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Sample records for folding thermodynamics visualized

  1. Kinetics and Thermodynamics of Membrane Protein Folding

    Directory of Open Access Journals (Sweden)

    Ernesto A. Roman

    2014-03-01

    Full Text Available Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field lag far behind. Although membrane proteins constitute about a third of the proteins encoded in known genomes, stability studies on membrane proteins have been impaired due to experimental limitations. Furthermore, no systematic experimental strategies are available for folding these biomolecules in vitro. Common denaturing agents such as chaotropes usually do not work on helical membrane proteins, and ionic detergents have been successful denaturants only in few cases. Refolding a membrane protein seems to be a craftsman work, which is relatively straightforward for transmembrane β-barrel proteins but challenging for α-helical membrane proteins. Additional complexities emerge in multidomain membrane proteins, data interpretation being one of the most critical. In this review, we will describe some recent efforts in understanding the folding mechanism of membrane proteins that have been reversibly refolded allowing both thermodynamic and kinetic analysis. This information will be discussed in the context of current paradigms in the protein folding field.

  2. 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.

  3. Folding and insertion thermodynamics of the transmembrane WALP peptide

    Energy Technology Data Exchange (ETDEWEB)

    Bereau, Tristan, E-mail: bereau@mpip-mainz.mpg.de [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany); Bennett, W. F. Drew [Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1 (Canada); Pfaendtner, Jim [Department of Chemical Engineering, University of Washington, Seattle, Washington 98195 (United States); Deserno, Markus [Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Karttunen, Mikko [Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MetaForum, 5600 MB Eindhoven (Netherlands)

    2015-12-28

    The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA){sub n} (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide’s insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.

  4. Folding and insertion thermodynamics of the transmembrane WALP peptide.

    Science.gov (United States)

    Bereau, Tristan; Bennett, W F Drew; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko

    2015-12-28

    The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum-in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.

  5. DNA Origami Folding Pathways: Implications for Design, Thermodynamics, and Kinetics

    Science.gov (United States)

    Majikes, Jacob Michael

    DNA nanotechnology implements the predictable self-assembly rules of DNA, allowing the adaptation of DNA from a biological tool for storage of genetic information to a biomimetic structural nanomaterial. DNA has been employed to organize organic and inorganic materials, as well as to create both static and dynamic nanostructures. Aided by the low cost of arbitrary sequence DNA oligomer synthesis and robust conjugation chemistries, DNA has developed as a promising nanofabrication tool. While under biological conditions the formation and thermodynamics of DNA are well known, nanotechnology applications typically lie well outside of those conditions. This dissertation presents a new scaffold (miniM13) for DNA nanostructures and three new protocols to probe the folding and formation of DNA nanostructures. Development of these novel techniques improves the molecular assembly toolkit to enable new and exciting experimental systems. (Abstract shortened by ProQuest.).

  6. Folding and insertion thermodynamics of the transmembrane WALP peptide

    CERN Document Server

    Bereau, Tristan; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko

    2015-01-01

    The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)$_n$(L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum---in contrast to both atomistic simulations and the alternative PLUM force field. Even tho...

  7. Teaching Differentials in Thermodynamics using Spatial Visualization

    CERN Document Server

    Wang, Chih-Yueh

    2011-01-01

    The greatest difficulty that is encountered by students in Thermodynamics classes is to find relationships between variables and solve a total differential equation that relates one thermodynamic state variable to two mutually-independent state variables. Rules of differentiation, including the total differential and the cyclic rule, are fundamental to solving thermodynamics problems. However, many students do not well understand such basic mathematics principles, because the underlying geometric meaning is unclear to them. Studies have shown that proficient symbolic techniques may become an obstacle to learning in a qualitative approach. Spatial visualization allows an emergence of new reasoning for students. In this investigation, the total differential rule and the cyclic rule are interpreted geometrically.

  8. 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

  9. Teaching Differentials in Thermodynamics Using Spatial Visualization

    Science.gov (United States)

    Wang, Chih-Yueh; Hou, Ching-Han

    2012-01-01

    The greatest difficulty that is encountered by students in thermodynamics classes is to find relationships between variables and to solve a total differential equation that relates one thermodynamic state variable to two mutually independent state variables. Rules of differentiation, including the total differential and the cyclic rule, are…

  10. Teaching Differentials in Thermodynamics Using Spatial Visualization

    Science.gov (United States)

    Wang, Chih-Yueh; Hou, Ching-Han

    2012-01-01

    The greatest difficulty that is encountered by students in thermodynamics classes is to find relationships between variables and to solve a total differential equation that relates one thermodynamic state variable to two mutually independent state variables. Rules of differentiation, including the total differential and the cyclic rule, are…

  11. Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Gorodkin, Jan; Backofen, Rolf

    2008-01-01

    Computational methods for determining the secondary structure of RNA sequences from given alignments are currently either based on thermodynamic folding, compensatory base pair substitutions or both. However, there is currently no approach that combines both sources of information in a single...... on a set of 46 well-curated Rfam families and its performance compared favorably to that of Pfold and RNAalifold....

  12. Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Gorodkin, Jan; Backofen, Rolf

    2008-01-01

    optimization problem. Here, we present a model that formally integrates both the energy-based and evolution-based approaches to predict the folding of multiple aligned RNA sequences. We have implemented an extended version of Pfold that identifies base pairs that have high probabilities of being conserved......Computational methods for determining the secondary structure of RNA sequences from given alignments are currently either based on thermodynamic folding, compensatory base pair substitutions or both. However, there is currently no approach that combines both sources of information in a single...... the corresponding probability of being single stranded. Furthermore, we found that structurally conserved RNA motifs are mostly supported by folding energies. Other problems (e.g. RNA-folding kinetics) may also benefit from employing the principles of the model we introduce. Our implementation, PETfold, was tested...

  13. 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%.

  14. Folding and self-assembly of polypeptides: Dynamics and thermodynamics from molecular simulation

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    Fluitt, Aaron Michael

    Empowered by their exquisite three-dimensional structures, or "folds," proteins carry out biological tasks with high specificity, efficiency, and fidelity. The fold that optimizes biological function represents a stable configuration of the constituent polypeptide molecule(s) under physiological conditions. Proteins and polypeptides are not static, however: battered by thermal motion, they explore a distribution of folds that is determined by the sequence of amino acids, the presence and identity of other molecules, and the thermodynamic conditions. In this dissertation, we apply molecular simulation techniques to the study of two polypeptides that have unusually diffuse distributions of folds under physiological conditions: polyglutamine (polyQ) and islet amyloid polypeptide (IAPP). Neither polyQ nor IAPP adopts a predominant fold in dilute aqueous solution, but at sufficient concentrations, both are prone to self-assemble into stable, periodic, and highly regular aggregate structures known as amyloid. The appearance of amyloid deposits of polyQ in the brain, and of IAPP in the pancreas, are associated with Huntington's disease and type 2 diabetes, respectively. A molecular view of the mechanism(s) by which polyQ and IAPP fold and self-assemble will enhance our understanding of disease pathogenesis, and it has the potential to accelerate the development of therapeutics that target early-stage aggregates. Using molecular simulations with spatial and temporal resolution on the atomic scale, we present analyses of the structural distributions of polyQ and IAPP under various conditions, both in and out of equilibrium. In particular, we examine amyloid fibers of polyQ, the IAPP dimer in solution, and single IAPP fragments at a lipid bilayer. We also benchmark the molecular models, or "force fields," available for such studies, and we introduce a novel simulation algorithm.

  15. Kinetics and Thermodynamics of Peptide (pHLIP) insertion and folding in a lipid bilayer

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    Andreev, Oleg; Karabadzhak, Alexander; Weerakkody, Dhammika; Markin, Vladislav; Engelman, Donald; Reshetnyak, Yana

    2009-03-01

    We study spontaneous insertion and folding across a lipid bilayer of moderately polar membrane peptide pHLIP - pH Low Insertion Peptide. pHLIP has three major states: soluble in water or bound to the surface of a lipid bilayer as an unstructured monomer, and inserted across the bilayer as a monomeric α-helix. We used fluorescence spectroscopy and isothermal titration calorimetry to calculate the transition energies between states. The free energy of binding to a surface of lipid bilayer is about -7 kcal/mol and the free energy of insertion and folding across a lipid bilayer at low pH is nearly -2 kcal/mol. We performed stopped-flow fluorescence and CD measurements to elucidate molecular mechanism of pHLIP insertion and folding within a lipid bilayer and to calculate the activation energy of formation of transmembrane helix. pHLIP also has utility as an agent to target diseased tissues and translocate molecules through the membrane into the cytoplasm of cells in environments with elevated levels of extracellular acidity, as in cancer and inflammation. We plan to discuss a number of related kinetics and thermodynamic parameters from our measurements.

  16. Thermodynamic Stabilization of the Folded Domain of Prion Protein Inhibits Prion Infection in Vivo

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    Qingzhong Kong

    2013-07-01

    Full Text Available Prion diseases, or transmissible spongiform encephalopathies (TSEs, are associated with the conformational conversion of the cellular prion protein, PrPC, into a protease-resistant form, PrPSc. Here, we show that mutation-induced thermodynamic stabilization of the folded, α-helical domain of PrPC has a dramatic inhibitory effect on the conformational conversion of prion protein in vitro, as well as on the propagation of TSE disease in vivo. Transgenic mice expressing a human prion protein variant with increased thermodynamic stability were found to be much more resistant to infection with the TSE agent than those expressing wild-type human prion protein, in both the primary passage and three subsequent subpassages. These findings not only provide a line of evidence in support of the protein-only model of TSEs but also yield insight into the molecular nature of the PrPC→PrPSc conformational transition, and they suggest an approach to the treatment of prion diseases.

  17. BiFold: visualizing decision-makers and choice in a common embedding space

    CERN Document Server

    Jiang, Yazhen; Sun, Jie

    2016-01-01

    The emerging domain of data-enabled science necessitates development of algorithms and tools to provide for knowledge discovery. Human interaction with data through well-constructed graphical representation can take special advantage of our visual processing system's ability to identify patterns. We develop a data visualization framework, called BiFold, for exploratory analysis of binary relationships between two groups of objects. Typical data examples would include voting records, organizational memberships, and pairwise associations, or other binary datasets. BiFold visualization provides a low dimensional embedding of the data in a way that captures similarity by visual nearness, analogous to Multidimensional Scaling (MDS). The unique and new feature of BiFold is its ability to simultaneously capture both the within-group and between-group relationships among the objects, significantly enhancing visual knowledge discovery. We benchmark BiFold using the classic Southern Women Dataset, where previously iden...

  18. Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry.

    Science.gov (United States)

    Vander Meulen, Kirk A; Butcher, Samuel E

    2012-03-01

    A novel isothermal titration calorimetry (ITC) method was applied to investigate RNA helical packing driven by the GAAA tetraloop-receptor interaction in magnesium and potassium solutions. Both the kinetics and thermodynamics were obtained in individual ITC experiments, and analysis of the kinetic data over a range of temperatures provided Arrhenius activation energies (ΔH(‡)) and Eyring transition state entropies (ΔS(‡)). The resulting rich dataset reveals strongly contrasting kinetic and thermodynamic profiles for this RNA folding system when stabilized by potassium versus magnesium. In potassium, association is highly exothermic (ΔH(25°C) = -41.6 ± 1.2 kcal/mol in 150 mM KCl) and the transition state is enthalpically barrierless (ΔH(‡) = -0.6 ± 0.5). These parameters are significantly positively shifted in magnesium (ΔH(25°C) = -20.5 ± 2.1 kcal/mol, ΔH(‡) = 7.3 ± 2.2 kcal/mol in 0.5 mM MgCl(2)). Mixed salt solutions approximating physiological conditions exhibit an intermediate thermodynamic character. The cation-dependent thermodynamic landscape may reflect either a salt-dependent unbound receptor conformation, or alternatively and more generally, it may reflect a small per-cation enthalpic penalty associated with folding-coupled magnesium uptake.

  19. Mathematics, Thermodynamics, and Modeling to Address Ten Common Misconceptions about Protein Structure, Folding, and Stability

    Science.gov (United States)

    Robic, Srebrenka

    2010-01-01

    To fully understand the roles proteins play in cellular processes, students need to grasp complex ideas about protein structure, folding, and stability. Our current understanding of these topics is based on mathematical models and experimental data. However, protein structure, folding, and stability are often introduced as descriptive, qualitative…

  20. Real-time kymographic imaging for visualizing human vocal-fold vibratory function

    NARCIS (Netherlands)

    Qiu, Qingjun; Schutte, Harm K.

    2007-01-01

    A stand-alone kymographic system for visualizing human vocal-fold vibration in real time is presented. By using a dual charge-coupled-device construction, the system not only provides kymographic images but also simultaneously presents structural images for navigating the endoscope to a desired posi

  1. Optimized Wang-Landau sampling of lattice polymers: ground state search and folding thermodynamics of HP model proteins.

    Science.gov (United States)

    Wüst, Thomas; Landau, David P

    2012-08-14

    Coarse-grained (lattice-) models have a long tradition in aiding efforts to decipher the physical or biological complexity of proteins. Despite the simplicity of these models, however, numerical simulations are often computationally very demanding and the quest for efficient algorithms is as old as the models themselves. Expanding on our previous work [T. Wüst and D. P. Landau, Phys. Rev. Lett. 102, 178101 (2009)], we present a complete picture of a Monte Carlo method based on Wang-Landau sampling in combination with efficient trial moves (pull, bond-rebridging, and pivot moves) which is particularly suited to the study of models such as the hydrophobic-polar (HP) lattice model of protein folding. With this generic and fully blind Monte Carlo procedure, all currently known putative ground states for the most difficult benchmark HP sequences could be found. For most sequences we could also determine the entire energy density of states and, together with suitably designed structural observables, explore the thermodynamics and intricate folding behavior in the virtually inaccessible low-temperature regime. We analyze the differences between random and protein-like heteropolymers for sequence lengths up to 500 residues. Our approach is powerful both in terms of robustness and speed, yet flexible and simple enough for the study of many related problems in protein folding.

  2. Optimized Wang-Landau sampling of lattice polymers: Ground state search and folding thermodynamics of HP model proteins

    Science.gov (United States)

    Wüst, Thomas; Landau, David P.

    2012-08-01

    Coarse-grained (lattice-) models have a long tradition in aiding efforts to decipher the physical or biological complexity of proteins. Despite the simplicity of these models, however, numerical simulations are often computationally very demanding and the quest for efficient algorithms is as old as the models themselves. Expanding on our previous work [T. Wüst and D. P. Landau, Phys. Rev. Lett. 102, 178101 (2009)], 10.1103/PhysRevLett.102.178101, we present a complete picture of a Monte Carlo method based on Wang-Landau sampling in combination with efficient trial moves (pull, bond-rebridging, and pivot moves) which is particularly suited to the study of models such as the hydrophobic-polar (HP) lattice model of protein folding. With this generic and fully blind Monte Carlo procedure, all currently known putative ground states for the most difficult benchmark HP sequences could be found. For most sequences we could also determine the entire energy density of states and, together with suitably designed structural observables, explore the thermodynamics and intricate folding behavior in the virtually inaccessible low-temperature regime. We analyze the differences between random and protein-like heteropolymers for sequence lengths up to 500 residues. Our approach is powerful both in terms of robustness and speed, yet flexible and simple enough for the study of many related problems in protein folding.

  3. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics

    Directory of Open Access Journals (Sweden)

    Giegerich Robert

    2004-08-01

    Full Text Available Abstract Background The general problem of RNA secondary structure prediction under the widely used thermodynamic model is known to be NP-complete when the structures considered include arbitrary pseudoknots. For restricted classes of pseudoknots, several polynomial time algorithms have been designed, where the O(n6time and O(n4 space algorithm by Rivas and Eddy is currently the best available program. Results We introduce the class of canonical simple recursive pseudoknots and present an algorithm that requires O(n4 time and O(n2 space to predict the energetically optimal structure of an RNA sequence, possible containing such pseudoknots. Evaluation against a large collection of known pseudoknotted structures shows the adequacy of the canonization approach and our algorithm. Conclusions RNA pseudoknots of medium size can now be predicted reliably as well as efficiently by the new algorithm.

  4. Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water.

    Science.gov (United States)

    Spolar, R S; Livingstone, J R; Record, M T

    1992-04-28

    This extension of the liquid hydrocarbon model seeks to quantify the thermodynamic contributions to protein stability from the removal of nonpolar and polar surface from water. Thermodynamic data for the transfer of hydrocarbons and organic amides from water to the pure liquid phase are analyzed to obtain contributions to the thermodynamics of folding from the reduction in water-accessible surface area. Although the removal of nonpolar surface makes the dominant contribution to the standard heat capacity change of folding (delta C0fold), here we show that inclusion of the contribution from removal of polar surface allows a quantitative prediction of delta C0fold within the uncertainty of the calorimetrically determined value. Moreover, analysis of the contribution of polar surface area to the enthalpy of transfer of liquid amides provides a means of estimating the contributions from changes in nonpolar and polar surface area as well as other factors to the enthalpy of folding (delta H0fold). In addition to estimates of delta H0fold, this extension of the liquid hydrocarbon model provides a thermodynamic explanation for the observation [Privalov, P. L., & Khechinashvili, N. N. (1974) J. Mol. Biol. 86, 665-684] that the specific enthalpy of folding (cal g-1) of a number of globular proteins converges to a common value at approximately 383 K. Because amounts of nonpolar and polar surface area buried by these proteins upon folding are found to be linear functions of molar mass, estimates of both delta C0fold and delta H0fold may be obtained given only the molar mass of the protein of interest.(ABSTRACT TRUNCATED AT 250 WORDS)

  5. Time Curves: Folding Time to Visualize Patterns of Temporal Evolution in Data.

    Science.gov (United States)

    Bach, Benjamin; Shi, Conglei; Heulot, Nicolas; Madhyastha, Tara; Grabowski, Tom; Dragicevic, Pierre

    2016-01-01

    We introduce time curves as a general approach for visualizing patterns of evolution in temporal data. Examples of such patterns include slow and regular progressions, large sudden changes, and reversals to previous states. These patterns can be of interest in a range of domains, such as collaborative document editing, dynamic network analysis, and video analysis. Time curves employ the metaphor of folding a timeline visualization into itself so as to bring similar time points close to each other. This metaphor can be applied to any dataset where a similarity metric between temporal snapshots can be defined, thus it is largely datatype-agnostic. We illustrate how time curves can visually reveal informative patterns in a range of different datasets.

  6. Folding thermodynamics of c-Myb DNA-binding domain in correlation with its α-helical contents.

    Science.gov (United States)

    Inaba, Satomi; Fukada, Harumi; Oda, Masayuki

    2016-01-01

    The conformational and thermal stabilities of the minimum functional unit for c-Myb DNA-binding domain, tandem repeat 2 and 3 (R2R3), were analyzed under different pH conditions, ranging from 4.0 to 7.5, using circular dichroism and differential scanning calorimetry. Secondary structure analysis showed that the solution pH largely affects the conformational stability of the protein domain. Of all conditions analyzed, the α-helical content was maximal at pH 6.5, and the thermal stability was highest at pH 5.0. Thermodynamic parameters for thermal unfolding of R2R3 were determined using differential scanning calorimetry, and the origin of folding thermodynamics at the different pHs and its correlation with the α-helical content were further analyzed. It should be noted that the α-helical content correlates well with the enthalpy change in the pH range from 4.5 to 7.5, suggesting that the strength of hydrogen bonds and salt bridges needed for maintenance of helical structure is related to enthalpy in the native state. Under physiological pH conditions, c-Myb R2R3 exists in the enthalpically unstable but entropically stable state. Due to loss of rigid structure and high stability, the protein can now obtain structural flexibility, befitting its function.

  7. Relevance of structural segregation and chain compaction for the thermodynamics of folding of a hydrophobic protein model.

    Science.gov (United States)

    Barbosa, Marco Aurélio A; de Araújo, Antônio F Pereira

    2003-05-01

    The relevance of inside-outside segregation and chain compaction for the thermodynamics of folding of a hydrophobic protein model is probed by complete enumeration of two-dimensional chains of up to 18 monomers in the square lattice. The exact computation of Z scores for uniquely designed sequences confirms that Z tends to decrease linearly with sigma square root of N, as previously suggested by theoretical analysis and Monte Carlo simulations, where sigma, the standard deviation of the number of contacts made by different monomers in the target structure, is a measure of structural segregation and N is the chain length. The probability that the target conformation is indeed the unique global energy minimum of the designed sequence is found to increase dramatically with sigma, approaching unity at maximal segregation. However, due to the huge number of conformations with sub-maximal values of sigma, which correspond to intermediate, only mildly discriminative, values of Z, in addition to significant oscillations of Z around its estimated value, the probability that a correctly designed sequence corresponds to a maximally segregated conformation is small. This behavior of Z also explains the observed relation between sigma and different measures of folding cooperativity of correctly designed sequences.

  8. Contribution of hydration to protein folding thermodynamics. I. The enthalpy of hydration.

    Science.gov (United States)

    Makhatadze, G I; Privalov, P L

    1993-07-20

    The enthalpy of hydration of polar and non-polar groups upon protein unfolding has been estimated for four globular proteins in the temperature range 5 to 125 degrees C, using structural information on the groups in these proteins exposed to water in the native and unfolded states and volume-corrected calorimetric information on the enthalpy and heat capacity of transfer into water of various model compounds. It has been shown that the enthalpy of hydration of polar groups greatly exceeds the enthalpy of hydration of non-polar groups. At low temperatures both these enthalpies are negative and change in opposite direction with increasing temperature. Subtracting the total enthalpy of hydration of polar and non-polar groups from the calorimetrically determined enthalpy of protein unfolding, the total enthalpy of internal interactions maintaining the native protein structure has been determined. Using thermodynamic information on the sublimation of organic crystals, the total enthalpy was divided into two components: one associated with the interactions between the non-polar groups (van der Waals interaction) and the rest associated with the interactions between polar groups (hydrogen bonding). This made it possible to estimate the overall enthalpies of disruption of contacts between the polar groups with their exposure to water and between the non-polar groups with their exposure to water. It appears that these enthalpies have opposite signs in the temperature range considered and change in opposite directions with increasing temperature. The enthalpy of transfer of non-polar groups from the protein interior into water is negative below 25 degrees C and positive above. The enthalpy of transfer of polar groups from the protein interior into water is positive at low temperatures and becomes negative at higher temperatures. Over the considered temperature range, however, the enthalpy of transfer of non-polar groups dominates. This results in a positive enthalpy of

  9. Airflow visualization in a model of human glottis near the self-oscillating vocal folds model

    Directory of Open Access Journals (Sweden)

    Horáček J.

    2011-06-01

    Full Text Available The contribution describes PIV (Particle Image Velocimetry measurement of airflow in the glottal region of complex physical models of the voice production that consist of 1 : 1 scaled models of the trachea, the self-oscillating vocal folds and the human vocal tract with acoustical spaces that correspond to the vowels /a:/, /u:/ and /i:/. The time-resolved PIV method was used for visualization of the airflow simultaneously with measurements of subglottal pressure, radiated acoustic pressure and vocal fold vibrations. The measurements were performed within a physiologically real range of mean airflow rate and fundamental phonation frequency. The images of the vibrating vocal folds during one oscillation period were recorded by the high-speed camera at the same time instants as the velocity fields measured by the PIV method.In the region above the models of the ventricular folds and of the epilaryngeal tube it is possible to detect large vortices with dimensions comparable with the channel cross-section and moving relatively slowly downstream. The vortices disappear in the narrower pharyngeal part of the vocal tract model where the flow is getting more uniform. The basic features of the coherent structures identified in the laryngeal cavity models in the interval of the measured airflow rates were found qualitatively similar for all three vowels investigated.

  10. Temperature dependence of strain energy and thermodynamic properties of V2 O5 -based single-walled nanotubes: Zone-folding approach.

    Science.gov (United States)

    Porsev, Vitaly V; Bandura, Andrei V; Evarestov, Robert A

    2016-06-15

    A zone-folding approach is applied to estimate the thermodynamic properties of V2 O5 -based nanotubes. The results obtained are compared with those from the direct calculations. It is shown that the zone-folding approximation allows an accurate estimation of nanotube thermodynamic properties and gives a gain in computation time compared to their direct calculations. Both approaches show that temperature effects do not change the relative stability of V2 O5 free layers and nanotubes derived from the α- and γ-phase. The internal energy thermal contributions into the strain energy of nanotubes are small and can be ignored. © 2016 Wiley Periodicals, Inc.

  11. 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

  12. 3D Visualization of Sheath Folds in Roman Marble from Ephesus, Turkey

    Science.gov (United States)

    Wex, Sebastian; Passchier, Cornelis W.; de Kemp, Eric A.; Ilhan, Sinan

    2013-04-01

    Excavation of a palatial 2nd century AD house (Terrace House Two) in the ancient city of Ephesus, Turkey in the 1970s produced 10.313 pieces of colored, folded marble which belonged to 54 marble plates of 1.6 cm thickness that originally covered the walls of the banquet hall of the house. The marble plates were completely reassembled and restored by a team of workers over the last 6 years. The plates were recognized as having been sawn from two separate large blocks of "Cipollino verde", a green mylonitized marble from Karystos on the Island of Euboea, Greece. After restoration, it became clear that all slabs had been placed on the wall in approximately the sequence in which they had been cut off by a Roman stone saw. As a result, the marble plates give a full 3D insight in the folded internal structure of 1m3 block of mylonite. The restoration of the slabs was recognized as a first, unique opportunity for detailed reconstruction of the 3D geometry of m-scale folds in mylonitized marble. Photographs were taken of each slab and used to reconstruct their exact arrangement within the originally quarried blocks. Outlines of layers were digitized and a full 3D reconstruction of the internal structure of the block was created using ArcMap and GOCAD. Fold structures in the block include curtain folds and multilayered sheath folds. Several different layers showing these structures were digitized on the photographs of the slab surfaces and virtually mounted back together within the model of the marble block. Due to the serial sectioning into slabs, with cm-scale spacing, the visualization of the 3D geometry of sheath folds was accomplished with a resolution better than 4 cm. Final assembled 3D images reveal how sheath folds emerge from continuous layers and show their overall consistency as well as a constant hinge line orientation of the fold structures. Observations suggest that a single deformation phase was responsible for the evolution of "Cipollino verde" structures

  13. 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.

  14. Discrete Frenet frame, inflection point solitons, and curve visualization with applications to folded proteins

    Science.gov (United States)

    Hu, Shuangwei; Lundgren, Martin; Niemi, Antti J.

    2011-06-01

    We develop a transfer matrix formalism to visualize the framing of discrete piecewise linear curves in three-dimensional space. Our approach is based on the concept of an intrinsically discrete curve. This enables us to more effectively describe curves that in the limit where the length of line segments vanishes approach fractal structures in lieu of continuous curves. We verify that in the case of differentiable curves the continuum limit of our discrete equation reproduces the generalized Frenet equation. In particular, we draw attention to the conceptual similarity between inflection points where the curvature vanishes and topologically stable solitons. As an application we consider folded proteins, their Hausdorff dimension is known to be fractal. We explain how to employ the orientation of Cβ carbons of amino acids along a protein backbone to introduce a preferred framing along the backbone. By analyzing the experimentally resolved fold geometries in the Protein Data Bank we observe that this Cβ framing relates intimately to the discrete Frenet framing. We also explain how inflection points (a.k.a. soliton centers) can be located in the loops and clarify their distinctive rôle in determining the loop structure of folded proteins.

  15. Museum as an integrated imaging device: visualization of ancient Kyoto cityscape from folding screen artifact

    Science.gov (United States)

    Miyata, Kimiyoshi; Oyabu, Umi; Kojima, Michihiro

    2012-03-01

    Museums hold cultural resources such as artworks, historical artifacts, and folklore materials. The National Museum of Japanese History holds over 200,000 of the cultural resources. A role of museum is to exhibit the cultural resources, therefore a museum could be referred to as a visualization device for the information society. In this research, visualization of a history image from cultural resources with interactive user interface will be mentioned. The material focused on is the oldest extant version of a genre of folding screen paintings that depict the thriving city of Kyoto in the four seasons, named Rekihaku's "Scenes In and Around Kyoto" designated as a nationally important cultural property in Japan. Over 1,400 people and a lot of residences, temples, and houses are drawn, and those are also information resource telling us about city scenes and people's life in Kyoto at that time. Historical researches were done by using a high resolution digital image obtained by a large scaled scanner, and scanned images are used for computer programs to visualize a history image of ancient Kyoto. Combinations between real materials and information provided by using the computer programs are also described in this research.

  16. Sudden unilateral visual loss after autologous fat injection into the nasolabial fold

    Directory of Open Access Journals (Sweden)

    Sang Hyouk Park

    2008-10-01

    Full Text Available Sang Hyouk Park, Hae Jung Sun, Kyung Seek ChoiDepartment of ophthalmology, Soonchunhyang University College of Medicine, Seoul, KoreaAbstract: A 27-year-old female presented with sudden visual loss of her right eye after receiving an autologous fat injection into the right nasolabial fold. Fundus examination of the right eye showed multiple whitish patchy lesions with macular edema. Fluorescein angiogram showed deterioration of choroidal circulation with patchy choroidal filling and arm-to-retina circulation time and retinal arteriovenous passage time were delayed to 30 seconds and 20 seconds, respectively. There was no response in flash visual evoked potential (VEP. High dose steroid therapy (methylprednisolone 1 g/day/i.v. was done and about 2 weeks later, the disc edema subsided and retinal arteriovenous passage time of fluorescein angiogram was normalized but there was no improvement in visual acuity. Absence of a cherry red spot, deterioration of choroidal circulation with patchy choroidal fillings seen in fluorescein angiogram, and no response in flash VEP suggests multiple choroidal infarction due to perfusion defect of the short posterior ciliary artery. The autologous fat injected is thought to have entered the dorsal nasal artery and the retrograde migration of the emboli to the ophthalmic artery might have caused the multiple occlusions of the short posterior ciliary artery.Keywords: autologous fat injection, ciliary artery occlusion, ischemic optic neuropathy

  17. Kinetic and thermodynamic analysis of the conformational folding process of SS-reduced bovine pancreatic ribonuclease A using a selenoxide reagent with high oxidizing ability.

    Science.gov (United States)

    Arai, Kenta; Kumakura, Fumio; Iwaoka, Michio

    2012-01-01

    Redox-coupled folding pathways of bovine pancreatic ribonuclease A (RNase A) with four intramolecular disulfide (SS) bonds comprise three phases: (I) SS formation to generate partially oxidized intermediate ensembles with no rigid folded structure; (II) SS rearrangement from the three SS intermediate ensemble (3S) to the des intermediates having three native SS linkages; (III) final oxidation of the last native SS linkage to generate native RNase A. We previously demonstrated that DHS(ox), a water-soluble selenoxide reagent for rapid and quantitative SS formation, allows clear separation of the three folding phases. In this study, the main conformational folding phase (phase II) has been extensively analyzed at pH 8.0 under a wide range of temperatures (5-45 °C), and thermodynamic and kinetic parameters for the four des intermediates were determined. The free-energy differences (ΔG) as a function of temperature suggested that the each SS linkage has different thermodynamic and kinetic roles in stability of the native structure. On the other hand, comparison of the rate constants and the activation energies for 3S → des with those reported for the conformational folding of SS-intact RNase A suggested that unfolded des species (desU) having three native SS linkages but not yet being folded are involved in very small amounts (SS-intact RNase A. It was revealed that DHS(ox) is useful for kinetic and thermodynamic analysis of the conformational folding process on the oxidative folding pathways of SS-reduced proteins.

  18. A new entropy model for RNA: part IV, The Minimum Free Energy (mFE and the thermodynamically most-probable folding pathway (TMPFP

    Directory of Open Access Journals (Sweden)

    Wayne Dawson

    2015-07-01

    Full Text Available Here we discuss four important questions (1 how can we be sure that the thermodynamically most-probable folding-pathway yields the minimum free energy for secondary structure using the dynamic programming algorithm (DPA approach, (2 what are its limitations, (3 how can we extend the DPA to find the minimum free energy with pseudoknots, and finally (4 what limitations can we expect to find in a DPA approach for pseudoknots. It is our supposition that some structures cannot be fit uniquely by the DPA, but may exist in real biology situations when disordered regions in the biomolecule are necessary. These regions would be identifiable by using suboptimal structure analysis. This grants us some qualitative tools to identify truly random RNA sequences, because such are likely to have greater degeneracy in their thermodynamically most-probable folding-pathway.

  19. Can you see what you feel? Color and folding properties affect visual-tactile material discrimination of fabrics.

    Science.gov (United States)

    Xiao, Bei; Bi, Wenyan; Jia, Xiaodan; Wei, Hanhan; Adelson, Edward H

    2016-01-01

    Humans can often estimate tactile properties of objects from vision alone. For example, during online shopping, we can often infer material properties of clothing from images and judge how the material would feel against our skin. What visual information is important for tactile perception? Previous studies in material perception have focused on measuring surface appearance, such as gloss and roughness, and using verbal reports of material attributes and categories. However, in real life, predicting tactile properties of an object might not require accurate verbal descriptions of its surface attributes or categories. In this paper, we use tactile perception as ground truth to measure visual material perception. Using fabrics as our stimuli, we measure how observers match what they see (photographs of fabric samples) with what they feel (physical fabric samples). The data shows that color has a significant main effect in that removing color significantly reduces accuracy, especially when the images contain 3-D folds. We also find that images of draped fabrics, which revealed 3-D shape information, achieved better matching accuracy than images with flattened fabrics. The data shows a strong interaction between color and folding conditions on matching accuracy, suggesting that, in 3-D folding conditions, the visual system takes advantage of chromatic gradients to infer tactile properties but not in flattened conditions. Together, using a visual-tactile matching task, we show that humans use folding and color information in matching the visual and tactile properties of fabrics.

  20. Visualization of chromatin folding patterns in chicken erythrocytes by atomic force microscopy (AFM)

    Institute of Scientific and Technical Information of China (English)

    QIANRUOLAN; ZHENGXIALIU; 等

    1997-01-01

    The organization of the higher order structure of chromatin in chicken erythrocytes has been examined with tapping-mode scanning force microscopy under conditions close to their native envirinment.Reproducible highresolution AFM images of chromatin compaction at several levels can be demonstrated.An extended beads-on-astring (width of - 15-20nm,height of - 2-3nm for each individual nucleosome) can be consistently observed.Furthermore,superbeade (width of - 40nm,height of - 7nm) are demonstrated.Visualization of the solenoid conformation at the level of 30nm chromatin fiber is attained either by using AFM or by using electron microscopy.In addition,tightly coiled chromatin fibers (- 50-60nm and - 90-110nm) can be revealed.Our data suggest that the chromatin in the interphase nucleus of chicken erythrocyte represents a high-order conformation and AFM provides useful high-resolution structural information concerning the folding pattern of interphase chromatin fibers.

  1. 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).

  2. 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

  3. Visualization of coupled protein folding and binding in bacteria and purification of the heterodimeric complex

    Science.gov (United States)

    Wang, Haoyong; Chong, Shaorong

    2003-01-01

    During overexpression of recombinant proteins in Escherichia coli, misfolded proteins often aggregate and form inclusion bodies. If an aggregation-prone recombinant protein is fused upstream (as an N-terminal fusion) to GFP, aggregation of the recombinant protein domain also leads to misfolding of the downstream GFP domain, resulting in a decrease or loss of fluorescence. We investigated whether the GFP domain could fold correctly if aggregation of the upstream protein domain was prevented in vivo by a coupled protein folding and binding interaction. Such interaction has been previously shown to occur between the E. coli integration host factors and , and between the domains of the general transcriptional coactivator cAMP response element binding protein (CREB)-binding protein and the activator for thyroid hormone and retinoid receptors. In this study, fusion of integration host factor or the CREB-binding protein domain upstream to GFP resulted in aggregation of the fusion protein. Coexpression of their respective partners, on the other hand, allowed soluble expression of the fusion protein and a dramatic increase in fluorescence. The study demonstrated that coupled protein folding and binding could be correlated to GFP fluorescence. A modified miniintein containing an affinity tag was inserted between the upstream protein domain and GFP to allow rapid purification and identification of the heterodimeric complex. The GFP coexpression fusion system may be used to identify novel protein-protein interactions that involve coupled folding and binding or protein partners that can solubilize aggregation-prone recombinant proteins.

  4. PTGIBBS—an EXCEL TM Visual Basic program for computing and visualizing thermodynamic functions and equilibria of rock-forming minerals

    Science.gov (United States)

    Brandelik, A.; Massonne, H.-J.

    2004-11-01

    PTGIBBS, a Visual Basic for Application program, was implemented in EXCEL TM. It calculates mineral equilibria and thermodynamic functions for diverse solid solution phases, including presentation in 2D- and 3D-plots. The program is also suitable for the calibration and subsequent application of geothermobarometers, because of its ability to simultaneously calculate a large number of equilibria of the same type. Options are provided for the application of various equations of state (EOS). The volume behavior of mineral phases as a function of pressure can be expressed, e.g. by the Murnaghan EOS. It is also possible to model order-disorder transitions and lambda heat capacity anomalies using a tricritical Landau model including pressure dependence. Thus, PTGIBBS can be used with different thermodynamic data sets. It can handle molecular mixing models and mixing-on-site models with a maximum of nine components for each solid solution phase. An event-driven, interactive operating mode was selected for easy application of the program. Another advantage is the implementation in EXCEL TM, resulting in a wide range of possible applications and the user-friendliness of PTGIBBS. The easy display of different thermodynamic functions and the simplicity with which input data sets can be changed may also be useful for teaching purposes.

  5. Teaching computers to fold proteins

    DEFF Research Database (Denmark)

    Winther, Ole; Krogh, Anders Stærmose

    2004-01-01

    A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages...

  6. Folding Thermodynamics and Mechanism of Five Trp-Cage Variants from Replica-Exchange MD Simulations with RSFF2 Force Field.

    Science.gov (United States)

    Zhou, Chen-Yang; Jiang, Fan; Wu, Yun-Dong

    2015-11-10

    To test whether our recently developed residue-specific force field RSFF2 can reproduce the mutational effect on the thermal stability of Trp-cage mini-protein and decipher its detailed folding mechanism, we carried out long-time replica-exchange molecular dynamics (REMD) simulations on five Trp-cage variants, including TC5b and TC10b. Initiated from their unfolded structures, the simulations not only well-reproduce their experimental structures but also their melting temperatures and folding enthalpies reasonably well. For each Trp-cage variant, the overall folding free energy landscape is apparently two-state, but some intermediate states can be observed when projected on more detailed coordinates. We also found different variants have the same major folding pathway, including the well formed PII-helix in the unfolded state, the formation of W6-P12/P18/P19 contacts and the α-helix before the transition state, the following formation of most native contacts, and the final native loop formation. The folding mechanism derived here is consistent with many previous simulations and experiments.

  7. Teaching computers to fold proteins

    OpenAIRE

    Winther, Ole; Krogh, Anders Stærmose

    2004-01-01

    A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages which are estimated by (generalized ensemble) Monte Carlo. We test the learning algorithm on a Lennard-Jones (LJ) force field with a torsional angle degrees-of-freedom and a single-atom side-chain. ...

  8. Extreme Folding

    Science.gov (United States)

    Demaine, Erik

    2012-02-01

    Our understanding of the mathematics and algorithms behind paper folding, and geometric folding in general, has increased dramatically over the past several years. These developments have found a surprisingly broad range of applications. In the art of origami, it has helped spur the technical origami revolution. In engineering and science, it has helped solve problems in areas such as manufacturing, robotics, graphics, and protein folding. On the recreational side, it has led to new kinds of folding puzzles and magic. I will give an overview of the mathematics and algorithms of folding, with a focus on new mathematics and sculpture.

  9. Visualization

    OpenAIRE

    Balon, Andreja

    1990-01-01

    The present thesis entails the field of visualization which is divided into visualization along traditional lines and visualization in computer science. As the psychological aspect of image is of vital importance for visualization, it is shortly described in the beginning. Visualization in computer science is divided into three main fields: scientific visualization, program visualization and visual programming. An explanation and examples of approach to applications are given for each field....

  10. Visualized and precise design of artificial small RNAs for regulating T7 RNA polymerase and enhancing recombinant protein folding in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Yujia Zhao

    2016-12-01

    Full Text Available Small non-coding RNAs (sRNAs have received much attention in recent years due to their unique biological properties, which can efficiently and specifically tune target gene expressions in bacteria. Inspired by natural sRNAs, recent works have proposed the use of artificial sRNAs (asRNAs as genetic tools to regulate desired gene that has been applied in several fields, such as metabolic engineering and bacterial physiology studies. However, the rational design of asRNAs is still a challenge. In this study, we proposed structure and length as two criteria to implement rational visualized and precise design of asRNAs. T7 expression system was one of the most useful recombinant protein expression systems. However, it was deeply limited by the formation of inclusion body. To settle this problem, we designed a series of asRNAs to inhibit the T7 RNA polymerase (Gene1 expression to balance the rate between transcription and folding of recombinant protein. Based on the heterologous expression of Aspergillus oryzae Li-3 glucuronidase in E. coli, the asRNA-antigene1-17bp can effectively decrease the inclusion body and increase the enzyme activity by 169.9%.

  11. 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.

  12. Ab initio RNA folding.

    Science.gov (United States)

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-17

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.

  13. PhasePlot: An Interactive Software Tool for Visualizing Phase Relations, Performing Virtual Experiments, and for Teaching Thermodynamic Concepts in Petrology

    Science.gov (United States)

    Ghiorso, M. S.

    2012-12-01

    The computer program PhasePlot was developed for Macintosh computers and released via the Mac App Store in December 2011. It permits the visualization of phase relations calculated from internally consistent thermodynamic data-model collections, including those from MELTS (Ghiorso and Sack, 1995, CMP 119, 197-212), pMELTS (Ghiorso et al., 2002, G-cubed 3, 10.1029/2001GC000217) and the deep mantle database of Stixrude and Lithgow-Bertelloni (2011, GJI 184, 1180-1213). The software allows users to enter a system bulk composition and a range of reference conditions, and then calculate a grid of phase relations. These relations may be visualized in a variety of ways including pseudosections, phase diagrams, phase proportion plots, and contour diagrams of phase compositions and abundances. The program interface is user friendly and the computations are fast on laptop-scale machines, which makes PhasePlot amenable to in-class demonstrations, as a tool in instructional laboratories, and as an aid in support of out-of-class exercises and research. Users focus on problem specification and interpretation of results rather than on manipulation and mechanics of computation. The software has been developed with NSF support and is free. The PhasePlot web site is at phaseplot.org where extensive user documentation, video tutorials and examples of use may be found. The original release of phase plot permitted calculations to be performed on pressure-, temperature-grids (P-T), by direct minimization of the Gibbs free energy of the system at each grid point. A revision of PhasePlot (scheduled for release to the Mac App Store in December 2012) extends capabilities to include pressure-, entropy-grids (P-S) by system enthalpy minimization, volume-, temperature-grids (V-T) by system Helmholtz energy minimization, and volume-,entropy-grids (V-S) by minimization of the Internal Energy of the system. P-S gridded results may be utilized to visualize phase relations as a function of heat

  14. How Does Your Protein Fold? Elucidating the Apomyoglobin Folding Pathway.

    Science.gov (United States)

    Dyson, H Jane; Wright, Peter E

    2017-01-17

    Although each type of protein fold and in some cases individual proteins within a fold classification can have very different mechanisms of folding, the underlying biophysical and biochemical principles that operate to cause a linear polypeptide chain to fold into a globular structure must be the same. In an aqueous solution, the protein takes up the thermodynamically most stable structure, but the pathway along which the polypeptide proceeds in order to reach that structure is a function of the amino acid sequence, which must be the final determining factor, not only in shaping the final folded structure, but in dictating the folding pathway. A number of groups have focused on a single protein or group of proteins, to determine in detail the factors that influence the rate and mechanism of folding in a defined system, with the hope that hypothesis-driven experiments can elucidate the underlying principles governing the folding process. Our research group has focused on the folding of the globin family of proteins, and in particular on the monomeric protein apomyoglobin. Apomyoglobin (apoMb) folds relatively slowly (∼2 s) via an ensemble of obligatory intermediates that form rapidly after the initiation of folding. The folding pathway can be dissected using rapid-mixing techniques, which can probe processes in the millisecond time range. Stopped-flow measurements detected by circular dichroism (CD) or fluorescence spectroscopy give information on the rates of folding events. Quench-flow experiments utilize the differential rates of hydrogen-deuterium exchange of amide protons protected in parts of the structure that are folded early; protection of amides can be detected by mass spectrometry or proton nuclear magnetic resonance spectroscopy (NMR). In addition, apoMb forms an intermediate at equilibrium at pH ∼ 4, which is sufficiently stable for it to be structurally characterized by solution methods such as CD, fluorescence and NMR spectroscopies, and the

  15. 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...

  16. Exploiting the downhill folding regime via experiment

    Science.gov (United States)

    Muñoz, Victor; Sadqi, Mourad; Naganathan, Athi N.; de Sancho, David

    2008-01-01

    Traditionally, folding experiments have been directed at determining equilibrium and relaxation rate constants of proteins that fold with two-state-like kinetics. More recently, the combination of free energy surface approaches inspired by theory with the discovery of proteins that fold in the downhill regime has greatly widened the battlefield for experimentalists. Downhill folding proteins cross very small or no free energy barrier at all so that all relevant partially folded conformations become experimentally accessible. From these combined efforts we now have tools to estimate the height of thermodynamic and kinetic folding barriers. Procedures to measure with atomic resolution the structural heterogeneity of conformational ensembles at varying unfolding degrees are also available. Moreover, determining the dynamic modes driving folding and how they change as folding proceeds is finally at our fingertips. These developments allow us to address via experiment fundamental questions such as the origin of folding cooperativity, the relationship between structure and stability, or how to engineer folding barriers. Moreover, the level of detail attained in this new breed of experiments should provide powerful benchmarks for computer simulations of folding and force-field refinement. PMID:19436488

  17. 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

  18. Exploring the mechanisms of protein folding

    CERN Document Server

    Xu, Ji; Ren, Ying; Li, Jinghai

    2013-01-01

    Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the exclusive dominant mechanism of protein folding, and attributes the structural transition from one characteristic state to another to energy barriers. Conversely, the concept of kinetic stability overemphasizes dominant mechanisms that are related to kinetic factors. This article explores the stability condition of protein structures from the viewpoint of meso-science, paying attention to the compromise in the competition between minimum free energy and other dominant mechanisms. Based on our study of complex systems, we propose that protein folding is a meso-scale, dissipative, nonlinear and non-equilibrium process that is dominated by the compromise between free energy and other dominant mechanisms such as environmental factors. Consequently, a protein shows dynamic structures,...

  19. Folding and Finding RNA Secondary Structure

    Science.gov (United States)

    Mathews, David H.; Moss, Walter N.; Turner, Douglas H.

    2010-01-01

    SUMMARY Optimal exploitation of the expanding database of sequences requires rapid finding and folding of RNAs. Methods are reviewed that automate folding and discovery of RNAs with algorithms that couple thermodynamics with chemical mapping, NMR, and/or sequence comparison. New functional noncoding RNAs in genome sequences can be found by combining sequence comparison with the assumption that functional noncoding RNAs will have more favorable folding free energies than other RNAs. When a new RNA is discovered, experiments and sequence comparison can restrict folding space so that secondary structure can be rapidly determined with the help of predicted free energies. In turn, secondary structure restricts folding in three dimensions, which allows modeling of three-dimensional structure. An example from a domain of a retrotransposon is described. Discovery of new RNAs and their structures will provide insights into evolution, biology, and design of therapeutics. Applications to studies of evolution are also reviewed. PMID:20685845

  20. 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.

  1. 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...

  2. Combined Isothermal Titration and Differential Scanning Calorimetry Define Three-State Thermodynamics of fALS-Associated Mutant Apo SOD1 Dimers and an Increased Population of Folded Monomer.

    Science.gov (United States)

    Broom, Helen R; Vassall, Kenrick A; Rumfeldt, Jessica A O; Doyle, Colleen M; Tong, Ming Sze; Bonner, Julia M; Meiering, Elizabeth M

    2016-01-26

    Many proteins are naturally homooligomers, homodimers most frequently. The overall stability of oligomeric proteins may be described in terms of the stability of the constituent monomers and the stability of their association; together, these stabilities determine the populations of different monomer and associated species, which generally have different roles in the function or dysfunction of the protein. Here we show how a new combined calorimetry approach, using isothermal titration calorimetry to define monomer association energetics together with differential scanning calorimetry to measure total energetics of oligomer unfolding, can be used to analyze homodimeric unmetalated (apo) superoxide dismutase (SOD1) and determine the effects on the stability of structurally diverse mutations associated with amyotrophic lateral sclerosis (ALS). Despite being located throughout the protein, all mutations studied weaken the dimer interface, while concomitantly either decreasing or increasing the marginal stability of the monomer. Analysis of the populations of dimer, monomer, and unfolded monomer under physiological conditions of temperature, pH, and protein concentration shows that all mutations promote the formation of folded monomers. These findings may help rationalize the key roles proposed for monomer forms of SOD1 in neurotoxic aggregation in ALS, as well as roles for other forms of SOD1. Thus, the results obtained here provide a valuable approach for the quantitative analysis of homooligomeric protein stabilities, which can be used to elucidate the natural and aberrant roles of different forms of these proteins and to improve methods for predicting protein stabilities.

  3. Covering folded shapes

    Directory of Open Access Journals (Sweden)

    Oswin Aichholzer

    2014-05-01

    Full Text Available Can folding a piece of paper flat make it larger? We explore whether a shape S must be scaled to cover a flat-folded copy of itself. We consider both single folds and arbitrary folds (continuous piecewise isometries \\(S\\to\\mathbb{R}^2\\. The underlying problem is motivated by computational origami, and is related to other covering and fixturing problems, such as Lebesgue's universal cover problem and force closure grasps. In addition to considering special shapes (squares, equilateral triangles, polygons and disks, we give upper and lower bounds on scale factors for single folds of convex objects and arbitrary folds of simply connected objects.

  4. Stochastic thermodynamics

    Science.gov (United States)

    Eichhorn, Ralf; Aurell, Erik

    2014-04-01

    'Stochastic thermodynamics as a conceptual framework combines the stochastic energetics approach introduced a decade ago by Sekimoto [1] with the idea that entropy can consistently be assigned to a single fluctuating trajectory [2]'. This quote, taken from Udo Seifert's [3] 2008 review, nicely summarizes the basic ideas behind stochastic thermodynamics: for small systems, driven by external forces and in contact with a heat bath at a well-defined temperature, stochastic energetics [4] defines the exchanged work and heat along a single fluctuating trajectory and connects them to changes in the internal (system) energy by an energy balance analogous to the first law of thermodynamics. Additionally, providing a consistent definition of trajectory-wise entropy production gives rise to second-law-like relations and forms the basis for a 'stochastic thermodynamics' along individual fluctuating trajectories. In order to construct meaningful concepts of work, heat and entropy production for single trajectories, their definitions are based on the stochastic equations of motion modeling the physical system of interest. Because of this, they are valid even for systems that are prevented from equilibrating with the thermal environment by external driving forces (or other sources of non-equilibrium). In that way, the central notions of equilibrium thermodynamics, such as heat, work and entropy, are consistently extended to the non-equilibrium realm. In the (non-equilibrium) ensemble, the trajectory-wise quantities acquire distributions. General statements derived within stochastic thermodynamics typically refer to properties of these distributions, and are valid in the non-equilibrium regime even beyond the linear response. The extension of statistical mechanics and of exact thermodynamic statements to the non-equilibrium realm has been discussed from the early days of statistical mechanics more than 100 years ago. This debate culminated in the development of linear response

  5. Origami - Folded Plate Structures

    OpenAIRE

    Buri, Hans Ulrich

    2010-01-01

    This research investigates new methods of designing folded plate structures that can be built with cross-laminated timber panels. Folded plate structures are attractive to both architects and engineers for their structural, spatial, and plastic qualities. Thin surfaces can be stiffened by a series of folds, and thus not only cover space, but also act as load bearing elements. The variation of light and shadow along the folded faces emphasizes the plas...

  6. The Folded t Distribution

    OpenAIRE

    Psarakis, Stelios; Panaretos, John

    1990-01-01

    Measurements are frequently recorder without their algebraic sign. As a consequence the underlying distribution of measurements is replaced by a distribution of absolute measurements. When the underlying distribution is t the resulting distribution is called the “folded-t distribution”. Here we study this distribution, we find the relationship between the folded-t distribution and a special case of the folded normal distribution and we derive relationships of the folded-t distribution to othe...

  7. 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...

  8. MODELS OF PROTEIN FOLDING

    Directory of Open Access Journals (Sweden)

    Unnati Ahluwalia

    2012-12-01

    Full Text Available In an attempt to explore the understanding of protein folding mechanism, various models have been proposed in the literature. Advances in recent experimental and computational techniques rationalized our understanding on some of the fundamental features of the protein folding pathways. The goal of this review is to revisit the various models and outline the essential aspects of the folding reaction.

  9. Effects of Folding on Metalloprotein Active Sites

    Science.gov (United States)

    Winkler, Jay R.; Wittung-Stafshede, Pernilla; Leckner, Johan; Malmstrom, Bo G.; Gray, Harry B.

    1997-04-01

    Experimental data for the unfolding of cytochrome c and azurin by guanidinium chloride (GuHCl) are used to construct free-energy diagrams for the folding of the oxidized and reduced proteins. With cytochrome c, the driving force for folding the reduced protein is larger than that for the oxidized form. Both the oxidized and the reduced folded forms of yeast cytochrome c are less stable than the corresponding states of the horse protein. Due to the covalent attachment of the heme and its fixed tetragonal coordination geometry, cytochrome c folding can be described by a two-state model. A thermodynamic cycle leads to an expression for the difference in self-exchange reorganization energies for the folded and unfolded proteins. The reorganization energy for electron exchange in the folded protein is approximately 0.5 eV smaller than that for a heme in aqueous solution. The finding that reduced azurin unfolds at lower GuHCl concentrations than the oxidized protein suggests that the coordination structure of copper is different in oxidized and reduced unfolded states: it is likely that the geometry of CuI in the unfolded protein is linear or trigonal, whereas CuII prefers to be tetragonal. The evidence indicates that protein folding lowers the azurin reorganization energy by roughly 1.7 eV relative to an aqueous Cu(1,10-phenanthroline)2{}2+/+ reference system.

  10. Fast protein folding kinetics

    Science.gov (United States)

    Gelman, Hannah; Gruebele, Martin

    2014-01-01

    Fast folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast folding proteins has provided insight into the mechanisms which allow some proteins to find their native conformation well less than 1 ms and has uncovered examples of theoretically predicted phenomena such as downhill folding. The study of fast folders also informs our understanding of even “slow” folding processes: fast folders are small, relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast folding proteins and provides an overview of the major findings of fast folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general as well as some work that is left to do. PMID:24641816

  11. A galaxy of folds.

    Science.gov (United States)

    Alva, Vikram; Remmert, Michael; Biegert, Andreas; Lupas, Andrei N; Söding, Johannes

    2010-01-01

    Many protein classification systems capture homologous relationships by grouping domains into families and superfamilies on the basis of sequence similarity. Superfamilies with similar 3D structures are further grouped into folds. In the absence of discernable sequence similarity, these structural similarities were long thought to have originated independently, by convergent evolution. However, the growth of databases and advances in sequence comparison methods have led to the discovery of many distant evolutionary relationships that transcend the boundaries of superfamilies and folds. To investigate the contributions of convergent versus divergent evolution in the origin of protein folds, we clustered representative domains of known structure by their sequence similarity, treating them as point masses in a virtual 2D space which attract or repel each other depending on their pairwise sequence similarities. As expected, families in the same superfamily form tight clusters. But often, superfamilies of the same fold are linked with each other, suggesting that the entire fold evolved from an ancient prototype. Strikingly, some links connect superfamilies with different folds. They arise from modular peptide fragments of between 20 and 40 residues that co-occur in the connected folds in disparate structural contexts. These may be descendants of an ancestral pool of peptide modules that evolved as cofactors in the RNA world and from which the first folded proteins arose by amplification and recombination. Our galaxy of folds summarizes, in a single image, most known and many yet undescribed homologous relationships between protein superfamilies, providing new insights into the evolution of protein domains.

  12. (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.

  13. 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...

  14. On Safe Folding

    NARCIS (Netherlands)

    Bossi, Annalisa; Cocco, Nicoletta; Etalle, Sandro; Bruynooghe, Maurice; Wirsing, Martin

    1993-01-01

    In [3] a general fold operation has been introduced for definite programs wrt computed answer substitution semantics. It differs from the fold operation defined by Tamaki and Sato in [26,25] because its application does not depend on the transformation history. This paper extends the results in [3

  15. Fast protein folding kinetics.

    Science.gov (United States)

    Gelman, Hannah; Gruebele, Martin

    2014-05-01

    Fast-folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast-folding proteins has provided insight into the mechanisms, which allow some proteins to find their native conformation well fast folders also informs our understanding of even 'slow' folding processes: fast folders are small; relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast-folding proteins and provides an overview of the major findings of fast-folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general, as well as some work that is left to do.

  16. Folding by Design

    Science.gov (United States)

    Dodd, Paul; Damasceno, Pablo; Glotzer, Sharon

    2014-03-01

    A form of self-assembly, ``self-folding'' presents an alternative approach to the creation of reconfigurable, responsive materials with applications ranging from robotics to drug design. However, the complexity of interactions present in biological and engineered systems that undergo folding makes it challenging to isolate the main factors controlling their assembly and dis-assembly. Here we use computer simulations of simple, minimalistic self-foldable structures and investigate their stochastic folding process. By dynamically accessing all the states that lead to, or inhibit, successful folding, we show that the mechanisms by which general stochastic systems can achieve their ``native'' structures can be identified and used to design rules for optimized folding propensity. Research supported by the National Science Foundation, Emerging Frontiers in Research and Innovation Award # EFRI-1240264.

  17. Effects of knots on protein folding properties.

    Directory of Open Access Journals (Sweden)

    Miguel A Soler

    Full Text Available This work explores the impact of knots, knot depth and motif of the threading terminus in protein folding properties (kinetics, thermodynamics and mechanism via extensive Monte Carlo simulations of lattice models. A knotted backbone has no effect on protein thermodynamic stability but it may affect key aspects of folding kinetics. In this regard, we found clear evidence for a functional advantage of knots: knots enhance kinetic stability because a knotted protein unfolds at a distinctively slower rate than its unknotted counterpart. However, an increase in knot deepness does not necessarily lead to more effective changes in folding properties. In this regard, a terminus with a non-trivial conformation (e.g. hairpin can have a more dramatic effect in enhancing kinetic stability than knot depth. Nevertheless, our results suggest that the probability of the denatured ensemble to keep knotted is higher for proteins with deeper knots, indicating that knot depth plays a role in determining the topology of the denatured state. Refolding simulations starting from denatured knotted conformations show that not every knot is able to nucleate folding and further indicate that the formation of the knotting loop is a key event in the folding of knotted trefoils. They also show that there are specific native contacts within the knotted core that are crucial to keep a native knotting loop in denatured conformations which otherwise have no detectable structure. The study of the knotting mechanism reveals that the threading of the knotting loop generally occurs towards late folding in conformations that exhibit a significant degree of structural consolidation.

  18. 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

  19. Protein-Folding Landscapes in Multi-Chain Systems

    Energy Technology Data Exchange (ETDEWEB)

    Cellmer, Troy; Bratko, Dusan; Prausnitz, John M.; Blanch, Harvey

    2005-06-20

    Computational studies of proteins have significantly improved our understanding of protein folding. These studies are normally carried out using chains in isolation. However, in many systems of practical interest, proteins fold in the presence of other molecules. To obtain insight into folding in such situations, we compare the thermodynamics of folding for a Miyazawa-Jernigan model 64-mer in isolation to results obtained in the presence of additional chains. The melting temperature falls as the chain concentration increases. In multi-chain systems, free-energy landscapes for folding show an increased preference for misfolded states. Misfolding is accompanied by an increase in inter-protein interactions; however, near the folding temperature, the transition from folded chains to misfolded and associated chains isentropically driven. A majority of the most probable inter-protein contacts are also native contacts, suggesting that native topology plays a role in early stages of aggregation.

  20. Folding of multidomain proteins: biophysical consequences of tethering even in apparently independent folding.

    Science.gov (United States)

    Arviv, Oshrit; Levy, Yaakov

    2012-12-01

    Most eukaryotic and a substantial fraction of prokaryotic proteins are composed of more than one domain. The tethering of these evolutionary, structural, and functional units raises, among others, questions regarding the folding process of conjugated domains. Studying the folding of multidomain proteins in silico enables one to identify and isolate the tethering-induced biophysical determinants that govern crosstalks generated between neighboring domains. For this purpose, we carried out coarse-grained and atomistic molecular dynamics simulations of two two-domain constructs from the immunoglobulin-like β-sandwich fold. Each of these was experimentally shown to behave as the "sum of its parts," that is, the thermodynamic and kinetic folding behavior of the constituent domains of these constructs seems to occur independently, with the folding of each domain uncoupled from the folding of its partner in the two-domain construct. We show that the properties of the individual domains can be significantly affected by conjugation to another domain. The tethering may be accompanied by stabilizing as well as destabilizing factors whose magnitude depends on the size of the interface, the length, and the flexibility of the linker, and the relative stability of the domains. Accordingly, the folding of a multidomain protein should not be viewed as the sum of the folding patterns of each of its parts, but rather, it involves abrogating several effects that lead to this outcome. An imbalance between these effects may result in either stabilization or destabilization owing to the tethering. Copyright © 2012 Wiley Periodicals, Inc.

  1. 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...

  2. 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...

  3. Vocal Fold Collision Modeling

    DEFF Research Database (Denmark)

    Granados, Alba; Brunskog, Jonas; Misztal, M. K.

    2015-01-01

    When vocal folds vibrate at normal speaking frequencies, collisions occurs. The numerics and formulations behind a position-based continuum model of contact is an active field of research in the contact mechanics community. In this paper, a frictionless three-dimensional finite element model...... of the vocal fold collision is proposed, which incorporates different procedures used in contact mechanics and mathematical optimization theories. The penalty approach and the Lagrange multiplier method are investigated. The contact force solution obtained by the penalty formulation is highly dependent...

  4. Simulations of Protein Folding

    CERN Document Server

    Cahill, M; Cahill, K E; Cahill, Michael; Fleharty, Mark; Cahill, Kevin

    2000-01-01

    We have developed a simple, phenomenological, Monte-Carlo code that predicts the three-dimensional structure of globular proteins from the DNA sequences that define them. We have applied this code to two small proteins, the villin headpiece (1VII) and cole1 rop (1ROP). Our code folded the 36-residue villin headpiece to a mean rms distance of less than 5 A from its native structure as revealed by NMR; it folded a 56-residue fragment of the protein cole1 rop to within 11 A of its native structure. The denatured starting configurations of these two proteins were, respectively, 29 A and 55 A distant from their native structures.

  5. Folding worlds between pages

    CERN Multimedia

    Meier, Matthias

    2010-01-01

    "We all remember pop-up books form our childhood. As fascinated as we were back then, we probably never imagined how much engineering know-how went into these books. Pop-up engineer Anton Radevsky has even managed to fold a 27-kilometre particle accelerator into a book" (4 pages)

  6. Folds and Etudes

    Science.gov (United States)

    Bean, Robert

    2007-01-01

    In this article, the author talks about "Folds" and "Etudes" which are images derived from anonymous typing exercises that he found in a used copy of "Touch Typing Made Simple". "Etudes" refers to the musical tradition of studies for a solo instrument, which is a typewriter. Typing exercises are repetitive attempts to type words and phrases…

  7. ProbFold

    DEFF Research Database (Denmark)

    Sahoo, Sudhakar; Świtnicki, Michał P; Pedersen, Jakob Skou

    2016-01-01

    ) with probabilistic graphical models. This approach allows rapid adaptation and integration of new probing data types. AVAILABILITY AND IMPLEMENTATION: ProbFold is implemented in C ++. Models are specified using simple textual formats. Data reformatting is done using separate C ++ programs. Source code, statically...

  8. Modelling the folding of DNA origami

    Science.gov (United States)

    Arbona, J. M.; Elezgaray, J.; Aimé, J. P.

    2012-10-01

    DNA-based nanostructures built from a long single-stranded DNA scaffold, known as DNA origamis, are at the basis of many applications. Despite their widespread development, many basic questions concerning the mechanisms of formation of DNA origamis have not yet been addressed. For instance, the robustness of different designs against factors such as the internal topology, or the influence of the staple pattern, are handled empirically. We have developed a model for the folding and melting processes of DNA origamis that is able to reproduce accurately several thermodynamic quantities measurable from UV absorption experiments. This model incorporates not only the origami sequence but also its topology. We show that cooperativity is key to quantitatively understand the folding process. The model can also be used to design a new distribution of crossovers that increases the robustness of the DNA template, a necessary step for technological development.

  9. 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.

  10. 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...

  11. 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…

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. The Fold of Commitment

    DEFF Research Database (Denmark)

    Raastrup Kristensen, Anders; Pedersen, Michael

    2016-01-01

    This paper serves two purposes. First, a rereading of Douglas McGregor’s An uneasy look at performance appraisal serves to show how McGregor’s conceptualization of commitment as a question of integrating personal goals with organizational purpose has helped shape founding the modern understanding...... of corporate community representation. Second, we suggest that French philosopher Gilles Deleuze’s concepts of fold, desire and interests can be useful in comprehending this modern form of corporate representation already present in McGregor’s text....

  18. Folding of Pollen Grains

    Science.gov (United States)

    Katifori, Eleni; Alben, Silas; Cerda, Enrique; Nelson, David; Dumais, Jacques

    2008-03-01

    At dehiscence, which occurs when the anther reaches maturity and opens, pollen grains dehydrate and their volume is reduced. The pollen wall deforms to accommodate the volume loss, and the deformation pathway depends on the initial turgid pollen grain geometry and the mechanical properties of the pollen wall. We demonstrate, using both experimental and theoretical approaches, that the design of the apertures (areas on the pollen wall where the stretching and the bending modulus are reduced) is critical for controlling the folding pattern, and ensures the pollen grain viability. An excellent fit to the experiments is obtained using a discretized version of the theory of thin elastic shells.

  19. 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.

  20. 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.

  1. Protein Folding: Search for Basic Physical Models

    Directory of Open Access Journals (Sweden)

    Ivan Y. Torshin

    2003-01-01

    Full Text Available How a unique three-dimensional structure is rapidly formed from the linear sequence of a polypeptide is one of the important questions in contemporary science. Apart from biological context of in vivo protein folding (which has been studied only for a few proteins, the roles of the fundamental physical forces in the in vitro folding remain largely unstudied. Despite a degree of success in using descriptions based on statistical and/or thermodynamic approaches, few of the current models explicitly include more basic physical forces (such as electrostatics and Van Der Waals forces. Moreover, the present-day models rarely take into account that the protein folding is, essentially, a rapid process that produces a highly specific architecture. This review considers several physical models that may provide more direct links between sequence and tertiary structure in terms of the physical forces. In particular, elaboration of such simple models is likely to produce extremely effective computational techniques with value for modern genomics.

  2. 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

  3. 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

  4. 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

  5. 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

  6. How the genome folds

    Science.gov (United States)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  7. Modern Analysis of Protein Folding by Differential Scanning Calorimetry.

    Science.gov (United States)

    Ibarra-Molero, Beatriz; Naganathan, Athi N; Sanchez-Ruiz, Jose M; Muñoz, Victor

    2016-01-01

    Differential scanning calorimetry (DSC) is a very powerful tool for investigating protein folding and stability because its experimental output reflects the energetics of all conformations that become minimally populated during thermal unfolding. Accordingly, analysis of DSC experiments with simple thermodynamic models has been key for developing our understanding of protein stability during the past five decades. The discovery of ultrafast folding proteins, which have naturally broad conformational ensembles and minimally cooperative unfolding, opens the possibility of probing the complete folding free energy landscape, including those conformations at the top of the barrier to folding, via DSC. Exploiting this opportunity requires high-quality experiments and the implementation of novel analytical methods based on statistical mechanics. Here, we cover the recent exciting developments in this front, describing the new analytical procedures in detail as well as providing experimental guidelines for performing such analysis.

  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. When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches.

    Science.gov (United States)

    Muñoz, Victor; Cerminara, Michele

    2016-09-01

    Protein folding research stalled for decades because conventional experiments indicated that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay between dynamics and energetics resulting in myriad microscopic pathways. Ultrafast kinetic methods turned the field upside down by providing the means to probe fundamental aspects of folding, test theoretical predictions and benchmark simulations. Accordingly, experimentalists could measure the timescales for all relevant folding motions, determine the folding speed limit and confirm that folding barriers are entropic bottlenecks. Moreover, a catalogue of proteins that fold extremely fast (microseconds) could be identified. Such fast-folding proteins cross shallow free energy barriers or fold downhill, and thus unfold with minimal co-operativity (gradually). A new generation of thermodynamic methods has exploited this property to map folding landscapes, interaction networks and mechanisms at nearly atomic resolution. In parallel, modern molecular dynamics simulations have finally reached the timescales required to watch fast-folding proteins fold and unfold in silico All of these findings have buttressed the fundamentals of protein folding predicted by theory, and are now offering the first glimpses at the underlying mechanisms. Fast folding appears to also have functional implications as recent results connect downhill folding with intrinsically disordered proteins, their complex binding modes and ability to moonlight. These connections suggest that the coupling between downhill (un)folding and binding enables such protein domains to operate analogically as conformational rheostats.

  10. RNA folding: structure prediction, folding kinetics and ion electrostatics.

    Science.gov (United States)

    Tan, Zhijie; Zhang, Wenbing; Shi, Yazhou; Wang, Fenghua

    2015-01-01

    Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

  11. 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

  12. 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.

  13. Graphene folding on flat substrates

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Xiaoming; Zhao, Yadong; Ke, Changhong, E-mail: cke@binghamton.edu [Department of Mechanical Engineering, State University of New York at Binghamton, Binghamton, New York 13902 (United States); Zhang, Liuyang; Wang, Xianqiao [College of Engineering, University of Georgia, Athens, Georgia 30602 (United States)

    2014-10-28

    We present a combined experimental-theoretical study of graphene folding on flat substrates. The structure and deformation of the folded graphene sheet are experimentally characterized by atomic force microscopy. The local graphene folding behaviors are interpreted based on nonlinear continuum mechanics modeling and molecular dynamics simulations. Our study on self-folding of a trilayer graphene sheet reports a bending stiffness of about 6.57 eV, which is about four times the reported values for monolayer graphene. Our results reveal that an intriguing free sliding phenomenon occurs at the interlayer van der Waals interfaces during the graphene folding process. This work demonstrates that it is a plausible venue to quantify the bending stiffness of graphene based on its self-folding conformation on flat substrates. The findings reported in this work are useful to a better understanding of the mechanical properties of graphene and in the pursuit of its applications.

  14. Traumatic chorioretinal folds treated with intra-vitreal triamcinolone injection

    Directory of Open Access Journals (Sweden)

    Kook Young Kim

    2013-01-01

    Full Text Available A 34-year-old male visited the hospital due to decreased visual acuity in the left eye following an injury from a car accident. In the left eye, best-corrected visual acuity (BCVA was hand motion and intraocular pressure (IOP was 8 mmHg. Choroidal vasodilation and chorioretinal folds were observed by spectral domain-optical coherence tomography (SD-OCT. Topical and systemic steroid treatments did not improve the chorioretinal folds. Twelve months after the injury, intra-vitreal triamcinolone (4 mg/0.1 ml was injected. Six months after intra-vitreal triamcinolone injection, BCVA in the left eye had improved to 20/100. Fundus examination showed improvement in retinal vascular tortuosity and SD-OCT revealed improvements in choroidal vasodilation and chorioretinal folds. Intra-vitreal triamcinolone injection (IVTI was effective against traumatic chorioretinal folds with no recurrence based on objective observation by fundus photography and SD-OCT.

  15. 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.

  16. 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.

  17. 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.

  18. Folding superfunnel to describe cooperative folding of interacting proteins.

    Science.gov (United States)

    Smeller, László

    2016-07-01

    This paper proposes a generalization of the well-known folding funnel concept of proteins. In the funnel model the polypeptide chain is treated as an individual object not interacting with other proteins. Since biological systems are considerably crowded, protein-protein interaction is a fundamental feature during the life cycle of proteins. The folding superfunnel proposed here describes the folding process of interacting proteins in various situations. The first example discussed is the folding of the freshly synthesized protein with the aid of chaperones. Another important aspect of protein-protein interactions is the folding of the recently characterized intrinsically disordered proteins, where binding to target proteins plays a crucial role in the completion of the folding process. The third scenario where the folding superfunnel is used is the formation of aggregates from destabilized proteins, which is an important factor in case of several conformational diseases. The folding superfunnel constructed here with the minimal assumption about the interaction potential explains all three cases mentioned above. Proteins 2016; 84:1009-1016. © 2016 Wiley Periodicals, Inc.

  19. 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

  20. 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.

  1. 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.

  2. Chemical Product Design: A new challenge of applied thermodynamics

    DEFF Research Database (Denmark)

    Abildskov, Jens; Kontogeorgis, Georgios

    2004-01-01

    try to describe and understand chemical products with traditional thermodynamic models, typically applicable to problems of petrochemical industries. The purpose of this article is two-fold: first to present some current and future challenges in thermodynamic modelling towards chemical product design......, and then to outline some specific examples from our research activities in the area of thermodynamics for chemical products. The examples cover rather diverse areas such as interrelation between thermodynamic and engineering properties in detergents (surfactants), paint thermodynamics and the development of models......Chemical products involving specialty chemicals and microstructured materials are often multicomponent systems. A number of five to 20 molecules is not unusual, comprising a range of different chemical compounds e.g. polymers, surfactants, solid particles and water. Milk is an example...

  3. Protein Stability, Folding and Misfolding in Human PGK1 Deficiency

    Directory of Open Access Journals (Sweden)

    Giovanna Valentini

    2013-12-01

    Full Text Available Conformational diseases are often caused by mutations, altering protein folding and stability in vivo. We review here our recent work on the effects of mutations on the human phosphoglycerate kinase 1 (hPGK1, with a particular focus on thermodynamics and kinetics of protein folding and misfolding. Expression analyses and in vitro biophysical studies indicate that disease-causing mutations enhance protein aggregation propensity. We found a strong correlation among protein aggregation propensity, thermodynamic stability, cooperativity and dynamics. Comparison of folding and unfolding properties with previous reports in PGKs from other species suggests that hPGK1 is very sensitive to mutations leading to enhance protein aggregation through changes in protein folding cooperativity and the structure of the relevant denaturation transition state for aggregation. Overall, we provide a mechanistic framework for protein misfolding of hPGK1, which is insightful to develop new therapeutic strategies aimed to target native state stability and foldability in hPGK1 deficient patients.

  4. Thermodynamic Model of Transcription Elongation

    Science.gov (United States)

    Tadigotla, Vasisht; O'Maoileidigh, Daibhid; Sengupta, Anirvan; Epshtein, Vitaly; Ebright, Richard; Nudler, Evgeny; Ruckenstein, Andrei

    2006-03-01

    We present a statistical mechanics approach to the prediction of backtracked pauses in prokaryotic transcription elongation derived from structural models of the transcription elongation complex (TEC). Our algorithm is based on the thermodynamic stability of TEC along the DNA template calculated from the sequence dependent free-energy of DNA-DNA, DNA-RNA and RNA-RNA base pairing associated with (a) the translocation and size fluctuations of the transcription bubble; (b) the changes in the DNA-RNA hybrid; and (c) the changes in the RNA folding free-energy. The calculations involve no adjustable parameters apart from a cutoff used to discriminate paused from non-paused complexes. When applied to 100 experimental pauses in transcription elongation by E. coli RNA polymerase on ten DNA templates the approach produces highly statistically significant results. Transcription elongation is an inherently kinetic process and a simplified kinetic model with the same predictive power is presented separately.

  5. Novel sequences propel familiar folds.

    Science.gov (United States)

    Jawad, Zahra; Paoli, Massimo

    2002-04-01

    Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.

  6. Equi-Gaussian Curvature Folding

    Indian Academy of Sciences (India)

    E M El-Kholy; El-Said R Lashin; Salama N Daoud

    2007-08-01

    In this paper we introduce a new type of folding called equi-Gaussian curvature folding of connected Riemannian 2-manifolds. We prove that the composition and the cartesian product of such foldings is again an equi-Gaussian curvature folding. In case of equi-Gaussian curvature foldings, $f:M→ P_n$, of an orientable surface onto a polygon $P_n$ we prove that (i) $f\\in\\mathcal{F}_{EG}(S^2)\\Leftrightarrow n=3$ (ii) $f\\in\\mathcal{F}_{EG}(T^2)\\Rightarrow n=4$ (iii) $f\\in\\mathcal{F}_{EG}(\\# 2T^2)\\Rightarrow n=5, 6$ and we generalize (iii) for $\\# nT^2$.

  7. 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.

  8. Ion concentration dependent tRNA folding energy landscapes

    Science.gov (United States)

    Li, Rongzhong; Cho, Samuel

    2013-03-01

    The RNA folding is highly dependent on the ionic conditions of its environment in the cell because the surrounding ions electrostatically screen the charged phosphates that line the RNA backbone. Recent studies (Cho, Pincus, and Thirumalai, PNAS, 2007; Biyun, Cho, and Thirumalai, JACS, 2011) demonstrated that the coarse-grained model we use accurately captures the RNA folding mechanisms by incorporating a Debye-Huckel potential to screen the electrostatics. We compare the ion-concentration dependent tRNA folding mechanism to the classical thermodynamic melting profiles of Crothers and co-workers, and we observe excellent agreement. We also supported our findings by performing empirical force field MD simulations with CHARMM and AMBER, and we observe remarkably comparable qualitative similarities between the average base-base distances from simulations and the empirically measured base-stacking potentials from the well-known Turner's Rules.

  9. 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.

  10. 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...

  11. Small scale folding observed in the NEEM ice core

    Science.gov (United States)

    Jansen, Daniela; Llorens, Maria-Gema; Westhoff, Julien; Steinbach, Florian; Bons, Paul D.; Kipfstuhl, Sepp; Griera, Albert; Weikusat, Ilka

    2015-04-01

    Disturbances on the centimeter scale in the layering of the NEEM ice core (North Greenland) can be mapped by means of visual stratigraphy as long as the ice does have a visual layering, such as, for example, cloudy bands. Different focal depths of the visual stratigraphy method allow, to a certain extent, a three dimensional view of the structures. In this study we present a structural analysis of the visible folds, discuss characteristics and frequency and present examples of typical fold structures. With this study we aim to quantify the potential impact of small scale folding on the integrity of climate proxy data. We also analyze the structures with regard to the stress environment under which they formed. The structures evolve from gentle waves at about 1700 m to overturned z-folds with increasing depth. Occasionally, the folding causes significant thickening of layers. Their shape indicates that they are passive features and are probably not initiated by rheology differences between layers. Layering is heavily disturbed and tracing of single layers is no longer possible below a depth of 2160 m. Lattice orientation distributions for the corresponding core sections were analyzed where available in addition to visual stratigraphy. The data show axial-plane parallel strings of grains with c.axis orientations that deviate from that of the matrix, which has more or less a single-maximum fabric at the depth where the folding occurs. We conclude from these data that folding is a consequence of deformation along localized shear planes and kink bands. The findings are compared with results from other deep ice cores. The observations presented are supplemented by microstructural modeling using a crystal plasticity code that reproduces deformation, applying a Fast Fourier Transform (FFT), coupled with ELLE to include dynamic recrystallization processes. The model results reproduce the development of bands of grains with a tilted orientation relative to the single maximum

  12. Folding gravitational-wave interferometers

    Science.gov (United States)

    Sanders, J. R.; Ballmer, Stefan W.

    2017-01-01

    The sensitivity of kilometer-scale terrestrial gravitational wave interferometers is limited by mirror coating thermal noise. Alternative interferometer topologies can mitigate the impact of thermal noise on interferometer noise curves. In this work, we explore the impact of introducing a single folding mirror into the arm cavities of dual-recycled Fabry–Perot interferometers. While simple folding alone does not reduce the mirror coating thermal noise, it makes the folding mirror the critical mirror, opening up a variety of design and upgrade options. Improvements to the folding mirror thermal noise through crystalline coatings or cryogenic cooling can increase interferometer range by as much as a factor of two over the Advanced LIGO reference design.

  13. 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

  14. 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

  15. 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

  16. 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

  17. Protein folding by motion planning

    Science.gov (United States)

    Thomas, Shawna; Song, Guang; Amato, Nancy M.

    2005-12-01

    We investigate a novel approach for studying protein folding that has evolved from robotics motion planning techniques called probabilistic roadmap methods (PRMs). Our focus is to study issues related to the folding process, such as the formation of secondary and tertiary structures, assuming we know the native fold. A feature of our PRM-based framework is that the large sets of folding pathways in the roadmaps it produces, in just a few hours on a desktop PC, provide global information about the protein's energy landscape. This is an advantage over other simulation methods such as molecular dynamics or Monte Carlo methods which require more computation and produce only a single trajectory in each run. In our initial studies, we obtained encouraging results for several small proteins. In this paper, we investigate more sophisticated techniques for analyzing the folding pathways in our roadmaps. In addition to more formally revalidating our previous results, we present a case study showing that our technique captures known folding differences between the structurally similar proteins G and L. This research was supported in part by NSF CAREER Award CCR-9624315, NSF Grants ACI-9872126, EIA-9975018, EIA-0103742, EIA-9805823, ACR-0113971, CCR-0113974, EIA-9810937, EIA-0079874 and the Texas Higher Education Coordinating Board grant ATP-000512-0261-2001. ST was supported in part by an NSF Graduate Research Fellowship. GS was supported in part by an IBM PhD Fellowship.

  18. Electrochemistry of folded graphene edges.

    Science.gov (United States)

    Ambrosi, Adriano; Bonanni, Alessandra; Pumera, Martin

    2011-05-01

    There is enormous interest in the investigation of electron transfer rates at the edges of graphene due to possible energy storage and sensing applications. While electrochemistry at the edges and the basal plane of graphene has been studied in the past, the new frontier is the electrochemistry of folded graphene edges. Here we describe the electrochemistry of folded graphene edges and compare it to that of open graphene edges. The materials were characterized in detail by high-resolution transmission electron microscopy, Raman spectroscopy, high-resolution X-ray photoelectron spectroscopy, electrochemical impedance spectroscopy and cyclic voltammetry. We found that the heterogeneous electron transfer rate is significantly lower on folded graphene edges compared to open edge sites for ferro/ferricyanide, and that electrochemical properties of open edges offer lower potential detection of biomarkers than the folded ones. It is apparent, therefore, that for sensing and biosensing applications the folded edges are less active than open edges, which should then be preferred for such applications. As folded edges are the product of thermal treatment of multilayer graphene, such thermal procedures should be avoided when fabricating graphene for electrochemical applications.

  19. The two dimensional fold test in paleomagnetism using ipython notebook

    Science.gov (United States)

    Setiabudidaya, Dedi; Piper, John D. A.

    2016-01-01

    One aspect of paleomagnetic analysis prone to controversy is the result of the fold test used to evaluate the age of a magnetisation component relative to the age of a structural event. Initially, the fold test was conducted by comparing the Fisherian precision parameter (k) to results from different limbs of a fold structure before and after tilt adjustment. To accommodate synfolding magnetisation, the tilt correction can be performed in stepwise fashion to both limbs simultaneously, here called one dimensional (1D) fold test. The two dimensional (2D) fold test described in this paper is carried out by applying stepwise tilt adjustment to each limb of the fold separately. The rationale for this is that tilts observed on contrasting limbs of deformed structure may not be synchronous or even belong to the same episode of deformation. A program for the procedure is presented here which generates two dimensional values of the k-parameter visually presented in contoured form. The use of ipython notebook enables this 2D fold test to be performed interactively and yield a more precise evaluation than the primitive 1D fold test.

  20. In vivo measurement of vocal fold surface resistance.

    Science.gov (United States)

    Mizuta, Masanobu; Kurita, Takashi; Dillon, Neal P; Kimball, Emily E; Garrett, C Gaelyn; Sivasankar, M Preeti; Webster, Robert J; Rousseau, Bernard

    2017-10-01

    A custom-designed probe was developed to measure vocal fold surface resistance in vivo. The purpose of this study was to demonstrate proof of concept of using vocal fold surface resistance as a proxy of functional tissue integrity after acute phonotrauma using an animal model. Prospective animal study. New Zealand White breeder rabbits received 120 minutes of airflow without vocal fold approximation (control) or 120 minutes of raised intensity phonation (experimental). The probe was inserted via laryngoscope and placed on the left vocal fold under endoscopic visualization. Vocal fold surface resistance of the middle one-third of the vocal fold was measured after 0 (baseline), 60, and 120 minutes of phonation. After the phonation procedure, the larynx was harvested and prepared for transmission electron microscopy. In the control group, vocal fold surface resistance values remained stable across time points. In the experimental group, surface resistance (X% ± Y% relative to baseline) was significantly decreased after 120 minutes of raised intensity phonation. This was associated with structural changes using transmission electron microscopy, which revealed damage to the vocal fold epithelium after phonotrauma, including disruption of the epithelium and basement membrane, dilated paracellular spaces, and alterations to epithelial microprojections. In contrast, control vocal fold specimens showed well-preserved stratified squamous epithelia. These data demonstrate the feasibility of measuring vocal fold surface resistance in vivo as a means of evaluating functional vocal fold epithelial barrier integrity. Device prototypes are in development for additional testing, validation, and for clinical applications in laryngology. NA Laryngoscope, 127:E364-E370, 2017. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  1. 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.

  2. 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 ...

  3. 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...

  4. 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.

  5. 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)

  6. 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.

  7. 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.

  8. 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...

  9. 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.

  10. 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.

  11. 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.

  12. 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)

  13. 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 ...

  14. 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.

  15. 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.

  16. 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.

  17. Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model.

    Science.gov (United States)

    Reddy, Govardhan; Thirumalai, D

    2015-08-27

    both the thermodynamics and kinetics of folding are not only in agreement with experiments but also provide missing details not resolvable in standard experiments. The key prediction that folding mechanism varies dramatically with pH is amenable to experimental tests.

  18. 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...

  19. 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.

  20. Differential equations and folding of $n$-mani-folds

    Directory of Open Access Journals (Sweden)

    I. Mousa

    2005-09-01

    Full Text Available In this paper we will describe some topological and geometric characters of $n$-manifold by using the properties of differential equations. The folding and unfolding of $n$-manifold into itself will be deduced from viewpoint of the differential equations.

  1. NoFold: RNA structure clustering without folding or alignment.

    Science.gov (United States)

    Middleton, Sarah A; Kim, Junhyong

    2014-11-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures.

  2. Mesoscale Modeling of Chromatin Folding

    Science.gov (United States)

    Schlick, Tamar

    2009-03-01

    Eukaryotic chromatin is the fundamental protein/nucleic acid unit that stores the genetic material. Understanding how chromatin fibers fold and unfold in physiological conditions is important for interpreting fundamental biological processes like DNA replication and transcription regulation. Using a mesoscopic model of oligonucleosome chains and tailored sampling protocols, we elucidate the energetics of oligonucleosome folding/unfolding and the role of each histone tail, linker histones, and divalent ions in regulating chromatin structure. The resulting compact topologies reconcile features of the zigzag model with straight linker DNAs with the solenoid model with bent linker DNAs for optimal fiber organization and reveal dynamic and energetic aspects involved.

  3. A similar in vitro and in cell lysate folding intermediate for the FF domain.

    Science.gov (United States)

    Latham, Michael P; Kay, Lewis E

    2014-09-23

    Understanding the mechanisms by which proteins fold into their three-dimensional structures, including a description of the intermediates that are formed during the folding process, remains a goal of protein science. Most studies are performed under carefully controlled conditions in which the folding reaction is monitored in a buffer solution that is far from the natural milieu of the cell. Here, we have used (13)C and (1)H relaxation dispersion NMR spectroscopy to study folding of the FF domain in both Escherichia coli and Saccharomyces cerevisiae cellular lysates. We find that a conformationally excited state is populated in both lysates, which is very similar in structure to a folding intermediate observed in previous studies in buffer, with the kinetics and thermodynamics of the interconversion between native and intermediate conformers somewhat changed. The results point to the importance of extending folding studies beyond the test tube yet emphasize that insights can be obtained through careful experiments recorded in controlled buffer solutions.

  4. Mapping the kinetic barriers of a Large RNA molecule's folding landscape.

    Science.gov (United States)

    Schlatterer, Jörg C; Martin, Joshua S; Laederach, Alain; Brenowitz, Michael

    2014-01-01

    The folding of linear polymers into discrete three-dimensional structures is often required for biological function. The formation of long-lived intermediates is a hallmark of the folding of large RNA molecules due to the ruggedness of their energy landscapes. The precise thermodynamic nature of the barriers (whether enthalpic or entropic) that leads to intermediate formation is still poorly characterized in large structured RNA molecules. A classic approach to analyzing kinetic barriers are temperature dependent studies analyzed with Eyring's transition state theory. We applied Eyring's theory to time-resolved hydroxyl radical (•OH) footprinting kinetics progress curves collected at eight temperature from 21.5 °C to 51 °C to characterize the thermodynamic nature of folding intermediate formation for the Mg(2+)-mediated folding of the Tetrahymena thermophila group I ribozyme. A common kinetic model configuration describes this RNA folding reaction over the entire temperature range studied consisting of primary (fast) transitions to misfolded intermediates followed by much slower secondary transitions, consistent with previous studies. Eyring analysis reveals that the primary transitions are moderate in magnitude and primarily enthalpic in nature. In contrast, the secondary transitions are daunting in magnitude and entropic in nature. The entropic character of the secondary transitions is consistent with structural rearrangement of the intermediate species to the final folded form. This segregation of kinetic control reveals distinctly different molecular mechanisms during the two stages of RNA folding and documents the importance of entropic barriers to defining rugged RNA folding landscapes.

  5. Mapping the kinetic barriers of a Large RNA molecule's folding landscape.

    Directory of Open Access Journals (Sweden)

    Jörg C Schlatterer

    Full Text Available The folding of linear polymers into discrete three-dimensional structures is often required for biological function. The formation of long-lived intermediates is a hallmark of the folding of large RNA molecules due to the ruggedness of their energy landscapes. The precise thermodynamic nature of the barriers (whether enthalpic or entropic that leads to intermediate formation is still poorly characterized in large structured RNA molecules. A classic approach to analyzing kinetic barriers are temperature dependent studies analyzed with Eyring's transition state theory. We applied Eyring's theory to time-resolved hydroxyl radical (•OH footprinting kinetics progress curves collected at eight temperature from 21.5 °C to 51 °C to characterize the thermodynamic nature of folding intermediate formation for the Mg(2+-mediated folding of the Tetrahymena thermophila group I ribozyme. A common kinetic model configuration describes this RNA folding reaction over the entire temperature range studied consisting of primary (fast transitions to misfolded intermediates followed by much slower secondary transitions, consistent with previous studies. Eyring analysis reveals that the primary transitions are moderate in magnitude and primarily enthalpic in nature. In contrast, the secondary transitions are daunting in magnitude and entropic in nature. The entropic character of the secondary transitions is consistent with structural rearrangement of the intermediate species to the final folded form. This segregation of kinetic control reveals distinctly different molecular mechanisms during the two stages of RNA folding and documents the importance of entropic barriers to defining rugged RNA folding landscapes.

  6. A new instrument for intraoperative assessment of individual vocal folds.

    Science.gov (United States)

    Heaton, James T; Kobler, James B; Hillman, Robert E; Zeitels, Steven M

    2005-07-01

    Intraoperative assessment of vocal fold vibration during phonomicrosurgery performed under general anesthesia may enhance surgical decision-making. We therefore developed and bench-tested a new device we refer to as the aerodynamic vocal fold driver (AVFD). The AVFD comprises a hand-held probe that uses airflow to drive individual vocal folds into phonatory-like vibration. This permits stroboscopic visualization of mucosal waves with simultaneous control of subglottal air pressure. In initial experiments to validate the technique, AVFD driven phonation and conventional whole-larynx phonation were compared using excised canine larynges (n = 14). Single vocal fold phonation using the AVFD and whole larynx phonation yielded similar, positive correlations between subglottal pressure and both amplitude and frequency of vibration. Experiments simulating vocal fold scar-related mucosal stiffening by subepithelial injection of fixative showed the expected elevation of phonation threshold pressures as measured with the AVFD. Likewise, unilateral tissue compression injury disrupted vocal fold vibration, and the AVFD was useful for quantifying improvement in the damaged vocal fold after repair with injection of cross-linked hyaluronic acid gel. These results show that this new instrument has the potential to provide novel and useful information for laryngeal experimentation and to improve phonosurgery.

  7. Bodies Folded in Migrant Crypts

    DEFF Research Database (Denmark)

    Galis, Vasilis; Tzokas, Spyros; Tympas, Aristotle

    2016-01-01

    and human migrants generates a dis/abled subject. In this context, dis/ability may be a cause or consequence of migration, both in physical/material (the folding of bodies in the crypt) and cultural/semiotic terms, and may become a barrier to accessing protection, to entering and/or crossing a country...

  8. Gothic Elements in Folding Beijing

    Institute of Scientific and Technical Information of China (English)

    Hua Yan

    2016-01-01

    The study claims that Folding Beijing can not only be read as science fiction but also as Gothic literature,in which perspective,Gothic Elements such as Gothic Setting, Gothic Wanderer and Transgressions,and Gothic Terror are discussed respectively.

  9. 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.

  10. 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<...

  11. 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

  12. 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)].

  13. 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 ...

  14. 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...

  15. 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...

  16. 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.

  17. 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.

  18. 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...

  19. 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.

  20. 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

  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. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. RNA folding on the 3D triangular lattice

    Directory of Open Access Journals (Sweden)

    Mayne Martin

    2009-11-01

    Full Text Available Abstract Background Difficult problems in structural bioinformatics are often studied in simple exact models to gain insights and to derive general principles. Protein folding, for example, has long been studied in the lattice model. Recently, researchers have also begun to apply the lattice model to the study of RNA folding. Results We present a novel method for predicting RNA secondary structures with pseudoknots: first simulate the folding dynamics of the RNA sequence on the 3D triangular lattice, next extract and select a set of disjoint base pairs from the best lattice conformation found by the folding simulation. Experiments on sequences from PseudoBase show that our prediction method outperforms the HotKnot algorithm of Ren, Rastegari, Condon and Hoos, a leading method for RNA pseudoknot prediction. Our method for RNA secondary structure prediction can be adapted into an efficient reconstruction method that, given an RNA sequence and an associated secondary structure, finds a conformation of the sequence on the 3D triangular lattice that realizes the base pairs in the secondary structure. We implemented a suite of computer programs for the simulation and visualization of RNA folding on the 3D triangular lattice. These programs come with detailed documentation and are accessible from the companion website of this paper at http://www.cs.usu.edu/~mjiang/rna/DeltaIS/. Conclusion Folding simulation on the 3D triangular lattice is effective method for RNA secondary structure prediction and lattice conformation reconstruction. The visualization software for the lattice conformations of RNA structures is a valuable tool for the study of RNA folding and is a great pedagogic device.

  9. 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

  10. 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)

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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…

  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. 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)

  19. 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…

  20. 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.

  1. 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.

  2. 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.

  3. Identification of Amino Acid Sequences with Good Folding Properties in an Off-Lattice Model

    CERN Document Server

    Irbäck, Anders; Potthast, Frank

    2008-01-01

    Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are found. The thermodynamic properties are found to be strongly sequence dependent in contrast to the kinetic ones. Hence, criteria for good folders are defined entirely in terms of thermodynamic fluctuations. With these criteria sequence patterns that fold well are isolated. For 300 chains with 20 randomly chosen binary residues approximately 10% meet these criteria. Also, an analysis is performed by means of statistical and artificial neural network methods from which it is concluded that the folding properties can be predicted to a certain degree given the binary numbers characterizing the sequences.

  4. Thermodynamics of Quantum Feedback Cooling

    Directory of Open Access Journals (Sweden)

    Pietro Liuzzo-Scorpo

    2016-02-01

    Full Text Available 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 two-fold: 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 to be key ingredients fuelling our spin refrigeration protocol. We report instead that a more general indicator of quantumness beyond entanglement, the so-called quantum discord, is closely related to the cooling performance.

  5. 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.

  6. 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.

  7. mRNA secondary structures fold sequentially but exchange rapidly in vivo.

    Directory of Open Access Journals (Sweden)

    Elisabeth M Mahen

    2010-02-01

    Full Text Available RNAs adopt defined structures to perform biological activities, and conformational transitions among alternative structures are critical to virtually all RNA-mediated processes ranging from metabolite-activation of bacterial riboswitches to pre-mRNA splicing and viral replication in eukaryotes. Mechanistic analysis of an RNA folding reaction in a biological context is challenging because many steps usually intervene between assembly of a functional RNA structure and execution of a biological function. We developed a system to probe mechanisms of secondary structure folding and exchange directly in vivo using self-cleavage to monitor competition between mutually exclusive structures that promote or inhibit ribozyme assembly. In previous work, upstream structures were more effective than downstream structures in blocking ribozyme assembly during transcription in vitro, consistent with a sequential folding mechanism. However, upstream and downstream structures blocked ribozyme assembly equally well in vivo, suggesting that intracellular folding outcomes reflect thermodynamic equilibration or that annealing of contiguous sequences is favored kinetically. We have extended these studies to learn when, if ever, thermodynamic stability becomes an impediment to rapid equilibration among alternative RNA structures in vivo. We find that a narrow thermodynamic threshold determines whether kinetics or thermodynamics govern RNA folding outcomes in vivo. mRNA secondary structures fold sequentially in vivo, but exchange between adjacent secondary structures is much faster in vivo than it is in vitro. Previous work showed that simple base-paired RNA helices dissociate at similar rates in vivo and in vitro so exchange between adjacent structures must occur through a different mechanism, one that likely involves facilitation of branch migration by proteins associated with nascent transcripts.

  8. 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.

  9. Funnels, Pathways and the Energy Landscape of Protein Folding A Synthesis

    CERN Document Server

    Bryngelson, J D; Socci, N D; Wolynes, P G

    1995-01-01

    The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation, that is, to the energy landscape. The statistical energy landscape approach explains when and why unique behaviors, such as specific folding pathways, occur in some proteins and more generally explains the distinction between folding processes common to all sequences and those peculiar to individual sequences. This approach also gives new, quantitative insights into the interpretation of experiments and simulations of protein folding thermodynamics and kinetics. Specifically, the picture provides simple explanations for folding as a two-state first-order phase transition, for the origin of metastable collapsed unfolded states and for the curved Arrhenius plots observed in both laboratory experiments and discrete lattice simulations. The relation of these quantitative ideas ...

  10. Teaching Thermodynamics with Physlets[R] in Introductory Physics

    Science.gov (United States)

    Cox, Anne J.; Belloni, Mario; Dancy, Melissa; Christian, Wolfgang

    2003-01-01

    This paper describes the use of interactive, Physlet[R]-based curricular material designed to help students learn concepts of thermodynamics with a particular focus on the use of kinetic theory models. These exercises help students visualize ideal gas particle dynamics and engine cycles, make concrete connections between mechanics and…

  11. Ventricular-Fold Dynamics in Human Phonation

    Science.gov (United States)

    Bailly, Lucie; Bernardoni, Nathalie Henrich; Müller, Frank; Rohlfs, Anna-Katharina; Hess, Markus

    2014-01-01

    Purpose: In this study, the authors aimed (a) to provide a classification of the ventricular-fold dynamics during voicing, (b) to study the aerodynamic impact of these motions on vocal-fold vibrations, and (c) to assess whether ventricular-fold oscillations could be sustained by aerodynamic coupling with the vocal folds. Method: A 72-sample…

  12. Synovial folds in equine articular process joints

    DEFF Research Database (Denmark)

    Thomsen, Line Nymann; Berg, Lise Charlotte; Markussen, Bo;

    2013-01-01

    Cervical synovial folds have been suggested as a potential cause of neck pain in humans. Little is known about the extent and characteristics of cervical synovial folds in horses.......Cervical synovial folds have been suggested as a potential cause of neck pain in humans. Little is known about the extent and characteristics of cervical synovial folds in horses....

  13. Folded MEMS approach to NMRG

    Science.gov (United States)

    Gundeti, Venu Madhav

    Atomic gyroscopes have a potential for good performance advantages and several attempts are being made to miniaturize them. This thesis describes the efforts made in implementing a Folded MEMS based NMRG. The micro implementations of all the essential components for NMRG (Nuclear Magnetic Resonance Gyroscope) are described in detail in regards to their design, fabrication, and characterization. A set of micro-scale Helmholtz coils are described and the homogeneity of the generated magnetic field is analyzed for different designs of heaters. The dielectric mirrors and metallic mirrors are compared in terms of reflectivity and polarization change up on reflection. A pyramid shaped folded backbone structure is designed, fabricated, and assembled along with all the required components. A novel double-folded structure 1/4th the size of original version is fabricated and assembled. Design and modeling details of a 5 layered shield with shielding factor > 106 and total volume of around 90 cc are also presented. A table top setup for characterization of atomic vapor cell is described in detail. A micro vapor cell based Rb magnetometer with a sensitivity of 108 pT/√Hz is demonstrated. The challenges due to DC heating are addressed and mitigated using an AC heater. Several experiments related to measuring the relaxation time of Xe are provided along with results. For Xe131, relaxation times of T1 = 23.78 sec, T2 = 18.06 sec and for Xe129, T1 = 21.65 sec and T2 = 20.45 sec are reported.

  14. Low Power Folded Cascode OTA

    Directory of Open Access Journals (Sweden)

    Swati Kundra

    2012-03-01

    Full Text Available Low power is one of the key research area in today’s electronic industry. Need of low power has created a major pattern shift in the field of electronics where power dissipation is equally important as area, performance etc. Several low power portable electronic equipments, low voltage design techniques havebeen developed and have driven analog designers to create techniques eg. Self cascode mosfet and stacking technique. For this aim in mind we designed a Folded Cascode using low power techniques and analyzed its various properties through the Spice simulations for 0.13 micron CMOS technology from TSMC and thesupply voltage 1.8V.

  15. Low Power Folded Cascode OTA

    Directory of Open Access Journals (Sweden)

    Swati Kundra

    2012-02-01

    Full Text Available Low power is one of the key research area in today’s electronic industry. Need of low power has created a major pattern shift in the field of electronics where power dissipation is equally important as area, performance etc. Several low power portable electronic equipments, low voltage design techniques have been developed and have driven analog designers to create techniques eg. Self cascode mosfet and stacking technique. For this aim in mind we designed a Folded Cascode using low power techniques and analyzed its various properties through the Spice simulations for 0.13 micron CMOS technology from TSMC and the supply voltage 1.8V.

  16. Probing possible downhill folding: native contact topology likely places a significant constraint on the folding cooperativity of proteins with approximately 40 residues.

    Science.gov (United States)

    Badasyan, Artem; Liu, Zhirong; Chan, Hue Sun

    2008-12-12

    Experiments point to appreciable variations in folding cooperativity among natural proteins with approximately 40 residues, indicating that the behaviors of these proteins are valuable for delineating the contributing factors to cooperative folding. To explore the role of native topology in a protein's propensity to fold cooperatively and how native topology might constrain the degree of cooperativity achievable by a given set of physical interactions, we compared folding/unfolding kinetics simulated using three classes of native-centric C(alpha) chain models with different interaction schemes. The approach was applied to two homologous 45-residue fragments from the peripheral subunit-binding domain family and a 39-residue fragment of the N-terminal domain of ribosomal protein L9. Free-energy profiles as functions of native contact number were computed to assess the heights of thermodynamic barriers to folding. In addition, chevron plots of folding/unfolding rates were constructed as functions of native stability to facilitate comparison with available experimental data. Although common Gō-like models with pairwise Lennard-Jones-type interactions generally fold less cooperatively than real proteins, the rank ordering of cooperativity predicted by these models is consistent with experiment for the proteins investigated, showing increasing folding cooperativity with increasing nonlocality of a protein's native contacts. Models that account for water-expulsion (desolvation) barriers and models with many-body (nonadditive) interactions generally entail higher degrees of folding cooperativity indicated by more linear model chevron plots, but the rank ordering of cooperativity remains unchanged. A robust, experimentally valid rank ordering of model folding cooperativity independent of the multiple native-centric interaction schemes tested here argues that native topology places significant constraints on how cooperatively a protein can fold.

  17. 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 ...

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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...

  3. 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...

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. Visual Impairment

    Science.gov (United States)

    ... Surgery? Choosing the Right Sport for You Shyness Visual Impairment KidsHealth > For Teens > Visual Impairment Print A A ... with the brain, making vision impossible. What Is Visual Impairment? Many people have some type of visual problem ...

  9. Visual field

    Science.gov (United States)

    Perimetry; Tangent screen exam; Automated perimetry exam; Goldmann visual field exam; Humphrey visual field exam ... Confrontation visual field exam : This is a quick and basic check of the visual field. The health care provider ...

  10. Determination of conformational entropy of fully and partially folded conformations of holo- and apomyoglobin.

    Science.gov (United States)

    Stadler, Andreas M; Koza, Michael Marek; Fitter, Jörg

    2015-01-08

    Holo- and apomyoglobin can be stabilized in native folded, partially folded molten globules (MGs) and denatured states depending on the solvent composition. Although the protein has been studied as a model system in the field of protein folding, little is known about the internal dynamics of the different structural conformations on the picosecond time scale. In a comparative experimental study we investigated the correlation between protein folding and dynamics on the picosecond time scale using incoherent quasielastic neutron scattering (QENS). The measured mean square displacements (MSDs) of conformational motions depend significantly on the secondary structure content of the protein, whereas the correlation times of the observed internal dynamics were found to be similar irrespective of the degree of folding. The conformational entropy difference ΔSconf between the folded conformations and the acid denatured state could be determined from the measured MSDs and was compared to the entropy difference ΔS obtained from thermodynamic parameters reported in the literature. The observed difference between ΔS and ΔSconf was attributed to the entropy difference ΔShydr of dynamically disordered water molecules of the hydration shell. The entropy content of the hydration water is significantly larger in the native folded proteins than in the partially folded MGs. We demonstrate the potential of incoherent neutron scattering for the investigation of the role of conformational dynamics in protein folding.

  11. 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.

  12. 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.

  13. Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model.

    Science.gov (United States)

    Mirny, L A; Abkevich, V; Shakhnovich, E I

    1996-01-01

    The role of intermediates in protein folding has been a matter of great controversy. Although it was widely believed that intermediates play a key role in minimizing the search problem associated with the Levinthal paradox, experimental evidence has been accumulating that small proteins fold fast without any detectable intermediates. We study the thermodynamics and kinetics of folding using a simple lattice model. Two folding sequences obtained by the design procedure exhibit different folding scenarios. The first sequence folds fast to the native state and does not exhibit any populated intermediates during folding. In contrast, the second sequence folds much slower, often being trapped in misfolded low-energy conformations. However, a small fraction of folding molecules for the second sequence fold on a fast track avoiding misfolded traps. In equilibrium at the same temperature the second sequence has a highly populated intermediate with structure similar to that of the kinetics intermediate. Our analysis suggests that intermediates may often destabilize native conformations and derail the folding process leading it to traps. Less-optimized sequences fold via parallel pathways involving misfolded intermediates. A better designed sequence is more stable in the native state and folds fast without intermediates in a two-state process.

  14. Stretching Folding Instability and Nanoemulsions

    CERN Document Server

    Chan, Chon U

    2009-01-01

    Here we show a folding-stretching instability in a microfluidic flow focusing device using silicon oil (100cSt) and water. The fluid dynamics video demonstrates an oscillating thread of oil focused by two co-flowing streams of water. We show several high-speed sequences of these oscillations with 30,000 frames/s. Once the thread is decelerated in a slower moving pool downstream an instability sets in and water-in-oil droplets are formed. We reveal the details of the pinch-off with 500,000 frames/s. The pinch-off is so repeatable that complex droplet patterns emerge. Some of droplets are below the resolution limit, thus smaller than 1 micrometer in diameter.

  15. Topological Solitons and Folded Proteins

    CERN Document Server

    Chernodub, M N; Niemi, Antti J

    2010-01-01

    We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by assembling the solitons together, one after another. We present a simple theoretical model that realizes our proposal and apply it to a number of biologically active proteins including 1VII, 2RB8, 3EBX (Protein Data Bank codes). In all the examples that we have considered we are able to construct solitons that reproduce secondary structural motifs such as alpha-helix-loop-alpha-helix and beta-sheet-loop-beta-sheet with an overall root-mean-square-distance accuracy of around 0.7 Angstrom or less for the central alpha-carbons, i.e. within the limits of current experimental accuracy.

  16. Protein folding and wring resonances

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1997-01-01

    The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested that prot......The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested...... that protein folding takes place when the amplitude of a wring excitation becomes so large that it is energetically favorable to bend the protein backbone. The condition under which such structural transformations can occur is found, and it is shown that both cold and hot denaturation (the unfolding...

  17. Optical coherence tomography imaging of chorioretinal folds associated with hypotony maculopathy following pars plana vitrectomy

    Directory of Open Access Journals (Sweden)

    Williams Jr BK

    2015-09-01

    Full Text Available Basil K Williams Jr, Jonathan S Chang, Harry W Flynn Jr Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA Abstract: Chorioretinal folds may occur as a consequence of hypotony and can be a cause of vision loss when associated with macular involvement. In this report, the spectral domain ocular coherence tomography imaging of three patients with chorioretinal folds before and after management are presented. The cases had unique presentations and each underwent different management approaches, but the results included improved visual acuities and lessened chorioretinal folds. Keywords: hypotony, chorioretinal folds, ocular coherence tomography

  18. Restructuring the vocal fold lamina propria with endoscopic microdissection.

    Science.gov (United States)

    Bartlett, Rebecca S; Hoffman, Henry T; Dailey, Seth H; Bock, Jonathan M; Klemuk, Sarah A; Askeland, Ryan W; Ahlrichs-Hanson, Jan S; Heaford, Andrew C; Thibeault, Susan L

    2013-11-01

    The purposes of this preclinical study were to investigate histologic and rheologic outcomes of Microendoscopy of Reinke's space (MERS)-guided minithyrotomy and to assess its instrumentation. Human cadaveric and in vivo animal study. Three human cadaveric larynges were treated with MERS-guided placement of Radiesse VoiceGel and immediately evaluated histologically for biomaterial location. In the second part of this investigation, two scarred porcine larynges were treated with MERS-guided placement of HyStem-VF and rheologically evaluated 6 weeks later. Student t tests determined differences in viscoelastic properties of treated/untreated vocal folds. Sialendoscopes and microendoscopes were subjectively compared for their visualization capacity. MERS imaged the subepithelial area and vocal ligament, guiding both tissue dissection and biomaterial positioning. Sialendoscopes provided adequate visualization and feature incorporated working channels. Enhanced image clarity was created in a gas-filled rather than saline-filled environment, per rater judgment. Histological analysis revealed desirable biomaterial positioning with MERS. Per rheological analysis, viscoelastic properties of the MERS-treated porcine vocal folds compared to uninjured vocal folds 6 weeks following treatment did not statistically differ. MERS-guided laryngoplasty using sialendoscopes yielded satisfactory biomaterial positioning in the short-term and normalized rheologic tissue properties in the long-term, contributing to proof of concept for MERS in the treatment of scarring. Strengths of MERS include direct, real-time visualization of Reinke's space and an ability to manipulate surgical instruments parallel to the vocal fold edge while maintaining an intact epithelium. Future work will explore the clinical utility of MERS for addressing scarring, sulcus vocalis, and other intracordal processes. Copyright © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

  19. Kinetics and thermodynamics of DNA polymerases with exonuclease proofreading

    Science.gov (United States)

    Gaspard, Pierre

    2016-04-01

    Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorporated nucleotide. The replication fidelity is shown to increase significantly thanks to this dependence at the basis of the mechanism of exonuclease proofreading. In particular, this dependence can provide up to a 100-fold lowering of the error probability under physiological conditions. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria.

  20. There and back again: Two views on the protein folding puzzle

    Science.gov (United States)

    Finkelstein, Alexei V.; Badretdin, Azat J.; Galzitskaya, Oxana V.; Ivankov, Dmitry N.; Bogatyreva, Natalya S.; Garbuzynskiy, Sergiy O.

    2017-07-01

    The ability of protein chains to spontaneously form their spatial structures is a long-standing puzzle in molecular biology. Experimentally measured folding times of single-domain globular proteins range from microseconds to hours: the difference (10-11 orders of magnitude) is the same as that between the life span of a mosquito and the age of the universe. This review describes physical theories of rates of overcoming the free-energy barrier separating the natively folded (N) and unfolded (U) states of protein chains in both directions: ;U-to-N; and ;N-to-U;. In the theory of protein folding rates a special role is played by the point of thermodynamic (and kinetic) equilibrium between the native and unfolded state of the chain; here, the theory obtains the simplest form. Paradoxically, a theoretical estimate of the folding time is easier to get from consideration of protein unfolding (the ;N-to-U; transition) rather than folding, because it is easier to outline a good unfolding pathway of any structure than a good folding pathway that leads to the stable fold, which is yet unknown to the folding protein chain. And since the rates of direct and reverse reactions are equal at the equilibrium point (as follows from the physical ;detailed balance; principle), the estimated folding time can be derived from the estimated unfolding time. Theoretical analysis of the ;N-to-U; transition outlines the range of protein folding rates in a good agreement with experiment. Theoretical analysis of folding (the ;U-to-N; transition), performed at the level of formation and assembly of protein secondary structures, outlines the upper limit of protein folding times (i.e., of the time of search for the most stable fold). Both theories come to essentially the same results; this is not a surprise, because they describe overcoming one and the same free-energy barrier, although the way to the top of this barrier from the side of the unfolded state is very different from the way from the

  1. The parallel universe of RNA folding.

    Science.gov (United States)

    Batey, R T; Doudna, J A

    1998-05-01

    How do large RNA molecules find their active conformations among a universe of possible structures? Two recent studies reveal that RNA folding is a rapid and ordered process, with surprising similarities to protein folding mechanisms.

  2. 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'.

  3. 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...

  4. 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

  5. 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

  6. 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

  7. 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.

  8. Entropy in molecular association and folding: Theory and computation

    Science.gov (United States)

    Brady, Gerald Patrick, Jr.

    1997-09-01

    This thesis addresses two central questions regarding entropy changes in protein folding and molecular recognition: (1) Can the entropy of a system be decomposed into individual components arising from particular atomic groups or physical interactions? and (2) Can molecular association thermodynamics be reliably calculated using current computational methods? To address the first question, the statistical-mechanical justification for entropy decomposition is theoretically investigated via 'cumulant' and 'beta-derivative' expansions of the entropy. The cumulant expansion demonstrates that entropy components may indeed be meaningfully ascribed to particular groups or interactions, although these components are coupled both explicitly via cross-terms and implicitly through the Boltzmann factor. The beta-derivative expansion (βDE) is shown to yield a complete decomposition of entropy, in that, the total entropy is completely partitioned amongst the contributing groups or interactions, with no individually unattributable cross- terms remaining. The question of calculating molecular association thermodynamics is examined via computational analysis of binding and solvation in a model peptide system. In particular, the gas ←⇔ crystal ←⇔ solution phase equilibrium thermodynamics of cyclic di-glycine (cGG) and cyclic di- alanine (cAA) is computed using a variety of techniques, and the results are compared to experimental data. The calculated cGG gas-to-solution free energy and gas-to- crystal enthalpy agree very well with experimental values; however, the gas-to-crystal entropy is overestimated by 15 eu. Of particular note, a reliable value of 14 eu is obtained for the association entropy barrier to gas ⇒ crystal transfer, the unfavorable net result of exchanging translational and rotational freedom in the gas phase for vibrational motion in the crystal. A mean-field Einstein Model underestimates the vibrational entropy of the crystal by 15 eu and, thus, appears

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. Understanding Protein Non-Folding

    Science.gov (United States)

    Uversky, Vladimir N.; Dunker, A. Keith

    2010-01-01

    This review describes the family of intrinsically disordered proteins, members of which fail to form rigid 3-D structures under physiological conditions, either along their entire lengths or only in localized regions. Instead, these intriguing proteins/regions exist as dynamic ensembles within which atom positions and backbone Ramachandran angles exhibit extreme temporal fluctuations without specific equilibrium values. Many of these intrinsically disordered proteins are known to carry out important biological functions which, in fact, depend on the absence of specific 3-D structure. The existence of such proteins does not fit the prevailing structure-function paradigm, which states that unique 3-D structure is a prerequisite to function. Thus, the protein structure-function paradigm has to be expanded to include intrinsically disordered proteins and alternative relationships among protein sequence, structure, and function. This shift in the paradigm represents a major breakthrough for biochemistry, biophysics and molecular biology, as it opens new levels of understanding with regard to the complex life of proteins. This review will try to answer the following questions: How were intrinsically disordered proteins discovered? Why don't these proteins fold? What is so special about intrinsic disorder? What are the functional advantages of disordered proteins/regions? What is the functional repertoire of these proteins? What are the relationships between intrinsically disordered proteins and human diseases? PMID:20117254

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. Elemental Composition Method in Thermodynamics of Multireaction Systems* (Ⅰ) Molar Number, Thermodynamic Properties and Partial Properties Relations

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    When species in the solution undergo multiple chemical reactions, the solution may be treated as a solution of all species actually present or as a hypothetical solution composed of elemental species. Based on the fundamental thermodynamic principle, the relationships of mole numbers, molar fractions, thermodynamic properties, partial molar properties, potential and fugacity between the hypothetical solution of elemental species and the equilibrated solution of actual species were derived. The hypothetical elemental solution provides a way of reducing the dimensionality of problem, simplifying the analysis and visualizing the phase behavior.

  5. 3D fold growth in transpression

    Science.gov (United States)

    Frehner, Marcel

    2016-12-01

    Geological folds in transpression are inherently 3D structures; hence their growth and rotation behavior is studied using 3D numerical finite-element simulations. Upright single-layer buckle folds in Newtonian materials are considered, which grow from an initial point-like perturbation due to a combination of in-plane shortening and shearing (i.e., transpression). The resulting fold growth exhibits three components: (1) fold amplification (vertical), (2) fold elongation (parallel to fold axis), and (3) sequential fold growth (perpendicular to axial plane) of new anti- and synforms adjacent to the initial fold. Generally, the fold growth rates are smaller for shearing-dominated than for shortening-dominated transpression. In spite of the growth rate, the folding behavior is very similar for the different convergence angles. The two lateral directions always exhibit similar growth rates implying that the bulk fold structure occupies an increasing roughly circular area. Fold axes are always parallel to the major horizontal principal strain axis (λ→max, i.e., long axis of the horizontal finite strain ellipse), which is initially also parallel to the major horizontal instantaneous stretching axis (ISA→max). After initiation, the fold axes rotate together with λ→max. Sequential folds appearing later do not initiate parallel to ISA→max, but parallel to λ→max, i.e. parallel to the already existing folds, and also rotate with λ→max. Therefore, fold axes do not correspond to passive material lines and hinge migration takes place as a consequence. The fold axis orientation parallel to λ→max is independent of convergence angle and viscosity ratio. Therefore, a triangular relationship between convergence angle, amount of shortening, and fold axis orientation exists. If two of these values are known, the third can be determined. This relationship is applied to the Zagros fold-and-thrust-belt to estimate the degree of strain partitioning between the Simply

  6. 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…

  7. Folding of Cu, Zn superoxide dismutase and Familial Amyotrophic Lateral Sclerosis

    CERN Document Server

    Khare, S D; Dokholyan, N V; Khare, Sagar D.; Ding, Feng; Dokholyan, Nikolay V.

    2003-01-01

    Cu,Zn superoxide dismutase (SOD1) has been implicated in the familial form of the neurodegenerative disease Amyotrophic Lateral Sclerosis (ALS). It has been suggested that mutant mediated SOD1 misfolding/aggregation is an integral part of the pathology of ALS. We study the folding thermodynamics and kinetics of SOD1 using a hybrid molecular dynamics approach. We reproduce the experimentally observed SOD1 folding thermodynamics and find that the residues which contribute the most to SOD1 thermal stability are also crucial for apparent two-state folding kinetics. Surprisingly, we find that these residues are located on the surface of the protein and not in the hydrophobic core. Mutations in some of the identified residues are found in patients with the disease. We argue that the identified residues may play an important role in aggregation. To further characterize the folding of SOD1, we study the role of cysteine residues in folding and find that non-native disulfide bond formation may significantly alter SOD1...

  8. Detecting Selection on Protein Stability through Statistical Mechanical Models of Folding and Evolution

    Directory of Open Access Journals (Sweden)

    Ugo Bastolla

    2014-03-01

    Full Text Available The properties of biomolecules depend both on physics and on the evolutionary process that formed them. These two points of view produce a powerful synergism. Physics sets the stage and the constraints that molecular evolution has to obey, and evolutionary theory helps in rationalizing the physical properties of biomolecules, including protein folding thermodynamics. To complete the parallelism, protein thermodynamics is founded on the statistical mechanics in the space of protein structures, and molecular evolution can be viewed as statistical mechanics in the space of protein sequences. In this review, we will integrate both points of view, applying them to detecting selection on the stability of the folded state of proteins. We will start discussing positive design, which strengthens the stability of the folded against the unfolded state of proteins. Positive design justifies why statistical potentials for protein folding can be obtained from the frequencies of structural motifs. Stability against unfolding is easier to achieve for longer proteins. On the contrary, negative design, which consists in destabilizing frequently formed misfolded conformations, is more difficult to achieve for longer proteins. The folding rate can be enhanced by strengthening short-range native interactions, but this requirement contrasts with negative design, and evolution has to trade-off between them. Finally, selection can accelerate functional movements by favoring low frequency normal modes of the dynamics of the native state that strongly correlate with the functional conformation change.

  9. Protein Folding under Mediation of Ordering Water: an Off-Lattice Gō-Like Model Study

    Institute of Scientific and Technical Information of China (English)

    ZUO Guang-Hong; HU Jun; FANG Hai-Ping

    2007-01-01

    @@ Water plays an important role in the structure and function of biomolecules. Water confined at the nanoscale usually exhibits phenomena not seen in bulk water, including the ice-like ordering structure on the surfaces of many substrates. We investigate the behaviour of protein folding in which the proteins are asssumed in an environment with ordering water by using of an off-lattice Gō-like model. It is found that in the physiological temperature, both the folding rate and the thermodynamic stability of the protein are greatly promoted by the existence of ordering of water.

  10. In-Situ Observation of Membrane Protein Folding during Cell-Free Expression.

    Directory of Open Access Journals (Sweden)

    Axel Baumann

    Full Text Available Proper insertion, folding and assembly of functional proteins in biological membranes are key processes to warrant activity of a living cell. Here, we present a novel approach to trace folding and insertion of a nascent membrane protein leaving the ribosome and penetrating the bilayer. Surface Enhanced IR Absorption Spectroscopy selectively monitored insertion and folding of membrane proteins during cell-free expression in a label-free and non-invasive manner. Protein synthesis was performed in an optical cell containing a prism covered with a thin gold film with nanodiscs on top, providing an artificial lipid bilayer for folding. In a pilot experiment, the folding pathway of bacteriorhodopsin via various secondary and tertiary structures was visualized. Thus, a methodology is established with which the folding reaction of other more complex membrane proteins can be observed during protein biosynthesis (in situ and in operando at molecular resolution.

  11. Anatomy and Histology of an Epicanthal Fold.

    Science.gov (United States)

    Park, Jae Woo; Hwang, Kun

    2016-06-01

    The aim of this study is to elucidate the precise anatomical and histological detail of the epicanthal fold.Thirty-two hemifaces of 16 Korean adult cadavers were used in this study (30 hemifaces with an epicanthal fold, 2 without an epicanthal fold). In 2 patients who had an epicanthoplasty, the epicanthal folds were sampled.In a dissection, the periorbital skin and subcutaneous tissues were removed and the epicanthal fold was observed in relation to each part of the orbicularis oculi muscle. Specimens including the epicanthal fold were embeddedin in paraffin, sectioned at 10 um, and stained with Hematoxylin-Eosin. The horizontal section in the level of the paplebral fissure was made and the prepared slides were observed under a light microscope.In the specimens without an epicanthal fold, no connection between the upper preseptal muscle and the lower preseptal muscle was found. In the specimens with an epicanthal fold, a connection of the upper preseptal muscle to the lower preseptal muscle was observed. It was present in all 15 hemifaces (100%). There was no connection between the pretarsal muscles. In a horizontal section, the epicanthal fold was composed of 3 compartments: an outer skin lining, a core structure, and an innerskin lining. The core structure was mainly composed of muscular fibers and fibrotic tissue and they were intermingled.Surgeons should be aware of the anatomical details of an epicanthal fold. In removing or reconstructing an epicanthal fold, the fibromuscular core band should also be removed or reconstructed.

  12. k-fold coloring of planar graphs

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A k-fold n-coloring of G is a mapping φ: V (G) → Zk(n) where Zk(n) is the collection of all ksubsets of {1,2,...,n} such that φ(u) ∩φ(v) = φ if uv ∈ E(G).If G has a k-fold n-coloring,i.e.,G is k-fold n-colorable.Let the smallest integer n such that G is k-fold n-colorable be the k-th chromatic number,denoted by χk(G).In this paper,we show that any outerplanar graph is k-fold 2k-colorable or k-fold χk(C*)-colorable,where C* is a shortest odd cycle of G.Moreover,we investigate that every planar graph with odd girth at least 10k-9(k 3) can be k-fold (2k + 1)-colorable.

  13. Estimation of protein folding free energy barriers from calorimetric data by multi-model Bayesian analysis.

    Science.gov (United States)

    Naganathan, Athi N; Perez-Jimenez, Raul; Muñoz, Victor; Sanchez-Ruiz, Jose M

    2011-10-14

    The realization that folding free energy barriers can be small enough to result in significant population of the species at the barrier top has sprouted in several methods to estimate folding barriers from equilibrium experiments. Some of these approaches are based on fitting the experimental thermogram measured by differential scanning calorimetry (DSC) to a one-dimensional representation of the folding free-energy surface (FES). Different physical models have been used to represent the FES: (1) a Landau quartic polynomial as a function of the total enthalpy, which acts as an order parameter; (2) the projection onto a structural order parameter (i.e. number of native residues or native contacts) of the free energy of all the conformations generated by Ising-like statistical mechanical models; and (3) mean-field models that define conformational entropy and stabilization energy as functions of a continuous local order parameter. The fundamental question that emerges is how can we obtain robust, model-independent estimates of the thermodynamic folding barrier from the analysis of DSC experiments. Here we address this issue by comparing the performance of various FES models in interpreting the thermogram of a protein with a marginal folding barrier. We chose the small α-helical protein PDD, which folds-unfolds in microseconds crossing a free energy barrier previously estimated as ~1 RT. The fits of the PDD thermogram to the various models and assumptions produce FES with a consistently small free energy barrier separating the folded and unfolded ensembles. However, the fits vary in quality as well as in the estimated barrier. Applying Bayesian probabilistic analysis we rank the fit performance using a statistically rigorous criterion that leads to a global estimate of the folding barrier and its precision, which for PDD is 1.3 ± 0.4 kJ mol(-1). This result confirms that PDD folds over a minor barrier consistent with the downhill folding regime. We have further

  14. How to fold intricately: using theory and experiments to unravel the properties of knotted proteins

    CERN Document Server

    Jackson, Sophie E; Micheletti, Cristian

    2016-01-01

    Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native state. Here, we review such developments by paying particular attention to the complementarity of experimental and computational studies. Key open issues that could be tackled with either or both approaches are finally pointed out.

  15. Vocal Fold Pathologies and Three-Dimensional Flow Separation Phenomena

    Science.gov (United States)

    Apostoli, Adam G.; Weiland, Kelley S.; Plesniak, Michael W.

    2013-11-01

    Polyps and nodules are two different pathologies, which are geometric abnormalities that form on the medial surface of the vocal folds, and have been shown to significantly disrupt a person's ability to communicate. Although the mechanism by which the vocal folds self-oscillate and the three-dimensional nature of the glottal jet has been studied, the effect of irregularities caused by pathologies is not fully understood. Examining the formation and evolution of vortical structures created by a geometric protuberance is important, not only for understanding the aerodynamic forces exerted by these structures on the vocal folds, but also in the treatment of the above-mentioned pathological conditions. Using a wall-mounted prolate hemispheroid with a 2:1 aspect ratio in cross flow, the present investigation considers three-dimensional flow separation induced by a model vocal fold polyp. Building on previous work using skin friction line visualization, both the velocity flow field and wall pressure measurements around the model polyp are presented and compared. Supported by the National Science Foundation, Grant No. CBET-1236351 and GW Center for Biomimetics and Bioinspired Engineering (COBRE).

  16. ETA-Graphics—an interface to endoreversible thermodynamics

    Science.gov (United States)

    Wagner, K.; Hoffmann, K. H.

    2015-03-01

    Endoreversible thermodynamics is a theory for the description of irreversible thermodynamic processes. In this theory a non-equilibrium system is divided into a set of reversible subsystems which interact irreversibly with one another by exchanging energy and extensive quantities. These extensities act as carriers for the energy. ETA-Graphics is a graphics-based interface to endoreversible thermodynamics that can be used as an educational aid. It enables students to visually design endoreversible systems by drawing reversible subsystems and connecting them with irreversible (or reversible) interactions. Through special dialogs users specify the properties of the system, e.g., in form of transport laws for energy and extensive quantities. Based on the input ETA-Graphics allows students to analyse the endoreversible systems and their properties. Therefore, performance measures, i.e., efficiency and total power output, are calculated. Additionally, graphical representations of the results are shown.

  17. 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.

  18. 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

  19. 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…

  20. 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…

  1. 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.

  2. 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

  3. Visual field asymmetries in visual evoked responses.

    Science.gov (United States)

    Hagler, Donald J

    2014-12-19

    Behavioral responses to visual stimuli exhibit visual field asymmetries, but cortical folding and the close proximity of visual cortical areas make electrophysiological comparisons between different stimulus locations problematic. Retinotopy-constrained source estimation (RCSE) uses distributed dipole models simultaneously constrained by multiple stimulus locations to provide separation between individual visual areas that is not possible with conventional source estimation methods. Magnetoencephalography and RCSE were used to estimate time courses of activity in V1, V2, V3, and V3A. Responses to left and right hemifield stimuli were not significantly different. Peak latencies for peripheral stimuli were significantly shorter than those for perifoveal stimuli in V1, V2, and V3A, likely related to the greater proportion of magnocellular input to V1 in the periphery. Consistent with previous results, sensor magnitudes for lower field stimuli were about twice as large as for upper field, which is only partially explained by the proximity to sensors for lower field cortical sources in V1, V2, and V3. V3A exhibited both latency and amplitude differences for upper and lower field responses. There were no differences for V3, consistent with previous suggestions that dorsal and ventral V3 are two halves of a single visual area, rather than distinct areas V3 and VP.

  4. Kinetic partitioning mechanism of HDV ribozyme folding

    Science.gov (United States)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2014-01-01

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  5. Viscoelastic properties of the false vocal fold

    Science.gov (United States)

    Chan, Roger W.

    2004-05-01

    The biomechanical properties of vocal fold tissues have been the focus of many previous studies, as vocal fold viscoelasticity critically dictates the acoustics and biomechanics of phonation. However, not much is known about the viscoelastic response of the ventricular fold or false vocal fold. It has been shown both clinically and in computer simulations that the false vocal fold may contribute significantly to the aerodynamics and sound generation processes of human voice production, with or without flow-induced oscillation of the false fold. To better understand the potential role of the false fold in phonation, this paper reports some preliminary measurements on the linear and nonlinear viscoelastic behavior of false vocal fold tissues. Linear viscoelastic shear properties of human false fold tissue samples were measured by a high-frequency controlled-strain rheometer as a function of frequency, and passive uniaxial tensile stress-strain response of the tissue samples was measured by a muscle lever system as a function of strain and loading rate. Elastic moduli (Young's modulus and shear modulus) of the false fold tissues were calculated from the measured data. [Work supported by NIH.

  6. Kinetic partitioning mechanism of HDV ribozyme folding

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing, E-mail: wbzhang@whu.edu.cn [Department of Physics, Wuhan University, Wuhan, Hubei 430072 (China)

    2014-01-14

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  7. Some aspects of vocal fold bowing.

    Science.gov (United States)

    Tanaka, S; Hirano, M; Chijiwa, K

    1994-05-01

    Bowing of the vocal fold frequently occurs in patients with vocal fold paralysis (VFP), those with sulcus vocalis, and those who have had laser surgery. Additionally, there are vocal folds that present bowing with no noticeable organic lesion. For the purpose of investigating the causes and mechanisms of vocal fold bowing, consecutive fiberscopic videorecordings of 127 patients with VFP, 33 with sulcus vocalis, 33 with laser surgery, and 33 with dysphonia having no clinically noticeable organic lesion were reviewed. Sixty-nine percent of the paralyzed vocal folds had bowing, and the occurrence of bowing was significantly related to the activity of the thyroarytenoid muscle as measured by electromyography. The cricothyroid activity had no significant relationship to vocal fold bowing. All vocal folds with sulcus presented with bowing. Thirty-five percent of the vocal folds that had had laser surgery had bowing. The extent of tissue removal was closely related to the occurrence of bowing. Twelve cases with no organic lesion had vocal fold bowing. Of these 12 patients, 8 were male and 9 were older than 60 years. Some aging process in the mucosa was presumed to be the cause of the bowing in this age group of patients without clinically noticeable organic lesions. Causes of vocal fold bowing in the younger group of patients without organic lesions were not determined in this study.

  8. 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...

  9. 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

  10. 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...

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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...

  17. 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.

  18. 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 ...

  19. 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...

  20. 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.

  1. On the usefulness of sheath folds as kinematic indicators

    Science.gov (United States)

    Reber, J. E.; Galland, O.; Dabrowski, M.; Schmid, D. W.; Cobbold, P. R.

    2012-04-01

    Sheath folds are cone-shaped structures that can be found in different rock types. They are mostly associated with shear zones. Even though they are three-dimensional structures they are most commonly recognized in nature in cross sections perpendicular to their stretching direction. These cross-sections exhibit so called eye-structures. The geometry of sheath folds has been used to deduce kinematic information such as strain, shear sense, and bulk strain type. However, how sheath folds form and how they evolve with increasing strain is still a matter of debate. We studied the development of sheath folds at the tip of a slip surface (weak inclusion) embedded in a layered matrix subjected to simple shear by means of analytical and experimental modeling. With this combined approach we tested the usefulness of sheath folds as indicators of strain, shear direction and bulk strain type. The analytical model is three-dimensional and based on an adapted external Eshelby solution. The slip surface is embedded in a homogeneous matrix, which is subjected to simple shear. Layers are introduced as passive markers for the visualization. With this method we tested the influence of the initial slip surface orientation (0°, 90°, or 135° with respect to the shear direction) and the number of layers on the evolving eye-structure. To study the effect of mechanical layering (viscosity contrast, layer thickness) on the geometry of the eye-structures we designed an experimental model using silicones as rock analogues. Although sheath folds are commonly considered as high strain markers, the analytical model shows that very little strain is needed to produce a sheath fold and the corresponding eye-pattern, and that the minimum strain is mainly dependent on the orientation of the slip surface and the number of layers. Our analytical as well as the experimental models revealed a sheath fold at both tips of the deformed slip surface. The two sheath folds show opposing closing direction

  2. 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

  3. Optical methods for measuring DNA folding

    Science.gov (United States)

    Smith, Adam D.; Ukogu, Obinna A.; Devenica, Luka M.; White, Elizabeth D.; Carter, Ashley R.

    2017-03-01

    One of the most important biological processes is the dynamic folding and unfolding of deoxyribonucleic acid (DNA). The folding process is crucial for DNA to fit within the boundaries of the cell, while the unfolding process is essential for DNA replication and transcription. To accommodate both processes, the cell employs a highly active folding mechanism that has been the subject of intense study over the last few decades. Still, many open questions remain. What are the pathways for folding or unfolding? How does the folding equilibrium shift? And, what is the energy landscape for a particular process? Here, we review these emerging questions and the in vitro, optical methods that have provided answers, introducing the topic for those physicists seeking to step into biology. Specifically, we discuss two iconic experiments for DNA folding, the tethered particle motion (TPM) experiment and the optical tweezers experiment.

  4. Structural features of protein folding nuclei.

    Science.gov (United States)

    Garbuzynskiy, S O; Kondratova, M S

    2008-03-05

    A crucial event of protein folding is the formation of a folding nucleus. We demonstrate the presence of a considerable coincidence between the location of folding nuclei and the location of so-called "root structural motifs", which have unique overall folds and handedness. In the case of proteins with a single root structural motif, the involvement in the formation of a folding nucleus is in average significantly higher for amino acids residues that are in root structural motifs, compared to residues in other parts of the protein. The tests carried out revealed that the observed difference is statistically reliable. Thus, a structural feature that corresponds to the protein folding nucleus is now found.

  5. Linking computation and experiments to study the role of charge-charge interactions in protein folding and stability

    Science.gov (United States)

    Makhatadze, George I.

    2017-02-01

    Over the past two decades there has been an increase in appreciation for the role of surface charge-charge interactions in protein folding and stability. The perception shifted from the belief that charge-charge interactions are not important for protein folding and stability to the near quantitative understanding of how these interactions shape the folding energy landscape. This led to the ability of computational approaches to rationally redesign surface charge-charge interactions to modulate thermodynamic properties of proteins. Here we summarize our progress in understanding the role of charge-charge interactions for protein stability using examples drawn from my own laboratory and touch upon unanswered questions.

  6. Implicit modeling of folds and overprinting deformation

    Science.gov (United States)

    Laurent, Gautier; Ailleres, Laurent; Grose, Lachlan; Caumon, Guillaume; Jessell, Mark; Armit, Robin

    2016-12-01

    Three-dimensional structural modeling is gaining importance for a broad range of quantitative geoscientific applications. However, existing approaches are still limited by the type of structural data they are able to use and by their lack of structural meaning. Most techniques heavily rely on spatial data for modeling folded layers, but are unable to completely use cleavage and lineation information for constraining the shape of modeled folds. This lack of structural control is generally compensated by expert knowledge introduced in the form of additional interpretive data such as cross-sections and maps. With this approach, folds are explicitly designed by the user instead of being derived from data. This makes the resulting structures subjective and deterministic. This paper introduces a numerical framework for modeling folds and associated foliations from typical field data. In this framework, a parametric description of fold geometry is incorporated into the interpolation algorithm. This way the folded geometry is implicitly derived from observed data, while being controlled through structural parameters such as fold wavelength, amplitude and tightness. A fold coordinate system is used to support the numerical description of fold geometry and to modify the behavior of classical structural interpolators. This fold frame is constructed from fold-related structural elements such as axial foliations, intersection lineations, and vergence. Poly-deformed terranes are progressively modeled by successively modeling each folding event going backward through time. The proposed framework introduces a new modeling paradigm, which enables the building of three-dimensional geological models of complex poly-deformed terranes. It follows a process based on the structural geologist approach and is able to produce geomodels that honor both structural data and geological knowledge.

  7. Calculation of the free energy and cooperativity of protein folding.

    Directory of Open Access Journals (Sweden)

    Alex Kentsis

    Full Text Available Calculation of the free energy of protein folding and delineation of its pre-organization are of foremost importance for understanding, predicting and designing biological macromolecules. Here, we introduce an energy smoothing variant of parallel tempering replica exchange Monte Carlo (REMS that allows for efficient configurational sampling of flexible solutes under the conditions of molecular hydration. Its usage to calculate the thermal stability of a model globular protein, Trp cage TC5b, achieves excellent agreement with experimental measurements. We find that the stability of TC5b is attained through the coupled formation of local and non-local interactions. Remarkably, many of these structures persist at high temperature, concomitant with the origin of native-like configurations and mesostates in an otherwise macroscopically disordered unfolded state. Graph manifold learning reveals that the conversion of these mesostates to the native state is structurally heterogeneous, and that the cooperativity of their formation is encoded largely by the unfolded state ensemble. In all, these studies establish the extent of thermodynamic and structural pre-organization of folding of this model globular protein, and achieve the calculation of macromolecular stability ab initio, as required for ab initio structure prediction, genome annotation, and drug design.

  8. Macromolecule-Assisted de novo Protein Folding

    Science.gov (United States)

    Choi, Seong Il; Son, Ahyun; Lim, Keo-Heun; Jeong, Hotcherl; Seong, Baik L.

    2012-01-01

    In the processes of protein synthesis and folding, newly synthesized polypeptides are tightly connected to the macromolecules, such as ribosomes, lipid bilayers, or cotranslationally folded domains in multidomain proteins, representing a hallmark of de novo protein folding environments in vivo. Such linkage effects on the aggregation of endogenous polypeptides have been largely neglected, although all these macromolecules have been known to effectively and robustly solubilize their linked heterologous proteins in fusion or display technology. Thus, their roles in the aggregation of linked endogenous polypeptides need to be elucidated and incorporated into the mechanisms of de novo protein folding in vivo. In the classic hydrophobic interaction-based stabilizing mechanism underlying the molecular chaperone-assisted protein folding, it has been assumed that the macromolecules connected through a simple linkage without hydrophobic interactions and conformational changes would make no effect on the aggregation of their linked polypeptide chains. However, an increasing line of evidence indicates that the intrinsic properties of soluble macromolecules, especially their surface charges and excluded volume, could be important and universal factors for stabilizing their linked polypeptides against aggregation. Taken together, these macromolecules could act as folding helpers by keeping their linked nascent chains in a folding-competent state. The folding assistance provided by these macromolecules in the linkage context would give new insights into de novo protein folding inside the cell. PMID:22949867

  9. 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.

  10. 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)

  11. Visual agnosia.

    Science.gov (United States)

    Álvarez, R; Masjuan, J

    2016-03-01

    Visual agnosia is defined as an impairment of object recognition, in the absence of visual acuity or cognitive dysfunction that would explain this impairment. This condition is caused by lesions in the visual association cortex, sparing primary visual cortex. There are 2 main pathways that process visual information: the ventral stream, tasked with object recognition, and the dorsal stream, in charge of locating objects in space. Visual agnosia can therefore be divided into 2 major groups depending on which of the two streams is damaged. The aim of this article is to conduct a narrative review of the various visual agnosia syndromes, including recent developments in a number of these syndromes.

  12. 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.

  13. Guiding the folding pathway of DNA origami.

    Science.gov (United States)

    Dunn, Katherine E; Dannenberg, Frits; Ouldridge, Thomas E; Kwiatkowska, Marta; Turberfield, Andrew J; Bath, Jonathan

    2015-09-03

    DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short 'staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its

  14. 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.

  15. 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...

  16. 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.

  17. 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.

  18. 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.

  19. New laryngoscope for quantitative high-speed imaging of human vocal folds vibration in the horizontal and vertical direction

    NARCIS (Netherlands)

    George, Nibu A.; de Mul, Frits F. M.; Qiu, Qingjun; Rakhorst, Gerhard; Schutte, Harm K.

    2008-01-01

    We report the design of a novel laser line-triangulation laryngoscope for the quantitative visualization of the three-dimensional movements of human vocal folds during phonation. This is the first successful in vivo recording of the three-dimensional movements of human vocal folds in absolute values

  20. APPLICATION OF FOLDED SURFACES IN CIVIL ENGINEERING

    Directory of Open Access Journals (Sweden)

    TOMA Ana Maria

    2015-06-01

    Full Text Available The paper presents the usage of folded surfaces as parts of a building system. This type of surfaces is not often used in constructions, even though the structures get to have a very special and spectacular design. The authors present some of the most known structures using the folded surfaces as a building component.

  1. Accelerated molecular dynamics simulations of protein folding.

    Science.gov (United States)

    Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew

    2015-07-30

    Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies.

  2. Monadic Maps and Folds for Arbitrary Datatypes

    NARCIS (Netherlands)

    Fokkinga, Maarten

    1994-01-01

    Each datatype constructor comes equiped not only with a so-called map and fold (catamorphism), as is widely known, but, under some condition, also with a kind of map and fold that are related to an arbitrary given monad. This result follows from the preservation of initiality under lifting

  3. The α/β hydrolase fold

    NARCIS (Netherlands)

    Ollis, David L.; Cheah, Eong; Cygler, Miroslaw; Dijkstra, Bauke; Frolow, Felix; Franken, Sybille M.; Harel, Michal; Remington, S. James; Silman, Israel; Schrag, Joseph; Sussman, Joel L.; Verschueren, Koen H.G.; Goldman, Adrian

    1992-01-01

    We have identified a new protein fold-the α/β hydrolase fold-that is common to several hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is similar: an α/β sheet, not barrel, of eight β-sheets connected by α-helices. These enzymes have diverge

  4. THE ALPHA/BETA-HYDROLASE FOLD

    NARCIS (Netherlands)

    OLLIS, DL; CHEAH, E; CYGLER, M; FROLOW, F; FRANKEN, SM; HAREL, M; REMINGTON, SJ; SILMAN, [No Value; SCHRAG, J; SUSSMAN, JL; VERSCHUEREN, KHG; GOLDMAN, A

    1992-01-01

    We have identified a new protein fold-the alpha/beta-hydrolase fold-that is common to several hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is similar: an alpha/beta-sheet, not barrel, of eight beta-sheets connected by alpha-helices. These

  5. A comparison of RNA folding measures

    DEFF Research Database (Denmark)

    Freyhult, E.; Gardner, P. P.; Moulton, V.

    2005-01-01

    Background In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs) fold in a more well-defined manner than random sequences. In this paper, we investigate several existing measures for how well an RNA sequence folds, and compare...

  6. Folded Plate Structures as Building Envelopes

    DEFF Research Database (Denmark)

    Falk, Andreas; Buelow, Peter von; Kirkegaard, Poul Henning

    2012-01-01

    This paper treats applications of cross-laminated timber (CLT) in structural systems for folded façade solutions. Previous work on CLT-based systems for folded roofs has shown a widening range of structural possibilities to develop timber-based shells. Geometric and material properties play, howe...

  7. Constructing a Rhombus through Paper Folding

    Science.gov (United States)

    Duatepe-Paksu, Asuman

    2017-01-01

    This paper presents an example of how paper folding can be used in a geometry class to support conceptual understanding. Specifically, it explains an activity that constructs a rhombus and explores its attributes by using paper folding. The steps of constructing a rhombus are described and some discussion questions are given to consolidate…

  8. Folded shapes with Super-Light Structures

    DEFF Research Database (Denmark)

    Castberg, Niels Andreas; Hertz, Kristian Dahl

    2012-01-01

    The use of folded shapes in structures has become more common, but it still costs problems because of construction issues and bending moments. The present paper deals with how the newly patented structural concept Super-Light structures (SLS) can be used to create folded shapes. SLS gives lighter...

  9. A comparison of RNA folding measures

    Directory of Open Access Journals (Sweden)

    Gardner Paul P

    2005-10-01

    Full Text Available Abstract Background In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs fold in a more well-defined manner than random sequences. In this paper, we investigate several existing measures for how well an RNA sequence folds, and compare the behaviour of these measures over a large range of Rfam ncRNA families. Such measures can be useful in, for example, identifying novel ncRNAs, and indicating the presence of alternate RNA foldings. Results Our analysis shows that ncRNAs, but not mRNAs, in general have lower minimal free energy (MFE than random sequences with the same dinucleotide frequency. Moreover, even when the MFE is significant, many ncRNAs appear to not have a unique fold, but rather several alternative folds, at least when folded in silico. Furthermore, we find that the six investigated measures are correlated to varying degrees. Conclusion Due to the correlations between the different measures we find that it is sufficient to use only two of them in RNA folding studies, one to test if the sequence in question has lower energy than a random sequence with the same dinucleotide frequency (the Z-score and the other to see if the sequence has a unique fold (the average base-pair distance, D.

  10. THE ALPHA/BETA-HYDROLASE FOLD

    NARCIS (Netherlands)

    OLLIS, DL; CHEAH, E; CYGLER, M; FROLOW, F; FRANKEN, SM; HAREL, M; REMINGTON, SJ; SILMAN, [No Value; SCHRAG, J; SUSSMAN, JL; VERSCHUEREN, KHG; GOLDMAN, A

    1992-01-01

    We have identified a new protein fold-the alpha/beta-hydrolase fold-that is common to several hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is similar: an alpha/beta-sheet, not barrel, of eight beta-sheets connected by alpha-helices. These

  11. The α/β hydrolase fold

    NARCIS (Netherlands)

    Ollis, David L.; Cheah, Eong; Cygler, Miroslaw; Dijkstra, Bauke; Frolow, Felix; Franken, Sybille M.; Harel, Michal; Remington, S. James; Silman, Israel; Schrag, Joseph; Sussman, Joel L.; Verschueren, Koen H.G.; Goldman, Adrian

    1992-01-01

    We have identified a new protein fold-the α/β hydrolase fold-that is common to several hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is similar: an α/β sheet, not barrel, of eight β-sheets connected by α-helices. These enzymes have diverge

  12. Folded shapes with Super-Light Structures

    DEFF Research Database (Denmark)

    Castberg, Niels Andreas; Hertz, Kristian Dahl

    2012-01-01

    The use of folded shapes in structures has become more common, but it still costs problems because of construction issues and bending moments. The present paper deals with how the newly patented structural concept Super-Light structures (SLS) can be used to create folded shapes. SLS gives lighter...

  13. Stochastic Resonance in Protein Folding Dynamics.

    Science.gov (United States)

    Davtyan, Aram; Platkov, Max; Gruebele, Martin; Papoian, Garegin A

    2016-05-04

    Although protein folding reactions are usually studied under static external conditions, it is likely that proteins fold in a locally fluctuating cellular environment in vivo. To mimic such behavior in in vitro experiments, the local temperature of the solvent can be modulated either harmonically or using correlated noise. In this study, coarse-grained molecular simulations are used to investigate these possibilities, and it is found that both periodic and correlated random fluctuations of the environment can indeed accelerate folding kinetics if the characteristic frequencies of the applied fluctuations are commensurate with the internal timescale of the folding reaction; this is consistent with the phenomenon of stochastic resonance observed in many other condensed-matter processes. To test this theoretical prediction, the folding dynamics of phosphoglycerate kinase under harmonic temperature fluctuations are experimentally probed using Förster resonance energy transfer fluorescence measurements. To analyze these experiments, a combination of theoretical approaches is developed, including stochastic simulations of folding kinetics and an analytical mean-field kinetic theory. The experimental observations are consistent with the theoretical predictions of stochastic resonance in phosphoglycerate kinase folding. When combined with an alternative experiment on the protein VlsE using a power spectrum analysis, elaborated in Dave et al., ChemPhysChem 2016, 10.1002/cphc.201501041, the overall data overwhelmingly point to the experimental confirmation of stochastic resonance in protein folding dynamics.

  14. Mis-folding and self-association: opportunities for alternative modes of self-recognition during the folding of TIM barrel proteins

    Science.gov (United States)

    Matthews, C. Robert

    2006-03-01

    The (βα)8 or TIM barrel motif is one of the most common in biology, represented in all three super-kingdoms of life. Detailed thermodynamic and kinetic analysis of the folding reactions of three members of the TIM barrel family of proteins reveal a common propensity to mis-fold to an off-pathway intermediate in less than a few milliseconds. The unfolding of this stopped-flow burst-phase intermediate controls access to an on-pathway intermediate that is highly-populated at moderate denaturant concentrations. Curiously, the equilibrium intermediate for two of the three nominally monomeric proteins spontaneously adopts a dimeric form; the native state of the third also dimerizes at micromolar concentrations. The early mis-folding reactions may reflect the rapid access to non-native folds enabled by the simple, repetitive βα topology of this motif. The propensity of stable forms, either intermediate or native, to form dimers may reflect a segment-swapping mechanism enabled by the modular folding of these single structural domain proteins. Off-pathway intermediates and non-native dimers serve as examples of important, alternative intra- or inter-molecular self-recognition events.

  15. Visual art and visual perception

    NARCIS (Netherlands)

    Koenderink, Jan J.

    2015-01-01

    Visual art and visual perception ‘Visual art’ has become a minor cul-de-sac orthogonal to THE ART of the museum directors and billionaire collectors. THE ART is conceptual, instead of visual. Among its cherished items are the tins of artist’s shit (Piero Manzoni, 1961, Merda d’Artista) “worth their

  16. 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.

  17. 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...

  18. 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...

  19. The robustness and innovability of protein folds.

    Science.gov (United States)

    Tóth-Petróczy, Agnes; Tawfik, Dan S

    2014-06-01

    Assignment of protein folds to functions indicates that >60% of folds carry out one or two enzymatic functions, while few folds, for example, the TIM-barrel and Rossmann folds, exhibit hundreds. Are there structural features that make a fold amenable to functional innovation (innovability)? Do these features relate to robustness--the ability to readily accumulate sequence changes? We discuss several hypotheses regarding the relationship between the architecture of a protein and its evolutionary potential. We describe how, in a seemingly paradoxical manner, opposite properties, such as high stability and rigidity versus conformational plasticity and structural order versus disorder, promote robustness and/or innovability. We hypothesize that polarity--differentiation and low connectivity between a protein's scaffold and its active-site--is a key prerequisite for innovability.

  20. The geometry and wetting of capillary folding

    CERN Document Server

    Péraud, Jean-Philippe

    2014-01-01

    Capillary forces are involved in a variety of natural phenomena, ranging from droplet breakup to the physics of clouds. The forces from surface tension can also be exploited in industrial application provided the length scales involved are small enough. Recent experimental investigations showed how to take advantage of capillarity to fold planar structures into three-dimensional configurations by selectively melting polymeric hinges joining otherwise rigid shapes. In this paper we use theoretical calculations to quantify the role of geometry and fluid wetting on the final folded state. Considering folding in two and three dimensions, studying both hydrophilic and hydrophobic situations with possible contact angle hysteresis, and addressing the shapes to be folded to be successively infinite, finite, curved, kinked, elastic, we are able to derive an overview of the geometrical parameter space available for capillary folding.

  1. Cooperative Tertiary Interaction Network Guides RNA Folding

    Energy Technology Data Exchange (ETDEWEB)

    Behrouzi, Reza; Roh, Joon Ho; Kilburn, Duncan; Briber, R.M.; Woodson, Sarah A. (JHU); (Maryland)

    2013-04-08

    Noncoding RNAs form unique 3D structures, which perform many regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme by single-base substitutions. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE. Double- and triple-mutant cycles show that most tertiary interactions have a small effect on the stability of the native state. Instead, the formation of core and peripheral structural motifs is cooperatively linked in near-native folding intermediates, and this cooperativity depends on the native helix orientation. The emergence of a cooperative interaction network at an early stage of folding suppresses nonnative structures and guides the search for the native state. We suggest that cooperativity in noncoding RNAs arose from natural selection of architectures conducive to forming a unique, stable fold.

  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. Thermodynamic and relativistic uncertainty relations

    Science.gov (United States)

    Artamonov, A. A.; Plotnikov, E. M.

    2017-01-01

    Thermodynamic uncertainty relation (UR) was verified experimentally. The experiments have shown the validity of the quantum analogue of the zeroth law of stochastic thermodynamics in the form of the saturated Schrödinger UR. We have also proposed a new type of UR for the relativistic mechanics. These relations allow us to consider macroscopic phenomena within the limits of the ratio of the uncertainty relations for different physical quantities.

  13. Thermodynamics of nonsingular bouncing universes

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, Pedro C. [Universidade Federal do Rio Grande do Norte, Escola de Ciencias e Tecnologia, Natal, Rio Grande do Norte (Brazil); Pavon, Diego [Universidad Autonoma de Barcelona, Departamento de Fisica, Bellaterra, Barcelona (Spain)

    2016-01-15

    Homogeneous and isotropic, nonsingular, bouncing world models are designed to evade the initial singularity at the beginning of the cosmic expansion. Here, we study the thermodynamics of the subset of these models governed by general relativity. Considering the entropy of matter and radiation and considering the entropy of the apparent horizon to be proportional to its area, we argue that these models do not respect the generalized second law of thermodynamics, also away from the bounce. (orig.)

  14. Thermodynamics from concepts to applications

    CERN Document Server

    Shavit, Arthur

    2008-01-01

    The book presents a logical methodology for solving problems in the context of conservation laws and property tables or equations. The authors elucidate the terms around which thermodynamics has historically developed, such as work, heat, temperature, energy, and entropy. Using a pedagogical approach that builds from basic principles to laws and eventually corollaries of the laws, the text enables students to think in clear and correct thermodynamic terms as well as solve real engineering problems.

  15. Thermodynamics of Asymptotically Conical Geometries.

    Science.gov (United States)

    Cvetič, Mirjam; Gibbons, Gary W; Saleem, Zain H

    2015-06-12

    We study the thermodynamical properties of a class of asymptotically conical geometries known as "subtracted geometries." We derive the mass and angular momentum from the regulated Komar integral and the Hawking-Horowitz prescription and show that they are equivalent. By deriving the asymptotic charges, we show that the Smarr formula and the first law of thermodynamics hold. We also propose an analog of Christodulou-Ruffini inequality. The analysis can be generalized to other asymptotically conical geometries.

  16. Generalization of Gibbs Entropy and Thermodynamic Relation

    OpenAIRE

    Park, Jun Chul

    2010-01-01

    In this paper, we extend Gibbs's approach of quasi-equilibrium thermodynamic processes, and calculate the microscopic expression of entropy for general non-equilibrium thermodynamic processes. Also, we analyze the formal structure of thermodynamic relation in non-equilibrium thermodynamic processes.

  17. Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins

    DEFF Research Database (Denmark)

    Kushon, S A; Jordan, J P; Seifert, J L

    2001-01-01

    structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic...

  18. Physical Intelligence and Thermodynamic Computing

    Directory of Open Access Journals (Sweden)

    Robert L. Fry

    2017-03-01

    Full Text Available This paper proposes that intelligent processes can be completely explained by thermodynamic principles. They can equally be described by information-theoretic principles that, from the standpoint of the required optimizations, are functionally equivalent. The underlying theory arises from two axioms regarding distinguishability and causality. Their consequence is a theory of computation that applies to the only two kinds of physical processes possible—those that reconstruct the past and those that control the future. Dissipative physical processes fall into the first class, whereas intelligent ones comprise the second. The first kind of process is exothermic and the latter is endothermic. Similarly, the first process dumps entropy and energy to its environment, whereas the second reduces entropy while requiring energy to operate. It is shown that high intelligence efficiency and high energy efficiency are synonymous. The theory suggests the usefulness of developing a new computing paradigm called Thermodynamic Computing to engineer intelligent processes. The described engineering formalism for the design of thermodynamic computers is a hybrid combination of information theory and thermodynamics. Elements of the engineering formalism are introduced in the reverse-engineer of a cortical neuron. The cortical neuron provides perhaps the simplest and most insightful example of a thermodynamic computer possible. It can be seen as a basic building block for constructing more intelligent thermodynamic circuits.

  19. Flow visualization

    CERN Document Server

    Merzkirch, Wolfgang

    1974-01-01

    Flow Visualization describes the most widely used methods for visualizing flows. Flow visualization evaluates certain properties of a flow field directly accessible to visual perception. Organized into five chapters, this book first presents the methods that create a visible flow pattern that could be investigated by visual inspection, such as simple dye and density-sensitive visualization methods. It then deals with the application of electron beams and streaming birefringence. Optical methods for compressible flows, hydraulic analogy, and high-speed photography are discussed in other cha

  20. Modulation of the multistate folding of designed TPR proteins through intrinsic and extrinsic factors.

    Science.gov (United States)

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

    2012-03-01

    Tetratricopeptide repeats (TPRs) are a class of all alpha-helical repeat proteins that are comprised of 34-aa helix-turn-helix motifs. These stack together to form nonglobular structures that are stabilized by short-range interactions from residues close in primary sequence. Unlike globular proteins, they have few, if any, long-range nonlocal stabilizing interactions. Several studies on designed TPR proteins have shown that this modular structure is reflected in their folding, that is, modular multistate folding is observed as opposed to two-state folding. Here we show that TPR multistate folding can be suppressed to approximate two-state folding through modulation of intrinsic stability or extrinsic environmental variables. This modulation was investigated by comparing the thermodynamic unfolding under differing buffer regimes of two distinct series of consensus-designed TPR proteins, which possess different intrinsic stabilities. A total of nine proteins of differing sizes and differing consensus TPR motifs were each thermally and chemically denatured and their unfolding monitored using differential scanning calorimetry (DSC) and CD/fluorescence, respectively. Analyses of both the DSC and chemical denaturation data show that reducing the total stability of each protein and repeat units leads to observable two-state unfolding. These data highlight the intimate link between global and intrinsic repeat stability that governs whether folding proceeds by an observably two-state mechanism, or whether partial unfolding yields stable intermediate structures which retain sufficient stability to be populated at equilibrium.

  1. Ultrafast folding of WW domains without structured aromatic clusters in the denatured state.

    Science.gov (United States)

    Ferguson, N; Johnson, C M; Macias, M; Oschkinat, H; Fersht, A

    2001-11-06

    Ultrafast-folding proteins are important for combining experiment and simulation to give complete descriptions of folding pathways. The WW domain family comprises small proteins with a three-stranded antiparallel beta-sheet topology. Previous studies on the 57-residue YAP 65 WW domain indicate the presence of residual structure in the chemically denatured state. Here we analyze three minimal core WW domains of 38-44 residues. There was little spectroscopic or thermodynamic evidence for residual structure in either their chemically or thermally denatured states. Folding and unfolding kinetics, studied by using rapid temperature-jump and continuous-flow techniques, show that each domain folds and unfolds very rapidly in a two-state transition through a highly compact transition state. Folding half-times were as short as 17 micros at 25 degrees C, within an order of magnitude of the predicted maximal rate of loop formation. The small size and topological simplicity of these domains, in conjunction with their very rapid two-state folding, may allow us to reduce the difference in time scale between experiment and theoretical simulation.

  2. Quantification of a Helical Origami Fold

    Science.gov (United States)

    Dai, Eric; Han, Xiaomin; Chen, Zi

    2015-03-01

    Origami, the Japanese art of paper folding, is traditionally viewed as an amusing pastime and medium of artistic expression. However, in recent years, origami has served as a source of inspiration for innovations in science and engineering. Here, we present the geometric and mechanical properties of a twisting origami fold. The origami structure created by the fold exhibits several interesting properties, including rigid foldibility, local bistability and finely tunable helical coiling, with control over pitch, radius and handedness of the helix. In addition, the pattern generated by the fold closely mimics the twist buckling patterns shown by thin materials, for example, a mobius strip. We use six parameters of the twisting origami pattern to generate a fully tunable graphical model of the fold. Finally, we present a mathematical model of the local bistability of the twisting origami fold. Our study elucidates the mechanisms behind the helical coiling and local bistability of the twisting origami fold, with potential applications in robotics and deployable structures. Acknowledgment to Branco Weiss Fellowship for funding.

  3. Mapping the Universe of RNA Tetraloop Folds.

    Science.gov (United States)

    Bottaro, Sandro; Lindorff-Larsen, Kresten

    2017-07-25

    We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG folds. We identify clusters corresponding to known tetraloop folds such as GGUG, RNYA, AGNN, and CUUG. These clusters are represented in a simple two-dimensional projection that recapitulates the relationship among the different folds. The cluster analysis also identifies 20 novel tetraloop folds that are peculiar to specific positions in ribosomal RNAs and that are stabilized by tertiary interactions. In our RNA tetraloop database we find a significant number of non-GNRA and non-UNCG sequences adopting the canonical GNRA and UNCG folds. Conversely, we find a significant number of GNRA and UNCG sequences adopting non-GNRA and non-UNCG folds. Our analysis demonstrates that there is not a simple one-to-one, but rather a many-to-many mapping between tetraloop sequence and tetraloop fold. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. Thermodynamics of firms' growth

    Science.gov (United States)

    Zambrano, Eduardo; Hernando, Alberto; 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 database 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 economic system for creating/destroying firms, and that can be used to measure the health of a capitalist-based economy. Indeed, our model predicts that when the exponent is larger than 1, creation of firms is favoured; when it is smaller than 1, destruction of firms is favoured instead; and when it equals 1 (matching Zipf's law), the system is in a full macroeconomic equilibrium, entailing ‘free’ creation and/or destruction of firms. For medium and smaller firm sizes, the dynamical regime changes, the whole distribution can no longer be fitted to a single simple analytical form and numerical prediction is required. Our model constitutes the basis for a full predictive framework regarding the economic evolution of an ensemble of firms. Such a structure can be potentially used to develop simulations and test hypothetical scenarios, such as economic crisis or the response to specific policy measures. PMID:26510828

  5. Pedagogical Visualization of a Nonideal Carnot Engine

    Directory of Open Access Journals (Sweden)

    Jonas Johansson

    2014-01-01

    Full Text Available We have implemented a visualization tool for the demonstration of a nonideal Carnot engine, operating at finite time. The cycle time can be varied using a slide bar and the pressure-volume, temperature-entropy, power-time, and efficiency-time diagrams change interactively and are shown on one screen. We have evaluated the visualization tool among engineering students at university level during an introductory course on thermodynamics and we review and discuss the outcome of the evaluation.

  6. Thermodynamics of noncommutative quantum Kerr black holes

    CERN Document Server

    Escamilla-Herrera, L F; Torres-Arenas, J

    2016-01-01

    Thermodynamic formalism for rotating black holes, characterized by noncommutative and quantum corrections, is constructed. From a fundamental thermodynamic relation, equations of state and thermodynamic response functions are explicitly given and the effect of noncommutativity and quantum correction is discussed. It is shown that the well known divergence exhibited in specific heat is not removed by any of these corrections. However, regions of thermodynamic stability are affected by noncommutativity, increasing the available states for which the system is thermodynamically stable.

  7. Thermodynamics and time-directional invariance

    OpenAIRE

    Klimenko, A. Y.; Maas, U.

    2012-01-01

    Time directions are not invariant in conventional thermodynamics. We broadly follow ideas of Ludwig Boltzmann and investigate implications of postulating time-directional invariance in thermodynamics. In this investigation, we require that thermodynamic descriptions are not changed under time reversal accompanied by replacement of matter by antimatter (i.e. CPT-invariant thermodynamics). The matter and antimatter are defined as thermodynamic concepts without detailing their physical structure...

  8. Investigating the thermodynamics of UNCG tetraloops using infrared spectroscopy.

    Science.gov (United States)

    Stancik, Aaron L; Brauns, Eric B

    2013-10-31

    Using infrared (IR) absorption spectroscopy, we have explored the folding thermodynamics of the UNCG class of RNA hairpin tetraloops (N = U, A, C, or G). Without the need to introduce non-native probes, IR spectroscopy makes it possible to distinguish specific structural elements such as base pairing versus base stacking or loop versus stem motions. Our results show that different structural components exhibit different thermodynamics. Specifically, we have found that tetraloop melting proceeds in a thermally sequential fashion, where base pairing in the stem is disrupted before (i.e., at a lower temperature) base stacking along the entire chain. In addition, for N = A, our data argue that the structure immediately surrounding adenine is particularly stable and melts at a higher temperature than either base-pairing or base-stacking interactions. Taken together, these results suggest that hairpin loop formation is not a simple two-state process, even in the equilibrium limit.

  9. Mechanical Models of Fault-Related Folding

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, A. M.

    2003-01-09

    The subject of the proposed research is fault-related folding and ground deformation. The results are relevant to oil-producing structures throughout the world, to understanding of damage that has been observed along and near earthquake ruptures, and to earthquake-producing structures in California and other tectonically-active areas. The objectives of the proposed research were to provide both a unified, mechanical infrastructure for studies of fault-related foldings and to present the results in computer programs that have graphical users interfaces (GUIs) so that structural geologists and geophysicists can model a wide variety of fault-related folds (FaRFs).

  10. Folded Plate Structures as Building Envelopes

    DEFF Research Database (Denmark)

    Falk, Andreas; Buelow, Peter von; Kirkegaard, Poul Henning

    2012-01-01

    This paper treats applications of cross-laminated timber (CLT) in structural systems for folded façade solutions. Previous work on CLT-based systems for folded roofs has shown a widening range of structural possibilities to develop timber-based shells. Geometric and material properties play......, however, an important role also for the enclosure, and climate and conceptual design procedures have been utilised to include these issues in early design phases. A current architectural trend proposes increasing complexity of the façades and in this context the paper proposes the application of folded...

  11. Melody discrimination and protein fold classification

    Directory of Open Access Journals (Sweden)

    Robert P. Bywater

    2016-10-01

    Full Text Available One of the greatest challenges in theoretical biophysics and bioinformatics is the identification of protein folds from sequence data. This can be regarded as a pattern recognition problem. In this paper we report the use of a melody generation software where the inputs are derived from calculations of evolutionary information, secondary structure, flexibility, hydropathy and solvent accessibility from multiple sequence alignment data. The melodies so generated are derived from the sequence, and by inference, of the fold, in ways that give each fold a sound representation that may facilitate analysis, recognition, or comparison with other sequences.

  12. Folding Kinetics of Riboswitch Transcriptional Terminators

    Science.gov (United States)

    Sauerwine, Benjamin; Widom, Michael

    2009-03-01

    Riboswitches control the expression of genes in bacteria by halting gene transcription or allowing it to proceed based on the presence of ligands in solution. A key feature of every riboswitch is a transcriptional terminator in which the messenger RNA folds into a secondary structure with the stem-loop structure of a hairpin. Through kinetic Monte Carlo simulation we show that terminators have been naturally selected to fold with high reliability on the time-scale of gene transcription. This efficient folding behavior is preserved among two classes of riboswitch and among two species of bacteria.

  13. Visual Servoing

    OpenAIRE

    Chaumette, Francois; Hutchinson, Seth; Corke, Peter

    2016-01-01

    International audience; This chapter introduces visual servo control, using computer vision data in the servo loop to control the motion of a robot. We first describe the basic techniques that are by now well established in the field. We give a general overview of the formulation of the visual servo control problem, and describe the two archetypal visual servo control schemes: image-based and pose-based visual servo control. We then discuss performance and stability issues that pertain to the...

  14. Chemical Energy and Exergy. An Introduction to Chemical Thermodynamics for Engineers

    Energy Technology Data Exchange (ETDEWEB)

    Sato, Norio [NS electrochemical Laboratory, Hokkaido University, Sapporo (Japan)

    2004-03-01

    This book is a beginners introduction to chemical thermodynamics for engineers. In the textbook efforts have been made to visualize as clearly as possible the main concepts of thermodynamic quantities such as enthalpy and entropy, thus making them more perceivable. Furthermore, intricate formulae in thermodynamics have been discussed as functionally unified sets of formulae to understand their meaning rather than to mathematically derive them in detail. In this textbook, the affinity of irreversible processes, defined by the second law of thermodynamics, has been treated as the main subject, rather than the equilibrium of chemical reactions. The concept of affinity is applicable in general not only to the processes of chemical reactions but also to all kinds of irreversible processes. This textbook also includes electrochemical thermodynamics in which, instead of the classical phenomenological approach, molecular science provides an advanced understanding of the reactions of charged particles such as ions and electrons at the electrodes. Recently, engineering thermodynamics has introduced a new thermodynamic potential called exergy, which essentially is related to the concept of the affinity of irreversible processes. This textbook discusses the relation between exergy and affinity and explains the exergy balance diagram and exergy vector diagram applicable to exergy analyses in chemical manufacturing processes. This textbook is written in the hope that the readers understand in a broad way the fundamental concepts of energy and exergy from chemical thermodynamics in practical applications. Finishing this book, the readers may easily step forward further into an advanced text of their specified line.

  15. Multiple folding pathways of proteins with shallow knots and co-translational folding

    CERN Document Server

    Chwastyk, Mateusz

    2015-01-01

    We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the single knot-loop events, we find novel, and dominant, two-loop mechanisms. We demonstrate that folding takes place in a range of temperatures and the conditions of most successful folding are at temperatures which are higher than those required for the fastest folding. We also demonstrate that nascent conditions are more favorable to knotting than off-ribosome folding.

  16. 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.

  17. Origami: Paper Folding--The Algorithmic Way.

    Science.gov (United States)

    Heukerott, Pamela Beth

    1988-01-01

    Describes origami, the oriental art of paper folding as an activity to teach upper elementary students concepts and skills in geometry involving polygons, angles, measurement, symmetry, and congruence. (PK)

  18. Folds--Offshore Santa Cruz, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the folds for the geologic and geomorphic map of the Offshore Santa Cruz map area, California. The vector data file is...

  19. Topology Explains Why Automobile Sunshades Fold Oddly

    Science.gov (United States)

    Feist, Curtis; Naimi, Ramin

    2009-01-01

    Automobile sunshades always fold into an "odd" number of loops. The explanation why involves elementary topology (braid theory and linking number, both explained in detail here with definitions and examples), and an elementary fact from algebra about symmetric group.

  20. Folds--Offshore Pigeon Point, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the folds for the geologic and geomorphic map of the Offshore Pigeon Point map area, California. The vector data file is...

  1. Folds--Offshore Santa Cruz, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the folds for the geologic and geomorphic map of the Offshore Santa Cruz map area, California. The vector data file is included...

  2. Folds--Offshore Scott Creek, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the folds for the geologic and geomorphic map of the Offshore of Scott Creek map area, California. The vector data file is...

  3. Self-folding miniature elastic electric devices

    Science.gov (United States)

    Miyashita, Shuhei; Meeker, Laura; Tolley, Michael T.; Wood, Robert J.; Rus, Daniela

    2014-09-01

    Printing functional materials represents a considerable impact on the access to manufacturing technology. In this paper we present a methodology and validation of print-and-self-fold miniature electric devices. Polyvinyl chloride laminated sheets based on metalized polyester film show reliable self-folding processes under a heat application, and it configures 3D electric devices. We exemplify this technique by fabricating fundamental electric devices, namely a resistor, capacitor, and inductor. Namely, we show the development of a self-folded stretchable resistor, variable resistor, capacitive strain sensor, and an actuation mechanism consisting of a folded contractible solenoid coil. Because of their pre-defined kinematic design, these devices feature elasticity, making them suitable as sensors and actuators in flexible circuits. Finally, an RLC circuit obtained from the integration of developed devices is demonstrated, in which the coil based actuator is controlled by reading a capacitive strain sensor.

  4. Folds--Offshore Santa Cruz, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the folds for the geologic and geomorphic map of the Offshore Santa Cruz map area, California. The vector data file is included...

  5. Folds--Offshore Pigeon Point, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the folds for the geologic and geomorphic map of the Offshore Pigeon Point map area, California. The vector data file is...

  6. Folds--Offshore Scott Creek, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the folds for the geologic and geomorphic map of the Offshore of Scott Creek map area, California. The vector data file is...

  7. Design Procedure for Compact Folded Waveguide Filters

    DEFF Research Database (Denmark)

    Dong, Yunfeng; Johansen, Tom Keinicke; Zhurbenko, Vitaliy;

    Waveguide filters are widely used in communication systems due to low losses and high power handling capabilities. One drawback of the conventional waveguide filters is their large size, especially for low-frequency and high-order realizations. It has been shown that the footprint of conventional...... waveguide resonators can be reduced to one quarter by folding the electric and magnetic fields inside the cavity (J. S. Hong, Microwave Symposium Digest, 2004, Vol. 1, pp. 213-216). This paper presents a novel systematic procedure for designing compact low-loss bandpass filters by using folded waveguide...... resonators. As a design example, a scaled version of a filter specified for a TETRA (Terrestrial Trunked Radio) system has been considered. The folded waveguide filter is designed to fulfil specific requirements, and the design procedure can be easily applied to other folded waveguide filter designs...

  8. Cotranslational folding of deeply knotted proteins

    CERN Document Server

    Chwastyk, Mateusz

    2015-01-01

    Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that cotranslational folding on a model ribosome may enhance the odds to form trefoil knots for protein YibK without any need to introduce any non-native contacts. The ribosome is represented by a repulsive wall that keeps elongating the protein. On-ribosome folding proceeds through a a slipknot conformation. We elucidate the mechanics and energetics of its formation. We show that the knotting probability in on-ribosome folding is a function of temperature and that there is an optimal temperature for the process. Our model often leads to the establishment of the native contacts without formation of the knot.

  9. Folds--Offshore Refugio Beach, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of SIM 3319 presents folds for the geologic and geomorphic map (see sheets 10, SIM 3319) of Offshore Refugio Beach, California. The vector data file is...

  10. Folds--Offshore of Santa Barbara, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of SIM 3281 presents data for folds for the geologic and geomorphic map (see sheet 10, SIM 3281) of the Offshore of Santa Barbara map area, California. The...

  11. Folds--Offshore of Carpinteria, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of SIM 3261 presents data for folds for the geologic and geomorphic map (see sheet 10, SIM 3261) of the Offshore of Carpinteria map area, California. The...

  12. Cycle 23 COS/NUV Fold Distribution

    Science.gov (United States)

    Wheeler, Thomas; Welty, Alan

    2017-07-01

    We summarize the Cycle 23 COS/NUV Fold Distribution for the Cosmic Origins Spectrograph's (COS) MAMA detector on the Hubble Space Telescope. The detector micro-channel plate's health state is determined and the results presented.

  13. Folds--Offshore of Ventura, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of SIM 3254 presents data for folds for the geologic and geomorphic map (see sheet 10, SIM 3254) of the Offshore of Ventura map area, California. The...

  14. Folds--Offshore of Santa Barbara, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of SIM 3281 presents data for folds for the geologic and geomorphic map (see sheet 10, SIM 3281) of the Offshore of Santa Barbara map area, California....

  15. Inverse Folding of RNA Pseudoknot Structures

    CERN Document Server

    Gao, James Z M; Reidys, Christian M

    2010-01-01

    Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \\pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These interactions are called pseudoknots and are observed across the whole spectrum of RNA functionalities. In the context of studying natural RNA structures, searching for new ribozymes and designing artificial RNA, it is of interest to find RNA sequences folding into a specific structure and to analyze their induced neutral networks. Since the established inverse folding algorithms, {\\tt RNAinverse}, {\\tt RNA-SSD} as well as {\\tt INFO-RNA} are limited to RNA secondary structures, we present in this paper the inverse folding algorithm {\\tt Inv} which can deal with 3-noncrossing, canonical pseudoknot structures. Results: In this paper we present the inverse folding algorithm {\\tt Inv}. We give a detailed analysis of {\\tt Inv}, including pseudocodes. We show that {\\tt Inv} allows to...

  16. Folds--Offshore Refugio Beach, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of SIM 3319 presents folds for the geologic and geomorphic map (see sheets 10, SIM 3319) of Offshore Refugio Beach, California. The vector data file is...

  17. Folds--Offshore of Santa Barbara, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of SIM 3281 presents data for folds for the geologic and geomorphic map (see sheet 10, SIM 3281) of the Offshore of Santa Barbara map area, California. The...

  18. Folds--Offshore of Carpinteria, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of SIM 3261 presents data for folds for the geologic and geomorphic map (see sheet 10, SIM 3261) of the Offshore of Carpinteria map area, California. The...

  19. Folds--Offshore of Ventura, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of SIM 3254 presents data for folds for the geologic and geomorphic map (see sheet 10, SIM 3254) of the Offshore of Ventura map area, California. The...

  20. Moments of the folded logistic distribution

    Institute of Scientific and Technical Information of China (English)

    Saralees Nadarajah; Samuel Kotz

    2007-01-01

    The recent paper by Cooray et al. introduced the folded logistic distribution. The moments properties given in the paper appear too complicated. In this note, a simple formula is derived in terms of the well known Lerch function.

  1. Cycle 22 COS/NUV Fold Distribution

    Science.gov (United States)

    Wheeler, T.; Welty, A.

    2016-09-01

    We summarize the Cycle 22 COS/NUV Fold Distribution for the Cosmic Origins Spectrograph's (COS) MAMA detector on the Hubble Space Telescope. The detector micro-channel plate's health state is determined and the results are presented.

  2. Protein Folding: A New Geometric Analysis

    OpenAIRE

    Simmons, Walter A.; Joel L. Weiner

    2008-01-01

    A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it is possible that so many initial configurations proceed to fold to a unique final configuration. We put energy and dynamical considerations temporarily aside and focus upon the geometry alone. We parameterize the structure of an idealized protein using the ...

  3. Folding defect affine Toda field theories

    CERN Document Server

    Robertson, C

    2013-01-01

    A folding process is applied to fused a^(1)_r defects to construct defects for the non-simply laced affi?ne Toda ?field theories of c^(1)_n, d^(2)_n and a^(2)_n at the classical level. Support for the hypothesis that these defects are integrable in the folded theories is provided by the observation that transmitted solitons retain their form. Further support is given by the demonstration that energy and momentum are conserved.

  4. [Congenital retinal folds in different clinical cases].

    Science.gov (United States)

    Munteanu, M

    2005-01-01

    We present 12 clinical cases of congenital retinal folds with different etiologies: posterior primitive vitreous persistency and hyperplasia (7 cases),retinocytoma (1 case). retinopathy of prematurity (1 case), astrocytoma of the retina (1 case), retinal vasculitis (1 case), Goldmann-Favre syndrome (1 case). Etiopathogenic and nosological aspects are discussed; the congenital retinal folds are interpreted as a symptom in a context of a congenital or acquired vitreo-retinal pathology.

  5. Some other algebraic properties of folded hypercubes

    CERN Document Server

    Mirafzal, S Morteza

    2011-01-01

    We construct explicity the automorphism group of the folded hypercube $FQ_n$ of dimension $n>3$, as a semidirect product of $N$ by $M$, where $N$ is isomorphic to the Abelian group $Z_2^n$, and $M$ is isomorphic to $Sym(n+1)$, the symmetric group of degree $n+1$, then we will show that the folded hypercube $FQ_n$ is a symmetric graph.

  6. Protein folding, protein homeostasis, and cancer

    Institute of Scientific and Technical Information of China (English)

    John H. Van Drie

    2011-01-01

    Proteins fold into their functional 3-dimensional structures from a linear amino acid sequence. In vitro this process is spontaneous; while in vivo it is orchestrated by a specialized set of proteins, called chaperones. Protein folding is an ongoing cellular process, as cellular proteins constantly undergo synthesis and degradation. Here emerging links between this process and cancer are reviewed. This perspective both yields insights into the current struggle to develop novel cancer chemotherapeutics and has implications for future chemotherapy discovery.

  7. Homology group on manifolds and their foldings

    Directory of Open Access Journals (Sweden)

    M. Abu-Saleem

    2010-03-01

    Full Text Available In this paper, we introduce the definition of the induced unfolding on the homology group. Some types of conditional foldings restricted on the elements of the homology groups are deduced. The effect of retraction on the homology group of a manifold is dicussed. The unfolding of variation curvature of manifolds on their homology group are represented. The relations between homology group of the manifold and its folding are deduced.

  8. Denatured-state energy landscapes of a protein structural database reveal the energetic determinants of a framework model for folding.

    Science.gov (United States)

    Wang, Suwei; Gu, Jenny; Larson, Scott A; Whitten, Steven T; Hilser, Vincent J

    2008-09-19

    Position-specific denatured-state thermodynamics were determined for a database of human proteins by use of an ensemble-based model of protein structure. The results of modeling denatured protein in this manner reveal important sequence-dependent thermodynamic properties in the denatured ensembles as well as fundamental differences between the denatured and native ensembles in overall thermodynamic character. The generality and robustness of these results were validated by performing fold-recognition experiments, whereby sequences were matched with their respective folds based on amino acid propensities for the different energetic environments in the protein, as determined through cluster analysis. Correlation analysis between structure and energetic information revealed that sequence segments destined for beta-sheet in the final native fold are energetically more predisposed to a broader repertoire of states than are sequence segments destined for alpha-helix. These results suggest that within the subensemble of mostly unstructured states, the energy landscapes are dominated by states in which parts of helices adopt structure, whereas structure formation for sequences destined for beta-strand is far less probable. These results support a framework model of folding, which suggests that, in general, the denatured state has evolutionarily evolved to avoid low-energy conformations in sequences that ultimately adopt beta-strand. Instead, the denatured state evolved so that sequence segments that ultimately adopt alpha-helix and coil will have a high intrinsic structure formation capability, thus serving as potential nucleation sites.

  9. Folding of non-Euclidean curved shells

    Science.gov (United States)

    Bende, Nakul; Evans, Arthur; Innes-Gold, Sarah; Marin, Luis; Cohen, Itai; Santangelo, Christian; Hayward, Ryan

    2015-03-01

    Origami-based folding of 2D sheets has been of recent interest for a variety of applications ranging from deployable structures to self-folding robots. Though folding of planar sheets follows well-established principles, folding of curved shells involves an added level of complexity due to the inherent influence of curvature on mechanics. In this study, we use principles from differential geometry and thin shell mechanics to establish fundamental rules that govern folding of prototypical creased shells. In particular, we show how the normal curvature of a crease line controls whether the deformation is smooth or discontinuous, and investigate the influence of shell thickness and boundary conditions. We show that snap-folding of shells provides a route to rapid actuation on time-scales dictated by the speed of sound. The simple geometric design principles developed can be applied at any length-scale, offering potential for bio-inspired soft actuators for tunable optics, microfluidics, and robotics. This work was funded by the National Science Foundation through EFRI ODISSEI-1240441 with additional support to S.I.-G. through the UMass MRSEC DMR-0820506 REU program.

  10. A Survey of Protein Fold Recognition Algorithms

    Directory of Open Access Journals (Sweden)

    M. S. Abual-Rub

    2008-01-01

    Full Text Available Problem statement: Predicting the tertiary structure of proteins from their linear sequence is really a big challenge in biology. This challenge is related to the fact that the traditional computational methods are not powerful enough to search for the correct structure in the huge conformational space. This inadequate capability of the computational methods, however, is a major obstacle in facing this problem. Trying to solve the problem of the protein fold recognition, most of the researchers have examined the use of the protein threading technique. This problem is known as NP-hard; researchers have used various methods such as neural networks, Monte Carlo, support vector machine and genetic algorithms to solve it. Some researchers tried the use of the parallel evolutionary methods for protein fold recognition but it is less well known. Approach: We reviewed various algorithms that have been developed for protein structure prediction by threading and fold recognition. Moreover, we provided a survey of parallel evolutionary methods for protein fold recognition. Results: The findings of this survey showed that evolutionary methods can be used to resolve the protein fold recognition problem. Conclusion: There are two aspects of protein fold recognition problem: First is the computational difficulty and second is that current energy functions are still not accurate enough to calculate the free energy of a given conformation.

  11. On the origin of the histone fold

    Directory of Open Access Journals (Sweden)

    Söding Johannes

    2007-03-01

    Full Text Available Abstract Background Histones organize the genomic DNA of eukaryotes into chromatin. The four core histone subunits consist of two consecutive helix-strand-helix motifs and are interleaved into heterodimers with a unique fold. We have searched for the evolutionary origin of this fold using sequence and structure comparisons, based on the hypothesis that folded proteins evolved by combination of an ancestral set of peptides, the antecedent domain segments. Results Our results suggest that an antecedent domain segment, corresponding to one helix-strand-helix motif, gave rise divergently to the N-terminal substrate recognition domain of Clp/Hsp100 proteins and to the helical part of the extended ATPase domain found in AAA+ proteins. The histone fold arose subsequently from the latter through a 3D domain-swapping event. To our knowledge, this is the first example of a genetically fixed 3D domain swap that led to the emergence of a protein family with novel properties, establishing domain swapping as a mechanism for protein evolution. Conclusion The helix-strand-helix motif common to these three folds provides support for our theory of an 'ancient peptide world' by demonstrating how an ancestral fragment can give rise to 3 different folds.

  12. Structural characteristics of novel protein folds.

    Directory of Open Access Journals (Sweden)

    Narcis Fernandez-Fuentes

    2010-04-01

    Full Text Available Folds are the basic building blocks of protein structures. Understanding the emergence of novel protein folds is an important step towards understanding the rules governing the evolution of protein structure and function and for developing tools for protein structure modeling and design. We explored the frequency of occurrences of an exhaustively classified library of supersecondary structural elements (Smotifs, in protein structures, in order to identify features that would define a fold as novel compared to previously known structures. We found that a surprisingly small set of Smotifs is sufficient to describe all known folds. Furthermore, novel folds do not require novel Smotifs, but rather are a new combination of existing ones. Novel folds can be typified by the inclusion of a relatively higher number of rarely occurring Smotifs in their structures and, to a lesser extent, by a novel topological combination of commonly occurring Smotifs. When investigating the structural features of Smotifs, we found that the top 10% of most frequent ones have a higher fraction of internal contacts, while some of the most rare motifs are larger, and contain a longer loop region.

  13. Geometric U-folds in four dimensions

    CERN Document Server

    Lazaroiu, C I

    2016-01-01

    We describe a general construction of geometric U-folds compatible with the global formulation of four-dimensional extended supergravity on a differentiable spin manifold. The topology of geometric U-folds depends on certain fiber bundles which encode how supergravity fields are globally glued together. Smooth non-trivial U-folds of this type can exist only in theories where both the scalar and space-time manifolds have non-trivial fundamental group and in addition the configuration of scalar fields of the solution is homotopically non-trivial. Nonetheless, certain geometric U-folds extend to simply-connected backgrounds containing localized sources. Consistency with string theory requires smooth geometric U-folds to be glued using subgroups of the effective discrete U-duality group, implying that the fundamental group of the scalar manifold of such solutions must be a subgroup of the latter. We construct simple examples of geometric U-folds in a generalization of the axion-dilaton model of N=2 supergravity c...

  14. Data visualization

    CERN Document Server

    Azzam, Tarek

    2013-01-01

    Do you communicate data and information to stakeholders? In Part 1, we introduce recent developments in the quantitative and qualitative data visualization field and provide a historical perspective on data visualization, its potential role in evaluation practice, and future directions. Part 2 delivers concrete suggestions for optimally using data visualization in evaluation, as well as suggestions for best practices in data visualization design. It focuses on specific quantitative and qualitative data visualization approaches that include data dashboards, graphic recording, and geographic information systems (GIS). Readers will get a step-by-step process for designing an effective data dashboard system for programs and organizations, and various suggestions to improve their utility.

  15. Mesoscopic non-equilibrium thermodynamics

    Directory of Open Access Journals (Sweden)

    Rubi, Jose' Miguel

    2008-02-01

    Full Text Available Basic concepts like energy, heat, and temperature have acquired a precise meaning after the development of thermodynamics. Thermodynamics provides the basis for understanding how heat and work are related and with the general rules that the macroscopic properties of systems at equilibrium follow. Outside equilibrium and away from macroscopic regimes most of those rules cannot be applied directly. In this paper we present recent developments that extend the applicability of thermodynamic concepts deep into mesoscopic and irreversible regimes. We show how the probabilistic interpretation of thermodynamics together with probability conservation laws can be used to obtain kinetic equations describing the evolution of the relevant degrees of freedom. This approach provides a systematic method to obtain the stochastic dynamics of a system directly from the knowledge of its equilibrium properties. A wide variety of situations can be studied in this way, including many that were thought to be out of reach of thermodynamic theories, such as non-linear transport in the presence of potential barriers, activated processes, slow relaxation phenomena, and basic processes in biomolecules, like translocation and stretching.

  16. Black hole thermodynamics in finite time

    CERN Document Server

    Gruber, Christine

    2016-01-01

    Finite-time thermodynamics provides the means to revisit ideal thermodynamic equilibrium processes in the light of reality and investigate the energetic "price of haste", i.e. the consequences of carrying out a process in finite time, when perfect equilibrium cannot be awaited due to economic reasons or the nature of the process. Employing the formalism of geometric thermodynamics, a lower bound on the energy dissipated during a process is derived from the thermodynamic length of that process. The notion of length is hereby defined via a metric structure on the space of equilibrium thermodynamics, spanned by a set of thermodynamic variables describing the system. Since the aim of finite-time thermodynamics is to obtain realistic limitations on idealized scenarios, it is a useful tool to reassess the efficiency of thermodynamic processes. We examine its implications for black hole thermodynamics, in particular scenarios inspired by the Penrose process, a thought experiment by which work can be extracted from a...

  17. Thermodynamics and time-directional invariance

    CERN Document Server

    Klimenko, A Y

    2012-01-01

    Time directions are not invariant in conventional thermodynamics. We broadly follow ideas of Ludwig Boltzmann and investigate implications of postulating time-directional invariance in thermodynamics. In this investigation, we require that thermodynamic descriptions are not changed under time reversal accompanied by replacement of matter by antimatter (i.e. CPT-invariant thermodynamics). The matter and antimatter are defined as thermodynamic concepts without detailing their physical structure. Our analysis stays within the limits of conceptual thermodynamics and leads to effective negative temperatures, to thermodynamic restrictions on time travel and to inherent antagonism of matter and antimatter. This antagonism is purely thermodynamic; it explains the difficulty in achieving thermodynamic equilibrium between matter and antimatter and does not postulate their mutual annihilation on contact. We believe that the conclusions of this work can be of interest not only for people researching or teaching thermodyn...

  18. Bridging Experiments and Native-Centric Simulations of a Downhill Folding Protein.

    Science.gov (United States)

    Naganathan, Athi N; De Sancho, David

    2015-11-25

    Experiments and atomistic simulations have independently contributed to the mechanistic understanding of protein folding. However, a coherent detailed picture explicitly combining both is currently lacking, a problem that seriously limits the amount of information that can be extracted. An alternative to atomistic models with physics-based potentials is the native-centric (i.e., Go̅ type) coarse-grained models, which for many years have been successfully employed to qualitatively understand features of protein folding energy landscapes. Again, quantitative validation of Go̅ models against experimental equilibrium unfolding curves is often not attempted. Here we use an atomistic topology-based model to study the folding mechanism of PDD, a protein that folds over a marginal thermodynamic barrier of ∼0.5 kBT at midpoint conditions. We find that the simulations are in exquisite agreement with several equilibrium experimental measurements including differential scanning calorimetry (DSC), an observable that is possibly the most challenging to reproduce from explicit-chain models. The dynamics, inferred using a detailed Markov state model, display a classical Chevron-like trend with a continuum of relaxation times under both folding and unfolding conditions, a signature feature of downhill folding. The number of populated microstates and the connectivity between them are shown to be temperature dependent with a maximum near the thermal denaturation midpoint, thus linking the macroscopic observation of a peak in the DSC profile of downhill folding proteins and the underlying microstate dynamics. The mechanistic picture derived from our analysis thus sheds light on the intricate and tunable nature of the downhill protein folding ensembles. In parallel, our work highlights the power of coarse-grained models to reproduce experiments at a quantitative level while also pointing at specific directions for their improvement.

  19. Bridging the Gap Between In Vitro and In Vivo RNA Folding

    Science.gov (United States)

    Leamy, Kathleen A.; Assmann, Sarah M.; Mathews, David H.; Bevilacqua, Philip C.

    2017-01-01

    Deciphering the folding pathways and predicting the structures of complex three-dimensional biomolecules is central to elucidating biological function. RNA is single-stranded, which gives it the freedom to fold into complex secondary and tertiary structures. These structures endow RNA with the ability to perform complex chemistries and functions ranging from enzymatic activity to gene regulation. Given that RNA is involved in many essential cellular processes, it is critical to understand how it folds and functions in vivo. Within the last few years, methods have been developed to probe RNA structures in vivo and genome-wide. These studies reveal that RNA often adopts very different structures in vivo and in vitro, and provide profound insights into RNA biology. Nonetheless, both in vitro and in vivo approaches have limitations: studies in the complex and uncontrolled cellular environment make it difficult to obtain insight into RNA folding pathways and thermodynamics, and studies in vitro often lack direct cellular relevance, leaving a gap in our knowledge of RNA folding in vivo. This gap is being bridged by biophysical and mechanistic studies of RNA structure and function under conditions that mimic the cellular environment. To date, most artificial cytoplasms have used various polymers as molecular crowding agents and a series of small molecules as cosolutes. Studies under such in vivo-like conditions are yielding fresh insights, such as cooperative folding of functional RNAs and increased activity of ribozymes. These observations are accounted for in part by molecular crowding effects and interactions with other molecules. In this review, we report milestones in RNA folding in vitro and in vivo and discuss ongoing experimental and computational efforts to bridge the gap between these two conditions in order to understand how RNA folds in the cell. PMID:27658939

  20. Frnakenstein: multiple target inverse RNA folding

    Directory of Open Access Journals (Sweden)

    Lyngsø Rune B

    2012-10-01

    Full Text Available Abstract Background RNA secondary structure prediction, or folding, is a classic problem in bioinformatics: given a sequence of nucleotides, the aim is to predict the base pairs formed in its three dimensional conformation. The inverse problem of designing a sequence folding into a particular target structure has only more recently received notable interest. With a growing appreciation and understanding of the functional and structural properties of RNA motifs, and a growing interest in utilising biomolecules in nano-scale designs, the interest in the inverse RNA folding problem is bound to increase. However, whereas the RNA folding problem from an algorithmic viewpoint has an elegant and efficient solution, the inverse RNA folding problem appears to be hard. Results In this paper we present a genetic algorithm approach to solve the inverse folding problem. The main aims of the development was to address the hitherto mostly ignored extension of solving the inverse folding problem, the multi-target inverse folding problem, while simultaneously designing a method with superior performance when measured on the quality of designed sequences. The genetic algorithm has been implemented as a Python program called Frnakenstein. It was benchmarked against four existing methods and several data sets totalling 769 real and predicted single structure targets, and on 292 two structure targets. It performed as well as or better at finding sequences which folded in silico into the target structure than all existing methods, without the heavy bias towards CG base pairs that was observed for all other top performing methods. On the two structure targets it also performed well, generating a perfect design for about 80% of the targets. Conclusions Our method illustrates that successful designs for the inverse RNA folding problem does not necessarily have to rely on heavy biases in base pair and unpaired base distributions. The design problem seems to become more

  1. 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.

  2. 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...

  3. Nanofluidics thermodynamic and transport properties

    CERN Document Server

    Michaelides, Efstathios E (Stathis)

    2014-01-01

    This volume offers a comprehensive examination of the subject of heat and mass transfer with nanofluids as well as a critical review of the past and recent research projects in this area. Emphasis is placed on the fundamentals of the transport processes using particle-fluid suspensions, such as nanofluids. The nanofluid research is examined and presented in a holistic way using a great deal of our experience with the subjects of continuum mechanics, statistical thermodynamics, and non-equilibrium thermodynamics of transport processes. Using a thorough database, the experimental, analytical, and numerical advances of recent research in nanofluids are critically examined and connected to past research with medium and fine particles as well as to functional engineering systems. Promising applications and technological issues of heat/mass transfer system design with nanofluids are also discussed. This book also: Provides a deep scientific analysis of nanofluids using classical thermodynamics and statistical therm...

  4. Non-hermitian quantum thermodynamics

    Science.gov (United States)

    Gardas, Bartłomiej; Deffner, Sebastian; Saxena, Avadh

    2016-03-01

    Thermodynamics is the phenomenological theory of heat and work. Here we analyze to what extent quantum thermodynamic relations are immune to the underlying mathematical formulation of quantum mechanics. As a main result, we show that the Jarzynski equality holds true for all non-hermitian quantum systems with real spectrum. This equality expresses the second law of thermodynamics for isothermal processes arbitrarily far from equilibrium. In the quasistatic limit however, the second law leads to the Carnot bound which is fulfilled even if some eigenenergies are complex provided they appear in conjugate pairs. Furthermore, we propose two setups to test our predictions, namely with strongly interacting excitons and photons in a semiconductor microcavity and in the non-hermitian tight-binding model.

  5. Non-hermitian quantum thermodynamics.

    Science.gov (United States)

    Gardas, Bartłomiej; Deffner, Sebastian; Saxena, Avadh

    2016-03-22

    Thermodynamics is the phenomenological theory of heat and work. Here we analyze to what extent quantum thermodynamic relations are immune to the underlying mathematical formulation of quantum mechanics. As a main result, we show that the Jarzynski equality holds true for all non-hermitian quantum systems with real spectrum. This equality expresses the second law of thermodynamics for isothermal processes arbitrarily far from equilibrium. In the quasistatic limit however, the second law leads to the Carnot bound which is fulfilled even if some eigenenergies are complex provided they appear in conjugate pairs. Furthermore, we propose two setups to test our predictions, namely with strongly interacting excitons and photons in a semiconductor microcavity and in the non-hermitian tight-binding model.

  6. Local non-equilibrium thermodynamics.

    Science.gov (United States)

    Jinwoo, Lee; Tanaka, Hajime

    2015-01-16

    Local Shannon entropy lies at the heart of modern thermodynamics, with much discussion of trajectory-dependent entropy production. When taken at both boundaries of a process in phase space, it reproduces the second law of thermodynamics over a finite time interval for small scale systems. However, given that entropy is an ensemble property, it has never been clear how one can assign such a quantity locally. Given such a fundamental omission in our knowledge, we construct a new ensemble composed of trajectories reaching an individual microstate, and show that locally defined entropy, information, and free energy are properties of the ensemble, or trajectory-independent true thermodynamic potentials. We find that the Boltzmann-Gibbs distribution and Landauer's principle can be generalized naturally as properties of the ensemble, and that trajectory-free state functions of the ensemble govern the exact mechanism of non-equilibrium relaxation.

  7. Thermodynamic Calculations for Systems Biocatalysis

    DEFF Research Database (Denmark)

    Abu, Rohana; Gundersen, Maria T.; Woodley, John M.

    2015-01-01

    on the basis of kinetics. However, many of the most interesting non-natural chemical reactions which could potentially be catalysed by enzymes, are thermodynamically unfavourable and are thus limited by the equilibrium position of the reaction. A good example is the enzyme ω-transaminase, which catalyses......‘Systems Biocatalysis’ is a term describing multi-enzyme processes in vitro for the synthesis of chemical products. Unlike in-vivo systems, such an artificial metabolism can be controlled in a highly efficient way in order to achieve a sufficiently favourable conversion for a given target product...... the transamination of a pro-chiral ketone into a chiral amine (interesting in many pharmaceutical applications). Here, the products are often less energetically stable than the reactants, meaning that the reaction may be thermodynamically unfavourable. As in nature, such thermodynamically-challenged reactions can...

  8. Complexation thermodynamics of modified cyclodextrins

    DEFF Research Database (Denmark)

    Schönbeck, Jens Christian Sidney; Westh, Peter; Holm, Rene

    2014-01-01

    Inclusion complexes between two bile salts and a range of differently methylated β-cyclodextrins were studied in an attempt to rationalize the complexation thermodynamics of modified cyclodextrins. Calorimetric titrations at a range of temperatures provided precise values of the enthalpies (ΔH......°), entropies (ΔS°), and heat capacities (ΔCp) of complexation, while molecular dynamics simulations assisted the interpretation of the obtained thermodynamic parameters. As previously observed for several types of modified cyclodextrins, the substituents at the rims of the cyclodextrin induced large changes......° and then a strong decrease when the degree of substitution exceeded some threshold. Exactly the same trend was observed for ΔCp. The dehydration of nonpolar surface, as quantified by the simulations, can to a large extent explain the variation in the thermodynamic parameters. The methyl substituents form additional...

  9. Statistical thermodynamics of clustered populations.

    Science.gov (United States)

    Matsoukas, Themis

    2014-08-01

    We present a thermodynamic theory for a generic population of M individuals distributed into N groups (clusters). We construct the ensemble of all distributions with fixed M and N, introduce a selection functional that embodies the physics that governs the population, and obtain the distribution that emerges in the scaling limit as the most probable among all distributions consistent with the given physics. We develop the thermodynamics of the ensemble and establish a rigorous mapping to regular thermodynamics. We treat the emergence of a so-called giant component as a formal phase transition and show that the criteria for its emergence are entirely analogous to the equilibrium conditions in molecular systems. We demonstrate the theory by an analytic model and confirm the predictions by Monte Carlo simulation.

  10. Hessian geometry and entanglement thermodynamics

    CERN Document Server

    Matsueda, Hiroaki

    2015-01-01

    We reconstruct entanglement thermodynamics by means of Hessian geometry, since this method exactly generalizes thermodynamics into much wider exponential family cases including quantum entanglement. Starting with the correct first law of entanglement thermodynamics, we derive that a proper choice of the Hessian potential leads to both of the entanglement entropy scaling for quantum critical systems and hyperbolic metric (or AdS space with imaginary time). We also derive geometric representation of the entanglement entropy in which the entropy is described as integration of local conserved current of information flowing across an entangling surface. We find that the entangling surface is equivalent to the domain boundary of the Hessian potential. This feature originates in a special property of critical systems in which we can identify the entanglement entropy with the Hessian potential after the second derivative by the canonical parameters, and this identification guarantees violation of extensive nature of ...

  11. Understanding the influence of codon translation rates on cotranslational protein folding.

    Science.gov (United States)

    O'Brien, Edward P; Ciryam, Prajwal; Vendruscolo, Michele; Dobson, Christopher M

    2014-05-20

    Protein domains can fold into stable tertiary structures while they are synthesized by the ribosome in a process known as cotranslational folding. If a protein does not fold cotranslationally, however, it has the opportunity to do so post-translationally, that is, after the nascent chain has been fully synthesized and released from the ribosome. The rate at which a ribosome adds an amino acid encoded by a particular codon to the elongating nascent chain can vary significantly and is called the codon translation rate. Recent experiments have illustrated the profound impact that codon translation rates can have on the cotranslational folding process and the acquisition of function by nascent proteins. Synonymous codon mutations in an mRNA molecule change the chemical identity of a codon and its translation rate without changing the sequence of the synthesized protein. This change in codon translation rate can, however, cause a nascent protein to malfunction as a result of cotranslational misfolding. In some situations, such dysfunction can have profound implications; for example, it can alter the substrate specificity of an ABC transporter protein, resulting in patients who are nonresponsive to chemotherapy treatment. Thus, codon translation rates are crucial in coordinating protein folding in a cellular environment and can affect downstream cellular processes that depend on the proper functioning of newly synthesized proteins. As the importance of codon translation rates makes clear, a necessary aspect of fully understanding cotranslational folding lies in considering the kinetics of the process in addition to its thermodynamics. In this Account, we examine the contributions that have been made to elucidating the mechanisms of cotranslational folding by using the theoretical and computational tools of chemical kinetics, molecular simulations, and systems biology. These efforts have extended our ability to understand, model, and predict the influence of codon

  12. Thermodynamic equivalence of spin systems

    Energy Technology Data Exchange (ETDEWEB)

    Beltman, J.M. (Katholieke Universiteit Nijmegen (Netherlands))

    1975-01-01

    The thermodynamic equilibrium properties of systems composed of classical spin /sup 1///sub 2/ particles (Ising spins) are studied. Given an interaction pattern between the Ising spins the main problem is to calculate the equilibrium state(s) of the system. The point put forward here is the existence of many thermodynamical equivalent spin coordinate systems. As a consequence of this phenomenon the interaction pattern of a system may be very intricate when described with respect to one spin coordinate system whereas it may become simple with respect to another one and vice versa. A systematic investigation of this phenomenon is made. (FR)

  13. Information thermodynamics on causal networks.

    Science.gov (United States)

    Ito, Sosuke; Sagawa, Takahiro

    2013-11-01

    We study nonequilibrium thermodynamics of complex information flows induced by interactions between multiple fluctuating systems. Characterizing nonequilibrium dynamics by causal networks (i.e., Bayesian networks), we obtain novel generalizations of the second law of thermodynamics and the fluctuation theorem, which include an informational quantity characterized by the topology of the causal network. Our result implies that the entropy production in a single system in the presence of multiple other systems is bounded by the information flow between these systems. We demonstrate our general result by a simple model of biochemical adaptation.

  14. Density perturbations with relativistic thermodynamics

    CERN Document Server

    Maartens, R

    1997-01-01

    We investigate cosmological density perturbations in a covariant and gauge- invariant formalism, incorporating relativistic causal thermodynamics to give a self-consistent description. The gradient of density inhomogeneities splits covariantly into a scalar part, a rotational vector part that is determined by the vorticity, and a tensor part that describes the shape. We give the evolution equations for these parts in the general dissipative case. Causal thermodynamics gives evolution equations for viswcous stress and heat flux, which are coupled to the density perturbation equation and to the entropy and temperature perturbation equations. We give the full coupled system in the general dissipative case, and simplify the system in certain cases.

  15. Thermodynamics of Dipolar Chain Systems

    DEFF Research Database (Denmark)

    R. Armstrong, J.; Zinner, Nikolaj Thomas; V. Fedorov, D.

    2012-01-01

    The thermodynamics of a quantum system of layers containing perpendicularly oriented dipolar molecules is studied within an oscillator approximation for both bosonic and fermionic species. The system is assumed to be built from chains with one molecule in each layer. We consider the effects...... numerically. Our findings indicate that thermodynamic observables, such as the heat capacity, can be used to probe the signatures of the intralayer interaction between chains. This should be relevant for near future experiments on polar molecules with strong dipole moments....

  16. Applied Thermodynamics: Grain Boundary Segregation

    Directory of Open Access Journals (Sweden)

    Pavel Lejček

    2014-03-01

    Full Text Available Chemical composition of interfaces—free surfaces and grain boundaries—is generally described by the Langmuir–McLean segregation isotherm controlled by Gibbs energy of segregation. Various components of the Gibbs energy of segregation, the standard and the excess ones as well as other thermodynamic state functions—enthalpy, entropy and volume—of interfacial segregation are derived and their physical meaning is elucidated. The importance of the thermodynamic state functions of grain boundary segregation, their dependence on volume solid solubility, mutual solute–solute interaction and pressure effect in ferrous alloys is demonstrated.

  17. Chapter 3: A fluorescent window into protein folding and aggregation in cells.

    Science.gov (United States)

    Ignatova, Zoya; Gierasch, Lila M

    2008-01-01

    Evolutionary selective pressures have tuned the efficiency of the protein-folding reaction in the crowded complex environment in the cell. Nevertheless, the fidelity of folding is imperfect, leading to off-pathway intermolecular interactions that compete with proper folding and to consequent formation of thermodynamically stable aggregates. Such aggregates constitute the histopathological hallmarks of many neurodegenerative pathologies. Yet, most of the approaches to characterize protein folding and/or misfolding are limited to in vitro conditions. Here, we describe a strategy to directly monitor the behavior of a protein in prokaryotic and eukaryotic cells. The method is based on incorporation of structurally non-perturbing, specific binding motifs for a bis-arsenical fluoroscein dye, FlAsH, in sites that result in distinct dye fluorescence signals for the folded and unfolded states of the protein under study. Our approach has been developed using as a case study the predominantly beta-sheet intracellular lipid-binding protein, cellular retinoic acid-binding protein, alone or as a chimera fused to the exon 1-encoded fragment of huntingtin, which harbors a polyglutamine repeat tract. We have designed protocols to label this protein in vivo and to monitor the resulting fluorescence signal, which reports on any misfolding transition and formation of aggregates, yielding quantitatively interpretable data.

  18. 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.

  19. Petrofabric test of viscous folding theory

    Science.gov (United States)

    Onasch, Charles M.

    1984-06-01

    Compression and extension axes are deduced from quartz deformation lamellae in a quartzite and a graywacke folded into an asymetrical syncline. Deformation lamellae fabrics in the two sandstones are distinctly different. In the graywacke, regardless of bedding orientation or position on the fold, compression axes are normal or nearly normal to the axial planar rough cleavage. Extension axes generally lie in the cleavage plane, parallel to dip. In most quartzite samples, compression axes are parallel or subparallel to bedding, at high angles to the fold axis and extension axes are normal to bedding. Two samples from the very base of the formation indicate compression parallel to the fold axis with extension parallel to bedding, at high angles to the fold axis. One of these two shows both patterns. The lamellae fabric geometry in these two samples suggests the presence of a neutral surface in the quartzite. The lamellae-derived compression and extension axes are in good agreement with the buckling behavior of a viscous layer (quartzite) embedded in a less viscous medium (graywacke and shale below and shale and carbonate above).

  20. Bifurcation of self-folded polygonal bilayers

    Science.gov (United States)

    Abdullah, Arif M.; Braun, Paul V.; Hsia, K. Jimmy

    2017-09-01

    Motivated by the self-assembly of natural systems, researchers have investigated the stimulus-responsive curving of thin-shell structures, which is also known as self-folding. Self-folding strategies not only offer possibilities to realize complicated shapes but also promise actuation at small length scales. Biaxial mismatch strain driven self-folding bilayers demonstrate bifurcation of equilibrium shapes (from quasi-axisymmetric doubly curved to approximately singly curved) during their stimulus-responsive morphing behavior. Being a structurally instable, bifurcation could be used to tune the self-folding behavior, and hence, a detailed understanding of this phenomenon is appealing from both fundamental and practical perspectives. In this work, we investigated the bifurcation behavior of self-folding bilayer polygons. For the mechanistic understanding, we developed finite element models of planar bilayers (consisting of a stimulus-responsive and a passive layer of material) that transform into 3D curved configurations. Our experiments with cross-linked Polydimethylsiloxane samples that change shapes in organic solvents confirmed our model predictions. Finally, we explored a design scheme to generate gripper-like architectures by avoiding the bifurcation of stimulus-responsive bilayers. Our research contributes to the broad field of self-assembly as the findings could motivate functional devices across multiple disciplines such as robotics, artificial muscles, therapeutic cargos, and reconfigurable biomedical devices.

  1. Folding at the birth of the nascent chain: coordinating translation with co-translational folding.

    Science.gov (United States)

    Zhang, Gong; Ignatova, Zoya

    2011-02-01

    In the living cells, the folding of many proteins is largely believed to begin co-translationally, during their biosynthesis at the ribosomes. In the ribosomal tunnel, the nascent peptide may establish local interactions and stabilize α-helical structures. Long-range contacts are more likely outside the ribosomes after release of larger segments of the nascent chain. Examples suggest that domains can attain native-like structure on the ribosome with and without population of folding intermediates. The co-translational folding is limited by the speed of the gradual extrusion of the nascent peptide which imposes conformational restraints on its folding landscape. Recent experimental and in silico modeling studies indicate that translation kinetics fine-tunes co-translational folding by providing a time delay for sequential folding of distinct portions of the nascent chain.

  2. Understanding the folding process of synthetic polymers by small-molecule folding agents

    Indian Academy of Sciences (India)

    S G Ramkumar; S Ramakrishnan

    2008-01-01

    Two acceptor containing polyimides PDI and NDI carrying pyromellitic diimide units and 1,4,5,8-naphthalene tetracarboxy diimide units, respectively, along with hexa(oxyethylene) (EO6) segments as linkers, were prepared from the corresponding dianhydrides and diamines. These polyimides were made to fold by interaction with specifically designed folding agents containing a dialkoxynaphthalene (DAN) donor linked to a carboxylic acid group. The alkali-metal counter-ion of the donor carboxylic acid upon complexation with the EO6 segment brings the DAN unit in the right location to induce a charge-transfer complex formation with acceptor units in the polymer backbone. This two-point interaction between the folding agent and the polymer backbone leads to a folding of the polymer chain, which was readily monitored by NMR titrations. The effect of various parameters, such as structures of the folding agent and polymer, and the solvent composition, on the folding propensities of the polymer was studied.

  3. Non-cylindrical fold growth in the Zagros fold and thrust belt (Kurdistan, NE-Iraq)

    Science.gov (United States)

    Bartl, Nikolaus; Bretis, Bernhard; Grasemann, Bernhard; Lockhart, Duncan

    2010-05-01

    The Zagros mountains extends over 1800 km from Kurdistan in N-Iraq to the Strait of Hormuz in Iran and is one of the world most promising regions for the future hydrocarbon exploration. The Zagros Mountains started to form as a result of the collision between the Eurasian and Arabian Plates, whose convergence began in the Late Cretaceous as part of the Alpine-Himalayan orogenic system. Geodetic and seismological data document that both plates are still converging and that the fold and thrust belt of the Zagros is actively growing. Extensive hydrocarbon exploration mainly focuses on the antiforms of this fold and thrust belt and therefore the growth history of the folds is of great importance. This work investigates by means of structural field work and quantitative geomorphological techniques the progressive fold growth of the Permam, Bana Bawi- and Safeen- Anticlines located in the NE of the city of Erbil in the Kurdistan region of Northern Iraq. This part of the Zagros fold and thrust belt belongs to the so-called Simply Folded Belt, which is dominated by gentle to open folding. Faults or fault related folds have only minor importance. The mechanical anisotropy of the formations consisting of a succession of relatively competent (massive dolomite and limestone) and incompetent (claystone and siltstone) sediments essentially controls the deformation pattern with open to gentle parallel folding of the competent layers and flexural flow folding of the incompetent layers. The characteristic wavelength of the fold trains is around 10 km. Due to faster erosion of the softer rock layers in the folded sequence, the more competent lithologies form sharp ridges with steeply sloping sides along the eroded flanks of the anticlines. Using an ASTER digital elevation model in combination with geological field data we quantified 250 drainage basins along the different limbs of the subcylindrical Permam, Bana Bawi- and Safeen- Anticlines. Geomorphological indices of the drainage

  4. The Risk of Vocal Fold Atrophy after Serial Corticosteroid Injections of the Vocal Fold.

    Science.gov (United States)

    Shi, Lucy L; Giraldez-Rodriguez, Laureano A; Johns, Michael M

    2016-11-01

    The aim of this study was to illustrate the risk of vocal fold atrophy in patients who receive serial subepithelial steroid injections for vocal fold scar. This study is a retrospective case report of two patients who underwent a series of weekly subepithelial infusions of 10 mg/mL dexamethasone for benign vocal fold lesion. Shortly after the procedures, both patients developed a weak and breathy voice. The first patient was a 53-year-old man with radiation-induced vocal fold stiffness. Six injections were performed unilaterally, and 1 week later, he developed unilateral vocal fold atrophy with new glottal insufficiency. The second patient was a 67-year-old woman with severe vocal fold inflammation related to laryngitis and calcinosis, Raynaud's phenomenon, esophagean dysmotility, sclerodactyly, and telangiectasia (CREST) syndrome. Five injections were performed bilaterally, and 1 week later, she developed bilateral vocal fold atrophy with a large midline glottal gap during phonation. In both cases, the steroid-induced vocal atrophy resolved spontaneously after 4 months. Serial subepithelial steroid infusions of the vocal folds, although safe in the majority of patients, carry the risk of causing temporary vocal fold atrophy when given at short intervals. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  5. Transversal Clifford gates on folded surface codes

    Science.gov (United States)

    Moussa, Jonathan E.

    2016-10-01

    Surface and color codes are two forms of topological quantum error correction in two spatial dimensions with complementary properties. Surface codes have lower-depth error detection circuits and well-developed decoders to interpret and correct errors, while color codes have transversal Clifford gates and better code efficiency in the number of physical qubits needed to achieve a given code distance. A formal equivalence exists between color codes and folded surface codes, but it does not guarantee the transferability of any of these favorable properties. However, the equivalence does imply the existence of constant-depth circuit implementations of logical Clifford gates on folded surface codes. We achieve and improve this result by constructing two families of folded surface codes with transversal Clifford gates. This construction is presented generally for qudits of any dimension. The specific application of these codes to universal quantum computation based on qubit fusion is also discussed.

  6. Experimental Identification of Downhill Protein Folding

    Science.gov (United States)

    Garcia-Mira, Maria M.; Sadqi, Mourad; Fischer, Niels; Sanchez-Ruiz, Jose M.; Muñoz, Victor

    2002-12-01

    Theory predicts the existence of barrierless protein folding. Without barriers, folding should be noncooperative and the degree of native structure should be coupled to overall protein stability. We investigated the thermal unfolding of the peripheral subunit binding domain from Escherichia coli's 2-oxoglutarate dehydrogenase multienzyme complex (termed BBL) with a combination of spectroscopic techniques and calorimetry. Each technique probed a different feature of protein structure. BBL has a defined three-dimensional structure at low temperatures. However, each technique showed a distinct unfolding transition. Global analysis with a statistical mechanical model identified BBL as a downhill-folding protein. Because of BBL's biological function, we propose that downhill folders may be molecular rheostats, in which effects could be modulated by altering the distribution of an ensemble of structures.

  7. Improvement of a Vocal Fold Imaging System

    Energy Technology Data Exchange (ETDEWEB)

    Krauter, K. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-02-01

    Medical professionals can better serve their patients through continual update of their imaging tools. A wide range of pathologies and disease may afflict human vocal cords or, as they’re also known, vocal folds. These diseases can affect human speech hampering the ability of the patient to communicate. Vocal folds must be opened for breathing and the closed to produce speech. Currently methodologies to image markers of potential pathologies are difficult to use and often fail to detect early signs of disease. These current methodologies rely on a strobe light and slower frame rate camera in an attempt to obtain images as the vocal folds travel over the full extent of their motion.

  8. Symmetric Circular Matchings and RNA Folding

    DEFF Research Database (Denmark)

    Hofacker, Ivo L.; Reidys, Christian; Stadler, Peter F.

    2012-01-01

    RNA secondary structures can be computed as optimal solutions of certain circular matching problems. An accurate treatment of this energy minimization problem has to account for the small --- but non-negligible --- entropic destabilization of secondary structures with non-trivial automorphisms....... Such intrinsic symmetries are typically excluded from algorithmic approaches, however, because the effects are small, they play a role only for RNAs with symmetries at sequence level, and they appear only in particular settings that are less frequently used in practical application, such as circular folding...... or the co-folding of two or more identical RNAs. Here, we show that the RNA folding problem with symmetry terms can still be solved with polynomial-time algorithms. Empirically, the fraction of symmetric ground state structures decreases with chain length, so that the error introduced by neglecting...

  9. Assessing Coupled Protein Folding and Binding Through Temperature-Dependent Isothermal Titration Calorimetry.

    Science.gov (United States)

    Sahu, Debashish; Bastidas, Monique; Lawrence, Chad W; Noid, William G; Showalter, Scott A

    2016-01-01

    Broad interest in the thermodynamic driving forces of coupled macromolecular folding and binding is motivated by the prevalence of disorder-to-order transitions observed when intrinsically disordered proteins (IDPs) bind to their partners. Isothermal titration calorimetry (ITC) is one of the few methods available for completely evaluating the thermodynamic parameters describing a protein-ligand binding event. Significantly, when the effective ΔH° for the coupled folding and binding process is determined by ITC in a temperature series, the constant-pressure heat capacity change (ΔCp) associated with these coupled equilibria is experimentally accessible, offering a unique opportunity to investigate the driving forces behind them. Notably, each of these molecular-scale events is often accompanied by strongly temperature-dependent enthalpy changes, even over the narrow temperature range experimentally accessible for biomolecules, making single temperature determinations of ΔH° less informative than typically assumed. Here, we will document the procedures we have adopted in our laboratory for designing, executing, and globally analyzing temperature-dependent ITC studies of coupled folding and binding in IDP interactions. As a biologically significant example, our recent evaluation of temperature-dependent interactions between the disordered tail of FCP1 and the winged-helix domain from Rap74 will be presented. Emphasis will be placed on the use of publically available analysis programs written in MATLAB that facilitate quantification of the thermodynamic forces governing IDP interactions. Although motivated from the perspective of IDPs, the experimental design principles and data fitting procedures presented here are general to the study of most noncooperative ligand binding equilibria. © 2016 Elsevier Inc. All rights reserved.

  10. Visualization Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Evaluates and improves the operational effectiveness of existing and emerging electronic warfare systems. By analyzing and visualizing simulation results...

  11. Stretching and folding mechanism in foams

    Energy Technology Data Exchange (ETDEWEB)

    Tufaile, Alberto [Escola de Artes, Ciencias e Humanidades, Soft Matter Laboratory, Universidade de Sao Paulo, 03828-000 Sao Paulo, SP (Brazil)], E-mail: tufaile@usp.br; Pedrosa Biscaia Tufaile, Adriana [Escola de Artes, Ciencias e Humanidades, Soft Matter Laboratory, Universidade de Sao Paulo, 03828-000 Sao Paulo, SP (Brazil)

    2008-10-13

    We have described the stretching and folding of foams in a vertical Hele-Shaw cell containing air and a surfactant solution, from a sequence of upside-down flips. Besides the fractal dimension of the foam, we have observed the logistic growth for the soap film length. The stretching and folding mechanism is present during the foam formation, and this mechanism is observed even after the foam has reached its respective maximum fractal dimension. Observing the motion of bubbles inside the foam, large bubbles present power spectrum associated with random walk motion in both directions, while the small bubbles are scattered like balls in a Galton board.

  12. Einstein's Field Equations as a Fold Bifurcation

    CERN Document Server

    Kohli, Ikjyot Singh

    2016-01-01

    It is shown that Einstein's field equations for \\emph{all} perfect-fluid $k=0$ FLRW cosmologies have the same form as the topological normal form of a fold bifurcation. In particular, we assume that the cosmological constant is a bifurcation parameter, and as such, fold bifurcation behaviour is shown to occur in a neighbourhood of Minkowski spacetime in the phase space. We show that as this cosmological constant parameter is varied, an expanding and contracting de Sitter universe \\emph{emerge} via this bifurcation.

  13. On thermodynamic limits of entropy densities

    NARCIS (Netherlands)

    Moriya, H; Van Enter, A

    1998-01-01

    We give some sufficient conditions which guarantee that the entropy density in the thermodynamic limit is equal to the thermodynamic limit of the entropy densities of finite-volume (local) Gibbs states.

  14. Thermodynamic parameters of elasticity and electrical conductivity ...

    African Journals Online (AJOL)

    Thermodynamic parameters of elasticity and electrical conductivity of reinforced natural rubber (nr) vulca nizates. ... Bulletin of the Chemical Society of Ethiopia ... The thermodynamic parameters (change in free energy of elasticity, DGe; ...

  15. From the test tube to the cell: exploring the folding and aggregation of a beta-clam protein.

    Science.gov (United States)

    Ignatova, Zoya; Krishnan, Beena; Bombardier, Jeffrey P; Marcelino, Anna Marie C; Hong, Jiang; Gierasch, Lila M

    2007-01-01

    A crucial challenge in present biomedical research is the elucidation of how fundamental processes like protein folding and aggregation occur in the complex environment of the cell. Many new physico-chemical factors like crowding and confinement must be considered, and immense technical hurdles must be overcome in order to explore these processes in vivo. Understanding protein misfolding and aggregation diseases and developing therapeutic strategies to these diseases demand that we gain mechanistic insight into behaviors and misbehaviors of proteins as they fold in vivo. We have developed a fluorescence approach using FlAsH labeling to study the thermodynamics of folding of a model beta-rich protein, cellular retinoic acid binding protein (CRABP) in Escherichia coli cells. The labeling approach has also enabled us to follow aggregation of a modified version of CRABP and chimeras between CRABP and huntingtin exon 1 with its glutamine repeat tract. In this article, we review our recent results using FlAsH labeling to study in-vivo folding and present new observations that hint at fundamental differences between the thermodynamics and kinetics of protein folding in vivo and in vitro.

  16. Conservation laws and thermodynamic efficiencies.

    Science.gov (United States)

    Benenti, Giuliano; Casati, Giulio; Wang, Jiao

    2013-02-15

    We show that generic systems with a single relevant conserved quantity reach the Carnot efficiency in the thermodynamic limit. Such a general result is illustrated by means of a diatomic chain of hard-point elastically colliding particles where the total momentum is the only relevant conserved quantity.

  17. One Antimatter— Two Possible Thermodynamics

    Directory of Open Access Journals (Sweden)

    Alexander Y. Klimenko

    2014-02-01

    Full Text Available Conventional thermodynamics, which is formulated for our world populated by radiation and matter, can be extended to describe physical properties of antimatter in two mutually exclusive ways: CP-invariant or CPT-invariant. Here we refer to invariance of physical laws under charge (C, parity (P and time reversal (T transformations. While in quantum field theory CPT invariance is a theorem confirmed by experiments, the symmetry principles applied to macroscopic phenomena or to the whole of the Universe represent only hypotheses. Since both versions of thermodynamics are different only in their treatment of antimatter, but are the same in describing our world dominated by matter, making a clear experimentally justified choice between CP invariance and CPT invariance in context of thermodynamics is not possible at present. This work investigates the comparative properties of the CP- and CPT-invariant extensions of thermodynamics (focusing on the latter, which is less conventional than the former and examines conditions under which these extensions can be experimentally tested.

  18. Thermodynamics of Oligonucleotide Duplex Melting

    Science.gov (United States)

    Schreiber-Gosche, Sherrie; Edwards, Robert A.

    2009-01-01

    Melting temperatures of oligonucleotides are useful for a number of molecular biology applications, such as the polymerase chain reaction (PCR). Although melting temperatures are often calculated with simplistic empirical equations, application of thermodynamics provides more accurate melting temperatures and an opportunity for students to apply…

  19. Jacobian's Thermodynamic Transforms Replacing Differentiation

    Institute of Scientific and Technical Information of China (English)

    邝钜炽; 张军

    2001-01-01

    The noteworthy work in this article consists in combiningcharacters of thermodynamic variables with Jacobian determinants to develop the three significant J transforms of thermodynamics,which seem not to have been reported except Eq.(12) until now.The significance of them is not only to offer us a new convenient tool for proofing puzzle but also to reveal the inner interrelations of thermodynamic variables,or to foretell the rules of variation of any thermodynamic variable following others.By all appearances,this can hardly be done by way of differentiation.%结合雅可比行列式和热力学变量的特性,率先导出了三个极为重要的雅可比热力学变换式,除(12)式外,其余尚未见报道.雅可比热力学变换的重要意义不仅体现在它为我们提供了一种证明难题的便利工具,而且还体现在其揭示了热力学变量间的内在联系,或预告某热力学量随其它热力学量变化的情况,显然此用微分法往往难以实现.

  20. Microscopic Models for Chemical Thermodynamics

    OpenAIRE

    Malyshev, Vadim A.

    2011-01-01

    We introduce an infinite particle system dynamics, which includes stochastic chemical kinetics models, the classical Kac model and free space movement. We study energy redistribution between two energy types (kinetic and chemical) in different time scales, similar to energy redistribution in the living organisms. One example is considered in great detail, where the model provides main formulas of chemical thermodynamics.

  1. Thermodynamics on the Molality Scale

    Science.gov (United States)

    Canagaratna, Sebastian G.; Maheswaran, M.

    2013-01-01

    For physical measurements, the compositions of solutions, especially electrolyte solutions, are expressed in terms of molality rather than mole fractions. The development of the necessary thermodynamic equations directly in terms of molality is not common in textbooks, and the treatment in the literature is not very systematic. We develop a…

  2. 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…

  3. THERMODYNAMICS USED IN ENVIRONMENTAL ENGINEERING

    Science.gov (United States)

    Thermodynamics is a science in which energy transformations are studied as well as their relationships to the changes in the chemical properties of a system. It is the fundamental basis of many engineering fields. The profession of environmental engineering is no exception. In pa...

  4. Thermodynamics of freezing and melting

    DEFF Research Database (Denmark)

    Pedersen, Ulf Rørbæk; Costigliola, Lorenzo; Bailey, Nicholas

    2016-01-01

    phases at a single thermodynamic state point provide the basis for calculating the pressure, density and entropy of fusion as functions of temperature along the melting line, as well as the variation along this line of the reduced crystalline vibrational mean-square displacement (the Lindemann ratio...

  5. Thermodynamics of asymptotically safe theories

    DEFF Research Database (Denmark)

    Rischke, Dirk H.; Sannino, Francesco

    2015-01-01

    We investigate the thermodynamic properties of a novel class of gauge-Yukawa theories that have recently been shown to be completely asymptotically safe, because their short-distance behaviour is determined by the presence of an interacting fixed point. Not only do all the coupling constants freeze...

  6. A Simple Statistical Thermodynamics Experiment

    Science.gov (United States)

    LoPresto, Michael C.

    2010-01-01

    Comparing the predicted and actual rolls of combinations of both two and three dice can help to introduce many of the basic concepts of statistical thermodynamics, including multiplicity, probability, microstates, and macrostates, and demonstrate that entropy is indeed a measure of randomness, that disordered states (those of higher entropy) are…

  7. Potential Functions in Chemical Thermodynamics

    Science.gov (United States)

    Araujo, Roger J.

    1998-11-01

    The first and second laws of thermodynamics are stated in equation form. The equation containing the combined laws is used to identify potential functions appropriate to various sets of constraints. An ion-exchange reaction and a redox reaction in a melt are considered as illustrations of the importance of using the potential function appropriate to the constraints.

  8. Microscopic Models for Chemical Thermodynamics

    CERN Document Server

    Malyshev, V A

    2011-01-01

    We introduce an infinite particle system dynamics, which includes stochastic chemical kinetics models, the classical Kac model and free space movement. We study energy redistribution between two energy types (kinetic and chemical) in different time scales, similar to energy redistribution in the living cell. One example is considered in great detail, where the model provides main formulas of chemical thermodynamics.

  9. Microscopic Models for Chemical Thermodynamics

    Science.gov (United States)

    Malyshev, V. A.

    2005-06-01

    We introduce an infinite particle system dynamics, which includes stochastic chemical kinetics models, the classical Kac model and free space movement. We study energy redistribution between two energy types (kinetic and chemical) in different time scales, similar to energy redistribution in the living cell. One example is considered in great detail, where the model provides main formulas of chemical thermodynamics.

  10. Monitoring of an RNA Multistep Folding Pathway by Isothermal Titration Calorimetry

    Science.gov (United States)

    Reymond, Cédric; Bisaillon, Martin; Perreault, Jean-Pierre

    2009-01-01

    Abstract Isothermal titration calorimetry was used to monitor the energetic landscape of a catalytic RNA, specifically that of the hepatitis delta virus ribozyme. Using mutants that isolated various tertiary interactions, the thermodynamic parameters of several ribozyme-substrate intermediates were determined. The results shed light on the impact of several tertiary interactions on the global structure of the ribozyme. In addition, the data indicate that the formation of the P1.1 pseudoknot is the limiting step of the molecular mechanism. Last, as illustrated here, isothermal titration calorimetry appears to be a method of choice for the elucidation of an RNA's folding pathway. PMID:19134473

  11. Monte Carlo simulations of the HP model (the "Ising model" of protein folding)

    Science.gov (United States)

    Li, Ying Wai; Wüst, Thomas; Landau, David P.

    2011-09-01

    Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free chains these proteins are known to first undergo a collapse "transition" to a globule state followed by a second "transition" into a native state. When placed in the proximity of an attractive surface, there is a competition between surface adsorption and folding that leads to an intriguing sequence of "transitions". These transitions depend upon the relative interaction strengths and are largely inaccessible to "standard" Monte Carlo methods.

  12. Chemical Thermodynamics and Information Theory with Applications

    CERN Document Server

    Graham, Daniel J

    2011-01-01

    Thermodynamics and information touch theory every facet of chemistry. However, the physical chemistry curriculum digested by students worldwide is still heavily skewed toward heat/work principles established more than a century ago. Rectifying this situation, Chemical Thermodynamics and Information Theory with Applications explores applications drawn from the intersection of thermodynamics and information theory--two mature and far-reaching fields. In an approach that intertwines information science and chemistry, this book covers: The informational aspects of thermodynamic state equations The

  13. Contact Geometry of Mesoscopic Thermodynamics and Dynamics

    Directory of Open Access Journals (Sweden)

    Miroslav Grmela

    2014-03-01

    Full Text Available The time evolution during which macroscopic systems reach thermodynamic equilibrium states proceeds as a continuous sequence of contact structure preserving transformations maximizing the entropy. This viewpoint of mesoscopic thermodynamics and dynamics provides a unified setting for the classical equilibrium and nonequilibrium thermodynamics, kinetic theory, and statistical mechanics. One of the illustrations presented in the paper is a new version of extended nonequilibrium thermodynamics with fluxes as extra state variables.

  14. Thermodynamics of statistical inference by cells.

    Science.gov (United States)

    Lang, Alex H; Fisher, Charles K; Mora, Thierry; Mehta, Pankaj

    2014-10-03

    The deep connection between thermodynamics, computation, and information is now well established both theoretically and experimentally. Here, we extend these ideas to show that thermodynamics also places fundamental constraints on statistical estimation and learning. To do so, we investigate the constraints placed by (nonequilibrium) thermodynamics on the ability of biochemical signaling networks to estimate the concentration of an external signal. We show that accuracy is limited by energy consumption, suggesting that there are fundamental thermodynamic constraints on statistical inference.

  15. 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

  16. Influence of denatured and intermediate states of folding on protein aggregation.

    Science.gov (United States)

    Fawzi, Nicolas L; Chubukov, Victor; Clark, Louis A; Brown, Scott; Head-Gordon, Teresa

    2005-04-01

    We simulate the aggregation thermodynamics and kinetics of proteins L and G, each of which self-assembles to the same alpha/beta [corrected] topology through distinct folding mechanisms. We find that the aggregation kinetics of both proteins at an experimentally relevant concentration exhibit both fast and slow aggregation pathways, although a greater proportion of protein G aggregation events are slow relative to those of found for protein L. These kinetic differences are correlated with the amount and distribution of intrachain contacts formed in the denatured state ensemble (DSE), or an intermediate state ensemble (ISE) if it exists, as well as the folding timescales of the two proteins. Protein G aggregates more slowly than protein L due to its rapidly formed folding intermediate, which exhibits native intrachain contacts spread across the protein, suggesting that certain early folding intermediates may be selected for by evolution due to their protective role against unwanted aggregation. Protein L shows only localized native structure in the DSE with timescales of folding that are commensurate with the aggregation timescale, leaving it vulnerable to domain swapping or nonnative interactions with other chains that increase the aggregation rate. Folding experiments that characterize the structural signatures of the DSE, ISE, or the transition state ensemble (TSE) under nonaggregating conditions should be able to predict regions where interchain contacts will be made in the aggregate, and to predict slower aggregation rates for proteins with contacts that are dispersed across the fold. Since proteins L and G can both form amyloid fibrils, this work also provides mechanistic and structural insight into the formation of prefibrillar species.

  17. Thermodynamic aspects of heat pipe operation

    Science.gov (United States)

    Richter, Robert; Gottschlich, Joseph

    1990-01-01

    An expanded heat pipe operating model is described which includes thermodynamic and heat transfer considerations to reconcile disparities between actual and theoretical heat pipe performances. The analysis shows that thermodynamic considerations can explain the observed heat pipe performance limitations. A full understanding of thermodynamic processes could lead to advanced concepts for thermal transport devices.

  18. Thermodynamics of chemical systems far from equilibrium

    Energy Technology Data Exchange (ETDEWEB)

    Ross, J. (Stanford Univ., CA (USA)); Garcia-Colin, L.S. (UAM-Iztapalapa, Postal (Mexico))

    1989-03-09

    A critique is presented of some recent work in this and other journals on the relation of thermodynamics to the mass action law of kinetics. For most chemical reactions, the thermodynamic variables change on the same time scale as the progress variable and there is no need for an extended thermodynamics.

  19. The Casimir Effect and Thermodynamic Instability

    OpenAIRE

    Widom, A.; Sassaroli, E.; Srivastava, Y. N.; Swain, J.

    1998-01-01

    One loop field theory calculations of free energies quite often yield violations of the stability conditions associated with the thermodynamic second law. Perhaps the best known example involves the equation of state of black holes. Here, it is pointed out that the Casimir force between two parallel conducting plates also violates a thermodynamic stability condition normally associated with the second law of thermodynamics.

  20. Chemical thermodynamics and the phase rule

    Energy Technology Data Exchange (ETDEWEB)

    Franzen, H.F.; Myers, C.E.

    1978-06-01

    An attempt is made to show that the Gibbs Phase Rule can, in a sense, be obtained without using chemical thermodynamics per se but by using an assumption which is implicit in applications of thermodynamics. This development will be followed by some comments on some important thermodynamic relationships with particular emphasis on the distinction between chemical components and chemical species.

  1. Glycoprotein folding in the endoplasmic reticulum

    NARCIS (Netherlands)

    Braakman, L.J.; Benham, A.M.

    2000-01-01

    Our understanding of eukaryotic protein folding in the endoplasmic reticulum has increased enormously over the last 5 years. In this review, we summarize some of the major research themes that have captivated researchers in this field during the last years of the 20th century. We follow the path of

  2. Amylose folding under the influence of lipids

    NARCIS (Netherlands)

    Lopez, Cesar A.; de Vries, Alex H.; Marrink, Siewert J.

    2012-01-01

    The molecular dynamics simulation technique was used to study the folding and complexation process of a short amylose fragment in the presence of lipids. In aqueous solution, the amylose chain remains as an extended left-handed helix. After the addition of lipids in the system, however, we observe s

  3. Folding and faulting of an elastic continuum

    Science.gov (United States)

    Gourgiotis, Panos A.

    2016-01-01

    Folding is a process in which bending is localized at sharp edges separated by almost undeformed elements. This process is rarely encountered in Nature, although some exceptions can be found in unusual layered rock formations (called ‘chevrons’) and seashell patterns (for instance Lopha cristagalli). In mechanics, the bending of a three-dimensional elastic solid is common (for example, in bulk wave propagation), but folding is usually not achieved. In this article, the route leading to folding is shown for an elastic solid obeying the couple-stress theory with an extreme anisotropy. This result is obtained with a perturbation technique, which involves the derivation of new two-dimensional Green's functions for applied concentrated force and moment. While the former perturbation reveals folding, the latter shows that a material in an extreme anisotropic state is also prone to a faulting instability, in which a displacement step of finite size emerges. Another failure mechanism, namely the formation of dilation/compaction bands, is also highlighted. Finally, a geophysical application to the mechanics of chevron formation shows how the proposed approach may explain the formation of natural structures. PMID:27118925

  4. MARATHON DESPITE UNILATERAL VOCAL FOLD PARALYSIS

    Directory of Open Access Journals (Sweden)

    Matthias Echternach

    2008-06-01

    Full Text Available The principal symptoms of unilateral vocal fold paralysis are hoarseness and difficulty in swallowing. Dyspnea is comparatively rare (Laccourreye et al., 2003. The extent to which unilateral vocal fold paralysis may lead to respiratory problems at all - in contrast to bilateral vocal fold paralysis- has not yet well been determined. On the one hand, inspiration is impaired with unilateral vocal fold paralysis; on the other hand, neither the position of the vocal fold paralysis nor the degree of breathiness correlates with respiratory parameters (Cantarella et al., 2003; 2005. The question of what respiratory stress a patient with a vocal fold paresis can endure has not yet been dealt with.A 43 year-old female patient was suffering from recurrent unspecific respiratory complaints for four months after physical activity. During training for a marathon, she experienced no difficulty in breathing. These unspecific respiratory complaints occurred only after athletic activity and persisted for hours. The patient observed neither an increased coughing nor a stridor. Her voice remained unaltered during the attacks, nor were there any signs of a symptomatic gastroesophageal reflux or infectious disease. A cardio-pulmonary and a radiological examination by means of an X-ray of the thorax also revealed no pathological phenomena. As antiallergic and antiobstructive therapy remained unsuccessful, a laryngological examination was performed in order to exclude a vocal cord dysfunction.Surprisingly enough, the laryngostroboscopy showed, as an initial description, a vocal fold paralysis of the left vocal fold in median position (Figure 1. The anamnestic background for the cause was unclear. The only clue was a thoracotomy on the left side due to a pleuritis in childhood. A subsequent laryngoscopic examination had never been performed. Good mucosa waves and amplitudes were shown bilateral with complete glottal closure. Neither in the acoustic analysis, nor in the

  5. Self-folding graphene-polymer bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Tao [Institute of Microelectronics, Tsinghua University, Beijing 100084 (China); Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Yoon, ChangKyu [Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Jin, Qianru [Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Li, Mingen [Department of Physics, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Liu, Zewen [Institute of Microelectronics, Tsinghua University, Beijing 100084 (China); Gracias, David H., E-mail: dgracias@jhu.edu [Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States)

    2015-05-18

    In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting.

  6. Self-folding graphene-polymer bilayers

    Science.gov (United States)

    Deng, Tao; Yoon, ChangKyu; Jin, Qianru; Li, Mingen; Liu, Zewen; Gracias, David H.

    2015-05-01

    In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting.

  7. Mapping the universe of RNA tetraloop folds

    DEFF Research Database (Denmark)

    Bottaro, Sandro; Lindorff-Larsen, Kresten

    2017-01-01

    We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG fold...

  8. Towards a systematic classification of protein folds

    DEFF Research Database (Denmark)

    Lindgård, Per-Anker; Bohr, Henrik

    1997-01-01

    in the usual protein data base coordinate format can be transformed into the proposed chain representation. Taking into account hydrophobic forces we have found a mechanism for the formation of domains with a unique fold containing predicted magic numbers {4,6,9,12,16,18,...} of secondary structures...

  9. Role of cofactors in metalloprotein folding.

    Science.gov (United States)

    Wilson, Corey J; Apiyo, David; Wittung-Stafshede, Pernilla

    2004-01-01

    Metals are commonly found as natural constituents of proteins. Since many such metals can interact specifically with their corresponding unfolded proteins in vitro , cofactor-binding prior to polypeptide folding may be a biological path to active metalloproteins. By interacting with the unfolded polypeptide, the metal may create local structure that initiates and directs the polypeptide-folding process. Here, we review recent literature that addresses the involvement of metals in protein-folding reactions in vitro . To date, the best characterized systems are simple one such as blue-copper proteins, heme-binding proteins, iron-sulfur-cluster proteins and synthetic metallopeptides. Taken together, the available data demonstrates that metals can play diverse roles: it is clear that many cofactors bind before polypeptide folding and influence the reaction; yet, some do not bind until a well-structured active site is formed. The significance of characterizing the effects of metals on protein conformational changes is underscored by the many human diseases that are directly linked to anomalous protein-metal interactions.

  10. Fold in Origami and Unfold Math

    Science.gov (United States)

    Georgeson, Joseph

    2011-01-01

    Students enjoy origami and like making everything from paper cranes to footballs out of small, colorful squares of paper. They can invent their own shapes and are intrigued by the polyhedrons that they can construct. Paper folding is fun, but where is the math? Unless teachers develop lessons that address mathematical objectives, origami could be…

  11. Fast Gravitational Wave Radiometry using Data Folding

    CERN Document Server

    Ain, Anirban; Mitra, Sanjit

    2015-01-01

    Gravitational Waves (GWs) from the early universe and unresolved astrophysical sources are expected to create a stochastic GW background (SGWB). The GW radiometer algorithm is well suited to probe such a background using data from ground based laser interferometric detectors. Radiometer analysis can be performed in different bases, e.g., isotropic, pixel or spherical harmonic. Each of these analyses possesses a common temporal symmetry which we exploit here to fold the whole dataset for every detector pair, typically a few hundred to a thousand days of data, to only one sidereal day, without any compromise in precision. We develop the algebra and a software pipeline needed to fold data, accounting for the effect of overlapping windows and non-stationary noise. We implement this on LIGO's fifth science run data and validate it by performing a standard anisotropic SGWB search on both folded and unfolded data. Folded data not only leads to orders of magnitude reduction in computation cost, but it results in a co...

  12. Understanding the role of the topology in protein folding by computational inverse folding experiments.

    Science.gov (United States)

    Mucherino, Antonio; Costantini, Susan; di Serafino, Daniela; D'Apuzzo, Marco; Facchiano, Angelo; Colonna, Giovanni

    2008-08-01

    Recent studies suggest that protein folding should be revisited as the emergent property of a complex system and that the nature allows only a very limited number of folds that seem to be strongly influenced by geometrical properties. In this work we explore the principles underlying this new view and show how helical protein conformations can be obtained starting from simple geometric considerations. We generated a large data set of C-alpha traces made of 65 points, by computationally solving a backbone model that takes into account only topological features of the all-alpha proteins; then, we built corresponding tertiary structures, by using the sequences associated to the crystallographic structures of four small globular all-alpha proteins from PDB, and analysed them in terms of structural and energetic properties. In this way we obtained four poorly populated sets of structures that are reasonably similar to the conformational states typical of the experimental PDB structures. These results show that our computational approach can capture the native topology of all-alpha proteins; furthermore, it generates backbone folds without the influence of the side chains and uses the protein sequence to select a specific fold among the generated folds. This agrees with the recent view that the backbone plays an important role in the protein folding process and that the amino acid sequence chooses its own fold within a limited total number of folds.

  13. Visual Thinking.

    Science.gov (United States)

    Arnheim, Rudolf

    Based on the more general principle that all thinking (including reasoning) is basically perceptual in nature, the author proposes that visual perception is not a passive recording of stimulus material but an active concern of the mind. He delineates the task of visually distinguishing changes in size, shape, and position and points out the…

  14. Visual search

    NARCIS (Netherlands)

    Toet, A.; Bijl, P.

    2003-01-01

    Visual search, with or without the aid of optical or electro-optical instruments, plays a significant role in various types of military and civilian operations (e.g., reconnaissance, surveillance, and search and rescue). Advance knowledge of human visual search and target acquisition performance is

  15. Visual Education

    DEFF Research Database (Denmark)

    Buhl, Mie; Flensborg, Ingelise

    2010-01-01

    The intrinsic breadth of various types of images creates new possibilities and challenges for visual education. The digital media have moved the boundaries between images and other kinds of modalities (e.g. writing, speech and sound) and have augmented the possibilities for integrating...... to emerge in the interlocutory space of a global visual repertoire and diverse local interpretations. The two perspectives represent challenges for future visual education which require visual competences, not only within the arts but also within the subjects of natural sciences, social sciences, languages...... the learning potential of images and visuality from two perspectives: 1) The perspective of digital media which are assumed to form an increasing part of experience and communication from the use of internet, tv and mobile devices. 2) The perspective of culture where images and visualisations are assumed...

  16. Visual Education

    DEFF Research Database (Denmark)

    Buhl, Mie; Flensborg, Ingelise

    2010-01-01

    The intrinsic breadth of various types of images creates new possibilities and challenges for visual education. The digital media have moved the boundaries between images and other kinds of modalities (e.g. writing, speech and sound) and have augmented the possibilities for integrating the functi......The intrinsic breadth of various types of images creates new possibilities and challenges for visual education. The digital media have moved the boundaries between images and other kinds of modalities (e.g. writing, speech and sound) and have augmented the possibilities for integrating...... to emerge in the interlocutory space of a global visual repertoire and diverse local interpretations. The two perspectives represent challenges for future visual education which require visual competences, not only within the arts but also within the subjects of natural sciences, social sciences, languages...

  17. Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein

    Science.gov (United States)

    Gruszka, Dominika T.; Whelan, Fiona; Farrance, Oliver E.; Fung, Herman K. H.; Paci, Emanuele; Jeffries, Cy M.; Svergun, Dmitri I.; Baldock, Clair; Baumann, Christoph G.; Brockwell, David J.; Potts, Jennifer R.; Clarke, Jane

    2015-06-01

    Bacteria exploit surface proteins to adhere to other bacteria, surfaces and host cells. Such proteins need to project away from the bacterial surface and resist significant mechanical forces. SasG is a protein that forms extended fibrils on the surface of Staphylococcus aureus and promotes host adherence and biofilm formation. Here we show that although monomeric and lacking covalent cross-links, SasG maintains a highly extended conformation in solution. This extension is mediated through obligate folding cooperativity of the intrinsically disordered E domains that couple non-adjacent G5 domains thermodynamically, forming interfaces that are more stable than the domains themselves. Thus, counterintuitively, the elongation of the protein appears to be dependent on the inherent instability of its domains. The remarkable mechanical strength of SasG arises from tandemly arrayed `clamp' motifs within the folded domains. Our findings reveal an elegant minimal solution for the assembly of monomeric mechano-resistant tethers of variable length.

  18. Phase transition in polypeptides: a step towards the understanding of protein folding

    DEFF Research Database (Denmark)

    Yakubovich, Alexander V.; Solov'yov, Ilia; Solov'yov, Andrey V.

    2006-01-01

    We present a formalism which turns out to be very successful in the description of the polypeptide folding. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely on fundamental physical principles. It describes...... essential thermodynamical properties of the system such as heat capacity, the phase transition temperature and others from the analysis of the polypeptide potential energy surface calculated within ab initio density functional theory and parameterized by two dihedral angles. This problem is viewed...... as a major breakthrough in the theoretical understanding of the protein folding process. Our conclusion is based on the comparison of the predictions of our theory with the results of several independent experiments....

  19. Inverse folding of RNA pseudoknot structures

    Directory of Open Access Journals (Sweden)

    Li Linda YM

    2010-06-01

    Full Text Available Abstract Background RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and G-U-base pairings (secondary structure and additional cross-serial base pairs. These interactions are called pseudoknots and are observed across the whole spectrum of RNA functionalities. In the context of studying natural RNA structures, searching for new ribozymes and designing artificial RNA, it is of interest to find RNA sequences folding into a specific structure and to analyze their induced neutral networks. Since the established inverse folding algorithms, RNAinverse, RNA-SSD as well as INFO-RNA are limited to RNA secondary structures, we present in this paper the inverse folding algorithm Inv which can deal with 3-noncrossing, canonical pseudoknot structures. Results In this paper we present the inverse folding algorithm Inv. We give a detailed analysis of Inv, including pseudocodes. We show that Inv allows to design in particular 3-noncrossing nonplanar RNA pseudoknot 3-noncrossing RNA structures-a class which is difficult to construct via dynamic programming routines. Inv is freely available at http://www.combinatorics.cn/cbpc/inv.html. Conclusions The algorithm Inv extends inverse folding capabilities to RNA pseudoknot structures. In comparison with RNAinverse it uses new ideas, for instance by considering sets of competing structures. As a result, Inv is not only able to find novel sequences even for RNA secondary structures, it does so in the context of competing structures that potentially exhibit cross-serial interactions.

  20. Folding and Fracturing of Rocks: the background

    Science.gov (United States)

    Ramsay, John G.

    2017-04-01

    This book was generated by structural geology teaching classes at Imperial College. I was appointed lecturer during 1957 and worked together with Dr Gilbert Wilson teaching basic structural geology at B.Sc level. I became convinced that the subject, being essentially based on geometric field observations, required a firm mathematical basis for its future development. In particular it seemed to me to require a very sound understanding of stress and strain. My field experience suggested that a knowledge of two- and three-demensional strain was critical in understanding natural tectonic processes. I found a rich confirmation for this in early publications of deformed fossils, oolitic limestones and spotted slates made by several geologists around the beginning of the 20th century (Sorby, Philips, Haughton, Harker) often using surprisingly sophisticated mathematical methods. These methods were discussed and elaborated in Folding and Fracturing of Rocks in a practical way. The geometric features of folds were related to folding mechanisms and the fold related small scale structures such as cleavage, schistosity and lineation explained in terms of rock strain. My work in the Scottish Highlands had shown just how repeated fold superposition could produce very complex geometric features, while further work in other localities suggested that such geometric complications are common in many orogenic zones. From the development of structural geological studies over the past decades it seems that the readers of this book have found many of the ideas set out are still of practical application. The mapping of these outcrop-scale structures should be emphasised in all field studies because they can be seen as ''fingerprints'' of regional scale tectonic processes. My own understanding of structural geology has been inspired by field work and I am of the opinion that future progress in understanding will be likewise based on careful observation and measurement of the features of