correspondence between almost all skew-symmetrizable mutation-finite cluster algebras and triangulated marked bordered surfaces.

  20. ARU – towards automatic unfolding of detector effects

    CERN Document Server

    Dembinski, H P

    2011-01-01

    This article presents the ARU algorithm, a general non-interactive algorithmfor the unfolding of detector effects (resolution effects, efficiency, non-linearresponse) from one-dimensional data distributions. ARU uses an unbinnedmaximum-likelihood fit with a weighted regularization term, based on the rel-ative information in the solution with respect to a reference distribution. Theoptimal regularization weight is found by minimizing the mean squared errorof the solution. The algorithm’s performance is demonstrated in a study of atoy data sets. The analysis shows that the bias on average is smaller than thestatistical uncertainties which are properly estimated by the fit.

  1. Natively unfolded domains in endocytosis: hooks, lines and linkers

    OpenAIRE

    Dafforn, Timothy R.; Smith, Corinne J I

    2004-01-01

    It is commonly assumed that a protein must adopt a tertiary structure to achieve its active native state and that regions of a protein that are devoid of α-helix or β-sheet structures are functionally inert. Although extended proline-rich regions are recognized as presenting binding motifs to, for example, Src homology 2 (SH2) and SH3 domains, the idea persists that natively unfolded regions in functional proteins are simply 'spacers' between the folded domains. Such a view has been challenge...

  2. Unfolding of Vortices into Topological Stripes in a Multiferroic Material

    Science.gov (United States)

    Wang, X.; Mostovoy, M.; Han, M. G.; Horibe, Y.; Aoki, T.; Zhu, Y.; Cheong, S.-W.

    2014-06-01

    Multiferroic hexagonal RMnO3 (R =rare earths) crystals exhibit dense networks of vortex lines at which six domain walls merge. While the domain walls can be readily moved with an applied electric field, the vortex cores so far have been impossible to control. Our experiments demonstrate that shear strain induces a Magnus-type force pulling vortices and antivortices in opposite directions and unfolding them into a topological stripe domain state. We discuss the analogy between this effect and the current-driven dynamics of vortices in superconductors and superfluids.

  3. Unfolded protein response in plants: one master, many questions.

    Science.gov (United States)

    Ruberti, Cristina; Kim, Sang-Jin; Stefano, Giovanni; Brandizzi, Federica

    2015-10-01

    To overcome endoplasmic reticulum (ER) stress, ER-localized stress sensors actuate distinct downstream organelle-nucleus signaling pathways to invoke a cytoprotective response, known as the unfolded protein response (UPR). Compared to yeast and metazoans, plant UPR studies are more recent but nevertheless fascinating. Here we discuss recent discoveries in plant UPR, highlight conserved and unique features of the plant UPR as well as critical yet-open questions whose answers will likely make significant contributions to the understanding plant ER stress management.

  4. Experimental thermodynamics experimental thermodynamics of non-reacting fluids

    CERN Document Server

    Neindre, B Le

    2013-01-01

    Experimental Thermodynamics, Volume II: Experimental Thermodynamics of Non-reacting Fluids focuses on experimental methods and procedures in the study of thermophysical properties of fluids. The selection first offers information on methods used in measuring thermodynamic properties and tests, including physical quantities and symbols for physical quantities, thermodynamic definitions, and definition of activities and related quantities. The text also describes reference materials for thermometric fixed points, temperature measurement under pressures, and pressure measurements. The publicatio

  5. Activation foils unfolding for neutron spectrometry: Comparison of different deconvolution methods

    Energy Technology Data Exchange (ETDEWEB)

    Tripathy, S.P. [Radiation Safety Systems Division, BARC, Mumbai 400085 (India)], E-mail: sam.tripathy@gmail.com; Sunil, C. [Radiation Safety Systems Division, BARC, Mumbai 400085 (India); Nandy, M. [Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata 700064 (India); Sarkar, P.K. [Radiation Safety Systems Division, BARC, Mumbai 400085 (India); Variable Energy Cyclotron Centre, 1/AF Bidhan Nagar, Kolkata 700064 (India); Sharma, D.N. [Radiation Safety Systems Division, BARC, Mumbai 400085 (India); Mukherjee, B. [Deutsches Elektronen-Synchrotron, LLRF Group, D-22607 Hamburg (Germany)

    2007-12-21

    The results obtained from the activation foils measurement are unfolded using two different deconvolution methods such as BUNKI and genetic algorithm (GA). The spectra produced by these codes agree fairly with each other and are comparable with that measured previously for the same system using NE213 liquid scintillator and by unfolding the neutron-induced proton pulse height distribution using two different methods, viz. FERDOR and BUNKI. The details of various unfolding procedures used in this work are reported in this paper.

  6. Molecular Dynamics Simulations of the Temperature Induced Unfolding of Crambin Follow the Arrhenius Equation.

    Science.gov (United States)

    Dalby, Andrew; Shamsir, Mohd Shahir

    2015-01-01

    Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation.

  7. Black Hole Thermodynamics in an Undergraduate Thermodynamics Course.

    Science.gov (United States)

    Parker, Barry R.; McLeod, Robert J.

    1980-01-01

    An analogy, which has been drawn between black hole physics and thermodynamics, is mathematically broadened in this article. Equations similar to the standard partial differential relations of thermodynamics are found for black holes. The results can be used to supplement an undergraduate thermodynamics course. (Author/SK)

  8. Correct thermodynamic forces in Tsallis thermodynamics: connection with Hill nanothermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Morales, Vladimir [Departament de Termodinamica, Universitat de Valencia, C/Dr. Moliner 50, E-46100 Burjassot (Spain)]. E-mail: vladimir.garcia@uv.es; Cervera, Javier [Departament de Termodinamica, Universitat de Valencia, C/Dr. Moliner 50, E-46100 Burjassot (Spain); Pellicer, Julio [Departament de Termodinamica, Universitat de Valencia, C/Dr. Moliner 50, E-46100 Burjassot (Spain)

    2005-02-28

    The equivalence between Tsallis thermodynamics and Hill's nanothermodynamics is established. The correct thermodynamic forces in Tsallis thermodynamics are pointed out. Through this connection we also find a general expression for the entropic index q which we illustrate with two physical examples, allowing in both cases to relate q to the underlying dynamics of the Hamiltonian systems.

  9. Thermodynamic properties of bulk and confined water

    Energy Technology Data Exchange (ETDEWEB)

    Mallamace, Francesco, E-mail: francesco.mallamace@unime.it [Dipartimento di Fisica e Scienza della Terra Università di Messina and CNISM, I-98168 Messina (Italy); Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215 (United States); Corsaro, Carmelo [Dipartimento di Fisica e Scienza della Terra Università di Messina and CNISM, I-98168 Messina (Italy); Mallamace, Domenico [Dipartimento di Scienze dell' Ambiente, della Sicurezza, del Territorio, degli Alimenti e della Salute, Università di Messina, I-98166 Messina (Italy); Vasi, Sebastiano; Vasi, Cirino [IPCF-CNR, I-98166 Messina (Italy); Stanley, H. Eugene [Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215 (United States)

    2014-11-14

    The thermodynamic response functions of water display anomalous behaviors. We study these anomalous behaviors in bulk and confined water. We use nuclear magnetic resonance (NMR) to examine the configurational specific heat and the transport parameters in both the thermal stable and the metastable supercooled phases. The data we obtain suggest that there is a behavior common to both phases: that the dynamics of water exhibit two singular temperatures belonging to the supercooled and the stable phase, respectively. One is the dynamic fragile-to-strong crossover temperature (T{sub L} ≃ 225 K). The second, T{sup *} ∼ 315 ± 5 K, is a special locus of the isothermal compressibility K{sub T}(T, P) and the thermal expansion coefficient α{sub P}(T, P) in the P–T plane. In the case of water confined inside a protein, we observe that these two temperatures mark, respectively, the onset of protein flexibility from its low temperature glass state (T{sub L}) and the onset of the unfolding process (T{sup *})

  10. A Hamiltonian approach to Thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Baldiotti, M.C., E-mail: baldiotti@uel.br [Departamento de Física, Universidade Estadual de Londrina, 86051-990, Londrina-PR (Brazil); Fresneda, R., E-mail: rodrigo.fresneda@ufabc.edu.br [Universidade Federal do ABC, Av. dos Estados 5001, 09210-580, Santo André-SP (Brazil); Molina, C., E-mail: cmolina@usp.br [Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, Av. Arlindo Bettio 1000, CEP 03828-000, São Paulo-SP (Brazil)

    2016-10-15

    In the present work we develop a strictly Hamiltonian approach to Thermodynamics. A thermodynamic description based on symplectic geometry is introduced, where all thermodynamic processes can be described within the framework of Analytic Mechanics. Our proposal is constructed on top of a usual symplectic manifold, where phase space is even dimensional and one has well-defined Poisson brackets. The main idea is the introduction of an extended phase space where thermodynamic equations of state are realized as constraints. We are then able to apply the canonical transformation toolkit to thermodynamic problems. Throughout this development, Dirac’s theory of constrained systems is extensively used. To illustrate the formalism, we consider paradigmatic examples, namely, the ideal, van der Waals and Clausius gases. - Highlights: • A strictly Hamiltonian approach to Thermodynamics is proposed. • Dirac’s theory of constrained systems is extensively used. • Thermodynamic equations of state are realized as constraints. • Thermodynamic potentials are related by canonical transformations.

  11. Thermodynamic stabilization of colloids

    NARCIS (Netherlands)

    Stol, R.J.; Bruyn, P.L. de

    1980-01-01

    An analysis is given of the conditions necessary for obtaining a thermodynamically stable dispersion (TSD) of solid particles in a continuous aqueous solution phase. The role of the adsorption of potential-determining ions at the planar interface in lowering the interfacial free energy (γ) to promot

  12. Thermodynamics of liquid metal

    Energy Technology Data Exchange (ETDEWEB)

    Kushnirenko, A.N.

    1988-01-01

    The thermodynamics of a liquid metal based on quantum-mechanical models of the crystal, electronic, and nuclear structures of the metal are derived in this paper. The models are based on such formulations as the Bohr radius, the Boltzmann constant, the Planck Law, the Fermi surface, and the Pauli principle.

  13. Thermodynamically Stable Pickering Emulsions

    NARCIS (Netherlands)

    Sacanna, S.; Kegel, W.K.; Philipse, A.P.

    2007-01-01

    We show that under appropriate conditions, mixtures of oil, water, and nanoparticles form thermodynamically stable oil-in-water emulsions with monodisperse droplet diameters in the range of 30–150 nm. This observation challenges current wisdom that so-called Pickering emulsions are at most metastabl

  14. Thermodynamical Arguments against Evolution

    Science.gov (United States)

    Rosenhouse, Jason

    2017-01-01

    The argument that the second law of thermodynamics contradicts the theory of evolution has recently been revived by anti-evolutionists. In its basic form, the argument asserts that whereas evolution implies that there has been an increase in biological complexity over time, the second law, a fundamental principle of physics, shows this to be…

  15. On Teaching Thermodynamics

    Science.gov (United States)

    Debbasch, F.

    2011-01-01

    The logical structure of classical thermodynamics is presented in a modern, geometrical manner. The first and second law receive clear, operatively oriented statements and the Gibbs free energy extremum principle is fully discussed. Applications relevant to chemistry, such as phase transitions, dilute solutions theory and, in particular, the law…

  16. The thermodynamics of portfolios

    OpenAIRE

    Edward W. Piotrowski; Jan Sladkowski

    2000-01-01

    We propose a new method of valuation of portfolios and their respective investing strategies. To this end we define a canonical ensemble of portfolios that allows to use the formalism of thermodynamics. (final version published in Acta Phys.Pol.B,32(2001)597-604)

  17. On Teaching Thermodynamics

    Science.gov (United States)

    Debbasch, F.

    2011-01-01

    The logical structure of classical thermodynamics is presented in a modern, geometrical manner. The first and second law receive clear, operatively oriented statements and the Gibbs free energy extremum principle is fully discussed. Applications relevant to chemistry, such as phase transitions, dilute solutions theory and, in particular, the law…

  18. Chemical thermodynamics. An introduction

    Energy Technology Data Exchange (ETDEWEB)

    Keszei, Ernoe [Budapest Univ. (Hungary). Dept. of Physical Chemistry

    2012-07-01

    Eminently suitable as a required textbook comprising complete material for or an undergraduate chemistry major course in chemical thermodynamics. Clearly explains details of formal derivations that students can easily follow and so master applied mathematical operations. Offers problems and solutions at the end of each chapter for self-test and self- or group study. This course-derived undergraduate textbook provides a concise explanation of the key concepts and calculations of chemical thermodynamics. Instead of the usual 'classical' introduction, this text adopts a straightforward postulatory approach that introduces thermodynamic potentials such as entropy and energy more directly and transparently. Structured around several features to assist students' understanding, Chemical Thermodynamics: - Develops applications and methods for the ready treatment of equilibria on a sound quantitative basis. - Requires minimal background in calculus to understand the text and presents formal derivations to the student in a detailed but understandable way. - Offers end-of-chapter problems (and answers) for self-testing and review and reinforcement, of use for self- or group study. This book is suitable as essential reading for courses in a bachelor and master chemistry program and is also valuable as a reference or textbook for students of physics, biochemistry and materials science.

  19. Thermodynamics in dynamical spacetimes

    CERN Document Server

    Tresguerres, Romualdo

    2013-01-01

    We derive a general formulation of the laws of irreversible thermodynamics in the presence of electromagnetism and gravity. For the handling of macroscopic material media, we use as a guide the field equations and the Noether identities of fundamental matter as deduced in the framework of gauge theories of the Poincar\\'e$\\otimes U(1)$ group.

  20. On the polymer physics origins of protein folding thermodynamics

    Science.gov (United States)

    Taylor, Mark P.; Paul, Wolfgang; Binder, Kurt

    2016-11-01

    A remarkable feature of the spontaneous folding of many small proteins is the striking similarity in the thermodynamics of the folding process. This process is characterized by simple two-state thermodynamics with large and compensating changes in entropy and enthalpy and a funnel-like free energy landscape with a free-energy barrier that varies linearly with temperature. One might attribute the commonality of this two-state folding behavior to features particular to these proteins (e.g., chain length, hydrophobic/hydrophilic balance, attributes of the native state) or one might suspect that this similarity in behavior has a more general polymer-physics origin. Here we show that this behavior is also typical for flexible homopolymer chains with sufficiently short range interactions. Two-state behavior arises from the presence of a low entropy ground (folded) state separated from a set of high entropy disordered (unfolded) states by a free energy barrier. This homopolymer model exhibits a funneled free energy landscape that reveals a complex underlying dynamics involving competition between folding and non-folding pathways. Despite the presence of multiple pathways, this simple physics model gives the robust result of two-state thermodynamics for both the cases of folding from a basin of expanded coil states and from a basin of compact globule states.

  1. Understanding how biodiversity unfolds through time under neutral theory.

    Science.gov (United States)

    Missa, Olivier; Dytham, Calvin; Morlon, Hélène

    2016-04-05

    Theoretical predictions for biodiversity patterns are typically derived under the assumption that ecological systems have reached a dynamic equilibrium. Yet, there is increasing evidence that various aspects of ecological systems, including (but not limited to) species richness, are not at equilibrium. Here, we use simulations to analyse how biodiversity patterns unfold through time. In particular, we focus on the relative time required for various biodiversity patterns (macroecological or phylogenetic) to reach equilibrium. We simulate spatially explicit metacommunities according to the Neutral Theory of Biodiversity (NTB) under three modes of speciation, which differ in how evenly a parent species is split between its two daughter species. We find that species richness stabilizes first, followed by species area relationships (SAR) and finally species abundance distributions (SAD). The difference in timing of equilibrium between these different macroecological patterns is the largest when the split of individuals between sibling species at speciation is the most uneven. Phylogenetic patterns of biodiversity take even longer to stabilize (tens to hundreds of times longer than species richness) so that equilibrium predictions from neutral theory for these patterns are unlikely to be relevant. Our results suggest that it may be unwise to assume that biodiversity patterns are at equilibrium and provide a first step in studying how these patterns unfold through time.

  2. A neutron spectrum unfolding code based on iterative procedures

    Energy Technology Data Exchange (ETDEWEB)

    Ortiz R, J. M.; Vega C, H. R., E-mail: morvymm@yahoo.com.mx [Universidad Autonoma de Zacatecas, Unidad Academica de Ingenieria Electrica, Apdo. Postal 336, 98000 Zacatecas (Mexico)

    2012-10-15

    In this work, the version 3.0 of the neutron spectrum unfolding code called Neutron Spectrometry and Dosimetry from Universidad Autonoma de Zacatecas (NSDUAZ), is presented. This code was designed in a graphical interface under the LabVIEW programming environment and it is based on the iterative SPUNIT iterative algorithm, using as entrance data, only the rate counts obtained with 7 Bonner spheres based on a {sup 6}Lil(Eu) neutron detector. The main features of the code are: it is intuitive and friendly to the user; it has a programming routine which automatically selects the initial guess spectrum by using a set of neutron spectra compiled by the International Atomic Energy Agency. Besides the neutron spectrum, this code calculates the total flux, the mean energy, H(10), h(10), 15 dosimetric quantities for radiation protection porpoises and 7 survey meter responses, in four energy grids, based on the International Atomic Energy Agency compilation. This code generates a full report in html format with all relevant information. In this work, the neutron spectrum of a {sup 241}AmBe neutron source on air, located at 150 cm from detector, is unfolded. (Author)

  3. Thermodynamics for the practicing engineer

    CERN Document Server

    Theodore, Louis; Vanvliet, Timothy

    2009-01-01

    This book concentrates specifically on the applications of thermodynamics, rather than the theory. It addresses both technical and pragmatic problems in the field, and covers such topics as enthalpy effects, equilibrium thermodynamics, non-ideal thermodynamics and energy conversion applications. Providing the reader with a working knowledge of the principles of thermodynamics, as well as experience in their application, it stands alone as an easy-to-follow self-teaching aid to practical applications and contains worked examples.

  4. The Unfolded Protein Response Regulates Uterine Myocyte Antioxidant Responsiveness During Pregnancy.

    Science.gov (United States)

    Ramnarayanan, Saiprasad; Kyathanahalli, Chandrashekara; Ingles, Judith; Park-York, MieJung; Jeyasuria, Pancharatnam; Condon, Jennifer C

    2016-12-01

    There is considerable evidence that implicates oxidative stress in the pathophysiology of human pregnancy complications. However, the role and the mechanism of maintaining an antioxidant prosurvival uterine environment during normal pregnancy is largely unresolved. Herein we report that the highly active uterine unfolded protein response plays a key role in promoting antioxidant activity in the uterine myocyte across gestation. The unfolded protein response (UPR) senses the accumulation of misfolded proteins in the endoplasmic reticulum (ER) and activates a signaling network that consists of the transmembrane protein kinase eukaryotic translation initiation factor 2 alpha kinase 3/PKR-like-ER kinase (EIF2AK3), which acts to decrease protein translation levels, allowing for a lowered need for protein folding during periods of ER stress. However, independent of its translational regulatory capacity, EIF2AK3-dependent signals elicit the activation of the transcription factor, nuclear factor erythroid 2-like 2 (NFE2L2) in response to oxidative stress. NFE2L2 binds to antioxidant response elements in the promoters of a variety of antioxidant genes that minimize the opportunities for generation of reactive oxygen intermediates. Our analysis demonstrates that in the absence of EIF2AK3, the uterine myocyte experiences increased levels of reactive oxygen species due to decreased NFE2L2 activation. Elevated levels of intracellular reactive oxygen species were observed in the EIF2AK3 null cells, and this was associated with the onset of apoptotic cell death. These findings confirm the prosurvival and antioxidant role of UPR-mediated EIF2AK3 activation in the context of the human uterine myocyte.

  5. IUPAC conference on chemical thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    1984-01-01

    The 39th Calorimetry Conference includes papers on the following typics: thermodynamic properties of various compounds and materials; measuring methods and equipment for determination of thermodynamic quantities; calculation of thermodynamic quantities. Fossil fuels, nuclear fuels, electrochemistry, photochemistry, and biochemistry are areas of applications which are emphasized.

  6. Elementary statistical thermodynamics a problems approach

    CERN Document Server

    Smith, Norman O

    1982-01-01

    This book is a sequel to my Chemical Thermodynamics: A Prob­ lems Approach published in 1967, which concerned classical thermodynamics almost exclusively. Most books on statistical thermodynamics now available are written either for the superior general chemistry student or for the specialist. The author has felt the need for a text which would bring the intermediate reader to the point where he could not only appreciate the roots of the subject but also have some facility in calculating thermodynamic quantities. Although statistical thermodynamics comprises an essential part of the college training of a chemist, its treatment in general physical chem­ istry texts is, of necessity, compressed to the point where the less competent student is unable to appreciate or comprehend its logic and beauty, and is reduced to memorizing a series of formulas. It has been my aim to fill this need by writing a logical account of the foundations and applications of the sub­ ject at a level which can be grasped by an under...

  7. Thermodynamics Insights for the Redshift Drift

    Science.gov (United States)

    Zhang, Ming-Jian; Liu, Wen-Biao

    2015-01-01

    The secular redshift drift is a potential measurement to directly probe the cosmic expansion. Previous study on the redshift drift mainly focused on the model-dependent simulation. Apparently, the physical insights on the redshift drift are very necessary. So in this paper, it is investigated using thermodynamics on the apparent, Hubble and event horizons. Thermodynamics could analytically present the model-independent upper bounds of redshift drift. For specific assumption on the cosmological parameters, we find that the thermodynamics bounds are nearly one order of magnitude larger than the expectation in standard ΛCDM model. We then examine ten observed redshift drift from Green Bank Telescope at redshift 0.09 < z < 0.69, and find that these observational results are inconsistent with the thermodynamics. The size of the errorbars on these measurements is about three orders of magnitude larger than the effect of thermodynamical bounds for the redshift drift. Obviously, we have not yet hit any instrumental systematics at the shift level of 1m s-1 yr-1.

  8. Industrial Requirements for Thermodynamics and Transport Properties

    DEFF Research Database (Denmark)

    Hendriks, Eric; Kontogeorgis, Georgios; Dohrn, Ralf

    2010-01-01

    . The main results are as follows. There is (still) an acute need for accurate, reliable, and thermodynamically consistent experimental data. Quality is more important than quantity. Similarly, there is a great need for reliable predictive, rather than correlative, models covering a wide range...... addressed to or written by industrial colleagues, are discussed initially. This provides the context of the survey and material with which the results of the survey can be compared. The results of the survey have been divided into the themes: data, models, systems, properties, education, and collaboration...... reactive systems (simultaneous chemical and physical equilibrium). Education in thermodynamics is perceived as key, for the future application of thermodynamics in the industry. A number of suggestions for improvement were made at all three levels (undergraduate, postgraduate, and professional development...

  9. Estimation Using an Enhancement Factor on Non Local Thermodynamic Equilibrium Behavior of High-lying Energy Levels of Neutral Atom in Argon Radio-Frequency Inductively-Coupled Plasma.

    Science.gov (United States)

    Wagatsuma, Kazuaki; Satoh, Kozue

    2016-01-01

    This paper describes a plasma-diagnostic method using an enhancement factor on the Boltzmann distribution among emission lines of iron atom in an argon radio-frequency inductively-coupled plasma (ICP). It indicated that Boltzmann plots of the atomic lines having lower excitation energies (3.4 to 4.8 eV) were well fitted on a straight line while those having more than 5.5 eV deviated upwards from a linear relationship. This observation could be explained by the fact that ICP is not in a complete thermodynamic equilibrium between direct excitation to energy levels of iron atom, ionization of iron atom, and radiative decay processes to the ground state. Especially, the recombination of iron ion with captured electron should accompany cascade de-excitations between closely-spaced excited levels just below the ionization limit, the rates of which become slower as a whole; as a result, these high-lying levels might be more populated than the low-lying levels as if a different LTE condition coexists on the high energy side. This overpopulation could be quantitatively estimated using an enhancement factor (EF), which was a ratio of the observed intensity to the expected value extrapolated from the normal distribution on the low energy side. The EFs were generally small (less than 3); therefore, the cascade de-excitation process would slightly contribute to the population of these excited levels. It could be considered from variations of the EF that the overpopulation proceeded to a larger extent at lower radio-frequency forward powers, at higher flow rates of the carrier gas, or at higher observation heights. The reason for this is that the kinetic energy of energetic particles, such as electrons, becomes reduced under all of these plasma conditions, thus enabling the high-lying levels to be more populated by cascade de-excitation processes from iron ion rather than by collisional excitation processes with the energetic particles. A similar Boltzmann analysis using the EF

  10. Reactive oxygen species-mediated unfolded protein response pathways in preimplantation embryos

    Science.gov (United States)

    Ali, Ihsan; Shah, Syed Zahid Ali; Jin, Yi; Li, Zhong-Shu; Ullah, Obaid

    2017-01-01

    Excessive production of reactive oxygen species (ROS) and endoplasmic reticulum (ER) stress-mediated responses are critical to embryonic development in the challenging in vitro environment. ROS production increases during early embryonic development with the increase in protein requirements for cell survival and growth. The ER is a multifunctional cellular organelle responsible for protein folding, modification, and cellular homeostasis. ER stress is activated by a variety of factors including ROS. Such stress leads to activation of the adaptive unfolded protein response (UPR), which restores homeostasis. However, chronic stress can exceed the toleration level of the ER, resulting in cellular apoptosis. In this review, we briefly describe the generation and impact of ROS in preimplantation embryo development, the ROS-mediated activation mechanism of the UPR via the ER, and the subsequent activation of signaling pathways following ER stress in preimplantation embryos. PMID:28057903

  11. Thermodynamics of High Temperature Plasmas

    Directory of Open Access Journals (Sweden)

    Ettore Minardi

    2009-03-01

    Full Text Available In this work we discuss how and to what extent the thermodynamic concepts and the thermodynamic formalism can be extended to the description of high temperature states of the plasma not necessarily associated with a Boltzmann distribution and with thermal equilibrium.The discussion is based on the “magnetic or electrostatic entropy concept”, an interpretative and predictive tool based on probability and information, defined in a suitably coarse-grained possibility space of all current density or of all electric charge density distributions under testable constraints, and whose variation properties are proven to be related under certain conditions to the equilibrium and the stability of the system. In the case of magnetic equilibrium the potentiality of the magnetic entropy concept is illustrated by comparing the predictions of the current density and pressure profiles with the observations in different tokamak machines and different tokamak regimes, as well as by showing how the equilibrium and the stability in devices as different as the reversed field pinch or the magnetic well are described by the variation properties of the same entropy functional applied to the different situations. In fact it emerges that the maximum of the entropy can be seen in these different cases as an optimization constraint for the minimum of the magnetic energy. The application of the entropy concept to the electrostatic processes shows in particular that the so-called reactive instabilities (non-dissipative, non-resonant instabilities with a marginal point admit a neighboring state with higher entropy and are therefore of special relevance from the point of view of the physical evolution of the system. In this case the thermodynamic formalism allows the introduction of the concept of “thermodynamic fluctuations” of the macroscopic charge density and provides a method for the calculation of the “thermodynamic” fluctuation levels both on the stable as

  12. Optimization of parameters for cerium(III) biosorption onto biowaste materials of animal and plant origin using 5-level Box-Behnken design:Equilibrium, kinetic, thermodynamic and regeneration studies

    Institute of Scientific and Technical Information of China (English)

    Jaya Sre Varsihini C; Devlina Das; Nilanjana Das

    2014-01-01

    Response surface methodology (RSM) employing 5-level Box-Behnken design was used to optimize the biosorption of ce-rium(III) onto biowaste materials of animal and plant origin viz. prawn carapace (PC) and corn style (CS). Various process parame-ters viz. pH (A:3.0-9.0), biomass dosage (B:0.05-0.35 g/L), initial metal concentration (C:50-350 mg/L), contact time (D:2-6 h) and temperature (E:20-60 °C) were chosen for optimization. A log transformation was suggested by the Box-Cox plot in the present case. A low p-value of<0.0001 validated the significance of the model. Maximum Ce(III) uptake of 218.3 mg/g for PC and 180.2 mg/g for CS was noted under optimum conditions. Among the equilibrium isotherms, Freundlich model was found to be the best fit-ted one suggesting a heterogeneous mode of biosorption on PC whereas Langmuir model showed the best fit suggesting homogene-ous mode of cerium biosorption on CS. This was further confirmed by scanning electron microscopy (SEM). Kinetic studies showed better applicability of pseudo-first order model suggesting physisorption as phenomena underlying the process. Film-diffusion was suggested by the non-linearity of the Boyd plot. Thermodynamic studies showed that the process was endothermic and spontaneous. FTIR analysis confirmed a major involvement of the participation of amide, amines, ketones and primary alcohol groups during Ce(III) biosorption. EDAX analysis confirmed the major participation of carbon group during Ce(III) biosorption. This was the first report on parameter optimization of Ce(III) biosorption onto biowaste materials using 5-level Box-Behnken experimental design which might be helpful for the recovery of Ce(III) from aqueous environment.

  13. Common modulation of limbic network activation underlies musical emotions as they unfold.

    Science.gov (United States)

    Singer, Neomi; Jacoby, Nori; Lin, Tamar; Raz, Gal; Shpigelman, Lavi; Gilam, Gadi; Granot, Roni Y; Hendler, Talma

    2016-11-01

    Music is a powerful means for communicating emotions among individuals. Here we reveal that this continuous stream of affective information is commonly represented in the brains of different listeners and that particular musical attributes mediate this link. We examined participants' brain responses to two naturalistic musical pieces using functional Magnetic Resonance imaging (fMRI). Following scanning, as participants listened to the musical pieces for a second time, they continuously indicated their emotional experience on scales of valence and arousal. These continuous reports were used along with a detailed annotation of the musical features, to predict a novel index of Dynamic Common Activation (DCA) derived from ten large-scale data-driven functional networks. We found an association between the unfolding music-induced emotionality and the DCA modulation within a vast network of limbic regions. The limbic-DCA modulation further corresponded with continuous changes in two temporal musical features: beat-strength and tempo. Remarkably, this "collective limbic sensitivity" to temporal features was found to mediate the link between limbic-DCA and the reported emotionality. An additional association with the emotional experience was found in a left fronto-parietal network, but only among a sub-group of participants with a high level of musical experience (>5years). These findings may indicate two processing-levels underlying the unfolding of common music emotionality; (1) a widely shared core-affective process that is confined to a limbic network and mediated by temporal regularities in music and (2) an experience based process that is rooted in a left fronto-parietal network that may involve functioning of the 'mirror-neuron system'. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Thermodynamic Function of Life

    CERN Document Server

    Michaelian, K

    2009-01-01

    Darwinian Theory depicts life as being overwhelmingly consumed by a fight for survival in a hostile environment. However, from a thermodynamic perspective, life is a dynamic, out of equilibrium process, stabilizing and coevolving in concert with its abiotic environment. The living component of the biosphere of greatest mass, the plants and cyanobacteria, are involved in the transpiration of vast amounts of water. Transpiration is part of the global water cycle, and it is this cycle that distinguishes Earth from its life barren neighboring planets, Venus and Mars. The water cycle, including the absorption of sunlight in the biosphere, is by far the greatest entropy producing process occurring on Earth. Life, from this perspective, can therefore be viewed as performing an important thermodynamic function; acting as a dynamic catalyst by aiding process such as the water cycle, hurricanes, and ocean and wind currents to produce entropy. The role of animals in this view is that of unwitting but dedicated servants ...

  15. Mechanics and thermodynamics

    CERN Document Server

    Demtröder, Wolfgang

    2017-01-01

    This introduction to classical mechanics and thermodynamics provides an accessible and clear treatment of the fundamentals. Starting with particle mechanics and an early introduction to special relativity this textbooks enables the reader to understand the basics in mechanics. The text is written from the experimental physics point of view, giving numerous real life examples and applications of classical mechanics in technology. This highly motivating presentation deepens the knowledge in a very accessible way. The second part of the text gives a concise introduction to rotational motion, an expansion to rigid bodies, fluids and gases. Finally, an extensive chapter on thermodynamics and a short introduction to nonlinear dynamics with some instructive examples intensify the knowledge of more advanced topics. Numerous problems with detailed solutions are perfect for self study.

  16. A commentary on thermodynamics

    CERN Document Server

    Day, William Alan

    1988-01-01

    The aim of this book is to comment on, and clarify, the mathematical aspects of the theory of thermodynamics. The standard presentations of the subject are often beset by a number of obscurities associated with the words "state", "reversible", "irreversible", and "quasi-static". This book is written in the belief that such obscurities are best removed not by the formal axiomatization of thermodynamics, but by setting the theory in the wider context of a genuine field theory which incorporates the effects of heat conduction and intertia, and proving appropriate results about the governing differential equations of this field theory. Even in the simplest one-dimensional case it is a nontrivial task to carry through the details of this program, and many challenging problems remain open.

  17. Thermodynamics, entropy and waterwheels

    CERN Document Server

    Bagnoli, Franco

    2016-01-01

    In textbooks, it is often repeated that Carnot arrived to the formulation of the second law of thermodynamics without knowing the first, using the caloric theory. In fact, in his book, R\\'eflexions sur la puissance motrice du feu, he often repeats that the "fall" of the caloric through a heat engine is equivalent to the fall of the water through a water wheel. Actually, one can play the analogy between thermal and hydraulic machines all the way down, and discover, with the help of the first principle and introducing the concept of the absolute height, what really "falls" through a waterwheel, i.e., the entropy. Adding a bit of relativity it is possible to extend the analogy to real machines and also to introduce the analogous of third law of thermodynamics.

  18. Thermodynamics of Crystalline States

    CERN Document Server

    Fujimoto, Minoru

    2013-01-01

    Thermodynamics is a well-established discipline of physics for properties of matter in thermal equilibrium with the surroundings. Applying to crystals, however, the laws encounter undefined properties of crystal lattice, which therefore need to be determined for a clear and well-defined description of crystalline states. Thermodynamics of Crystalline States explores the roles played by order variables and dynamic lattices in crystals in a wholly new way. The book begins by clarifying basic concepts for stable crystals. Next, binary phase transitions are discussed to study collective motion of order variables, as described mostly as classical phenomena. New to this edition is the examination of magnetic crystals, where magnetic symmetry is essential for magnetic phase transitions. The multi-electron system is also discussed  theoretically, as a quantum-mechanical example, for superconductivity in metallic crystals. Throughout the book, the role played by the lattice is emphasized and studied in-depth. Thermod...

  19. Prediction of change in protein unfolding rates upon point mutations in two state proteins.

    Science.gov (United States)

    Chaudhary, Priyashree; Naganathan, Athi N; Gromiha, M Michael

    2016-09-01

    Studies on protein unfolding rates are limited and challenging due to the complexity of unfolding mechanism and the larger dynamic range of the experimental data. Though attempts have been made to predict unfolding rates using protein sequence-structure information there is no available method for predicting the unfolding rates of proteins upon specific point mutations. In this work, we have systematically analyzed a set of 790 single mutants and developed a robust method for predicting protein unfolding rates upon mutations (Δlnku) in two-state proteins by combining amino acid properties and knowledge-based classification of mutants with multiple linear regression technique. We obtain a mean absolute error (MAE) of 0.79/s and a Pearson correlation coefficient (PCC) of 0.71 between predicted unfolding rates and experimental observations using jack-knife test. We have developed a web server for predicting protein unfolding rates upon mutation and it is freely available at https://www.iitm.ac.in/bioinfo/proteinunfolding/unfoldingrace.html. Prominent features that determine unfolding kinetics as well as plausible reasons for the observed outliers are also discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Application of long-range order to predict unfolding rates of two-state proteins.

    Science.gov (United States)

    Harihar, B; Selvaraj, S

    2011-03-01

    Predicting the experimental unfolding rates of two-state proteins and models describing the unfolding rates of these proteins is quite limited because of the complexity present in the unfolding mechanism and the lack of experimental unfolding data compared with folding data. In this work, 25 two-state proteins characterized by Maxwell et al. (Protein Sci 2005;14:602–616) using a consensus set of experimental conditions were taken, and the parameter long-range order (LRO) derived from their three-dimensional structures were related with their experimental unfolding rates ln(k(u)). From the total data set of 30 proteins used by Maxwell et al. (Protein Sci 2005;14:602–616), five slow-unfolding proteins with very low unfolding rates were considered to be outliers and were not included in our data set. Except all beta structural class, LRO of both the all-alpha and mixed-class proteins showed a strong inverse correlation of r = -0.99 and -0.88, respectively, with experimental ln(k(u)). LRO shows a correlation of -0.62 with experimental ln(k(u)) for all-beta proteins. For predicting the unfolding rates, a simple statistical method has been used and linear regression equations were developed for individual structural classes of proteins using LRO, and the results obtained showed a better agreement with experimental results. Copyright © 2010 Wiley-Liss, Inc.

  1. Unfolding Mixed-Symmetry Fields in AdS and the BMV Conjecture I. General Formalism

    CERN Document Server

    Boulanger, Nicolas; Sundell, Per

    2009-01-01

    We present some generalities of unfolded on-shell dynamics that are useful in analyzing the BMV conjecture for mixed-symmetry fields in constantly curved backgrounds. In particular we discuss the unfolded notion of local degrees of freedom in theories with and without gravity and with and without massive deformation parameters, using the language of Weyl zero-form modules and their duals.

  2. Unfolding Semantics of the Untyped λ-Calculus with lectrec-Calculus with letrec

    NARCIS (Netherlands)

    Rochel, J.

    2016-01-01

    We investigate the relationship between finite terms in lambda-letrec, the lambda calculus with letrec, and the infinite lambda terms they express. We say that a lambda-letrec term expresses a lambda term if the latter can be obtained as an infinite unfolding of the former. Unfolding is the process

  3. Experimental parameterization of an energy function for the simulation of unfolded proteins

    DEFF Research Database (Denmark)

    Norgaard, A.B.; Ferkinghoff-Borg, Jesper; Lindorff-Larsen, K.

    2008-01-01

    The determination of conformational preferences in unfolded and disordered proteins is an important challenge in structural biology. We here describe an algorithm to optimize energy functions for the simulation of unfolded proteins. The procedure is based on the maximum likelihood principle...... and can be applied to a range of experimental data and energy functions including the force fields used in molecular dynamics simulations....

  4. Comparison of intra-organellar chaperone capacity for dealing with stress-induced protein unfolding

    NARCIS (Netherlands)

    Hageman, Jurre; Vos, Michel J.; van Waarde, Maria A. W. H.; Kampinga, Harm H.

    2007-01-01

    Molecular chaperones are essential for cells to prevent that partially unfolded proteins form non-functional, toxic aggregates. This requirement is increased when cells experience protein unfolding stresses and such could affect all compartments in the eukaryotic cell. Whether all organelles are equ

  5. The Application of an Unfolding Model of the PIRT Type to the Measurement of Attitude.

    Science.gov (United States)

    Andrich, David

    1988-01-01

    A simple probabilistic model for unfolding data collected by a direct response design in which responses were scored dichotomously was applied to the measurement of attitudes toward capital punishment. Responses conformed to the unfolding mechanism. Scale values of the statements were statistically equivalent to those of Thurstone's methods. (SLD)

  6. Using Data Augmentation and Markov Chain Monte Carlo for the Estimation of Unfolding Response Models

    Science.gov (United States)

    Johnson, Matthew S.; Junker, Brian W.

    2003-01-01

    Unfolding response models, a class of item response theory (IRT) models that assume a unimodal item response function (IRF), are often used for the measurement of attitudes. Verhelst and Verstralen (1993)and Andrich and Luo (1993) independently developed unfolding response models by relating the observed responses to a more common monotone IRT…

  7. Unfolding Case-Based Practicum Curriculum Infusing Crisis, Trauma, and Disaster Preparation

    Science.gov (United States)

    Greene, Catie A.; Williams, Amy E.; Harris, Pamela N.; Travis, Sterling P.; Kim, Sharon Y.

    2016-01-01

    The authors evaluated an unfolding case-based approach to a practicum in counseling course infusing crisis, trauma, and disaster preparation for changes in students' crisis self-efficacy across a semester. The course, informed by constructivist-developmental pedagogy and centered on the unfolding case, resulted in significant increases in…

  8. Mechanical unfolding of ribose binding protein and its comparison with other periplasmic binding proteins.

    Science.gov (United States)

    Kotamarthi, Hema Chandra; Narayan, Satya; Ainavarapu, Sri Rama Koti

    2014-10-01

    Folding and unfolding studies on large, multidomain proteins are still rare despite their high abundance in genomes of prokaryotes and eukaryotes. Here, we investigate the unfolding properties of a 271 residue, two-domain ribose binding protein (RBP) from the bacterial periplasm using single-molecule force spectroscopy. We observe that RBP predominately unfolds via a two-state pathway with an unfolding force of ∼80 pN and an unfolding contour length of ∼95 nm. Only a small population (∼15%) of RBP follows three-state pathways. The ligand binding neither increases the mechanical stability nor influences the unfolding flux of RBP through different pathways. The kinetic partitioning between two-state and three-state pathways, which has been reported earlier for other periplasmic proteins, is also observed in RBP, albeit to a lesser extent. These results provide important insights into the mechanical stability and unfolding processes of large two-domain proteins and highlight the contrasting features upon ligand binding. Protein structural topology diagrams are used to explain the differences in the mechanical unfolding behavior of RBP with other periplasmic binding proteins.

  9. The construction of periodic unfolding operators on some compact Riemannian manifolds

    DEFF Research Database (Denmark)

    Dobberschütz, Sören; Böhm, Michael

    2014-01-01

    The notion of periodic unfolding has become a standard tool in the theory of periodic homogenization. However, all the results obtained so far are only applicable to the "flat" Euclidean space R n. In this paper, we present a generalization of the method of periodic unfolding applicable to struct...

  10. Thermodynamic Origin of Life

    OpenAIRE

    Michaelian, K.

    2009-01-01

    Understanding the thermodynamic function of life may shed light on its origin. Life, as are all irreversible processes, is contingent on entropy production. Entropy production is a measure of the rate of the tendency of Nature to explore available microstates. The most important irreversible process generating entropy in the biosphere, and thus facilitating this exploration, is the absorption and transformation of sunlight into heat. Here we hypothesize that life began, and persists today, as...

  11. Thermodynamics and emergent universe

    CERN Document Server

    Ghosh, Saumya

    2016-01-01

    We show that in the isentropic scenario the first order thermodynamical particle creation model gives an emergent universe solution even when the chemical potential is non-zero. However there exists no emergent universe scenario in the second order non-equilibrium theory for the particle creation model. We then point out a correspondence between the particle creation model with barotropic equation of state and the equation of state giving rise to an emergent universe without particle creation in spatially flat FRW cosmology.

  12. Thermodynamics of Organic Compounds

    Science.gov (United States)

    1979-01-01

    General Techniques for Combustion of Liquid/Soli. Organic Compounds by Oxygen Bomb Calorimetry by Arthur J. Head, William D. Good, and Ccrnelius...Mosselman, Chap. 8; Combustion of Liquid/Solid Organic Compounds with Non-Metallic Hetero-Atoms by Arthur J. Head and William D. Good, Chap. 9; in...0 Box 95085 Washington, DC 20234 Los Angeles, CA 90045 National Bureau of Standards CINDAS Chemical Thermodynamics Division Purdue University

  13. Black Hole Thermodynamics

    Science.gov (United States)

    Israel, Werner

    This chapter reviews the conceptual developments on black hole thermodynamics and the attempts to determine the origin of black hole entropy in terms of their horizon area. The brick wall model and an operational approach are discussed. An attempt to understand at the microlevel how the quantum black hole acquires its thermal properties is included. The chapter concludes with some remarks on the extension of these techniques to describing the dynamical process of black hole evaporation.

  14. Unit 5. Thermodynamics (Summary)

    OpenAIRE

    Beléndez Vázquez, Augusto

    2012-01-01

    Summary of the "Unit 5. Thermodynamics" of course "Physical Foundations of Engineering I". Degree in Sound and Image Engineering, in Telecommunications. Polytechnic School of the University of Alicante Resumen del "Tema 5. Termodinámica" de la asignatura "Fundamentos Físicos de la Ingeniería I". Grado en Ingeniería en Sonido e Imagen en Telecomunicaciones. Escuela Politécnica Superior. Universidad de Alicante.

  15. Teaching the Quantal Exposition of the Unified Quantum Theory of Mechanics and Thermodynamics

    OpenAIRE

    von Spakovsky, Michael R.

    2006-01-01

    The author presents his experience in teaching at a graduate level the quantal exposition of a new non-statistically based paradigm of physics and thermodynamics. This paradigm, called the Unified Quantum Theory of Mechanics and Thermodynamics, applies to all systems large or small (including one particle systems) either in a state of thermodynamic (i.e. stable) equilibrium or not in a state of thermodynamic equilibrium. It uses as its primitives inertial mass, force, and time and in...

  16. Thermodynamical Arguments Against Evolution

    Science.gov (United States)

    Rosenhouse, Jason

    2017-02-01

    The argument that the second law of thermodynamics contradicts the theory of evolution has recently been revived by anti-evolutionists. In its basic form, the argument asserts that whereas evolution implies that there has been an increase in biological complexity over time, the second law, a fundamental principle of physics, shows this to be impossible. Scientists have responded primarily by noting that the second law does not rule out increases in complexity in open systems, and since the Earth receives energy from the Sun, it is an open system. This reply is correct as far as it goes, and it adequately rebuts the most crude versions of the second law argument. However, it is insufficient against more sophisticated versions, and it leaves many relevant aspects of thermodynamics unexplained. We shall consider the history of the argument, explain the nuances various anti-evolution writers have brought to it, and offer thorough explanations for why the argument is fallacious. We shall emphasize in particular that the second law is best viewed as a mathematical statement. Since anti-evolutionists never make use of the mathematical structure of thermodynamics, invocations of the second law never contribute anything substantive to their discourse.

  17. Nonequilibrium thermodynamics of nucleation

    Energy Technology Data Exchange (ETDEWEB)

    Schweizer, M., E-mail: marco.schweizer@math.ethz.ch [ETH Zurich, Department of Materials, Polymer Physics, Vladimir-Prelog-Weg 2, 8093 Zurich (Switzerland); Sagis, L. M. C., E-mail: leonard.sagis@wur.nl [ETH Zurich, Department of Materials, Polymer Physics, Vladimir-Prelog-Weg 2, 8093 Zurich (Switzerland); Food Physics Group, Wageningen University, Bornse Weilanden, 6708 WG Wageningen (Netherlands)

    2014-12-14

    We present a novel approach to nucleation processes based on the GENERIC framework (general equation for the nonequilibrium reversible-irreversible coupling). Solely based on the GENERIC structure of time-evolution equations and thermodynamic consistency arguments of exchange processes between a metastable phase and a nucleating phase, we derive the fundamental dynamics for this phenomenon, based on continuous Fokker-Planck equations. We are readily able to treat non-isothermal nucleation even when the nucleating cores cannot be attributed intensive thermodynamic properties. In addition, we capture the dynamics of the time-dependent metastable phase being continuously expelled from the nucleating phase, and keep rigorous track of the volume corrections to the dynamics. Within our framework the definition of a thermodynamic nuclei temperature is manifest. For the special case of nucleation of a gas phase towards its vapor-liquid coexistence, we illustrate that our approach is capable of reproducing recent literature results obtained by more microscopic considerations for the suppression of the nucleation rate due to nonisothermal effects.

  18. A thermodynamic study of Abeta(16-21) dissociation from a fibril using computer simulations

    Science.gov (United States)

    Dias, Cristiano; Mahmoudinobar, Farbod; Su, Zhaoqian

    Here, I will discuss recent all-atom molecular dynamics simulations with explicit water in which we studied the thermodynamic properties of Abeta(16-21) dissociation from an amyloid fibril. Changes in thermodynamics quantities, e.g., entropy, enthalpy, and volume, are computed from the temperature dependence of the free-energy computed using the umbrella sampling method. We find similarities and differences between the thermodynamics of peptide dissociation and protein unfolding. Similarly to protein unfolding, Abeta(16-21) dissociation is characterized by an unfavorable change in enthalpy, a favorable change in the entropic energy, and an increase in the heat capacity. A main difference is that peptide dissociation is characterized by a weak enthalpy-entropy compensation. We characterize dock and lock states of the peptide based on the solvent accessible surface area. The Lennard-Jones energy of the system is observed to increase continuously in lock and dock states as the peptide dissociates. The electrostatic energy increases in the lock state and it decreases in the dock state as the peptide dissociates. These results will be discussed as well as their implication for fibril growth.

  19. Unfolding and Refolding Embodiment into the Landscape of Ubiquitous Computing

    DEFF Research Database (Denmark)

    Schick, Lea; Malmborg, Lone

    2009-01-01

    how these are to an increasing extent focusing on sociality, context-awareness, relations, affects, connectedness, and collectivity we will examine how these new technological movements can change our perception of embodiment towards a distributed and shared one. By examining interactive textiles......This paper advocates the future of the body as a distributed and shared embodiment; an unfolded body that doesn’t end at one's skin, but emerges as intercorporeality between bodies and the technological environment. Looking at new tendencies within interaction design and ubiquitous computing to see...... as part of a future rising landscape of multi-sensory networks we will exemplify how the new technologies can shutter dichotomies and challenge traditional notions of embodiment and the subject. Finally, we show how this ‘new embodiment’ manifests Deleuze’s philosophy of the body as something unstable...

  20. Unfolding Education for Sustainable Development as Didactic Thinking and Practice

    Directory of Open Access Journals (Sweden)

    Katrine Dahl Madsen

    2013-09-01

    Full Text Available This article’s primary objective is to unfold how teachers translate education for sustainable development (ESD in a school context. The article argues that exploring tensions, ruptures and openings apparent in this meeting is crucial for the development of existing teaching practices in relation to ESD. The article draws on doctoral research involving interviews with researchers and teachers who have collaborated in ESD research and development projects at primary and secondary schools in two different countries, Denmark and Ireland. It is the teachers’ perspectives on the projects which form the analytical foundation; thus, it is the practices as seen from the ‘inside’. Furthermore, ESD practices are considered in a broader societal perspective, pointing to the critical power of the practice lens.

  1. Using unfolding case studies in a subject-centered classroom.

    Science.gov (United States)

    Day, Lisa

    2011-08-01

    The recently published report of the Carnegie Foundation's National Study of Nursing Education points out significant problems with classroom teaching in schools of nursing. This article suggests Palmer's idea of the subject-centered classroom as a way to transform nursing school classrooms into collaborative learning communities. For Palmer, the subject is the big idea of nursing practice-the nurse-patient/client/family/community relationship-that should take the lead in stimulating inquiry and discussion. The article goes on to describe how teachers can develop and use unfolding case studies to bring the subject to the center of the classroom. By doing so, the classroom becomes a place where students learn a sense of salience, develop their clinical imagination, and begin their formation as professional nurses.

  2. Thermal unfolding of a Ca- and Lanthanide-binding protein

    Energy Technology Data Exchange (ETDEWEB)

    Fahmy, Karim [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Biophysics; Goettfert, M. [Technische Univ. Dresden (Germany); Knoeppel, J.

    2017-06-01

    The MIIA (metal ion-induced autocleavage)-domain of the protein Vic001052 from the pathogen Vibrio coralliilyticus, comprises 173 amino acids and exhibits Ca-dependent autoproteolytic activity. It shows homology to nodulation proteins which are secreted by Rhizobiacea into plant host cells where they exert Ca-dependent functions. We have studied the structural and energetic aspects of metal protein interactions of the MIIA domain which appear attractive for engineering metal-binding synthetic peptides. Using a non-cleavable MIIA domain construct, we detected very similar structural changes upon binding to Ca{sup 2+} and Eu{sup 3+}. The thermal denaturation of the Ca-bound state was studied by circular dichroism spectroscopy. The metal-bound folded state unfolds reversibly into an unstructured metal-free state similar to the metal-free state at room temperature.

  3. Tannin-assisted aggregation of natively unfolded proteins

    Science.gov (United States)

    Zanchi, D.; Narayanan, T.; Hagenmuller, D.; Baron, A.; Guyot, S.; Cabane, B.; Bouhallab, S.

    2008-06-01

    Tannin-protein interactions are essentially physical: hydrophobic and hydrogen-bond-mediated. We explored the tannin-assisted protein aggregation on the case of β-casein, which is a natively unfolded protein known for its ability to form micellar aggregates. We used several tannins with specified length. Our SAXS results show that small tannins increase the number of proteins per micelle, but keeping their size constant. It leads to a tannin-assisted compactization of micelles. Larger tannins, with linear dimensions greater than the crown width of micelles, lead to the aggregation of micelles by a bridging effect. Experimental results can be understood within a model where tannins are treated as effective enhancers of hydrophobic attraction between specific sites in proteins.

  4. Nanoconfined circular and linear DNA - equilibrium conformations and unfolding kinetics

    CERN Document Server

    Alizadehheidari, M; Noble, C; Reiter-Schad, M; Nyberg, L K; Fritzsche, J; Mehlig, B; Tegenfeldt, J O; Ambjörnsson, T; Persson, F; Westerlund, F

    2016-01-01

    Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to linear configuration as a light-induced double strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to which extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA....

  5. The Unfolded Protein Response in Chronic Obstructive Pulmonary Disease.

    Science.gov (United States)

    Kelsen, Steven G

    2016-04-01

    Accumulation of nonfunctional and potentially cytotoxic, misfolded proteins in chronic obstructive pulmonary disease (COPD) is believed to contribute to lung cell apoptosis, inflammation, and autophagy. Because of its fundamental role as a quality control system in protein metabolism, the "unfolded protein response" (UPR) is of potential importance in the pathogenesis of COPD. The UPR comprises a series of transcriptional, translational, and post-translational processes that decrease protein synthesis while enhancing protein folding capacity and protein degradation. Several studies have suggested that the UPR contributes to lung cell apoptosis and lung inflammation in at least some subjects with human COPD. However, information on the prevalence of the UPR in subjects with COPD, the lung cells that manifest a UPR, and the role of the UPR in the pathogenesis of COPD is extremely limited and requires additional study.

  6. Unfolding the fast neutron spectra of a BC501A liquid scintillation detector using GRAVEL method

    CERN Document Server

    Chen, Yonghao; Lei, Jiarong; An, Li; Zhang, Xiaodong; Shao, Jianxiong; Zheng, Pu; Wang, Xinhua

    2013-01-01

    Accurate knowledge of the neutron energy spectra is useful in basic research and applications. The overall procedure of measuring and unfolding the fast neutron energy spectra with BC501A liquid scintillation detector is described. The recoil proton spectrum of Am-Be neutrons was obtained experimentally. With the NRESP7 code, the response matrix of detector was simulated. Combining the recoil proton spectrum and response matrix, the unfolding of neutron spectra was performed by GRAVEL iterative algorithm. A MatLab program based on the GRAVEL method was developed. The continuous neutron spectrum of Am-Be source and monoenergetic neutron spectrum of D-T source have been unfolded successfully and are in good agreement with their standard reference spectra. The unfolded Am-Be spectrum are more accurate than the spectra unfolded by artificial neural networks in recent years.

  7. Unfolding the fast neutron spectra of a BC501A liquid scintillation detector using GRAVEL method

    Science.gov (United States)

    Chen, YongHao; Chen, XiMeng; Lei, JiaRong; An, Li; Zhang, XiaoDong; Shao, JianXiong; Zheng, Pu; Wang, XinHua

    2014-10-01

    Accurate knowledge of the neutron energy spectra is useful in basic research and applications. The overall procedure of measuring and unfolding the fast neutron energy spectra with BC501A liquid scintillation detector is described. The recoil proton spectrum of 241Am-Be neutrons was obtained experimentally. With the NRESP7 code, the response matrix of detector was simulated. Combining the recoil proton spectrum and response matrix, the unfolding of neutron spectra was performed by GRAVEL iterative algorithm. A MatLab program based on the GRAVEL method was developed. The continuous neutron spectrum of 241Am-Be source and monoenergetic neutron spectrum of D-T source have been unfolded successfully and are in good agreement with their standard reference spectra. The unfolded 241Am-Be spectrum are more accurate than the spectra unfolded by artificial neural networks in recent years.

  8. A new neutron energy spectrum unfolding code using a two steps genetic algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Shahabinejad, H., E-mail: shahabinejad1367@yahoo.com; Hosseini, S.A.; Sohrabpour, M.

    2016-03-01

    A new neutron spectrum unfolding code TGASU (Two-steps Genetic Algorithm Spectrum Unfolding) has been developed to unfold the neutron spectrum from a pulse height distribution which was calculated using the MCNPX-ESUT computational Monte Carlo code. To perform the unfolding process, the response matrices were generated using the MCNPX-ESUT computational code. Both one step (common GA) and two steps GAs have been implemented to unfold the neutron spectra. According to the obtained results, the new two steps GA code results has shown closer match in all energy regions and particularly in the high energy regions. The results of the TGASU code have been compared with those of the standard spectra, LSQR method and GAMCD code. The results of the TGASU code have been demonstrated to be more accurate than that of the existing computational codes for both under-determined and over-determined problems.

  9. The unfolded protein response has a protective role in yeast models of classic galactosemia

    Directory of Open Access Journals (Sweden)

    Evandro A. De-Souza

    2014-01-01

    Full Text Available Classic galactosemia is a human autosomal recessive disorder caused by mutations in the GALT gene (GAL7 in yeast, which encodes the enzyme galactose-1-phosphate uridyltransferase. Here we show that the unfolded protein response pathway is triggered by galactose in two yeast models of galactosemia: lithium-treated cells and the gal7Δ mutant. The synthesis of galactose-1-phosphate is essential to trigger the unfolded protein response under these conditions because the deletion of the galactokinase-encoding gene GAL1 completely abolishes unfolded protein response activation and galactose toxicity. Impairment of the unfolded protein response in both yeast models makes cells even more sensitive to galactose, unmasking its cytotoxic effect. These results indicate that endoplasmic reticulum stress is induced under galactosemic conditions and underscores the importance of the unfolded protein response pathway to cellular adaptation in these models of classic galactosemia.

  10. The unfolded protein response has a protective role in yeast models of classic galactosemia.

    Science.gov (United States)

    De-Souza, Evandro A; Pimentel, Felipe S A; Machado, Caio M; Martins, Larissa S; da-Silva, Wagner S; Montero-Lomelí, Mónica; Masuda, Claudio A

    2014-01-01

    Classic galactosemia is a human autosomal recessive disorder caused by mutations in the GALT gene (GAL7 in yeast), which encodes the enzyme galactose-1-phosphate uridyltransferase. Here we show that the unfolded protein response pathway is triggered by galactose in two yeast models of galactosemia: lithium-treated cells and the gal7Δ mutant. The synthesis of galactose-1-phosphate is essential to trigger the unfolded protein response under these conditions because the deletion of the galactokinase-encoding gene GAL1 completely abolishes unfolded protein response activation and galactose toxicity. Impairment of the unfolded protein response in both yeast models makes cells even more sensitive to galactose, unmasking its cytotoxic effect. These results indicate that endoplasmic reticulum stress is induced under galactosemic conditions and underscores the importance of the unfolded protein response pathway to cellular adaptation in these models of classic galactosemia.

  11. A new neutron energy spectrum unfolding code using a two steps genetic algorithm

    Science.gov (United States)

    Shahabinejad, H.; Hosseini, S. A.; Sohrabpour, M.

    2016-03-01

    A new neutron spectrum unfolding code TGASU (Two-steps Genetic Algorithm Spectrum Unfolding) has been developed to unfold the neutron spectrum from a pulse height distribution which was calculated using the MCNPX-ESUT computational Monte Carlo code. To perform the unfolding process, the response matrices were generated using the MCNPX-ESUT computational code. Both one step (common GA) and two steps GAs have been implemented to unfold the neutron spectra. According to the obtained results, the new two steps GA code results has shown closer match in all energy regions and particularly in the high energy regions. The results of the TGASU code have been compared with those of the standard spectra, LSQR method and GAMCD code. The results of the TGASU code have been demonstrated to be more accurate than that of the existing computational codes for both under-determined and over-determined problems.

  12. The Unfolding of Value Sources During Online Business Model Transformation

    Directory of Open Access Journals (Sweden)

    Nadja Hoßbach

    2016-12-01

    Full Text Available Purpose: In the magazine publishing industry, viable online business models are still rare to absent. To prepare for the ‘digital future’ and safeguard their long-term survival, many publishers are currently in the process of transforming their online business model. Against this backdrop, this study aims to develop a deeper understanding of (1 how the different building blocks of an online business model are transformed over time and (2 how sources of value creation unfold during this transformation process. Methodology: To answer our research question, we conducted a longitudinal case study with a leading German business magazine publisher (called BIZ. Data was triangulated from multiple sources including interviews, internal documents, and direct observations. Findings: Based on our case study, we nd that BIZ used the transformation process to differentiate its online business model from its traditional print business model along several dimensions, and that BIZ’s online business model changed from an efficiency- to a complementarity- to a novelty-based model during this process. Research implications: Our findings suggest that different business model transformation phases relate to different value sources, questioning the appropriateness of value source-based approaches for classifying business models. Practical implications: The results of our case study highlight the need for online-offline business model differentiation and point to the important distinction between service and product differentiation. Originality: Our study contributes to the business model literature by applying a dynamic and holistic perspective on the link between online business model changes and unfolding value sources.

  13. The Unfolding of Equivariant Bifurcation Problems with Two Types of State Variables in the Presence of Parameter Symmetry

    Institute of Scientific and Technical Information of China (English)

    Deng Lan CUI; Yang Cheng LI

    2006-01-01

    The unfolding of equivariant bifurcation problems with two types of state variables under the action of group (ж) (Г, △) is discussed by using DA-algebraic tools. One of the main results is the equivariant versal unfolding theorem.

  14. Structural and dynamical characterization of a biologically active unfolded fibronectin-binding protein from Staphylococcus aureus.

    Science.gov (United States)

    Penkett, C J; Redfield, C; Jones, J A; Dodd, I; Hubbard, J; Smith, R A; Smith, L J; Dobson, C M

    1998-12-01

    A 130-residue fragment (D1-D4) taken from a fibronectin-binding protein of Staphylococcus aureus, which contains four fibronectin-binding repeats and is unfolded but biologically active at neutral pH, has been studied extensively by NMR spectroscopy. Using heteronuclear multidimensional techniques, the conformational properties of D1-D4 have been defined at both a global and a local level. Diffusion studies give an average effective radius of 26.2 +/- 0.1 A, approximately 75% larger than that expected for a globular protein of this size. Analysis of chemical shift, 3JHNalpha coupling constant, and NOE data show that the experimental parameters agree well overall with values measured in short model peptides and with predictions from a statistical model for a random coil. Sequences where specific features give deviations from these predictions for a random coil have however been identified. These arise from clustering of hydrophobic side chains and electrostatic interactions between charged groups. 15N relaxation studies demonstrate that local fluctuations of the chain are the dominant motional process that gives rise to relaxation of the 15N nuclei, with a persistence length of approximately 7-10 residues for the segmental motion. The consequences of the structural and dynamical properties of this unfolded protein for its biological role of binding to fibronectin have been considered. It is found that the regions of the sequence involved in binding have a high propensity for populating extended conformations, a feature that would allow a number of both charged and hydrophobic groups to be presented to fibronectin for highly specific binding.

  15. Thermodynamics of quantum feedback cooling

    CERN Document Server

    Liuzzo-Scorpo, Pietro; Schmidt, Rebecca; Adesso, Gerardo

    2015-01-01

    The ability to initialize quantum registers in pure states lies at the core of many applications of quantum technologies, from sensing to quantum information processing and computation. In this paper we tackle the problem of increasing the polarization bias of an ensemble of two-level register spins by means of joint coherent manipulations, involving a second ensemble of ancillary spins, and energy dissipation into an external heat bath. We formulate this spin refrigeration protocol, akin to algorithmic cooling, in the general language of quantum feedback control, and identify the relevant thermodynamic variables involved. Our analysis is twofold: On the one hand, we assess the optimality of the protocol by means of suitable figures of merit, accounting for both its work cost and effectiveness. On the other hand, we characterise the nature of correlations built up between the register and the ancilla. In particular, we observe that neither the amount of classical correlations nor the quantum entanglement seem...

  16. Thermodynamics of adaptive molecular resolution

    Science.gov (United States)

    Delgado-Buscalioni, R.

    2016-11-01

    A relatively general thermodynamic formalism for adaptive molecular resolution (AMR) is presented. The description is based on the approximation of local thermodynamic equilibrium and considers the alchemic parameter λ as the conjugate variable of the potential energy difference between the atomistic and coarse-grained model Φ=U(1)-U(0). The thermodynamic formalism recovers the relations obtained from statistical mechanics of H-AdResS (Español et al., J. Chem. Phys. 142, 064115, 2015 (doi:10.1063/1.4907006)) and provides relations between the free energy compensation and thermodynamic potentials. Inspired by this thermodynamic analogy, several generalizations of AMR are proposed, such as the exploration of new Maxwell relations and how to treat λ and Φ as `real' thermodynamic variables. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

  17. The postulates of gravitational thermodynamics

    CERN Document Server

    Martínez, E A

    1996-01-01

    The general principles and logical structure of a thermodynamic formalism that incorporates strongly self-gravitating systems are presented. This framework generalizes and simplifies the formulation of thermodynamics developed by Callen. The definition of extensive variables, the homogeneity properties of intensive parameters, and the fundamental problem of gravitational thermodynamics are discussed in detail. In particular, extensive parameters include quasilocal quantities and are naturally incorporated into a set of basic general postulates for thermodynamics. These include additivity of entropies (Massieu functions) and the generalized second law. Fundamental equations are no longer homogeneous first-order functions of their extensive variables. It is shown that the postulates lead to a formal resolution of the fundamental problem despite non-additivity of extensive parameters and thermodynamic potentials. Therefore, all the results of (gravitational) thermodynamics are an outgrowth of these postulates. T...

  18. Thermodynamics of Thermoelectric Materials

    Science.gov (United States)

    Doak, Jeff W.

    One challenge facing society is the responsible use of our energy resources. Increasing the efficiency of energy generation provides one path to solving this challenge. One commonality among most current energy generation methods is that waste heat is generated during the generation process. Thermoelectrics can provide a solution to increasing the efficiency of power generation and automotive systems by converting waste heat directly to electricity. The current barrier to implementation of thermoelectric systems is the low efficiencies of underlying thermoelectric materials. The efficiency of a thermoelectric material depends on the electronic and thermal transport properties of the material; a good thermoelectric material should be an electronic conductor and a thermal insulator, traits which generally oppose one another. The thermal properties of a thermoelectric material can be improved by forming nanoscale precipitates with the material which scatter phonons, reducing the thermal conductivity. The electronic properties of a thermoelectric material can be improved by doping the material to increase the electronic conductivity or by alloying the material to favorably alter its band structure. The ability of these chemical modifications to affect the thermoelectric efficiency of material are ultimately governed by the chemical thermodynamics of the system. PbTe is a prototypical thermoelectric material: Alloying PbTe with PbS (or other materials) creates nanostructures which scatter phonons and reduce the lattice thermal conductivity. Doping PbTe with Na increases the hole concentration, increasing the electronic conductivity. In this work, we investigate the thermodynamics of PbTe and similar systems using first principles to understand the underlying mechanisms controlling the formation of nanostructures and the amount of doping allowed in these systems. In this work we: 1) investigate the thermodynamics of pseudo-binary alloys of IV--VI systems to identify the

  19. Chemical thermodynamics of uranium

    Energy Technology Data Exchange (ETDEWEB)

    Grenthe, I.; Fuger, J.; Lemire, R.J.; Muller, A.B.; Nguyen-Trung Cregu, C.; Wanner, H.

    1992-01-01

    A comprehensive overview on the chemical thermodynamics of those elements that are of particular importance in the safety assessment of radioactive waste disposal systems is provided. This is the first volume in a series of critical reviews to be published on this subject. The book provides an extensive compilation of chemical thermodynamic data for uranium. A description of procedures for activity corrections and uncertainty estimates is given. A critical discussion of data needed for nuclear waste management assessments, including areas where significant gaps of knowledge exist is presented. A detailed inventory of chemical thermodynamic data for inorganic compounds and complexes of uranium is listed. Data and their uncertainty limits are recommended for 74 aqueous complexes and 199 solid and 31 gaseous compounds containing uranium, and on 52 aqueous and 17 solid auxiliary species containing no uranium. The data are internally consistent and compatible with the CODATA Key Values. The book contains a detailed discussion of procedures used for activity factor corrections in aqueous solution, as well as including methods for making uncertainty estimates. The recommended data have been prepared for use in environmental geochemistry. Containing contributions written by experts the chapters cover various subject areas such a s: oxide and hydroxide compounds and complexes, the uranium nitrides, the solid uranium nitrates and the arsenic-containing uranium compounds, uranates, procedures for consistent estimation of entropies, gaseous and solid uranium halides, gaseous uranium oxides, solid phosphorous-containing uranium compounds, alkali metal uranates, uncertainties, standards and conventions, aqueous complexes, uranium minerals dealing with solubility products and ionic strength corrections. The book is intended for nuclear research establishments and consulting firms dealing with uranium mining and nuclear waste disposal, as well as academic and research institutes.

  20. Thermodynamics of irreversible physicochemical processes

    Science.gov (United States)

    Bulatov, N. K.; Lundin, A. B.

    The main principles of the phenomenological thermodynamics of irreversible processes are expounded in close relation to concepts of classical phenomenological thermodynamics, and the most important thermodynamic equations of state are presented. These principles are then used in describing various physicochemical processes, including chemical transformations, structural relaxation, heat conduction, electrical conductivity, diffusion, and sedimentation in homogeneous, continuous, and discontinuous systems. Other processes discussed include filtration, electrical osmosis, heat transfer, and the mechanocaloric effect.

  1. Thermodynamic aspects of rock friction

    CERN Document Server

    Mitsui, Noa

    2013-01-01

    Rate- and state-dependent friction law for velocity-step tests is analyzed from a thermodynamic point of view. A simple macroscopic non-equilibrium thermodynamic model with a single internal variable reproduces instantaneous jump and relaxation. Velocity weakening appears as a consequence of a plasticity related nonlinear coefficient. Permanent part of displacement corresponds to plastic strain, and relaxation effects are analogous to creep in thermodynamic rheology.

  2. Practical Chemical Thermodynamics for Geoscientists

    CERN Document Server

    Fegley, Jr, Bruce

    2012-01-01

    Practical Chemical Thermodynamics for Geoscientists covers classical chemical thermodynamics and focuses on applications to practical problems in the geosciences, environmental sciences, and planetary sciences. This book will provide a strong theoretical foundation for students, while also proving beneficial for earth and planetary scientists seeking a review of thermodynamic principles and their application to a specific problem. Strong theoretical foundation and emphasis on applicationsNumerous worked examples in each chapterBrief historical summaries and biographies of key thermodynamicist

  3. On thermodynamic and microscopic reversibility

    Energy Technology Data Exchange (ETDEWEB)

    Crooks, Gavin E.

    2011-07-12

    The word 'reversible' has two (apparently) distinct applications in statistical thermodynamics. A thermodynamically reversible process indicates an experimental protocol for which the entropy change is zero, whereas the principle of microscopic reversibility asserts that the probability of any trajectory of a system through phase space equals that of the time reversed trajectory. However, these two terms are actually synonymous: a thermodynamically reversible process is microscopically reversible, and vice versa.

  4. Thermodynamics of Rubber Elasticity

    Science.gov (United States)

    Pellicer, J.; Manzanares, J. A.; Zúñiga, J.; Utrillas, P.; Fernández, J.

    2001-02-01

    A thermodynamic study of an isotropic rubber band under uniaxial stress is presented on the basis of its equation of state. The behavior of the rubber band is compared with both that of an ideal elastomer and that of an ideal gas, considering the generalized Joule's law as the ideality criterion. First, the thermal expansion of rubber at constant stress and the change in the stress with temperature at constant length are described. Thermoelastic inversion is then considered, and the experimental observations are easily rationalized. Finally, the temperature changes observed in the adiabatic stretching of a rubber band are evaluated from the decrease of entropy with length.

  5. Principles of thermodynamics

    CERN Document Server

    Kaufman, Myron

    2002-01-01

    Ideal for one- or two-semester courses that assume elementary knowledge of calculus, This text presents the fundamental concepts of thermodynamics and applies these to problems dealing with properties of materials, phase transformations, chemical reactions, solutions and surfaces. The author utilizes principles of statistical mechanics to illustrate key concepts from a microscopic perspective, as well as develop equations of kinetic theory. The book provides end-of-chapter question and problem sets, some using Mathcad™ and Mathematica™; a useful glossary containing important symbols, definitions, and units; and appendices covering multivariable calculus and valuable numerical methods.

  6. Time and Thermodynamics

    CERN Document Server

    Kirkland, Kyle

    2007-01-01

    Temperature is vital to the health and welfare of all living beings, and Earth's temperature varies considerably from place to place. Early humans could only live in warm areas such as the tropics. Although modern humans have the technology to keep their houses and offices warm even in cold environments, the growth and development of civilization has created unintentional effects. Cities are warmer than their surrounding regions, and on a global scale, Earth is experiencing rising temperatures. Thus, the science of thermodynamics offers an important tool to study these effects. "Time and

  7. Interfacial solvation thermodynamics

    Science.gov (United States)

    Ben-Amotz, Dor

    2016-10-01

    Previous studies have reached conflicting conclusions regarding the interplay of cavity formation, polarizability, desolvation, and surface capillary waves in driving the interfacial adsorptions of ions and molecules at air-water interfaces. Here we revisit these questions by combining exact potential distribution results with linear response theory and other physically motivated approximations. The results highlight both exact and approximate compensation relations pertaining to direct (solute-solvent) and indirect (solvent-solvent) contributions to adsorption thermodynamics, of relevance to solvation at air-water interfaces, as well as a broader class of processes linked to the mean force potential between ions, molecules, nanoparticles, proteins, and biological assemblies.

  8. Thermodynamic Stability of Nanobubbles

    CERN Document Server

    Attard, Phil

    2015-01-01

    The observed stability of nanobubbles contradicts the well-known result in classical nucleation theory, that the critical radius is both microscopic and thermodynamically unstable. Here nanoscopic stability is shown to be the combined result of two non-classical mechanisms. It is shown that the surface tension decreases with increasing supersaturation, and that this gives a nanoscopic critical radius. Whilst neither a free spherical bubble nor a hemispherical bubble mobile on an hydrophobic surface are stable, it is shown that an immobilized hemispherical bubble with a pinned contact rim is stable and that the total entropy is a maximum at the critical radius.

  9. Thermodynamics of Accelerating Black Holes.

    Science.gov (United States)

    Appels, Michael; Gregory, Ruth; Kubizňák, David

    2016-09-23

    We address a long-standing problem of describing the thermodynamics of an accelerating black hole. We derive a standard first law of black hole thermodynamics, with the usual identification of entropy proportional to the area of the event horizon-even though the event horizon contains a conical singularity. This result not only extends the applicability of black hole thermodynamics to realms previously not anticipated, it also opens a possibility for studying novel properties of an important class of exact radiative solutions of Einstein equations describing accelerated objects. We discuss the thermodynamic volume, stability, and phase structure of these black holes.

  10. Molecular thermodynamics of nonideal fluids

    CERN Document Server

    Lee, Lloyd L

    2013-01-01

    Molecular Thermodynamics of Nonideal Fluids serves as an introductory presentation for engineers to the concepts and principles behind and the advances in molecular thermodynamics of nonideal fluids. The book covers related topics such as the laws of thermodynamics; entropy; its ensembles; the different properties of the ideal gas; and the structure of liquids. Also covered in the book are topics such as integral equation theories; theories for polar fluids; solution thermodynamics; and molecular dynamics. The text is recommended for engineers who would like to be familiarized with the concept

  11. Dynamics and Thermodynamics of Nanoclusters

    Directory of Open Access Journals (Sweden)

    Karo Michaelian

    2015-10-01

    Full Text Available The dynamic and thermodynamic properties of nanoclusters are studied in two different environments: the canonical and microcanonical ensembles. A comparison is made to thermodynamic properties of the bulk. It is shown that consistent and reproducible results on nanoclusters can only be obtained in the canonical ensemble. Nanoclusters in the microcanonical ensemble are trapped systems, and inconsistencies will be found if thermodynamic formalism is applied. An analytical model is given for the energy dependence of the phase space volume of nanoclusters, which allows the prediction of both dynamical and thermodynamical properties.

  12. Thermodynamics of Accelerating Black Holes

    CERN Document Server

    Appels, Michael; Kubiznak, David

    2016-01-01

    We address a long-standing problem of describing the thermodynamics of a charged accelerating black hole. We derive a standard first law of black hole thermodynamics, with the usual identification of entropy proportional to the area of the event horizon -- even though the event horizon contains a conical singularity. This result not only extends the applicability of black hole thermodynamics to realms previously not anticipated, it also opens a possibility for studying novel properties of an important class of exact radiative solutions of Einstein equations describing accelerated objects. We discuss the thermodynamic volume, stability and phase structure of these black holes.

  13. Thermodynamics of Accelerating Black Holes

    Science.gov (United States)

    Appels, Michael; Gregory, Ruth; KubizÅák, David

    2016-09-01

    We address a long-standing problem of describing the thermodynamics of an accelerating black hole. We derive a standard first law of black hole thermodynamics, with the usual identification of entropy proportional to the area of the event horizon—even though the event horizon contains a conical singularity. This result not only extends the applicability of black hole thermodynamics to realms previously not anticipated, it also opens a possibility for studying novel properties of an important class of exact radiative solutions of Einstein equations describing accelerated objects. We discuss the thermodynamic volume, stability, and phase structure of these black holes.

  14. Multiple unfolding intermediates of human placental alkaline phosphatase in equilibrium urea denaturation.

    Science.gov (United States)

    Hung, H C; Chang, G G

    2001-12-01

    Alkaline phosphatase is an enzyme with a typical alpha/beta hydrolase fold. The conformational stability of the human placental alkaline phosphatase was examined with the chemical denaturant urea. The red shifts of fluorescence spectra show a complex unfolding process involving multiple equilibrium intermediates indicating differential stability of the subdomains of the enzyme. None of these unfolding intermediates were observed in the presence of 83 mM NaCl, indicating the importance of ionic interactions in the stabilization of the unfolding intermediates. Guanidinium chloride, on the other hand, could stabilize one of the unfolding intermediates, which is not a salt effect. Some of the unfolding intermediates were also observed in circular dichroism spectroscopy, which clearly indicates steady loss of helical structure during unfolding, but very little change was observed for the beta strand content until the late stage of the unfolding process. The enzyme does not lose its phosphate-binding ability after substantial tertiary structure changes, suggesting that the substrate-binding region is more resistant to chemical denaturant than the other structural domains. Global analysis of the fluorescence spectral change demonstrated the following folding-unfolding process of the enzyme: N I(1) I(2) I(3) I(4) I(5) D. These discrete intermediates are stable at urea concentrations of 2.6, 4.1, 4.7, 5.5, 6.6, and 7.7 M, respectively. These intermediates are further characterized by acrylamide and/or potassium iodide quenching of the intrinsic fluorescence of the enzyme and by the hydrophobic probes, 1-anilinonaphthalene-8-sulfonic acid and 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid. The stepwise unfolding process was interpreted by the folding energy landscape in terms of the unique structure of the enzyme. The rigid central beta-strand domain is surrounded by the peripheral alpha-helical and coil structures, which are marginally stable toward a chemical

  15. Biochemical Thermodynamics under near Physiological Conditions

    Science.gov (United States)

    Mendez, Eduardo

    2008-01-01

    The recommendations for nomenclature and tables in Biochemical Thermodynamics approved by IUBMB and IUPAC in 1994 can be easily introduced after the chemical thermodynamic formalism. Substitution of the usual standard thermodynamic properties by the transformed ones in the thermodynamic equations, and the use of appropriate thermodynamic tables…

  16. VERSAL UNFOLDING OF EQUIVARIANT BIFURCATION PROBLEMS IN MORE GENERAL CASE UNDER TWO EQUIVALENT GROUPS

    Institute of Scientific and Technical Information of China (English)

    Li Yangcheng; He Wei

    2008-01-01

    For the unfolding of equivariant bifurcation problems with two types of state variables in the presence of parameter symmetry, the versa[ unfolding theorem with re-spect to left-right equivalence is obtained by using the related methods and techniques in the singularity theory of smooth map-germs. The corresponding results in [4, 9] can be considered as its special cases. A relationship between the versal unfolding w.r.t, left-right equivalence and the versal deformation w.r.t, contact equivalence is established.

  17. Comparison of Inactivation and Unfolding of Calf Intestinal Alkaline Phosphatase in Guanidinium Chloride Solution

    Institute of Scientific and Technical Information of China (English)

    张英侠; 闫淑莲; 刘永利; 席宏伟; 周海梦

    2002-01-01

    The changes in activity and unfolding of calf intestinal alkaline phosphatase (CIP) during denaturation in guanidinium chloride solutions of different concentrations were investigated using ultraviolet difference absorption spectra and fluorescence emission spectra. Unfolding and inactivation rate constants were measured and compared. The inactivation course is much faster than that of unfolding, which suggests that the active site of CIP containing two zinc ions and one magnesium ion is situated in a limited and flexible region of the enzyme molecule, which is more fragile to the denaturant than the protein as a whole.

  18. Mapping of unfolding states of integral helical membrane proteins by GPS-NMR and scattering techniques

    DEFF Research Database (Denmark)

    Calcutta, Antonello; Jessen, Christian Moestrup; Behrens, Manja Annette;

    2012-01-01

    Membrane proteins are vital for biological function, and their action is governed by structural properties critically depending on their interactions with the membranes. This has motivated considerable interest in studies of membrane protein folding and unfolding. Here the structural changes...... induced by unfolding of an integral membrane protein, namely TFE-induced unfolding of KcsA solubilized by the n-dodecyl ß-d-maltoside (DDM) surfactant is investigated by the recently introduced GPS-NMR (Global Protein folding State mapping by multivariate NMR) (Malmendal et al., PlosONE 5, e10262 (2010...

  19. NSDUAZ unfolding package for neutron spectrometry and dosimetry with Bonner spheres

    Energy Technology Data Exchange (ETDEWEB)

    Vega C, H. R.; Martinez B, M. R. [Universidad Autonoma de Zacatecas, Unidad Academica de Estudios Nucleares, Calle Cipres No. 10, Fracc. La Penuela, 98068 Zacatecas (Mexico); Ortiz R, J. M., E-mail: fermineutron@yahoo.com [Universidad Autonoma de Zacatecas, Unidad Academica de Ingenieria Electrica, Av. Ramon Lopez Velarde 801, Col. Centro, 98000 Zacatecas (Mexico)

    2011-10-15

    NSDUAZ (Neutron Spectrometry and Dosimetry for the Universidad Autonoma de Zacatecas) is a user friendly neutron unfolding package for Bonner sphere spectrometer with {sup 6}Lil(Eu) developed under Lab View environment. Unfolding is carried out using a recursive iterative procedure with the SPUNIT algorithm, where the starting spectrum is obtained from a library initial guess spectrum to start the iterations, the package include a statistical procedure based on the count rates relative to the count rate in the 8 inches-diameter sphere to select the initial spectrum. Neutron spectrum is unfolded in 32 energy groups ranging from 10{sup -8} up to 231.2 MeV. (Author)

  20. Thermodynamics of spinning branes and their dual field theories

    DEFF Research Database (Denmark)

    Harmark, Troels; Obers, N. A.

    2000-01-01

    We discuss general spinning p-branes of string and M-theory and use their thermodynamics along with the correspondence between near-horizon brane solutions and field theories with 16 supercharges to describe the thermodynamic behavior of these theories in the presence of voltages under the R...... limits are remarkably close and (ii) The tree-level R^4 corrections to the spinning D3-brane generate a decrease in the free energy at strong coupling towards the weak coupling result. We also comment on the generalization to spinning brane bound states and their thermodynamics, which are relevant...

  1. Decrease in membrane phospholipid unsaturation induces unfolded protein response.

    Science.gov (United States)

    Ariyama, Hiroyuki; Kono, Nozomu; Matsuda, Shinji; Inoue, Takao; Arai, Hiroyuki

    2010-07-16

    Various kinds of fatty acids are distributed in membrane phospholipids in mammalian cells and tissues. The degree of fatty acid unsaturation in membrane phospholipids affects many membrane-associated functions and can be influenced by diet and by altered activities of lipid-metabolizing enzymes such as fatty acid desaturases. However, little is known about how mammalian cells respond to changes in phospholipid fatty acid composition. In this study we showed that stearoyl-CoA desaturase 1 (SCD1) knockdown increased the amount of saturated fatty acids and decreased that of monounsaturated fatty acids in phospholipids without affecting the amount or the composition of free fatty acid and induced unfolded protein response (UPR), evidenced by increased expression of C/EBP homologous protein (CHOP) and glucose-regulated protein 78 (GRP78) mRNAs and splicing of Xbox-binding protein 1 (XBP1) mRNA. SCD1 knockdown-induced UPR was rescued by various unsaturated fatty acids and was enhanced by saturated fatty acid. Lysophosphatidylcholine acyltransferase 3 (LPCAT3), which incorporates preferentially polyunsaturated fatty acids into phosphatidylcholine, was up-regulated in SCD1 knockdown cells. Knockdown of LPCAT3 synergistically enhanced UPR with SCD1 knockdown. Finally we showed that palmitic acid-induced UPR was significantly enhanced by LPCAT3 knockdown as well as SCD1 knockdown. These results suggest that a decrease in membrane phospholipid unsaturation induces UPR.

  2. Unfolding X-ray spectra using a flat panel detector.

    Science.gov (United States)

    Gallardo, Sergio; Juste, Belén; Pozuelo, Fausto; Ródenas, José; Querol, Andrea; Verdú, Gumersindo

    2013-01-01

    It is difficult to measure the energy spectrum of X-ray tubes due to the pile up effect produced by the high fluence of photons. Using attenuating materials, appropriate detector devices and the Monte Carlo method, primary X-ray spectrum of these devices can be estimated. In this work, a flat panel detector with a PMMA wedge has been used to obtain a dose curve corresponding to certain working conditions of a radiodiagnostic X-ray tube. The relation between the dose curve recorded by the flat panel and the primary X-ray spectrum is defined by a response function. Normally this function can be approximated by a matrix, which can be obtained by means of the Monte Carlo method. Knowing the measured dose curve and the response matrix, the primary X-ray spectrum can be unfolded. However, there are some problems that strongly affect the applicability of this method: i.e. technical features of the flat panel and inherent characteristics of the involved radiation physics (ill-posed problem). Both aspects are analyzed in this work, concluding that the proposed method can be applied with an acceptable accuracy for spectra without characteristic lines, for instance, tungsten anode in the 50-70 kVp range.

  3. An Unfolding Method for X-ray Spectro-Polarimetry

    CERN Document Server

    Kislat, Fabian; Zajczyk, Anna; Krawczynski, Henric

    2014-01-01

    X-ray polarimetry has great scientific potential and new experiments, such as X-Calibur, PoGOLite, XIPE, and GEMS, will not only be orders of magnitude more sensitive than previous missions, but also provide the capability to measure polarization over a wide energy range. However, the measured spectra depend on the collection area, detector responses, and, in case of balloon-borne experiments, the absorption of X-rays in the atmosphere, all of which are energy dependent. Combined with the typically steep source spectra, this leads to significant biases that need to be taken into account to correctly reconstruct energy-resolved polarization properties. In this paper, we present a method based on an iterative unfolding algorithm that makes it possible to simultaneously reconstruct the energy spectrum and the polarization properties as a function of true photon energy. We apply the method to a simulated X-Calibur data set and show that it is able to recover both the energy spectrum and the energy-dependent polar...

  4. The role of the unfolded protein response in diabetes mellitus.

    Science.gov (United States)

    Iwawaki, Takao; Oikawa, Daisuke

    2013-05-01

    The endoplasmic reticulum (ER) plays a key role in the synthesis and modification of secretory and membrane proteins in all eukaryotic cells. Under normal conditions, these proteins are correctly folded and assembled in the ER. However, when cells are exposed to environmental factors such as overproduction of ER proteins, viral infections, or glucose deprivation, the secretory and membrane proteins can accumulate in unfolded or misfolded forms in the lumen of the ER, and consequently, cause stress in the ER. To maintain cellular homeostasis, cells induce several responses to ER stress. In mammalian cells, ER stress responses are induced by a diversity of signal pathways. There are three ER-located transmembrane proteins that play important roles in mammalian ER stress responses: activating transcription factor 6, inositol-requiring protein 1, and protein kinase RNA-like endoplasmic reticulum kinase. ER stress is linked to various diseases, including diabetes. This review highlights the particular importance of ER stress-responsive molecules in insulin biosynthesis, glyconeogenesis, insulin resistance, glucose intolerance, and pancreatic β-cell apoptosis. An understanding of the pathogenic mechanism of diabetes from the aspect of ER stress is crucial in formulating therapeutic strategies.

  5. New insights into the unfolded protein response in stem cells.

    Science.gov (United States)

    Yang, Yanzhou; Cheung, Hoi Hung; Tu, JiaJie; Miu, Kai Kei; Chan, Wai Yee

    2016-08-16

    The unfolded protein response (UPR) is an evolutionarily conserved adaptive mechanism to increase cell survival under endoplasmic reticulum (ER) stress conditions. The UPR is critical for maintaining cell homeostasis under physiological and pathological conditions. The vital functions of the UPR in development, metabolism and immunity have been demonstrated in several cell types. UPR dysfunction activates a variety of pathologies, including cancer, inflammation, neurodegenerative disease, metabolic disease and immune disease. Stem cells with the special ability to self-renew and differentiate into various somatic cells have been demonstrated to be present in multiple tissues. These cells are involved in development, tissue renewal and certain disease processes. Although the role and regulation of the UPR in somatic cells has been widely reported, the function of the UPR in stem cells is not fully known, and the roles and functions of the UPR are dependent on the stem cell type. Therefore, in this article, the potential significances of the UPR in stem cells, including embryonic stem cells, tissue stem cells, cancer stem cells and induced pluripotent cells, are comprehensively reviewed. This review aims to provide novel insights regarding the mechanisms associated with stem cell differentiation and cancer pathology.

  6. The Unfolded Protein Response in Amelogenesis and Enamel Pathologies

    Directory of Open Access Journals (Sweden)

    Steven J. Brookes

    2017-09-01

    Full Text Available During the secretory phase of their life-cycle, ameloblasts are highly specialized secretory cells whose role is to elaborate an extracellular matrix that ultimately confers both form and function to dental enamel, the most highly mineralized of all mammalian tissues. In common with many other “professional” secretory cells, ameloblasts employ the unfolded protein response (UPR to help them cope with the large secretory cargo of extracellular matrix proteins transiting their ER (endoplasmic reticulum/Golgi complex and so minimize ER stress. However, the UPR is a double-edged sword, and, in cases where ER stress is severe and prolonged, the UPR switches from pro-survival to pro-apoptotic mode. The purpose of this review is to consider the role of the ameloblast UPR in the biology and pathology of amelogenesis; specifically in respect of amelogenesis imperfecta (AI and fluorosis. Some forms of AI appear to correspond to classic proteopathies, where pathological intra-cellular accumulations of protein tip the UPR toward apoptosis. Fluorosis also involves the UPR and, while not of itself a classic proteopathic disease, shares some common elements through the involvement of the UPR. The possibility of therapeutic intervention by pharmacological modulation of the UPR in AI and fluorosis is also discussed.

  7. THE THERMODYNAMIC CHARACTER OF INFORMATION

    Directory of Open Access Journals (Sweden)

    Popova T.M.

    2010-04-01

    Full Text Available The article includes data concerning application of one of the universal method of the modern science based on fundamental thermodynamic laws to analyze the efficiency of the information processes. The comparison of the information and thermodynamic processes brought the author to the basic conclusion of the energetic character of information.

  8. Fundamental functions in equilibrium thermodynamics

    NARCIS (Netherlands)

    Horst, H.J. ter

    1987-01-01

    In the standard presentations of the principles of Gibbsian equilibrium thermodynamics one can find several gaps in the logic. For a subject that is as widely used as equilibrium thermodynamics, it is of interest to clear up such questions of mathematical rigor. In this paper it is shown that using

  9. Thermodynamics from Car to Kitchen

    Science.gov (United States)

    Auty, Geoff

    2014-01-01

    The historical background to the laws of thermodynamics is explained using examples we can all observe in the world around us, focusing on motorised transport, refrigeration and solar heating. This is not to be considered as an academic article. The purpose is to improve understanding of thermodynamics rather than impart new knowledge, and for…

  10. Thermodynamics from Car to Kitchen

    Science.gov (United States)

    Auty, Geoff

    2014-01-01

    The historical background to the laws of thermodynamics is explained using examples we can all observe in the world around us, focusing on motorised transport, refrigeration and solar heating. This is not to be considered as an academic article. The purpose is to improve understanding of thermodynamics rather than impart new knowledge, and for…

  11. Thermodynamics of light and sound

    Directory of Open Access Journals (Sweden)

    G. M. Kremer

    1991-05-01

    Full Text Available This paper presents a thermodynamic theory of light and sound. It demonstrates that extended thermodynamics permits the explicit calculation of the main part of the equations of balance of energy for photons and phonons. Wave speeds are calculated and the limiting cases of near-equilibrium and free streaming are discussed.

  12. Thermodynamics of the Earth

    Energy Technology Data Exchange (ETDEWEB)

    Stacey, Frank D [CSIRO Exploration and Mining, PO Box 883, Kenmore, Qld. 4069 (Australia)], E-mail: Frank.Stacey@csiro.au

    2010-04-15

    Applications of elementary thermodynamic principles to the dynamics of the Earth lead to robust, quantitative conclusions about the tectonic effects that arise from convection. The grand pattern of motion conveys deep heat to the surface, generating mechanical energy with a thermodynamic efficiency corresponding to that of a Carnot engine operating over the adiabatic temperature gradient between the heat source and sink. Referred to the total heat flux derived from the Earth's silicate mantle, the efficiency is 24% and the power generated, 7.7 x 10{sup 12} W, causes all the material deformation apparent as plate tectonics and the consequent geological processes. About 3.5% of this is released in seismic zones but little more than 0.2% as seismic waves. Even major earthquakes are only localized hiccups in this motion. Complications that arise from mineral phase transitions can be used to illuminate details of the motion. There are two superimposed patterns of convection, plate subduction and deep mantle plumes, driven by sources of buoyancy, negative and positive respectively, at the top and bottom of the mantle. The patterns of motion are controlled by the viscosity contrasts (>10{sup 4} : 1) at these boundaries and are self-selected as the least dissipative mechanisms of heat transfer for convection in a body with very strong viscosity variation. Both are subjects of the thermodynamic efficiency argument. Convection also drives the motion in the fluid outer core that generates the geomagnetic field, although in that case there is an important energy contribution by compositional separation, as light solute is rejected by the solidifying inner core and mixed into the outer core, a process referred to as compositional convection. Uncertainty persists over the core energy balance because thermal conduction is a drain on core energy that has been a subject of diverse estimates, with attendant debate over the need for radiogenic heat in the core. The geophysical

  13. Moessbauer spectroscopic evidence on the heme binding to the proximal histidine in unfolded carbonmonoxy myoglobin by guanidine hydrochloride

    Energy Technology Data Exchange (ETDEWEB)

    Harami, Taikan, E-mail: harami.taikan@jaea.go.jp [Japan Atomic Energy Agency (Japan); Kitao, Shinji; Kobayashi, Yasuhiro [Kyoto University, Research Reactor Institute (Japan); Mitsui, Takaya [Japan Atomic Energy Agency (Japan)

    2008-01-15

    The unfolded heme structure in myoglobin is controversial because of no chance of direct X-ray structure analyses. The unfolding of carbonmonoxy myoglobin (MbCO) by guanidine hydrochloride (GdnHCl) was studied by the Moessbauer spectroscopy. The spectra show the presence of a sort of spectrum in the unfolded MbCO, independent on the concentration of GdnHCl from 1 to 6 M and the increase of the fraction of unfolded MbCO, depending on the GdnHCl concentration. The isomer shift of the iron of heme in the unfolded MbCO was identified to be different from that of the native MbCO as the globin structure in Mb collapses under the unfolded conditions. This result and the existing related Moessbauer data proved that the heme in the unfolded MbCO may remain coordinated to the proximal histidine.

  14. Phenol oxidation by mushroom waste extracts: a kinetic and thermodynamic study.

    Science.gov (United States)

    Pigatto, Gisele; Lodi, Alessandra; Aliakbarian, Bahar; Converti, Attilio; da Silva, Regildo Marcio Gonçalves; Palma, Mauri Sérgio Alves

    2013-09-01

    Tyrosinase activity of mushroom extracts was checked for their ability to degrade phenol. Phenol oxidation kinetics was investigated varying temperature from 10 to 60 °C and the initial values of pH, enzyme activity and phenol concentration in the ranges 4.5-8.5, 1.43-9.54 U/mL and 50-600 mg/L, respectively. Thermodynamic parameters of phenol oxidation and tyrosinase reversible inactivation were estimated. Tyrosinase thermostability was also investigated through residual activity tests after extracts exposition at 20-50 °C, whose results allowed exploring the thermodynamics of enzyme irreversible thermoinactivation. This study is the first attempt to separate the effects of reversible unfolding and irreversible denaturation of tyrosinase on its activity. Extracts were finally tested on a real oil mill wastewater.

  15. Application of differential scanning calorimetry to measure the differential binding of ions, water and protons in the unfolding of DNA molecules.

    Science.gov (United States)

    Olsen, Chris M; Shikiya, Ronald; Ganugula, Rajkumar; Reiling-Steffensmeier, Calliste; Khutsishvili, Irine; Johnson, Sarah E; Marky, Luis A

    2016-05-01

    The overall stability of DNA molecules globally depends on base-pair stacking, base-pairing, polyelectrolyte effect and hydration contributions. In order to understand how they carry out their biological roles, it is essential to have a complete physical description of how the folding of nucleic acids takes place, including their ion and water binding. To investigate the role of ions, water and protons in the stability and melting behavior of DNA structures, we report here an experimental approach i.e., mainly differential scanning calorimetry (DSC), to determine linking numbers: the differential binding of ions (Δnion), water (ΔnW) and protons (ΔnH(+)) in the helix-coil transition of DNA molecules. We use DSC and temperature-dependent UV spectroscopic techniques to measure the differential binding of ions, water, and protons for the unfolding of a variety of DNA molecules: salmon testes DNA (ST-DNA), one dodecamer, one undecamer and one decamer duplexes, nine hairpin loops, and two triplexes. These methods can be applied to any conformational transition of a biomolecule. We determined complete thermodynamic profiles, including all three linking numbers, for the unfolding of each molecule. The favorable folding of a DNA helix results from a favorable enthalpy-unfavorable entropy compensation. DSC thermograms and UV melts as a function of salt, osmolyte and proton concentrations yielded releases of ions and water. Therefore, the favorable folding of each DNA molecule results from the formation of base-pair stacks and uptake of both counterions and water molecules. In addition, the triplex with C(+)GC base triplets yielded an uptake of protons. Furthermore, the folding of a DNA duplex is accompanied by a lower uptake of ions and a similar uptake of four water molecules as the DNA helix gets shorter. In addition, the oligomer duplexes and hairpin thermodynamic data suggest ion and water binding depends on the DNA sequence rather than DNA composition. Copyright

  16. Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip?

    Science.gov (United States)

    Geschwindner, Stefan; Ulander, Johan; Johansson, Patrik

    2015-08-27

    The use of ligand binding thermodynamics has been proposed as a potential success factor to accelerate drug discovery. However, despite the intuitive appeal of optimizing binding enthalpy, a number of factors complicate routine use of thermodynamic data. On a macroscopic level, a range of experimental parameters including temperature and buffer choice significantly influence the observed thermodynamic signatures. On a microscopic level, solute effects, structural flexibility, and cooperativity lead to nonlinear changes in enthalpy. This multifactorial character hides essential enthalpy contributions of intermolecular contacts, making them experimentally nonobservable. In this perspective, we present three case studies, reflect on some key factors affecting thermodynamic signatures, and investigate their relation to the hydrophobic effect, enthalpy-entropy compensation, lipophilic ligand efficiency, and promiscuity. The studies highlight that enthalpy and entropy cannot be used as direct end points but can together with calculations increase our understanding of ligand binding and identify interesting outliers that do not behave as expected.

  17. Structural characteristic of the initial unfolded state on refolding determines catalytic efficiency of the folded protein in presence of osmolytes.

    Directory of Open Access Journals (Sweden)

    Marina Warepam

    Full Text Available Osmolytes are low molecular weight organic molecules accumulated by organisms to assist proper protein folding, and to provide protection to the structural integrity of proteins under denaturing stress conditions. It is known that osmolyte-induced protein folding is brought by unfavorable interaction of osmolytes with the denatured/unfolded states. The interaction of osmolyte with the native state does not significantly contribute to the osmolyte-induced protein folding. We have therefore investigated if different denatured states of a protein (generated by different denaturing agents interact differently with the osmolytes to induce protein folding. We observed that osmolyte-assisted refolding of protein obtained from heat-induced denatured state produces native molecules with higher enzyme activity than those initiated from GdmCl- or urea-induced denatured state indicating that the structural property of the initial denatured state during refolding by osmolytes determines the catalytic efficiency of the folded protein molecule. These conclusions have been reached from the systematic measurements of enzymatic kinetic parameters (Km and kcat, thermodynamic stability (Tm and ΔHm and secondary and tertiary structures of the folded native proteins obtained from refolding of various denatured states (due to heat-, urea- and GdmCl-induced denaturation of RNase-A in the presence of various osmolytes.

  18. Applied thermodynamics: A new frontier for biotechnology

    DEFF Research Database (Denmark)

    Mollerup, Jørgen

    2006-01-01

    The scientific career of one of the most outstanding scientists in molecular thermodynamics, Professor John M. Prausnitz at Berkeley, reflects the change in the agenda of molecular thermodynamics, from hydrocarbon chemistry to biotechnology. To make thermodynamics a frontier for biotechnology...

  19. Equilibrium thermodynamics - Callen’s postulational approach

    NARCIS (Netherlands)

    Jongschaap, Robert J.J.; Öttinger, Hans Christian

    2001-01-01

    In order to provide the background for nonequilibrium thermodynamics, we outline the fundamentals of equilibrium thermodynamics. Equilibrium thermodynamics must not only be obtained as a special case of any acceptable nonequilibrium generalization but, through its shining example, it also elucidates

  20. Thermodynamic properties of cryogenic fluids

    CERN Document Server

    Leachman, Jacob; Lemmon, Eric; Penoncello, Steven

    2017-01-01

    This update to a classic reference text provides practising engineers and scientists with accurate thermophysical property data for cryogenic fluids. The equations for fifteen important cryogenic fluids are presented in a basic format, accompanied by pressure-enthalpy and temperature-entropy charts and tables of thermodynamic properties. It begins with a chapter introducing the thermodynamic relations and functional forms for equations of state, and goes on to describe the requirements for thermodynamic property formulations, needed for the complete definition of the thermodynamic properties of a fluid. The core of the book comprises extensive data tables and charts for the most commonly-encountered cryogenic fluids. This new edition sees significant updates to the data presented for air, argon, carbon monoxide, deuterium, ethane, helium, hydrogen, krypton, nitrogen and xenon. The book supports and complements NIST’s REFPROP - an interactive database and tool for the calculation of thermodynamic propertie...

  1. A Hamiltonian approach to Thermodynamics

    CERN Document Server

    Baldiotti, M C; Molina, C

    2016-01-01

    In the present work we develop a strictly Hamiltonian approach to Thermodynamics. A thermodynamic description based on symplectic geometry is introduced, where all thermodynamic processes can be described within the framework of Analytic Mechanics. Our proposal is constructed ontop of a usual symplectic manifold, where phase space is even dimensional and one has well-defined Poisson brackets. The main idea is the introduction of an extended phase space where thermodynamic equations of state are realized as constraints. We are then able to apply the canonical transformation toolkit to thermodynamic problems. Throughout this development, Dirac's theory of constrained systems is extensively used. To illustrate the formalism, we consider paradigmatic examples, namely, the ideal, van der Waals and Clausius gases.

  2. Thermodynamic cost of acquiring information.

    Science.gov (United States)

    Micadei, Kaonan; Serra, Roberto M; Céleri, Lucas C

    2013-12-01

    Connections between information theory and thermodynamics have proven to be very useful to establish bounding limits for physical processes. Ideas such as Landauer's erasure principle and information-assisted work extraction have greatly contributed not only to broadening our understanding about the fundamental limits imposed by nature, but also paving the way for practical implementations of information-processing devices. The intricate information-thermodynamics relation also entails a fundamental limit on parameter estimation, establishing a thermodynamic cost for information acquisition. We show that the amount of information that can be encoded in a physical system by means of a unitary process is limited by the dissipated work during the implementation of the process. This includes a thermodynamic tradeoff for information acquisition. Likewise, the information acquisition process is ultimately limited by the second law of thermodynamics. This tradeoff for information acquisition may find applications in several areas of knowledge.

  3. Applied statistical thermodynamics

    CERN Document Server

    Lucas, Klaus

    1991-01-01

    The book guides the reader from the foundations of statisti- cal thermodynamics including the theory of intermolecular forces to modern computer-aided applications in chemical en- gineering and physical chemistry. The approach is new. The foundations of quantum and statistical mechanics are presen- ted in a simple way and their applications to the prediction of fluid phase behavior of real systems are demonstrated. A particular effort is made to introduce the reader to expli- cit formulations of intermolecular interaction models and to show how these models influence the properties of fluid sy- stems. The established methods of statistical mechanics - computer simulation, perturbation theory, and numerical in- tegration - are discussed in a style appropriate for newcom- ers and are extensively applied. Numerous worked examples illustrate how practical calculations should be carried out.

  4. Cooling by Thermodynamic Induction

    Science.gov (United States)

    Patitsas, S. N.

    2017-03-01

    A method is described for cooling conductive channels to below ambient temperature. The thermodynamic induction principle dictates that the electrically biased channel will cool if the electrical conductance decreases with temperature. The extent of this cooling is calculated in detail for both cases of ballistic and conventional transport with specific calculations for carbon nanotubes and conventional metals, followed by discussions for semiconductors, graphene, and metal-insulator transition systems. A theorem is established for ballistic transport stating that net cooling is not possible. For conventional transport, net cooling is possible over a broad temperature range, with the range being size-dependent. A temperature clamping scheme for establishing a metastable nonequilibrium stationary state is detailed and followed with discussion of possible applications to on-chip thermoelectric cooling in integrated circuitry and quantum computer systems.

  5. Cooling by Thermodynamic Induction

    Science.gov (United States)

    Patitsas, S. N.

    2016-11-01

    A method is described for cooling conductive channels to below ambient temperature. The thermodynamic induction principle dictates that the electrically biased channel will cool if the electrical conductance decreases with temperature. The extent of this cooling is calculated in detail for both cases of ballistic and conventional transport with specific calculations for carbon nanotubes and conventional metals, followed by discussions for semiconductors, graphene, and metal-insulator transition systems. A theorem is established for ballistic transport stating that net cooling is not possible. For conventional transport, net cooling is possible over a broad temperature range, with the range being size-dependent. A temperature clamping scheme for establishing a metastable nonequilibrium stationary state is detailed and followed with discussion of possible applications to on-chip thermoelectric cooling in integrated circuitry and quantum computer systems.

  6. Thermodynamic Origin of Life

    CERN Document Server

    Michaelian, K

    2009-01-01

    Understanding the thermodynamic function of life may shed light on its origin. Out of equilibrium structuring in space and time is contingent on continuous entropy production. Entropy production is a measure of the rate of the natural tendency of Nature to explore all available microstates. The process producing the greatest amount of entropy in the biosphere is the absorption and transformation of sunlight, leading to the transpiration of water by plants and cyanobacteria. Here we hypothesize that life began, and exists today, as a dynamic catalyst for the absorption and transformation of sunlight into heat, which could then be efficiently harvested by the water cycle, hurricanes, and ocean and wind currents. RNA and DNA are the most efficient of all known molecules for absorbing the ultraviolet light that could have penetrated the dense early atmosphere, and are extremely rapid in transforming this light into heat that can be readily absorbed by liquid water. The origin and evolution of life was thus driven...

  7. Thermodynamics of anisotropic branes

    Energy Technology Data Exchange (ETDEWEB)

    Ávila, Daniel [Departamento de Física, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P. 70-542, México D.F. 04510 (Mexico); Fernández, Daniel [Max-Planck-Institut für Physik,Föhringer Ring 6, 80805 München (Germany); Patiño, Leonardo [Departamento de Física, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P. 70-542, México D.F. 04510 (Mexico); Trancanelli, Diego [Institute of Physics, University of São Paulo,05314-970 São Paulo (Brazil)

    2016-11-22

    We study the thermodynamics of flavor D7-branes embedded in an anisotropic black brane solution of type IIB supergravity. The flavor branes undergo a phase transition between a ‘Minkowski embedding’, in which they lie outside of the horizon, and a ‘black hole embedding’, in which they fall into the horizon. This transition depends on the black hole temperature, its degree of anisotropy, and the mass of the flavor degrees of freedom. It happens either at a critical temperature or at a critical anisotropy. A general lesson we learn from this analysis is that the anisotropy, in this particular realization, induces similar effects as the temperature. In particular, increasing the anisotropy bends the branes more and more into the horizon. Moreover, we observe that the transition becomes smoother for higher anisotropies.

  8. Covariant Thermodynamics and Relativity

    CERN Document Server

    Lopez-Monsalvo, C S

    2011-01-01

    This thesis deals with the dynamics of irreversible processes within the context of the general theory of relativity. In particular, we address the problem of the 'infinite' speed of propagation of thermal disturbances in a dissipative fluid. The present work builds on the multi-fluid variational approach to relativistic dissipation, pioneered by Carter, and provides a dynamical theory of heat conduction. The novel property of such approach is the thermodynamic interpretation associated with a two-fluid system whose constituents are matter and entropy. The dynamics of this model leads to a relativistic generalisation of the Cattaneo equation; the constitutive relation for causal heat transport. A comparison with the Israel and Stewart model is presented and its equivalence is shown. This discussion provides new insights into the not-well understood definition of a non-equilibrium temperature. The variational approach to heat conduction presented in this thesis constitutes a mathematically promising formalism ...

  9. Thermodynamics and energy conversion

    CERN Document Server

    Struchtrup, Henning

    2014-01-01

    This textbook gives a thorough treatment of engineering thermodynamics with applications to classical and modern energy conversion devices.   Some emphasis lies on the description of irreversible processes, such as friction, heat transfer and mixing, and the evaluation of the related work losses. Better use of resources requires high efficiencies, therefore the reduction of irreversible losses should be seen as one of the main goals of a thermal engineer. This book provides the necessary tools.   Topics include: car and aircraft engines,  including Otto, Diesel and Atkinson cycles, by-pass turbofan engines, ramjet and scramjet;  steam and gas power plants, including advanced regenerative systems, solar tower, and compressed air energy storage; mixing and separation, including reverse osmosis, osmotic powerplants, and carbon sequestration; phase equilibrium and chemical equilibrium, distillation, chemical reactors, combustion processes, and fuel cells; the microscopic definition of entropy.    The book i...

  10. Experimental Milestones in the Discovery of Molecular Chaperones as Polypeptide Unfolding Enzymes.

    Science.gov (United States)

    Finka, Andrija; Mattoo, Rayees U H; Goloubinoff, Pierre

    2016-06-01

    Molecular chaperones control the cellular folding, assembly, unfolding, disassembly, translocation, activation, inactivation, disaggregation, and degradation of proteins. In 1989, groundbreaking experiments demonstrated that a purified chaperone can bind and prevent the aggregation of artificially unfolded polypeptides and use ATP to dissociate and convert them into native proteins. A decade later, other chaperones were shown to use ATP hydrolysis to unfold and solubilize stable protein aggregates, leading to their native refolding. Presently, the main conserved chaperone families Hsp70, Hsp104, Hsp90, Hsp60, and small heat-shock proteins (sHsps) apparently act as unfolding nanomachines capable of converting functional alternatively folded or toxic misfolded polypeptides into harmless protease-degradable or biologically active native proteins. Being unfoldases, the chaperones can proofread three-dimensional protein structures and thus control protein quality in the cell. Understanding the mechanisms of the cellular unfoldases is central to the design of new therapies against aging, degenerative protein conformational diseases, and specific cancers.

  11. A Quasi-Metric Approach to Multidimensional Unfolding for Reducing the Occurrence of Degenerate Solutions.

    Science.gov (United States)

    Kim, Chulwan; Rangaswamy, Arvind; DeSarbo, Wayne S.

    1999-01-01

    Presents an approach to multidimensional unfolding that reduces the occurrence of degenerate solutions and conducts a Monte Carlo study to demonstrate the superiority of the new method to the ALSCAL and KYST nonmetric procedures for student preference data. (SLD)

  12. The unfolding of God’s revelation in Hebrews 1:1–2a

    Directory of Open Access Journals (Sweden)

    Albert Coetsee

    2016-04-01

    Full Text Available In the introduction to his sermon, the writer of Hebrews suggests that God’s revelation unfolded from his so-called ‘Old Testament’ revelation to his ‘New Testament’ revelation in his Son (Heb. 1:1–2a. By doing a thorough exegesis of Hebrews 1:1–2a, the author’s view of such an unfolding revelation is confirmed. From this conclusion, certain hermeneutical implications of the unfolding of God’s revelation are drawn for believers and scholars today. Among others, it is determined that God’s revelation is progressive, that his revelation in his Son is superior, climactic and final, and that God’s final revelation in his Son can only be understood within the context of his Old Testament revelation, and vice versa.Keywords: Hebrews; Hebrews 1:1-2a; unfolding; revelation; hermeneutics

  13. Protein unfolding versus β-sheet separation in spider silk nanocrystals

    Science.gov (United States)

    Alam, Parvez

    2014-03-01

    In this communication a mechanism for spider silk strain hardening is proposed. Shear failure of β-sheet nanocrystals is the first failure mode that gives rise to the creation of smaller nanocrystals, which are of higher strength and stiffness. β-sheet unfolding requires more energy than nanocrystal separation in a shear mode of failure. As a result, unfolding occurs after the nanocrystals separate in shear. β-sheet unfolding yields a secondary strain hardening effect once the β-sheet conformation is geometrically stable and acts like a unidirectional fibre in a fibre reinforced composite. The mechanism suggested herein is based on molecular dynamics calculations of residual inter-β-sheet separation strengths against residual intra-β-sheet unfolding strengths.

  14. Thermal unfolding of myoglobin in the Landau-Ginzburg-Wilson approach

    Science.gov (United States)

    Peng, Xubiao; Sieradzan, Adam K.; Niemi, Antti J.

    2016-12-01

    The Landau-Ginzburg-Wilson paradigm is applied to model the low-temperature crystallographic C α backbone structure of sperm whale myoglobin. The Glauber protocol is employed to simulate its response to an increase in ambient temperature. The myoglobin is found to unfold from its native state by a succession of α -helical intermediates, fully in line with the observed folding and unfolding patterns in denaturation experiments. In particular, a molten globule intermediate is identified with experimentally correct attributes. A detailed, experimentally testable contact map is constructed to characterize the specifics of the unfolding pathway, including the formation of long-range interactions. The results reveal how the unfolding process of a protein is driven by the interplay between, and a successive melting of, its modular secondary structure components.

  15. Natively unfolded human prothymosin alpha adopts partially folded collapsed conformation at acidic pH.

    Science.gov (United States)

    Uversky, V N; Gillespie, J R; Millett, I S; Khodyakova, A V; Vasiliev, A M; Chernovskaya, T V; Vasilenko, R N; Kozlovskaya, G D; Dolgikh, D A; Fink, A L; Doniach, S; Abramov, V M

    1999-11-09

    Prothymosin alpha has previously been shown to be unfolded at neutral pH, thus belonging to a growing family of "natively unfolded" proteins. The structural properties and conformational stability of recombinant human prothymosin alpha were characterized at neutral and acidic pH by gel filtration, SAXS, circular dichroism, ANS fluorescence, (1)H NMR, and resistance to urea-induced unfolding. Interestingly, prothymosin alpha underwent a cooperative transition from the unfolded state into a partially folded conformation on lowering the pH. This conformation of prothymosin alpha is a compact denatured state, with structural properties different from those of the molten globule. The formation of alpha-helical structure by the glutamic acid-rich elements of the protein accompanied by the partial hydrophobic collapse is expected at lower pH due to the neutralization of the negatively charged residues. It is possible that such conformational changes may be associated with the protein function.

  16. Mechanical unfolding of RNA: From hairpins to structures with internal multiloops

    CERN Document Server

    Hyeon, Changbong

    2007-01-01

    Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes, using laser optical tweezer (LOT) experiments have begun to reveal the features of the energy landscape that cannot be easily explored using conventional experiments. Upon application of constant force ($f$), RNA hairpins undergo cooperative transitions from folded to unfolded states whereas subdomains of ribozymes unravel one at a time. Here, we use a self-organized polymer (SOP) model and Brownian dynamics simulations to probe mechanical unfolding at constant force and constant-loading rate of four RNA structures of varying complexity. Our work shows (i) the response of RNA to force is largely determined by the native structure; (ii) only by probing mechanical unfolding over a wide range of forces can the underlying energy landscape be fully explored.

  17. Thermodynamics of fragment binding.

    Science.gov (United States)

    Ferenczy, György G; Keserű, György M

    2012-04-23

    The ligand binding pockets of proteins have preponderance of hydrophobic amino acids and are typically within the apolar interior of the protein; nevertheless, they are able to bind low complexity, polar, water-soluble fragments. In order to understand this phenomenon, we analyzed high resolution X-ray data of protein-ligand complexes from the Protein Data Bank and found that fragments bind to proteins with two near optimal geometry H-bonds on average. The linear extent of the fragment binding site was found not to be larger than 10 Å, and the H-bonding region was found to be restricted to about 5 Å on average. The number of conserved H-bonds in proteins cocrystallized with multiple different fragments is also near to 2. These fragment binding sites that are able to form limited number of strong H-bonds in a hydrophobic environment are identified as hot spots. An estimate of the free-energy gain of H-bond formation versus apolar desolvation supports that fragment sized compounds need H-bonds to achieve detectable binding. This suggests that fragment binding is mostly enthalpic that is in line with their observed binding thermodynamics documented in Isothermal Titration Calorimetry (ITC) data sets and gives a thermodynamic rationale for fragment based approaches. The binding of larger compounds tends to more rely on apolar desolvation with a corresponding increase of the entropy content of their binding free-energy. These findings explain the reported size-dependence of maximal available affinity and ligand efficiency both behaving differently in the small molecule region featured by strong H-bond formation and in the larger molecule region featured by apolar desolvation.

  18. Sequence-Specific Solvent Accessibilities of Protein Residues in Unfolded Protein Ensembles

    OpenAIRE

    Bernadó, Pau,; Blackledge, Martin; Sancho, Javier

    2006-01-01

    Protein stability cannot be understood without the correct description of the unfolded state. We present here an efficient method for accurate calculation of atomic solvent exposures for denatured protein ensembles. The method used to generate the ensembles has been shown to reproduce diverse biophysical experimental data corresponding to natively and chemically unfolded proteins. Using a data set of 19 nonhomologous proteins containing from 98 to 579 residues, we report average accessibiliti...

  19. Solving inverse problems with the unfolding program TRUEE: Examples in astroparticle physics

    CERN Document Server

    Milke, Natalie; Klepser, Stefan; Mazin, Daniel; Blobel, Volker; Rhode, Wolfgang; 10.1016/j.nima.2012.08.105

    2012-01-01

    The unfolding program TRUEE is a software package for the numerical solution of inverse problems. The algorithm was fi?rst applied in the FORTRAN77 program RUN. RUN is an event-based unfolding algorithm which makes use of the Tikhonov regularization. It has been tested and compared to di?fferent unfolding applications and stood out with notably stable results and reliable error estimation. TRUEE is a conversion of RUN to C++, which works within the powerful ROOT framework. The program has been extended for more user-friendliness and delivers unfolding results which are identical to RUN. Beside the simplicity of the installation of the software and the generation of graphics, there are new functions, which facilitate the choice of unfolding parameters and observables for the user. In this paper, we introduce the new unfolding program and present its performance by applying it to two exemplary data sets from astroparticle physics, taken with the MAGIC telescopes and the IceCube neutrino detector, respectively.

  20. Long-Range Contacts in Unfolding of Two-State Proteins.

    Science.gov (United States)

    Samuel, Selvaraj; Balasubramanian, Harihar

    2017-01-01

    Predicting the unfolding rates of proteins remains complicated due to the intricacy present in the unfolding pathway of proteins and further it was observed that the experimental unfolding data were less while compared to folding kinetics. The aim of our present work is to show the variation in long-range contacts observed in various sequence separation bins belonging to all-α, all-β and mixed structural classes of 52 two-state proteins. In this work linear regression technique have been used and regression equations were developed using long-range contacts observed from various sequence separation bins. Also nine topological parameters developed from the 3-D structures of proteins are related with their experimental unfolding rates and their variation in correlation coefficient is observed before and after structural classification. The present work aims to show that long-range contacts formed between residues which are sequentially far and spatially close in the 3-D structure of proteins play a crucial role in the unfolding mechanism of proteins. Also importance of long-range contacts in various experimental and theoretical studies of protein folding along with NMR studies of the unfolded non-native states of proteins have been discussed. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  1. A highly compliant protein native state with a spontaneous-like mechanical unfolding pathway.

    Science.gov (United States)

    Heidarsson, Pétur O; Valpapuram, Immanuel; Camilloni, Carlo; Imparato, Alberto; Tiana, Guido; Poulsen, Flemming M; Kragelund, Birthe B; Cecconi, Ciro

    2012-10-17

    The mechanical properties of proteins and their force-induced structural changes play key roles in many biological processes. Previous studies have shown that natively folded proteins are brittle under tension, unfolding after small mechanical deformations, while partially folded intermediate states, such as molten globules, are compliant and can deform elastically a great amount before crossing the transition state barrier. Moreover, under tension proteins appear to unfold through a different sequence of events than during spontaneous unfolding. Here, we describe the response to force of the four-α-helix acyl-CoA binding protein (ACBP) in the low-force regime using optical tweezers and ratcheted molecular dynamics simulations. The results of our studies reveal an unprecedented mechanical behavior of a natively folded protein. ACBP displays an atypical compliance along two nearly orthogonal pulling axes, with transition states located almost halfway between the unfolded and folded states. Surprisingly, the deformability of ACBP is greater than that observed for the highly pliant molten globule intermediate states. Furthermore, when manipulated from the N- and C-termini, ACBP unfolds by populating a transition state that resembles that observed during chemical denaturation, both for structure and position along the reaction coordinate. Our data provide the first experimental evidence of a spontaneous-like mechanical unfolding pathway of a protein. The mechanical behavior of ACBP is discussed in terms of topology and helix propensity.

  2. Mode decomposition based on crystallographic symmetry in the band-unfolding method

    Science.gov (United States)

    Ikeda, Yuji; Carreras, Abel; Seko, Atsuto; Togo, Atsushi; Tanaka, Isao

    2017-01-01

    The band-unfolding method is widely used to calculate the effective band structures of a disordered system from its supercell model. The unfolded band structures show the crystallographic symmetry of the underlying structure, where the difference of chemical components and the local atomic relaxation are ignored. However, it has still been difficult to decompose the unfolded band structures into the modes based on the crystallographic symmetry of the underlying structure, and therefore detailed analyses of the unfolded band structures have been restricted. In this study, a procedure to decompose the unfolded band structures according to the small representations (SRs) of the little groups is developed. The decomposition is performed using the projection operators for SRs derived from the group representation theory. The current method is employed to investigate the phonon band structure of disordered face-centered-cubic Cu0.75Au0.25 , which has large variations of atomic masses and force constants among the atomic sites due to the chemical disorder. In the unfolded phonon band structure, several peculiar behaviors such as discontinuous and split branches are found in the decomposed modes corresponding to specific SRs. They are found to occur because different combinations of the chemical elements contribute to different regions of frequency.

  3. Resveratrol-induced cytotoxicity in human Burkitt's lymphoma cells is coupled to the unfolded protein response

    Directory of Open Access Journals (Sweden)

    Yan Ying

    2010-08-01

    Full Text Available Abstract Background Resveratrol (RES, a natural phytoalexin found at high levels in grapes and red wine, has been shown to induce anti-proliferation and apoptosis of human cancer cell lines. However, the underlying molecular mechanisms are at present only partially understood. Method The effects of RES on activation of unfolded protein responses (UPR were evaluated using Western blotting, semi-quantitative and real-time RT-PCR. Cell death was evaluated using Annexin V/PI staining and subsequent FACS. Results Similar as tunicamycin, treatment with RES lead to the activation of all 3 branches of the UPR, with early splicing of XBP-1 indicative of IRE1 activation, phosphorylation of eIF2α consistent with ER resident kinase (PERK activation, activating transcription factor 6 (ATF6 splicing, and increase in expression levels of the downstream molecules GRP78/BiP, GRP94 and CHOP/GADD153 in human Burkitt's lymphoma Raji and Daudi cell lines. RES was shown to induce cell death, which could be attenuated by thwarting upregulation of CHOP. Conclusions Our data suggest that activation of the apoptotic arm of the UPR and its downstream effector CHOP/GADD153 is involved, at least in part, in RES-induced apoptosis in Burkitt's lymphoma cells.

  4. Unfolding the resident-invader dynamics of similar strategies.

    Science.gov (United States)

    Dercole, Fabio; Geritz, Stefan A H

    2016-04-01

    We investigate the competition between two groups of similar agents in the restricted, but classical context of unstructured populations varying in continuous time in an isolated, homogeneous, and constant abiotic environment. Individual behavioral and phenotypic traits are quantified by one-dimensional strategies and intra- as well as inter-specific interactions are described in the vicinity of a stationary regime. Some known results are revisited: invasion by a new strategy generically implies the substitution of the former resident; and resident-invader coexistence is possible close to singular strategies-the stationary points of the invasion fitness-and is generically protected-each of the two competing groups can invade the other. An (almost known) old conjecture is shown true: competition close to a singular strategy is "essentially Lotka-Volterra"-dominance of one strategy, protected coexistence at an intermediate equilibrium, and mutual exclusion are the generic outcomes. And the unfolding of the competition scenarios is completed with the analysis of three degenerate singular strategies-characterized by vanishing second-order fitness derivatives-near which resident-invader coexistence can be unprotected. Our approach is based on the series expansion of a generic demographic model, w.r.t. the small strategy difference between the two competing groups, and on known results on time-scale separation and bifurcation theories. The analysis is carried out up to third order and is extendable to any order. For each order, explicit genericity conditions under which higher orders can be neglected are derived and, interestingly, they are known prior to invasion. An important result is that degeneracies up to third-order are required to have more than one stable way of coexistence. Such degeneracies can be due to particular symmetries in the model formulation, and breaking the genericity conditions provides a direct way to draw biological interpretations. The developed

  5. ABCB10 depletion reduces unfolded protein response in mitochondria.

    Science.gov (United States)

    Yano, Masato

    2017-04-29

    Mitochondria have many functions, including ATP generation. The electron transport chain (ETC) and the coupled ATP synthase generate ATP by consuming oxygen. Reactive oxygen species (ROS) are also produced by ETC, and ROS damage deoxyribonucleic acids, membrane lipids and proteins. Recent analysis indicate that mitochondrial unfolded protein response (UPR(mt)), which enhances expression of mitochondrial chaperones and proteases to remove damaged proteins, is activated when damaged proteins accumulate in the mitochondria. In Caenorhabditis elegans, HAF-1, a putative ortholog of human ABCB10, plays an essential role in signal transduction from mitochondria to nuclei to enhance UPR(mt). Therefore, it is possible that ABCB10 has a role similar to that of HAF-1. However, it has not been reported whether ABCB10 is a factor in the signal transduction pathway to enhance UPR(mt). In this study, ABCB10 was depleted in HepG2 cells using small interfering RNA (siRNA), and the effect was examined. ABCB10 depletion upregulated ROS and the expression of ROS-detoxifying enzymes (SOD2, GSTA1, and GSTA2), and SESN3, a protein induced by ROS to protect the cell from oxidative stress. In addition, ABCB10 depletion significantly decreased expression of UPR(mt)-related mitochondrial chaperones (HSPD1 and DNAJA3), and a mitochondrial protease (LONP1). However, the putative activity of ABCB10 to export peptides from mitochondria was not lost by ABCB10 depletion. Altogether, these data suggest that ABCB10 is involved in UPR(mt) signaling pathway similar to that of HAF-1, although ABCB10 probably does not participate in peptide export from mitochondria. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Chemical thermodynamics: principles and applications

    Energy Technology Data Exchange (ETDEWEB)

    Ott, J. Bevan; Boerio-Goates, Juliana [Brigham Young Univ., Provo, UT (United States)

    2000-06-01

    Chemical Thermodynamics: Principles and Applications presents a thorough development of the principles of thermodynamics--an old science to which the authors include the most modem applications, along with those of importance in developing the science and those of historical interest. The text is written in an informal but rigorous style, including anecdotes about some of the great thermodynamicists (with some of whom the authors have had a personal relationship), and focuses on 'real' systems in the discussion and figures, in contrast to the generic examples that are often used in other textbooks. The book provides a basic review of thermodynamic principles, equations, and applications of broad interest. It covers the development of thermodynamics as one of the pre-eminent examples of an exact science. A discussion of the standard state that emphasizes its significance and usefulness is also included, as well as a more rigorous and indepth treatment of thermodynamics. Outlines the development of the principles of thermodynamics, including the most modem applications along with those of importance in developing the science and those of historical interest . Provides a basic review of thermodynamic principles, equations, and applications of broad interest. Treats thermodynamics as one of the preeminent examples of an exact science. Provides a more rigorous and indepth treatment of thermodynamics and discussion of a wider variety of applications than are found in more broadly based physical chemistry undergraduate textbooks. Includes examples in the text and exercises and problems at the end of each chapter to assist the student in learning the subject. (Author)

  7. Modern thermodynamics - New concepts based on the second law of thermodynamics

    Institute of Scientific and Technical Information of China (English)

    Jitao Wang

    2009-01-01

    Thermodynamics is a core part of science.Nearly all scientists should have a basic knowledge of thermodynamics.Thermodynamics is a science of development,and is a viewpoint of scientific development in natural sciences.Achievement of thermodynamics has influence not only on natural sciences,but also on social sciences and philosophy.Fundamental concepts and definitions are very important for any discipline of science,so what is classical thermodynamics and what is modern thermodynamics have become the key points of puzzledom in thermodynamics.In this paper,after clarification of fundamental concept in thermodynamics,a complete basic modern classification of thermodynamics is naturally obtained.It is suggested that extended Carnot theorem and dissipation decrease theorem,together with the laws of thermodynamics,are the most fundamental theorems in thermodynamics discipline.Nondissipative thermodynamics is a new field besides equilibrium thermodynamics belonging to the equal part of the second law of thermodynamics.

  8. Influence of precipitating agents on thermodynamic parameters of protein crystallization solutions.

    Science.gov (United States)

    Stavros, Philemon; Saridakis, Emmanuel; Nounesis, George

    2016-09-01

    X-ray crystallography is the most powerful method for determining three-dimensional structures of proteins to (near-)atomic resolution, but protein crystallization is a poorly explained and often intractable phenomenon. Differential Scanning Calorimetry was used to measure the thermodynamic parameters (ΔG, ΔH, ΔS) of temperature-driven unfolding of two globular proteins, lysozyme, and ribonuclease A, in various salt solutions. The mixtures were categorized into those that were conducive to crystallization of the protein and those that were not. It was found that even fairly low salt concentrations had very large effects on thermodynamic parameters. High concentrations of salts conducive to crystallization stabilized the native folded forms of proteins, whereas high concentrations of salts that did not crystallize them tended to destabilize them. Considering the ΔH and TΔS contributions to the ΔG of unfolding separately, high concentrations of crystallizing salts were found to enthalpically stabilize and entropically destabilize the protein, and vice-versa for the noncrystallizing salts. These observations suggest an explanation, in terms of protein stability and entropy of hydration, of why some salts are good crystallization agents for a given protein and others are not. This in turn provides theoretical insight into the process of protein crystallization, suggesting ways of predicting and controlling it. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 642-652, 2016.

  9. Thermodynamic Metrics and Optimal Paths

    Energy Technology Data Exchange (ETDEWEB)

    Sivak, David; Crooks, Gavin

    2012-05-08

    A fundamental problem in modern thermodynamics is how a molecular-scale machine performs useful work, while operating away from thermal equilibrium without excessive dissipation. To this end, we derive a friction tensor that induces a Riemannian manifold on the space of thermodynamic states. Within the linear-response regime, this metric structure controls the dissipation of finite-time transformations, and bestows optimal protocols with many useful properties. We discuss the connection to the existing thermodynamic length formalism, and demonstrate the utility of this metric by solving for optimal control parameter protocols in a simple nonequilibrium model.

  10. Statistical Thermodynamics of Disperse Systems

    DEFF Research Database (Denmark)

    Shapiro, Alexander

    1996-01-01

    Principles of statistical physics are applied for the description of thermodynamic equilibrium in disperse systems. The cells of disperse systems are shown to possess a number of non-standard thermodynamic parameters. A random distribution of these parameters in the system is determined....... On the basis of this distribution, it is established that the disperse system has an additional degree of freedom called the macro-entropy. A large set of bounded ideal disperse systems allows exact evaluation of thermodynamic characteristics. The theory developed is applied to the description of equilibrium...

  11. The Thermodynamic Properties of Cubanite

    Science.gov (United States)

    Berger, E. L.; Lauretta, D. S.; Keller, L. P.

    2012-01-01

    CuFe2S3 exists in two polymorphs, a low-temperature orthorhombic form (cubanite) and a high-temperature cubic form (isocubanite). Cubanite has been identified in the CI-chondrite and Stardust collections. However, the thermodynamic properties of cubanite have neither been measured nor estimated. Our derivation of a thermodynamic model for cubanite allows constraints to be placed on the formation conditions. This data, along with the temperature constraint afforded by the crystal structure, can be used to assess the environments in which cubanite formation is (or is not) thermodynamically favored.

  12. Vector Theory in Relativistic Thermodynamics

    Institute of Scientific and Technical Information of China (English)

    刘泽文

    1994-01-01

    It is pointed out that five defects occur in Planck-Einstein’s relativistic thermodynamics (P-E theory). A vector theory in relativistic thermodynamics (VTRT) is established. Defining the internal energy as a 4-vector, and supposing the entropy and the number of. particles to be invariants we have derived the transformations of all quantities, and subsequently got the Lagrangian and 4-D forms of thermodynamic laws. In order to test the new theory, several exact solutions with classical limits are given. The VTRT is free from the defects of the P-E theory.

  13. Legendre transforms in chemical thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Alberty, R.A. (Massachusetts Inst. of Technology, Cambridge, MA (United States). Dept. of Chemistry)

    After introductory remarks on chemical thermodynamics, independent variables, and natural variables, the paper discusses the following: Callen's nomenclature for Legendre transformed thermodynamic potentials; Transforms for chemical work (gas reactions, biochemical reactions, and ligand binding and denaturation of macromolecules); Transforms for gravitational and centrifugal work; Transforms for mechanical work (tensile stress and shear stress); Transforms for surface work; Transforms for work of electrical transport (fundamental equations, thermodynamic properties and chemical reactions, and derivation of the equation for the membrane potential); Transforms for work of electric polarization; and Transforms for work of magnetic polarization. 92 references.

  14. Uterine endoplasmic reticulum stress and its unfolded protein response may regulate caspase 3 activation in the pregnant mouse uterus.

    Directory of Open Access Journals (Sweden)

    Arvind Suresh

    Full Text Available We have previously proposed that uterine caspase-3 may modulate uterine contractility in a gestationally regulated fashion. The objective of this study was to determine the mechanism by which uterine caspase-3 is activated and consequently controlled in the pregnant uterus across gestation. Utilizing the mouse uterus as our gestational model we examined the intrinsic and extrinsic apoptotic signaling pathways and the endoplasmic reticulum stress response as potential activators of uterine caspase-3 at the transcriptional and translational level. Our study revealed robust activation of the uterine myocyte endoplasmic reticulum stress response and its adaptive unfolded protein response during pregnancy coinciding respectively with increased uterine caspase-3 activity and its withdrawal to term. In contrast the intrinsic and extrinsic apoptotic signaling pathways remained inactive across gestation. We speculate that physiological stimuli experienced by the pregnant uterus likely potentiates the uterine myocyte endoplasmic reticulum stress response resulting in elevated caspase-3 activation, which is isolated to the pregnant mouse myometrium. However as term approaches, activation of an elevated adaptive unfolded protein response acts to limit the endoplasmic reticulum stress response inhibiting caspase-3 resulting in its decline towards term. We speculate that these events have the capacity to regulate gestational length in a caspase-3 dependent manner.

  15. Uterine endoplasmic reticulum stress and its unfolded protein response may regulate caspase 3 activation in the pregnant mouse uterus.

    Science.gov (United States)

    Suresh, Arvind; Subedi, Kalpana; Kyathanahalli, Chandrashekara; Jeyasuria, Pancharatnam; Condon, Jennifer C

    2013-01-01

    We have previously proposed that uterine caspase-3 may modulate uterine contractility in a gestationally regulated fashion. The objective of this study was to determine the mechanism by which uterine caspase-3 is activated and consequently controlled in the pregnant uterus across gestation. Utilizing the mouse uterus as our gestational model we examined the intrinsic and extrinsic apoptotic signaling pathways and the endoplasmic reticulum stress response as potential activators of uterine caspase-3 at the transcriptional and translational level. Our study revealed robust activation of the uterine myocyte endoplasmic reticulum stress response and its adaptive unfolded protein response during pregnancy coinciding respectively with increased uterine caspase-3 activity and its withdrawal to term. In contrast the intrinsic and extrinsic apoptotic signaling pathways remained inactive across gestation. We speculate that physiological stimuli experienced by the pregnant uterus likely potentiates the uterine myocyte endoplasmic reticulum stress response resulting in elevated caspase-3 activation, which is isolated to the pregnant mouse myometrium. However as term approaches, activation of an elevated adaptive unfolded protein response acts to limit the endoplasmic reticulum stress response inhibiting caspase-3 resulting in its decline towards term. We speculate that these events have the capacity to regulate gestational length in a caspase-3 dependent manner.

  16. Site-specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution

    Science.gov (United States)

    Silva, R. A. G. D.; Kubelka, Jan; Bour, Petr; Decatur, Sean M.; Keiderling, Timothy A.

    2000-01-01

    Understanding the detailed mechanism of protein folding requires dynamic, site-specific stereochemical information. The short time response of vibrational spectroscopies allows evaluation of the distribution of populations in rapid equilibrium as the peptide unfolds. Spectral shifts associated with isotopic labels along with local stereochemical sensitivity of vibrational circular dichroism (VCD) allow determination of the segment sequence of unfolding. For a series of alanine-rich peptides that form α-helices in aqueous solution, we used isotopic labeling and VCD to demonstrate that the α-helix noncooperatively unwinds from the ends with increasing temperature. For these blocked peptides, the C-terminal is frayed at 5°C. Ab initio level theoretical simulations of the IR and VCD band shapes are used to analyze the spectra and to confirm the conformation of the labeled components. The VCD signals associated with the labeled residues are amplified by coupling to the nonlabeled parts of the molecule. Thus small labeled segments are detectable and stereochemically defined in moderately large peptides in this report of site-specific peptide VCD conformational analysis. PMID:10880566

  17. Thermal stability and unfolding pathways of hyperthermophilic and mesophilic periplasmic binding proteins studied by molecular dynamics simulation.

    Science.gov (United States)

    Chen, Lin; Li, Xue; Wang, Ruige; Fang, Fengqin; Yang, Wanli; Kan, Wei

    2016-07-01

    The ribose binding protein (RBP), a sugar-binding periplasmic protein, is involved in the transport and signaling processes in both prokaryotes and eukaryotes. Although several cellular and structural studies have been reported, a description of the thermostability of RBP at the molecular level remains elusive. Focused on the hyperthermophilic Thermoytoga maritima RBP (tmRBP) and mesophilic Escherichia coli homolog (ecRBP), we applied molecular dynamics simulations at four different temperatures (300, 380, 450, and 500 K) to obtain a deeper insight into the structural features responsible for the reduced thermostability of the ecRBP. The simulations results indicate that there are distinct structural differences in the unfolding pathway between the two homologs and the ecRBP unfolds faster than the hyperthermophilic homologs at certain temperatures in accordance with the lower thermal stability found experimentally. Essential dynamics analysis uncovers that the essential subspaces of ecRBP and tmRBP are non-overlapping and these two proteins show different directions of motion within the simulations trajectories. Such an understanding is required for designing efficient proteins with characteristics for a particular application.

  18. Thermodynamical string fragmentation

    Science.gov (United States)

    Fischer, Nadine; Sjöstrand, Torbjörn

    2017-01-01

    The observation of heavy-ion-like behaviour in pp collisions at the LHC suggests that more physics mechanisms are at play than traditionally assumed. The introduction e.g. of quark-gluon plasma or colour rope formation can describe several of the observations, but as of yet there is no established paradigm. In this article we study a few possible modifications to the Pythia event generator, which describes a wealth of data but fails for a number of recent observations. Firstly, we present a new model for generating the transverse momentum of hadrons during the string fragmentation process, inspired by thermodynamics, where heavier hadrons naturally are suppressed in rate but obtain a higher average transverse momentum. Secondly, close-packing of strings is taken into account by making the temperature or string tension environment-dependent. Thirdly, a simple model for hadron rescattering is added. The effect of these modifications is studied, individually and taken together, and compared with data mainly from the LHC. While some improvements can be noted, it turns out to be nontrivial to obtain effects as big as required, and further work is called for.

  19. Thermodynamical String Fragmentation

    CERN Document Server

    Fischer, Nadine

    2016-01-01

    The observation of heavy-ion-like behaviour in pp collisions at the LHC suggests that more physics mechanisms are at play than traditionally assumed. The introduction e.g. of quark-gluon plasma or colour rope formation can describe several of the observations, but as of yet there is no established paradigm. In this article we study a few possible modifications to the Pythia event generator, which describes a wealth of data but fails for a number of recent observations. Firstly, we present a new model for generating the transverse momentum of hadrons during the string fragmentation process, inspired by thermodynamics, where heavier hadrons naturally are suppressed in rate but obtain a higher average transverse momentum. Secondly, close-packing of strings is taken into account by making the temperature or string tension environment-dependent. Thirdly, a simple model for hadron rescattering is added. The effect of these modifications is studied, individually and taken together, and compared with data mainly from...

  20. Thermodynamics of firms' growth

    CERN Document Server

    Zambrano, Eduardo; Fernandez-Bariviera, Aurelio; Hernando, Ricardo; Plastino, Angelo

    2015-01-01

    The distribution of firms' growth and firms' sizes is a topic under intense scrutiny. In this paper we show that a thermodynamic model based on the Maximum Entropy Principle, with dynamical prior information, can be constructed that adequately describes the dynamics and distribution of firms' growth. Our theoretical framework is tested against a comprehensive data-base of Spanish firms, which covers to a very large extent Spain's economic activity with a total of 1,155,142 firms evolving along a full decade. We show that the empirical exponent of Pareto's law, a rule often observed in the rank distribution of large-size firms, is explained by the capacity of the economic system for creating/destroying firms, and can be used to measure the health of a capitalist-based economy. Indeed, our model predicts that when the exponent is larger that 1, creation of firms is favored; when it is smaller that 1, destruction of firms is favored instead; and when it equals 1 (matching Zipf's law), the system is in a full mac...

  1. Thermodynamic investigations of protein's behaviour with ionic liquids in aqueous medium studied by isothermal titration calorimetry.

    Science.gov (United States)

    Bharmoria, Pankaj; Kumar, Arvind

    2016-05-01

    While a number of reports appear on ionic liquids-proteins interactions, their thermodynamic behaviour using suitable technique like isothermal titration calorimetry is not systematically presented. Isothermal titration calorimetry (ITC) is a key technique which can directly measure the thermodynamic contribution of IL binding to protein, particularly the enthalpy, heat capacities and binding stoichiometry. Ionic liquids (ILs), owing to their unique and tunable physicochemical properties have been the central area of scientific research besides graphene in the last decade, and growing unabated. Their encounter with proteins in the biological system is inevitable considering their environmental discharge though most of them are recyclable for a number of cycles. In this article we will cover the thermodynamics of proteins upon interaction with ILs as osmolyte and surfactant. The up to date literature survey of IL-protein interactions using isothermal titration calorimetry will be discussed and parallel comparison with the results obtained for such studies with other techniques will be highlighted to demonstrate the accuracy of ITC technique. Net stability of proteins can be obtained from the difference in the free energy (ΔG) of the native (folded) and denatured (unfolded) state using the Gibbs-Helmholtz equation (ΔG=ΔH-TΔS). Isothermal titration calorimetry can directly measure the heat changes upon IL-protein interactions. Calculation of other thermodynamic parameters such as entropy, binding constant and free energy depends upon the proper fitting of the binding isotherms using various fitting models. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Program calculation of thermodynamic properties

    Science.gov (United States)

    Gill, Walter; Filho, Fernando Fachini; Ribeirodeoliveira, Ronaldo

    1986-12-01

    The determination of the thermodynamic properties are examined through the basic equations such as: state equation (Beattie-Bridgeman Form), saturation pressure equation, specific heat constant pressure or constant volume equation, and specific volume or density of liquid equation.

  3. Thermodynamic efficiency of solar concentrators.

    Science.gov (United States)

    Shatz, Narkis; Bortz, John; Winston, Roland

    2010-04-26

    The optical thermodynamic efficiency is a comprehensive metric that takes into account all loss mechanisms associated with transferring flux from the source to the target phase space, which may include losses due to inadequate design, non-ideal materials, fabrication errors, and less than maximal concentration. We discuss consequences of Fermat's principle of geometrical optics and review étendue dilution and optical loss mechanisms associated with nonimaging concentrators. We develop an expression for the optical thermodynamic efficiency which combines the first and second laws of thermodynamics. As such, this metric is a gold standard for evaluating the performance of nonimaging concentrators. We provide examples illustrating the use of this new metric for concentrating photovoltaic systems for solar power applications, and in particular show how skewness mismatch limits the attainable optical thermodynamic efficiency.

  4. Thermodynamic black di-rings

    CERN Document Server

    Iguchi, Hideo

    2010-01-01

    Previously the five dimensional $S^1$-rotating black rings have been superposed in concentric way by some solitonic methods and regular systems of two $S^1$-rotating black rings were constructed by the authors and then Evslin and Krishnan (we called these solutions black di-rings). In this place we show some characteristics of the solutions of five dimensional black di-rings, especially in thermodynamic equilibrium. After the summary of the di-ring expressions and their physical quantities, first we comment on the equivalence of the two different solution-sets of the black di-rings. Then the existence of thermodynamic black di-rings are shown, in which both iso-thermality and iso-rotation between the inner black ring and the outer black ring are realized. We also give detailed analysis of peculiar properties of the thermodynamic black di-ring including discussion about a certain kind of thermodynamic stability (instability) of the system.

  5. On the Mathematics of Thermodynamics

    CERN Document Server

    Cooper, J B

    2011-01-01

    We show that the mathematical structure of Gibbsian thermodynamics flows from the following simple elements: the state space of a thermodynamical substance is a measure space together with two orderings (corresponding to "warmer than" and "adiabatically accessible from") which satisfy certain plausible physical axioms and an area condition which was introduced by Paul Samuelson. We show how the basic identities of thermodynamics, in particular the Maxwell relations, follow and so the existence of energy, free energy, enthalpy and the Gibbs potential function. We also discuss some questions which we have not found dealt with in the literature, such as the amount of information required to reconstruct the equations of state of a substance and a systematic approach to thermodynamical identities.

  6. Experimental approaches to membrane thermodynamics

    DEFF Research Database (Denmark)

    Westh, Peter

    2009-01-01

    Thermodynamics describes a system on the macroscopic scale, yet it is becoming an important tool for the elucidation of many specific molecular aspects of membrane properties. In this note we discuss this application of thermodynamics, and give a number of examples on how thermodynamic measuremen...... have contributed to the understanding of specific membrane phenomena. We mainly focus on non-specific interactions of bilayers and small molecules (water and solutes) in the surrounding solvent, and the changes in membrane properties they bring about. Differences between thermodynamic...... and stoichiometric (structural) definitions of non-specific binding or partitioning are emphasized, and it is concluded that this distinction is important for weak, but not for strong, interactions....

  7. Shock Thermodynamic Applied Research Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Shock Thermodynamic Applied Research Facility (STAR) facility, within Sandia’s Solid Dynamic Physics Department, is one of a few institutions in the world with a...

  8. Review of selenium thermodynamic data

    Science.gov (United States)

    Cowan, C. E.

    1988-02-01

    This report assesses the accuracy and completeness of available thermodynamic data on selenium. A review of experimental methods from published literature on selenium thermodynamic data focused on chemical reactions responsible for the formation of both aqueous complexes and solid phases of selenate, selenite, and selenide. The reviewer selected best data values, based on the methods used for estimating thermodynamic data. After inclusion of these values into the MINTEQ model, a validation study evaluated model performance for selenite and selenide solid phases. Lack of selenate data precluded model validation for this compound. The review furnished data on 22 aqueous complexes of selenite, 15 of selenide, and 17 of selenate, as well as 21 solid phases of selenite, 20 of selenide and 8 of selenate. These data proved inadequate to represent the formation of species in the solid phase. The validation study gave inconclusive predictions of selenite and selenide solubility and could not be used to assess the accuracy or completeness of the thermodynamic data.

  9. Shock Thermodynamic Applied Research Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Shock Thermodynamic Applied Research Facility (STAR) facility, within Sandia’s Solid Dynamic Physics Department, is one of a few institutions in the world with...

  10. Association theories for complex thermodynamics

    DEFF Research Database (Denmark)

    Kontogeorgis, Georgios; Rafiqul Gani

    2013-01-01

    Thermodynamics of complex systems (e.g. with associating molecules, multicomponent mixtures, multiphase equilibria, wide ranges of conditions, estimation of many different properties simultaneously) is a topic of great importance in chemical engineering and for a wide range of industrial...... promising direction for a general and useful for engineering purposes modeling of complex thermodynamics is via the use of association theories e.g. those based on chemical theory (like APACT), or on the lattice theory (like NRHB) or those based on perturbation theory (like SAFT and CPA). The purpose...... applications. While specialized models can handle different cases, even complex ones, with the advent of powerful theories and computers there is the hope that a single or a few models could be suitable for a general modeling of complex thermodynamics. After more than 100 years with active use of thermodynamic...

  11. Entropy Function for Multifractal Thermodynamics

    Institute of Scientific and Technical Information of China (English)

    QiuhuaZENG

    1999-01-01

    The theory on multifractal thermodynamics has been studied by the method of series expansion.The method is able to overcome the shortages of Kohmoto's steepest desent method and the results have general meanings.

  12. Molecular Dynamics Simulations of Cytochrome c un-folding in AOT Reverse Micelles: the first steps

    CERN Document Server

    Abel, Stéphane; Marchi, Massimo

    2009-01-01

    This paper explores the reduced form of horse cytochrome c confined in reverse micelles (RM) of so-dium bis-(2-ethylhexyl) sulfosuccinate (AOT) in isooctane by molecular dynamics simulation. RMs of two sizes were constructed at a water content of Wo = [H2O]/[AOT] = 5.5 and 9.1. Our results show that the protein secondary structure and the heme conformation both depend on micellar hydration. At low hydration, the protein structure and the heme moiety remain stable, whereas at high water content the protein becomes unstable and starts to unfold. At Wo = 9.1, according to the X-ray structure, conforma-tional changes are mainly localized on protein loops and around the heme moiety, where we observe a partial opening of the heme crevice. These findings suggest that within our time window (10 ns), the structural changes observed at the heme level are the first steps of the protein denaturation process, pre-viously described experimentally in micellar solutions. In addition, a specific binding of AOT molecules to a ...

  13. Inter-regulation of the unfolded protein response and auxin signaling.

    Science.gov (United States)

    Chen, Yani; Aung, Kyaw; Rolčík, Jakub; Walicki, Kathryn; Friml, Jiří; Brandizzi, Federica

    2014-01-01

    The unfolded protein response (UPR) is a signaling network triggered by overload of protein-folding demand in the endoplasmic reticulum (ER), a condition termed ER stress. The UPR is critical for growth and development; nonetheless, connections between the UPR and other cellular regulatory processes remain largely unknown. Here, we identify a link between the UPR and the phytohormone auxin, a master regulator of plant physiology. We show that ER stress triggers down-regulation of auxin receptors and transporters in Arabidopsis thaliana. We also demonstrate that an Arabidopsis mutant of a conserved ER stress sensor IRE1 exhibits defects in the auxin response and levels. These data not only support that the plant IRE1 is required for auxin homeostasis, they also reveal a species-specific feature of IRE1 in multicellular eukaryotes. Furthermore, by establishing that UPR activation is reduced in mutants of ER-localized auxin transporters, including PIN5, we define a long-neglected biological significance of ER-based auxin regulation. We further examine the functional relationship of IRE1 and PIN5 by showing that an ire1 pin5 triple mutant enhances defects of UPR activation and auxin homeostasis in ire1 or pin5. Our results imply that the plant UPR has evolved a hormone-dependent strategy for coordinating ER function with physiological processes.

  14. Endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) in plants.

    Science.gov (United States)

    Wan, Shucen; Jiang, Liwen

    2016-05-01

    Being a major factory for protein synthesis, assembly, and export, the endoplasmic reticulum (ER) has a precise and robust ER quality control (ERQC) system monitoring its product line. However, when organisms are subjected to environmental stress, whether biotic or abiotic, the levels of misfolded proteins may overwhelm the ERQC system, tilting the balance between the capacity of and demand for ER quality control and resulting in a scenario termed ER stress. Intense or prolonged ER stress may cause damage to the ER as well as to other organelles, or even lead to cell death in extreme cases. To avoid such serious consequences, cells activate self-rescue programs to restore protein homeostasis in the ER, either through the enhancement of protein-folding and degradation competence or by alleviating the demands for such reactions. These are collectively called the unfolded protein response (UPR). Long investigated in mammalian cells and yeasts, the UPR is also of great interest to plant scientists. Among the three branches of UPR discovered in mammals, two have been studied in plants with plant homologs existing of the ER-membrane-associated activating transcription factor 6 (ATF6) and inositol-requiring enzyme 1 (IRE1). This review discusses the molecular mechanisms of these two types of UPR in plants, as well as the consequences of insufficient UPR, with a focus on experiments using model plants.

  15. Borrelidin Induces the Unfolded Protein Response in Oral Cancer Cells and Chop-Dependent Apoptosis.

    Science.gov (United States)

    Sidhu, Alpa; Miller, Justin R; Tripathi, Ashootosh; Garshott, Danielle M; Brownell, Amy L; Chiego, Daniel J; Arevang, Carl; Zeng, Qinghua; Jackson, Leah C; Bechler, Shelby A; Callaghan, Michael U; Yoo, George H; Sethi, Seema; Lin, Ho-Sheng; Callaghan, Joseph H; Tamayo-Castillo, Giselle; Sherman, David H; Kaufman, Randal J; Fribley, Andrew M

    2015-11-12

    Oral squamous cell carcinoma (OSCC) is the most common cancer affecting the oral cavity, and US clinics will register about 30,000 new patients in 2015. Current treatment modalities include chemotherapy, surgery, and radiotherapy, which often result in astonishing disfigurement. Cancers of the head and neck display enhanced levels of glucose-regulated proteins and translation initiation factors associated with endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). Previous work demonstrated that chemically enforced UPR could overwhelm these adaptive features and selectively kill malignant cells. The threonyl-tRNA synthetase (ThRS) inhibitor borrelidin and two congeners were discovered in a cell-based chemical genomic screen. Borrelidin increased XBP1 splicing and led to accumulation of phosphorylated eIF2α and UPR-associated genes, prior to death in panel of OSCC cells. Murine embryonic fibroblasts (MEFs) null for GCN2 and PERK were less able to accumulate UPR markers and were resistant to borrelidin. This study demonstrates that UPR induction is a feature of ThRS inhibition and adds to a growing body of literature suggesting ThRS inhibitors might selectively target cancer cells.

  16. Yokukansan inhibits neuronal death during ER stress by regulating the unfolded protein response.

    Directory of Open Access Journals (Sweden)

    Toru Hiratsuka

    Full Text Available BACKGROUND: Recently, several studies have reported Yokukansan (Tsumura TJ-54, a traditional Japanese medicine, as a potential new drug for the treatment of Alzheimer's disease (AD. Endoplasmic reticulum (ER stress is known to play an important role in the pathogenesis of AD, particularly in neuronal death. Therefore, we examined the effect of Yokukansan on ER stress-induced neurotoxicity and on familial AD-linked presenilin-1 mutation-associated cell death. METHODS: We employed the WST-1 assay and monitored morphological changes to evaluate cell viability following Yokukansan treatment or treatment with its components. Western blotting and PCR were used to observe the expression levels of GRP78/BiP, caspase-4 and C/EBP homologous protein. RESULTS: Yokukansan inhibited neuronal death during ER stress, with Cnidii Rhizoma (Senkyu, a component of Yokukansan, being particularly effective. We also showed that Yokukansan and Senkyu affect the unfolded protein response following ER stress and that these drugs inhibit the activation of caspase-4, resulting in the inhibition of ER stress-induced neuronal death. Furthermore, we found that the protective effect of Yokukansan and Senkyu against ER stress could be attributed to the ferulic acid content of these two drugs. CONCLUSIONS: Our results indicate that Yokukansan, Senkyu and ferulic acid are protective against ER stress-induced neuronal cell death and may provide a possible new treatment for AD.

  17. Conformational properties of the unfolded state of Im7 in nondenaturing conditions.

    Science.gov (United States)

    Pashley, Clare L; Morgan, Gareth J; Kalverda, Arnout P; Thompson, Gary S; Kleanthous, Colin; Radford, Sheena E

    2012-02-17

    The unfolded ensemble in aqueous solution represents the starting point of protein folding. Characterisation of this species is often difficult since the native state is usually predominantly populated at equilibrium. Previous work has shown that the four-helix protein, Im7 (immunity protein 7), folds via an on-pathway intermediate. While the transition states and folding intermediate have been characterised in atomistic detail, knowledge of the unfolded ensemble under the same ambient conditions remained sparse. Here, we introduce destabilising amino acid substitutions into the sequence of Im7, such that the unfolded state becomes predominantly populated at equilibrium in the absence of denaturant. Using far- and near-UV CD, fluorescence, urea titration and heteronuclear NMR experiments, we show that three amino acid substitutions (L18A-L19A-L37A) are sufficient to prevent Im7 folding, such that the unfolded state is predominantly populated at equilibrium. Using measurement of chemical shifts, (15)N transverse relaxation rates and sedimentation coefficients, we show that the unfolded species of L18A-L19A-L37A deviates significantly from random-coil behaviour. Specifically, we demonstrate that this unfolded species is compact (R(h)=25 Å) relative to the urea-denatured state (R(h)≥30 Å) and contains local clusters of hydrophobic residues in regions that correspond to the four helices in the native state. Despite these interactions, there is no evidence for long-range stabilising tertiary interactions or persistent helical structure. The results reveal an unfolded ensemble that is conformationally restricted in regions of the polypeptide chain that ultimately form helices I, II and IV in the native state.

  18. The Intrinsic Dynamics and Unfolding Process of an Antibody Fab Fragment Revealed by Elastic Network Model

    Directory of Open Access Journals (Sweden)

    Ji-Guo Su

    2015-12-01

    Full Text Available Antibodies have been increasingly used as pharmaceuticals in clinical treatment. Thermal stability and unfolding process are important properties that must be considered in antibody design. In this paper, the structure-encoded dynamical properties and the unfolding process of the Fab fragment of the phosphocholine-binding antibody McPC603 are investigated by use of the normal mode analysis of Gaussian network model (GNM. Firstly, the temperature factors for the residues of the protein were calculated with GNM and then compared with the experimental measurements. A good result was obtained, which provides the validity for the use of GNM to study the dynamical properties of the protein. Then, with this approach, the mean-square fluctuation (MSF of the residues, as well as the MSF in the internal distance (MSFID between all pairwise residues, was calculated to investigate the mobility and flexibility of the protein, respectively. It is found that the mobility and flexibility of the constant regions are higher than those of the variable regions, and the six complementarity-determining regions (CDRs in the variable regions also exhibit relative large mobility and flexibility. The large amplitude motions of the CDRs are considered to be associated with the immune function of the antibody. In addition, the unfolding process of the protein was simulated by iterative use of the GNM. In our method, only the topology of protein native structure is taken into account, and the protein unfolding process is simulated through breaking the native contacts one by one according to the MSFID values between the residues. It is found that the flexible regions tend to unfold earlier. The sequence of the unfolding events obtained by our method is consistent with the hydrogen-deuterium exchange experimental results. Our studies imply that the unfolding behavior of the Fab fragment of antibody McPc603 is largely determined by the intrinsic dynamics of the protein.

  19. Microscopic dynamics of water around unfolded structures of barstar at room temperature

    Energy Technology Data Exchange (ETDEWEB)

    Pal, Somedatta; Chakraborty, Kaushik; Khatua, Prabir; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302 (India)

    2015-02-07

    The breaking of the native structure of a protein and its influences on the dynamic response of the surrounding solvent is an important issue in protein folding. In this work, we have carried out atomistic molecular dynamics simulations to unfold the protein barstar at two different temperatures (400 K and 450 K). The two unfolded forms obtained at such high temperatures are further studied at room temperature to explore the effects of nonuniform unfolding of the protein secondary structures along two different pathways on the microscopic dynamical properties of the surface water molecules. It is demonstrated that though the structural transition of the protein in general results in less restricted water motions around its segments, but there are evidences of formation of new conformational motifs upon unfolding with increasingly confined environment around them, thereby resulting in further restricted water mobility in their hydration layers. Moreover, it is noticed that the effects of nonuniform unfolding of the protein segments on the relaxation times of the protein–water (PW) and the water–water (WW) hydrogen bonds are correlated with hindered hydration water motions. However, the kinetics of breaking and reformation of such hydrogen bonds are found to be influenced differently at the interface. It is observed that while the effects of unfolding on the PW hydrogen bond kinetics seem to be minimum, but the kinetics involving the WW hydrogen bonds around the protein segments exhibit noticeably heterogeneous characteristics. We believe that this is an important observation, which can provide valuable insights on the origin of heterogeneous influence of unfolding of a protein on the microscopic properties of its hydration water.

  20. Force-induced unfolding of fibronectin in the extracellular matrix of living cells.

    Directory of Open Access Journals (Sweden)

    Michael L Smith

    2007-10-01

    Full Text Available Whether mechanically unfolded fibronectin (Fn is present within native extracellular matrix fibrils is controversial. Fn extensibility under the influence of cell traction forces has been proposed to originate either from the force-induced lengthening of an initially compact, folded quaternary structure as is found in solution (quaternary structure model, where the dimeric arms of Fn cross each other, or from the force-induced unfolding of type III modules (unfolding model. Clarification of this issue is central to our understanding of the structural arrangement of Fn within fibrils, the mechanism of fibrillogenesis, and whether cryptic sites, which are exposed by partial protein unfolding, can be exposed by cell-derived force. In order to differentiate between these two models, two fluorescence resonance energy transfer schemes to label plasma Fn were applied, with sensitivity to either compact-to-extended conformation (arm separation without loss of secondary structure or compact-to-unfolded conformation. Fluorescence resonance energy transfer studies revealed that a significant fraction of fibrillar Fn within a three-dimensional human fibroblast matrix is partially unfolded. Complete relaxation of Fn fibrils led to a refolding of Fn. The compactly folded quaternary structure with crossed Fn arms, however, was never detected within extracellular matrix fibrils. We conclude that the resting state of Fn fibrils does not contain Fn molecules with crossed-over arms, and that the several-fold extensibility of Fn fibrils involves the unfolding of type III modules. This could imply that Fn might play a significant role in mechanotransduction processes.