Sample records for spectroscopic thermodynamic microscopic

  1. Global Passivity in Microscopic Thermodynamics

    NASA Astrophysics Data System (ADS)

    Uzdin, Raam; Rahav, Saar

    2018-04-01

    The main thread that links classical thermodynamics and the thermodynamics of small quantum systems is the celebrated Clausius inequality form of the second law. However, its application to small quantum systems suffers from two cardinal problems. (i) The Clausius inequality does not hold when the system and environment are initially correlated—a commonly encountered scenario in microscopic setups. (ii) In some other cases, the Clausius inequality does not provide any useful information (e.g., in dephasing scenarios). We address these deficiencies by developing the notion of global passivity and employing it as a tool for deriving thermodynamic inequalities on observables. For initially uncorrelated thermal environments the global passivity framework recovers the Clausius inequality. More generally, global passivity provides an extension of the Clausius inequality that holds even in the presences of strong initial system-environment correlations. Crucially, the present framework provides additional thermodynamic bounds on expectation values. To illustrate the role of the additional bounds, we use them to detect unaccounted heat leaks and weak feedback operations ("Maxwell demons") that the Clausius inequality cannot detect. In addition, it is shown that global passivity can put practical upper and lower bounds on the buildup of system-environment correlations for dephasing interactions. Our findings are highly relevant for experiments in various systems such as ion traps, superconducting circuits, atoms in optical cavities, and more.

  2. Biochemical activity of a fluorescent dye rhodamine 6G: Molecular modeling, electrochemical, spectroscopic and thermodynamic studies.

    PubMed

    Al Masum, Abdulla; Chakraborty, Maharudra; Ghosh, Soumen; Laha, Dipranjan; Karmakar, Parimal; Islam, Md Maidul; Mukhopadhyay, Subrata

    2016-11-01

    Interaction of CT DNA with Rhodamine 6G (R6G) has been studied using molecular docking, electrochemical, spectroscopic and thermodynamic methods. From the study, it was illustrated that Rhodamine 6G binds to the minor groove of CT DNA. The binding was cooperative in nature. Circular voltametric study showed significant change in peak current and peak potential due to complexation. All the studies showed that the binding constant was in the order of 10 6 M -1 . Circular dichroic spectra showed significant conformational change on binding and DNA unwind during binding. Thermodynamic study showed that binding was favored by negative enthalpy and positive entropy change. From thermodynamic study it was also observed that several positive and negative free energies played significant role during binding and the unfavorable conformational free energy change was overcame by highly negative hydrophobic and salt dependent free energy changes. The experimental results were further validated using molecular docking study and the effect of structure on binding has been studied theoretically. From docking study it was found that the hydrophobic interaction and hydrogen bonds played a significant role during binding. The dye was absorbed by cell and this phenomenon was studied using fluorescent microscope. Cell survivability test showed that the dye active against Human Breast Cancer cells MDA-MB 468. ROS study showed that the activity is due to the production of reactive oxygen. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Insight into the microscopic structure of an AdS black hole from a thermodynamical phase transition.

    PubMed

    Wei, Shao-Wen; Liu, Yu-Xiao

    2015-09-11

    Comparing with an ordinary thermodynamic system, we investigate the possible microscopic structure of a charged anti-de Sitter black hole completely from the thermodynamic viewpoint. The number density of the black hole molecules is introduced to measure the microscopic degrees of freedom of the black hole. We found that the number density suffers a sudden change accompanied by a latent heat when the black hole system crosses the small-large black hole coexistence curve, while when the system passes the critical point, it encounters a second-order phase transition with a vanishing latent heat due to the continuous change of the number density. Moreover, the thermodynamic scalar curvature suggests that there is a weak attractive interaction between two black hole molecules. These phenomena might cast new insight into the underlying microscopic structure of a charged anti-de Sitter black hole.

  4. Conformational Contribution to Thermodynamics of Binding in Protein-Peptide Complexes through Microscopic Simulation

    PubMed Central

    Das, Amit; Chakrabarti, J.; Ghosh, Mahua

    2013-01-01

    We extract the thermodynamics of conformational changes in biomacromolecular complexes from the distributions of the dihedral angles of the macromolecules. These distributions are obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. The conformational thermodynamics data we obtained for calmodulin-peptide complexes using our methodology corroborate well with the experimentally observed conformational and binding entropies. The conformational free-energy changes and their contributions for different peptide-binding regions of calmodulin are evaluated microscopically. PMID:23528087

  5. Grasping the Second Law of Thermodynamics at University: The Consistency of Macroscopic and Microscopic Explanations

    ERIC Educational Resources Information Center

    Leinonen, Risto; Asikainen, Mervi A.; Hirvonen, Pekka E.

    2015-01-01

    This study concentrates on evaluating the consistency of upper-division students' use of the second law of thermodynamics at macroscopic and microscopic levels. Data were collected by means of a paper and pencil test (N = 48) focusing on the macroscopic and microscopic features of the second law concerned with heat transfer processes. The data…

  6. Apertureless near-field/far-field CW two-photon microscope for biological and material imaging and spectroscopic applications.

    PubMed

    Nowak, Derek B; Lawrence, A J; Sánchez, Erik J

    2010-12-10

    We present the development of a versatile spectroscopic imaging tool to allow for imaging with single-molecule sensitivity and high spatial resolution. The microscope allows for near-field and subdiffraction-limited far-field imaging by integrating a shear-force microscope on top of a custom inverted microscope design. The instrument has the ability to image in ambient conditions with optical resolutions on the order of tens of nanometers in the near field. A single low-cost computer controls the microscope with a field programmable gate array data acquisition card. High spatial resolution imaging is achieved with an inexpensive CW multiphoton excitation source, using an apertureless probe and simplified optical pathways. The high-resolution, combined with high collection efficiency and single-molecule sensitive optical capabilities of the microscope, are demonstrated with a low-cost CW laser source as well as a mode-locked laser source.

  7. Microscopic thermodynamics with levitated nanoparticles (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Gieseler, Jan; Jain, Vijay; Moritz, Clemens; Dellago, Christoph; Quidant, Romain; Novotny, Lukas

    2016-09-01

    Micsospheres trapped in liquid by so called optical tweezers have been established as useful tools to study microscopic thermodynamics. Since the sphere is in direct contact with the liquid, it is strongly coupled to the thermal bath and its dynamics is dominated by thermal fluctuations. In contrast, here we use an optically trapped nanoparticle in vacuum to study fluctuations of a system that is coupled only weakly to the thermal bath. The weak coupling allows us to resolve the ballistic dynamics and to control its motion via modulation of the trapping beam, thereby preparing it in a highly non-thermal state. We develop a theory for the effective Hamiltonian that describes the system dynamics in this state and show that all the relevant parameters can be controlled in situ. This tunability allows us to study classical fluctuation theorems for different effective Hamiltonians and for varying coupling to the thermal bath ranging over several orders of magnitude. The ultimate goal, however, is to completely suppress the effect of the thermal bath and to prepare the levitated nanoparticle in a quantum mechanical state. Our most recent result indicate that this regime is now within reach.

  8. Black hole thermodynamics under the microscope

    NASA Astrophysics Data System (ADS)

    Falls, Kevin; Litim, Daniel F.

    2014-04-01

    A coarse-grained version of the effective action is used to study the thermodynamics of black holes, interpolating from largest to smallest masses. The physical parameters of the black hole are linked to the running couplings by thermodynamics, and the corresponding equation of state includes quantum corrections for temperature, specific heat, and entropy. If quantum gravity becomes asymptotically safe, the state function predicts conformal scaling in the limit of small horizon area and bounds on black hole mass and temperature. A metric-based derivation for the equation of state and quantum corrections to the thermodynamical, statistical, and phenomenological definition of entropy are also given. Further implications and limitations of our study are discussed.

  9. Construction and performance of a dilution-refrigerator based spectroscopic-imaging scanning tunneling microscope.

    PubMed

    Singh, U R; Enayat, M; White, S C; Wahl, P

    2013-01-01

    We report on the set-up and performance of a dilution-refrigerator based spectroscopic imaging scanning tunneling microscope. It operates at temperatures below 10 mK and in magnetic fields up to 14T. The system allows for sample transfer and in situ cleavage. We present first-results demonstrating atomic resolution and the multi-gap structure of the superconducting gap of NbSe(2) at base temperature. To determine the energy resolution of our system we have measured a normal metal/vacuum/superconductor tunneling junction consisting of an aluminum tip on a gold sample. Our system allows for continuous measurements at base temperature on time scales of up to ≈170 h.

  10. Single nanoparticle tracking spectroscopic microscope

    DOEpatents

    Yang, Haw [Moraga, CA; Cang, Hu [Berkeley, CA; Xu, Cangshan [Berkeley, CA; Wong, Chung M [San Gabriel, CA

    2011-07-19

    A system that can maintain and track the position of a single nanoparticle in three dimensions for a prolonged period has been disclosed. The system allows for continuously imaging the particle to observe any interactions it may have. The system also enables the acquisition of real-time sequential spectroscopic information from the particle. The apparatus holds great promise in performing single molecule spectroscopy and imaging on a non-stationary target.

  11. Thermodynamic and Spectroscopic Investigation of Interactions between Reactive Red 223 and Reactive Orange 122 Anionic Dyes and Cetyltrimethyl Ammonium Bromide (CTAB) Cationic Surfactant in Aqueous Solution

    PubMed Central

    Irfan, Muhammad; Usman, Muhammad; Mansha, Asim; Rasool, Nasir; Ibrahim, Muhammad; Rana, Usman Ali; Siddiq, Mohammad; Zia-Ul-Haq, Muhammad; Jaafar, Hawa Z. E.; Khan, Salah Ud-Din

    2014-01-01

    The present study describes the conductometric and spectroscopic study of the interaction of reactive anionic dyes, namely, reactive red 223 and reactive orange 122 with the cationic surfactant cetyltrimethyl ammonium bromide (CTAB). In a systematic investigation, the electrical conductivity data was used to calculate various thermodynamic parameters such as free energy (ΔG), enthalpy (ΔH), and the entropy (ΔS) of solubilization. The trend of change in these thermodynamic quantities indicates toward the entropy driven solubilization process. Moreover, the results from spectroscopic data reveal high degree of solubilization, with strong interactions observed in the cases of both dyes and the CTAB. The spontaneous nature of solubilization and binding was evident from the observed negative values of free energies (ΔG p and ΔG b). PMID:25243216

  12. Spectroscopic and thermodynamic studies on ferulic acid - Alpha-2-macroglobulin interaction

    NASA Astrophysics Data System (ADS)

    Rehman, Ahmed Abdur; Sarwar, Tarique; Arif, Hussain; Ali, Syed Saqib; Ahsan, Haseeb; Tabish, Mohammad; Khan, Fahim Halim

    2017-09-01

    Ferulic acid is a major phenolic acid found in numerous plant species in conjugated form. It binds to enzymes and oligomeric proteins and modifies their structure and function. This study was designed to examine the interaction of ferulic acid, an active ingredient of some important medicines, with α2M, a key serum proteinase, under physiological conditions. The mechanism of interaction was studied by spectroscopic techniques such as, UV-visible absorption, fluorescence spectroscopy, circular dichroism along with isothermal titration calorimetry. Fluorescence quenching of α2M by ferulic acid demonstrated the formation of α2M-ferulic acid complex by static quenching mechanism. Binding parameters calculated by Stern-Volmer method showed that ferulic acid binds to α2M with moderate affinity of the order of ∼104 M-1. The thermodynamic signatures reveal that binding was enthalpy driven and hydrogen bonding played a major role in ferulic acid-α2M binding. CD spectra analysis suggests very little conformational changes in α2M on ferulic acid binding.

  13. Laser apparatus and method for microscopic and spectroscopic analysis and processing of biological cells

    DOEpatents

    Gourley, Paul L.; Gourley, Mark F.

    1997-01-01

    An apparatus and method for microscopic and spectroscopic analysis and processing of biological cells. The apparatus comprises a laser having an analysis region within the laser cavity for containing one or more biological cells to be analyzed. The presence of a cell within the analysis region in superposition with an activated portion of a gain medium of the laser acts to encode information about the cell upon the laser beam, the cell information being recoverable by an analysis means that preferably includes an array photodetector such as a CCD camera and a spectrometer. The apparatus and method may be used to analyze biomedical cells including blood cells and the like, and may include processing means for manipulating, sorting, or eradicating cells after analysis thereof.

  14. Laser apparatus and method for microscopic and spectroscopic analysis and processing of biological cells

    DOEpatents

    Gourley, P.L.; Gourley, M.F.

    1997-03-04

    An apparatus and method are disclosed for microscopic and spectroscopic analysis and processing of biological cells. The apparatus comprises a laser having an analysis region within the laser cavity for containing one or more biological cells to be analyzed. The presence of a cell within the analysis region in superposition with an activated portion of a gain medium of the laser acts to encode information about the cell upon the laser beam, the cell information being recoverable by an analysis means that preferably includes an array photodetector such as a CCD camera and a spectrometer. The apparatus and method may be used to analyze biomedical cells including blood cells and the like, and may include processing means for manipulating, sorting, or eradicating cells after analysis. 20 figs.

  15. Characterization of the binding of shikonin to human immunoglobulin using scanning electron microscope, molecular modeling and multi-spectroscopic methods.

    PubMed

    He, Wenying; Ye, Xinyu; Yao, Xiaojun; Wu, Xiuli; Lin, Qiang; Huang, Guolei; Hua, Yingjie; Hui, Yang

    2015-11-05

    Shikonin, one of the active components isolated from the root of Arnebia euchroma (Royle) Johnst, have anti-tumor, anti-bacterial and anti-inflammatory activities and has been used clinically in phlebitis and vascular purpura. In the present work, the interaction of human immunoglobulin (HIg) with shikonin has been investigated by using scanning electron microscope (SEM), Fourier transform infrared (FT-IR) spectroscopy, fluorescence polarization, synchronous and 3D fluorescence spectroscopy in combination with molecular modeling techniques under physiological conditions with drug concentrations of 3.33-36.67 μM. The results of SEM exhibited visually the special effect on aggregation behavior of the complex formed between HIg and shikonin. The fluorescence polarization values indicated that shikonin molecules were found in a motionally unrestricted environment introduced by HIg. Molecular docking showed the shikonin moiety bound to the hydrophobic cavity of HIg, and there are four hydrogen-bonding interactions between shikonin and the residues of protein. The synchronous and 3D fluorescence spectra confirmed that shikonin could quench the intrinsic fluorescence of HIg and has an effect on the microenvironment around HIg in aqueous solution. The changes in the secondary structure of HIg were estimated by qualitative and quantitative FT-IR spectroscopic analysis. The binding constants and thermodynamic parameters for shikonin-HIg systems were obtained under different temperatures (300 K, 310 K and 320 K). The above results revealed the binding mechanism of shikonin and HIg at the ultrastructure and molecular level. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Thermodynamics of urban population flows.

    PubMed

    Hernando, A; Plastino, A

    2012-12-01

    Orderliness, reflected via mathematical laws, is encountered in different frameworks involving social groups. Here we show that a thermodynamics can be constructed that macroscopically describes urban population flows. Microscopic dynamic equations and simulations with random walkers underlie the macroscopic approach. Our results might be regarded, via suitable analogies, as a step towards building an explicit social thermodynamics.

  17. A comparison of microscopic and spectroscopic identification methods for analysis of microplastics in environmental samples.

    PubMed

    Song, Young Kyoung; Hong, Sang Hee; Jang, Mi; Han, Gi Myung; Rani, Manviri; Lee, Jongmyoung; Shim, Won Joon

    2015-04-15

    The analysis of microplastics in various environmental samples requires the identification of microplastics from natural materials. The identification technique lacks a standardized protocol. Herein, stereomicroscope and Fourier transform infrared spectroscope (FT-IR) identification methods for microplastics (<1mm) were compared using the same samples from the sea surface microlayer (SML) and beach sand. Fragmented microplastics were significantly (p<0.05) underestimated and fiber was significantly overestimated using the stereomicroscope both in the SML and beach samples. The total abundance by FT-IR was higher than by microscope both in the SML and beach samples, but they were not significantly (p>0.05) different. Depending on the number of samples and the microplastic size range of interest, the appropriate identification method should be determined; selecting a suitable identification method for microplastics is crucial for evaluating microplastic pollution. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Binding of Phenazinium Dye Safranin T to Polyriboadenylic Acid: Spectroscopic and Thermodynamic Study

    PubMed Central

    Roy, Snigdha; Das, Suman

    2014-01-01

    Here, we report results from experiments designed to explore the association of the phenazinium dye safranin T (ST, 3,7-diamino-2,8-dimethyl-5-phenylphenazinium chloride) with single and double stranded form of polyriboadenylic acid (hereafter poly-A) using several spectroscopic techniques. We demonstrate that the dye binds to single stranded polyriboadenylic acid (hereafter ss poly-A) with high affinity while it does not interact at all with the double stranded (ds) form of the polynucleotide. Fluorescence and absorption spectral studies reveal the molecular aspects of binding of ST to single stranded form of the polynucleotide. This observation is also supported by the circular dichroism study. Thermodynamic data obtained from temperature dependence of binding constant reveals that association is driven by negative enthalpy change and opposed by negative entropy change. Ferrocyanide quenching studies have shown intercalative binding of ST to ss poly-A. Experiments on viscosity measurements confirm the binding mode of the dye to be intercalative. The effect of [Na+] ion concentration on the binding process suggests the role of electrostatic forces in the complexation. Present studies reveal the utility of the dye in probing nucleic acid structure. PMID:24498422

  19. Binding of phenazinium dye safranin T to polyriboadenylic acid: spectroscopic and thermodynamic study.

    PubMed

    Pradhan, Ankur Bikash; Haque, Lucy; Roy, Snigdha; Das, Suman

    2014-01-01

    Here, we report results from experiments designed to explore the association of the phenazinium dye safranin T (ST, 3,7-diamino-2,8-dimethyl-5-phenylphenazinium chloride) with single and double stranded form of polyriboadenylic acid (hereafter poly-A) using several spectroscopic techniques. We demonstrate that the dye binds to single stranded polyriboadenylic acid (hereafter ss poly-A) with high affinity while it does not interact at all with the double stranded (ds) form of the polynucleotide. Fluorescence and absorption spectral studies reveal the molecular aspects of binding of ST to single stranded form of the polynucleotide. This observation is also supported by the circular dichroism study. Thermodynamic data obtained from temperature dependence of binding constant reveals that association is driven by negative enthalpy change and opposed by negative entropy change. Ferrocyanide quenching studies have shown intercalative binding of ST to ss poly-A. Experiments on viscosity measurements confirm the binding mode of the dye to be intercalative. The effect of [Na⁺] ion concentration on the binding process suggests the role of electrostatic forces in the complexation. Present studies reveal the utility of the dye in probing nucleic acid structure.

  20. Surprises in low dimensional spin 1/2 magnets - from crystal chemistry to microscopic magnetic models of complex oxides

    NASA Astrophysics Data System (ADS)

    Rosner, Helge

    2011-03-01

    A microscopic understanding of the structure-properties relation in crystalline materials is a main goal of modern solid state chemistry and physics. Due to their peculiar magnetism, low dimensional spin 1/2 systems are often highly sensitive to structural details. Seemingly unimportant structural details can be crucial for the magnetic ground state of a compound, especially in the case of competing interactions, frustration and near-degeneracy. Here, we present for selected, complex Cu 2+ systems that a first principles based approach can reliably provide the correct magnetic model, especially in cases where the interpretation of experimental data meets serious difficulties or fails. We demonstrate that the magnetism of low dimensional insulators crucially depends on the magnetically active orbitals which are determined by details of the ligand field of the magnetic cation. Our theoretical results are in very good agreement with thermodynamic and spectroscopic data and provide deep microscopic insight into topical low dimensional magnets.

  1. Uranium(VI) Binding Forms in Selected Human Body Fluids: Thermodynamic Calculations versus Spectroscopic Measurements.

    PubMed

    Osman, Alfatih A A; Geipel, Gerhard; Barkleit, Astrid; Bernhard, Gert

    2015-02-16

    Human exposure to uranium increasingly becomes a subject of interest in many scientific disciplines such as environmental medicine, toxicology, and radiation protection. Knowledge about uranium chemical binding forms(speciation) in human body fluids can be of great importance to understand not only its biokinetics but also its relevance in risk assessment and in designing decorporation therapy in the case of accidental overexposure. In this study, thermodynamic calculations of uranium speciation in relevant simulated and original body fluids were compared with spectroscopic data after ex-situ uranium addition. For the first time, experimental data on U(VI) speciation in body fluids (saliva, sweat, urine) was obtained by means of cryogenic time-resolved laser-induced fluorescence spectroscopy (cryo-TRLFS) at 153 K. By using the time dependency of fluorescence decay and the band positions of the emission spectra, various uranyl complexes were demonstrated in the studied samples. The variations of the body fluids in terms of chemical composition, pH, and ionic strength resulted in different binding forms of U(VI). The speciation of U(VI) in saliva and in urine was affected by the presence of bioorganic ligands, whereas in sweat, the distribution depends mainly on inorganic ligands. We also elucidated the role of biological buffers, i.e., phosphate (H(2)PO(4−)/HPO(4)(2−)) on U(VI) distribution, and the system Ca(2+)/UO(2)(2+)/PO(4)(3−) was discussed in detail in both saliva and urine. The theoretical speciation calculations of the main U(VI) species in the investigated body fluids were significantly consistent with the spectroscopic data. Laser fluorescence spectroscopy showed success and reliability for direct determination of U(VI) in such biological matrices with the possibility for further improvement.

  2. Spectro-refractometry of individual microscopic objects using swept-source quantitative phase imaging.

    PubMed

    Jung, Jae-Hwang; Jang, Jaeduck; Park, Yongkeun

    2013-11-05

    We present a novel spectroscopic quantitative phase imaging technique with a wavelength swept-source, referred to as swept-source diffraction phase microscopy (ssDPM), for quantifying the optical dispersion of microscopic individual samples. Employing the swept-source and the principle of common-path interferometry, ssDPM measures the multispectral full-field quantitative phase imaging and spectroscopic microrefractometry of transparent microscopic samples in the visible spectrum with a wavelength range of 450-750 nm and a spectral resolution of less than 8 nm. With unprecedented precision and sensitivity, we demonstrate the quantitative spectroscopic microrefractometry of individual polystyrene beads, 30% bovine serum albumin solution, and healthy human red blood cells.

  3. Probing the inhibitory potency of epigallocatechin gallate against human γB-crystallin aggregation: Spectroscopic, microscopic and simulation studies

    NASA Astrophysics Data System (ADS)

    Chaudhury, Susmitnarayan; Dutta, Anirudha; Bag, Sudipta; Biswas, Pranandita; Das, Amit Kumar; Dasgupta, Swagata

    2018-03-01

    Aggregation of human ocular lens proteins, the crystallins is believed to be one of the key reasons for age-onset cataract. Previous studies have shown that human γD-crystallin forms amyloid like fibres under conditions of low pH and elevated temperature. In this article, we have investigated the aggregation propensity of human γB-crystallin in absence and presence of epigallocatechin gallate (EGCG), in vitro, when exposed to stressful conditions. We have used different spectroscopic and microscopic techniques to elucidate the inhibitory effect of EGCG towards aggregation. The experimental results have been substantiated by molecular dynamics simulation studies. We have shown that EGCG possesses inhibitory potency against the aggregation of human γB-crystallin at low pH and elevated temperature.

  4. Stochastic Independence as a Resource for Small-Scale Thermodynamics

    NASA Astrophysics Data System (ADS)

    Lostaglio, Matteo; Mueller, Markus P.; Pastena, Michele

    It is well-known in thermodynamics that the creation of correlations costs work. It seems then a truism that if a thermodynamic transformation A --> B is impossible, so will be any transformation that in sending A to B also correlates among them some auxiliary systems C. Surprisingly, we show that this is not the case for non-equilibrium thermodynamics of microscopic systems. On the contrary, the creation of correlations greatly extends the set of accessible states, to the point that we can perform on individual systems and in a single shot any transformation that would otherwise be possible only if the number of systems involved was very large. We also show that one only ever needs to create a vanishingly small amount of correlations (as measured by mutual information) among a small number of auxiliary systems (never more than three). The many, severe constraints of microscopic thermodynamics are reduced to the sole requirement that the non-equilibrium free energy decreases in the transformation. This shows that, in principle, reliable extraction of work equal to the free energy of a system can be performed by microscopic engines.

  5. Stochastic Independence as a Resource in Small-Scale Thermodynamics

    NASA Astrophysics Data System (ADS)

    Lostaglio, Matteo; Müller, Markus P.; Pastena, Michele

    2015-10-01

    It is well known in thermodynamics that the creation of correlations costs work. It seems then a truism that if a thermodynamic transformation A →B is impossible, so will be any transformation that in sending A to B also correlates among them some auxiliary systems C . Surprisingly, we show that this is not the case for nonequilibrium thermodynamics of microscopic systems. On the contrary, the creation of correlations greatly extends the set of accessible states, to the point that we can perform on individual systems and in a single shot any transformation that would otherwise be possible only if the number of systems involved was very large. We also show that one only ever needs to create a vanishingly small amount of correlations (as measured by mutual information) among a small number of auxiliary systems (never more than three). The many, severe constraints of microscopic thermodynamics are reduced to the sole requirement that the nonequilibrium free energy decreases in the transformation. This shows that, in principle, reliable extraction of work equal to the free energy of a system can be performed by microscopic engines.

  6. Thermodynamic and Spectroscopic Studies of Trivalent f -element Complexation with Ethylenediamine- N,N '-di(acetylglycine)- N,N '-diacetic Acid

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Heathman, Colt R.; Grimes, Travis S.; Zalupski, Peter R.

    In this study, the coordination behavior and thermodynamic features of complexation of trivalent lanthanides and americium by ethylenediamine- N,N'-di(acetylglycine)- N,N'-diacetic acid (EDDAG-DA) (bisamide-substituted-EDTA) were investigated by potentiometric and spectroscopic techniques. Acid dissociation constants (K a) and complexation constants (β) of lanthanides (except Pm) were determined by potentiometric analysis. Absorption spectroscopy was used to determine stability constants for the binding of trivalent americium and neodymium by EDDAG-DA under similar conditions. The potentiometry revealed 5 discernible protonation constants and 3 distinct metal–ligand complexes (identified as ML –, MHL, and MH 2L +). Time-resolved fluorescence studies of Eu-(EDDAG-DA) solutions (at varying pH) identifiedmore » a constant inner-sphere hydration number of 3, suggesting that glycine functionalities contained in the amide pendant arms are not involved in metal complexation and are protonated under more acidic conditions. The thermodynamic studies identified that f-element coordination by EDDAG-DA is similar to that observed for ethylenediamine- N,N,N',N'-tetraacetic acid (EDTA). However, coordination via two amidic oxygens of EDDAG-DA lowers its trivalent f-element complex stability by roughly 3 orders of magnitude relative to EDTA.« less

  7. Thermodynamic and Spectroscopic Studies of Trivalent f -element Complexation with Ethylenediamine- N,N '-di(acetylglycine)- N,N '-diacetic Acid

    DOE PAGES

    Heathman, Colt R.; Grimes, Travis S.; Zalupski, Peter R.

    2016-03-21

    In this study, the coordination behavior and thermodynamic features of complexation of trivalent lanthanides and americium by ethylenediamine- N,N'-di(acetylglycine)- N,N'-diacetic acid (EDDAG-DA) (bisamide-substituted-EDTA) were investigated by potentiometric and spectroscopic techniques. Acid dissociation constants (K a) and complexation constants (β) of lanthanides (except Pm) were determined by potentiometric analysis. Absorption spectroscopy was used to determine stability constants for the binding of trivalent americium and neodymium by EDDAG-DA under similar conditions. The potentiometry revealed 5 discernible protonation constants and 3 distinct metal–ligand complexes (identified as ML –, MHL, and MH 2L +). Time-resolved fluorescence studies of Eu-(EDDAG-DA) solutions (at varying pH) identifiedmore » a constant inner-sphere hydration number of 3, suggesting that glycine functionalities contained in the amide pendant arms are not involved in metal complexation and are protonated under more acidic conditions. The thermodynamic studies identified that f-element coordination by EDDAG-DA is similar to that observed for ethylenediamine- N,N,N',N'-tetraacetic acid (EDTA). However, coordination via two amidic oxygens of EDDAG-DA lowers its trivalent f-element complex stability by roughly 3 orders of magnitude relative to EDTA.« less

  8. [Authentication of Trace Material Evidence in Forensic Science Field with Infrared Microscopic Technique].

    PubMed

    Jiang, Zhi-quan; Hu, Ke-liang

    2016-03-01

    In the field of forensic science, conventional infrared spectral analysis technique is usually unable to meet the detection requirements, because only very a few trace material evidence with diverse shapes and complex compositions, can be extracted from the crime scene. Infrared microscopic technique is developed based on a combination of Fourier-transform infrared spectroscopic technique and microscopic technique. Infrared microscopic technique has a lot of advantages over conventional infrared spectroscopic technique, such as high detection sensitivity, micro-area analysisand nondestructive examination. It has effectively solved the problem of authentication of trace material evidence in the field of forensic science. Additionally, almost no external interference is introduced during measurements by infrared microscopic technique. It can satisfy the special need that the trace material evidence must be reserved for witness in court. It is illustrated in detail through real case analysis in this experimental center that, infrared microscopic technique has advantages in authentication of trace material evidence in forensic science field. In this paper, the vibration features in infrared spectra of material evidences, including paints, plastics, rubbers, fibers, drugs and toxicants, can be comparatively analyzed by means of infrared microscopic technique, in an attempt to provide powerful spectroscopic evidence for qualitative diagnosis of various criminal and traffic accident cases. The experimental results clearly suggest that infrared microscopic technique has an incomparable advantage and it has become an effective method for authentication of trace material evidence in the field of forensic science.

  9. Dilational symmetry-breaking in thermodynamics

    NASA Astrophysics Data System (ADS)

    Lin, Chris L.; Ordóñez, Carlos R.

    2017-04-01

    Using thermodynamic relations and dimensional analysis we derive a general formula for the thermodynamical trace 2{ E}-DP for nonrelativistic systems and { E}-DP for relativistic systems, where D is the number of spatial dimensions, in terms of the microscopic scales of the system within the grand canonical ensemble. We demonstrate the formula for several cases, including anomalous systems which develop scales through dimensional transmutation. Using this relation, we make explicit the connection between dimensional analysis and the virial theorem. This paper is focused mainly on the non-relativistic aspects of this relation.

  10. Macromolecular Competition Titration Method: Accessing Thermodynamics of the Unmodified Macromolecule–Ligand Interactions Through Spectroscopic Titrations of Fluorescent Analogs

    PubMed Central

    Bujalowski, Wlodzimierz; Jezewska, Maria J.

    2011-01-01

    Analysis of thermodynamically rigorous binding isotherms provides fundamental information about the energetics of the ligand–macromolecule interactions and often an invaluable insight about the structure of the formed complexes. The Macromolecular Competition Titration (MCT) method enables one to quantitatively obtain interaction parameters of protein–nucleic acid interactions, which may not be available by other methods, particularly for the unmodified long polymer lattices and specific nucleic acid substrates, if the binding is not accompanied by adequate spectroscopic signal changes. The method can be applied using different fluorescent nucleic acids or fluorophores, although the etheno-derivatives of nucleic acid are especially suitable as they are relatively easy to prepare, have significant blue fluorescence, their excitation band lies far from the protein absorption spectrum, and the modification eliminates the possibility of base pairing with other nucleic acids. The MCT method is not limited to the specific size of the reference nucleic acid. Particularly, a simple analysis of the competition titration experiments is described in which the fluorescent, short fragment of nucleic acid, spanning the exact site-size of the protein–nucleic acid complex, and binding with only a 1:1 stoichiometry to the protein, is used as a reference macromolecule. Although the MCT method is predominantly discussed as applied to studying protein–nucleic acid interactions, it can generally be applied to any ligand–macromolecule system by monitoring the association reaction using the spectroscopic signal originating from the reference macromolecule in the presence of the competing macromolecule, whose interaction parameters with the ligand are to be determined. PMID:21195223

  11. Black Hole Thermodynamics and Lorentz Symmetry

    NASA Astrophysics Data System (ADS)

    Jacobson, Ted; Wall, Aron C.

    2010-08-01

    Recent developments point to a breakdown in the generalized second law of thermodynamics for theories with Lorentz symmetry violation. It appears possible to construct a perpetual motion machine of the second kind in such theories, using a black hole to catalyze the conversion of heat to work. Here we describe and extend the arguments leading to that conclusion. We suggest the inference that local Lorentz symmetry may be an emergent property of the macroscopic world with origins in a microscopic second law of causal horizon thermodynamics.

  12. Large area fabrication of plasmonic nanoparticle grating structure by conventional scanning electron microscope

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sudheer,, E-mail: sudheer@rrcat.gov.in; Tiwari, P.; Rai, V. N.

    Plasmonic nanoparticle grating (PNG) structure of different periods has been fabricated by electron beam lithography using silver halide based transmission electron microscope film as a substrate. Conventional scanning electron microscope is used as a fabrication tool for electron beam lithography. Optical microscope and energy dispersive spectroscopy (EDS) have been used for its morphological and elemental characterization. Optical characterization is performed by UV-Vis absorption spectroscopic technique.

  13. LEAD SORPTION ON RUTHENIUM OXIDE: A MACROSCOPIC AND SPECTROSCOPIC STUDY

    EPA Science Inventory

    The sorption and desorption of Pb on RuO2 xH2O were examined kinetically and thermodynamically via spectroscopic and macroscopic investigations. X-ray absorption spectroscopy (XAS) was employed to determine the sorption mechanism with regard to identity of nearest atomic neighbo...

  14. Correcting the spectroscopic surface gravity using transits and asteroseismology. No significant effect on temperatures or metallicities with ARES and MOOG in local thermodynamic equilibrium

    NASA Astrophysics Data System (ADS)

    Mortier, A.; Sousa, S. G.; Adibekyan, V. Zh.; Brandão, I. M.; Santos, N. C.

    2014-12-01

    Context. Precise stellar parameters (effective temperature, surface gravity, metallicity, stellar mass, and radius) are crucial for several reasons, amongst which are the precise characterization of orbiting exoplanets and the correct determination of galactic chemical evolution. The atmospheric parameters are extremely important because all the other stellar parameters depend on them. Using our standard equivalent-width method on high-resolution spectroscopy, good precision can be obtained for the derived effective temperature and metallicity. The surface gravity, however, is usually not well constrained with spectroscopy. Aims: We use two different samples of FGK dwarfs to study the effect of the stellar surface gravity on the precise spectroscopic determination of the other atmospheric parameters. Furthermore, we present a straightforward formula for correcting the spectroscopic surface gravities derived by our method and with our linelists. Methods: Our spectroscopic analysis is based on Kurucz models in local thermodynamic equilibrium, performed with the MOOG code to derive the atmospheric parameters. The surface gravity was either left free or fixed to a predetermined value. The latter is either obtained through a photometric transit light curve or derived using asteroseismology. Results: We find first that, despite some minor trends, the effective temperatures and metallicities for FGK dwarfs derived with the described method and linelists are, in most cases, only affected within the errorbars by using different values for the surface gravity, even for very large differences in surface gravity, so they can be trusted. The temperatures derived with a fixed surface gravity continue to be compatible within 1 sigma with the accurate results of the infrared flux method (IRFM), as is the case for the unconstrained temperatures. Secondly, we find that the spectroscopic surface gravity can easily be corrected to a more accurate value using a linear function with the

  15. Thermodynamic and spectroscopic study of Al3+ interaction with glycine, l-cysteine and tranexamic acid in aqueous solution.

    PubMed

    Cardiano, Paola; Giacobello, Fausta; Giuffrè, Ottavia; Sammartano, Silvio

    2017-11-01

    In this paper a thermodynamic and spectroscopic study on the interaction between Al 3+ and glycine (Gly), l-cysteine (Cys), tranexamic acid (Tranex) is reported. Speciation models have been obtained by processing potentiometric titration data to determine stability constants of the species formed in aqueous solution at T=298.15K, 0.15≤I/molL -1 ≤1 in NaCl. Thermodynamic formation parameters have been obtained from calorimetric titration data, at T=298.15K, I=0.15molL -1 using NaCl as ionic medium. Al 3+ -Cys system was also investigated by spectrophotometric and 1 H NMR measurements. 1 H NMR experiments were performed on Al 3+ -Tranex system as well. Different speciation models have been observed for the three systems. The results showed the formation of MLH, ML and M 2 L 2 (OH) 2 species for Gly, ML, M 2 L and MLOH for Cys, MLH and MLOH for Tranex. The formed species are quite stable, i.e. for ML, logβ=7.18, 11.91 for Gly and Cys, respectively, at I=0.15molL -1 and T=298.15K. For all the systems the dependence of formation constants on ionic strength over the range 0.1-1molL -1 is reported. The sequestering ability of the ligands under study was also evaluated by pL 0.5 empiric parameter. For Gly, Cys and Tranex, pL 0.5 =2.51, 3.74, 3.91 respectively, at pH=5, I=0.15molL -1 and T=298.15K. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Microcomputer Calculation of Thermodynamic Properties from Molecular Parameters of Gases.

    ERIC Educational Resources Information Center

    Venugopalan, Mundiyath

    1990-01-01

    Described in this article is a problem-solving activity which integrates the application of microcomputers with the learning of physical chemistry. Students use the program with spectroscopic data to calculate the thermodynamic properties and compare them with the values from the thermochemical tables. (Author/KR)

  17. Deciphering the interaction of bovine heart cystatin with ZnO nanoparticles: Spectroscopic and thermodynamic approach.

    PubMed

    Sohail, Aamir; Faraz, Mohd; Arif, Hussain; Bhat, Sheraz Ahmad; Siddiqui, Azad Alam; Bano, Bilqees

    2017-02-01

    ZnO-NPs have been widely used in biomedical fields such as therapeutics, cellular imaging, and drug delivery. However, the risk of exposure of nanoparticles to the biological system is not well understood. Nanoparticle-protein interaction is pivotal to understand their biological behavior and predict nanoparticle toxicity that is crucial for its safer applications. In the present study zinc oxide nanoparticles (ZnO-NPs) were synthesized and subjected to interact with buffalo heart cystatin (BHC), purified from buffalo heart, to assess the effect(s) of ZnO-NPs on the structure and function of BHC. In vitro toxicity assessments revealed that BHC, upon interaction with ZnO-NPs, led to the altered protein conformation and perturbed function. A decrease in the anti-papain activity of BHC was observed. Spectroscopic studies demonstrated that formation of BHC-ZnO-NPs complex accompanied by structural changes in BHC along with a significant decrease in its α-helical content. ITC determined the thermodynamic parameters of binding between ZnO-NPs and BHC quantitatively. Increased surface hydrophobicity (change in the tertiary structure) was observed by ANS fluorescence that demonstrated the formation of molten globular intermediates that were found to be stable without any signs of aggregation as depicted by ThT fluorescence. TEM images gave the physical evidence of the formation of ZnO-NPs-BHC corona. Copyright © 2016. Published by Elsevier B.V.

  18. Thermodynamics of Biological Processes

    PubMed Central

    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

  19. Surface Tension: Mechanics, Thermodynamics, and Relaxation Times

    NASA Astrophysics Data System (ADS)

    Tovbin, Yu. K.

    2018-06-01

    A microscopic analysis is presented of the existing definitions of equilibrium surface tension, which can be divided into two types: mechanical and thermodynamic. Each type of definition can be studied from the presentation below according to thermodynamic hypotheses or molecular calculations. An analysis of the planar interface is given and its generalization for curved (spherical) interfaces is considered. The distinction between approaches describing the surface tension of metastable and equilibrium droplets is discussed. Based on nonequilibrium thermodynamics, it is shown that the introduction of metastable droplets is due to a violation of the relationship between the times of impulse and chemical potential relaxation in condensed phases. Problems of calculating the surface tension in nonequilibrium situations are created.

  20. Thermodynamic curvature for a two-parameter spin model with frustration.

    PubMed

    Ruppeiner, George; Bellucci, Stefano

    2015-01-01

    Microscopic models of realistic thermodynamic systems usually involve a number of parameters, not all of equal macroscopic relevance. We examine a decorated (1+3) Ising spin chain containing two microscopic parameters: a stiff parameter K mediating the long-range interactions, and a sloppy J operating within local spin groups. We show that K dominates the macroscopic behavior, with varying J having only a weak effect, except in regions where J brings about transitions between phases through its conditioning of the local spin groups with which K interacts. We calculate the heat capacity C(H), the magnetic susceptibility χ(T), and the thermodynamic curvature R. For large |J/K|, we identify four magnetic phases: ferromagnetic, antiferromagnetic, and two ferrimagnetic, according to the signs of K and J. We argue that for characterizing these phases, the strongest picture is offered by the thermodynamic geometric invariant R, proportional to the correlation length ξ. This picture has correspondences to other cases, such as fluids.

  1. Lagrangian formulation of irreversible thermodynamics and the second law of thermodynamics.

    PubMed

    Glavatskiy, K S

    2015-05-28

    We show that the equations which describe irreversible evolution of a system can be derived from a variational principle. We suggest a Lagrangian, which depends on the properties of the normal and the so-called "mirror-image" system. The Lagrangian is symmetric in time and therefore compatible with microscopic reversibility. The evolution equations in the normal and mirror-imaged systems are decoupled and describe therefore independent irreversible evolution of each of the systems. The second law of thermodynamics follows from a symmetry of the Lagrangian. Entropy increase in the normal system is balanced by the entropy decrease in the mirror-image system, such that there exists an "integral of evolution" which is a constant. The derivation relies on the property of local equilibrium, which states that the local relations between the thermodynamic quantities in non-equilibrium are the same as in equilibrium.

  2. Toxicity evaluations of nanoclays and thermally degraded byproducts through spectroscopical and microscopical approaches

    PubMed Central

    Wagner, Alixandra; Eldawud, Reem; White, Andrew; Agarwal, Sushant; Stueckle, Todd A.; Sierros, Konstantinos A.; Rojanasakul, Yon; Gupta, Rakesh K.; Dinu, Cerasela Zoica

    2016-01-01

    Background Montmorillonite is a type of nanoclay that originates from the clay fraction of the soil and is incorporated into polymers to form nanocomposites with enhanced mechanical strength, barrier, and flammability properties used for food packaging, automotive, and medical devices. However, with implementation in such consumer applications, the interaction of montmorillonite-based composites or derived byproducts with biological systems needs to be investigated. Methods Herein we examined the potential of Cloisite Na+ (pristine) and Cloisite 30B (organically modified montmorillonite nanoclay) and their thermally degraded byproducts’ to induce toxicity in model human lung epithelial cells. The experimental set-up mimicked biological exposure in manufacturing and disposal areas and employed cellular treatments with occupationally relevant doses of nanoclays previously characterized using spectroscopical and microscopical approaches. For nanoclay-cellular interactions and for cellular analyses respectively, biosensorial-based analytical platforms were used, with induced cellular changes being confirmed via live cell counts, viability assays, and cell imaging. Results Our analysis of byproducts’ chemical and physical properties revealed both structural and functional changes. Real-time high throughput analyses of exposed cellular systems confirmed that nanoclay induced significant toxic effects, with Cloisite 30B showing time-dependent decreases in live cell count and cellular viability relative to control and pristine nanoclay, respectively. Byproducts produced less toxic effects; all treatments caused alterations in the cell morphology upon exposure. Conclusions Our morphological, behavioral, and viability cellular changes show that nanoclays have the potential to produce toxic effects when used both in manufacturing or disposal environments. General significance The reported toxicological mechanisms prove the extensibility of a biosensorial-based platform

  3. Ab initio atomistic thermodynamics study on the oxidation mechanism of binary and ternary alloy surfaces

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liu, Shi-Yu, E-mail: buaasyliu@gmail.com; Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong; Liu, Shiyang

    Utilizing a combination of ab initio density-functional theory and thermodynamics formalism, we have established the microscopic mechanisms for oxidation of the binary and ternary alloy surfaces and provided a clear explanation for the experimental results of the oxidation. We construct three-dimensional surface phase diagrams (SPDs) for oxygen adsorption on three different Nb-X(110) (X = Ti, Al or Si) binary alloy surfaces. On the basis of the obtained SPDs, we conclude a general microscopic mechanism for the thermodynamic oxidation, that is, under O-rich conditions, a uniform single-phase SPD (type I) and a nonuniform double-phase SPD (type II) correspond to the sustainedmore » complete selective oxidation and the non-sustained partial selective oxidation by adding the X element, respectively. Furthermore, by revealing the framework of thermodynamics for the oxidation mechanism of ternary alloys through the comparison of the surface energies of two separated binary alloys, we provide an understanding for the selective oxidation behavior of the Nb ternary alloy surfaces. Using these general microscopic mechanisms, one could predict the oxidation behavior of any binary and multi-component alloy surfaces based on thermodynamics considerations.« less

  4. A microscopic insight from conformational thermodynamics to functional ligand binding in proteins.

    PubMed

    Sikdar, Samapan; Chakrabarti, J; Ghosh, Mahua

    2014-12-01

    We show that the thermodynamics of metal ion-induced conformational changes aid to understand the functions of protein complexes. This is illustrated in the case of a metalloprotein, alpha-lactalbumin (aLA), a divalent metal ion binding protein. We use the histograms of dihedral angles of the protein, generated from all-atom molecular dynamics simulations, to calculate conformational thermodynamics. The thermodynamically destabilized and disordered residues in different conformational states of a protein are proposed to serve as binding sites for ligands. This is tested for β-1,4-galactosyltransferase (β4GalT) binding to the Ca(2+)-aLA complex, in which the binding residues are known. Among the binding residues, the C-terminal residues like aspartate (D) 116, glutamine (Q) 117, tryptophan (W) 118 and leucine (L) 119 are destabilized and disordered and can dock β4GalT onto Ca(2+)-aLA. No such thermodynamically favourable binding residues can be identified in the case of the Mg(2+)-aLA complex. We apply similar analysis to oleic acid binding and predict that the Ca(2+)-aLA complex can bind to oleic acid through the basic histidine (H) 32 of the A2 helix and the hydrophobic residues, namely, isoleucine (I) 59, W60 and I95, of the interfacial cleft. However, the number of destabilized and disordered residues in Mg(2+)-aLA are few, and hence, the oleic acid binding to Mg(2+)-bound aLA is less stable than that to the Ca(2+)-aLA complex. Our analysis can be generalized to understand the functionality of other ligand bound proteins.

  5. Thermodynamics of transport through the ammonium transporter Amt-1 investigated with free energy calculations.

    PubMed

    Ullmann, R Thomas; Andrade, Susana L A; Ullmann, G Matthias

    2012-08-16

    Amt-1 from Archaeoglobus fulgidus (AfAmt-1) belongs to the Amt/Rh family of ammonium/ammonia transporting membrane proteins. The transport mode and the precise microscopic permeation mechanism utilized by these proteins are intensely debated. Open questions concern the identity of the transported substrate (ammonia and/or ammonium) and whether the transport is passive or active. To address these questions, we studied the overall thermodynamics of the different transport modes as a function of the environmental conditions. Then, we investigated the thermodynamics of the underlying microscopic transport mechanisms with free energy calculations within a continuum electrostatics model. The formalism developed for this purpose is of general utility in the calculation of binding free energies for ligands with multiple protonation forms or other binding forms. The results of our calculations are compared to the available experimental and theoretical data on Amt/Rh proteins and discussed in light of the current knowledge on the physiological conditions experienced by microorganisms and plants. We found that microscopic models of electroneutral and electrogenic transport modes are in principle thermodynamically viable. However, only the electrogenic variants have a net thermodynamic driving force under the physiological conditions experienced by microorganisms and plants. Thus, the transport mechanism of AfAmt-1 is most likely electrogenic.

  6. Microscopic approaches to liquid nitromethane detonation properties.

    PubMed

    Hervouët, Anaïs; Desbiens, Nicolas; Bourasseau, Emeric; Maillet, Jean-Bernard

    2008-04-24

    In this paper, thermodynamic and chemical properties of nitromethane are investigated using microscopic simulations. The Hugoniot curve of the inert explosive is computed using Monte Carlo simulations with a modified version of the adaptative Erpenbeck equation of state and a recently developed intermolecular potential. Molecular dynamic simulations of nitromethane decomposition have been performed using a reactive potential, allowing the calculation of kinetic rate constants and activation energies. Finally, the Crussard curve of detonation products as well as thermodynamic properties at the Chapman-Jouguet (CJ) point are computed using reactive ensemble Monte Carlo simulations. Results are in good agreement with both thermochemical calculations and experimental measurements.

  7. Lagrangian formulation of irreversible thermodynamics and the second law of thermodynamics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Glavatskiy, K. S.

    We show that the equations which describe irreversible evolution of a system can be derived from a variational principle. We suggest a Lagrangian, which depends on the properties of the normal and the so-called “mirror-image” system. The Lagrangian is symmetric in time and therefore compatible with microscopic reversibility. The evolution equations in the normal and mirror-imaged systems are decoupled and describe therefore independent irreversible evolution of each of the systems. The second law of thermodynamics follows from a symmetry of the Lagrangian. Entropy increase in the normal system is balanced by the entropy decrease in the mirror-image system, such thatmore » there exists an “integral of evolution” which is a constant. The derivation relies on the property of local equilibrium, which states that the local relations between the thermodynamic quantities in non-equilibrium are the same as in equilibrium.« less

  8. Spectroscopic imaging of biomaterials and biological systems with FTIR microscopy or with quantum cascade lasers.

    PubMed

    Kimber, James A; Kazarian, Sergei G

    2017-10-01

    Spectroscopic imaging of biomaterials and biological systems has received increased interest within the last decade because of its potential to aid in the detection of disease using biomaterials/biopsy samples and to probe the states of live cells in a label-free manner. The factors behind this increased attention include the availability of improved infrared microscopes and systems that do not require the use of a synchrotron as a light source, as well as the decreasing costs of these systems. This article highlights the current technical challenges and future directions of mid-infrared spectroscopic imaging within this field. Specifically, these are improvements in spatial resolution and spectral quality through the use of novel added lenses and computational algorithms, as well as quantum cascade laser imaging systems, which offer advantages over traditional Fourier transform infrared systems with respect to the speed of acquisition and field of view. Overcoming these challenges will push forward spectroscopic imaging as a viable tool for disease diagnostics and medical research. Graphical abstract Absorbance images of a biopsy obtained using an FTIR imaging microscope with and without an added lens, and also using a QCL microscope with high-NA objective.

  9. High-Definition Infrared Spectroscopic Imaging

    PubMed Central

    Reddy, Rohith K.; Walsh, Michael J.; Schulmerich, Matthew V.; Carney, P. Scott; Bhargava, Rohit

    2013-01-01

    The quality of images from an infrared (IR) microscope has traditionally been limited by considerations of throughput and signal-to-noise ratio (SNR). An understanding of the achievable quality as a function of instrument parameters, from first principals is needed for improved instrument design. Here, we first present a model for light propagation through an IR spectroscopic imaging system based on scalar wave theory. The model analytically describes the propagation of light along the entire beam path from the source to the detector. The effect of various optical elements and the sample in the microscope is understood in terms of the accessible spatial frequencies by using a Fourier optics approach and simulations are conducted to gain insights into spectroscopic image formation. The optimal pixel size at the sample plane is calculated and shown much smaller than that in current mid-IR microscopy systems. A commercial imaging system is modified, and experimental data are presented to demonstrate the validity of the developed model. Building on this validated theoretical foundation, an optimal sampling configuration is set up. Acquired data were of high spatial quality but, as expected, of poorer SNR. Signal processing approaches were implemented to improve the spectral SNR. The resulting data demonstrated the ability to perform high-definition IR imaging in the laboratory by using minimally-modified commercial instruments. PMID:23317676

  10. High-definition infrared spectroscopic imaging.

    PubMed

    Reddy, Rohith K; Walsh, Michael J; Schulmerich, Matthew V; Carney, P Scott; Bhargava, Rohit

    2013-01-01

    The quality of images from an infrared (IR) microscope has traditionally been limited by considerations of throughput and signal-to-noise ratio (SNR). An understanding of the achievable quality as a function of instrument parameters, from first principals is needed for improved instrument design. Here, we first present a model for light propagation through an IR spectroscopic imaging system based on scalar wave theory. The model analytically describes the propagation of light along the entire beam path from the source to the detector. The effect of various optical elements and the sample in the microscope is understood in terms of the accessible spatial frequencies by using a Fourier optics approach and simulations are conducted to gain insights into spectroscopic image formation. The optimal pixel size at the sample plane is calculated and shown much smaller than that in current mid-IR microscopy systems. A commercial imaging system is modified, and experimental data are presented to demonstrate the validity of the developed model. Building on this validated theoretical foundation, an optimal sampling configuration is set up. Acquired data were of high spatial quality but, as expected, of poorer SNR. Signal processing approaches were implemented to improve the spectral SNR. The resulting data demonstrated the ability to perform high-definition IR imaging in the laboratory by using minimally-modified commercial instruments.

  11. Microscopic approaches to quantum nonequilibriumthermodynamics and information

    DTIC Science & Technology

    2018-02-09

    Microscopic approaches to quantum non- equilibrium thermodynamics and information The views, opinions and/or findings contained in this report are... information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering...and maintaining the data needed, and completing and reviewing the collection of information . Send comments regarding this burden estimate or any other

  12. Ballistic-Electron-Emission Microscope

    NASA Technical Reports Server (NTRS)

    Kaiser, William J.; Bell, L. Douglas

    1990-01-01

    Ballistic-electron-emission microscope (BEEM) employs scanning tunneling-microscopy (STM) methods for nondestructive, direct electrical investigation of buried interfaces, such as interface between semiconductor and thin metal film. In BEEM, there are at least three electrodes: emitting tip, biasing electrode, and collecting electrode, receiving current crossing interface under investigation. Signal-processing device amplifies electrode signals and converts them into form usable by computer. Produces spatial images of surface by scanning tip; in addition, provides high-resolution images of buried interface under investigation. Spectroscopic information extracted by measuring collecting-electrode current as function of one of interelectrode voltages.

  13. Coherent anti-Stokes Raman scattering spectroscope/microscope based on a widely tunable laser source

    NASA Astrophysics Data System (ADS)

    Dementjev, A.; Gulbinas, V.; Serbenta, A.; Kaucikas, M.; Niaura, G.

    2010-03-01

    We present a coherent anti-Stokes Raman scattering (CARS) microscope based on a robust and simple laser source. A picosecond laser operating in a cavity dumping regime at the 1 MHz repetition rate was used to pump a traveling wave optical parametric generator, which serves as a two-color excitation light source for the CARS microscope. We demonstrate the ability of the presented CARS microscope to measure CARS spectra and images by using several detection schemes.

  14. Living Matter Observations with a Novel Hyperspectral Supercontinuum Confocal Microscope for VIS to Near-IR Reflectance Spectroscopy

    PubMed Central

    Bertani, Francesca R.; Ferrari, Luisa; Mussi, Valentina; Botti, Elisabetta; Costanzo, Antonio; Selci, Stefano

    2013-01-01

    A broad range hyper-spectroscopic microscope fed by a supercontinuum laser source and equipped with an almost achromatic optical layout is illustrated with detailed explanations of the design, implementation and data. The real novelty of this instrument, a confocal spectroscopic microscope capable of recording high resolution reflectance data in the VIS-IR spectral range from about 500 nm to 2.5 μm wavelengths, is the possibility of acquiring spectral data at every physical point as defined by lateral coordinates, X and Y, as well as at a depth coordinate, Z, as obtained by the confocal optical sectioning advantage. With this apparatus we collect each single scanning point as a whole spectrum by combining two linear spectral detector arrays, one CCD for the visible range, and one InGaAs infrared array, simultaneously available at the sensor output channel of the home made instrument. This microscope has been developed for biomedical analysis of human skin and other similar applications. Results are shown illustrating the technical performances of the instrument and the capability in extracting information about the composition and the structure of different parts or compartments in biological samples as well as in solid statematter. A complete spectroscopic fingerprinting of samples at microscopic level is shown possible by using statistical analysis on raw data or analytical reflectance models based on Abelés matrix transfer methods. PMID:24233077

  15. Conservation laws and symmetries in stochastic thermodynamics.

    PubMed

    Polettini, Matteo; Bulnes-Cuetara, Gregory; Esposito, Massimiliano

    2016-11-01

    Phenomenological nonequilibrium thermodynamics describes how fluxes of conserved quantities, such as matter, energy, and charge, flow from outer reservoirs across a system and how they irreversibly degrade from one form to another. Stochastic thermodynamics is formulated in terms of probability fluxes circulating in the system's configuration space. The consistency of the two frameworks is granted by the condition of local detailed balance, which specifies the amount of physical quantities exchanged with the reservoirs during single transitions between configurations. We demonstrate that the topology of the configuration space crucially determines the number of independent thermodynamic affinities (forces) that the reservoirs generate across the system and provides a general algorithm that produces the fundamental affinities and their conjugate currents contributing to the total dissipation, based on the interplay between macroscopic conservations laws for the currents and microscopic symmetries of the affinities.

  16. Physico-chemical properties of aqueous drug solutions: From the basic thermodynamics to the advanced experimental and simulation results.

    PubMed

    Bellich, Barbara; Gamini, Amelia; Brady, John W; Cesàro, Attilio

    2018-04-05

    The physical chemical properties of aqueous solutions of model compounds are illustrated in relation to hydration and solubility issues by using three perspectives: thermodynamic, spectroscopic and molecular dynamics simulations. The thermodynamic survey of the fundamental backgrounds of concentration dependence and experimental solubility results show some peculiar behavior of aqueous solutions with several types of similar solutes. Secondly, the use of a variety of experimental spectroscopic devices, operating under different experimental conditions of dimension and frequency, has produced a large amount of structural and dynamic data on aqueous solutions showing the richness of the information produced, depending on where and how the experiment is carried out. Finally, the use of molecular dynamics computational work is presented to highlight how the different types of solute functional groups and surface topologies organize adjacent water molecules differently. The highly valuable contribution of computer simulation studies in providing molecular explanations for experimental deductions, either of a thermodynamic or spectroscopic nature, is shown to have changed the current knowledge of many aqueous solution processes. While this paper is intended to provide a collective view on the latest literature results, still the presentation aims at a tutorial explanation of the potentials of the three methodologies in the field of aqueous solutions of pharmaceutical molecules. Copyright © 2018. Published by Elsevier B.V.

  17. Thermodynamic analysis and purifying an amorphous phase of frozen crystallization centers

    NASA Astrophysics Data System (ADS)

    Lysov, V. I.; Tsaregradskaya, T. L.; Turkov, O. V.; Saenko, G. V.

    2017-12-01

    The possibility of dissolving frozen crystallization centers in amorphous alloys of the Fe-B system is considered by means of thermodynamic calculations. This can in turn improve the thermal stability of an amorphous alloy. The effect isothermal annealing has on the thermal stability of multicomponent amorphous alloys based on iron is investigated via the highly sensitive dilatometric technique, measurements of microsolidity, and electron microscopic investigations. The annealing temperature is determined empirically on the basis of the theses of the thermodynamic theory of the high temperature stability of multicomponent amorphous alloys, according to which there exists a range of temperatures that is characterized by a negative difference between the chemical potentials of phases in a heterogeneous amorphous matrix-frozen crystallization centers system. The thermodynamic condition of the possible dissolution of frozen crystallization centers is thus met. It is shown that introducing regimes of thermal processing allows us to expand the ranges of the thermal stability of iron-based amorphous alloys by 20-40 K through purifying an amorphous matrix of frozen crystallization centers. This conclusion is proved via electron microscopic investigations.

  18. A Hamiltonian approach for the Thermodynamics of AdS black holes

    NASA Astrophysics Data System (ADS)

    Baldiotti, M. C.; Fresneda, R.; Molina, C.

    2017-07-01

    In this work we study the Thermodynamics of D-dimensional Schwarzschild-anti de Sitter (SAdS) black holes. The minimal Thermodynamics of the SAdS spacetime is briefly discussed, highlighting some of its strong points and shortcomings. The minimal SAdS Thermodynamics is extended within a Hamiltonian approach, by means of the introduction of an additional degree of freedom. We demonstrate that the cosmological constant can be introduced in the thermodynamic description of the SAdS black hole with a canonical transformation of the Schwarzschild problem, closely related to the introduction of an anti-de Sitter thermodynamic volume. The treatment presented is consistent, in the sense that it is compatible with the introduction of new thermodynamic potentials, and respects the laws of black hole Thermodynamics. By demanding homogeneity of the thermodynamic variables, we are able to construct a new equation of state that completely characterizes the Thermodynamics of SAdS black holes. The treatment naturally generates phenomenological constants that can be associated with different boundary conditions in underlying microscopic theories. A whole new set of phenomena can be expected from the proposed generalization of SAdS Thermodynamics.

  19. Thermodynamic constraints on fluctuation phenomena

    NASA Astrophysics Data System (ADS)

    Maroney, O. J. E.

    2009-12-01

    The relationships among reversible Carnot cycles, the absence of perpetual motion machines, and the existence of a nondecreasing globally unique entropy function form the starting point of many textbook presentations of the foundations of thermodynamics. However, the thermal fluctuation phenomena associated with statistical mechanics has been argued to restrict the domain of validity of this basis of the second law of thermodynamics. Here we demonstrate that fluctuation phenomena can be incorporated into the traditional presentation, extending rather than restricting the domain of validity of the phenomenologically motivated second law. Consistency conditions lead to constraints upon the possible spectrum of thermal fluctuations. In a special case this uniquely selects the Gibbs canonical distribution and more generally incorporates the Tsallis distributions. No particular model of microscopic dynamics need be assumed.

  20. Thermodynamic constraints on fluctuation phenomena.

    PubMed

    Maroney, O J E

    2009-12-01

    The relationships among reversible Carnot cycles, the absence of perpetual motion machines, and the existence of a nondecreasing globally unique entropy function form the starting point of many textbook presentations of the foundations of thermodynamics. However, the thermal fluctuation phenomena associated with statistical mechanics has been argued to restrict the domain of validity of this basis of the second law of thermodynamics. Here we demonstrate that fluctuation phenomena can be incorporated into the traditional presentation, extending rather than restricting the domain of validity of the phenomenologically motivated second law. Consistency conditions lead to constraints upon the possible spectrum of thermal fluctuations. In a special case this uniquely selects the Gibbs canonical distribution and more generally incorporates the Tsallis distributions. No particular model of microscopic dynamics need be assumed.

  1. Quantum thermodynamic cycles and quantum heat engines. II.

    PubMed

    Quan, H T

    2009-04-01

    We study the quantum-mechanical generalization of force or pressure, and then we extend the classical thermodynamic isobaric process to quantum-mechanical systems. Based on these efforts, we are able to study the quantum version of thermodynamic cycles that consist of quantum isobaric processes, such as the quantum Brayton cycle and quantum Diesel cycle. We also consider the implementation of the quantum Brayton cycle and quantum Diesel cycle with some model systems, such as single particle in a one-dimensional box and single-mode radiation field in a cavity. These studies lay the microscopic (quantum-mechanical) foundation for Szilard-Zurek single-molecule engine.

  2. Stochastic thermodynamics

    NASA Astrophysics Data System (ADS)

    Eichhorn, Ralf; Aurell, Erik

    2014-04-01

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

  3. Irreversible thermodynamic analysis and application for molecular heat engines

    NASA Astrophysics Data System (ADS)

    Lucia, Umberto; Açıkkalp, Emin

    2017-09-01

    Is there a link between the macroscopic approach to irreversibility and microscopic behaviour of the systems? Consumption of free energy keeps the system away from a stable equilibrium. Entropy generation results from the redistribution of energy, momentum, mass and charge. This concept represents the essence of the thermodynamic approach to irreversibility. Irreversibility is the result of the interaction between systems and their environment. The aim of this paper is to determine lost works in a molecular engine and compare results with macro (classical) heat engines. Firstly, irreversible thermodynamics are reviewed for macro and molecular cycles. Secondly, irreversible thermodynamics approaches are applied for a quantum heat engine with -1/2 spin system. Finally, lost works are determined for considered system and results show that macro and molecular heat engines obey same limitations. Moreover, a quantum thermodynamic approach is suggested in order to explain the results previously obtained from an atomic viewpoint.

  4. Molecular Thermodynamics for Cell Biology as Taught with Boxes

    ERIC Educational Resources Information Center

    Mayorga, Luis S.; Lopez, Maria Jose; Becker, Wayne M.

    2012-01-01

    Thermodynamic principles are basic to an understanding of the complex fluxes of energy and information required to keep cells alive. These microscopic machines are nonequilibrium systems at the micron scale that are maintained in pseudo-steady-state conditions by very sophisticated processes. Therefore, several nonstandard concepts need to be…

  5. Molecular spectroscopic and thermodynamic studies on the interaction of anti-platelet drug ticlopidine with calf thymus DNA

    NASA Astrophysics Data System (ADS)

    Afrin, Shumaila; Rahman, Yusra; Sarwar, Tarique; Husain, Mohammed Amir; Ali, Abad; Shamsuzzaman; Tabish, Mohammad

    2017-11-01

    Ticlopidine is an anti-platelet drug which belongs to the thienopyridine structural family and exerts its effect by functioning as an ADP receptor inhibitor. Ticlopidine inhibits the expression of TarO gene in S. aureus and may provide protection against MRSA. Groove binding agents are known to disrupt the transcription factor DNA complex and consequently inhibit gene expression. Understanding the mechanism of interaction of ticlopidine with DNA can prove useful in the development of a rational drug designing system. At present, there is no such study on the interaction of anti-platelet drugs with nucleic acids. A series of biophysical experiments were performed to ascertain the binding mode between ticlopidine and calf thymus DNA. UV-visible and fluorescence spectroscopic experiments confirmed the formation of a complex between ticlopidine and calf thymus DNA. Moreover, the values of binding constant were found to be in the range of 103 M- 1, which is indicative of groove binding between ticlopidine and calf thymus DNA. These results were further confirmed by studying the effect of denaturation on double stranded DNA, iodide quenching, viscometric studies, thermal melting profile as well as CD spectral analysis. The thermodynamic profile of the interaction was also determined using isothermal titration calorimetric studies. The reaction was found to be endothermic and the parameters obtained were found to be consistent with those of known groove binders. In silico molecular docking studies further corroborated well with the experimental results.

  6. THERMODYNAMICS OF THE ACTINIDES

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cunningham, Burris B.

    1962-04-01

    Recent work on the thermodynamic properties of the transplutonium elements is presented and discussed in relation to trends in thermodynamic properties of the actinide series. Accurate values are given for room temperature lattice parameters of two crystallographic forms, (facecentred cubic) fcc and dhcp (double-hexagonal closepacked), of americium metal and for the coefficients of thermal expansion between 157 and 878 deg K (dhcp) and 295 to 633 deg K (fcc). The meiting point of the metal, and its magnetic susceptibility between 77 and 823 deg K are reported and the latter compared with theoretical values for the tripositive ion calculated frommore » spectroscopic data. Similar data (crystallography, meiting point and magnetic susceptibility) are given for metallic curium. A value for the heat of formation of americium monoxide is reported in conjunction with crystallographic data on the monoxide and mononitride. A revision is made in the current value for the heat of formation of Am/O/sub 2/ and for the potential of the Am(III)-Am(IV) couple. The crystal structures and lattice parameters are reported for the trichloride, oxychloride and oxides of californium. (auth)« less

  7. Microscopic and macroscopic spectral peculiarities of cutaneous tumours

    NASA Astrophysics Data System (ADS)

    Borisova, Ekaterina; Genova, Tsanislava; Troyanova, Petranka; Terziev, Ivan; Zakharov, Valery; Bratchenko, Ivan; Lomova, Maria; Gorin, Dmitry; Avramov, Latchezar

    2017-12-01

    Autofluorescence spectral and confocal microscopic measurements were made on different cutaneous neoplastic lesions, namely basal cell carcinoma, squamous cell carcinoma, malignant melanoma, and their dysplastic forms - keratoacantoma, dysplastic nevi and benign lesions related - basal cell papiloma, seboreic keratosa and compound nevi using excitation at 405 nm. Spectroscopic investigations were made on in vivo and ex vivo tissue samples, and confocal microscopy investigations were made on ex vivo and eosin-haematoxilin stained thin slices of the tumours detected. Correlation between the spectral data received and the microscopic features observed was found, related to the morphological and biochemical alterations during neoplasia growth. Specific spectral features observed in each type of lesion investigated on micro and macro level would be presented and discussed.

  8. The second law of thermodynamics under unitary evolution and external operations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ikeda, Tatsuhiko N., E-mail: ikeda@cat.phys.s.u-tokyo.ac.jp; Physics Department, Boston University, Boston, MA 02215; Sakumichi, Naoyuki

    The von Neumann entropy cannot represent the thermodynamic entropy of equilibrium pure states in isolated quantum systems. The diagonal entropy, which is the Shannon entropy in the energy eigenbasis at each instant of time, is a natural generalization of the von Neumann entropy and applicable to equilibrium pure states. We show that the diagonal entropy is consistent with the second law of thermodynamics upon arbitrary external unitary operations. In terms of the diagonal entropy, thermodynamic irreversibility follows from the facts that quantum trajectories under unitary evolution are restricted by the Hamiltonian dynamics and that the external operation is performed withoutmore » reference to the microscopic state of the system.« less

  9. Planetary Surface Analysis Using Fast Laser Spectroscopic Techniques: Combined Microscopic Raman, LIBS, and Fluorescence Spectroscopy

    NASA Astrophysics Data System (ADS)

    Blacksberg, J.; Rossman, G. R.; Maruyama, Y.; Charbon, E.

    2011-12-01

    In situ exploration of planetary surfaces has to date required multiple techniques that, when used together, yield important information about their formation histories and evolution. We present a time-resolved laser spectroscopic technique that could potentially collect complementary sets of data providing information on mineral structure, composition, and hydration state. Using a picosecond-scale pulsed laser and a fast time-resolved detector we can simultaneously collect spectra from Raman, Laser Induced Breakdown Spectroscopy (LIBS), and fluorescence emissions that are separated in time due to the unique decay times of each process. The use of a laser with high rep rate (40 KHz) and low pulse energy (1 μJ/pulse) allows us to rapidly collect high signal to noise Raman spectra while minimizing sample damage. Increasing the pulse energy by about an order of magnitude creates a microscopic plasma near the surface and enables the collection of LIBS spectra at an unusually high rep rate and low pulse energy. Simultaneously, broader fluorescence peaks can be detected with lifetimes varying from nanosecond to microsecond. We will present Raman, LIBS, and fluorescence spectra obtained on natural mineral samples such as sulfates, clays, pyroxenes and carbonates that are of interest for Mars mineralogy. We demonstrate this technique using a photocathode-based streak camera detector as well as a newly-developed solid state Single Photon Avalanche Diode (SPAD) sensor array based on Complementary Metal-Oxide Semiconductor (CMOS) technology. We will discuss the impact of system design and detector choice on science return of a potential planetary surface mission, with a specific focus on size, weight, power, and complexity. The research described here was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (NASA).

  10. Pre-microscope tunnelling — Inspiration or constraint?

    NASA Astrophysics Data System (ADS)

    Walmsley, D. G.

    1987-03-01

    Before the microscope burst upon the scene, tunnelling had established for itself a substantial niche in the repertoire of the solid state physicist. Over a period of 20 years it has contributed importantly to our understanding of many systems. It elucidated the superconducting state, first by a direct display of the energy gap then by providing detailed information on the phonon spectra and electron-phonon coupling strength in junction electrodes. Its use as a phonon spectrometer was subsequently extended to semiconductors and to the oxides of insulating barriers. Eventually the vibrational spectra of monolayer organic and inorganic adsorbates became amenable with rich scientific rewards. In a few cases electronic transitions have been observed. Plasmon excitation by tunnelling electrons led to insights on the electron loss function in metals at visible frequencies and provided along the way an intriguing light emitting device. With the advent of the microscope it is now appropriate to enquire how much of this experience can profitably be carried over to the new environment. Are we constrained just to repeat the experiments in a new configuration? Happily no. The microscope offers us topographical and spectroscopic information of a new order. One might next ask how great is the contact between the two disciplines? We explore this question and seek to establish where the pre-microscope experience can be helpful in inspiring our use of this marvellous new facility that we know as the scanning tunnelling microscope.

  11. The second laws of quantum thermodynamics.

    PubMed

    Brandão, Fernando; Horodecki, Michał; Ng, Nelly; Oppenheim, Jonathan; Wehner, Stephanie

    2015-03-17

    The second law of thermodynamics places constraints on state transformations. It applies to systems composed of many particles, however, we are seeing that one can formulate laws of thermodynamics when only a small number of particles are interacting with a heat bath. Is there a second law of thermodynamics in this regime? Here, we find that for processes which are approximately cyclic, the second law for microscopic systems takes on a different form compared to the macroscopic scale, imposing not just one constraint on state transformations, but an entire family of constraints. We find a family of free energies which generalize the traditional one, and show that they can never increase. The ordinary second law relates to one of these, with the remainder imposing additional constraints on thermodynamic transitions. We find three regimes which determine which family of second laws govern state transitions, depending on how cyclic the process is. In one regime one can cause an apparent violation of the usual second law, through a process of embezzling work from a large system which remains arbitrarily close to its original state. These second laws are relevant for small systems, and also apply to individual macroscopic systems interacting via long-range interactions. By making precise the definition of thermal operations, the laws of thermodynamics are unified in this framework, with the first law defining the class of operations, the zeroth law emerging as an equivalence relation between thermal states, and the remaining laws being monotonicity of our generalized free energies.

  12. The second laws of quantum thermodynamics

    PubMed Central

    Brandão, Fernando; Horodecki, Michał; Ng, Nelly; Oppenheim, Jonathan; Wehner, Stephanie

    2015-01-01

    The second law of thermodynamics places constraints on state transformations. It applies to systems composed of many particles, however, we are seeing that one can formulate laws of thermodynamics when only a small number of particles are interacting with a heat bath. Is there a second law of thermodynamics in this regime? Here, we find that for processes which are approximately cyclic, the second law for microscopic systems takes on a different form compared to the macroscopic scale, imposing not just one constraint on state transformations, but an entire family of constraints. We find a family of free energies which generalize the traditional one, and show that they can never increase. The ordinary second law relates to one of these, with the remainder imposing additional constraints on thermodynamic transitions. We find three regimes which determine which family of second laws govern state transitions, depending on how cyclic the process is. In one regime one can cause an apparent violation of the usual second law, through a process of embezzling work from a large system which remains arbitrarily close to its original state. These second laws are relevant for small systems, and also apply to individual macroscopic systems interacting via long-range interactions. By making precise the definition of thermal operations, the laws of thermodynamics are unified in this framework, with the first law defining the class of operations, the zeroth law emerging as an equivalence relation between thermal states, and the remaining laws being monotonicity of our generalized free energies. PMID:25675476

  13. The biocompatibility of carbon hydroxyapatite/β-glucan composite for bone tissue engineering studied with Raman and FTIR spectroscopic imaging.

    PubMed

    Sroka-Bartnicka, Anna; Kimber, James A; Borkowski, Leszek; Pawlowska, Marta; Polkowska, Izabela; Kalisz, Grzegorz; Belcarz, Anna; Jozwiak, Krzysztof; Ginalska, Grazyna; Kazarian, Sergei G

    2015-10-01

    The spectroscopic approaches of FTIR imaging and Raman mapping were applied to the characterisation of a new carbon hydroxyapatite/β-glucan composite developed for bone tissue engineering. The composite is an artificial bone material with an apatite-forming ability for the bone repair process. Rabbit bone samples were tested with an implanted bioactive material for a period of several months. Using spectroscopic and chemometric methods, we were able to determine the presence of amides and phosphates and the distribution of lipid-rich domains in the bone tissue, providing an assessment of the composite's bioactivity. Samples were also imaged in transmission using an infrared microscope combined with a focal plane array detector. CaF2 lenses were also used on the infrared microscope to improve spectral quality by reducing scattering artefacts, improving chemometric analysis. The presence of collagen and lipids at the bone/composite interface confirmed biocompatibility and demonstrate the suitability of FTIR microscopic imaging with lenses in studying these samples. It confirmed that the composite is a very good background for collagen growth and increases collagen maturity with the time of the bone growth process. The results indicate the bioactive and biocompatible properties of this composite and demonstrate how Raman and FTIR spectroscopic imaging have been used as an effective tool for tissue characterisation.

  14. Spectroscopic identification of individual fluorophores using photoluminescence excitation spectra.

    PubMed

    Czerski, J; Colomb, W; Cannataro, F; Sarkar, S K

    2018-01-25

    The identity of a fluorophore can be ambiguous if other fluorophores or nonspecific fluorescent impurities have overlapping emission spectra. The presence of overlapping spectra makes it difficult to differentiate fluorescent species using discrete detection channels and unmixing of spectra. The unique absorption and emission signatures of fluorophores provide an opportunity for spectroscopic identification. However, absorption spectroscopy may be affected by scattering, whereas fluorescence emission spectroscopy suffers from signal loss by gratings or other dispersive optics. Photoluminescence excitation spectra, where excitation is varied and emission is detected at a fixed wavelength, allows hyperspectral imaging with a single emission filter for high signal-to-background ratio without any moving optics on the emission side. We report a high throughput method for measuring the photoluminescence excitation spectra of individual fluorophores using a tunable supercontinuum laser and prism-type total internal reflection fluorescence microscope. We used the system to measure and sort the photoluminescence excitation spectra of individual Alexa dyes, fluorescent nanodiamonds (FNDs), and fluorescent polystyrene beads. We used a Gaussian mixture model with maximum likelihood estimation to objectively separate the spectra. Finally, we spectroscopically identified different species of fluorescent nanodiamonds with overlapping spectra and characterized the heterogeneity of fluorescent nanodiamonds of varying size. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

  15. Spectroscopic study of intermolecular complexes between FAD and some β-carboline derivatives

    NASA Astrophysics Data System (ADS)

    Codoñer, Armando; Monzó, Isidro S.; Tomás, Francisco; Valero, Rosa

    The formation of molecular complexes between flavine adenine dinucleotide (FAD) and some β-carboline derivatives [antidepressant drugs that have a pronounced inhibition of monoamine oxidase (MAO)] has been studied by using electronic absorption and fluorescence spectroscopic methods. Thermodynamic parameters have been determined from the values of association constants for the molecular complexes at various temperatures. The influence of substituents in the β-carboline molecule on the stability of the complexes formed was also investigated.

  16. Thermodynamic, Spectroscopic, and Computational Studies of f -Element Complexation by N -Hydroxyethyl-diethylenetriamine- N,N ', N ", N"-tetraacetic Acid

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Grimes, Travis S.; Heathman, Colt R.; Jansone-Popova, Santa

    Potentiometric and spectroscopic techniques were combined with DFT calculations to probe the coordination environment and determine thermodynamic features of trivalent f-element complexation by N-hydroxyethyl-diethylenetriamine-N,N',N",N"-tetraacetic acid, HEDTTA. Ligand protonation constants and lanthanide stability constants were determined using potentiometry. Five protonation constants were accessible in I = 2.0 M (H +/Na +)ClO 4. UV–vis spectroscopy was used to determine stability constants for Nd 3+ and Am 3+ complexation with HEDTTA. Luminescence spectroscopy indicates two water molecules in the inner coordination sphere of the Eu/HEDTTA complex, suggesting HEDTTA is heptadentate. Luminescence data was supported by DFT calculations, which demonstrate that substitution of themore » acetate pendant arm by a N-hydroxyethyl group weakens the metal–nitrogen bond. This bond elongation is reflected in HEDTTA’s ability to differentiate trivalent actinides from trivalent lanthanides. The trans-lanthanide Ln/HEDTTA complex stability trend is analogous to Ln/DTPA complexation; however, the loss of one chelate ring resulting from structural substitution weakens the complexation by ~3 orders of magnitude. Successful separation of trivalent americium from trivalent lanthanides was demonstrated when HEDTTA was utilized as aqueous holdback complexant in a liquid–liquid system. Time-dependent extraction studies for HEDTTA were compared to diethylenetriamine-N,N,N',N",N"-pentaacetic acid (DTPA) and N-hydroxyethyl-ethylenediamine-N,N',N'-triacetic acid (HEDTA). The results presented here indicate substantially enhanced phase-transfer kinetic rates for mixtures containing HEDTTA.« less

  17. Thermodynamic, Spectroscopic, and Computational Studies of f -Element Complexation by N -Hydroxyethyl-diethylenetriamine- N,N ', N ", N"-tetraacetic Acid

    DOE PAGES

    Grimes, Travis S.; Heathman, Colt R.; Jansone-Popova, Santa; ...

    2017-01-24

    Potentiometric and spectroscopic techniques were combined with DFT calculations to probe the coordination environment and determine thermodynamic features of trivalent f-element complexation by N-hydroxyethyl-diethylenetriamine-N,N',N",N"-tetraacetic acid, HEDTTA. Ligand protonation constants and lanthanide stability constants were determined using potentiometry. Five protonation constants were accessible in I = 2.0 M (H +/Na +)ClO 4. UV–vis spectroscopy was used to determine stability constants for Nd 3+ and Am 3+ complexation with HEDTTA. Luminescence spectroscopy indicates two water molecules in the inner coordination sphere of the Eu/HEDTTA complex, suggesting HEDTTA is heptadentate. Luminescence data was supported by DFT calculations, which demonstrate that substitution of themore » acetate pendant arm by a N-hydroxyethyl group weakens the metal–nitrogen bond. This bond elongation is reflected in HEDTTA’s ability to differentiate trivalent actinides from trivalent lanthanides. The trans-lanthanide Ln/HEDTTA complex stability trend is analogous to Ln/DTPA complexation; however, the loss of one chelate ring resulting from structural substitution weakens the complexation by ~3 orders of magnitude. Successful separation of trivalent americium from trivalent lanthanides was demonstrated when HEDTTA was utilized as aqueous holdback complexant in a liquid–liquid system. Time-dependent extraction studies for HEDTTA were compared to diethylenetriamine-N,N,N',N",N"-pentaacetic acid (DTPA) and N-hydroxyethyl-ethylenediamine-N,N',N'-triacetic acid (HEDTA). The results presented here indicate substantially enhanced phase-transfer kinetic rates for mixtures containing HEDTTA.« less

  18. Surface conservation laws at microscopically diffuse interfaces.

    PubMed

    Chu, Kevin T; Bazant, Martin Z

    2007-11-01

    In studies of interfaces with dynamic chemical composition, bulk and interfacial quantities are often coupled via surface conservation laws of excess surface quantities. While this approach is easily justified for microscopically sharp interfaces, its applicability in the context of microscopically diffuse interfaces is less theoretically well-established. Furthermore, surface conservation laws (and interfacial models in general) are often derived phenomenologically rather than systematically. In this article, we first provide a mathematically rigorous justification for surface conservation laws at diffuse interfaces based on an asymptotic analysis of transport processes in the boundary layer and derive general formulae for the surface and normal fluxes that appear in surface conservation laws. Next, we use nonequilibrium thermodynamics to formulate surface conservation laws in terms of chemical potentials and provide a method for systematically deriving the structure of the interfacial layer. Finally, we derive surface conservation laws for a few examples from diffusive and electrochemical transport.

  19. An original method to determine complex refractive index of liquids by spectroscopic ellipsometry and illustrated applications

    NASA Astrophysics Data System (ADS)

    Stchakovsky, M.; Battie, Y.; Naciri, A. En

    2017-11-01

    We present a method to characterize optical properties of liquids by spectroscopic ellipsometry. The experiments use a specific liquid cell that avoids disturbance of waves at air-liquid interface and allows the determination of the real and the imaginary part of the refractive index, with a sensitivity of the latter below 10-4. The method is illustrated by results obtained with a spectroscopic phase modulation ellipsometer on several liquids such as deionised water, microscope oil and protein solution. Comparisons of the method with standard techniques are given.

  20. EEL spectroscopic tomography: towards a new dimension in nanomaterials analysis.

    PubMed

    Yedra, Lluís; Eljarrat, Alberto; Arenal, Raúl; Pellicer, Eva; Cabo, Moisés; López-Ortega, Alberto; Estrader, Marta; Sort, Jordi; Baró, Maria Dolors; Estradé, Sònia; Peiró, Francesca

    2012-11-01

    Electron tomography is a widely spread technique for recovering the three dimensional (3D) shape of nanostructured materials. Using a spectroscopic signal to achieve a reconstruction adds a fourth chemical dimension to the 3D structure. Up to date, energy filtering of the images in the transmission electron microscope (EFTEM) is the usual spectroscopic method even if most of the information in the spectrum is lost. Unlike EFTEM tomography, the use of electron energy-loss spectroscopy (EELS) spectrum images (SI) for tomographic reconstruction retains all chemical information, and the possibilities of this new approach still remain to be fully exploited. In this article we prove the feasibility of EEL spectroscopic tomography at low voltages (80 kV) and short acquisition times from data acquired using an aberration corrected instrument and data treatment by Multivariate Analysis (MVA), applied to Fe(x)Co((3-x))O(4)@Co(3)O(4) mesoporous materials. This approach provides a new scope into materials; the recovery of full EELS signal in 3D. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Future constraints on halo thermodynamics from combined Sunyaev-Zel'dovich measurements

    NASA Astrophysics Data System (ADS)

    Battaglia, Nicholas; Ferraro, Simone; Schaan, Emmanuel; Spergel, David N.

    2017-11-01

    The improving sensitivity of measurements of the kinetic Sunyaev-Zel'dovich (SZ) effect opens a new window into the thermodynamic properties of the baryons in halos. We propose a methodology to constrain these thermodynamic properties by combining the kinetic SZ, which is an unbiased probe of the free electron density, and the thermal SZ, which probes their thermal pressure. We forecast that our method constrains the average thermodynamic processes that govern the energetics of galaxy evolution like energetic feedback across all redshift ranges where viable halos sample are available. Current Stage-3 cosmic microwave background (CMB) experiments like AdvACT and SPT-3G can measure the kSZ and tSZ to greater than 100σ if combined with a DESI-like spectroscopic survey. Such measurements translate into percent-level constraints on the baryonic density and pressure profiles and on the feedback and non-thermal pressure support parameters for a given ICM model. This in turn will provide critical thermodynamic tests for sub-grid models of feedback in cosmological simulations of galaxy formation. The high fidelity measurements promised by the next generation CMB experiment, CMB-S4, allow one to further sub-divide these constraints beyond redshift into other classifications, like stellar mass or galaxy type.

  2. Global spectroscopic survey of cloud thermodynamic phase at high spatial resolution, 2005-2015

    NASA Astrophysics Data System (ADS)

    Thompson, David R.; Kahn, Brian H.; Green, Robert O.; Chien, Steve A.; Middleton, Elizabeth M.; Tran, Daniel Q.

    2018-02-01

    The distribution of ice, liquid, and mixed phase clouds is important for Earth's planetary radiation budget, impacting cloud optical properties, evolution, and solar reflectivity. Most remote orbital thermodynamic phase measurements observe kilometer scales and are insensitive to mixed phases. This under-constrains important processes with outsize radiative forcing impact, such as spatial partitioning in mixed phase clouds. To date, the fine spatial structure of cloud phase has not been measured at global scales. Imaging spectroscopy of reflected solar energy from 1.4 to 1.8 µm can address this gap: it directly measures ice and water absorption, a robust indicator of cloud top thermodynamic phase, with spatial resolution of tens to hundreds of meters. We report the first such global high spatial resolution survey based on data from 2005 to 2015 acquired by the Hyperion imaging spectrometer onboard NASA's Earth Observer 1 (EO-1) spacecraft. Seasonal and latitudinal distributions corroborate observations by the Atmospheric Infrared Sounder (AIRS). For extratropical cloud systems, just 25 % of variance observed at GCM grid scales of 100 km was related to irreducible measurement error, while 75 % was explained by spatial correlations possible at finer resolutions.

  3. Role of quantum coherence in the thermodynamics of energy transfer

    NASA Astrophysics Data System (ADS)

    Henao, Ivan; Serra, Roberto M.

    2018-06-01

    Recent research on the thermodynamic arrow of time, at the microscopic scale, has questioned the universality of its direction. Theoretical studies showed that quantum correlations can be used to revert the natural heat flow (from the hot body to the cold one), posing an apparent challenge to the second law of thermodynamics. Such an "anomalous" heat current was observed in a recent experiment (K. Micadei et al., arXiv:1711.03323), by employing two spin systems initially quantum correlated. Nevertheless, the precise relationship between this intriguing phenomenon and the initial conditions that allow it is not fully evident. Here, we address energy transfer in a wider perspective, identifying a nonclassical contribution that applies to the reversion of the heat flow as well as to more general forms of energy exchange. We derive three theorems that describe the energy transfer between two microscopic systems, for arbitrary initial bipartite states. Using these theorems, we obtain an analytical bound showing that certain type of quantum coherence can optimize such a process, outperforming incoherent states. This genuine quantum advantage is corroborated through a characterization of the energy transfer between two qubits. For this system, it is shown that a large enough amount of coherence is necessary and sufficient to revert the thermodynamic arrow of time. As a second crucial consequence of the presented theorems, we introduce a class of nonequilibrium states that only allow unidirectional energy flow. In this way, we broaden the set where the standard Clausius statement of the second law applies.

  4. Thermodynamics of information exchange between two coupled quantum dots

    NASA Astrophysics Data System (ADS)

    Kutvonen, Aki; Sagawa, Takahiro; Ala-Nissila, Tapio

    2016-03-01

    We propose a setup based on two coupled quantum dots where thermodynamics of a measurement can be quantitatively characterized. The information obtained in the measurement can be utilized by performing feedback in a manner apparently breaking the second law of thermodynamics. In this way the setup can be operated as a Maxwell's demon, where both the measurement and feedback are performed separately by controlling an external parameter. This is analogous to the case of the original Szilard engine. Since the setup contains both the microscopic demon and the engine itself, the operation of the whole measurement-feedback cycle can be explained in detail at the level of single realizations. In addition, we derive integral fluctuation relations for both the bare and coarse-grained entropy productions in the setup.

  5. Anterior chamber blood cell differentiation using spectroscopic optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Qian, Ruobing; McNabb, Ryan P.; Kuo, Anthony N.; Izatt, Joseph A.

    2018-02-01

    There is great clinical importance in identifying cellular responses in the anterior chamber (AC) which can indicate signs of hyphema (an accumulation of red blood cells (RBCs)) or aberrant intraocular inflammation (an accumulation of white blood cells (WBCs)). These responses are difficult to diagnose and require specialized equipment such as ophthalmic microscopes and specialists trained in examining the eye. In this work, we applied spectroscopic OCT to differentiate between RBCs and subtypes of WBCs, including neutrophils, lymphocytes and monocytes, both in vitro and in ACs of porcine eyes. We located and tracked single cells in OCT volumetric images, and extracted the spectroscopic data of each cell from the detected interferograms using short-time Fourier Transform (STFT). A look-up table of Mie spectra was generated and used to correlate the spectroscopic data of single cells to their characteristic sizes. The accuracy of the method was first validated on 10um polystyrene microspheres. For RBCs and subtypes of WBCs, the extracted size distributions based on the best Mie spectra fit were significantly different between each cell type by using the Wilcoxon rank-sum test. A similar size distribution of neutrophils was also acquired in the measurements of cells introduced into the ACs of porcine eyes, further supporting spectroscopic OCT for potentially differentiating and quantifying blood cell types in the AC in vivo.

  6. Thermodynamic and transport properties of frozen and reacting pH2-oH2 mixtures

    NASA Technical Reports Server (NTRS)

    Carter, H. G.; Bullock, R. E.

    1972-01-01

    Application of experimental state data and spectroscopic term values shows that the thermodynamic and transport properties of reacting pH2-oH2 mixtures are considerably different than those of chemically frozen pH2 at temperatures below 300 R. Calculated H-S data also show that radiation-induced pH2-oH2 equilibration at constant enthalpy produces a temperature drop of at least 28 R, corresponding to an ideal shaft work loss of 15% or more for a turbine operating downstream from the point of conversion. Aside from differences in thermodynamic and transport properties, frozen pH2-oH2 mixtures may differ from pure pH2 on a purely hydrodynamical basis.

  7. Plum pudding random medium model of biological tissue toward remote microscopy from spectroscopic light scattering

    PubMed Central

    Xu, Min

    2017-01-01

    Biological tissue has a complex structure and exhibits rich spectroscopic behavior. There has been no tissue model until now that has been able to account for the observed spectroscopy of tissue light scattering and its anisotropy. Here we present, for the first time, a plum pudding random medium (PPRM) model for biological tissue which succinctly describes tissue as a superposition of distinctive scattering structures (plum) embedded inside a fractal continuous medium of background refractive index fluctuation (pudding). PPRM faithfully reproduces the wavelength dependence of tissue light scattering and attributes the “anomalous” trend in the anisotropy to the plum and the powerlaw dependence of the reduced scattering coefficient to the fractal scattering pudding. Most importantly, PPRM opens up a novel venue of quantifying the tissue architecture and microscopic structures on average from macroscopic probing of the bulk with scattered light alone without tissue excision. We demonstrate this potential by visualizing the fine microscopic structural alterations in breast tissue (adipose, glandular, fibrocystic, fibroadenoma, and ductal carcinoma) deduced from noncontact spectroscopic measurement. PMID:28663913

  8. Exact analytical thermodynamic expressions for a Brownian heat engine

    NASA Astrophysics Data System (ADS)

    Taye, Mesfin Asfaw

    2015-09-01

    The nonequilibrium thermodynamics feature of a Brownian motor operating between two different heat baths is explored as a function of time t . Using the Gibbs entropy and Schnakenberg microscopic stochastic approach, we find exact closed form expressions for the free energy, the rate of entropy production, and the rate of entropy flow from the system to the outside. We show that when the system is out of equilibrium, it constantly produces entropy and at the same time extracts entropy out of the system. Its entropy production and extraction rates decrease in time and saturate to a constant value. In the long time limit, the rate of entropy production balances the rate of entropy extraction, and at equilibrium both entropy production and extraction rates become zero. Furthermore, via the present model, many thermodynamic theories can be checked.

  9. Exact analytical thermodynamic expressions for a Brownian heat engine.

    PubMed

    Taye, Mesfin Asfaw

    2015-09-01

    The nonequilibrium thermodynamics feature of a Brownian motor operating between two different heat baths is explored as a function of time t. Using the Gibbs entropy and Schnakenberg microscopic stochastic approach, we find exact closed form expressions for the free energy, the rate of entropy production, and the rate of entropy flow from the system to the outside. We show that when the system is out of equilibrium, it constantly produces entropy and at the same time extracts entropy out of the system. Its entropy production and extraction rates decrease in time and saturate to a constant value. In the long time limit, the rate of entropy production balances the rate of entropy extraction, and at equilibrium both entropy production and extraction rates become zero. Furthermore, via the present model, many thermodynamic theories can be checked.

  10. Routes towards an abstract thermodynamics in the late nineteenth century

    NASA Astrophysics Data System (ADS)

    Bordoni, Stefano

    2013-12-01

    Two different traditions of research emerged from Rudolf Clausius's version of thermodynamics. While James Clerk Maxwell and Ludwig Boltzmann pursued the integration of thermodynamics with the kinetic theory of gases, others relied on a macroscopic and more abstract approach that set aside specific mechanical models. This second approach blossomed in about two decades in different countries of Europe and in the United States. François Massieu, Josiah Willard Gibbs, Hermann Helmholtz, and then Pierre Duhem explored the connections between the contents of thermodynamics and the formal structures of analytical mechanics. Others like the young Max Planck and Arthur von Oettingen pursued a sort of formal symmetry between thermal and mechanical variables. In the British Isles, Joseph John Thomson developed a dynamical approach to physics and chemistry, making use of the tools of abstract mechanics without excluding microscopic motions. Some developments were logically interconnected, as it was for Massieu's, Gibbs's, Helmholtz's, and Duhem's, even though they occurred in a largely independent manner. Duhem put forward the most original and most systematic reinterpretation of thermodynamics, which involved a bold upgrading of analytical mechanics and a bold mathematical unification of physics and chemistry. A strong commitment to unification was one of the hallmarks of all these theoretical researches.

  11. The ALBA spectroscopic LEEM-PEEM experimental station: layout and performance

    PubMed Central

    Aballe, Lucia; Foerster, Michael; Pellegrin, Eric; Nicolas, Josep; Ferrer, Salvador

    2015-01-01

    The spectroscopic LEEM-PEEM experimental station at the CIRCE helical undulator beamline, which started user operation at the ALBA Synchrotron Light Facility in 2012, is presented. This station, based on an Elmitec LEEM III microscope with electron imaging energy analyzer, permits surfaces to be imaged with chemical, structural and magnetic sensitivity down to a lateral spatial resolution better than 20 nm with X-ray excited photoelectrons and 10 nm in LEEM and UV-PEEM modes. Rotation around the surface normal and application of electric and (weak) magnetic fields are possible in the microscope chamber. In situ surface preparation capabilities include ion sputtering, high-temperature flashing, exposure to gases, and metal evaporation with quick evaporator exchange. Results from experiments in a variety of fields and imaging modes will be presented in order to illustrate the ALBA XPEEM capabilities. PMID:25931092

  12. Microscopic insight into thermodynamics of conformational changes of SAP-SLAM complex in signal transduction cascade.

    PubMed

    Samanta, Sudipta; Mukherjee, Sanchita

    2017-04-28

    The signalling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, associate with SLAM-associated protein (SAP)-related molecules, composed of single SH2 domain architecture. SAP activates Src-family kinase Fyn after SLAM ligation, resulting in a SLAM-SAP-Fyn complex, where, SAP binds the Fyn SH3 domain that does not involve canonical SH3 or SH2 interactions. This demands insight into this SAP mediated signalling cascade. Thermodynamics of the conformational changes are extracted from the histograms of dihedral angles obtained from the all-atom molecular dynamics simulations of this structurally well characterized SAP-SLAM complex. The results incorporate the binding induced thermodynamic changes of individual amino acid as well as the secondary structural elements of the protein and the solvent. Stabilization of the peptide partially comes through a strong hydrogen bonding network with the protein, while hydrophobic interactions also play a significant role where the peptide inserts itself into a hydrophobic cavity of the protein. SLAM binding widens SAP's second binding site for Fyn, which is the next step in the signal transduction cascade. The higher stabilization and less fluctuation of specific residues of SAP in the Fyn binding site, induced by SAP-SLAM complexation, emerge as the key structural elements to trigger the recognition of SAP by the SH3 domain of Fyn. The thermodynamic quantification of the protein due to complexation not only throws deeper understanding in the established mode of SAP-SLAM interaction but also assists in the recognition of the relevant residues of the protein responsible for alterations in its activity.

  13. Microscopic insight into thermodynamics of conformational changes of SAP-SLAM complex in signal transduction cascade

    NASA Astrophysics Data System (ADS)

    Samanta, Sudipta; Mukherjee, Sanchita

    2017-04-01

    The signalling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, associate with SLAM-associated protein (SAP)-related molecules, composed of single SH2 domain architecture. SAP activates Src-family kinase Fyn after SLAM ligation, resulting in a SLAM-SAP-Fyn complex, where, SAP binds the Fyn SH3 domain that does not involve canonical SH3 or SH2 interactions. This demands insight into this SAP mediated signalling cascade. Thermodynamics of the conformational changes are extracted from the histograms of dihedral angles obtained from the all-atom molecular dynamics simulations of this structurally well characterized SAP-SLAM complex. The results incorporate the binding induced thermodynamic changes of individual amino acid as well as the secondary structural elements of the protein and the solvent. Stabilization of the peptide partially comes through a strong hydrogen bonding network with the protein, while hydrophobic interactions also play a significant role where the peptide inserts itself into a hydrophobic cavity of the protein. SLAM binding widens SAP's second binding site for Fyn, which is the next step in the signal transduction cascade. The higher stabilization and less fluctuation of specific residues of SAP in the Fyn binding site, induced by SAP-SLAM complexation, emerge as the key structural elements to trigger the recognition of SAP by the SH3 domain of Fyn. The thermodynamic quantification of the protein due to complexation not only throws deeper understanding in the established mode of SAP-SLAM interaction but also assists in the recognition of the relevant residues of the protein responsible for alterations in its activity.

  14. Development and Optical Testing of the Camera, Hand Lens, and Microscope Probe with Scannable Laser Spectroscopy (CHAMP-SLS)

    NASA Technical Reports Server (NTRS)

    Mungas, Greg S.; Gursel, Yekta; Sepulveda, Cesar A.; Anderson, Mark; La Baw, Clayton; Johnson, Kenneth R.; Deans, Matthew; Beegle, Luther; Boynton, John

    2008-01-01

    Conducting high resolution field microscopy with coupled laser spectroscopy that can be used to selectively analyze the surface chemistry of individual pixels in a scene is an enabling capability for next generation robotic and manned spaceflight missions, civil, and military applications. In the laboratory, we use a range of imaging and surface preparation tools that provide us with in-focus images, context imaging for identifying features that we want to investigate at high magnification, and surface-optical coupling that allows us to apply optical spectroscopic analysis techniques for analyzing surface chemistry particularly at high magnifications. The camera, hand lens, and microscope probe with scannable laser spectroscopy (CHAMP-SLS) is an imaging/spectroscopy instrument capable of imaging continuously from infinity down to high resolution microscopy (resolution of approx. 1 micron/pixel in a final camera format), the closer CHAMP-SLS is placed to a feature, the higher the resultant magnification. At hand lens to microscopic magnifications, the imaged scene can be selectively interrogated with point spectroscopic techniques such as Raman spectroscopy, microscopic Laser Induced Breakdown Spectroscopy (micro-LIBS), laser ablation mass-spectrometry, Fluorescence spectroscopy, and/or Reflectance spectroscopy. This paper summarizes the optical design, development, and testing of the CHAMP-SLS optics.

  15. Thermodynamics of H-bonding in alcohols and water. The mobile order theory as opposed to the classical multicomponent order theories

    NASA Astrophysics Data System (ADS)

    Huyskens, P.; Kapuku, F.; Colemonts-Vandevyvere, C.

    1990-09-01

    In liquids the partners of H bonds constantly change. As a consequence the entities observed by IR spectroscopy are not the same as those considered for thermodynamic properties. For the latter, the H-bonds are shared by all the molecules. The thermodynamic "monomeric fraction", γ, the time fraction during which an alcohol molecule is vaporizable, is the square root of the spectroscopic monomeric fraction, and is the fraction of molecules which, during a time interval of 10 -14 s, have their hydroxylic proton and their lone pairs free. The classical thermodynamic treatments of Mecke and Prigogine consider the spectroscopic entities as real thermodynamic entities. Opposed to this, the mobile order theory considers all the formal molecules as equal but with a reduction of the entropy due to the fact that during a fraction 1-γ of the time, the OH proton follows a neighbouring oxygen atom on its journey through the liquid. Mobile order theory and classic multicomponent treatment lead, in binary mixtures of the associated substance A with the inert substance S, to expressions of the chemical potentials μ A and μ S that are fundamentally different. However, the differences become very important only when the molar volumes overlineVS and overlineVA differ by a factor larger than 2. As a consequence the equations of the classic theory can still fit the experimental vapour pressure data of mixtures of liquid alcohols and liquid alkanes. However, the solubilities of solid alkanes in water for which overlineVS > 3 overlineVA are only correctly predicted by the mobile order theory.

  16. The spectroscopic search for the trace aerosols in the planetary atmospheres - the results of numerical simulations

    NASA Astrophysics Data System (ADS)

    Blecka, Maria I.

    2010-05-01

    The passive remote spectrometric methods are important in examinations the atmospheres of planets. The radiance spectra inform us about values of thermodynamical parameters and composition of the atmospheres and surfaces. The spectral technology can be useful in detection of the trace aerosols like biological substances (if present) in the environments of the planets. We discuss here some of the aspects related to the spectroscopic search for the aerosols and dust in planetary atmospheres. Possibility of detection and identifications of biological aerosols with a passive InfraRed spectrometer in an open-air environment is discussed. We present numerically simulated, based on radiative transfer theory, spectroscopic observations of the Earth atmosphere. Laboratory measurements of transmittance of various kinds of aerosols, pollens and bacterias were used in modeling.

  17. Signatures of Solvation Thermodynamics in Spectra of Intermolecular Vibrations

    PubMed Central

    2017-01-01

    This study explores the thermodynamic and vibrational properties of water in the three-dimensional environment of solvated ions and small molecules using molecular simulations. The spectrum of intermolecular vibrations in liquid solvents provides detailed information on the shape of the local potential energy surface, which in turn determines local thermodynamic properties such as the entropy. Here, we extract this information using a spatially resolved extension of the two-phase thermodynamics method to estimate hydration water entropies based on the local vibrational density of states (3D-2PT). Combined with an analysis of solute–water and water–water interaction energies, this allows us to resolve local contributions to the solvation enthalpy, entropy, and free energy. We use this approach to study effects of ions on their surrounding water hydrogen bond network, its spectrum of intermolecular vibrations, and resulting thermodynamic properties. In the three-dimensional environment of polar and nonpolar functional groups of molecular solutes, we identify distinct hydration water species and classify them by their characteristic vibrational density of states and molecular entropies. In each case, we are able to assign variations in local hydration water entropies to specific changes in the spectrum of intermolecular vibrations. This provides an important link for the thermodynamic interpretation of vibrational spectra that are accessible to far-infrared absorption and Raman spectroscopy experiments. Our analysis provides unique microscopic details regarding the hydration of hydrophobic and hydrophilic functional groups, which enable us to identify interactions and molecular degrees of freedom that determine relevant contributions to the solvation entropy and consequently the free energy. PMID:28783431

  18. Structural, conformational and thermodynamic aspects of groove-directed-intercalation of flavopiridol into DNA.

    PubMed

    Ray, Bhumika; Agarwal, Shweta; Lohani, Neelam; Rajeswari, Moganty R; Mehrotra, Ranjana

    2016-11-01

    Certain plant-derived alkaloids and flavonoids have shown propitious cytotoxic acitvity against different types of cancer, having deoxyribose nucleic acid (DNA) as their main cellular target. Flavopiridol, a semi-synthetic derivative of rohitukine (a natural compound isolated from Dysoxylum binectariferum plant), has attained much attention owing to its anticancer potential against various haematological malignancies and solid tumours. This work focuses on investigating interaction between flavopiridol and DNA at molecular level in order to decipher its underlying mechanism of action, which is not well understood. To define direct influence of flavopiridol on the structural, conformational and thermodynamic aspects of DNA, various spectroscopic and calorimetric techniques have been used. ATR-FTIR and SERS spectral outcomes indicate a novel insight into groove-directed-intercalation of flavopiridol into DNA via direct binding with nitrogenous bases guanine (C6=O6) and thymine (C2=O2) in DNA groove together with slight external binding to its sugar-phosphate backbone. Circular dichroism spectral analysis of flavopiridol-DNA complexes suggests perturbation in native B-conformation of DNA and its transition into C-form, which may be localized up to a few base pairs of DNA. UV-visible spectroscopic results illustrate dual binding mode of flavopiridol when interacts with DNA having association constant, Ka = 1.18 × 10(4) M(-1). This suggests moderate type of interaction between flavopiridol and DNA. Further, UV melting analysis also supports spectroscopic outcomes. Thermodynamically, flavopiridol-DNA complexation is an enthalpy-driven exothermic process. These conclusions drawn from this study could be helpful in unveiling mechanism of cytoxicity induced by flavopiridol that can be further applied in the development of flavonoid-based new chemotherapeutics with more specificity and better efficacy.

  19. Coarse-grained forms for equations describing the microscopic motion of particles in a fluid.

    PubMed

    Das, Shankar P; Yoshimori, Akira

    2013-10-01

    Exact equations of motion for the microscopically defined collective density ρ(x,t) and the momentum density ĝ(x,t) of a fluid have been obtained in the past starting from the corresponding Langevin equations representing the dynamics of the fluid particles. In the present work we average these exact equations of microscopic dynamics over the local equilibrium distribution to obtain stochastic partial differential equations for the coarse-grained densities with smooth spatial and temporal dependence. In particular, we consider Dean's exact balance equation for the microscopic density of a system of interacting Brownian particles to obtain the basic equation of the dynamic density functional theory with noise. Our analysis demonstrates that on thermal averaging the dependence of the exact equations on the bare interaction potential is converted to dependence on the corresponding thermodynamic direct correlation functions in the coarse-grained equations.

  20. Microscopic, Transport and Thermodynamic properties of Ca10(Pt3As8)((Fe1-xTMx)2As2)5 (TM=Co, Ni) single crystals

    NASA Astrophysics Data System (ADS)

    Jiang, Shan; Ni, Ni

    2015-03-01

    Here we report detailed microscopic, transport and thermodynamic measurements on two series of high quality single crystals Ca10(Pt3As8)((Fe1-xTMx)2As2)5 (TM=Co, Ni). With electron doping on Fe sites, the structural/magnetic phase transitions in the parent compound were suppressed at a rate of roughly -7K per 0.01Co doping and -9K per 0.01Ni doping. Superconductivity emerges in the region of 0 . 048 < x < 0 . 20 for Co doping with optimal Tc of 13.5K (x = 0 . 11) while it occurs in the region of 0 . 035 < x < 0 . 11 for Ni doping with optimal Tc of 9.6K (x = 0 . 064). No coexistence of AFM and SC is observed, which is different from the well-studied 122 Fe-pnictides but reminiscent the one of La1111. The comparison of the effect between Co- and Ni- doping on 10-3-8 shows that rigid band approximation is likely working for these two dopants in this superconducting family.

  1. [Progress in Raman spectroscopic measurement of methane hydrate].

    PubMed

    Xu, Feng; Zhu, Li-hua; Wu, Qiang; Xu, Long-jun

    2009-09-01

    Complex thermodynamics and kinetics problems are involved in the methane hydrate formation and decomposition, and these problems are crucial to understanding the mechanisms of hydrate formation and hydrate decomposition. However, it was difficult to accurately obtain such information due to the difficulty of measurement since methane hydrate is only stable under low temperature and high pressure condition, and until recent years, methane hydrate has been measured in situ using Raman spectroscopy. Raman spectroscopy, a non-destructive and non-invasive technique, is used to study vibrational modes of molecules. Studies of methane hydrate using Raman spectroscopy have been developed over the last decade. The Raman spectra of CH4 in vapor phase and in hydrate phase are presented in this paper. The progress in the research on methane hydrate formation thermodynamics, formation kinetics, decomposition kinetics and decomposition mechanism based on Raman spectroscopic measurements in the laboratory and deep sea are reviewed. Formation thermodynamic studies, including in situ observation of formation condition of methane hydrate, analysis of structure, and determination of hydrate cage occupancy and hydration numbers by using Raman spectroscopy, are emphasized. In the aspect of formation kinetics, research on variation in hydrate cage amount and methane concentration in water during the growth of hydrate using Raman spectroscopy is also introduced. For the methane hydrate decomposition, the investigation associated with decomposition mechanism, the mutative law of cage occupancy ratio and the formulation of decomposition rate in porous media are described. The important aspects for future hydrate research based on Raman spectroscopy are discussed.

  2. Reaction cycle and thermodynamics in bacteriorhodopsin

    NASA Technical Reports Server (NTRS)

    Lanyi, J. K.

    1992-01-01

    Light causes the all-trans to 13-cis isomerization of the retinal in bacteriorhodopsin; the thermal relaxation leading back to the initial state drives proton transport first via proton transfer between the retinal Schiff base and D85 and then between the Schiff base and D96. The reaction sequence and thermodynamics of this photocycle are described by measuring time-resolved absorption changes with a gated multichannel analyzer between 100 ns and 100 ms, at six temperatures between 5 degrees C and 30 degrees C. Analysis of the energetics of the chromophore reaction sequence is on the basis of a recently proposed model (Varo & Lanyi, Biochemistry 30, 5016-5022, 1991) which consists of a single cycle and many reversible reactions: BR -hv-->K<==>L<==>M1-->M2<==>N<==>O-->BR. The existence of the M1-->M2 reaction, which functions as the switch in the proton transfer, is confirmed by spectroscopic evidence. The calculated thermodynamic parameters indicate that the exchange of free energy between the protein and the protons is at the switch step. Further, a large entropy decrease at this reaction suggests a protein conformation change which will conserve delta G for driving the completion of the reaction cycle. The results provide insights to mechanism and energy coupling in this system, with possible relevance to the general question of how ion pumps function.

  3. The thermodynamical foundation of electronic conduction in solids

    NASA Astrophysics Data System (ADS)

    Bringuier, E.

    2018-03-01

    In elementary textbooks, the microscopic justification of Ohm’s local law in a solid medium starts with Drude’s classical model of electron transport and next discusses the quantum-dynamical and statistical amendments. In this paper, emphasis is laid instead upon the thermodynamical background motivated by the Joule-Lenz heating effect accompanying conduction and the fact that the conduction electrons are thermalized at the lattice temperature. Both metals and n-type semiconductors are considered; but conduction under a magnetic field is not. Proficiency in second-year thermodynamics and vector analysis is required from an undergraduate university student in physics so that the content of the paper can be taught to third-year students. The necessary elements of quantum mechanics are posited in this paper without detailed justification. We start with the equilibrium-thermodynamic notion of the chemical potential of the electron gas, the value of which distinguishes metals from semiconductors. Then we turn to the usage of the electrochemical potential in the description of near-equilibrium electron transport. The response of charge carriers to the electrochemical gradient involves the mobility, which is the reciprocal of the coefficient of the effective friction force opposing the carrier drift. Drude’s calculation of mobility is restated with the dynamical requirements of quantum physics. Where the carrier density is inhomogeneous, there appears diffusion, the coefficient of which is thermodynamically related to the mobility. Next, it is remarked that the release of heat was ignored in Drude’s original model. In this paper, the flow of Joule heat is handled thermodynamically within an energy balance where the voltage generator, the conduction electrons and the host lattice are involved in an explicit way. The notion of dissipation is introduced as the rate of entropy creation in a steady state. The body of the paper is restricted to the case of one

  4. Thermodynamic Diagrams

    NASA Astrophysics Data System (ADS)

    Chaston, Scot

    1999-02-01

    Thermodynamic data such as equilibrium constants, standard cell potentials, molar enthalpies of formation, and standard entropies of substances can be a very useful basis for an organized presentation of knowledge in diverse areas of applied chemistry. Thermodynamic data can become particularly useful when incorporated into thermodynamic diagrams that are designed to be easy to recall, to serve as a basis for reconstructing previous knowledge, and to determine whether reactions can occur exergonically or only with the help of an external energy source. Few students in our chemistry-based courses would want to acquire the depth of knowledge or rigor of professional thermodynamicists. But they should nevertheless learn how to make good use of thermodynamic data in their professional occupations that span the chemical, biological, environmental, and medical laboratory fields. This article discusses examples of three thermodynamic diagrams that have been developed for this purpose. They are the thermodynamic energy account (TEA), the total entropy scale, and the thermodynamic scale diagrams. These diagrams help in the teaching and learning of thermodynamics by bringing the imagination into the process of developing a better understanding of abstract thermodynamic functions, and by allowing the reader to keep track of specialist thermodynamic discourses in the literature.

  5. Spectroscopic studies of nanomaterials with a liquid-helium-free high-stability cryogenic scanning tunneling microscope

    NASA Astrophysics Data System (ADS)

    Kislitsyn, Dmitry Anatolevich

    This dissertation presents results of a project bringing Scanning Tunneling Microscope (STM) into a regime of unlimited operational time at cryogenic conditions. Freedom from liquid helium consumption was achieved and technical characteristics of the instrument are reported, including record low noise for a scanning probe instrument coupled to a close-cycle cryostat, which allows for atomically resolved imaging, and record low thermal drift. Subsequent studies showed that the new STM opened new prospects in nanoscience research by enabling Scanning Tunneling Spectroscopic (STS) spatial mapping to reveal details of the electronic structure in real space for molecules and low-dimensional nanomaterials, for which this depth of investigation was previously prohibitively expensive. Quantum-confined electronic states were studied in single-walled carbon nanotubes (SWCNTs) deposited on the Au(111) surface. Localization on the nanometer-scale was discovered to produce a local vibronic manifold resulting from the localization-enhanced electron-vibrational coupling. STS showed the vibrational overtones, identified as D-band Kekule vibrational modes and K-point transverse out-of plane phonons. This study experimentally connected the properties of well-defined localized electronic states to the properties of associated vibronic states. Electronic structures of alkyl-substituted oligothiophenes with different backbone lengths were studied and correlated with torsional conformations assumed on the Au(111) surface. The molecules adopted distinct planar conformations with alkyl ligands forming cis- or trans-mutual orientations and at higher coverage self-assembled into ordered structures, binding to each other via interdigitated alkyl ligands. STS maps visualized, in real space, particle-in-a-box-like molecular orbitals. Shorter quaterthiophenes have substantially varying orbital energies because of local variations in surface reactivity. Different conformers of longer

  6. Interaction of methotrexate with trypsin analyzed by spectroscopic and molecular modeling methods

    NASA Astrophysics Data System (ADS)

    Wang, Yanqing; Zhang, Hongmei; Cao, Jian; Zhou, Qiuhua

    2013-11-01

    Trypsin is one of important digestive enzymes that have intimate correlation with human health and illness. In this work, the interaction of trypsin with methotrexate was investigated by spectroscopic and molecular modeling methods. The results revealed that methotrexate could interact with trypsin with about one binding site. Methotrexate molecule could enter into the primary substrate-binding pocket, resulting in inhibition of trypsin activity. Furthermore, the thermodynamic analysis implied that electrostatic force, hydrogen bonding, van der Waals and hydrophobic interactions were the main interactions for stabilizing the trypsin-methotrexate system, which agreed well with the results from the molecular modeling study.

  7. Molecular Thermodynamics for Cell Biology as Taught with Boxes

    PubMed Central

    Mayorga, Luis S.; López, María José; Becker, Wayne M.

    2012-01-01

    Thermodynamic principles are basic to an understanding of the complex fluxes of energy and information required to keep cells alive. These microscopic machines are nonequilibrium systems at the micron scale that are maintained in pseudo-steady-state conditions by very sophisticated processes. Therefore, several nonstandard concepts need to be taught to rationalize why these very ordered systems proliferate actively all over our planet in seeming contradiction to the second law of thermodynamics. We propose a model consisting of boxes with different shapes that contain small balls that are in constant motion due to a stream of air blowing from below. This is a simple macroscopic system that can be easily visualized by students and that can be understood as mimicking the behavior of a set of molecules exchanging energy. With such boxes, the basic concepts of entropy, enthalpy, and free energy can be taught while reinforcing a molecular understanding of the concepts and stressing the stochastic nature of the thermodynamic laws. In addition, time-related concepts, such as reaction rates and activation energy, can be readily visualized. Moreover, the boxes provide an intuitive way to introduce the role in cellular organization of “information” and Maxwell's demons operating under nonequilibrium conditions. PMID:22383615

  8. Molecular thermodynamics for cell biology as taught with boxes.

    PubMed

    Mayorga, Luis S; López, María José; Becker, Wayne M

    2012-01-01

    Thermodynamic principles are basic to an understanding of the complex fluxes of energy and information required to keep cells alive. These microscopic machines are nonequilibrium systems at the micron scale that are maintained in pseudo-steady-state conditions by very sophisticated processes. Therefore, several nonstandard concepts need to be taught to rationalize why these very ordered systems proliferate actively all over our planet in seeming contradiction to the second law of thermodynamics. We propose a model consisting of boxes with different shapes that contain small balls that are in constant motion due to a stream of air blowing from below. This is a simple macroscopic system that can be easily visualized by students and that can be understood as mimicking the behavior of a set of molecules exchanging energy. With such boxes, the basic concepts of entropy, enthalpy, and free energy can be taught while reinforcing a molecular understanding of the concepts and stressing the stochastic nature of the thermodynamic laws. In addition, time-related concepts, such as reaction rates and activation energy, can be readily visualized. Moreover, the boxes provide an intuitive way to introduce the role in cellular organization of "information" and Maxwell's demons operating under nonequilibrium conditions.

  9. Pushing the physical limits of spectroscopic imaging for new biology and better medicine (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Cheng, Ji-Xin

    2017-02-01

    In vivo molecular spectroscopic imaging is not a simple addition of a spectrometer to a microscope. Innovations are needed to break the physical limits in sensitivity, depth, speed and resolution perspectives. I will present our most recent advances in modality development, biological application, and clinical translation. My talk will focus on the development of mid-infrared photothermal microscope for depth-resolved vibrational imaging of living cells (Science Advances, in press), the discovery of a metabolic signature in cancer stem cells by hyperspectral stimulated Raman scattering imaging (Cell Stem Cell, in press), and the development of an intravascular vibrational photoacoustic catheter for label-free sensing of lipid laden plaques (Scientific Report 2016, 6:25236).

  10. Protein Denaturation on p-T Axes--Thermodynamics and Analysis.

    PubMed

    Smeller, László

    2015-01-01

    Proteins are essential players in the vast majority of molecular level life processes. Since their structure is in most cases substantial for their correct function, study of their structural changes attracted great interest in the past decades. The three dimensional structure of proteins is influenced by several factors including temperature, pH, presence of chaotropic and cosmotropic agents, or presence of denaturants. Although pressure is an equally important thermodynamic parameter as temperature, pressure studies are considerably less frequent in the literature, probably due to the technical difficulties associated to the pressure studies. Although the first steps in the high-pressure protein study have been done 100 years ago with Bridgman's ground breaking work, the field was silent until the modern spectroscopic techniques allowed the characterization of the protein structural changes, while the protein was under pressure. Recently a number of proteins were studied under pressure, and complete pressure-temperature phase diagrams were determined for several of them. This review summarizes the thermodynamic background of the typical elliptic p-T phase diagram, its limitations and the possible reasons for deviations of the experimental diagrams from the theoretical one. Finally we show some examples of experimentally determined pressure-temperature phase diagrams.

  11. Low-energy nuclear spectroscopy in a microscopic multiphonon approach

    NASA Astrophysics Data System (ADS)

    Lo Iudice, N.; Ponomarev, V. Yu; Stoyanov, Ch; Sushkov, A. V.; Voronov, V. V.

    2012-04-01

    The low-lying spectra of heavy nuclei are investigated within the quasiparticle-phonon model. This microscopic approach goes beyond the quasiparticle random-phase approximation by treating a Hamiltonian of separable form in a microscopic multiphonon basis. It is therefore able to describe the anharmonic features of collective modes as well as the multiphonon states, whose experimental evidence is continuously growing. The method can be put in close correspondence with the proton-neutron interacting boson model. By associating the microscopic isoscalar and isovector quadrupole phonons with proton-neutron symmetric and mixed-symmetry quadrupole bosons, respectively, the microscopic states can be classified, just as in the algebraic model, according to their phonon content and their symmetry. In addition, these states disclose the nuclear properties which are to be ascribed to genuine shell effects, not included in the algebraic approach. Due to its flexibility, the method can be implemented numerically for systematic studies of spectroscopic properties throughout entire regions of vibrational nuclei. The spectra and multipole transition strengths so computed are in overall good agreement with the experimental data. By exploiting the correspondence of the method with the interacting boson model, it is possible to embed the microscopic states into this algebraic frame and, therefore, face the study of nuclei far from shell closures, not directly accessible to merely microscopic approaches. Here, it is shown how this task is accomplished through systematic investigations of magnetic dipole and, especially, electric dipole modes along paths moving from the vibrational to the transitional regions. The method is very well suited to the study of well-deformed nuclei. It provides reliable descriptions of low-lying magnetic as well as electric multipole modes of nuclei throughout the rare-earth and actinide regions. Attention is focused here on the low-lying 0+ states

  12. Structure and spectroscopic properties of neutral and cationic tetratomic [C,H,N,Zn] isomers: A theoretical study

    NASA Astrophysics Data System (ADS)

    Redondo, Pilar; Largo, Antonio; Vega-Vega, Álvaro; Barrientos, Carmen

    2015-05-01

    The structure and spectroscopic parameters of the most relevant [C,H,N,Zn] isomers have been studied employing high-level quantum chemical methods. For each isomer, we provide predictions for their molecular structure, thermodynamic stabilities as well as vibrational and rotational spectroscopic parameters which could eventually help in their experimental detection. In addition, we have carried out a detailed study of the bonding situations by means of a topological analysis of the electron density in the framework of the Bader's quantum theory of atoms in molecules. The analysis of the relative stabilities and spectroscopic parameters suggests two linear isomers of the neutral [C,H,N,Zn] composition, namely, cyanidehydridezinc HZnCN (1Σ) and hydrideisocyanidezinc HZnNC (1Σ), as possible candidates for experimental detections. For the cationic [C,H,N,Zn]+ composition, the most stable isomers are the ion-molecule complexes arising from the direct interaction of the zinc cation with either the nitrogen or carbon atom of either hydrogen cyanide or hydrogen isocyanide, namely, HCNZn+ (2Σ) and HCNZn+ (2Σ).

  13. Black Hole Thermodynamics in an Undergraduate Thermodynamics Course.

    ERIC Educational Resources Information Center

    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)

  14. A spectroscopic and thermodynamic study of porphyrin/DNA supramolecular assemblies.

    PubMed Central

    Pasternack, R F; Goldsmith, J I; Szép, S; Gibbs, E J

    1998-01-01

    Assemblies of trans-bis(N-methylpyridinium-4-yl)diphenylporphine ions on the surface of calf thymus DNA have been studied using several spectroscopic techniques: absorbance, circular dichroism, and resonance light scattering. The aggregation equilibrium can be treated as a two-state system-monomer and assembly-each bound to the nucleic acid template. The aggregate absorption spectrum in the Soret region is resolved into two bands of Lorentzian line shape, while the DNA-bound monomer spectrum in this region is composed of two Gaussian bands. The Beer-Lambert law is obeyed by both porphyrin forms. The assembly is also characterized by an extremely large, bisignate induced circular dichroism (CD) profile and by enhanced resonance light scattering (RLS). Both the CD and RLS intensities depend linearly on aggregate concentration. The RLS result is consistent with a model for the aggregates as being either of a characteristic size or of a fixed distribution of sizes, independent of total porphyrin concentration or ionic strength. Above threshold values of concentration and ionic strength, the mass action expression for the equilibrium has a particularly simple form: K' = cac-1; where cac is defined as the "critical assembly concentration."offe dependence of the cac upon temperature and ionic strength (NaCl) has been investigated at a fixed DNA concentration. The value of the cac scales as the inverse square of the sodium chloride concentration and, from temperature dependence studies, the aggregation process is shown to be exothermic. PMID:9675203

  15. Observation of the origin of d0 magnetism in ZnO nanostructures using X-ray-based microscopic and spectroscopic techniques

    NASA Astrophysics Data System (ADS)

    Singh, Shashi B.; Wang, Yu-Fu; Shao, Yu-Cheng; Lai, Hsuan-Yu; Hsieh, Shang-Hsien; Limaye, Mukta V.; Chuang, Chen-Hao; Hsueh, Hung-Chung; Wang, Hsaiotsu; Chiou, Jau-Wern; Tsai, Hung-Ming; Pao, Chih-Wen; Chen, Chia-Hao; Lin, Hong-Ji; Lee, Jyh-Fu; Wu, Chun-Te; Wu, Jih-Jen; Pong, Way-Faung; Ohigashi, Takuji; Kosugi, Nobuhiro; Wang, Jian; Zhou, Jigang; Regier, Tom; Sham, Tsun-Kong

    2014-07-01

    Efforts have been made to elucidate the origin of d0 magnetism in ZnO nanocactuses (NCs) and nanowires (NWs) using X-ray-based microscopic and spectroscopic techniques. The photoluminescence and O K-edge and Zn L3,2-edge X-ray-excited optical luminescence spectra showed that ZnO NCs contain more defects than NWs do and that in ZnO NCs, more defects are present at the O sites than at the Zn sites. Specifically, the results of O K-edge scanning transmission X-ray microscopy (STXM) and the corresponding X-ray-absorption near-edge structure (XANES) spectroscopy demonstrated that the impurity (non-stoichiometric) region in ZnO NCs contains a greater defect population than the thick region. The intensity of O K-edge STXM-XANES in the impurity region is more predominant in ZnO NCs than in NWs. The increase in the unoccupied (occupied) density of states at/above (at/below) the conduction-band minimum (valence-band maximum) or the Fermi level is related to the population of defects at the O sites, as revealed by comparing the ZnO NCs to the NWs. The results of O K-edge and Zn L3,2-edge X-ray magnetic circular dichroism demonstrated that the origin of magnetization is attributable to the O 2p orbitals rather than the Zn d orbitals. Further, the local density approximation (LDA) + U verified that vacancies in the form of dangling or unpaired 2p states (due to Zn vacancies) induced a significant local spin moment in the nearest-neighboring O atoms to the defect center, which was determined from the uneven local spin density by analyzing the partial density of states of O 2p in ZnO.Efforts have been made to elucidate the origin of d0 magnetism in ZnO nanocactuses (NCs) and nanowires (NWs) using X-ray-based microscopic and spectroscopic techniques. The photoluminescence and O K-edge and Zn L3,2-edge X-ray-excited optical luminescence spectra showed that ZnO NCs contain more defects than NWs do and that in ZnO NCs, more defects are present at the O sites than at the Zn sites

  16. 21 CFR 884.6190 - Assisted reproductive microscopes and microscope accessories.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... contrast microscopes, dissecting microscopes and inverted stage microscopes. (b) Classification. Class I... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Assisted reproductive microscopes and microscope... Devices § 884.6190 Assisted reproductive microscopes and microscope accessories. (a) Identification...

  17. Communication: Mechanochemical fluctuation theorem and thermodynamics of self-phoretic motors

    NASA Astrophysics Data System (ADS)

    Gaspard, Pierre; Kapral, Raymond

    2017-12-01

    Microscopic dynamical aspects of the propulsion of nanomotors by self-phoretic mechanisms are considered. Propulsion by self-diffusiophoresis relies on the mechanochemical coupling between the fluid velocity field and the concentration fields induced by asymmetric catalytic reactions on the motor surface. The consistency between the thermodynamics of this coupling and the microscopic reversibility of the underlying molecular dynamics is investigated. For this purpose, a mechanochemical fluctuation theorem for the joint probability to find the motor at position r after n reactive events have occurred during the time interval t is derived, starting from coupled Langevin equations for the translational, rotational, and chemical fluctuations of self-phoretic motors. An important result that follows from this analysis is the identification of an effect that is reciprocal to self-propulsion by diffusiophoresis, which leads to a dependence of the reaction rate on the value of an externally applied force.

  18. Complexity theory and physical unification: From microscopic to oscopic level

    NASA Astrophysics Data System (ADS)

    Pavlos, G. P.; Iliopoulos, A. C.; Karakatsanis, L. P.; Tsoutsouras, V. G.; Pavlos, E. G.

    During the last two decades, low dimensional chaotic or self-organized criticality (SOC) processes have been observed by our group in many different physical systems such as space plasmas, the solar or the magnetospheric dynamics, the atmosphere, earthquakes, the brain activity as well as in informational systems. All these systems are complex systems living far from equilibrium with strong self-organization and phase transition character. The theoretical interpretation of these natural phenomena needs a deeper insight into the fundamentals of complexity theory. In this study, we try to give a synoptic description of complexity theory both at the microscopic and at the oscopic level of the physical reality. Also, we propose that the self-organization observed oscopically is a phenomenon that reveals the strong unifying character of the complex dynamics which includes thermodynamical and dynamical characteristics in all levels of the physical reality. From this point of view, oscopical deterministic and stochastic processes are closely related to the microscopical chaos and self-organization. In this study the scientific work of scientists such as Wilson, Nicolis, Prigogine, Hooft, Nottale, El Naschie, Castro, Tsallis, Chang and others is used for the development of a unified physical comprehension of complex dynamics from the microscopic to the oscopic level.

  19. Spectroscopic and thermodynamic insights into the interaction between proflavine and human telomeric G-quadruplex DNA.

    PubMed

    Kumar, Vivek; Sengupta, Abhigyan; Gavvala, Krishna; Koninti, Raj Kumar; Hazra, Partha

    2014-09-25

    The G-quadruplex (GQ-DNA), an alternative structure motif of DNA, has emerged as a novel and exciting target for anticancer drug discovery. GQ-DNA formed in the presence of monovalent cations (Na(+)/K(+)) by human telomeric DNA is a point of interest due to their direct relevance for cellular aging and abnormal cell growths. Small molecules that selectively target and stabilize G-quadruplex structures are considered to be potential therapeutic anticancer agents. Herein, we probe G-quadruplex and proflavine (a well-known DNA intercalator, hence acting as an anticarcinogen) association through steady state and time-resolved fluorescence spectroscopy to explore the effect of stabilization of GQ-DNA by this well-known DNA intercalator. The structural modifications of G-quadruplex upon binding are highlighted through circular dichroism (CD) spectra. Moreover, a detailed insight into the thermodynamics of this interaction has been provided though isothermal titration calorimetry (ITC) studies. The thermodynamic parameters obtained from ITC help to gain knowledge about the nature as well as the driving forces of binding. This present study shows that proflavine (PF) can act as a stabilizer of telomeric GQ-DNA through an entropically as well as enthalpically feasible process with high binding affinity and thereby can be considered as a potential telomerase inhibitor.

  20. Early history of extended irreversible thermodynamics (1953-1983): An exploration beyond local equilibrium and classical transport theory

    NASA Astrophysics Data System (ADS)

    Lebon, G.; Jou, D.

    2015-06-01

    This paper gives a historical account of the early years (1953-1983) of extended irreversible thermodynamics (EIT). The salient features of this formalism are to upgrade the thermodynamic fluxes of mass, momentum, energy, and others, to the status of independent variables, and to explore the consistency between generalized transport equations and a generalized version of the second law of thermodynamics. This requires going beyond classical irreversible thermodynamics by redefining entropy and entropy flux. EIT provides deeper foundations, closer relations with microscopic formalisms, a wider spectrum of applications, and a more exciting conceptual appeal to non-equilibrium thermodynamics. We first recall the historical contributions by Maxwell, Cattaneo, and Grad on generalized transport equations. A thermodynamic theory wide enough to cope with such transport equations was independently proposed between 1953 and 1983 by several authors, each emphasizing different kinds of problems. In 1983, the first international meeting on this theory took place in Bellaterra (Barcelona). It provided the opportunity for the various authors to meet together for the first time and to discuss the common points and the specific differences of their previous formulations. From then on, a large amount of applications and theoretical confirmations have emerged. From the historical point of view, the emergence of EIT has been an opportunity to revisit the foundations and to open new avenues in thermodynamics, one of the most classical and well consolidated physical theories.

  1. Enhanced optical coupling and Raman scattering via microscopic interface engineering

    NASA Astrophysics Data System (ADS)

    Thompson, Jonathan V.; Hokr, Brett H.; Kim, Wihan; Ballmann, Charles W.; Applegate, Brian E.; Jo, Javier A.; Yamilov, Alexey; Cao, Hui; Scully, Marlan O.; Yakovlev, Vladislav V.

    2017-11-01

    Spontaneous Raman scattering is an extremely powerful tool for the remote detection and identification of various chemical materials. However, when those materials are contained within strongly scattering or turbid media, as is the case in many biological and security related systems, the sensitivity and range of Raman signal generation and detection is severely limited. Here, we demonstrate that through microscopic engineering of the optical interface, the optical coupling of light into a turbid material can be substantially enhanced. This improved coupling facilitates the enhancement of the Raman scattering signal generated by molecules within the medium. In particular, we detect at least two-orders of magnitude more spontaneous Raman scattering from a sample when the pump laser light is focused into a microscopic hole in the surface of the sample. Because this approach enhances both the interaction time and interaction region of the laser light within the material, its use will greatly improve the range and sensitivity of many spectroscopic techniques, including Raman scattering and fluorescence emission detection, inside highly scattering environments.

  2. Influence of atomic kinetics in the simulation of plasma microscopic properties and thermal instabilities for radiative bow shock experiments.

    PubMed

    Espinosa, G; Rodríguez, R; Gil, J M; Suzuki-Vidal, F; Lebedev, S V; Ciardi, A; Rubiano, J G; Martel, P

    2017-03-01

    Numerical simulations of laboratory astrophysics experiments on plasma flows require plasma microscopic properties that are obtained by means of an atomic kinetic model. This fact implies a careful choice of the most suitable model for the experiment under analysis. Otherwise, the calculations could lead to inaccurate results and inappropriate conclusions. First, a study of the validity of the local thermodynamic equilibrium in the calculation of the average ionization, mean radiative properties, and cooling times of argon plasmas in a range of plasma conditions of interest in laboratory astrophysics experiments on radiative shocks is performed in this work. In the second part, we have made an analysis of the influence of the atomic kinetic model used to calculate plasma microscopic properties of experiments carried out on magpie on radiative bow shocks propagating in argon. The models considered were developed assuming both local and nonlocal thermodynamic equilibrium and, for the latter situation, we have considered in the kinetic model different effects such as external radiation field and plasma mixture. The microscopic properties studied were the average ionization, the charge state distributions, the monochromatic opacities and emissivities, the Planck mean opacity, and the radiative power loss. The microscopic study was made as a postprocess of a radiative-hydrodynamic simulation of the experiment. We have also performed a theoretical analysis of the influence of these atomic kinetic models in the criteria for the onset possibility of thermal instabilities due to radiative cooling in those experiments in which small structures were experimentally observed in the bow shock that could be due to this kind of instability.

  3. Influence of atomic kinetics in the simulation of plasma microscopic properties and thermal instabilities for radiative bow shock experiments

    NASA Astrophysics Data System (ADS)

    Espinosa, G.; Rodríguez, R.; Gil, J. M.; Suzuki-Vidal, F.; Lebedev, S. V.; Ciardi, A.; Rubiano, J. G.; Martel, P.

    2017-03-01

    Numerical simulations of laboratory astrophysics experiments on plasma flows require plasma microscopic properties that are obtained by means of an atomic kinetic model. This fact implies a careful choice of the most suitable model for the experiment under analysis. Otherwise, the calculations could lead to inaccurate results and inappropriate conclusions. First, a study of the validity of the local thermodynamic equilibrium in the calculation of the average ionization, mean radiative properties, and cooling times of argon plasmas in a range of plasma conditions of interest in laboratory astrophysics experiments on radiative shocks is performed in this work. In the second part, we have made an analysis of the influence of the atomic kinetic model used to calculate plasma microscopic properties of experiments carried out on magpie on radiative bow shocks propagating in argon. The models considered were developed assuming both local and nonlocal thermodynamic equilibrium and, for the latter situation, we have considered in the kinetic model different effects such as external radiation field and plasma mixture. The microscopic properties studied were the average ionization, the charge state distributions, the monochromatic opacities and emissivities, the Planck mean opacity, and the radiative power loss. The microscopic study was made as a postprocess of a radiative-hydrodynamic simulation of the experiment. We have also performed a theoretical analysis of the influence of these atomic kinetic models in the criteria for the onset possibility of thermal instabilities due to radiative cooling in those experiments in which small structures were experimentally observed in the bow shock that could be due to this kind of instability.

  4. Thermodynamics of Terrestrial Evolution

    PubMed Central

    Kirkaldy, J. S.

    1965-01-01

    The causal element of biological evolution and development can be understood in terms of a potential function which is generalized from the variational principles of irreversible thermodynamics. This potential function is approximated by the rate of entropy production in a configuration space which admits of macroscopic excursions by fluctuation and regression as well as microscopic ones. Analogously to Onsager's dissipation function, the potential takes the form of a saddle surface in this configuration space. The path of evolution following from an initial high dissipation state within the fixed constraint provided by the invariant energy flux from the sun tends toward the stable saddle point by a series of spontaneous regressions which lower the entropy production rate and by an alternating series of spontaneous fluctuations which introduce new internal constraints and lead to a higher entropy production rate. The potential thus rationalizes the system's observed tendency toward “chemical imperialism” (high dissipation) while simultaneously accommodating the development of “dynamic efficiency” and complication (low dissipation). PMID:5884019

  5. Magnetic fingerprint of individual Fe4 molecular magnets under compression by a scanning tunnelling microscope

    NASA Astrophysics Data System (ADS)

    Burgess, Jacob A. J.; Malavolti, Luigi; Lanzilotto, Valeria; Mannini, Matteo; Yan, Shichao; Ninova, Silviya; Totti, Federico; Rolf-Pissarczyk, Steffen; Cornia, Andrea; Sessoli, Roberta; Loth, Sebastian

    2015-09-01

    Single-molecule magnets (SMMs) present a promising avenue to develop spintronic technologies. Addressing individual molecules with electrical leads in SMM-based spintronic devices remains a ubiquitous challenge: interactions with metallic electrodes can drastically modify the SMM's properties by charge transfer or through changes in the molecular structure. Here, we probe electrical transport through individual Fe4 SMMs using a scanning tunnelling microscope at 0.5 K. Correlation of topographic and spectroscopic information permits identification of the spin excitation fingerprint of intact Fe4 molecules. Building from this, we find that the exchange coupling strength within the molecule's magnetic core is significantly enhanced. First-principles calculations support the conclusion that this is the result of confinement of the molecule in the two-contact junction formed by the microscope tip and the sample surface.

  6. Lanthanide and transition metal complexes of bioactive coumarins: molecular modeling and spectroscopic studies.

    PubMed

    Georgieva, I; Mihaylov, Tz; Trendafilova, N

    2014-06-01

    The present paper summarizes theoretical and spectroscopic investigations on a series of active coumarins and their lanthanide and transition metal complexes with application in medicine and pharmacy. Molecular modeling as well as IR, Raman, NMR and electronic spectral simulations at different levels of theory were performed to obtain important molecular descriptors: total energy, formation energy, binding energy, stability, conformations, structural parameters, electron density distribution, molecular electrostatic potential, Fukui functions, atomic charges, and reactive indexes. The computations are performed both in gas phase and in solution with consideration of the solvent effect on the molecular structural and energetic parameters. The investigations have shown that the advanced computational methods are reliable for prediction of the metal-coumarin binding mode, electron density distribution, thermodynamic properties as well as the strength and nature of the metal-coumarin interaction (not experimentally accessible) and correctly interpret the experimental spectroscopic data. Known results from biological tests for cytotoxic, antimicrobial, anti-fungal, spasmolytic and anti-HIV activities on the studied metal complexes are reported and discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Microscopic analysis of currency and stock exchange markets.

    PubMed

    Kador, L

    1999-08-01

    Recently it was shown that distributions of short-term price fluctuations in foreign-currency exchange exhibit striking similarities to those of velocity differences in turbulent flows. Similar profiles represent the spectral-diffusion behavior of impurity molecules in disordered solids at low temperatures. It is demonstrated that a microscopic statistical theory of the spectroscopic line shapes can be applied to the other two phenomena. The theory interprets the financial data in terms of information which becomes available to the traders and their reactions as a function of time. The analysis shows that there is no characteristic time scale in financial markets, but that instead stretched-exponential or algebraic memory functions yield good agreement with the price data. For an algebraic function, the theory yields truncated Lévy distributions which are often observed in stock exchange markets.

  8. Microscopic analysis of currency and stock exchange markets

    NASA Astrophysics Data System (ADS)

    Kador, L.

    1999-08-01

    Recently it was shown that distributions of short-term price fluctuations in foreign-currency exchange exhibit striking similarities to those of velocity differences in turbulent flows. Similar profiles represent the spectral-diffusion behavior of impurity molecules in disordered solids at low temperatures. It is demonstrated that a microscopic statistical theory of the spectroscopic line shapes can be applied to the other two phenomena. The theory interprets the financial data in terms of information which becomes available to the traders and their reactions as a function of time. The analysis shows that there is no characteristic time scale in financial markets, but that instead stretched-exponential or algebraic memory functions yield good agreement with the price data. For an algebraic function, the theory yields truncated Lévy distributions which are often observed in stock exchange markets.

  9. Microscope basics.

    PubMed

    Sluder, Greenfield; Nordberg, Joshua J

    2013-01-01

    This chapter provides information on how microscopes work and discusses some of the microscope issues to be considered in using a video camera on the microscope. There are two types of microscopes in use today for research in cell biology-the older finite tube-length (typically 160mm mechanical tube length) microscopes and the infinity optics microscopes that are now produced. The objective lens forms a magnified, real image of the specimen at a specific distance from the objective known as the intermediate image plane. All objectives are designed to be used with the specimen at a defined distance from the front lens element of the objective (the working distance) so that the image formed is located at a specific location in the microscope. Infinity optics microscopes differ from the finite tube-length microscopes in that the objectives are designed to project the image of the specimen to infinity and do not, on their own, form a real image of the specimen. Three types of objectives are in common use today-plan achromats, plan apochromats, and plan fluorite lenses. The concept of mounting video cameras on the microscope is also presented in the chapter. Copyright © 2003 Elsevier Inc. All rights reserved.

  10. Microscopic video observation of capillary vessel systems using diffuse back lighting

    NASA Astrophysics Data System (ADS)

    Sakai, Minako; Arai, Hiroki; Iwai, Toshiaki

    2017-04-01

    We have been developing a simple and practical video microscopy system based on absorption spectra of biological substance to perform spectroscopic observation of living tissues. The diffuse backlighting effect is actively used in the developed system, which is generated by multiple light scattering in the tissue. It is demonstrated that the light specularly reflected from the skin surface can be completely suppressed in the microscopic observation and the biological activity of the capillary vessel systems distributed under the skin can be successfully observed. As a result, we can confirm the effectiveness of the video microscopy system using diffuse backlighting and the applicability of our developed system.

  11. The optical method for determining the thermodynamic parameters of hot gases

    NASA Astrophysics Data System (ADS)

    Egorov, O. V.; Voitsekhovskaya, O. K.; Kashirskii, D. E.; Tsvyk, R. Sh.; Sazanovich, V. M.; Sherstobitov, M. V.

    2014-11-01

    The research conducted on the thermodynamic parameters of a flame was based on its experimental transmission spectra in the 2.7 μm and 4.3 μm ranges. To produce the flame, alcohol was burned under atmospheric conditions. The hot gases resulting from the burning of ethanol (H2O, CO, and CO2) were accelerated and spun by the rotation of an impeller. The optical method developed by the authors was employed for predicting the temperature and partial pressure of the hot gases. The results demonstrate the practical significance of the method suggested. The spectroscopic database HITEMP 2010 was used for all line-by-line calculations presented in the article.

  12. Thermodynamics and folding pathway of tetraloop receptor-mediated RNA helical packing

    PubMed Central

    Vander Meulen, Kirk A.; Davis, Jared H.; Foster, Trenton R.; Record, M. Thomas; Butcher, Samuel E.

    2008-01-01

    Summary Little is known about the thermodynamic forces that drive the folding pathways of higher order RNA structure. In this study, we employ calorimetric (ITC and DSC) and spectroscopic (NMR and UV) methods to characterize the thermodynamics of the GAAA tetraloop – receptor interaction, utilizing a previously described bivalent construct. ITC studies indicate that the bivalent interaction is enthalpy-driven and highly stable, with a binding constant (Kobs) of 5.5 × 106 M−1 and enthalpy (ΔHobs°) of −33.8 kcal/mol at 45°C in 20 mM KCl and 2 mM MgCl2. Thus we derive the ΔHobs° for a single tetraloop-receptor interaction to be −16.9 kcal/mol at these conditions. UV absorbance data indicate that an increase in base stacking quality contributes to the enthalpy of complex formation. These highly favorable thermodynamics are consistent with the known critical role for the tetraloop-receptor motif in the folding of large RNAs. Additionally, a significant heat capacity change (ΔCp,obs°) of −0.24 kcal·mol−1·K−1 was determined by ITC. DSC and UV monitored thermal denaturation experiments indicate that the bivalent tetraloop-receptor construct follows a minimally 5–state unfolding pathway, and suggest the observed ΔCp,obs° for the interaction results from a temperature-dependent unbound receptor RNA structure. PMID:18845162

  13. Tables and charts of equilibrium thermodynamic properties of ammonia for temperatures from 500 to 50,000 K.

    NASA Technical Reports Server (NTRS)

    Simmonds, A. L.; Miller, C. G., III; Nealy, J. E.

    1976-01-01

    Equilibrium thermodynamic properties for pure ammonia were generated for a range of temperature from 500 to 50,000 K and pressure from 0.01 to 40 MN/sq m and are presented in tabulated and graphical form. Properties include pressure, temperature, density, enthalpy, speed of sound, entropy, molecular-weight ratio, specific heat at constant pressure, specific heat at constant volume, isentropic exponent, and species mole fractions. These properties were calculated by the method which is based on minimization of the Gibbs free energy. The data presented herein are for an 18-species ammonia model. Heats of formation and spectroscopic constants used as input data are presented. Comparison of several thermodynamic properties calculated with the present program and a second computer code is performed for a range of pressure and for temperatures up to 30,000 K.

  14. Methodology of Thermodynamics

    ERIC Educational Resources Information Center

    Mohan, Gyan

    1969-01-01

    Presents a systematization of the mathematical formulae in thermodynamics. From the set of thermodynamic variables, four equations are derived which contain the total mathematical jargon of thermodynamics. (LC)

  15. Scanning Tunneling Spectroscope Use in Electrocatalysis Testing

    PubMed Central

    Knutsen, Turid

    2010-01-01

    The relationship between the electrocatalytic properties of an electrode and its ability to transfer electrons between the electrode and a metallic tip in a scanning tunneling microscope (STM) is investigated. The alkaline oxygen evolution reaction (OER) was used as a test reaction with four different metallic glasses, Ni78Si8B14, Ni70Mo20Si5B5, Ni58Co20Si10B12, and Ni25Co50Si15B10, as electrodes. The electrocatalytic properties of the electrodes were determined. The electrode surfaces were then investigated with an STM. A clear relationship between the catalytic activity of an electrode toward the OER and its tunneling characteristics was found. The use of a scanning tunneling spectroscope (STS) in electrocatalytic testing may increase the efficiency of the optimization of electrochemical processes.

  16. Versatile variable temperature and magnetic field scanning probe microscope for advanced material research

    NASA Astrophysics Data System (ADS)

    Jung, Jin-Oh; Choi, Seokhwan; Lee, Yeonghoon; Kim, Jinwoo; Son, Donghyeon; Lee, Jhinhwan

    2017-10-01

    We have built a variable temperature scanning probe microscope (SPM) that covers 4.6 K-180 K and up to 7 T whose SPM head fits in a 52 mm bore magnet. It features a temperature-controlled sample stage thermally well isolated from the SPM body in good thermal contact with the liquid helium bath. It has a 7-sample-holder storage carousel at liquid helium temperature for systematic studies using multiple samples and field emission targets intended for spin-polarized spectroscopic-imaging scanning tunneling microscopy (STM) study on samples with various compositions and doping conditions. The system is equipped with a UHV sample preparation chamber and mounted on a two-stage vibration isolation system made of a heavy concrete block and a granite table on pneumatic vibration isolators. A quartz resonator (qPlus)-based non-contact atomic force microscope (AFM) sensor is used for simultaneous STM/AFM operation for research on samples with highly insulating properties such as strongly underdoped cuprates and strongly correlated electron systems.

  17. Biophysical influence of coumarin 35 on bovine serum albumin: Spectroscopic study

    NASA Astrophysics Data System (ADS)

    Bayraktutan, Tuğba; Onganer, Yavuz

    2017-01-01

    The binding mechanism and protein-fluorescence probe interactions between bovine serum albumin (BSA) and coumarin 35 (C35) was investigated by using UV-Vis absorption and fluorescence spectroscopies since they remain major research topics in biophysics. The spectroscopic data indicated that a fluorescence quenching process for BSA-C35 system was occurred. The fluorescence quenching processes were analyzed using Stern-Volmer method. In this regard, Stern-Volmer quenching constants (KSV) and binding constants were calculated at different temperatures. The distance r between BSA (donor) and C35 (acceptor) was determined by exploiting fluorescence resonance energy transfer (FRET) method. Synchronous fluorescence spectra were also studied to observe information about conformational changes. Moreover, thermodynamics parameters were calculated for better understanding of interactions and conformational changes of the system.

  18. Thermodynamic properties of hydrate phases immersed in ice phase

    NASA Astrophysics Data System (ADS)

    Belosludov, V. R.; Subbotin, O. S.; Krupskii, D. S.; Ikeshoji, T.; Belosludov, R. V.; Kawazoe, Y.; Kudoh, J.

    2006-01-01

    Thermodynamic properties and the pressure of hydrate phases immersed in the ice phase with the aim to understand the nature of self-preservation effect of methane hydrate in the framework of macroscopic and microscopic molecular models was studied. It was show that increasing of pressure is happen inside methane hydrate phases immersed in the ice phase under increasing temperature and if the ice structure does not destroy, the methane hydrate will have larger pressure than ice phase. This is because of the thermal expansion of methane hydrate in a few times larger than ice one. The thermal expansion of the hydrate is constrained by the thermal expansion of ice because it can remain in a region of stability within the methane hydrate phase diagram. The utter lack of preservation behavior in CS-II methane- ethane hydrate can be explain that the thermal expansion of ethane-methane hydrate coincide with than ice one it do not pent up by thermal expansion of ice. The pressure and density during the crossing of interface between ice and hydrate was found and dynamical and thermodynamic stability of this system are studied in accordance with relation between ice phase and hydrate phase.

  19. Calibration method for spectroscopic systems

    DOEpatents

    Sandison, David R.

    1998-01-01

    Calibration spots of optically-characterized material placed in the field of view of a spectroscopic system allow calibration of the spectroscopic system. Response from the calibration spots is measured and used to calibrate for varying spectroscopic system operating parameters. The accurate calibration achieved allows quantitative spectroscopic analysis of responses taken at different times, different excitation conditions, and of different targets.

  20. Calibration method for spectroscopic systems

    DOEpatents

    Sandison, D.R.

    1998-11-17

    Calibration spots of optically-characterized material placed in the field of view of a spectroscopic system allow calibration of the spectroscopic system. Response from the calibration spots is measured and used to calibrate for varying spectroscopic system operating parameters. The accurate calibration achieved allows quantitative spectroscopic analysis of responses taken at different times, different excitation conditions, and of different targets. 3 figs.

  1. Design and performance of an ultra-high vacuum scanning tunneling microscope operating at dilution refrigerator temperatures and high magnetic fields.

    PubMed

    Misra, S; Zhou, B B; Drozdov, I K; Seo, J; Urban, L; Gyenis, A; Kingsley, S C J; Jones, H; Yazdani, A

    2013-10-01

    We describe the construction and performance of a scanning tunneling microscope capable of taking maps of the tunneling density of states with sub-atomic spatial resolution at dilution refrigerator temperatures and high (14 T) magnetic fields. The fully ultra-high vacuum system features visual access to a two-sample microscope stage at the end of a bottom-loading dilution refrigerator, which facilitates the transfer of in situ prepared tips and samples. The two-sample stage enables location of the best area of the sample under study and extends the experiment lifetime. The successful thermal anchoring of the microscope, described in detail, is confirmed through a base temperature reading of 20 mK, along with a measured electron temperature of 250 mK. Atomically resolved images, along with complementary vibration measurements, are presented to confirm the effectiveness of the vibration isolation scheme in this instrument. Finally, we demonstrate that the microscope is capable of the same level of performance as typical machines with more modest refrigeration by measuring spectroscopic maps at base temperature both at zero field and in an applied magnetic field.

  2. Thermodynamics of Bioreactions.

    PubMed

    Held, Christoph; Sadowski, Gabriele

    2016-06-07

    Thermodynamic principles have been applied to enzyme-catalyzed reactions since the beginning of the 1930s in an attempt to understand metabolic pathways. Currently, thermodynamics is also applied to the design and analysis of biotechnological processes. The key thermodynamic quantity is the Gibbs energy of reaction, which must be negative for a reaction to occur spontaneously. However, the application of thermodynamic feasibility studies sometimes yields positive Gibbs energies of reaction even for reactions that are known to occur spontaneously, such as glycolysis. This article reviews the application of thermodynamics in enzyme-catalyzed reactions. It summarizes the basic thermodynamic relationships used for describing the Gibbs energy of reaction and also refers to the nonuniform application of these relationships in the literature. The review summarizes state-of-the-art approaches that describe the influence of temperature, pH, electrolytes, solvents, and concentrations of reacting agents on the Gibbs energy of reaction and, therefore, on the feasibility and yield of biological reactions.

  3. Binding of copper to lysozyme: Spectroscopic, isothermal titration calorimetry and molecular docking studies

    NASA Astrophysics Data System (ADS)

    Jing, Mingyang; Song, Wei; Liu, Rutao

    2016-07-01

    Although copper is essential to all living organisms, its potential toxicity to human health have aroused wide concerns. Previous studies have reported copper could alter physical properties of lysozyme. The direct binding of copper with lysozyme might induce the conformational and functional changes of lysozyme and then influence the body's resistance to bacterial attack. To better understand the potential toxicity and toxic mechanisms of copper, the interaction of copper with lysozyme was investigated by biophysical methods including multi-spectroscopic measurements, isothermal titration calorimetry (ITC), molecular docking study and enzyme activity assay. Multi-spectroscopic measurements proved that copper quenched the intrinsic fluorescence of lysozyme in a static process accompanied by complex formation and conformational changes. The ITC results indicated that the binding interaction was a spontaneous process with approximately three thermodynamical binding sites at 298 K and the hydrophobic force is the predominant driven force. The enzyme activity was obviously inhibited by the addition of copper with catalytic residues Glu 35 and Asp 52 locating at the binding sites. This study helps to elucidate the molecular mechanism of the interaction between copper and lysozyme and provides reference for toxicological studies of copper.

  4. Oligomerization in As (III) sulfide solutions: Theoretical constraints and spectroscopic evidence

    NASA Astrophysics Data System (ADS)

    Helz, George R.; Tossell, John A.; Charnock, John M.; Pattrick, Richard A. D.; Vaughan, David J.; David Garner, C.

    1995-11-01

    Bond distances, vibrational frequencies, gas-phase energetics, and proton affinities for various thioarsenite molecules and ions are predicted from molecular orbital theory and used to interpret EXAFS and Raman spectra of dissolved thioarsenites in undersaturated, alkaline 1 M NaHS solutions. From MO predictions, Raman peaks at 325 and 412 cm - are assigned to AsS(SH) 2- and a peak at 382 cm - to AsS 2(SH) 2- At alkaline pH, As-S distances in dissolved thioarsenites are 2.21-2.23 Å and no statistically significant As-As interactions are recorded, consistent with predominance of the monomers, AsS(SH) 2- and AsS 2(SH ) 2-. Estimated proton affinities suggest that thioarsenites with a negative charge greater than 2 are unstable in water. In seeming contradiction to this spectroscopic evidence, a new analysis of published solubility studies reinforces previous inferences that the trimer, As 3S 4(SH) 2-, is the predominant thioarsenite in systems saturated with As 2S 3. Previously proposed dimeric species of the form, H xAs2S 4x- , are rejected based on predicted thermodynamic properties. Dimer plus tetramer combinations also are rejected. Estimated free energies for AsS (OH)(SH) - and AsS(SH) 2- are presented. We reconcile the spectroscopic and solubility evidence by showing that in undersaturated solutions monomers can become thermodynamically favored over oligomers. This pattern should be looked for in other sulfide systems as well. Sulfidic natural waters are in many cases undersaturated with respect to AS 2S 3 phases, so monomeric thioarsenites could be more important in nature than the trimers that have been characterized in saturated solutions. EXAFS spectra show that amorphous AS 2S 3 resembles orpiment in the first shell around As, but that higher shells are disordered. Disorder may be caused by occasional realgar-like, As-As bonds, consistent with the observation that amorphous AS 2S 3 is slightly S deficient.

  5. Formation, Physicochemical Characterization, and Thermodynamic Stability of the Amorphous State of Drugs and Excipients.

    PubMed

    Martino, Piera Di; Magnoni, Federico; Peregrina, Dolores Vargas; Gigliobianco, Maria Rosa; Censi, Roberta; Malaj, Ledjan

    2016-01-01

    Drugs and excipients used for pharmaceutical applications generally exist in the solid (crystalline or amorphous) state, more rarely as liquid materials. In some cases, according to the physicochemical nature of the molecule, or as a consequence of specific technological processes, a compound may exist exclusively in the amorphous state. In other cases, as a consequence of specific treatments (freezing and spray drying, melting and co-melting, grinding and compression), the crystalline form may convert into a completely or partially amorphous form. An amorphous material shows physical and thermodynamic properties different from the corresponding crystalline form, with profound repercussions on its technological performance and biopharmaceutical properties. Several physicochemical techniques such as X-ray powder diffraction, thermal methods of analysis, spectroscopic techniques, gravimetric techniques, and inverse gas chromatography can be applied to characterize the amorphous form of a compound (drug or excipient), and to evaluate its thermodynamic stability. This review offers a survey of the technologies used to convert a crystalline solid into an amorphous form, and describes the most important techniques for characterizing the amorphous state of compounds of pharmaceutical interest.

  6. Thermodynamics of Radiation Modes

    ERIC Educational Resources Information Center

    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…

  7. FAST CARS: Engineering a laser spectroscopic technique for rapid identification of bacterial spores

    PubMed Central

    Scully, M. O.; Kattawar, G. W.; Lucht, R. P.; Opatrný, T.; Pilloff, H.; Rebane, A.; Sokolov, A. V.; Zubairy, M. S.

    2002-01-01

    Airborne contaminants, e.g., bacterial spores, are usually analyzed by time-consuming microscopic, chemical, and biological assays. Current research into real-time laser spectroscopic detectors of such contaminants is based on e.g., resonance fluorescence. The present approach derives from recent experiments in which atoms and molecules are prepared by one (or more) coherent laser(s) and probed by another set of lasers. However, generating and using maximally coherent oscillation in macromolecules having an enormous number of degrees of freedom is challenging. In particular, the short dephasing times and rapid internal conversion rates are major obstacles. However, adiabatic fast passage techniques and the ability to generate combs of phase-coherent femtosecond pulses provide tools for the generation and utilization of maximal quantum coherence in large molecules and biopolymers. We call this technique FAST CARS (femtosecond adaptive spectroscopic techniques for coherent anti-Stokes Raman spectroscopy), and the present article proposes and analyses ways in which it could be used to rapidly identify preselected molecules in real time. PMID:12177405

  8. High-definition Fourier transform infrared spectroscopic imaging of prostate tissue

    NASA Astrophysics Data System (ADS)

    Wrobel, Tomasz P.; Kwak, Jin Tae; Kadjacsy-Balla, Andre; Bhargava, Rohit

    2016-03-01

    Histopathology forms the gold standard for cancer diagnosis and therapy, and generally relies on manual examination of microscopic structural morphology within tissue. Fourier-Transform Infrared (FT-IR) imaging is an emerging vibrational spectroscopic imaging technique, especially in a High-Definition (HD) format, that provides the spatial specificity of microscopy at magnifications used in diagnostic surgical pathology. While it has been shown for standard imaging that IR absorption by tissue creates a strong signal where the spectrum at each pixel is a quantitative "fingerprint" of the molecular composition of the sample, here we show that this fingerprint also enables direct digital pathology without the need for stains or dyes for HD imaging. An assessment of the potential of HD imaging to improve diagnostic pathology accuracy is presented.

  9. Stochastic thermodynamics and entropy production of chemical reaction systems

    NASA Astrophysics Data System (ADS)

    Tomé, Tânia; de Oliveira, Mário J.

    2018-06-01

    We investigate the nonequilibrium stationary states of systems consisting of chemical reactions among molecules of several chemical species. To this end, we introduce and develop a stochastic formulation of nonequilibrium thermodynamics of chemical reaction systems based on a master equation defined on the space of microscopic chemical states and on appropriate definitions of entropy and entropy production. The system is in contact with a heat reservoir and is placed out of equilibrium by the contact with particle reservoirs. In our approach, the fluxes of various types, such as the heat and particle fluxes, play a fundamental role in characterizing the nonequilibrium chemical state. We show that the rate of entropy production in the stationary nonequilibrium state is a bilinear form in the affinities and the fluxes of reaction, which are expressed in terms of rate constants and transition rates, respectively. We also show how the description in terms of microscopic states can be reduced to a description in terms of the numbers of particles of each species, from which follows the chemical master equation. As an example, we calculate the rate of entropy production of the first and second Schlögl reaction models.

  10. Advanced classical thermodynamics

    NASA Astrophysics Data System (ADS)

    Emanuel, George

    The theoretical and mathematical foundations of thermodynamics are presented in an advanced text intended for graduate engineering students. Chapters are devoted to definitions and postulates, the fundamental equation, equilibrium, the application of Jacobian theory to thermodynamics, the Maxwell equations, stability, the theory of real gases, critical-point theory, and chemical thermodynamics. Diagrams, graphs, tables, and sample problems are provided.

  11. Thermodynamic holography.

    PubMed

    Wei, Bo-Bo; Jiang, Zhan-Feng; Liu, Ren-Bao

    2015-10-19

    The holographic principle states that the information about a volume of a system is encoded on the boundary surface of the volume. Holography appears in many branches of physics, such as optics, electromagnetism, many-body physics, quantum gravity, and string theory. Here we show that holography is also an underlying principle in thermodynamics, a most important foundation of physics. The thermodynamics of a system is fully determined by its partition function. We prove that the partition function of a finite but arbitrarily large system is an analytic function on the complex plane of physical parameters, and therefore the partition function in a region on the complex plane is uniquely determined by its values along the boundary. The thermodynamic holography has applications in studying thermodynamics of nano-scale systems (such as molecule engines, nano-generators and macromolecules) and provides a new approach to many-body physics.

  12. Microscopic Description of Thermodynamics of Lipid Membrane at Liquid-Gel Phase Transition

    NASA Astrophysics Data System (ADS)

    Kheyfets, B.; Galimzyanov, T.; Mukhin, S.

    2018-05-01

    A microscopic model of the lipid membrane is constructed that provides analytically tractable description of the physical mechanism of the first order liquid-gel phase transition. We demonstrate that liquid-gel phase transition is cooperative effect of the three major interactions: inter-lipid van der Waals attraction, steric repulsion and hydrophobic tension. The model explicitly shows that temperature-dependent inter-lipid steric repulsion switches the system from liquid to gel phase when the temperature decreases. The switching manifests itself in the increase of lateral compressibility of the lipids as the temperature decreases, making phase with smaller area more preferable below the transition temperature. The model gives qualitatively correct picture of abrupt change at transition temperature of the area per lipid, membrane thickness and volume per hydrocarbon group in the lipid chains. The calculated dependence of phase transition temperature on lipid chain length is in quantitative agreement with experimental data. Steric repulsion between the lipid molecules is shown to be the only driver of the phase transition, as van der Waals attraction and hydrophobic tension are weakly temperature dependent.

  13. Local thermodynamic equilibrium in a laser-induced plasma evidenced by blackbody radiation

    NASA Astrophysics Data System (ADS)

    Hermann, Jörg; Grojo, David; Axente, Emanuel; Craciun, Valentin

    2018-06-01

    We show that the plasma produced by laser ablation of solid materials in specific conditions has an emission spectrum that is characterized by the saturation of the most intense spectral lines at the blackbody radiance. The blackbody temperature equals the excitation temperature of atoms and ions, proving directly and unambiguously a plasma in local thermodynamic equilibrium. The present investigations take benefit from the very rich and intense emission spectrum generated by ablation of a nickel-chromium-molybdenum alloy. This alternative and direct proof of the plasma equilibrium state re-opens the perspectives of quantitative material analyses via calibration-free laser-induced breakdown spectroscopy. Moreover, the unique properties of this laser-produced plasma promote its use as radiation standard for intensity calibration of spectroscopic instruments.

  14. Contact symmetries and Hamiltonian thermodynamics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bravetti, A., E-mail: bravetti@correo.nucleares.unam.mx; Lopez-Monsalvo, C.S., E-mail: cesar.slm@correo.nucleares.unam.mx; Nettel, F., E-mail: Francisco.Nettel@roma1.infn.it

    It has been shown that contact geometry is the proper framework underlying classical thermodynamics and that thermodynamic fluctuations are captured by an additional metric structure related to Fisher’s Information Matrix. In this work we analyse several unaddressed aspects about the application of contact and metric geometry to thermodynamics. We consider here the Thermodynamic Phase Space and start by investigating the role of gauge transformations and Legendre symmetries for metric contact manifolds and their significance in thermodynamics. Then we present a novel mathematical characterization of first order phase transitions as equilibrium processes on the Thermodynamic Phase Space for which the Legendremore » symmetry is broken. Moreover, we use contact Hamiltonian dynamics to represent thermodynamic processes in a way that resembles the classical Hamiltonian formulation of conservative mechanics and we show that the relevant Hamiltonian coincides with the irreversible entropy production along thermodynamic processes. Therefore, we use such property to give a geometric definition of thermodynamically admissible fluctuations according to the Second Law of thermodynamics. Finally, we show that the length of a curve describing a thermodynamic process measures its entropy production.« less

  15. Fluctuating Thermodynamics for Biological Processes

    NASA Astrophysics Data System (ADS)

    Ham, Sihyun

    Because biomolecular processes are largely under thermodynamic control, dynamic extension of thermodynamics is necessary to uncover the mechanisms and driving factors of fluctuating processes. The fluctuating thermodynamics technology presented in this talk offers a practical means for the thermodynamic characterization of conformational dynamics in biomolecules. The use of fluctuating thermodynamics has the potential to provide a comprehensive picture of fluctuating phenomena in diverse biological processes. Through the application of fluctuating thermodynamics, we provide a thermodynamic perspective on the misfolding and aggregation of the various proteins associated with human diseases. In this talk, I will present the detailed concepts and applications of the fluctuating thermodynamics technology for elucidating biological processes. This work was supported by Samsung Science and Technology Foundation under Project Number SSTF-BA1401-13.

  16. A 350 mK, 9 T scanning tunneling microscope for the study of superconducting thin films on insulating substrates and single crystals.

    PubMed

    Kamlapure, Anand; Saraswat, Garima; Ganguli, Somesh Chandra; Bagwe, Vivas; Raychaudhuri, Pratap; Pai, Subash P

    2013-12-01

    We report the construction and performance of a low temperature, high field scanning tunneling microscope (STM) operating down to 350 mK and in magnetic fields up to 9 T, with thin film deposition and in situ single crystal cleaving capabilities. The main focus lies on the simple design of STM head and a sample holder design that allows us to get spectroscopic data on superconducting thin films grown in situ on insulating substrates. Other design details on sample transport, sample preparation chamber, and vibration isolation schemes are also described. We demonstrate the capability of our instrument through the atomic resolution imaging and spectroscopy on NbSe2 single crystal and spectroscopic maps obtained on homogeneously disordered NbN thin film.

  17. Reconstruction of explicit structural properties at the nanoscale via spectroscopic microscopy

    NASA Astrophysics Data System (ADS)

    Cherkezyan, Lusik; Zhang, Di; Subramanian, Hariharan; Taflove, Allen; Backman, Vadim

    2016-02-01

    The spectrum registered by a reflected-light bright-field spectroscopic microscope (SM) can quantify the microscopically indiscernible, deeply subdiffractional length scales within samples such as biological cells and tissues. Nevertheless, quantification of biological specimens via any optical measures most often reveals ambiguous information about the specific structural properties within the studied samples. Thus, optical quantification remains nonintuitive to users from the diverse fields of technique application. In this work, we demonstrate that the SM signal can be analyzed to reconstruct explicit physical measures of internal structure within label-free, weakly scattering samples: characteristic length scale and the amplitude of spatial refractive-index (RI) fluctuations. We present and validate the reconstruction algorithm via finite-difference time-domain solutions of Maxwell's equations on an example of exponential spatial correlation of RI. We apply the validated algorithm to experimentally measure structural properties within isolated cells from two genetic variants of HT29 colon cancer cell line as well as within a prostate tissue biopsy section. The presented methodology can lead to the development of novel biophotonics techniques that create two-dimensional maps of explicit structural properties within biomaterials: the characteristic size of macromolecular complexes and the variance of local mass density.

  18. Fluctuations of thermodynamic quantities calculated from the fundamental equation of thermodynamics

    NASA Astrophysics Data System (ADS)

    Yan, Zijun; Chen, Jincan

    1992-02-01

    On the basis of the probability distribution of the various values of the fluctuation and the fundamental equation of thermodynamics of any given system, a simple and useful method of calculating the fluctuations is presented. By using the method, the fluctuations of thermodynamic quantities can be directly determined from the fundamental equation of thermodynamics. Finally, some examples are given to illustrate the use of the method.

  19. Spectroscopic properties in Er3+-doped germanotellurite glasses and glass ceramics for mid-infrared laser materials.

    PubMed

    Kang, Shiliang; Xiao, Xiudi; Pan, Qiwen; Chen, Dongdan; Qiu, Jianrong; Dong, Guoping

    2017-03-07

    Transparent Er 3+ -doped germanotellurite glass ceramics (GCs) with variable Te/Ge ratio were prepared by controllable heat-treated process. X-ray diffraction (XRD) and transmission electron microscope (TEM) confirmed the formation of nanocrystals in glass matrix. Raman spectra were used to investigate the evolution of glass structure and photon energy. Fourier transform infrared (FTIR) spectra were introduced to characterize the change of hydroxyl group (OH - ) content. Enhanced 2.7 μm emission was achieved from Er 3+ -doped GCs upon excitation with a 980 nm laser diode (LD), and the influence of GeO 2 concentration and heat-treated temperature on the spectroscopic properties were also discussed in detail. It is found that the present Er 3+ -doped GC possesses large stimulated emission cross section at around 2.7 μm (0.85 × 10 -20  cm 2 ). The advantageous spectroscopic characteristics suggest that the obtained GC may be a promising material for mid-infrared fiber lasers.

  20. Spectroscopic properties in Er3+-doped germanotellurite glasses and glass ceramics for mid-infrared laser materials

    PubMed Central

    Kang, Shiliang; Xiao, Xiudi; Pan, Qiwen; Chen, Dongdan; Qiu, Jianrong; Dong, Guoping

    2017-01-01

    Transparent Er3+-doped germanotellurite glass ceramics (GCs) with variable Te/Ge ratio were prepared by controllable heat-treated process. X-ray diffraction (XRD) and transmission electron microscope (TEM) confirmed the formation of nanocrystals in glass matrix. Raman spectra were used to investigate the evolution of glass structure and photon energy. Fourier transform infrared (FTIR) spectra were introduced to characterize the change of hydroxyl group (OH−) content. Enhanced 2.7 μm emission was achieved from Er3+-doped GCs upon excitation with a 980 nm laser diode (LD), and the influence of GeO2 concentration and heat-treated temperature on the spectroscopic properties were also discussed in detail. It is found that the present Er3+-doped GC possesses large stimulated emission cross section at around 2.7 μm (0.85 × 10−20 cm2). The advantageous spectroscopic characteristics suggest that the obtained GC may be a promising material for mid-infrared fiber lasers. PMID:28266570

  1. Characterization of titanyl phthalocyanine (TiOPc) thin films by microscopic and spectroscopic method

    NASA Astrophysics Data System (ADS)

    Skonieczny, R.; Makowiecki, J.; Bursa, B.; Krzykowski, A.; Szybowicz, M.

    2018-02-01

    The titanyl phthalocyanine (TiOPc) thin film deposited on glass, silicon and gold substrate have been studied using Raman spectroscopy, atomic force microscopy (AFM), absorption and profilometry measurements. The TiOPc thin layers have been deposited at room temperature by the quasi-molecular beam evaporation technique. The Raman spectra have been recorded using micro Raman system equipped with a confocal microscope. Using surface Raman mapping techni que with polarized Raman spectra the polymorphic forms of the TiOPc thin films distribution have been obtained. The AFM height and phase image were examined in order to find surface features and morphology of the thin films. Additionally to compare experimental results, structure optimization and vibrational spectra calculation of single TiOPc molecule were performed using DFT calculations. The received results showed that the parameters like polymorphic form, grain size, roughness of the surface in TiOPc thin films can well characterize the obtained organic thin films structures in terms of their use in optoelectronics and photovoltaics devices.

  2. Low temperature IR spectroscopic study of torsional vibrations of taurine

    NASA Astrophysics Data System (ADS)

    Bajaj, Naini; Bhatt, Himal; Vishwakarma, S. R.; Thomas, Susy; Murli, C.; Deo, M. N.

    2018-04-01

    The hydrogen bonding network in amino acids can give information about the structural stability under varying thermodynamic conditions such as temperature and pressure. We have carried out low temperature IR spectroscopic studies on Taurine, an amino acid with various bio-chemical applications in physiology and synthesis, in order to observe the behaviour of torsional modes, i.e. τ(CSH) and τ(NH3), which are very sensitive to the hydrogen bonding interactions. It was observed that the CSH torsional mode showed splitting at low temperature of nearly 250 K and the bandwidth shows linear temperature dependence, which can be attributed to anharmonicity. Another torsional mode, τ(NH3) showed no splitting, but the bandwidth has non-linear temperature dependence. This can be due to orientational changes at low temperature. These observations are strong evidences for a hydrogen bond reorientation induced phase transition at 250 K.

  3. Nonequilibrium thermodynamics and a fluctuation theorem for individual reaction steps in a chemical reaction network

    NASA Astrophysics Data System (ADS)

    Pal, Krishnendu; Das, Biswajit; Banerjee, Kinshuk; Gangopadhyay, Gautam

    2015-09-01

    We have introduced an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the propensities of the individual elementary reactions and the corresponding reverse reactions. The method is a microscopic formulation of the dissipation function in terms of the relative entropy or Kullback-Leibler distance which is based on the analogy of phase space trajectory with the path of elementary reactions in a network of chemical process. We have introduced here a fluctuation theorem valid for each opposite pair of elementary reactions which is useful in determining the contribution of each sub-reaction on the nonequilibrium thermodynamics of overall reaction. The methodology is applied to an oligomeric enzyme kinetics at a chemiostatic condition that leads the reaction to a nonequilibrium steady state for which we have estimated how each step of the reaction is energy driven or entropy driven to contribute to the overall reaction.

  4. Electrochemical and spectroscopic effects of mixed substituents in bis(phenolate)–copper(II) galactose oxidase model complexes

    PubMed Central

    Pratt, Russell C.; Lyons, Christopher T.; Wasinger, Erik C.; Stack, T. Daniel. P.

    2012-01-01

    Non-symmetric substitution of salen (1R1,R2) and reduced salen (2R1,R2) CuII-phenoxyl complexes with a combination of -tBu, -SiPr, and -OMe substituents leads to dramatic differences in their redox and spectroscopic properties, providing insight into the influence of the cysteine-modified tyrosine cofactor in the enzyme galactose oxidase (GO). Using a modified Marcus-Hush analysis, the oxidized copper complexes are characterized as Class II mixed-valent due to the electronic differentiation between the two substituted phenolates. Sulfur K-edge X-ray absorption spectroscopy (XAS) assesses the degree of radical delocalization onto the single sulfur atom of non-symmetric [1tBu,SMe]+ at 7%, consistent with other spectroscopic and electrochemical results that suggest preferential oxidation of the -SMe bearing phenolate. Estimates of the thermodynamic free-energy difference between the two localized states (ΔG∘) and reorganizational energies (λR1R2) of [1R1,R2]+ and [2R1,R2]+ leads to accurate predictions of the spectroscopically observed IVCT transition energies. Application of the modified Marcus-Hush analysis to GO using parameters determined for [2R1,R2]+ predicts a νmax of ~ 13600 cm−1, well within the energy range of the broad Vis-NIR band displayed by the enzyme. PMID:22471355

  5. Thermodynamics and combustion modeling

    NASA Technical Reports Server (NTRS)

    Zeleznik, Frank J.

    1986-01-01

    Modeling fluid phase phenomena blends the conservation equations of continuum mechanics with the property equations of thermodynamics. The thermodynamic contribution becomes especially important when the phenomena involve chemical reactions as they do in combustion systems. The successful study of combustion processes requires (1) the availability of accurate thermodynamic properties for both the reactants and the products of reaction and (2) the computational capabilities to use the properties. A discussion is given of some aspects of the problem of estimating accurate thermodynamic properties both for reactants and products of reaction. Also, some examples of the use of thermodynamic properties for modeling chemically reacting systems are presented. These examples include one-dimensional flow systems and the internal combustion engine.

  6. A Hamiltonian approach to Thermodynamics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Baldiotti, M.C., E-mail: baldiotti@uel.br; Fresneda, R., E-mail: rodrigo.fresneda@ufabc.edu.br; Molina, C., E-mail: cmolina@usp.br

    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 extensivelymore » 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.« less

  7. Discrete Thermodynamics

    DOE PAGES

    Margolin, L. G.; Hunter, A.

    2017-10-18

    Here, we consider the dependence of velocity probability distribution functions on the finite size of a thermodynamic system. We are motivated by applications to computational fluid dynamics, hence discrete thermodynamics. We then begin by describing a coarsening process that represents geometric renormalization. Then, based only on the requirements of conservation, we demonstrate that the pervasive assumption of local thermodynamic equilibrium is not form invariant. We develop a perturbative correction that restores form invariance to second-order in a small parameter associated with macroscopic gradients. Finally, we interpret the corrections in terms of unresolved kinetic energy and discuss the implications of ourmore » results both in theory and as applied to numerical simulation.« less

  8. Discrete Thermodynamics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Margolin, L. G.; Hunter, A.

    Here, we consider the dependence of velocity probability distribution functions on the finite size of a thermodynamic system. We are motivated by applications to computational fluid dynamics, hence discrete thermodynamics. We then begin by describing a coarsening process that represents geometric renormalization. Then, based only on the requirements of conservation, we demonstrate that the pervasive assumption of local thermodynamic equilibrium is not form invariant. We develop a perturbative correction that restores form invariance to second-order in a small parameter associated with macroscopic gradients. Finally, we interpret the corrections in terms of unresolved kinetic energy and discuss the implications of ourmore » results both in theory and as applied to numerical simulation.« less

  9. Evolution in thermodynamics

    NASA Astrophysics Data System (ADS)

    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. Infrared and Raman Spectroscopic Studies of the Antimicrobial Effects of Garlic Concentrates and Diallyl Constituents on Foodborne Pathogens

    PubMed Central

    Lu, Xiaonan; Rasco, Barbara A.; Kang, Dong-Hyun; Jabal, Jamie M.F.; Aston, D. Eric; Konkel, Michael E.

    2012-01-01

    The antimicrobial effects of garlic (Allium sativum) extract (25, 50, 75, 100, and 200 μl/ml) and diallyl sulfide (5, 10 and 20 μM) on Listeria monocytogenes and Escherichia coli O157:H7 cultivated in tryptic soy broth at 4, 22 and 35°C for up to 7 days were investigated. L. monocytogenes was more resistant to garlic extract and diallyl compounds treatment than E. coli O157:H7. Fourier transform Infrared (FT-IR) spectroscopy indicated that diallyl constituents contributed more to the antimicrobial effect than phenolic compounds. This effect was verified by Raman spectroscopy and Raman mapping on single bacteria. Scanning electron microscope (SEM) and transmission electron microscope (TEM) showed cell membrane damage consistent with spectroscopic observation. The degree of bacterial cell injury could be quantified using chemometric methods. PMID:21553849

  11. Thermal-Wave Microscope

    NASA Technical Reports Server (NTRS)

    Jones, Robert E.; Kramarchuk, Ihor; Williams, Wallace D.; Pouch, John J.; Gilbert, Percy

    1989-01-01

    Computer-controlled thermal-wave microscope developed to investigate III-V compound semiconductor devices and materials. Is nondestructive technique providing information on subsurface thermal features of solid samples. Furthermore, because this is subsurface technique, three-dimensional imaging also possible. Microscope uses intensity-modulated electron beam of modified scanning electron microscope to generate thermal waves in sample. Acoustic waves generated by thermal waves received by transducer and processed in computer to form images displayed on video display of microscope or recorded on magnetic disk.

  12. Growth and spectroscopic, thermodynamic and nonlinear optical studies of L-threonine phthalate crystal

    NASA Astrophysics Data System (ADS)

    Theras, J. Elberin Mary; Kalaivani, D.; Jayaraman, D.; Joseph, V.

    2015-10-01

    L-threonine phthalate (LTP) single crystal has been grown using a solution growth technique at room temperature. Single crystal X-ray diffraction analysis reveals that LTP crystallizes in monoclinic crystal system with space group C2/c. The optical absorption studies show that the crystal is transparent in the entire visible region with a cut-off wavelength 309 nm. The optical band gap is found to be 4.05 eV. The functional groups of the synthesized compound have been identified by FTIR spectral analysis. The functional groups present in the material were also confirmed by FT-RAMAN spectroscopy. Surface morphology and the presence of various elements were studied by SEM-EDAX analysis. The thermal stability of LTP single crystal has been analyzed by TGA/DTA studies. The thermodynamic parameters such as activation energy, entropy, enthalpy and Gibbs free energy were determined for the grown material using TG data and Coats-Redfern relation. Since the grown crystal is centrosymmetric, Z-Scan studies were carried out for analyzing the third order nonlinear optical property. The nonlinear absorption coefficient, nonlinear refractive index and susceptibility have been measured using Z-Scan technique.

  13. Biochemical Thermodynamics under near Physiological Conditions

    ERIC Educational Resources Information Center

    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…

  14. Spectroscopic characterization of N = 9 armchair graphene nanoribbons

    DOE PAGES

    Senkovskiy, B. V.; Haberer, D.; Usachov, D. Yu.; ...

    2017-07-03

    In this study, we investigate the N = 9 atoms wide armchair-type graphene nanoribbons (9-AGNRs) by performing a comprehensive spectroscopic and microscopic characterization of this novel material. In particular, we use X-ray photoelectron, near edge X-ray absorption fine structure, scanning tunneling, polarized Raman and angle-resolved photoemission (ARPES) spectroscopies. The ARPES measurements are aided by calculations of the photoemission matrix elements which yield the position in k space having the strongest photoemission cross section. Comparison with well-studied narrow N = 7 AGNRs shows that the effective electron mass in 9-AGNRs is reduced by two times and the valence band maximum ismore » shifted to lower binding energy by ~0.6 eV. In polarized Raman measurements of the aligned 9-AGNR, we reveal anisotropic signal depending upon the phonon symmetry. To conclude, our results indicate the 9-AGNRs are a novel 1D semiconductor with a high potential in nanoelectronic applications.« less

  15. Effects of Calcium Ions on the Thermostability and Spectroscopic Properties of the LH1-RC Complex from a New Thermophilic Purple Bacterium Allochromatium tepidum.

    PubMed

    Kimura, Yukihiro; Lyu, Shuwen; Okoshi, Akira; Okazaki, Koudai; Nakamura, Natsuki; Ohashi, Akira; Ohno, Takashi; Kobayashi, Manami; Imanishi, Michie; Takaichi, Shinichi; Madigan, Michael T; Wang-Otomo, Zheng-Yu

    2017-05-18

    The light harvesting-reaction center (LH1-RC) complex from a new thermophilic purple sulfur bacterium Allochromatium (Alc.) tepidum was isolated and characterized by spectroscopic and thermodynamic analyses. The purified Alc. tepidum LH1-RC complex showed a high thermostability comparable to that of another thermophilic purple sulfur bacterium Thermochromatium tepidum, and spectroscopic characteristics similar to those of a mesophilic bacterium Alc. vinosum. Approximately 4-5 Ca 2+ per LH1-RC were detected by inductively coupled plasma atomic emission spectroscopy and isothermal titration calorimetry. Upon removal of Ca 2+ , the denaturing temperature of the Alc. tepidum LH1-RC complex dropped accompanied by a blue-shift of the LH1 Q y absorption band. The effect of Ca 2+ was also observed in the resonance Raman shift of the C3-acetyl νC═O band of bacteriochlorophyll-a, indicating changes in the hydrogen-bonding interactions between the pigment and LH1 polypeptides. Thermodynamic parameters for the Ca 2+ -binding to the Alc. tepidum LH1-RC complex indicated that this reaction is predominantly driven by the largely favorable electrostatic interactions that counteract the unfavorable negative entropy change. Our data support a hypothesis that Alc. tepidum may be a transitional organism between mesophilic and thermophilic purple bacteria and that Ca 2+ is one of the major keys to the thermostability of LH1-RC complexes in purple bacteria.

  16. Theory of BCS-BEC Crossover in Ultracold Fermi Gases: Insights into Thermodynamical and Spectroscopic Experiments

    NASA Astrophysics Data System (ADS)

    Levin, Kathryn

    2009-05-01

    In this talk we summarize our theoretical understanding of the atomic Fermi superfluids with an emphasis on understanding current experiments. We compare and contrast different theoretical approaches for dealing with finite temperature, and discuss their respective implications for these trapped gases. Armed with a basic picture of the thermodynamics we turn to a variety of different measurements based on radio frequency spectroscopy, including both momentum integrated and momentum resolved experiments. As recently reviewed in arXiv 0810.1940 and 0810.1938, we show how a broad range of experimental phenomena can be accomodated within our natural extension of the BCS-Leggett ground state to finite temperature, and briefly touch on the applicability of BCS-BEC crossover theory to the high temperature superconductors. Co-authors: Qijin Chen, Yan He and Chih-Chun Chien

  17. Surface imaging microscope

    NASA Astrophysics Data System (ADS)

    Rogala, Eric W.; Bankman, Isaac N.

    2008-04-01

    The three-dimensional shapes of microscopic objects are becoming increasingly important for battlespace CBRNE sensing. Potential applications of microscopic 3D shape observations include characterization of biological weapon particles and manufacturing of micromechanical components. Aerosol signatures of stand-off lidar systems, using elastic backscatter or polarization, are dictated by the aerosol particle shapes and sizes that must be well characterized in the lab. A low-cost, fast instrument for 3D surface shape microscopy will be a valuable point sensor for biological particle sensing applications. Both the cost and imaging durations of traditional techniques such as confocal microscopes, atomic force microscopes, and electron scanning microscopes are too high. We investigated the feasibility of a low-cost, fast interferometric technique for imaging the 3D surface shape of microscopic objects at frame rates limited only by the camera in the system. The system operates at two laser wavelengths producing two fringe images collected simultaneously by a digital camera, and a specialized algorithm we developed reconstructs the surface map of the microscopic object. The current implementation assembled to test the concept and develop the new 3D reconstruction algorithm has 0.25 micron resolution in the x and y directions, and about 0.1 micron accuracy in the z direction, as tested on a microscopic glass test object manufactured with etching techniques. We describe the interferometric instrument, present the reconstruction algorithm, and discuss further development.

  18. Nonlocal effects in nonisothermal hydrodynamics from the perspective of beyond-equilibrium thermodynamics.

    PubMed

    Hütter, Markus; Brader, Joseph M

    2009-06-07

    We examine the origins of nonlocality in a nonisothermal hydrodynamic formulation of a one-component fluid of particles that exhibit long-range correlations, e.g., due to a spherically symmetric, long-range interaction potential. In order to furnish the continuum modeling with physical understanding of the microscopic interactions and dynamics, we make use of systematic coarse graining from the microscopic to the continuum level. We thus arrive at a thermodynamically admissible and closed set of evolution equations for the densities of momentum, mass, and internal energy. From the consideration of an illustrative special case, the following main conclusions emerge. There are two different source terms in the momentum balance. The first is a body force, which in special circumstances can be related to the functional derivative of a nonlocal Helmholtz free energy density with respect to the mass density. The second source term is proportional to the temperature gradient, multiplied by the nonlocal entropy density. These two source terms combine into a pressure gradient only in the absence of long-range effects. In the irreversible contributions to the time evolution, the nonlocal contributions arise since the self-correlations of the stress tensor and heat flux, respectively, are nonlocal as a result of the microscopic nonlocal correlations. Finally, we point out specific points that warrant further discussions.

  19. Conformational, electronic, and spectroscopic characterization of isophthalic acid (monomer and dimer structures) experimentally and by DFT

    NASA Astrophysics Data System (ADS)

    Bardak, F.; Karaca, C.; Bilgili, S.; Atac, A.; Mavis, T.; Asiri, A. M.; Karabacak, M.; Kose, E.

    2016-08-01

    Isophthalic acid (C6H4(CO2H)2) is a noteworthy organic compound widely used in coating and synthesis of resins and the production of commercially important polymers such as drink plastic bottles. The effects of isophthalic acid (IPA) on human health, toxicology, and biodegradability are the main focus of many researchers. Because structural and spectroscopic investigation of molecules provides a deep understanding of interactional behaviors of compounds, this study stands for exploring those features. Therefore, the spectroscopic, structural, electronic, and thermodynamical properties of IPA were thoroughly studied in this work experimentally using UV-Vis, 1H and 13C NMR, FT-IR, FT-Raman and theoretically via DFT and TD-DFT calculations. The UV-Vis absorption spectrum in water was taken in the region 200-400 nm. The NMR chemical shifts (1H and 13C) were recorded in DMSO solution. The infrared and Raman spectra of the solid IPA were recorded in the range of 4000-400 cm- 1 and 3500-50 cm- 1, respectively. DFT and TD-DFT calculations were performed at the level of B3LYP/6-311++G(d,p) in determination of geometrical structure, electronic structure analysis and normal mode. The 13C and 1H nuclear magnetic resonance (NMR) spectra were estimated by using the gauge-invariant atomic orbital (GIAO) method. The scaled quantum mechanics (SQM) method was used to determine the total energy distribution (TED) to assign the vibrational modes accurately. Weak interactions such as hydrogen bonding and Van der Walls were analyzed via reduced density gradient (RDG) analysis in monomeric and dimeric forms. Furthermore, the excitation energies, density of state (DOS) diagram, thermodynamical properties, molecular electro-static potential (MEP), and nonlinear optical (NLO) properties were obtained.

  20. Statistical Thermodynamics and Microscale Thermophysics

    NASA Astrophysics Data System (ADS)

    Carey, Van P.

    1999-08-01

    Many exciting new developments in microscale engineering are based on the application of traditional principles of statistical thermodynamics. In this text Van Carey offers a modern view of thermodynamics, interweaving classical and statistical thermodynamic principles and applying them to current engineering systems. He begins with coverage of microscale energy storage mechanisms from a quantum mechanics perspective and then develops the fundamental elements of classical and statistical thermodynamics. Subsequent chapters discuss applications of equilibrium statistical thermodynamics to solid, liquid, and gas phase systems. The remainder of the book is devoted to nonequilibrium thermodynamics of transport phenomena and to nonequilibrium effects and noncontinuum behavior at the microscale. Although the text emphasizes mathematical development, Carey includes many examples and exercises to illustrate how the theoretical concepts are applied to systems of scientific and engineering interest. In the process he offers a fresh view of statistical thermodynamics for advanced undergraduate and graduate students, as well as practitioners, in mechanical, chemical, and materials engineering.

  1. Comparative study of image contrast in scanning electron microscope and helium ion microscope.

    PubMed

    O'Connell, R; Chen, Y; Zhang, H; Zhou, Y; Fox, D; Maguire, P; Wang, J J; Rodenburg, C

    2017-12-01

    Images of Ga + -implanted amorphous silicon layers in a 110 n-type silicon substrate have been collected by a range of detectors in a scanning electron microscope and a helium ion microscope. The effects of the implantation dose and imaging parameters (beam energy, dwell time, etc.) on the image contrast were investigated. We demonstrate a similar relationship for both the helium ion microscope Everhart-Thornley and scanning electron microscope Inlens detectors between the contrast of the images and the Ga + density and imaging parameters. These results also show that dynamic charging effects have a significant impact on the quantification of the helium ion microscope and scanning electron microscope contrast. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

  2. Microscopic dynamics of charge separation at the aqueous electrochemical interface.

    PubMed

    Kattirtzi, John A; Limmer, David T; Willard, Adam P

    2017-12-19

    We have used molecular simulation and methods of importance sampling to study the thermodynamics and kinetics of ionic charge separation at a liquid water-metal interface. We have considered this process using canonical examples of two different classes of ions: a simple alkali-halide pair, Na + I - , or classical ions, and the products of water autoionization, H 3 O + OH - , or water ions. We find that for both ion classes, the microscopic mechanism of charge separation, including water's collective role in the process, is conserved between the bulk liquid and the electrode interface. However, the thermodynamic and kinetic details of the process differ between these two environments in a way that depends on ion type. In the case of the classical ion pairs, a higher free-energy barrier to charge separation and a smaller flux over that barrier at the interface result in a rate of dissociation that is 40 times slower relative to the bulk. For water ions, a slightly higher free-energy barrier is offset by a higher flux over the barrier from longer lived hydrogen-bonding patterns at the interface, resulting in a rate of association that is similar both at and away from the interface. We find that these differences in rates and stabilities of charge separation are due to the altered ability of water to solvate and reorganize in the vicinity of the metal interface.

  3. Arsenic removal by Japanese oak wood biochar in aqueous solutions and well water: Investigating arsenic fate using integrated spectroscopic and microscopic techniques.

    PubMed

    Niazi, Nabeel Khan; Bibi, Irshad; Shahid, Muhammad; Ok, Yong Sik; Shaheen, Sabry M; Rinklebe, Jörg; Wang, Hailong; Murtaza, Behzad; Islam, Ejazul; Farrakh Nawaz, M; Lüttge, Andreas

    2018-04-15

    In this study, we examined the sorption of arsenite (As(III)) and arsenate (As(V)) to Japanese oak wood-derived biochar (OW-BC) in aqueous solutions, and determined its efficiency to remove As from As-contaminated well water. Results revealed that, among the four sorption isotherm models, Langmuir model showed the best fit to describe As(III) and As(V) sorption on OW-BC, with slightly greater sorption affinity for As(V) compared to As(III) (Q L =3.89 and 3.16mgg -1 ; R 2 =0.91 and 0.85, respectively). Sorption edge experiments indicated that the maximum As removal was 81% and 84% for As(III)- and As(V)-OW-BC systems at pH7 and 6, respectively, which decreased above these pH values (76-69% and 80-58%). Surface functional groups, notably OH, COOH, CO, CH 3 , were involved in As sequestration by OW-BC, suggesting the surface complexation/precipitation and/or electrostatic interaction of As on OW-BC surface. Arsenic K-edge X-ray absorption near edge structure (XANES) spectroscopy indicated that 36% of the added As(III) was partially oxidized to As(V) in the As(III) sorption experiment, and in As(V) sorption experiment, 48% of As(V) was, albeit incompletely, reduced to As(III) on OW-BC surface. Application of OW-BC to As-contaminated well water (As: 27-144μgL -1 ; n=10) displayed that 92 to 100% of As was depleted despite in the presence of co-occurring competing anions (e.g., SO 4 2- , CO 3 2- , PO 4 3- ). This study shows that OW-BC has a great potential to remove As from solution and drinking (well) water. Overall, the combination of macroscopic sorption data and integrated spectroscopic and microscopic techniques highlight that the fate of As on biochar involves complex redox transformation and association with surface functional moieties in aquatic systems, thereby providing crucial information required for implication of biochar in environmental remediation programs. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Spectroscopic and thermodynamic properties of molecular hydrogen dissolved in water at pressures up to 200 MPa

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Borysow, Jacek, E-mail: jborysow@mtu.edu; Rosso, Leonardo del; Celli, Milva

    2014-04-28

    We have measured the Raman Q-branch of hydrogen in a solution with water at a temperature of about 280 K and at pressures from 20 to 200 MPa. From a least-mean-square fitting analysis of the broad Raman Q-branch, we isolated the contributions from the four lowest individual roto-vibrational lines. The vibrational lines were narrower than the pure rotational Raman lines of hydrogen dissolved in water measured previously, but significantly larger than in the gas. The separations between these lines were found to be significantly smaller than in gaseous hydrogen and their widths were slightly increasing with pressure. The lines weremore » narrowing with increasing rotational quantum number. The Raman frequencies of all roto-vibrational lines were approaching the values of gas phase hydrogen with increasing pressure. Additionally, from the comparison of the integrated intensity signal of Q-branch of hydrogen to the integrated Raman signal of the water bending mode, we have obtained the concentration of hydrogen in a solution with water along the 280 K isotherm. Hydrogen solubility increases slowly with pressure, and no deviation from a smooth behaviour was observed, even reaching thermodynamic conditions very close to the transition to the stable hydrogen hydrate. The analysis of the relative hydrogen concentration in solution on the basis of a simple thermodynamic model has allowed us to obtain the molar volume for the hydrogen gas/water solution. Interestingly, the volume relative to one hydrogen molecule in solution does not decrease with pressure and, at high pressure, is larger than the volume pertinent to one molecule of water. This is in favour of the theory of hydrophobic solvation, for which a larger and more stable structure of the water molecules is expected around a solute molecule.« less

  5. Spectroscopic and thermodynamic properties of molecular hydrogen dissolved in water at pressures up to 200 MPa.

    PubMed

    Borysow, Jacek; del Rosso, Leonardo; Celli, Milva; Moraldi, Massimo; Ulivi, Lorenzo

    2014-04-28

    We have measured the Raman Q-branch of hydrogen in a solution with water at a temperature of about 280 K and at pressures from 20 to 200 MPa. From a least-mean-square fitting analysis of the broad Raman Q-branch, we isolated the contributions from the four lowest individual roto-vibrational lines. The vibrational lines were narrower than the pure rotational Raman lines of hydrogen dissolved in water measured previously, but significantly larger than in the gas. The separations between these lines were found to be significantly smaller than in gaseous hydrogen and their widths were slightly increasing with pressure. The lines were narrowing with increasing rotational quantum number. The Raman frequencies of all roto-vibrational lines were approaching the values of gas phase hydrogen with increasing pressure. Additionally, from the comparison of the integrated intensity signal of Q-branch of hydrogen to the integrated Raman signal of the water bending mode, we have obtained the concentration of hydrogen in a solution with water along the 280 K isotherm. Hydrogen solubility increases slowly with pressure, and no deviation from a smooth behaviour was observed, even reaching thermodynamic conditions very close to the transition to the stable hydrogen hydrate. The analysis of the relative hydrogen concentration in solution on the basis of a simple thermodynamic model has allowed us to obtain the molar volume for the hydrogen gas/water solution. Interestingly, the volume relative to one hydrogen molecule in solution does not decrease with pressure and, at high pressure, is larger than the volume pertinent to one molecule of water. This is in favour of the theory of hydrophobic solvation, for which a larger and more stable structure of the water molecules is expected around a solute molecule.

  6. Spectroscopic and thermodynamic properties of molecular hydrogen dissolved in water at pressures up to 200 MPa

    NASA Astrophysics Data System (ADS)

    Borysow, Jacek; del Rosso, Leonardo; Celli, Milva; Moraldi, Massimo; Ulivi, Lorenzo

    2014-04-01

    We have measured the Raman Q-branch of hydrogen in a solution with water at a temperature of about 280 K and at pressures from 20 to 200 MPa. From a least-mean-square fitting analysis of the broad Raman Q-branch, we isolated the contributions from the four lowest individual roto-vibrational lines. The vibrational lines were narrower than the pure rotational Raman lines of hydrogen dissolved in water measured previously, but significantly larger than in the gas. The separations between these lines were found to be significantly smaller than in gaseous hydrogen and their widths were slightly increasing with pressure. The lines were narrowing with increasing rotational quantum number. The Raman frequencies of all roto-vibrational lines were approaching the values of gas phase hydrogen with increasing pressure. Additionally, from the comparison of the integrated intensity signal of Q-branch of hydrogen to the integrated Raman signal of the water bending mode, we have obtained the concentration of hydrogen in a solution with water along the 280 K isotherm. Hydrogen solubility increases slowly with pressure, and no deviation from a smooth behaviour was observed, even reaching thermodynamic conditions very close to the transition to the stable hydrogen hydrate. The analysis of the relative hydrogen concentration in solution on the basis of a simple thermodynamic model has allowed us to obtain the molar volume for the hydrogen gas/water solution. Interestingly, the volume relative to one hydrogen molecule in solution does not decrease with pressure and, at high pressure, is larger than the volume pertinent to one molecule of water. This is in favour of the theory of hydrophobic solvation, for which a larger and more stable structure of the water molecules is expected around a solute molecule.

  7. A single-photon fluorescence and multi-photon spectroscopic study of atherosclerotic lesions

    NASA Astrophysics Data System (ADS)

    Smith, Michael S. D.; Ko, Alex C. T.; Ridsdale, Andrew; Schattka, Bernie; Pegoraro, Adrian; Hewko, Mark D.; Shiomi, Masashi; Stolow, Albert; Sowa, Michael G.

    2009-06-01

    In this study we compare the single-photon autofluorescence and multi-photon emission spectra obtained from the luminal surface of healthy segments of artery with segments where there are early atherosclerotic lesions. Arterial tissue was harvested from atherosclerosis-prone WHHL-MI rabbits (Watanabe heritable hyperlipidemic rabbit-myocardial infarction), an animal model which mimics spontaneous myocardial infarction in humans. Single photon fluorescence emission spectra of samples were acquired using a simple spectrofluorometer set-up with 400 nm excitation. Samples were also investigated using a home built multi-photon microscope based on a Ti:sapphire femto-second oscillator. The excitation wavelength was set at 800 nm with a ~100 femto-second pulse width. Epi-multi-photon spectroscopic signals were collected through a fibre-optics coupled spectrometer. While the single-photon fluorescence spectra of atherosclerotic lesions show minimal spectroscopic difference from those of healthy arterial tissue, the multi-photon spectra collected from atherosclerotic lesions show marked changes in the relative intensity of two-photon excited fluorescence (TPEF) and second-harmonic generation (SHG) signals when compared with those from healthy arterial tissue. The observed sharp increase of the relative SHG signal intensity in a plaque is in agreement with the known pathology of early lesions which have increased collagen content.

  8. Modeling nanostructural surface modifications in metal cutting by an approach of thermodynamic irreversibility: Derivation and experimental validation

    NASA Astrophysics Data System (ADS)

    Buchkremer, S.; Klocke, F.

    2017-01-01

    Performance and operational safety of many metal parts in engineering depend on their surface integrity. During metal cutting, large thermomechanical loads and high gradients of the loads concerning time and location act on the surfaces and may yield significant structural material modifications, which alter the surface integrity. In this work, the derivation and validation of a model of nanostructural surface modifications in metal cutting are presented. For the first time in process modeling, initiation and kinetics of these modifications are predicted using a thermodynamic potential, which considers the interdependent developments of plastic work, dissipation, heat conduction and interface energy as well as the associated productions and flows of entropy. The potential is expressed based on the free Helmholtz energy. The irreversible thermodynamic state changes in the workpiece surface are homogenized over the volume in order to bridge the gap between discrete phenomena involved with the initiation and kinetics of dynamic recrystallization and its macroscopic implications for surface integrity. The formulation of the thermodynamic potential is implemented into a finite element model of orthogonal cutting of steel AISI 4140. Close agreement is achieved between predicted nanostructures and those obtained in transmission electron microscopical investigations of specimen produced in cutting experiments.

  9. Thermodynamics of adaptive molecular resolution.

    PubMed

    Delgado-Buscalioni, R

    2016-11-13

    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 variablesThis article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

  10. Thermodynamics of adaptive molecular resolution

    NASA Astrophysics Data System (ADS)

    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'.

  11. Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Carra,J.; McHugh, C.; Mulligan, S.

    2007-01-01

    We found that amide ligands can bind weakly but specifically to the ricin active site, producing significant shifts in positions of the critical active site residues Arg180 and Tyr80. These results indicate that fragment-based drug discovery methods are capable of identifying minimal bonding determinants of active-site side-chain rearrangements and the mechanistic origins of spectroscopic shifts. Our results suggest that tryptophan fluorescence provides a sensitive probe for the geometric relationship of arginine-tryptophan pairs, which often have significant roles in protein function. Using the unusual characteristics of the RTA system, we measured the still controversial thermodynamic changes of site-specific urea binding tomore » a protein, results that are relevant to understanding the physical mechanisms of protein denaturation.« less

  12. Usefulness of charge-transfer complexation for the assessment of sympathomimetic drugs: Spectroscopic properties of drug ephedrine hydrochloride complexed with some π-acceptors

    NASA Astrophysics Data System (ADS)

    Refat, Moamen S.; Ibrahim, Omar B.; Saad, Hosam A.; Adam, Abdel Majid A.

    2014-05-01

    Recently, ephedrine (Eph) assessment in food products, pharmaceutical formulations, human fluids of athletes and detection of drug toxicity and abuse, has gained a growing interest. To provide basic data that can be used to assessment of Eph quantitatively based on charge-transfer (CT) complexation, the CT complexes of Eph with 7‧,8,8‧-tetracyanoquinodimethane (TCNQ), dichlorodicyanobenzoquinone (DDQ), 1,3-dinitrobenzene (DNB) or tetrabromothiophene (TBT) were synthesized and spectroscopically investigated. The newly synthesized complexes have been characterized via elemental analysis, IR, Raman, 1H NMR, and UV-visible spectroscopy. The formation constant (KCT), molar extinction coefficient (εCT) and other spectroscopic data have been determined using the Benesi-Hildebrand method and its modifications. The sharp, well-defined Bragg reflections at specific 2θ angles have been identified from the powder X-ray diffraction patterns. Thermal decomposition behavior of these complexes was also studied, and their kinetic thermodynamic parameters were calculated with Coats-Redfern and Horowitz-Metzger equations.

  13. A detailed spectroscopic study on the interaction of Rhodamine 6G with human hemoglobin.

    PubMed

    Mandal, Paulami; Bardhan, Munmun; Ganguly, Tapan

    2010-05-03

    UV-vis, time-resolved fluorescence and circular dichroism spectroscopic investigations have been made to reveal the nature of the interactions between xanthene dye Rhodamine 6G and the well known protein hemoglobin. From the analysis of the steady-state and time-resolved fluorescence quenching of Rhodamine 6G in aqueous solutions in presence of hemoglobin, it is revealed that the quenching is static in nature. The primary binding pattern between Rhodamine and hemoglobin has been interpreted as combined effect of hydrophobic association and electrostatic interaction. The binding constants, number of binding sites and thermodynamic parameters at various pH of the environment have been computed. The binding average distance between the energy donor Rhodamine and acceptor hemoglobin has been determined from the Forster's theory. Copyright 2010 Elsevier B.V. All rights reserved.

  14. Spectroscopic analysis and control

    DOEpatents

    Tate; , James D.; Reed, Christopher J.; Domke, Christopher H.; Le, Linh; Seasholtz, Mary Beth; Weber, Andy; Lipp, Charles

    2017-04-18

    Apparatus for spectroscopic analysis which includes a tunable diode laser spectrometer having a digital output signal and a digital computer for receiving the digital output signal from the spectrometer, the digital computer programmed to process the digital output signal using a multivariate regression algorithm. In addition, a spectroscopic method of analysis using such apparatus. Finally, a method for controlling an ethylene cracker hydrogenator.

  15. SpectraPlot.com: Integrated spectroscopic modeling of atomic and molecular gases

    NASA Astrophysics Data System (ADS)

    Goldenstein, Christopher S.; Miller, Victor A.; Mitchell Spearrin, R.; Strand, Christopher L.

    2017-10-01

    SpectraPlot is a web-based application for simulating spectra of atomic and molecular gases. At the time this manuscript was written, SpectraPlot consisted of four primary tools for calculating: (1) atomic and molecular absorption spectra, (2) atomic and molecular emission spectra, (3) transition linestrengths, and (4) blackbody emission spectra. These tools currently employ the NIST ASD, HITRAN2012, and HITEMP2010 databases to perform line-by-line simulations of spectra. SpectraPlot employs a modular, integrated architecture, enabling multiple simulations across multiple databases and/or thermodynamic conditions to be visualized in an interactive plot window. The primary objective of this paper is to describe the architecture and spectroscopic models employed by SpectraPlot in order to provide its users with the knowledge required to understand the capabilities and limitations of simulations performed using SpectraPlot. Further, this manuscript discusses the accuracy of several underlying approximations used to decrease computational time, in particular, the use of far-wing cutoff criteria.

  16. L-shell spectroscopic diagnostics of radiation from krypton HED plasma sources.

    PubMed

    Petkov, E E; Safronova, A S; Kantsyrev, V L; Shlyaptseva, V V; Rawat, R S; Tan, K S; Beiersdorfer, P; Hell, N; Brown, G V

    2016-11-01

    X-ray spectroscopy is a useful tool for diagnosing plasma sources due to its non-invasive nature. One such source is the dense plasma focus (DPF). Recent interest has developed to demonstrate its potential application as a soft x-ray source. We present the first spectroscopic studies of krypton high energy density plasmas produced on a 3 kJ DPF device in Singapore. In order to diagnose spectral features, and to obtain a more comprehensive understanding of plasma parameters, a new non-local thermodynamic equilibrium L-shell kinetic model for krypton was developed. It has the capability of incorporating hot electrons, with different electron distribution functions, in order to examine the effects that they have on emission spectra. To further substantiate the validity of this model, it is also benchmarked with data gathered from experiments on the electron beam ion trap (EBIT) at Lawrence Livermore National Laboratory, where data were collected using the high resolution EBIT calorimeter spectrometer.

  17. L-shell spectroscopic diagnostics of radiation from krypton HED plasma sources

    DOE PAGES

    Petkov, E. E.; Safronova, A. S.; Kantsyrev, V. L.; ...

    2016-08-09

    We report that X-ray spectroscopy is a useful tool for diagnosing plasma sources due to its non-invasive nature. One such source is the dense plasma focus (DPF). Recent interest has developed to demonstrate its potential application as a soft x-ray source. We present the first spectroscopic studies of krypton high energy density plasmas produced on a 3 kJ DPF device in Singapore. In order to diagnose spectral features, and to obtain a more comprehensive understanding of plasma parameters, a new non-local thermodynamic equilibrium L-shell kinetic model for krypton was developed. It has the capability of incorporating hot electrons, with differentmore » electron distribution functions, in order to examine the effects that they have on emission spectra. Finally, to further substantiate the validity of this model, it is also benchmarked with data gathered from experiments on the electron beam ion trap (EBIT) at Lawrence Livermore National Laboratory, where data were collected using the high resolution EBIT calorimeter spectrometer.« less

  18. L-shell spectroscopic diagnostics of radiation from krypton HED plasma sources

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Petkov, E. E., E-mail: emilp@unr.edu; Safronova, A. S.; Kantsyrev, V. L.

    2016-11-15

    X-ray spectroscopy is a useful tool for diagnosing plasma sources due to its non-invasive nature. One such source is the dense plasma focus (DPF). Recent interest has developed to demonstrate its potential application as a soft x-ray source. We present the first spectroscopic studies of krypton high energy density plasmas produced on a 3 kJ DPF device in Singapore. In order to diagnose spectral features, and to obtain a more comprehensive understanding of plasma parameters, a new non-local thermodynamic equilibrium L-shell kinetic model for krypton was developed. It has the capability of incorporating hot electrons, with different electron distribution functions,more » in order to examine the effects that they have on emission spectra. To further substantiate the validity of this model, it is also benchmarked with data gathered from experiments on the electron beam ion trap (EBIT) at Lawrence Livermore National Laboratory, where data were collected using the high resolution EBIT calorimeter spectrometer.« less

  19. High vacuum tip-enhanced Raman spectroscope based on a scanning tunneling microscope.

    PubMed

    Fang, Yurui; Zhang, Zhenglong; Sun, Mengtao

    2016-03-01

    In this paper, we present the construction of a high-vacuum tip-enhanced Raman spectroscopy (HV-TERS) system that allows in situ sample preparation and measurement. A detailed description of the prototype instrument is presented with experimental validation of its use and novel ex situ experimental results using the HV-TERS system. The HV-TERS system includes three chambers held under a 10(-7) Pa vacuum. The three chambers are an analysis chamber, a sample preparation chamber, and a fast loading chamber. The analysis chamber is the core chamber and contains a scanning tunneling microscope (STM) and a Raman detector coupled with a 50 × 0.5 numerical aperture objective. The sample preparation chamber is used to produce single-crystalline metal and sub-monolayer molecular films by molecular beam epitaxy. The fast loading chamber allows ex situ preparation of samples for HV-TERS analysis. Atomic resolution can be achieved by the STM on highly ordered pyrolytic graphite. We demonstrate the measurement of localized temperature using the Stokes and anti-Stokes TERS signals from a monolayer of 1,2-benzenedithiol on a gold film using a gold tip. Additionally, plasmonic catalysis can be monitored label-free at the nanoscale using our device. Moreover, the HV-TERS experiments show simultaneously activated infrared and Raman vibrational modes, Fermi resonance, and some other non-linear effects that are not observed in atmospheric TERS experiments. The high spatial and spectral resolution and pure environment of high vacuum are beneficial for basic surface studies.

  20. High vacuum tip-enhanced Raman spectroscope based on a scanning tunneling microscope

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fang, Yurui; Bionanophotonics, Department of Applied Physics, Chalmers University of Technology, Göteborg, SE 41296; Zhang, Zhenglong

    2016-03-15

    In this paper, we present the construction of a high-vacuum tip-enhanced Raman spectroscopy (HV-TERS) system that allows in situ sample preparation and measurement. A detailed description of the prototype instrument is presented with experimental validation of its use and novel ex situ experimental results using the HV-TERS system. The HV-TERS system includes three chambers held under a 10{sup −7} Pa vacuum. The three chambers are an analysis chamber, a sample preparation chamber, and a fast loading chamber. The analysis chamber is the core chamber and contains a scanning tunneling microscope (STM) and a Raman detector coupled with a 50 ×more » 0.5 numerical aperture objective. The sample preparation chamber is used to produce single-crystalline metal and sub-monolayer molecular films by molecular beam epitaxy. The fast loading chamber allows ex situ preparation of samples for HV-TERS analysis. Atomic resolution can be achieved by the STM on highly ordered pyrolytic graphite. We demonstrate the measurement of localized temperature using the Stokes and anti-Stokes TERS signals from a monolayer of 1,2-benzenedithiol on a gold film using a gold tip. Additionally, plasmonic catalysis can be monitored label-free at the nanoscale using our device. Moreover, the HV-TERS experiments show simultaneously activated infrared and Raman vibrational modes, Fermi resonance, and some other non-linear effects that are not observed in atmospheric TERS experiments. The high spatial and spectral resolution and pure environment of high vacuum are beneficial for basic surface studies.« less

  1. Shock compression dynamics under a microscope.

    NASA Astrophysics Data System (ADS)

    Dlott, Dana

    2015-06-01

    We have developed a tabletop laser flyer launch system1 that solves many of the problems that plagued previous efforts. Using a novel mechanism where a spatially-uniform laser pulse creates a shock in a glass substrate just underneath a metal foil, we can launch tiny (0.7 mm diameter x 100 μm thick) flyers at speeds ranging from 0-5 km/s and the foils are flat, cold and intact. This tabletop launch system, where we often launch 100 flyers per day, provides a platform for a wide variety of time-resolved spectroscopies. The shocked material is viewed by a microscope objective that transmits near-infrared light from a photon Doppler velocimeter to monitor the flyer, and collects the light for spectroscopic and video images. Fluorescent probes, which have been highly developed for the biomedical sciences, have proven especially useful for these experiments. Using emission measurements, we have investigated the fundamental mechanisms of many shock wave effects including: viscoelastic compression of high molecular weight polymers, visualization of shocks in porous media such as sand, where we can observe the behavior of individual grains of sand, shock attenuation by passing the shock through reactive materials that undergo endothermic chemical reactions, and shock initiation of nanoenergetic materials.

  2. Coherence and measurement in quantum thermodynamics

    PubMed Central

    Kammerlander, P.; Anders, J.

    2016-01-01

    Thermodynamics is a highly successful macroscopic theory widely used across the natural sciences and for the construction of everyday devices, from car engines to solar cells. With thermodynamics predating quantum theory, research now aims to uncover the thermodynamic laws that govern finite size systems which may in addition host quantum effects. Recent theoretical breakthroughs include the characterisation of the efficiency of quantum thermal engines, the extension of classical non-equilibrium fluctuation theorems to the quantum regime and a new thermodynamic resource theory has led to the discovery of a set of second laws for finite size systems. These results have substantially advanced our understanding of nanoscale thermodynamics, however putting a finger on what is genuinely quantum in quantum thermodynamics has remained a challenge. Here we identify information processing tasks, the so-called projections, that can only be formulated within the framework of quantum mechanics. We show that the physical realisation of such projections can come with a non-trivial thermodynamic work only for quantum states with coherences. This contrasts with information erasure, first investigated by Landauer, for which a thermodynamic work cost applies for classical and quantum erasure alike. Repercussions on quantum work fluctuation relations and thermodynamic single-shot approaches are also discussed. PMID:26916503

  3. Coherence and measurement in quantum thermodynamics.

    PubMed

    Kammerlander, P; Anders, J

    2016-02-26

    Thermodynamics is a highly successful macroscopic theory widely used across the natural sciences and for the construction of everyday devices, from car engines to solar cells. With thermodynamics predating quantum theory, research now aims to uncover the thermodynamic laws that govern finite size systems which may in addition host quantum effects. Recent theoretical breakthroughs include the characterisation of the efficiency of quantum thermal engines, the extension of classical non-equilibrium fluctuation theorems to the quantum regime and a new thermodynamic resource theory has led to the discovery of a set of second laws for finite size systems. These results have substantially advanced our understanding of nanoscale thermodynamics, however putting a finger on what is genuinely quantum in quantum thermodynamics has remained a challenge. Here we identify information processing tasks, the so-called projections, that can only be formulated within the framework of quantum mechanics. We show that the physical realisation of such projections can come with a non-trivial thermodynamic work only for quantum states with coherences. This contrasts with information erasure, first investigated by Landauer, for which a thermodynamic work cost applies for classical and quantum erasure alike. Repercussions on quantum work fluctuation relations and thermodynamic single-shot approaches are also discussed.

  4. Coherence and measurement in quantum thermodynamics

    NASA Astrophysics Data System (ADS)

    Kammerlander, P.; Anders, J.

    2016-02-01

    Thermodynamics is a highly successful macroscopic theory widely used across the natural sciences and for the construction of everyday devices, from car engines to solar cells. With thermodynamics predating quantum theory, research now aims to uncover the thermodynamic laws that govern finite size systems which may in addition host quantum effects. Recent theoretical breakthroughs include the characterisation of the efficiency of quantum thermal engines, the extension of classical non-equilibrium fluctuation theorems to the quantum regime and a new thermodynamic resource theory has led to the discovery of a set of second laws for finite size systems. These results have substantially advanced our understanding of nanoscale thermodynamics, however putting a finger on what is genuinely quantum in quantum thermodynamics has remained a challenge. Here we identify information processing tasks, the so-called projections, that can only be formulated within the framework of quantum mechanics. We show that the physical realisation of such projections can come with a non-trivial thermodynamic work only for quantum states with coherences. This contrasts with information erasure, first investigated by Landauer, for which a thermodynamic work cost applies for classical and quantum erasure alike. Repercussions on quantum work fluctuation relations and thermodynamic single-shot approaches are also discussed.

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

    PubMed Central

    Tischer, Alexander; Auton, Matthew

    2013-01-01

    We have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea-induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea–temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two-state character. Global analysis of the urea–temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of and that define a complex temperature dependence of the m-value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea-denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions. PMID:23813497

  6. Cryogenic immersion microscope

    DOEpatents

    Le Gros, Mark; Larabell, Carolyn A.

    2010-12-14

    A cryogenic immersion microscope whose objective lens is at least partially in contact with a liquid reservoir of a cryogenic liquid, in which reservoir a sample of interest is immersed is disclosed. When the cryogenic liquid has an index of refraction that reduces refraction at interfaces between the lens and the sample, overall resolution and image quality are improved. A combination of an immersion microscope and x-ray microscope, suitable for imaging at cryogenic temperatures is also disclosed.

  7. Thermodynamically efficient solar concentrators

    NASA Astrophysics Data System (ADS)

    Winston, Roland

    2012-10-01

    Non-imaging Optics is the theory of thermodynamically efficient optics and as such depends more on thermodynamics than on optics. Hence in this paper a condition for the "best" design is proposed based on purely thermodynamic arguments, which we believe has profound consequences for design of thermal and even photovoltaic systems. This new way of looking at the problem of efficient concentration depends on probabilities, the ingredients of entropy and information theory while "optics" in the conventional sense recedes into the background.

  8. The OpenCalphad thermodynamic software interface.

    PubMed

    Sundman, Bo; Kattner, Ursula R; Sigli, Christophe; Stratmann, Matthias; Le Tellier, Romain; Palumbo, Mauro; Fries, Suzana G

    2016-12-01

    Thermodynamic data are needed for all kinds of simulations of materials processes. Thermodynamics determines the set of stable phases and also provides chemical potentials, compositions and driving forces for nucleation of new phases and phase transformations. Software to simulate materials properties needs accurate and consistent thermodynamic data to predict metastable states that occur during phase transformations. Due to long calculation times thermodynamic data are frequently pre-calculated into "lookup tables" to speed up calculations. This creates additional uncertainties as data must be interpolated or extrapolated and conditions may differ from those assumed for creating the lookup table. Speed and accuracy requires that thermodynamic software is fully parallelized and the Open-Calphad (OC) software is the first thermodynamic software supporting this feature. This paper gives a brief introduction to computational thermodynamics and introduces the basic features of the OC software and presents four different application examples to demonstrate its versatility.

  9. Electrochemical thermodynamic measurement system

    DOEpatents

    Reynier, Yvan [Meylan, FR; Yazami, Rachid [Los Angeles, CA; Fultz, Brent T [Pasadena, CA

    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. Thermodynamics and evolution.

    PubMed

    Demetrius, L

    2000-09-07

    The science of thermodynamics is concerned with understanding the properties of inanimate matter in so far as they are determined by changes in temperature. The Second Law asserts that in irreversible processes there is a uni-directional increase in thermodynamic entropy, a measure of the degree of uncertainty in the thermal energy state of a randomly chosen particle in the aggregate. The science of evolution is concerned with understanding the properties of populations of living matter in so far as they are regulated by changes in generation time. Directionality theory, a mathematical model of the evolutionary process, establishes that in populations subject to bounded growth constraints, there is a uni-directional increase in evolutionary entropy, a measure of the degree of uncertainty in the age of the immediate ancestor of a randomly chosen newborn. This article reviews the mathematical basis of directionality theory and analyses the relation between directionality theory and statistical thermodynamics. We exploit an analytic relation between temperature, and generation time, to show that the directionality principle for evolutionary entropy is a non-equilibrium extension of the principle of a uni-directional increase of thermodynamic entropy. The analytic relation between these directionality principles is consistent with the hypothesis of the equivalence of fundamental laws as one moves up the hierarchy, from a molecular ensemble where the thermodynamic laws apply, to a population of replicating entities (molecules, cells, higher organisms), where evolutionary principles prevail. Copyright 2000 Academic Press.

  11. Reproducible fabrication and applications of superconducting scanning tunneling microscope tips

    NASA Astrophysics Data System (ADS)

    Naaman, Ofer; Teizer, Winfried; Dynes, Robert C.

    2001-03-01

    We report on a method developed in our lab, for the fabrication of superconducting scanning tunneling microscope (STM) tips in a reproducible fashion. The fabrication process relies on sequential deposition of superconducting Pb and a proximity-coupled Ag capping layer onto a Pt/Ir tip. The tips were characterized by tunneling into both normal-metal and superconducting films, and the results confirm that the tips are superconducting with Tc and Δ close to that of bulk lead. The lead phonon structure in the tunneling density of states was observed, indicating a single step tunneling process. In an attempt to form STM Josephson junctions, we used our tips to form S/I/S junctions with R_NN ~50-100 kΩ. Results from spectroscopic measurements of these junctions at 2.0 K are discussed within the framework of the Ivanchenko and Zil'berman theory (Soviet Physics JETP, vol.28, 1272; 1969) of Josephson tunneling in the presence of strong phase fluctuations.

  12. Microscopic dynamics of charge separation at the aqueous electrochemical interface

    PubMed Central

    Kattirtzi, John A.; Limmer, David T.; Willard, Adam P.

    2017-01-01

    We have used molecular simulation and methods of importance sampling to study the thermodynamics and kinetics of ionic charge separation at a liquid water–metal interface. We have considered this process using canonical examples of two different classes of ions: a simple alkali–halide pair, Na+I−, or classical ions, and the products of water autoionization, H3O+OH−, or water ions. We find that for both ion classes, the microscopic mechanism of charge separation, including water’s collective role in the process, is conserved between the bulk liquid and the electrode interface. However, the thermodynamic and kinetic details of the process differ between these two environments in a way that depends on ion type. In the case of the classical ion pairs, a higher free-energy barrier to charge separation and a smaller flux over that barrier at the interface result in a rate of dissociation that is 40 times slower relative to the bulk. For water ions, a slightly higher free-energy barrier is offset by a higher flux over the barrier from longer lived hydrogen-bonding patterns at the interface, resulting in a rate of association that is similar both at and away from the interface. We find that these differences in rates and stabilities of charge separation are due to the altered ability of water to solvate and reorganize in the vicinity of the metal interface. PMID:28698368

  13. Microscopic colitis syndrome.

    PubMed Central

    Veress, B; Löfberg, R; Bergman, L

    1995-01-01

    The colorectal biopsy specimens from 30 patients with chronic watery diarrhoea but normal endoscopic and radiographic findings were studied by light microscopy, morphometry, immunohistochemistry, and two patients with electron microscopy. The histological changes in the colorectum were originally diagnosed in six patients as lymphocytic colitis and in 24 patients as collagenous colitis. The analysis of the specimens for this study could delineate three distinct groups of microscopic colitis: lymphocytic colitis (six patients), collagenous colitis without lymphocytic attack on the surface epithelium (seven patients), and a mixed form presenting with both thickening of the collagen plate and increased number of intraepithelial lymphocytes (17 patients). No transformation was seen from one type to another during follow up of six patients for four to seven years. Increased numbers of active pericryptal myofibroblasts were found with the electron microscope in one patient with mixed microscopic colitis showing also myofibroblasts entrapped within the collagen layer. Hitherto undescribed flat mucosa of the ileum was found in one patient with lymphocytic colitis and both flat mucosa and thickening of the collagen plate in the ileum were seen in one patient with the mixed form of the disease. In another patient with mixed microscopic colitis, normalisation of the colorectal morphology occurred after temporary loop ileostomy, followed by the reappearance of both diarrhoea, inflammation, and thickening of the collagen plate after the ileostomy was reversed. No association was found between non-steroid anti-inflammatory drug (NSAID) consumption and collagenous or mixed microscopic colitis. The primary cause of microscopic colitis is probably an immunological reaction to luminal antigen/s, perhaps of ileal origin. The engagement of the pericryptal myofibroblasts in the disease process might result in the development of the various forms of microscopic colitis. An inverse

  14. The OpenCalphad thermodynamic software interface

    PubMed Central

    Sundman, Bo; Kattner, Ursula R; Sigli, Christophe; Stratmann, Matthias; Le Tellier, Romain; Palumbo, Mauro; Fries, Suzana G

    2017-01-01

    Thermodynamic data are needed for all kinds of simulations of materials processes. Thermodynamics determines the set of stable phases and also provides chemical potentials, compositions and driving forces for nucleation of new phases and phase transformations. Software to simulate materials properties needs accurate and consistent thermodynamic data to predict metastable states that occur during phase transformations. Due to long calculation times thermodynamic data are frequently pre-calculated into “lookup tables” to speed up calculations. This creates additional uncertainties as data must be interpolated or extrapolated and conditions may differ from those assumed for creating the lookup table. Speed and accuracy requires that thermodynamic software is fully parallelized and the Open-Calphad (OC) software is the first thermodynamic software supporting this feature. This paper gives a brief introduction to computational thermodynamics and introduces the basic features of the OC software and presents four different application examples to demonstrate its versatility. PMID:28260838

  15. Spectroscopic Chemical Analysis Methods and Apparatus

    NASA Technical Reports Server (NTRS)

    Hug, William F.; Reid, Ray D.

    2012-01-01

    This invention relates to non-contact spectroscopic methods and apparatus for performing chemical analysis and the ideal wavelengths and sources needed for this analysis. It employs deep ultraviolet (200- to 300-nm spectral range) electron-beam-pumped wide bandgap semiconductor lasers, incoherent wide bandgap semiconductor lightemitting devices, and hollow cathode metal ion lasers. Three achieved goals for this innovation are to reduce the size (under 20 L), reduce the weight [under 100 lb (.45 kg)], and reduce the power consumption (under 100 W). This method can be used in microscope or macroscope to provide measurement of Raman and/or native fluorescence emission spectra either by point-by-point measurement, or by global imaging of emissions within specific ultraviolet spectral bands. In other embodiments, the method can be used in analytical instruments such as capillary electrophoresis, capillary electro-chromatography, high-performance liquid chromatography, flow cytometry, and related instruments for detection and identification of unknown analytes using a combination of native fluorescence and/or Raman spectroscopic methods. This design provides an electron-beampumped semiconductor radiation-producing method, or source, that can emit at a wavelength (or wavelengths) below 300 nm, e.g. in the deep ultraviolet between about 200 and 300 nm, and more preferably less than 260 nm. In some variations, the method is to produce incoherent radiation, while in other implementations it produces laser radiation. In some variations, this object is achieved by using an AlGaN emission medium, while in other implementations a diamond emission medium may be used. This instrument irradiates a sample with deep UV radiation, and then uses an improved filter for separating wavelengths to be detected. This provides a multi-stage analysis of the sample. To avoid the difficulties related to producing deep UV semiconductor sources, a pumping approach has been developed that uses

  16. Ultra-High Resolution Spectroscopic Remote Sensing: A Microscope on Planetary Atmospheres

    NASA Technical Reports Server (NTRS)

    Kostiuk, Theodor

    2010-01-01

    Remote sensing of planetary atmospheres is not complete without studies of all levels of the atmosphere, including the dense cloudy- and haze filled troposphere, relatively clear and important stratosphere and the upper atmosphere, which are the first levels to experience the effects of solar radiation. High-resolution spectroscopy can provide valuable information on these regions of the atmosphere. Ultra-high spectral resolution studies can directly measure atmospheric winds, composition, temperature and non-thermal phenomena, which describe the physics and chemistry of the atmosphere. Spectroscopy in the middle to long infrared wavelengths can also probe levels where dust of haze limit measurements at shorter wavelength or can provide ambiguous results on atmospheric species abundances or winds. A spectroscopic technique in the middle infrared wavelengths analogous to a radio receiver. infrared heterodyne spectroscopy [1], will be describe and used to illustrate the detailed study of atmospheric phenomena not readily possible with other methods. The heterodyne spectral resolution with resolving power greater than 1,000.000 measures the true line shapes of emission and absorption lines in planetary atmospheres. The information on the region of line formation is contained in the line shapes. The absolute frequency of the lines can be measured to I part in 100 ,000,000 and can be used to accurately measure the Doppler frequency shift of the lines, directly measuring the line-of-sight velocity of the gas to --Im/s precision (winds). The technical and analytical methods developed and used to measure and analyze infrared heterodyne measurements will be described. Examples of studies on Titan, Venus, Mars, Earth, and Jupiter will be presented. 'These include atmospheric dynamics on slowly rotating bodies (Titan [2] and Venus [3] and temperature, composition and chemistry on Mars 141, Venus and Earth. The discovery and studies of unique atmospheric phenomena will also be

  17. Deformability of adsorbents during adsorption and principles of the thermodynamics of solid-phase systems

    NASA Astrophysics Data System (ADS)

    Tovbin, Yu. K.

    2017-09-01

    A microscopic theory of adsorption, based on a discrete continuum lattice gas model for noninert (including deformable) adsorbents that change their lattice parameters during adsorption, is presented. Cases of the complete and partial equilibrium states of the adsorbent are considered. In the former, the adsorbent consists of coexisting solid and vapor phases of adsorbent components, and the adsorbate is a mobile component of the vapor phase with an arbitrary density (up to that of the liquid adsorbate phase). The adsorptive transitioning to the bound state changes the state of the near-surface region of the adsorbent. In the latter, there are no equilibrium components of the adsorbent between the solid and vapor phases. The adsorbent state is shown to be determined by its prehistory, rather than set by chemical potentials of vapor of its components. Relations between the microscopic theory and thermodynamic interpretations are discussed: (1) adsorption on an open surface, (2) two-dimensional stratification of the adsorbate mobile phase on an open homogeneous surface, (3) small microcrystals in vacuum and the gas phase, and (4) adsorption in porous systems.

  18. Black hole chemistry: thermodynamics with Lambda

    NASA Astrophysics Data System (ADS)

    Kubizňák, David; Mann, Robert B.; Teo, Mae

    2017-03-01

    We review recent developments on the thermodynamics of black holes in extended phase space, where the cosmological constant is interpreted as thermodynamic pressure and treated as a thermodynamic variable in its own right. In this approach, the mass of the black hole is no longer regarded as internal energy, rather it is identified with the chemical enthalpy. This leads to an extended dictionary for black hole thermodynamic quantities; in particular a notion of thermodynamic volume emerges for a given black hole spacetime. This volume is conjectured to satisfy the reverse isoperimetric inequality—an inequality imposing a bound on the amount of entropy black hole can carry for a fixed thermodynamic volume. New thermodynamic phase transitions naturally emerge from these identifications. Namely, we show that black holes can be understood from the viewpoint of chemistry, in terms of concepts such as Van der Waals fluids, reentrant phase transitions, and triple points. We also review the recent attempts at extending the AdS/CFT dictionary in this setting, discuss the connections with horizon thermodynamics, applications to Lifshitz spacetimes, and outline possible future directions in this field.

  19. Thermodynamics of Accelerating Black Holes.

    PubMed

    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. Thermodynamics of organic compounds

    NASA Astrophysics Data System (ADS)

    Gammon, B. E.; Smith, N. K.

    1982-11-01

    This research program consisted of an integrated and interrelated effort of basic and applied research in chemical thermodynamics and thermochemistry. Knowledge of variation of physical and thermodynamic properties with molecular structure was used to select compounds for study that because of high ring strain or unusual steric effects may have good energy characteristics per unit volume or per unit mass and thus be useful in the synthesis of high energy fuels. These materials were synthesized, and their thermodynamic properties were evaluated. In cooperation with researcher at Wright-Patterson Air Force Base, ramjet fuels currently in use were subjected to careful thermodynamic evaluation by measurements of heat capacity, enthalpy of combustion and vapor pressure. During the last year of this effort, seven kerosene-type fuels produced by British Petroleum and seven jet fuels produced from shale oil were studied.

  1. Thermodynamic Constraints Improve Metabolic Networks.

    PubMed

    Krumholz, Elias W; Libourel, Igor G L

    2017-08-08

    In pursuit of establishing a realistic metabolic phenotypic space, the reversibility of reactions is thermodynamically constrained in modern metabolic networks. The reversibility constraints follow from heuristic thermodynamic poise approximations that take anticipated cellular metabolite concentration ranges into account. Because constraints reduce the feasible space, draft metabolic network reconstructions may need more extensive reconciliation, and a larger number of genes may become essential. Notwithstanding ubiquitous application, the effect of reversibility constraints on the predictive capabilities of metabolic networks has not been investigated in detail. Instead, work has focused on the implementation and validation of the thermodynamic poise calculation itself. With the advance of fast linear programming-based network reconciliation, the effects of reversibility constraints on network reconciliation and gene essentiality predictions have become feasible and are the subject of this study. Networks with thermodynamically informed reversibility constraints outperformed gene essentiality predictions compared to networks that were constrained with randomly shuffled constraints. Unconstrained networks predicted gene essentiality as accurately as thermodynamically constrained networks, but predicted substantially fewer essential genes. Networks that were reconciled with sequence similarity data and strongly enforced reversibility constraints outperformed all other networks. We conclude that metabolic network analysis confirmed the validity of the thermodynamic constraints, and that thermodynamic poise information is actionable during network reconciliation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  2. In situ study of live specimens in an environmental scanning electron microscope.

    PubMed

    Tihlaříková, Eva; Neděla, Vilém; Shiojiri, Makoto

    2013-08-01

    In this paper we introduce new methodology for the observation of living biological samples in an environmental scanning electron microscope (ESEM). The methodology is based on an unconventional initiation procedure for ESEM chamber pumping, free from purge-flood cycles, and on the ability to control thermodynamic processes close to the sample. The gradual and gentle change of the working environment from air to water vapor enables the study of not only living samples in dynamic in situ experiments and their manifestation of life (sample walking) but also its experimentally stimulated physiological reactions. Moreover, Monte Carlo simulations of primary electron beam energy losses in a water layer on the sample surface were studied; consequently, the influence of the water thickness on radiation, temperature, or chemical damage of the sample was considered.

  3. Morphological and spectroscopic analysis of cellulose nanocrystals extracted from oil palm empty fruit bunch fiber

    NASA Astrophysics Data System (ADS)

    Dasan, Y. K.; Bhat, A. H.; Faiz, A.

    2015-07-01

    This work evaluates the use of oil palm empty fruit bunch (OPEFB) fiber as a source of cellulose to obtain nanocrystalline cellulose (CNC) by acid hydrolysis reaction. The raw OPEFB fibers were pretreated with aqueous Sodium hydroxide at 80°C followed by bleaching treatment and further hydrolyzed with Sulphuric acid at 45°C with limited range of hydrolysis time and acid concentration. The resulting CNC's were characterized for spectroscopic, crystallographic and morphological properties using Fourier Transform Infrared Spectroscopy (FTIR), X-ray Diffractometer (XRD), Transmission Electron Microscope (TEM) and Atomic Force Microscopy (AFM). Finding of this study shows that the properties of CNC's are strongly dependent on the hydrolysis time and acid concentration.

  4. Synthesis, crystal structure investigation, spectroscopic characterizations and DFT computations on a novel 1-(2-chloro-4-phenylquinolin-3-yl)ethanone

    NASA Astrophysics Data System (ADS)

    Murugavel, S.; Stephen, C. S. Jacob Prasanna; Subashini, R.; Reddy, H. Raveendranatha; AnanthaKrishnan, Dhanabalan

    2016-10-01

    The title compound 1-(2-chloro-4-phenylquinolin-3-yl)ethanone (CPQE) was synthesised effectively by chlorination of 3-acetyl-4-phenylquinolin-2(1H)-one (APQ) using POCl3 reagent. Structural and vibrational spectroscopic studies were performed by utilizing single crystal X-ray diffraction, FTIR and NMR spectral analysis along with DFT method utilizing GAUSSIAN‧ 03 software. Veda program has been employed to perform a detailed interpretation of vibrational spectra. Mulliken population analyses on atomic charges, MEP, HOMO-LUMO, NBO, Global chemical reactivity descriptors and thermodynamic properties have been examined by (DFT/B3LYP) method with the 6-311G(d,p) basis set level.

  5. Thermodynamic aspect in using modified Boltzmann model as an acoustic probe for URu2Si2

    NASA Astrophysics Data System (ADS)

    Kwang-Hua, Chu Rainer

    2018-05-01

    The approximate system of equations describing ultrasonic attenuation propagating in many electrons of the heavy-fermion materials URu2Si2 under high magnetic fields were firstly derived and then calculated based on the modified Boltzmann model considering the microscopic contributions due to electronic fluids. A system of nonlinear partial differential coupled with integral equations were linearized firstly and approximately solved considering the perturbed thermodynamic equilibrium states. Our numerical data were compared with previous measurements using non-dimensional or normalized physical values. The rather good fit of our numerical calculations with experimental measurements confirms our present approach.

  6. Spectroscopic survey of southern hemisphere white dwarfs. II. Spectroscopic data for forty-one southern white dwarfs

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wegner, G.

    New spectroscopic data on 41 southern white dwarfs are presented. Most of these stars have not teen previously observed spectroscopically. Spectral types, as well as equivalent widths and line profiles for a few selected lines, are given. (auth)

  7. Spectroscopic database

    NASA Technical Reports Server (NTRS)

    Husson, N.; Barbe, A.; Brown, L. R.; Carli, B.; Goldman, A.; Pickett, H. M.; Roche, A. E.; Rothman, L. S.; Smith, M. A. H.

    1985-01-01

    Several aspects of quantitative atmospheric spectroscopy are considered, using a classification of the molecules according to the gas amounts in the stratosphere and upper troposphere, and reviews of quantitative atmospheric high-resolution spectroscopic measurements and field measurements systems are given. Laboratory spectroscopy and spectral analysis and prediction are presented with a summary of current laboratory spectroscopy capabilities. Spectroscopic data requirements for accurate derivation of atmospheric composition are discussed, where examples are given for space-based remote sensing experiments of the atmosphere: the ATMOS (Atmospheric Trace Molecule) and UARS (Upper Atmosphere Research Satellite) experiment. A review of the basic parameters involved in the data compilations; a summary of information on line parameter compilations already in existence; and a summary of current laboratory spectroscopy studies are used to assess the data base.

  8. Thermodynamics and statistical mechanics. [thermodynamic properties of gases

    NASA Technical Reports Server (NTRS)

    1976-01-01

    The basic thermodynamic properties of gases are reviewed and the relations between them are derived from the first and second laws. The elements of statistical mechanics are then formulated and the partition function is derived. The classical form of the partition function is used to obtain the Maxwell-Boltzmann distribution of kinetic energies in the gas phase and the equipartition of energy theorem is given in its most general form. The thermodynamic properties are all derived as functions of the partition function. Quantum statistics are reviewed briefly and the differences between the Boltzmann distribution function for classical particles and the Fermi-Dirac and Bose-Einstein distributions for quantum particles are discussed.

  9. Phytochemical, spectroscopic and density functional theory study of Diospyrin, and non-bonding interactions of Diospyrin with atmospheric gases

    NASA Astrophysics Data System (ADS)

    Fazl-i-Sattar; Ullah, Zakir; Ata-ur-Rahman; Rauf, Abdur; Tariq, Muhammad; Tahir, Asif Ali; Ayub, Khurshid; Ullah, Habib

    2015-04-01

    Density functional theory (DFT) and phytochemical study of a natural product, Diospyrin (DO) have been carried out. A suitable level of theory was developed, based on correlating the experimental and theoretical data. Hybrid DFT method at B3LYP/6-31G (d,p) level of theory is employed for obtaining the electronic, spectroscopic, inter-molecular interaction and thermodynamic properties of DO. The exact structure of DO is confirmed from the nice validation of the theory and experiment. Non-covalent interactions of DO with different atmospheric gases such as NH3, CO2, CO, and H2O were studied to find out its electroactive nature. The experimental and predicted geometrical parameters, IR and UV-vis spectra (B3LYP/6-31+G (d,p) level of theory) show excellent correlation. Inter-molecular non-bonding interaction of DO with atmospheric gases is investigated through geometrical parameters, electronic properties, charge analysis, and thermodynamic parameters. Electronic properties include, ionization potential (I.P.), electron affinities (E.A.), electrostatic potential (ESP), density of states (DOS), HOMO, LUMO, and band gap. All these characterizations have corroborated each other and confirmed the presence of non-covalent nature in DO with the mentioned gases.

  10. Binding of caffeine with caffeic acid and chlorogenic acid using fluorescence quenching, UV/vis and FTIR spectroscopic techniques.

    PubMed

    Belay, Abebe; Kim, Hyung Kook; Hwang, Yoon-Hwae

    2016-03-01

    The interactions of caffeine (CF) with chlorogenic acid (CGA) and caffeic acid (CFA) were investigated by fluorescence quenching, UV/vis and Fourier transform infrared (FTIR) spectroscopic techniques. The results of the study indicated that the fluorescence quenching between caffeine and hydroxycinnamic acids could be rationalized in terms of static quenching or the formation of non-fluorescent CF-CFA and CF-CGA complexes. From fluorescence quenching spectral analysis, the quenching constant (KSV), quenching rate constant (kq), number of binding sites (n), thermodynamic properties and conformational changes of the interaction were determined. The quenching constants (KSV) between CF and CGA, CFA are 1.84 × 10(4) and 1.04 × 10(4) L/mol at 298 K and their binding site n is ~ 1. Thermodynamic parameters determined using the Van't Hoff equation indicated that hydrogen bonds and van der Waal's forces have a major role in the reaction of caffeine with caffeic acid and chlorogenic acid. The 3D fluorescence, UV/vis and FTIR spectra also showed that the binding of CF with CFA and CGA induces conformational changes in CFA and CGA. Copyright © 2015 John Wiley & Sons, Ltd.

  11. Spectroscopic analysis on the resveratrol-DNA binding interactions at physiological pH

    NASA Astrophysics Data System (ADS)

    Zhang, Shufang; Sun, Xuejun; Jing, Zhihong; Qu, Fengli

    2011-11-01

    The interaction of resveratrol with calf thymus deoxyribonucleic acid (ctDNA) under physiological conditions (Tris-HCl buffer solutions, pH 7.4) was studied by spectroscopy, fluorescence spectroscopy and viscosity measurement method, respectively. Results indicated that a complex of resveratrol with ctDNA was formed with a binding constant of K17 °C = 5.49 × 10 3 L mol -1 and K37 °C = 1.90 × 10 4 L mol -1. The fluorescence quenching mechanism of acridine orange (AO)-ctDNA by resveratrol was shown to be a static quenching type. The thermodynamic parameters of the complex were calculated by a double reciprocal method: ΔHms=4.64×10 J mol, ΔSms=231.8 J K mol and ΔGms=-2.54×10 J mol (37 °C). Spectroscopic techniques together with viscosity determination provided evidences of intercalation mode of binding for the interaction between resveratrol and ctDNA.

  12. Spectroscopic and magnetic properties of Fe2+ (3d6; S = 2) ions in Fe(NH4)2(SO4)2·6H2O - Modeling zero-field splitting and Zeeman electronic parameters by microscopic spin Hamiltonian approach

    NASA Astrophysics Data System (ADS)

    Zając, Magdalena; Rudowicz, Czesław; Ohta, Hitoshi; Sakurai, Takahiro

    2018-03-01

    Utilizing the package MSH/VBA, based on the microscopic spin Hamiltonian (MSH) approach, spectroscopic and magnetic properties of Fe2+ (3d6; S = 2) ions at (nearly) orthorhombic sites in Fe(NH4)2(SO4)2·6H2O (FASH) are modeled. The zero-field splitting (ZFS) parameters and the Zeeman electronic (Ze) factors are predicted for wide ranges of values of the microscopic parameters, i.e. the spin-orbit (λ), spin-spin (ρ) coupling constants, and the crystal-field (ligand-field) energy levels (Δi) within the 5D multiplet. This enables to consider the dependence of the ZFS parameters bkq (in the Stevens notation), or the conventional ones (e.g., D and E), and the Zeeman factors gi on λ, ρ, and Δi. By matching the theoretical SH parameters and the experimental ones measured by electron magnetic resonance (EMR), the values of λ, ρ, and Δi best describing Fe2+ ions in FASH are determined. The novel aspect is prediction of the fourth-rank ZFS parameters and the ρ(spin-spin)-related contributions, not considered in previous studies. The higher-order contributions to the second- and fourth-rank ZFSPs are found significant. The MSH predictions provide guidance for high-magnetic field and high-frequency EMR (HMF-EMR) measurements and enable assessment of suitability of FASH for application as high-pressure probes for HMF-EMR studies. The method employed here and the present results may be also useful for other structurally related Fe2+ (S = 2) systems.

  13. Spectroscopic Study on the Interaction of 4-dimethylaminochalcones with Phospholipids

    NASA Astrophysics Data System (ADS)

    Tomečková, V.; Revická, M.; Sassen, A.; Veliká, B.; Stupák, M.; Perjési, P.

    2014-11-01

    The ultraviolet-visible and fluorescence spectroscopic properties of 4'-dimethylaminochalcone ( 1a) and its cyclic analogs 2a-4a have been studied in the presence of phospholipid vesicles (i.e., egg yolk lecithin and dipalmitoylpho sphatidylcholine), bovine serum albumin (BSA), and lipoprotein particles (i.e., bovine serum albumin plus egg yolk lecithin). The spectral results showed that compounds 1a-4a formed hydrophobic interactions with the phospholipids, lipoproteins, and BSA at the polar/nonpolar interface. Compounds 3a and 4a exhibited the strongest hydrophobic interactions of all of the compounds tested towards the phospholipids. Compound 2a gave the best fluorescent fluorophore indicating interactions with the lipids, lipoproteins, and proteins. Fluorescent microscopic imaging of breast cancer cells treated with compounds 1a-4a revealed that they could be used to stain all of the cellular components and destroy the nuclear structure. Compounds 1a-4a were found to be concentrated predominantly on the surfaces of the liposomes and lipoproteins.

  14. Spectroscopic optical coherence tomography for ex vivo brain tumor analysis

    NASA Astrophysics Data System (ADS)

    Lenz, Marcel; Krug, Robin; Dillmann, Christopher; Gerling, Alexandra; Gerhardt, Nils C.; Welp, Hubert; Schmieder, Kirsten; Hofmann, Martin R.

    2017-02-01

    For neurosurgeries precise tumor resection is essential for the subsequent recovery of the patients since nearby healthy tissue that may be harmed has a huge impact on the life quality after the surgery. However, so far no satisfying methodology has been established to assist the surgeon during surgery to distinguish between healthy and tumor tissue. Optical Coherence Tomography (OCT) potentially enables non-contact in vivo image acquisition at penetration depths of 1-2 mm with a resolution of approximately 1-15 μm. To analyze the potential of OCT for distinction between brain tumors and healthy tissue, we used a commercially available Thorlabs Callisto system to measure healthy tissue and meningioma samples ex vivo. All samples were measured with the OCT system and three dimensional datasets were generated. Afterwards they were sent to the pathology for staining with hematoxylin and eosin and then investigated with a bright field microscope to verify the tissue type. This is the actual gold standard for ex vivo analysis. The images taken by the OCT system exhibit variations in the structure for different tissue types, but these variations may not be objectively evaluated from raw OCT images. Since an automated distinction between tumor and healthy tissue would be highly desirable to guide the surgeon, we applied Spectroscopic Optical Coherence Tomography to further enhance the differences between the tissue types. Pattern recognition and machine learning algorithms were applied to classify the derived spectroscopic information. Finally, the classification results are analyzed in comparison to the histological analysis of the samples.

  15. Virtual reality microscope versus conventional microscope regarding time to diagnosis: an experimental study.

    PubMed

    Randell, Rebecca; Ruddle, Roy A; Mello-Thoms, Claudia; Thomas, Rhys G; Quirke, Phil; Treanor, Darren

    2013-01-01

      To create and evaluate a virtual reality (VR) microscope that is as efficient as the conventional microscope, seeking to support the introduction of digital slides into routine practice.   A VR microscope was designed and implemented by combining ultra-high-resolution displays with VR technology, techniques for fast interaction, and high usability. It was evaluated using a mixed factorial experimental design with technology and task as within-participant variables and grade of histopathologist as a between-participant variable. Time to diagnosis was similar for the conventional and VR microscopes. However, there was a significant difference in the mean magnification used between the two technologies, with participants working at a higher level of magnification on the VR microscope.   The results suggest that, with the right technology, efficient use of digital pathology for routine practice is a realistic possibility. Further work is required to explore what magnification is required on the VR microscope for histopathologists to identify diagnostic features, and the effect on this of the digital slide production process. © 2012 Blackwell Publishing Limited.

  16. Thermodynamics of statistical inference by cells.

    PubMed

    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.

  17. The head-mounted microscope.

    PubMed

    Chen, Ting; Dailey, Seth H; Naze, Sawyer A; Jiang, Jack J

    2012-04-01

    Microsurgical equipment has greatly advanced since the inception of the microscope into the operating room. These advancements have allowed for superior surgical precision and better post-operative results. This study focuses on the use of the Leica HM500 head-mounted microscope for the operating phonosurgeon. The head-mounted microscope has an optical zoom from 2× to 9× and provides a working distance from 300 mm to 700 mm. The headpiece, with its articulated eyepieces, adjusts easily to head shape and circumference, and offers a focus function, which is either automatic or manually controlled. We performed five microlaryngoscopic operations utilizing the head-mounted microscope with successful results. By creating a more ergonomically favorable operating posture, a surgeon may be able to obtain greater precision and success in phonomicrosurgery. Phonomicrosurgery requires the precise manipulation of long-handled cantilevered instruments through the narrow bore of a laryngoscope. The head-mounted microscope shortens the working distance compared with a stand microscope, thereby increasing arm stability, which may improve surgical precision. Also, the head-mounted design permits flexibility in head position, enabling operator comfort, and delaying musculoskeletal fatigue. A head-mounted microscope decreases the working distance and provides better ergonomics in laryngoscopic microsurgery. These advances provide the potential to promote precision in phonomicrosurgery. Copyright © 2011 The American Laryngological, Rhinological, and Otological Society, Inc.

  18. Microbial diversity arising from thermodynamic constraints

    PubMed Central

    Großkopf, Tobias; Soyer, Orkun S

    2016-01-01

    The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments. PMID:27035705

  19. Kinetics of Electrocatalytic Reactions from First-Principles: A Critical Comparison with the Ab Initio Thermodynamics Approach.

    PubMed

    Exner, Kai S; Over, Herbert

    2017-05-16

    Multielectron processes in electrochemistry require the stabilization of reaction intermediates (RI) at the electrode surface after every elementary reaction step. Accordingly, the bond strengths of these intermediates are important for assessing the catalytic performance of an electrode material. Current understanding of microscopic processes in modern electrocatalysis research is largely driven by theory, mostly based on ab initio thermodynamics considerations, where stable reaction intermediates at the electrode surface are identified, while the actual free energy barriers (or activation barriers) are ignored. This simple approach is popular in electrochemistry in that the researcher has a simple tool at hand in successfully searching for promising electrode materials. The ab initio TD approach allows for a rough but fast screening of the parameter space with low computational cost. However, ab initio thermodynamics is also frequently employed (often, even based on a single binding energy only) to comprehend on the activity and on the mechanism of an electrochemical reaction. The basic idea is that the activation barrier of an endergonic reaction step consists of a thermodynamic part and an additional kinetically determined barrier. Assuming that the activation barrier scales with thermodynamics (so-called Brønsted-Polanyi-Evans (BEP) relation) and the kinetic part of the barrier is small, ab initio thermodynamics may provide molecular insights into the electrochemical reaction kinetics. However, for many electrocatalytic reactions, these tacit assumptions are violated so that ab initio thermodynamics will lead to contradictions with both experimental data and ab initio kinetics. In this Account, we will discuss several electrochemical key reactions, including chlorine evolution (CER), oxygen evolution reaction (OER), and oxygen reduction (ORR), where ab initio kinetics data are available in order to critically compare the results with those derived from a

  20. Thermodynamic Properties of Low-Density {}^{132}Xe Gas in the Temperature Range 165-275 K

    NASA Astrophysics Data System (ADS)

    Akour, Abdulrahman

    2018-01-01

    The method of static fluctuation approximation was used to calculate selected thermodynamic properties (internal energy, entropy, energy capacity, and pressure) for xenon in a particularly low-temperature range (165-270 K) under different conditions. This integrated microscopic study started from an initial basic assumption as the main input. The basic assumption in this method was to replace the local field operator with its mean value, then numerically solve a closed set of nonlinear equations using an iterative method, considering the Hartree-Fock B2-type dispersion potential as the most appropriate potential for xenon. The results are in very good agreement with those of an ideal gas.

  1. The Homemade Microscope.

    ERIC Educational Resources Information Center

    Baker, Roger C., Jr.

    1991-01-01

    Directions for the building of a pocket microscope that will make visible the details of insect structure and living bacteria are described. Background information on the history of microscopes and lenses is provided. The procedures for producing various types of lenses are included. (KR)

  2. VESUVIO: a novel instrument for performing spectroscopic studies in condensed matter with eV neutrons at the ISIS facility

    NASA Astrophysics Data System (ADS)

    Senesi, R.; Andreani, C.; Bowden, Z.; Colognesi, D.; Degiorgi, E.; Fielding, A. L.; Mayers, J.; Nardone, M.; Norris, J.; Praitano, M.; Rhodes, N. J.; Stirling, W. G.; Tomkinson, J.; Uden, C.

    2000-03-01

    The VESUVIO project aims to provide unique prototype instrumentation at the ISIS-pulsed neutron source and to establish a routine experimental and theoretical program in neutron scattering spectroscopy at eV energies. This instrumentation will be specifically designed for high momentum, (20 Å-11 eV) inelastic neutron scattering studies of microscopic dynamical processes in materials and will represent a unique facility for EU researchers. It will allow to derive single-particle kinetic energies and single-particle momentum distributions, n(p), providing additional and/or complementary information to other neutron inelastic spectroscopic techniques.

  3. Third law of thermodynamics as a key test of generalized entropies.

    PubMed

    Bento, E P; Viswanathan, G M; da Luz, M G E; Silva, R

    2015-02-01

    The laws of thermodynamics constrain the formulation of statistical mechanics at the microscopic level. The third law of thermodynamics states that the entropy must vanish at absolute zero temperature for systems with nondegenerate ground states in equilibrium. Conversely, the entropy can vanish only at absolute zero temperature. Here we ask whether or not generalized entropies satisfy this fundamental property. We propose a direct analytical procedure to test if a generalized entropy satisfies the third law, assuming only very general assumptions for the entropy S and energy U of an arbitrary N-level classical system. Mathematically, the method relies on exact calculation of β=dS/dU in terms of the microstate probabilities p(i). To illustrate this approach, we present exact results for the two best known generalizations of statistical mechanics. Specifically, we study the Kaniadakis entropy S(κ), which is additive, and the Tsallis entropy S(q), which is nonadditive. We show that the Kaniadakis entropy correctly satisfies the third law only for -1<κ<+1, thereby shedding light on why κ is conventionally restricted to this interval. Surprisingly, however, the Tsallis entropy violates the third law for q<1. Finally, we give a concrete example of the power of our proposed method by applying it to a paradigmatic system: the one-dimensional ferromagnetic Ising model with nearest-neighbor interactions.

  4. Thermodynamic Analysis of Nickel(II) and Zinc(II) Adsorption to Biochar.

    PubMed

    Alam, Md Samrat; Gorman-Lewis, Drew; Chen, Ning; Flynn, Shannon L; Ok, Yong Sik; Konhauser, Kurt O; Alessi, Daniel S

    2018-05-21

    While numerous studies have investigated metal uptake from solution by biochar, few of these have developed a mechanistic understanding of the adsorption reactions that occur at the biochar surface. In this study, we explore a combined modeling and spectroscopic approach for the first time to describe the molecular level adsorption of Ni(II) and Zn(II) to five types of biochar. Following thorough characterization, potentiometric titrations were carried out to measure the proton (H + ) reactivity of each biochar, and the data was used to develop protonation models. Surface complexation modeling (SCM) supported by synchrotron-based extended X-ray absorption fine structure (EXAFS) was then used to gain insights into the molecular scale metal-biochar surface reactions. The SCM approach was combined with isothermal titration calorimetry (ITC) data to determine the thermodynamic driving forces of metal adsorption. Our results show that the reactivity of biochar toward Ni(II) and Zn(II) directly relates to the site densities of biochar. EXAFS along with FT-IR analyses, suggest that Ni(II) and Zn(II) adsorption occurred primarily through proton-active carboxyl (-COOH) and hydroxyl (-OH) functional groups on the biochar surface. SCM-ITC analyses revealed that the enthalpies of protonation are exothermic and Ni(II) and Zn(II) complexes with biochar surface are slightly exothermic to slightly endothermic. The results obtained from these combined approaches contribute to the better understanding of molecular scale metal adsorption onto the biochar surface, and will facilitate the further development of thermodynamics-based, predictive approaches to biochar removal of metals from contaminated water.

  5. Thermodynamics--A Practical Subject.

    ERIC Educational Resources Information Center

    Jones, Hugh G.

    1984-01-01

    Provides a simplified, synoptic overview of the area of thermodynamics, enumerating and explaining the four basic laws, and introducing the mathematics involved in a stepwise fashion. Discusses such basic tools of thermodynamics as enthalpy, entropy, Helmholtz free energy, and Gibbs free energy, and their uses in problem solving. (JM)

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

    PubMed

    Tischer, Alexander; Auton, Matthew

    2013-09-01

    We have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea-induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea-temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two-state character. Global analysis of the urea-temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of ΔH0 and ΔCP0 that define a complex temperature dependence of the m-value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea-denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions. © 2013 The Protein Society.

  7. Thermodynamic modeling of melts in the system Na 2O-NaAlO 2-SiO 2-F 2O -1

    NASA Astrophysics Data System (ADS)

    Dolejš, David; Baker, Don R.

    2005-12-01

    Fluorine is a common volatile element in magmatic-hydrothermal systems, but its solution mechanisms and thermodynamic description in highly polymerized silicate melts are poorly known. We have developed a thermodynamic model for fluorosilicate liquids that links experimentally determined phase equilibria and spectroscopic information on melt structure. The model is applicable to crystallization of fluoride minerals, fluoride-silicate immiscibility in natural felsic melts, and metallurgical processes. Configurational properties of fluorosilicate melts are described by mixing on three site levels (sublattices): (1) alkali fluoride, polyhedral aluminofluoride and silicofluoride species and nonbridging terminations of the aluminosilicate network, (2) alkali-aluminate and silicate tetrahedra within the network and (3) bridging oxygen, nonbridging oxygen and terminal fluorine atoms on tetrahedral apices of the network. Abundances of individual chemical species are described by a homogeneous equilibrium representing melt depolymerization: F - (free) + O 0 (bridging) = F 0 (terminal) + O - (nonbridging) which corresponds to a replacement of an oxygen bridging two tetrahedra by a pair of terminations, one with F and the other with an O and a charge-balancing Na. In cryolite-bearing systems two additional interaction mechanisms occur: (1) the self-dissociation of octahedral aluminofluoride complexes: [AlF 6] = [AlF 4] + 2 [F], and (2) the short-range order between (O,F)-corners and (Si,NaAl)-centers of tetrahedra: Si-O-Si + 2 [NaAl]-F = [NaAl]-O-[NaAl] + 2 Si-F. Portrayal of these equilibria in ternary Thompson reaction space allows for the decrease in the number of interaction mechanisms by linearly combining melt depolymerization with tetrahedral short-range order. In this formulation, the nonideal thermodynamic properties are represented by reaction energies of homogeneous equilibria, thus defining directly individual chemical species concentrations and configurational

  8. Time-dependent entropy evolution in microscopic and macroscopic electromagnetic relaxation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Baker-Jarvis, James

    This paper is a study of entropy and its evolution in the time and frequency domains upon application of electromagnetic fields to materials. An understanding of entropy and its evolution in electromagnetic interactions bridges the boundaries between electromagnetism and thermodynamics. The approach used here is a Liouville-based statistical-mechanical theory. I show that the microscopic entropy is reversible and the macroscopic entropy satisfies an H theorem. The spectral entropy development can be very useful for studying the frequency response of materials. Using a projection-operator based nonequilibrium entropy, different equations are derived for the entropy and entropy production and are applied tomore » the polarization, magnetization, and macroscopic fields. I begin by proving an exact H theorem for the entropy, progress to application of time-dependent entropy in electromagnetics, and then apply the theory to relevant applications in electromagnetics. The paper concludes with a discussion of the relationship of the frequency-domain form of the entropy to the permittivity, permeability, and impedance.« less

  9. Proper alignment of the microscope.

    PubMed

    Rottenfusser, Rudi

    2013-01-01

    The light microscope is merely the first element of an imaging system in a research facility. Such a system may include high-speed and/or high-resolution image acquisition capabilities, confocal technologies, and super-resolution methods of various types. Yet more than ever, the proverb "garbage in-garbage out" remains a fact. Image manipulations may be used to conceal a suboptimal microscope setup, but an artifact-free image can only be obtained when the microscope is optimally aligned, both mechanically and optically. Something else is often overlooked in the quest to get the best image out of the microscope: Proper sample preparation! The microscope optics can only do its job when its design criteria are matched to the specimen or vice versa. The specimen itself, the mounting medium, the cover slip, and the type of immersion medium (if applicable) are all part of the total optical makeup. To get the best results out of a microscope, understanding the functions of all of its variable components is important. Only then one knows how to optimize these components for the intended application. Different approaches might be chosen to discuss all of the microscope's components. We decided to follow the light path which starts with the light source and ends at the camera or the eyepieces. To add more transparency to this sequence, the section up to the microscope stage was called the "Illuminating Section", to be followed by the "Imaging Section" which starts with the microscope objective. After understanding the various components, we can start "working with the microscope." To get the best resolution and contrast from the microscope, the practice of "Koehler Illumination" should be understood and followed by every serious microscopist. Step-by-step instructions as well as illustrations of the beam path in an upright and inverted microscope are included in this chapter. A few practical considerations are listed in Section 3. Copyright © 2013 Elsevier Inc. All rights

  10. Thermodynamics of weight loss diets.

    PubMed

    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.

  11. Thermodynamics of weight loss diets

    PubMed Central

    Fine, Eugene J; Feinman, Richard D

    2004-01-01

    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. PMID:15588283

  12. Thermodynamically consistent model calibration in chemical kinetics

    PubMed Central

    2011-01-01

    Background The dynamics of biochemical reaction systems are constrained by the fundamental laws of thermodynamics, which impose well-defined relationships among the reaction rate constants characterizing these systems. Constructing biochemical reaction systems from experimental observations often leads to parameter values that do not satisfy the necessary thermodynamic constraints. This can result in models that are not physically realizable and may lead to inaccurate, or even erroneous, descriptions of cellular function. Results We introduce a thermodynamically consistent model calibration (TCMC) method that can be effectively used to provide thermodynamically feasible values for the parameters of an open biochemical reaction system. The proposed method formulates the model calibration problem as a constrained optimization problem that takes thermodynamic constraints (and, if desired, additional non-thermodynamic constraints) into account. By calculating thermodynamically feasible values for the kinetic parameters of a well-known model of the EGF/ERK signaling cascade, we demonstrate the qualitative and quantitative significance of imposing thermodynamic constraints on these parameters and the effectiveness of our method for accomplishing this important task. MATLAB software, using the Systems Biology Toolbox 2.1, can be accessed from http://www.cis.jhu.edu/~goutsias/CSS lab/software.html. An SBML file containing the thermodynamically feasible EGF/ERK signaling cascade model can be found in the BioModels database. Conclusions TCMC is a simple and flexible method for obtaining physically plausible values for the kinetic parameters of open biochemical reaction systems. It can be effectively used to recalculate a thermodynamically consistent set of parameter values for existing thermodynamically infeasible biochemical reaction models of cellular function as well as to estimate thermodynamically feasible values for the parameters of new models. Furthermore, TCMC can

  13. Mailing microscope slides

    USDA-ARS?s Scientific Manuscript database

    Many insects feed agriculturally important crops, trees, and ornamental plants and cause millions of dollars of damage annually. Identification for some of these require the preparation of a microscope slide for examination. There are times when a microscope slide may need to be sent away to a speci...

  14. Real-Time Measurement of Nanotube Resonator Fluctuations in an Electron Microscope

    PubMed Central

    2017-01-01

    Mechanical resonators based on low-dimensional materials provide a unique platform for exploring a broad range of physical phenomena. The mechanical vibrational states are indeed extremely sensitive to charges, spins, photons, and adsorbed masses. However, the roadblock is often the readout of the resonator, because the detection of the vibrational states becomes increasingly difficult for smaller resonators. Here, we report an unprecedentedly sensitive method to detect nanotube resonators with effective masses in the 10–20 kg range. We use the beam of an electron microscope to resolve the mechanical fluctuations of a nanotube in real-time for the first time. We obtain full access to the thermally driven Brownian motion of the resonator, both in space and time domains. Our results establish the viability of carbon nanotube resonator technology at room temperature and pave the way toward the observation of novel thermodynamics regimes and quantum effects in nanomechanics. PMID:28186773

  15. Thermodynamic Studies for Drug Design and Screening

    PubMed Central

    Garbett, Nichola C.; Chaires, Jonathan B.

    2012-01-01

    Introduction A key part of drug design and development is the optimization of molecular interactions between an engineered drug candidate and its binding target. Thermodynamic characterization provides information about the balance of energetic forces driving binding interactions and is essential for understanding and optimizing molecular interactions. Areas covered This review discusses the information that can be obtained from thermodynamic measurements and how this can be applied to the drug development process. Current approaches for the measurement and optimization of thermodynamic parameters are presented, specifically higher throughput and calorimetric methods. Relevant literature for this review was identified in part by bibliographic searches for the period 2004 – 2011 using the Science Citation Index and PUBMED and the keywords listed below. Expert opinion The most effective drug design and development platform comes from an integrated process utilizing all available information from structural, thermodynamic and biological studies. Continuing evolution in our understanding of the energetic basis of molecular interactions and advances in thermodynamic methods for widespread application are essential to realize the goal of thermodynamically-driven drug design. Comprehensive thermodynamic evaluation is vital early in the drug development process to speed drug development towards an optimal energetic interaction profile while retaining good pharmacological properties. Practical thermodynamic approaches, such as enthalpic optimization, thermodynamic optimization plots and the enthalpic efficiency index, have now matured to provide proven utility in design process. Improved throughput in calorimetric methods remains essential for even greater integration of thermodynamics into drug design. PMID:22458502

  16. The scanning tunnelling microscope as an operative tool: doing physics and chemistry with single atoms and molecules.

    PubMed

    Rieder, Karl-Heinz; Meyer, Gerhard; Hla, Saw-Wai; Moresco, Francesca; Braun, Kai F; Morgenstern, Karina; Repp, Jascha; Foelsch, Stefan; Bartels, Ludwig

    2004-06-15

    The scanning tunnelling microscope, initially invented to image surfaces down to the atomic scale, has been further developed in the last few years to an operative tool, with which atoms and molecules can be manipulated at will at low substrate temperatures in different manners to create and investigate artificial structures, whose properties can be investigated employing spectroscopic dI/dV measurements. The tunnelling current can be used to selectively break chemical bonds, but also to induce chemical association. These possibilities give rise to startling new opportunities for physical and chemical experiments on the single atom and single molecule level. Here we provide a short overview on recent results obtained with these techniques.

  17. Microscope collision protection apparatus

    DOEpatents

    DeNure, Charles R.

    2001-10-23

    A microscope collision protection apparatus for a remote control microscope which protects the optical and associated components from damage in the event of an uncontrolled collision with a specimen, regardless of the specimen size or shape. In a preferred embodiment, the apparatus includes a counterbalanced slide for mounting the microscope's optical components. This slide replaces the rigid mounts on conventional upright microscopes with a precision ball bearing slide. As the specimen contacts an optical component, the contacting force will move the slide and the optical components mounted thereon. This movement will protect the optical and associated components from damage as the movement causes a limit switch to be actuated, thereby stopping all motors responsible for the collision.

  18. Supramolecular interactions of nonsteroidal anti-inflammatory drug in nanochannels of molecular containers: a spectroscopic, thermogravimetric and microscopic investigation.

    PubMed

    Maity, Banibrata; Chatterjee, Aninda; Ahmed, Sayeed Ashique; Seth, Debabrata

    2014-11-10

    Supramolecular host-guest complexation between the nonsteroidal anti-inflammatory drug indomethacin (IMC) and molecular containers were investigated. The weakly fluorescent drug molecule becomes highly fluorescent on complexation with different molecular containers, and time-resolved fluorescence emission spectroscopy reveals that the lifetime components of IMC significantly increase in the presence of molecular containers, compared with the lifetimes in neat water. The respective solid host-guest complexes were synthesised and characterised by Fourier transform infrared and (1) H nuclear magnetic resonance spectroscopic analysis. Microscopy techniques were used to analyse modifications of the surface morphology, owing to the formation of supramolecular complexes. The effect of the molecular container on the optical properties of IMC has also been investigated to determine the effect of nanochannels of different size and structure. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Morphological and spectroscopic analysis of cellulose nanocrystals extracted from oil palm empty fruit bunch fiber

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dasan, Y. K., E-mail: aamir.bhat@petronas.com.my; Bhat, A. H., E-mail: aamir.bhat@petronas.com.my; Faiz, A., E-mail: faizahmad@petronas.com.my

    2015-07-22

    This work evaluates the use of oil palm empty fruit bunch (OPEFB) fiber as a source of cellulose to obtain nanocrystalline cellulose (CNC) by acid hydrolysis reaction. The raw OPEFB fibers were pretreated with aqueous Sodium hydroxide at 80°C followed by bleaching treatment and further hydrolyzed with Sulphuric acid at 45°C with limited range of hydrolysis time and acid concentration. The resulting CNC’s were characterized for spectroscopic, crystallographic and morphological properties using Fourier Transform Infrared Spectroscopy (FTIR), X-ray Diffractometer (XRD), Transmission Electron Microscope (TEM) and Atomic Force Microscopy (AFM). Finding of this study shows that the properties of CNC’s aremore » strongly dependent on the hydrolysis time and acid concentration.« less

  20. The enlightened microscope: re-enactment and analysis of projections with eighteenth-century solar microscopes.

    PubMed

    Heering, Peter

    2008-09-01

    Solar microscopes and their techniques attracted particular attention in the second half of the eighteenth century. This paper investigates the grounds for this interest. After a general introduction to the solar microscope, it discusses the use of original instruments to gain access to the visual culture of solar microscopes and the issues raised by these reenactments. Experiences involved in this process serve as a basis for reassessing the original source materials. Thence emerges a different account of the meaning of the solar microscope in the eighteenth century and possible reasons for its popularity.

  1. Available Energy via Nonequilibrium Thermodynamics.

    ERIC Educational Resources Information Center

    Woollett, E. L.

    1979-01-01

    Presents basic relations involving the concept of available energy that are derived from the local equations of nonequilibrium thermodynamics. The equations and applications of the local thermodynamic equilibrium LTD model are also presented. (HM)

  2. X ray microscope assembly and alignment support and advanced x ray microscope design and analysis

    NASA Technical Reports Server (NTRS)

    Shealy, David L.

    1991-01-01

    Considerable efforts have been devoted recently to the design, analysis, fabrication, and testing of spherical Schwarzschild microscopes for soft x ray application in microscopy and projection lithography. The spherical Schwarzschild microscope consists of two concentric spherical mirrors configured such that the third order spherical aberration and coma are zero. Since multilayers are used on the mirror substrates for x ray applications, it is desirable to have only two reflecting surfaces in a microscope. In order to reduce microscope aberrations and increase the field of view, generalized mirror surface profiles have been considered in this investigation. Based on incoherent and sine wave modulation transfer function (MTF) calculations, the object plane resolution of a microscope has been analyzed as a function of the object height and numerical aperture (NA) of the primary for several spherical Schwarzschild, conic, and aspherical head reflecting two mirror microscope configurations.

  3. Thermodynamic origin of nonimaging optics

    NASA Astrophysics Data System (ADS)

    Jiang, Lun; Winston, Roland

    2016-10-01

    Nonimaging optics is the theory of thermodynamically efficient optics and as such depends more on thermodynamics than on optics. Hence, in this paper, a condition for the "best" design is proposed based on purely thermodynamic arguments, which we believe has profound consequences for the designs of thermal and even photovoltaic systems. This way of looking at the problem of efficient concentration depends on probabilities, the ingredients of entropy and information theory, while "optics" in the conventional sense recedes into the background. Much of the paper is pedagogical and retrospective. Some of the development of flowline designs will be introduced at the end and the connection between the thermodynamics and flowline design will be graphically presented. We will conclude with some speculative directions of where the ideas might lead.

  4. Thermodynamic efficiency of solar concentrators.

    PubMed

    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.

  5. Integration of a high-NA light microscope in a scanning electron microscope.

    PubMed

    Zonnevylle, A C; Van Tol, R F C; Liv, N; Narvaez, A C; Effting, A P J; Kruit, P; Hoogenboom, J P

    2013-10-01

    We present an integrated light-electron microscope in which an inverted high-NA objective lens is positioned inside a scanning electron microscope (SEM). The SEM objective lens and the light objective lens have a common axis and focal plane, allowing high-resolution optical microscopy and scanning electron microscopy on the same area of a sample simultaneously. Components for light illumination and detection can be mounted outside the vacuum, enabling flexibility in the construction of the light microscope. The light objective lens can be positioned underneath the SEM objective lens during operation for sub-10 μm alignment of the fields of view of the light and electron microscopes. We demonstrate in situ epifluorescence microscopy in the SEM with a numerical aperture of 1.4 using vacuum-compatible immersion oil. For a 40-nm-diameter fluorescent polymer nanoparticle, an intensity profile with a FWHM of 380 nm is measured whereas the SEM performance is uncompromised. The integrated instrument may offer new possibilities for correlative light and electron microscopy in the life sciences as well as in physics and chemistry. © 2013 The Authors Journal of Microscopy © 2013 Royal Microscopical Society.

  6. Interaction of Lysozyme with Rhodamine B: A combined analysis of spectroscopic & molecular docking.

    PubMed

    Millan, Sabera; Satish, Lakkoji; Kesh, Sandeep; Chaudhary, Yatendra S; Sahoo, Harekrushna

    2016-09-01

    The interaction of Rhodamine B (RB) with Lysozyme (Lys) was investigated by different optical spectroscopic techniques such as absorption, fluorescence, and circular-dichroism (CD), along with molecular docking studies. The fluorescence results (including steady-state and time-resolved mode) revealed that the addition of RB effectively causes strong quenching of intrinsic fluorescence in Lysozyme and mostly, by the static quenching mechanism. Different binding and thermodynamic parameters were calculated at different temperatures and the binding constant value was found to be 2963.54Lmol(-1) at 25°C. The average distance (r0) was found to be 3.31nm according to Förster's theory of non-radiative energy transfer between Lysozyme and RB. The conformational change in Lysozyme during interaction with RB was confirmed from absorbance, synchronous fluorescence, and circular dichroism measurements. Finally, molecular docking studies were done to confirm that the dye binds with Lysozyme. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Hydrophobicity and thermodynamic response for aqueous solutions of amphiphiles

    NASA Astrophysics Data System (ADS)

    Zemánková, Katerina; Troncoso, Jacobo; Cerdeiriña, Claudio A.; Romaní, Luis; Anisimov, Mikhail A.

    2016-06-01

    The anomalous behavior of aqueous solutions of amphiphiles in the water-rich region is analyzed via a phenomenological approach that utilizes the isobaric heat capacity Cp as an experimental probe. We report extensive data for solutions of 14 amphiphiles as a function of temperature at atmospheric pressure. Beyond that, Cp data but also isobaric thermal expansivities and isothermal compressibilities for three solutions of tert-butanol as a function of both temperature and pressure are presented. Results rule out the possibility that the observed phenomenology is associated with the anomalous thermodynamics of pure water. Indeed, our Cp data, quantitatively consistent with recent spectroscopic analyses, suggest that water-mediated interactions between the nonpolar parts of amphiphiles are at the origin of anomalies, with the effects of such "hydrophobic aggregation" being observed at mole fractions as small as 0.01. Physicochemical details like the size, the electronic charge distribution and the geometry of amphiphile molecules as well as third-order derivatives of the Gibbs energy and the associated Koga lines support the above claims while they further contribute to characterizing the role of hydrophobicity in these phenomena. Progress with a view to gain a deeper, more concrete understanding remains.

  8. Microscopic and spectroscopic evaluation of novel PLGA-chitosan Nanoplexes as an ocular delivery system.

    PubMed

    Jain, Gaurav K; Pathan, Shadab A; Akhter, Sohail; Jayabalan, Nirmal; Talegaonkar, Sushma; Khar, Roop K; Ahmad, Farhan J

    2011-02-01

    The interaction of PLGA-chitosan Nanoplexes with ocular mucosa was investigated ex vivo and in vivo to assess their potential as ocular delivery system. Fluorescent Rhodamine Nanoplexes (Rd-Nanoplexes) were prepared by ionotropic gelation method. The size and morphology of Nanoplexes was investigated by TEM, SEM and PCS. The corneal retention, uptake and penetration of Nanoplexes were analyzed by spectrofluorimetry and confocal microscopy. Corneas from Rd-Nanoplexes-treated rabbits were evaluated for the in vivo uptake and ocular tolerance. The Nanoplexes prepared were round with a mean diameter of 115.6±17nm and the encapsulation efficiency of Rd was 59.4±2.5%. Data from ex vivo and in vivo studies showed that the amounts of Rd in the cornea were significantly higher for Nanoplexes than for a control Rd solution, these amounts being fairly constant for up to 24h. Confocal microscopy of the corneas revealed paracellular and transcellular uptake of the Nanoplexes. The uptake mechanism postulated was adsorptive-mediated endocytosis and opening of the tight junctions between epithelial cells. No alteration was microscopically observed after ocular surface exposure to Nanoplexes. Taken together, these data demonstrate that Nanoplexes are potentially useful as ocular drug carriers. Copyright © 2010 Elsevier B.V. All rights reserved.

  9. The antiproliferative activity of di-2-pyridylketone dithiocarbamate is partly attributed to catalase inhibition: detailing the interaction by spectroscopic methods.

    PubMed

    Li, Cuiping; Liu, Youxun; Fu, Yun; Huang, Tengfei; Kang, Lixia; Li, Changzheng

    2017-08-22

    The bioactivity of drugs is attributed to their interaction with biological molecules, embodied in either their direct or indirect influence on enzyme activity and conformation. Di-2-pyridylketone hydrazine dithiocarbamate (DpdtC) exhibits significant antitumor activity in our preliminary study. We speculated that its activity may partly stem from enzyme inhibition due to strong metal chelating ability. To this end, we assessed its effect on catalase from erythrocytes and found evidence of inhibition, which was further confirmed by ROS determination in vivo. Thus, detailing the interaction between the agent and catalase via spectroscopic methods and molecular docking was required to obtain information on both the dynamics and thermodynamic parameters. The Lineweaver-Burk plot implied an uncompetitive pattern between DpdtC and catalase from beef liver, and IC 50 = ∼7 μM. The thermodynamic parameters from fluorescence quenching measurements indicated that DpdtC could bind to catalase with moderate affinity (K a = approximately 10 4 M -1 ). CD spectra revealed that DpdtC could significantly disrupt the secondary structure of catalase. Docking studies indicated that DpdtC bound to a flexible region of catalase, involving hydrogen bonds and salt bond; this was consistent with thermodynamic results from spectral investigations. Our data clearly showed that catalase inhibition of DpdtC was not due to direct chelation of iron from heme (killing), but through an allosteric effect. Thus, it can be concluded that the antiproliferative activity of DpdtC is partially attributed to its catalase inhibition.

  10. Local equilibrium and the second law of thermodynamics for irreversible systems with thermodynamic inertia.

    PubMed

    Glavatskiy, K S

    2015-10-28

    Validity of local equilibrium has been questioned for non-equilibrium systems which are characterized by delayed response. In particular, for systems with non-zero thermodynamic inertia, the assumption of local equilibrium leads to negative values of the entropy production, which is in contradiction with the second law of thermodynamics. In this paper, we address this question by suggesting a variational formulation of irreversible evolution of a system with non-zero thermodynamic inertia. We introduce the Lagrangian, which depends on the properties of the normal and the so-called "mirror-image" systems. We show that the standard evolution equations, in particular, the Maxwell-Cattaneo-Vernotte equation, can be derived from the variational procedure without going beyond the assumption of local equilibrium. We also argue that the second law of thermodynamics in non-equilibrium should be understood as a consequence of the variational procedure and the property of local equilibrium. For systems with instantaneous response this leads to the standard requirement of the local instantaneous entropy production being always positive. However, if a system is characterized by delayed response, the formulation of the second law of thermodynamics should be altered. In particular, the quantity, which is always positive, is not the instantaneous entropy production, but the entropy production averaged over a proper time interval.

  11. Spectroscopic profiling and computational study of the binding of tschimgine: A natural monoterpene derivative, with calf thymus DNA

    NASA Astrophysics Data System (ADS)

    Khajeh, Masoumeh Ashrafi; Dehghan, Gholamreza; Dastmalchi, Siavoush; Shaghaghi, Masoomeh; Iranshahi, Mehrdad

    2018-03-01

    DNA is a major target for a number of anticancer substances. Interaction studies between small molecules and DNA are essential for rational drug designing to influence main biological processes and also introducing new probes for the assay of DNA. Tschimgine (TMG) is a monoterpene derivative with anticancer properties. In the present study we tried to elucidate the interaction of TMG with calf thymus DNA (CT-DNA) using different spectroscopic methods. UV-visible absorption spectrophotometry, fluorescence and circular dichroism (CD) spectroscopies as well as molecular docking study revealed formation of complex between TMG and CT-DNA. Binding constant (Kb) between TMG and DNA was 2.27 × 104 M- 1, that is comparable to groove binding agents. The fluorescence spectroscopic data revealed that the quenching mechanism of fluorescence of TMG by CT-DNA is static quenching. Thermodynamic parameters (ΔH < 0 and ΔS < 0) at different temperatures indicated that van der Waals forces and hydrogen bonds were involved in the binding process of TMG with CT-DNA. Competitive binding assay with methylene blue (MB) and Hoechst 33258 using fluorescence spectroscopy displayed that TMG possibly binds to the minor groove of CT-DNA. These observations were further confirmed by CD spectral analysis, viscosity measurements and molecular docking.

  12. Robotic autopositioning of the operating microscope.

    PubMed

    Oppenlander, Mark E; Chowdhry, Shakeel A; Merkl, Brandon; Hattendorf, Guido M; Nakaji, Peter; Spetzler, Robert F

    2014-06-01

    Use of the operating microscope has become pervasive since its introduction to the neurosurgical world. Neuronavigation fused with the operating microscope has allowed accurate correlation of the focal point of the microscope and its location on the downloaded imaging study. However, the robotic ability of the Pentero microscope has not been utilized to orient the angle of the microscope or to change its focal length to hone in on a predefined target. To report a novel technology that allows automatic positioning of the operating microscope onto a set target and utilization of a planned trajectory, either determined with the StealthStation S7 by using preoperative imaging or intraoperatively with the microscope. By utilizing the current motorized capabilities of the Zeiss OPMI Pentero microscope, a robotic autopositioning feature was developed in collaboration with Surgical Technologies, Medtronic, Inc. (StealthStation S7). The system is currently being tested at the Barrow Neurological Institute. Three options were developed for automatically positioning the microscope: AutoLock Current Point, Align Parallel to Plan, and Point to Plan Target. These options allow the microscope to pivot around the lesion, hover in a set plane parallel to the determined trajectory, or rotate and point to a set target point, respectively. Integration of automatic microscope positioning into the operative workflow has potential to increase operative efficacy and safety. This technology is best suited for precise trajectories and entry points into deep-seated lesions.

  13. Scanning evanescent electro-magnetic microscope

    DOEpatents

    Xiang, Xiao-Dong; Gao, Chen; Schultz, Peter G.; Wei, Tao

    2003-01-01

    A novel scanning microscope is described that uses near-field evanescent electromagnetic waves to probe sample properties. The novel microscope is capable of high resolution imaging and quantitative measurements of the electrical properties of the sample. The inventive scanning evanescent wave electromagnetic microscope (SEMM) can map dielectric constant, tangent loss, conductivity, complex electrical impedance, and other electrical parameters of materials. The quantitative map corresponds to the imaged detail. The novel microscope can be used to measure electrical properties of both dielectric and electrically conducting materials.

  14. Scanning evanescent electro-magnetic microscope

    DOEpatents

    Xiang, Xiao-Dong; Gao, Chen

    2001-01-01

    A novel scanning microscope is described that uses near-field evanescent electromagnetic waves to probe sample properties. The novel microscope is capable of high resolution imaging and quantitative measurements of the electrical properties of the sample. The inventive scanning evanescent wave electromagnetic microscope (SEMM) can map dielectric constant, tangent loss, conductivity, complex electrical impedance, and other electrical parameters of materials. The quantitative map corresponds to the imaged detail. The novel microscope can be used to measure electrical properties of both dielectric and electrically conducting materials.

  15. Calorimetry of a Bose–Einstein-condensed photon gas

    PubMed Central

    Damm, Tobias; Schmitt, Julian; Liang, Qi; Dung, David; Vewinger, Frank; Weitz, Martin; Klaers, Jan

    2016-01-01

    Phase transitions, as the condensation of a gas to a liquid, are often revealed by a discontinuous behaviour of thermodynamic quantities. For liquid helium, for example, a divergence of the specific heat signals the transition from the normal fluid to the superfluid state. Apart from liquid helium, determining the specific heat of a Bose gas has proven to be a challenging task, for example, for ultracold atomic Bose gases. Here we examine the thermodynamic behaviour of a trapped two-dimensional photon gas, a system that allows us to spectroscopically determine the specific heat and the entropy of a nearly ideal Bose gas from the classical high temperature to the Bose-condensed quantum regime. The critical behaviour at the phase transition is clearly revealed by a cusp singularity of the specific heat. Regarded as a test of quantum statistical mechanics, our results demonstrate a quantitative agreement with its predictions at the microscopic level. PMID:27090978

  16. The Thermodynamic Properties of Cubanite

    NASA Technical Reports Server (NTRS)

    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. Thermodynamic metrics and optimal paths.

    PubMed

    Sivak, David A; Crooks, Gavin E

    2012-05-11

    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.

  18. Raman spectroscopic analysis of a 'noli me tangere' painting.

    PubMed

    Hibberts, Stephen; Edwards, Howell G M; Abdel-Ghani, Mona; Vandenabeele, Peter

    2016-12-13

    The discovery of an oil painting in seriously damaged condition with an important historical and a heterodox detail with possible origins in the late fifteenth century has afforded the opportunity for Raman microscopic analysis prior to its restoration being undertaken. The painting depicts a risen Christ following His crucifixion in a 'noli me tangere' pose with three women in an Italian terrace garden with a stone balustrade overlooking a rural landscape and an undoubted view of late-medieval Florence. The picture has suffered much abuse and is in very poor condition, which is possibly attributable to its controversial portrayal of a polydactylic Christ with six toes on His right foot. By the late sixteenth century, after the Council of Trent, this portrayal would almost certainly have been frowned upon by the Church authorities or more controversially as a depiction of the holy. Raman spectroscopic analysis of the pigments places the painting as being consistent chronologically with the Renaissance period following the identification of cinnabar, haematite, red lead, lead white, goethite, verdigris, caput mortuum and azurite with no evidence of more modern synthetic pigments or of modern restoration having been carried out. An interesting pigment mixture found here is that of the organic dye carmine and cinnabar to produce a particular bright red pigment coloration. Stratigraphic examination of the paint fragments has demonstrated the presence of an orange resin layer immediately on top of the canvas substrate, effectively rendering the pigment as a sandwich between this substratal resin and the overlying varnish. The Raman spectroscopic evidence clearly indicates that an attribution of the artwork to the Renaissance is consistent with the scientific analysis of the pigment composition.This article is part of the themed issue 'Raman spectroscopy in art and archaeology'. © 2016 The Author(s).

  19. Raman spectroscopic analysis of a `noli me tangere' painting

    NASA Astrophysics Data System (ADS)

    Hibberts, Stephen; Edwards, Howell G. M.; Abdel-Ghani, Mona; Vandenabeele, Peter

    2016-12-01

    The discovery of an oil painting in seriously damaged condition with an important historical and a heterodox detail with possible origins in the late fifteenth century has afforded the opportunity for Raman microscopic analysis prior to its restoration being undertaken. The painting depicts a risen Christ following His crucifixion in a `noli me tangere' pose with three women in an Italian terrace garden with a stone balustrade overlooking a rural landscape and an undoubted view of late-medieval Florence. The picture has suffered much abuse and is in very poor condition, which is possibly attributable to its controversial portrayal of a polydactylic Christ with six toes on His right foot. By the late sixteenth century, after the Council of Trent, this portrayal would almost certainly have been frowned upon by the Church authorities or more controversially as a depiction of the holy. Raman spectroscopic analysis of the pigments places the painting as being consistent chronologically with the Renaissance period following the identification of cinnabar, haematite, red lead, lead white, goethite, verdigris, caput mortuum and azurite with no evidence of more modern synthetic pigments or of modern restoration having been carried out. An interesting pigment mixture found here is that of the organic dye carmine and cinnabar to produce a particular bright red pigment coloration. Stratigraphic examination of the paint fragments has demonstrated the presence of an orange resin layer immediately on top of the canvas substrate, effectively rendering the pigment as a sandwich between this substratal resin and the overlying varnish. The Raman spectroscopic evidence clearly indicates that an attribution of the artwork to the Renaissance is consistent with the scientific analysis of the pigment composition. This article is part of the themed issue "Raman spectroscopy in art and archaeology".

  20. Non-hermitian quantum thermodynamics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gardas, Bartłomiej; Deffner, Sebastian; Saxena, Avadh

    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. Lastly, we propose two setups to test our predictions,more » namely with strongly interacting excitons and photons in a semiconductor microcavity and in the non-hermitian tight-binding model.« less

  1. Non-hermitian quantum thermodynamics

    DOE PAGES

    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. Lastly, we propose two setups to test our predictions,more » namely with strongly interacting excitons and photons in a semiconductor microcavity and in the non-hermitian tight-binding model.« less

  2. eQuilibrator--the biochemical thermodynamics calculator.

    PubMed

    Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

    2012-01-01

    The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like 'how much Gibbs energy is released by ATP hydrolysis at pH 5?' are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use.

  3. eQuilibrator—the biochemical thermodynamics calculator

    PubMed Central

    Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

    2012-01-01

    The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like ‘how much Gibbs energy is released by ATP hydrolysis at pH 5?’ are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use. PMID:22064852

  4. Unsupervised data mining in nanoscale x-ray spectro-microscopic study of NdFeB magnet

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Duan, Xiaoyue; Yang, Feifei; Antono, Erin

    Novel developments in X-ray based spectro-microscopic characterization techniques have increased the rate of acquisition of spatially resolved spectroscopic data by several orders of magnitude over what was possible a few years ago. This accelerated data acquisition, with high spatial resolution at nanoscale and sensitivity to subtle differences in chemistry and atomic structure, provides a unique opportunity to investigate hierarchically complex and structurally heterogeneous systems found in functional devices and materials systems. However, handling and analyzing the large volume data generated poses significant challenges. Here we apply an unsupervised data-mining algorithm known as DBSCAN to study a rare-earth element based permanentmore » magnet material, Nd 2Fe 14B. We are able to reduce a large spectro-microscopic dataset of over 300,000 spectra to 3, preserving much of the underlying information. Scientists can easily and quickly analyze in detail three characteristic spectra. Our approach can rapidly provide a concise representation of a large and complex dataset to materials scientists and chemists. For instance, it shows that the surface of common Nd 2Fe 14B magnet is chemically and structurally very different from the bulk, suggesting a possible surface alteration effect possibly due to the corrosion, which could affect the material’s overall properties.« less

  5. Unsupervised data mining in nanoscale x-ray spectro-microscopic study of NdFeB magnet

    DOE PAGES

    Duan, Xiaoyue; Yang, Feifei; Antono, Erin; ...

    2016-09-29

    Novel developments in X-ray based spectro-microscopic characterization techniques have increased the rate of acquisition of spatially resolved spectroscopic data by several orders of magnitude over what was possible a few years ago. This accelerated data acquisition, with high spatial resolution at nanoscale and sensitivity to subtle differences in chemistry and atomic structure, provides a unique opportunity to investigate hierarchically complex and structurally heterogeneous systems found in functional devices and materials systems. However, handling and analyzing the large volume data generated poses significant challenges. Here we apply an unsupervised data-mining algorithm known as DBSCAN to study a rare-earth element based permanentmore » magnet material, Nd 2Fe 14B. We are able to reduce a large spectro-microscopic dataset of over 300,000 spectra to 3, preserving much of the underlying information. Scientists can easily and quickly analyze in detail three characteristic spectra. Our approach can rapidly provide a concise representation of a large and complex dataset to materials scientists and chemists. For instance, it shows that the surface of common Nd 2Fe 14B magnet is chemically and structurally very different from the bulk, suggesting a possible surface alteration effect possibly due to the corrosion, which could affect the material’s overall properties.« less

  6. Geometry and symmetry in non-equilibrium thermodynamic systems

    NASA Astrophysics Data System (ADS)

    Sonnino, Giorgio

    2017-06-01

    The ultimate aim of this series of works is to establish the closure equations, valid for thermodynamic systems out from the Onsager region, and to describe the geometry and symmetry in thermodynamic systems far from equilibrium. Geometry of a non-equilibrium thermodynamic system is constructed by taking into account the second law of thermodynamics and by imposing the validity of the Glansdorff-Prigogine Universal Criterion of Evolution. These two constraints allow introducing the metrics and the affine connection of the Space of the Thermodynamic Forces, respectively. The Lie group associated to the nonlinear Thermodynamic Coordinate Transformations (TCT) leaving invariant both the entropy production σ and the Glansdorff-Prigogine dissipative quantity P, is also described. The invariance under TCT leads to the formulation of the Thermodynamic Covariance Principle (TCP): The nonlinear closure equations, i.e. the flux-force relations, must be covariant under TCT. In other terms, the fundamental laws of thermodynamics should be manifestly covariant under transformations between the admissible thermodynamic forces (i.e. under TCT). The symmetry properties of a physical system are intimately related to the conservation laws characterizing the thermodynamic system. Noether's theorem gives a precise description of this relation. The macroscopic theory for closure relations, based on this geometrical description and subject to the TCP, is referred to as the Thermodynamic Field Theory (TFT). This theory ensures the validity of the fundamental theorems for systems far from equilibrium.

  7. Immersion-scanning-tunneling-microscope for long-term variable-temperature experiments at liquid-solid interfaces

    NASA Astrophysics Data System (ADS)

    Ochs, Oliver; Heckl, Wolfgang M.; Lackinger, Markus

    2018-05-01

    Fundamental insights into the kinetics and thermodynamics of supramolecular self-assembly on surfaces are uniquely gained by variable-temperature high-resolution Scanning-Tunneling-Microscopy (STM). Conventionally, these experiments are performed with standard ambient microscopes extended with heatable sample stages for local heating. However, unavoidable solvent evaporation sets a technical limit on the duration of these experiments, hence prohibiting long-term experiments. These, however, would be highly desirable to provide enough time for temperature stabilization and settling of drift but also to study processes with inherently slow kinetics. To overcome this dilemma, we propose a STM that can operate fully immersed in solution. The instrument is mounted onto the lid of a hermetically sealed heatable container that is filled with the respective solution. By closing the container, both the sample and microscope are immersed in solution. Thereby solvent evaporation is eliminated and an environment for long-term experiments with utmost stable and controllable temperatures between room-temperature and 100 °C is provided. Important experimental requirements for the immersion-STM and resulting design criteria are discussed, the strategy for protection against corrosive media is described, the temperature stability and drift behavior are thoroughly characterized, and first long-term high resolution experiments at liquid-solid interfaces are presented.

  8. Spectroscopic and chemical reactivity analysis of D-Myo-Inositol using quantum chemical approach and its experimental verification

    NASA Astrophysics Data System (ADS)

    Mishra, Devendra P.; Srivastava, Anchal; Shukla, R. K.

    2017-07-01

    This paper describes the spectroscopic (^1H and ^{13}C NMR, FT-IR and UV-Visible), chemical, nonlinear optical and thermodynamic properties of D-Myo-Inositol using quantum chemical technique and its experimental verification. The structural parameters of the compound are determined from the optimized geometry by B3LYP method with 6 {-}311{+}{+}G(d,p) basis set. It was found that the optimized parameters thus obtained are almost in agreement with the experimental ones. A detailed interpretation of the infrared spectra of D-Myo-Inositol is also reported in the present work. After optimization, the proton and carbon NMR chemical shifts of the studied compound are calculated using GIAO and 6 {-}311{+}{+}G(d,p) basis set. The search of organic materials with improved charge transfer properties requires precise quantum chemical calculations of space-charge density distribution, state and transition dipole moments and HOMO-LUMO states. The nature of the transitions in the observed UV-Visible spectrum of the compound has been studied by the time-dependent density functional theory (TD-DFT). The global reactivity descriptors like chemical potential, electronegativity, hardness, softness and electrophilicity index, have been calculated using DFT. The thermodynamic calculation related to the title compound was also performed at B3LYP/ 6 {-}311{+}{+}G(d,p) level of theory. The standard statistical thermodynamic functions like heat capacity at constant pressure, entropy and enthalpy change were obtained from the theoretical harmonic frequencies of the optimized molecule. It is observed that the values of heat capacity, entropy and enthalpy increase with increase in temperature from 100 to 1000 K, which is attributed to the enhancement of molecular vibration with the increase in temperature.

  9. Microscopic insights into the NMR relaxation based protein conformational entropy meter

    PubMed Central

    Kasinath, Vignesh; Sharp, Kim A.; Wand, A. Joshua

    2013-01-01

    Conformational entropy is a potentially important thermodynamic parameter contributing to protein function. Quantitative measures of conformational entropy are necessary for an understanding of its role but have been difficult to obtain. An empirical method that utilizes changes in conformational dynamics as a proxy for changes in conformational entropy has recently been introduced. Here we probe the microscopic origins of the link between conformational dynamics and conformational entropy using molecular dynamics simulations. Simulation of seven pro! teins gave an excellent correlation with measures of side-chain motion derived from NMR relaxation. The simulations show that the motion of methyl-bearing side-chains are sufficiently coupled to that of other side chains to serve as excellent reporters of the overall side-chain conformational entropy. These results tend to validate the use of experimentally accessible measures of methyl motion - the NMR-derived generalized order parameters - as a proxy from which to derive changes in protein conformational entropy. PMID:24007504

  10. Thermodynamics and kinetics of molecular motors.

    PubMed

    Astumian, R Dean

    2010-06-02

    Molecular motors are first and foremost molecules, governed by the laws of chemistry rather than of mechanics. The dynamical behavior of motors based on chemical principles can be described as a random walk on a network of states. A key insight is that any molecular motor in solution explores all possible motions and configurations at thermodynamic equilibrium. By using input energy and chemical design to prevent motion that is not wanted, what is left behind is the motion that is desired. This review is focused on two-headed motors such as kinesin and Myosin V that move on a polymeric track. By use of microscopic reversibility, it is shown that the ratio between the number of forward steps and the number of backward steps in any sufficiently long time period does not directly depend on the mechanical properties of the linker between the two heads. Instead, this ratio is governed by the relative chemical specificity of the heads in the front-versus-rear position for the fuel, adenosine triphosphate and its products, adenosine diphosphate and inorganic phosphate. These insights have been key factors in the design of biologically inspired synthetic molecular walkers constructed out of DNA or out of small organic molecules. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  11. Black hole thermodynamics

    NASA Astrophysics Data System (ADS)

    Carlip, S.

    2014-10-01

    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 paper, 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.

  12. Phytochemical, spectroscopic and density functional theory study of Diospyrin, and non-bonding interactions of Diospyrin with atmospheric gases.

    PubMed

    Fazl-i-Sattar; Ullah, Zakir; Ata-ur-Rahman; Rauf, Abdur; Tariq, Muhammad; Tahir, Asif Ali; Ayub, Khurshid; Ullah, Habib

    2015-04-15

    Density functional theory (DFT) and phytochemical study of a natural product, Diospyrin (DO) have been carried out. A suitable level of theory was developed, based on correlating the experimental and theoretical data. Hybrid DFT method at B3LYP/6-31G (d,p) level of theory is employed for obtaining the electronic, spectroscopic, inter-molecular interaction and thermodynamic properties of DO. The exact structure of DO is confirmed from the nice validation of the theory and experiment. Non-covalent interactions of DO with different atmospheric gases such as NH3, CO2, CO, and H2O were studied to find out its electroactive nature. The experimental and predicted geometrical parameters, IR and UV-vis spectra (B3LYP/6-31+G (d,p) level of theory) show excellent correlation. Inter-molecular non-bonding interaction of DO with atmospheric gases is investigated through geometrical parameters, electronic properties, charge analysis, and thermodynamic parameters. Electronic properties include, ionization potential (I.P.), electron affinities (E.A.), electrostatic potential (ESP), density of states (DOS), HOMO, LUMO, and band gap. All these characterizations have corroborated each other and confirmed the presence of non-covalent nature in DO with the mentioned gases. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Stochastic thermodynamics of fluctuating density fields: Non-equilibrium free energy differences under coarse-graining

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Leonard, T.; Lander, B.; Seifert, U.

    2013-11-28

    We discuss the stochastic thermodynamics of systems that are described by a time-dependent density field, for example, simple liquids and colloidal suspensions. For a time-dependent change of external parameters, we show that the Jarzynski relation connecting work with the change of free energy holds if the time evolution of the density follows the Kawasaki-Dean equation. Specifically, we study the work distributions for the compression and expansion of a two-dimensional colloidal model suspension implementing a practical coarse-graining scheme of the microscopic particle positions. We demonstrate that even if coarse-grained dynamics and density functional do not match, the fluctuation relations for themore » work still hold albeit for a different, apparent, change of free energy.« less

  14. X-ray laser microscope apparatus

    DOEpatents

    Suckewer, Szymon; DiCicco, Darrell S.; Hirschberg, Joseph G.; Meixler, Lewis D.; Sathre, Robert; Skinner, Charles H.

    1990-01-01

    A microscope consisting of an x-ray contact microscope and an optical microscope. The optical, phase contrast, microscope is used to align a target with respect to a source of soft x-rays. The source of soft x-rays preferably comprises an x-ray laser but could comprise a synchrotron or other pulse source of x-rays. Transparent resist material is used to support the target. The optical microscope is located on the opposite side of the transparent resist material from the target and is employed to align the target with respect to the anticipated soft x-ray laser beam. After alignment with the use of the optical microscope, the target is exposed to the soft x-ray laser beam. The x-ray sensitive transparent resist material whose chemical bonds are altered by the x-ray beam passing through the target mater GOVERNMENT LICENSE RIGHTS This invention was made with government support under Contract No. De-FG02-86ER13609 awarded by the Department of Energy. The Government has certain rights in this invention.

  15. An intraoperative spectroscopic imaging system for quantification of Protoporphyrin IX during glioma surgery (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Angulo-Rodríguez, Leticia M.; Laurence, Audrey; Jermyn, Michael; Sheehy, Guillaume; Sibai, Mira; Petrecca, Kevin; Roberts, David W.; Paulsen, Keith D.; Wilson, Brian C.; Leblond, Frédéric

    2016-03-01

    Cancer tissue often remains after brain tumor resection due to the inability to detect the full extent of cancer during surgery, particularly near tumor boundaries. Commercial systems are available for intra-operative real-time aminolevulenic acid (ALA)-induced protoporphyrin IX (PpIX) fluorescence imaging. These are standard white-light neurosurgical microscopes adapted with optical components for fluorescence excitation and detection. However, these instruments lack sensitivity and specificity, which limits the ability to detect low levels of PpIX and distinguish it from tissue auto-fluorescence. Current systems also cannot provide repeatable and un-biased quantitative fluorophore concentration values because of the unknown and highly variable light attenuation by tissue. We present a highly sensitive spectroscopic fluorescence imaging system that is seamlessly integrated onto a neurosurgical microscope. Hardware and software were developed to achieve through-microscope spatially-modulated illumination for 3D profilometry and to use this information to extract tissue optical properties to correct for the effects of tissue light attenuation. This gives pixel-by-pixel quantified fluorescence values and improves detection of low PpIX concentrations. This is achieved using a high-sensitivity Electron Multiplying Charge Coupled Device (EMCCD) with a Liquid Crystal Tunable Filter (LCTF) whereby spectral bands are acquired sequentially; and a snapshot camera system with simultaneous acquisition of all bands is used for profilometry and optical property recovery. Sensitivity and specificity to PpIX is demonstrated using brain tissue phantoms and intraoperative human data acquired in an on-going clinical study using PpIX fluorescence to guide glioma resection.

  16. Zinc complexation in chloride-rich hydrothermal fluids (25-600 °C): A thermodynamic model derived from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Mei, Yuan; Sherman, David M.; Liu, Weihua; Etschmann, Barbara; Testemale, Denis; Brugger, Joël

    2015-02-01

    The solubility of zinc minerals in hydrothermal fluids is enhanced by chloride complexation of Zn2+. Thermodynamic models of these complexation reactions are central to models of Zn transport and ore formation. However, existing thermodynamic models, derived from solubility measurements, are inconsistent with spectroscopic measurements of Zn speciation. Here, we used ab initio molecular dynamics simulations (with the PBE exchange-correlation functional) to predict the speciation of Zn-Cl complexes from 25 to 600 °C. We also obtained in situ XAS measurements of Zn-Cl solutions at 30-600 °C. Qualitatively, the simulations reproduced the main features derived from in situ XANES and EXAFS measurements: octahedral to tetrahedral transition with increasing temperature and salinity, stability of ZnCl42- at high chloride concentration up to ⩾500 °C, and increasing stability of the trigonal planar [ZnCl3]- complex at high temperature. Having confirmed the dominant species, we directly determined the stability constants for the Zn-Cl complexes using thermodynamic integration along constrained Zn-Cl distances in a series of MD simulations. We corrected our stability constants to infinite dilution using the b-dot model for the activity coefficients of the solute species. In order to compare the ab initio results with experiments, we need to re-model the existing solubility data using the species we identified in our MD simulations. The stability constants derived from refitting published experimental data are in reasonable agreement with those we obtained using ab initio MD simulations. Our new thermodynamic model accurately predicts the experimentally observed changes in ZnO(s) and ZnCO3(s) solubility as a function of chloride concentration from 200 (Psat) to 600 °C (2000 bar). This study demonstrates that metal speciation and geologically useful stability constants can be derived for species in hydrothermal fluids from ab initio MD simulations even at the generalized

  17. Application of thermodynamics to silicate crystalline solutions

    NASA Technical Reports Server (NTRS)

    Saxena, S. K.

    1972-01-01

    A review of thermodynamic relations is presented, describing Guggenheim's regular solution models, the simple mixture, the zeroth approximation, and the quasi-chemical model. The possibilities of retrieving useful thermodynamic quantities from phase equilibrium studies are discussed. Such quantities include the activity-composition relations and the free energy of mixing in crystalline solutions. Theory and results of the study of partitioning of elements in coexisting minerals are briefly reviewed. A thermodynamic study of the intercrystalline and intracrystalline ion exchange relations gives useful information on the thermodynamic behavior of the crystalline solutions involved. Such information is necessary for the solution of most petrogenic problems and for geothermometry. Thermodynamic quantities for tungstates (CaWO4-SrWO4) are calculated.

  18. Martian Microscope

    NASA Technical Reports Server (NTRS)

    2004-01-01

    The microscopic imager (circular device in center) is in clear view above the surface at Meridiani Planum, Mars, in this approximate true-color image taken by the panoramic camera on the Mars Exploration Rover Opportunity. The image was taken on the 9th sol of the rover's journey. The microscopic imager is located on the rover's instrument deployment device, or arm. The arrow is pointing to the lens of the instrument. Note the dust cover, which flips out to the left of the lens, is open. This approximated color image was created using the camera's violet and infrared filters as blue and red.

  19. Nonequilibrium thermodynamics of restricted Boltzmann machines.

    PubMed

    Salazar, Domingos S P

    2017-08-01

    In this work, we analyze the nonequilibrium thermodynamics of a class of neural networks known as restricted Boltzmann machines (RBMs) in the context of unsupervised learning. We show how the network is described as a discrete Markov process and how the detailed balance condition and the Maxwell-Boltzmann equilibrium distribution are sufficient conditions for a complete thermodynamics description, including nonequilibrium fluctuation theorems. Numerical simulations in a fully trained RBM are performed and the heat exchange fluctuation theorem is verified with excellent agreement to the theory. We observe how the contrastive divergence functional, mostly used in unsupervised learning of RBMs, is closely related to nonequilibrium thermodynamic quantities. We also use the framework to interpret the estimation of the partition function of RBMs with the annealed importance sampling method from a thermodynamics standpoint. Finally, we argue that unsupervised learning of RBMs is equivalent to a work protocol in a system driven by the laws of thermodynamics in the absence of labeled data.

  20. Single molecule thermodynamics in biological motors.

    PubMed

    Taniguchi, Yuichi; Karagiannis, Peter; Nishiyama, Masayoshi; Ishii, Yoshiharu; Yanagida, Toshio

    2007-04-01

    Biological molecular machines use thermal activation energy to carry out various functions. The process of thermal activation has the stochastic nature of output events that can be described according to the laws of thermodynamics. Recently developed single molecule detection techniques have allowed each distinct enzymatic event of single biological machines to be characterized providing clues to the underlying thermodynamics. In this study, the thermodynamic properties in the stepping movement of a biological molecular motor have been examined. A single molecule detection technique was used to measure the stepping movements at various loads and temperatures and a range of thermodynamic parameters associated with the production of each forward and backward step including free energy, enthalpy, entropy and characteristic distance were obtained. The results show that an asymmetry in entropy is a primary factor that controls the direction in which the motor will step. The investigation on single molecule thermodynamics has the potential to reveal dynamic properties underlying the mechanisms of how biological molecular machines work.

  1. Local equilibrium and the second law of thermodynamics for irreversible systems with thermodynamic inertia

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Glavatskiy, K. S.

    Validity of local equilibrium has been questioned for non-equilibrium systems which are characterized by delayed response. In particular, for systems with non-zero thermodynamic inertia, the assumption of local equilibrium leads to negative values of the entropy production, which is in contradiction with the second law of thermodynamics. In this paper, we address this question by suggesting a variational formulation of irreversible evolution of a system with non-zero thermodynamic inertia. We introduce the Lagrangian, which depends on the properties of the normal and the so-called “mirror-image” systems. We show that the standard evolution equations, in particular, the Maxwell-Cattaneo-Vernotte equation, can bemore » derived from the variational procedure without going beyond the assumption of local equilibrium. We also argue that the second law of thermodynamics in non-equilibrium should be understood as a consequence of the variational procedure and the property of local equilibrium. For systems with instantaneous response this leads to the standard requirement of the local instantaneous entropy production being always positive. However, if a system is characterized by delayed response, the formulation of the second law of thermodynamics should be altered. In particular, the quantity, which is always positive, is not the instantaneous entropy production, but the entropy production averaged over a proper time interval.« less

  2. The Scanning Optical Microscope.

    ERIC Educational Resources Information Center

    Sheppard, C. J. R.

    1978-01-01

    Describes the principle of the scanning optical microscope and explains its advantages over the conventional microscope in the improvement of resolution and contrast, as well as the possibility of producing a picture from optical harmonies generated within the specimen.

  3. Difference rule-a new thermodynamic principle: prediction of standard thermodynamic data for inorganic solvates.

    PubMed

    Jenkins, H Donald Brooke; Glasser, Leslie

    2004-12-08

    We present a quite general thermodynamic "difference" rule, derived from thermochemical first principles, quantifying the difference between the standard thermodynamic properties, P, of a solid n-solvate (or n-hydrate), n-S, containing n molecules of solvate, S (water or other) and the corresponding solid parent (unsolvated) salt: [P[n-solvate] - P[parent

  4. Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives.

    PubMed

    Rokob, Tibor András; Srnec, Martin; Rulíšek, Lubomír

    2012-05-21

    In the last decade, we have witnessed substantial progress in the development of quantum chemical methodologies. Simultaneously, robust solvation models and various combined quantum and molecular mechanical (QM/MM) approaches have become an integral part of quantum chemical programs. Along with the steady growth of computer power and, more importantly, the dramatic increase of the computer performance to price ratio, this has led to a situation where computational chemistry, when exercised with the proper amount of diligence and expertise, reproduces, predicts, and complements the experimental data. In this perspective, we review some of the latest achievements in the field of theoretical (quantum) bioinorganic chemistry, concentrating mostly on accurate calculations of the spectroscopic and physico-chemical properties of open-shell bioinorganic systems by wave-function (ab initio) and DFT methods. In our opinion, the one-to-one mapping between the calculated properties and individual molecular structures represents a major advantage of quantum chemical modelling since this type of information is very difficult to obtain experimentally. Once (and only once) the physico-chemical, thermodynamic and spectroscopic properties of complex bioinorganic systems are quantitatively reproduced by theoretical calculations may we consider the outcome of theoretical modelling, such as reaction profiles and the various decompositions of the calculated parameters into individual spatial or physical contributions, to be reliable. In an ideal situation, agreement between theory and experiment may imply that the practical problem at hand, such as the reaction mechanism of the studied metalloprotein, can be considered as essentially solved.

  5. [Thermodynamics of the origin of life, evolution and aging].

    PubMed

    Gladyshev, G P

    2014-01-01

    Briefly discusses the history of the search of thermodynamic approach to explain the origin of life, evolution and aging of living beings. The origin of life is the result of requirement by the quasi-equilibrium hierarchical thermodynamics, in particular, the supramolecular thermodynamics. The evolution and aging of living beings is accompanied with changes of chemical and supramolecular compositions of living bodies, as well as with changes in the composition and structure of all hierarchies of the living world. The thermodynamic principle of substance stability predicts the existence of a single genetic code in our universe. The thermodynamic theory optimizes physiology and medicine and recommends antiaging diets and medicines. Hierarchical thermodynamics forms the design diversity of culture and art. The thermodynamic theory of origin of life, evolution and aging is the development of Clausius-Gibbs thermodynamics. Hierarchical thermodynamics is the mirror of Darwin-Wallace's-theory.

  6. Thermodynamic efficiency of nonimaging concentrators

    NASA Astrophysics Data System (ADS)

    Shatz, Narkis; Bortz, John; Winston, Roland

    2009-08-01

    The purpose of a nonimaging concentrator is to transfer maximal flux from the phase space of a source to that of a target. A concentrator's performance can be expressed relative to a thermodynamic reference. We discuss consequences of Fermat's principle of geometrical optics. We review étendue dilution and optical loss mechanisms associated with nonimaging concentrators, especially for the photovoltaic (PV) role. We introduce the concept of optical thermodynamic efficiency which is a performance metric combining the first and second laws of thermodynamics. 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. As such, this metric is a gold standard for evaluating the performance of nonimaging concentrators. Examples are provided to illustrate the use of this new metric. In particular we discuss concentrating PV systems for solar power applications.

  7. Adsorption properties of biomass-based activated carbon prepared with spent coffee grounds and pomelo skin by phosphoric acid activation

    NASA Astrophysics Data System (ADS)

    Ma, Xiaodong; Ouyang, Feng

    2013-03-01

    Activated carbon prepared from spent coffee grounds and pomelo skin by phosphoric acid activation had been employed as the adsorbent for ethylene and n-butane at room temperature. Prepared activated carbon was characterized by means of nitrogen adsorption-desorption, X-ray powder diffraction, scanning electron microscope and Fourier transform infrared spectroscope. It was confirmed that pore structure played an important role during the adsorption testes. Adsorption isotherms of ethylene and n-butane fitted well with Langmuir equation. The prepared samples owned better adsorption capacity for n-butane than commercial activated carbon. Isosteric heats of adsorptions at different coverage were calculated through Clausius-Clapeyron equation. Micropore filling effect was explained in a thermodynamic way.

  8. The Scanning Optical Microscope: An Overview

    NASA Astrophysics Data System (ADS)

    Kino, G. S.; Corte, T. R.; Xiao, G. Q.

    1988-07-01

    In the last few years there has been a resurgence in research on optical microscopes. One reason stems from the invention of the acoustic microscope by Quate and Lemons,1 and the realization that some of the same principles could be applied to the optical microscope. The acoustic microscope has better transverse definition for the same wavelength than the standard optical microscope and at the same time has far better range definition. Consequently, Kompfner, who was involved with the work on the early acoustic microscope, decided to try out similar scanning microscope principles with optics, and started a group with Wilson and Sheppard to carry out such research at Oxford.2 Sometime earlier, Petran et a13 had invented the tandem scanning microscope which used many of the same principles. Now, in our laboratory at Stanford, these ideas on the tandem scanning microscope and the scanning optical microscope are converging. Another aspect of this work, which stems from the earlier experience with the acoustic microscope, involves measurement of both phase and amplitude of the optical beam. It is also possible to use scanned optical microscopy for other purposes. For instance, an optical beam can be used to excite electrons and holes in semiconductors, and the generated current can be measured. By scanning the optical beam over the semiconductor, an image can be obtained of the regions where there is strong or weak electron hole generation. This type of microscope is called OBIC (Optical Beam Induced Current). A second application involves fluorescent imaging of biological materials. Here we have the excellent range definition of a scanning optical microscope which eliminates unwanted glare from regions of the material where the beam is unfocused.3 A third application is focused on the heating effect of the light beam. With such a system, images can be obtained which are associated with changes in the thermal properties of a material, changes in recombination rates in

  9. Spectroscopic properties of a two-dimensional time-dependent Cepheid model. I. Description and validation of the model

    NASA Astrophysics Data System (ADS)

    Vasilyev, V.; Ludwig, H.-G.; Freytag, B.; Lemasle, B.; Marconi, M.

    2017-10-01

    Context. Standard spectroscopic analyses of Cepheid variables are based on hydrostatic one-dimensional model atmospheres, with convection treated using various formulations of mixing-length theory. Aims: This paper aims to carry out an investigation of the validity of the quasi-static approximation in the context of pulsating stars. We check the adequacy of a two-dimensional time-dependent model of a Cepheid-like variable with focus on its spectroscopic properties. Methods: With the radiation-hydrodynamics code CO5BOLD, we construct a two-dimensional time-dependent envelope model of a Cepheid with Teff = 5600 K, log g = 2.0, solar metallicity, and a 2.8-day pulsation period. Subsequently, we perform extensive spectral syntheses of a set of artificial iron lines in local thermodynamic equilibrium. The set of lines allows us to systematically study effects of line strength, ionization stage, and excitation potential. Results: We evaluate the microturbulent velocity, line asymmetry, projection factor, and Doppler shifts. The microturbulent velocity, averaged over all lines, depends on the pulsational phase and varies between 1.5 and 2.7 km s-1. The derived projection factor lies between 1.23 and 1.27, which agrees with observational results. The mean Doppler shift is non-zero and negative, -1 km s-1, after averaging over several full periods and lines. This residual line-of-sight velocity (related to the "K-term") is primarily caused by horizontal inhomogeneities, and consequently we interpret it as the familiar convective blueshift ubiquitously present in non-pulsating late-type stars. Limited statistics prevent firm conclusions on the line asymmetries. Conclusions: Our two-dimensional model provides a reasonably accurate representation of the spectroscopic properties of a short-period Cepheid-like variable star. Some properties are primarily controlled by convective inhomogeneities rather than by the Cepheid-defining pulsations. Extended multi-dimensional modelling

  10. Thermodynamic equilibrium-air correlations for flowfield applications

    NASA Technical Reports Server (NTRS)

    Zoby, E. V.; Moss, J. N.

    1981-01-01

    Equilibrium-air thermodynamic correlations have been developed for flowfield calculation procedures. A comparison between the postshock results computed by the correlation equations and detailed chemistry calculations is very good. The thermodynamic correlations are incorporated in an approximate inviscid flowfield code with a convective heating capability for the purpose of defining the thermodynamic environment through the shock layer. Comparisons of heating rates computed by the approximate code and a viscous-shock-layer method are good. In addition to presenting the thermodynamic correlations, the impact of several viscosity models on the convective heat transfer is demonstrated.

  11. On Thermodynamic Constraints upon Turbulence Modeling

    NASA Astrophysics Data System (ADS)

    Huang, Yu-Ning; Durst, Franz

    2000-11-01

    Turbulence is a continuum phenomenon which can be described within the framework of continuum mechanics. Such foundation has the potential for improving turbulence modeling, making it less heuristic and more rational. In the present research, we consider the compatibility of turbulence modeling with the second law of thermodynamics. We show that the Clausius-Planck inequality, as an expression of the principle of entropy growth, places a thermodynamic restriction upon the turbulence modeling of an incompressible Navier-Stokes fluid in an isothermal temperature field. This thermodynamic restriction is given in the form of an inequality, which ensures non-negativeness of the mean internal dissipation. As an illustration, we show the thermodynamic constraints on the modeling of a few typical homogeneous turbulent flows.

  12. Method and apparatus for differential spectroscopic atomic-imaging using scanning tunneling microscopy

    DOEpatents

    Kazmerski, Lawrence L.

    1990-01-01

    A Method and apparatus for differential spectroscopic atomic-imaging is disclosed for spatial resolution and imaging for display not only individual atoms on a sample surface, but also bonding and the specific atomic species in such bond. The apparatus includes a scanning tunneling microscope (STM) that is modified to include photon biasing, preferably a tuneable laser, modulating electronic surface biasing for the sample, and temperature biasing, preferably a vibration-free refrigerated sample mounting stage. Computer control and data processing and visual display components are also included. The method includes modulating the electronic bias voltage with and without selected photon wavelengths and frequency biasing under a stabilizing (usually cold) bias temperature to detect bonding and specific atomic species in the bonds as the STM rasters the sample. This data is processed along with atomic spatial topography data obtained from the STM raster scan to create a real-time visual image of the atoms on the sample surface.

  13. Spectroscopic study on variations in illite surface properties after acid-base titration.

    PubMed

    Liu, Wen-xin; Coveney, R M; Tang, Hong-xiao

    2003-07-01

    FT-IR, Raman microscopy, XRD, 29Si and 27Al MAS NMR, were used to investigate changes in surface properties of a natural illite sample after acid-base potentiometric titration. The characteristic XRD lines indicated the presence of surface Al-Si complexes, preferable to Al(OH)3 precipitates. In the microscopic Raman spectra, the vibration peaks of Si-O and Al-O bonds diminished as a result of treatment with acid, then increased after hydroxide back titration. The varied ratio of signal intensity between (IV)Al and (VI)Al species in 27Al MAS NMR spectra, together with the stable BET surface area after acidimetric titration, suggested that edge faces and basal planes in the layer structure of illite participated in dissolution of structural components. The combined spectroscopic evidence demonstrated that the reactions between illite surfaces and acid-leaching silicic acid and aluminum ions should be considered in the model description of surface acid-base properties of the aqueous illite.

  14. Thermodynamics of Enzyme-Catalyzed Reactions Database

    National Institute of Standards and Technology Data Gateway

    SRD 74 Thermodynamics of Enzyme-Catalyzed Reactions Database (Web, free access)   The Thermodynamics of Enzyme-Catalyzed Reactions Database contains thermodynamic data on enzyme-catalyzed reactions that have been recently published in the Journal of Physical and Chemical Reference Data (JPCRD). For each reaction the following information is provided: the reference for the data, the reaction studied, the name of the enzyme used and its Enzyme Commission number, the method of measurement, the data and an evaluation thereof.

  15. Limits of predictions in thermodynamic systems: a review

    NASA Astrophysics Data System (ADS)

    Marsland, Robert, III; England, Jeremy

    2018-01-01

    The past twenty years have seen a resurgence of interest in nonequilibrium thermodynamics, thanks to advances in the theory of stochastic processes and in their thermodynamic interpretation. Fluctuation theorems provide fundamental constraints on the dynamics of systems arbitrarily far from thermal equilibrium. Thermodynamic uncertainty relations bound the dissipative cost of precision in a wide variety of processes. Concepts of excess work and excess heat provide the basis for a complete thermodynamics of nonequilibrium steady states, including generalized Clausius relations and thermodynamic potentials. But these general results carry their own limitations: fluctuation theorems involve exponential averages that can depend sensitively on unobservably rare trajectories; steady-state thermodynamics makes use of a dual dynamics that lacks any direct physical interpretation. This review aims to present these central results of contemporary nonequilibrium thermodynamics in such a way that the power of each claim for making physical predictions can be clearly assessed, using examples from current topics in soft matter and biophysics.

  16. Non-equilibrium thermodynamics in cells.

    PubMed

    Jülicher, Frank; Grill, Stephan W; Salbreux, Guillaume

    2018-03-15

    We review the general hydrodynamic theory of active soft materials that is motivated in partic- ular by biological matter. We present basic concepts of irreversible thermodynamics of spatially extended multicomponent active systems. Starting from the rate of entropy production, we iden- tify conjugate thermodynamic fluxes and forces and present generic constitutive equations of polar active fluids and active gels. We also discuss angular momentum conservation which plays a role in the the physics of active chiral gels. The irreversible thermodynamics of active gels provides a general framework to discuss the physics that underlies a wide variety of biological processes in cells and in multicellular tissues. © 2018 IOP Publishing Ltd.

  17. Neutron Spectroscopic Factors from Transfer Reactions

    NASA Astrophysics Data System (ADS)

    Lee, Jenny; Tsang, M. B.

    2007-05-01

    We have extracted the ground state to ground state neutron spectroscopic factors for 80 nuclei ranging in Z from 3 to 24 by analyzing the past measurements of the angular distributions from (d,p) and (p,d) reactions. We demonstrate an approach that provides systematic and consistent values with a minimum of assumptions. A three-body model with global optical potentials and standard geometry of n-potential is applied. For the 60 nuclei where modern shell model calculations are available, such analysis reproduces, to within 20%, the experimental spectroscopic factors for most nuclei. If we constraint the nucleon-target optical potential and the geometries of the bound neutron-wave function with the modern Hartree-Fock calculations, our deduced neutron spectroscopic factors are reduced by 30% on average.

  18. A DVD Spectroscope: A Simple, High-Resolution Classroom Spectroscope

    ERIC Educational Resources Information Center

    Wakabayashi, Fumitaka; Hamada, Kiyohito

    2006-01-01

    Digital versatile disks (DVDs) have successfully made up an inexpensive but high-resolution spectroscope suitable for classroom experiments that can easily be made with common material and gives clear and fine spectra of various light sources and colored material. The observed spectra can be photographed with a digital camera, and such images can…

  19. Thermodynamics of Inozemtsev's elliptic spin chain

    NASA Astrophysics Data System (ADS)

    Klabbers, Rob

    2016-06-01

    We study the thermodynamic behaviour of Inozemtsev's long-range elliptic spin chain using the Bethe ansatz equations describing the spectrum of the model in the infinite-length limit. We classify all solutions of these equations in that limit and argue which of these solutions determine the spectrum in the thermodynamic limit. Interestingly, some of the solutions are not selfconjugate, which puts the model in sharp contrast to one of the model's limiting cases, the Heisenberg XXX spin chain. Invoking the string hypothesis we derive the thermodynamic Bethe ansatz equations (TBA-equations) from which we determine the Helmholtz free energy in thermodynamic equilibrium and derive the associated Y-system. We corroborate our results by comparing numerical solutions of the TBA-equations to a direct computation of the free energy for the finite-length hamiltonian. In addition we confirm numerically the interesting conjecture put forward by Finkel and González-López that the original and supersymmetric versions of Inozemtsev's elliptic spin chain are equivalent in the thermodynamic limit.

  20. Thermodynamic properties of water solvating biomolecular surfaces

    NASA Astrophysics Data System (ADS)

    Heyden, Matthias

    Changes in the potential energy and entropy of water molecules hydrating biomolecular interfaces play a significant role for biomolecular solubility and association. Free energy perturbation and thermodynamic integration methods allow calculations of free energy differences between two states from simulations. However, these methods are computationally demanding and do not provide insights into individual thermodynamic contributions, i.e. changes in the solvent energy or entropy. Here, we employ methods to spatially resolve distributions of hydration water thermodynamic properties in the vicinity of biomolecular surfaces. This allows direct insights into thermodynamic signatures of the hydration of hydrophobic and hydrophilic solvent accessible sites of proteins and small molecules and comparisons to ideal model surfaces. We correlate dynamic properties of hydration water molecules, i.e. translational and rotational mobility, to their thermodynamics. The latter can be used as a guide to extract thermodynamic information from experimental measurements of site-resolved water dynamics. Further, we study energy-entropy compensations of water at different hydration sites of biomolecular surfaces. This work is supported by the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft.

  1. Quantum thermodynamics of general quantum processes.

    PubMed

    Binder, Felix; Vinjanampathy, Sai; Modi, Kavan; Goold, John

    2015-03-01

    Accurately describing work extraction from a quantum system is a central objective for the extension of thermodynamics to individual quantum systems. The concepts of work and heat are surprisingly subtle when generalizations are made to arbitrary quantum states. We formulate an operational thermodynamics suitable for application to an open quantum system undergoing quantum evolution under a general quantum process by which we mean a completely positive and trace-preserving map. We derive an operational first law of thermodynamics for such processes and show consistency with the second law. We show that heat, from the first law, is positive when the input state of the map majorizes the output state. Moreover, the change in entropy is also positive for the same majorization condition. This makes a strong connection between the two operational laws of thermodynamics.

  2. Mars Life? - Microscopic Structures

    NASA Technical Reports Server (NTRS)

    1996-01-01

    In the center of this electron microscope image of a small chip from a meteorite are several tiny structures that are possible microscopic fossils of primitive, bacteria-like organisms that may have lived on Mars more than 3.6 billion years ago. A two-year investigation by a NASA research team found organic molecules, mineral features characteristic of biological activity and possible microscopic fossils such as these inside of an ancient Martian rock that fell to Earth as a meteorite. The largest possible fossils are less than 1/100th the diameter of a human hair in size while most are ten times smaller.

  3. Mars Life? - Microscopic Structures

    NASA Image and Video Library

    1996-08-09

    In the center of this electron microscope image of a small chip from a meteorite are several tiny structures that are possible microscopic fossils of primitive, bacteria-like organisms that may have lived on Mars more than 3.6 billion years ago. http://photojournal.jpl.nasa.gov/catalog/PIA00283

  4. A Scale-Invariant Model of Statistical Mechanics and Modified Forms of the First and the Second Laws of Thermodynamics

    NASA Technical Reports Server (NTRS)

    Sohrab, Siavash H.; Pitch, Nancy (Technical Monitor)

    1999-01-01

    A scale-invariant statistical theory of fields is presented that leads to invariant definition of density, velocity, temperature, and pressure, The definition of Boltzmann constant is introduced as k(sub k) = m(sub k)v(sub k)c = 1.381 x 10(exp -23) J x K(exp -1), suggesting that the Kelvin absolute temperature scale is equivalent to a length scale. Two new state variables called the reversible heat Q(sub rev) = TS and the reversible work W(sub rev) = PV are introduced. The modified forms of the first and second law of thermodynamics are presented. The microscopic definition of heat (work) is presented as the kinetic energy due to the random (peculiar) translational, rotational, and pulsational motions. The Gibbs free energy of an element at scale Beta is identified as the total system energy at scale (Beta-1), thus leading to an invariant form of the first law of thermodynamics U(sub Beta) = Q(sub Beta) - W(sub Beta) +N(e3)U(sub Beta-1).

  5. Thermodynamics from Car to Kitchen

    ERIC Educational Resources Information Center

    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…

  6. Study of the interaction of deoxynivalenol with human serum albumin by spectroscopic technique and molecular modelling.

    PubMed

    Li, Yuqin; Wang, Hao; Jia, Baoxiu; Liu, Caihong; Liu, Ke; Qi, Yongxiu; Hu, Zhide

    2013-01-01

    The mechanism of interaction between deoxynivalenol (DON) and human serum albumin (HSA) was studied using spectroscopic methods including fluorescence spectra, UV-VIS, Fourier transform infrared (FT-IR) and circular dichroism (CD). The quenching mechanism was investigated in terms of the association constants, number of binding sites and basic thermodynamic parameters. The distance between the HSA donor and the acceptor DON was 2.80 nm as derived from fluorescence resonance energy transfer. The secondary structure compositions of free HSA and its DON complexes were estimated by the FT-IR spectra. Alteration of the secondary protein structure in the presence of DON was confirmed by UV-VIS and CD spectroscopy. Molecular modelling revealed that a DON-protein complex was stabilised by hydrophobic forces and hydrogen bonding. It was potentially useful for elucidating the toxigenicity of DON when combined with biomolecular function effect, transmembrane transport, toxicological testing and the other experiments.

  7. Scanning Miniature Microscopes without Lenses

    NASA Technical Reports Server (NTRS)

    Wang, Yu

    2009-01-01

    The figure schematically depicts some alternative designs of proposed compact, lightweight optoelectronic microscopes that would contain no lenses and would generate magnified video images of specimens. Microscopes of this type were described previously in Miniature Microscope Without Lenses (NPO - 20218), NASA Tech Briefs, Vol. 22, No. 8 (August 1998), page 43 and Reflective Variants of Miniature Microscope Without Lenses (NPO 20610), NASA Tech Briefs, Vol. 26, No. 9 (September 1999), page 6a. To recapitulate: In the design and construction of a microscope of this type, the focusing optics of a conventional microscope are replaced by a combination of a microchannel filter and a charge-coupled-device (CCD) image detector. Elimination of focusing optics reduces the size and weight of the instrument and eliminates the need for the time-consuming focusing operation. The microscopes described in the cited prior articles contained two-dimensional CCDs registered with two-dimensional arrays of microchannels and, as such, were designed to produce full two-dimensional images, without need for scanning. The microscopes of the present proposal would contain one-dimensional (line image) CCDs registered with linear arrays of microchannels. In the operation of such a microscope, one would scan a specimen along a line perpendicular to the array axis (in other words, one would scan in pushbroom fashion). One could then synthesize a full two-dimensional image of the specimen from the line-image data acquired at one-pixel increments of position along the scan. In one of the proposed microscopes, a beam of unpolarized light for illuminating the specimen would enter from the side. This light would be reflected down onto the specimen by a nonpolarizing beam splitter attached to the microchannels at their lower ends. A portion of the light incident on the specimen would be reflected upward, through the beam splitter and along the microchannels, to form an image on the CCD. If the

  8. Operating microscopes: past, present, and future.

    PubMed

    Uluç, Kutluay; Kujoth, Gregory C; Başkaya, Mustafa K

    2009-09-01

    The operating microscope is a fixture of modern surgical facilities, and it is a critically important factor in the success of many of the most complex and difficult surgical interventions used in medicine today. The rise of this key surgical tool reflects advances in understanding the principles of optics and vision that have occurred over centuries. The development of reading spectacles in the late 13th century led to the construction of early compound microscopes in the 16th and 17th centuries by Lippershey, Janssen, Galileo, Hooke, and others. Perhaps surprisingly, Leeuwenhoek's simple microscopes of this era offered improved performance over his contemporaries' designs. The intervening years saw improvements that reduced the spherical and chromatic aberrations present in compound microscopes. By the late 19th century, Carl Zeiss and Ernst Abbe ushered the compound microscope into the beginnings of the modern era of commercial design and production. The introduction of the microscope into the operating room by Nylén in 1921 initiated a revolution in surgical practice that gained momentum throughout the 1950s with multiple refinements, the introduction of the Zeiss OPMI series, and Kurze's application of the microscope to neurosurgery in 1957. Many of the refinements of the last 50 years have greatly improved the handling and practical operation of the surgical microscope, considerations which are equally important to its optical performance. Today's sophisticated operating microscopes allow for advanced real-time angiographic and tumor imaging. In this paper the authors discuss what might be found in the operating rooms of tomorrow.

  9. MicroRaman, PXRD, EDS and microscopic investigation of magnesium calcite biomineral phases. The case of sea urchin biominerals

    NASA Astrophysics Data System (ADS)

    Borzęcka-Prokop, B.; Wesełucha-Birczyńska, A.; Koszowska, E.

    2007-02-01

    This study concerns Mg-calcite characterization (and in particular molecular structure and microstructural studies of mineral phases) of a sea urchin mineralised test and spines. Sea urchins are spiny sea animals (kingdom Animalia, phylum Echinodermata, class Echinoidea). Microscopic observations, SEM, EDS, PXRD and spectroscopic microRaman methods have been applied to characterize the biomineral parts of the sea urchin. The latter technique is very useful in research of biological systems and especially suitable for monitoring differences within biomineral phases exhibiting varieties of morphological forms. Crystalline magnesium calcium carbonate, Mg xCa 1- xCO 3 (magnesian calcite; space group R-3 cH; a = 4.9594(8) Å, c = 16.886(6) Å), has been identified as the predominant biomineral component.

  10. Thermodynamic laws apply to brain function.

    PubMed

    Salerian, Alen J

    2010-02-01

    Thermodynamic laws and complex system dynamics govern brain function. Thus, any change in brain homeostasis by an alteration in brain temperature, neurotransmission or content may cause region-specific brain dysfunction. This is the premise for the Salerian Theory of Brain built upon a new paradigm for neuropsychiatric disorders: the governing influence of neuroanatomy, neurophysiology, thermodynamic laws. The principles of region-specific brain function thermodynamics are reviewed. The clinical and supporting evidence including the paradoxical effects of various agents that alter brain homeostasis is demonstrated.

  11. Thermodynamic Volume in AdS/CFT

    NASA Astrophysics Data System (ADS)

    Kim, Kyung Kiu; Ahn, Byoungjoon

    2018-01-01

    In this note, we study on extended thermodynamics of AdS black holes by varying cosmological constant. We found and discussed pressure and volume of both bulk and boundary physics through AdS/CFT correspondence. In particular, we derive the relation between thermodynamic volume and a chemical potential for M2 brane dual to four dimensional AdS space. In addition, we show that thermodynamic volume of hyperbolic black hole is related to `entanglement pressure' coming from a generalized first law of entanglement entropy.

  12. D-amino acids inhibit initial bacterial adhesion: thermodynamic evidence.

    PubMed

    Xing, Su-Fang; Sun, Xue-Fei; Taylor, Alicia A; Walker, Sharon L; Wang, Yi-Fu; Wang, Shu-Guang

    2015-04-01

    Bacterial biofilms are structured communities of cells enclosed in a self-produced hydrated polymeric matrix that can adhere to inert or living surfaces. D-Amino acids were previously identified as self-produced compounds that mediate biofilm disassembly by causing the release of the protein component of the polymeric matrix. However, whether exogenous D-amino acids could inhibit initial bacterial adhesion is still unknown. Here, the effect of the exogenous amino acid D-tyrosine on initial bacterial adhesion was determined by combined use of chemical analysis, force spectroscopic measurement, and theoretical predictions. The surface thermodynamic theory demonstrated that the total interaction energy increased with more D-tyrosine, and the contribution of Lewis acid-base interactions relative to the change in the total interaction energy was much greater than the overall nonspecific interactions. Finally, atomic force microscopy analysis implied that the hydrogen bond numbers and adhesion forces decreased with the increase in D-tyrosine concentrations. D-Tyrosine contributed to the repulsive nature of the cell and ultimately led to the inhibition of bacterial adhesion. This study provides a new way to regulate biofilm formation by manipulating the contents of D-amino acids in natural or engineered systems. © 2014 Wiley Periodicals, Inc.

  13. Inflight thermodynamic properties

    NASA Technical Reports Server (NTRS)

    Brown, S. C.; Daniels, G. E.; Johnson, D. L.; Smith, O. E.

    1973-01-01

    The inflight thermodynamic parameters (temperature, pressure, and density) of the atmosphere are presented. Mean and extreme values of the thermodynamic parameters given here can be used in application of many aerospace problems, such as: (1) research and planning and engineering design of remote earth sensing systems; (2) vehicle design and development; and (3) vehicle trajectory analysis, dealing with vehicle thrust, dynamic pressure, aerodynamic drag, aerodynamic heating, vibration, structural and guidance limitations, and reentry analysis. Atmospheric density plays a very important role in most of the above problems. A subsection on reentry is presented, giving atmospheric models to be used for reentry heating, trajectory, etc., analysis.

  14. The Theory of Thermodynamic Systems with Internal Variables of State: Necessary and Sufficient Conditions for Compliance with the Second Law of Thermodynamics

    NASA Astrophysics Data System (ADS)

    Shnip, A. I.

    2018-01-01

    Based on the entropy-free thermodynamic approach, a generalized theory of thermodynamic systems with internal variables of state is being developed. For the case of nonlinear thermodynamic systems with internal variables of state and linear relaxation, the necessary and sufficient conditions have been proved for fulfillment of the second law of thermodynamics in entropy-free formulation which, according to the basic theorem of the theory, are also necessary and sufficient for the existence of a thermodynamic potential. Moreover, relations of correspondence between thermodynamic systems with memory and systems with internal variables of state have been established, as well as some useful relations in the spaces of states of both types of systems.

  15. Thermodynamically consistent Langevin dynamics with spatially correlated noise predicting frictionless regime and transient attraction effect

    NASA Astrophysics Data System (ADS)

    Majka, M.; Góra, P. F.

    2016-10-01

    While the origins of temporal correlations in Langevin dynamics have been thoroughly researched, the understanding of spatially correlated noise (SCN) is rather incomplete. In particular, very little is known about the relation between friction and SCN. In this article, starting from the microscopic, deterministic model, we derive the analytical formula for the spatial correlation function in the particle-bath interactions. This expression shows that SCN is the inherent component of binary mixtures, originating from the effective (entropic) interactions. Further, employing this spatial correlation function, we postulate the thermodynamically consistent Langevin equation driven by the Gaussian SCN and calculate the adequate fluctuation-dissipation relation. The thermodynamical consistency is achieved by introducing the spatially variant friction coefficient, which can be also derived analytically. This coefficient exhibits a number of intriguing properties, e.g., the singular behavior for certain types of interactions. Eventually, we apply this new theory to the system of two charged particles in the presence of counter-ions. Such particles interact via the screened-charge Yukawa potential and the inclusion of SCN leads to the emergence of the anomalous frictionless regime. In this regime the particles can experience active propulsion leading to the transient attraction effect. This effect suggests a nonequilibrium mechanism facilitating the molecular binding of the like-charged particles.

  16. Automatic Focus Adjustment of a Microscope

    NASA Technical Reports Server (NTRS)

    Huntsberger, Terrance

    2005-01-01

    AUTOFOCUS is a computer program for use in a control system that automatically adjusts the position of an instrument arm that carries a microscope equipped with an electronic camera. In the original intended application of AUTOFOCUS, the imaging microscope would be carried by an exploratory robotic vehicle on a remote planet, but AUTOFOCUS could also be adapted to similar applications on Earth. Initially control software other than AUTOFOCUS brings the microscope to a position above a target to be imaged. Then the instrument arm is moved to lower the microscope toward the target: nominally, the target is approached from a starting distance of 3 cm in 10 steps of 3 mm each. After each step, the image in the camera is subjected to a wavelet transform, which is used to evaluate the texture in the image at multiple scales to determine whether and by how much the microscope is approaching focus. A focus measure is derived from the transform and used to guide the arm to bring the microscope to the focal height. When the analysis reveals that the microscope is in focus, image data are recorded and transmitted.

  17. Localized and Spectroscopic Orbitals: Squirrel Ears on Water.

    ERIC Educational Resources Information Center

    Martin, R. Bruce

    1988-01-01

    Reexamines the electronic structure of water considering divergent views. Discusses several aspects of molecular orbital theory using spectroscopic molecular orbitals and localized molecular orbitals. Gives examples for determining lowest energy spectroscopic orbitals. (ML)

  18. The Thermodynamics of Black Holes.

    PubMed

    Wald, Robert M

    2001-01-01

    We review the present status of black hole thermodynamics. Our review includes discussion of classical black hole thermodynamics, Hawking radiation from black holes, the generalized second law, and the issue of entropy bounds. A brief survey also is given of approaches to the calculation of black hole entropy. We conclude with a discussion of some unresolved open issues.

  19. Thermodynamics-Based Metabolic Flux Analysis

    PubMed Central

    Henry, Christopher S.; Broadbelt, Linda J.; Hatzimanikatis, Vassily

    2007-01-01

    A new form of metabolic flux analysis (MFA) called thermodynamics-based metabolic flux analysis (TMFA) is introduced with the capability of generating thermodynamically feasible flux and metabolite activity profiles on a genome scale. TMFA involves the use of a set of linear thermodynamic constraints in addition to the mass balance constraints typically used in MFA. TMFA produces flux distributions that do not contain any thermodynamically infeasible reactions or pathways, and it provides information about the free energy change of reactions and the range of metabolite activities in addition to reaction fluxes. TMFA is applied to study the thermodynamically feasible ranges for the fluxes and the Gibbs free energy change, ΔrG′, of the reactions and the activities of the metabolites in the genome-scale metabolic model of Escherichia coli developed by Palsson and co-workers. In the TMFA of the genome scale model, the metabolite activities and reaction ΔrG′ are able to achieve a wide range of values at optimal growth. The reaction dihydroorotase is identified as a possible thermodynamic bottleneck in E. coli metabolism with a ΔrG′ constrained close to zero while numerous reactions are identified throughout metabolism for which ΔrG′ is always highly negative regardless of metabolite concentrations. As it has been proposed previously, these reactions with exclusively negative ΔrG′ might be candidates for cell regulation, and we find that a significant number of these reactions appear to be the first steps in the linear portion of numerous biosynthesis pathways. The thermodynamically feasible ranges for the concentration ratios ATP/ADP, NAD(P)/NAD(P)H, and \\documentclass[10pt]{article} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{pmc} \\pagestyle{empty} \\oddsidemargin -1.0in \\begin{document} \\begin

  20. Spectroscopic profiling and computational study of the binding of tschimgine: A natural monoterpene derivative, with calf thymus DNA.

    PubMed

    Khajeh, Masoumeh Ashrafi; Dehghan, Gholamreza; Dastmalchi, Siavoush; Shaghaghi, Masoomeh; Iranshahi, Mehrdad

    2018-03-05

    DNA is a major target for a number of anticancer substances. Interaction studies between small molecules and DNA are essential for rational drug designing to influence main biological processes and also introducing new probes for the assay of DNA. Tschimgine (TMG) is a monoterpene derivative with anticancer properties. In the present study we tried to elucidate the interaction of TMG with calf thymus DNA (CT-DNA) using different spectroscopic methods. UV-visible absorption spectrophotometry, fluorescence and circular dichroism (CD) spectroscopies as well as molecular docking study revealed formation of complex between TMG and CT-DNA. Binding constant (K b ) between TMG and DNA was 2.27×10 4 M -1 , that is comparable to groove binding agents. The fluorescence spectroscopic data revealed that the quenching mechanism of fluorescence of TMG by CT-DNA is static quenching. Thermodynamic parameters (ΔH<0 and ΔS<0) at different temperatures indicated that van der Waals forces and hydrogen bonds were involved in the binding process of TMG with CT-DNA. Competitive binding assay with methylene blue (MB) and Hoechst 33258 using fluorescence spectroscopy displayed that TMG possibly binds to the minor groove of CT-DNA. These observations were further confirmed by CD spectral analysis, viscosity measurements and molecular docking. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Biophysical study on the interaction of ceftriaxone sodium with bovine serum albumin using spectroscopic methods.

    PubMed

    Pan, Jiongwei; Ye, Zaiting; Cai, Xiaoping; Wang, Liangxing; Cao, Zhuo

    2012-12-01

    The interaction of ceftriaxone sodium (CS), a cephalosporin antibiotic, with the major transport protein, bovine serum albumin (BSA), was investigated using different spectroscopic techniques such as fluorescence, circular dichroism (CD), and UV-vis spectroscopy. Values of binding parameters for BSA-CS interaction in terms of binding constant and number of binding sides were found to be 9.00 × 10(3), 3.24 × 10(3), and 2.30 × 10(3) M(-1) at 281, 301, and 321 K, respectively. Thermodynamic analysis of the binding data obtained at different temperatures showed that the binding process was spontaneous and was primarily mediated by van der Waals force or hydrogen bonding. CS binding to BSA caused secondary structural alterations in the protein as revealed by CD results. The distance between CS and Trp of BSA was determined as 3.23 nm according to the Förster resonance energy transfer theory. © 2012 Wiley Periodicals, Inc.

  2. A Student-Built Scanning Tunneling Microscope

    ERIC Educational Resources Information Center

    Ekkens, Tom

    2015-01-01

    Many introductory and nanotechnology textbooks discuss the operation of various microscopes including atomic force (AFM), scanning tunneling (STM), and scanning electron microscopes (SEM). In a nanotechnology laboratory class, students frequently utilize microscopes to obtain data without a thought about the detailed operation of the tool itself.…

  3. Thermodynamic DFT analysis of natural gas.

    PubMed

    Neto, Abel F G; Huda, Muhammad N; Marques, Francisco C; Borges, Rosivaldo S; Neto, Antonio M J C

    2017-08-01

    Density functional theory was performed for thermodynamic predictions on natural gas, whose B3LYP/6-311++G(d,p), B3LYP/6-31+G(d), CBS-QB3, G3, and G4 methods were applied. Additionally, we carried out thermodynamic predictions using G3/G4 averaged. The calculations were performed for each major component of seven kinds of natural gas and to their respective air + natural gas mixtures at a thermal equilibrium between room temperature and the initial temperature of a combustion chamber during the injection stage. The following thermodynamic properties were obtained: internal energy, enthalpy, Gibbs free energy and entropy, which enabled us to investigate the thermal resistance of fuels. Also, we estimated an important parameter, namely, the specific heat ratio of each natural gas; this allowed us to compare the results with the empirical functions of these parameters, where the B3LYP/6-311++G(d,p) and G3/G4 methods showed better agreements. In addition, relevant information on the thermal and mechanic resistance of natural gases were investigated, as well as the standard thermodynamic properties for the combustion of natural gas. Thus, we show that density functional theory can be useful for predicting the thermodynamic properties of natural gas, enabling the production of more efficient compositions for the investigated fuels. Graphical abstract Investigation of the thermodynamic properties of natural gas through the canonical ensemble model and the density functional theory.

  4. Transmission electron microscope CCD camera

    DOEpatents

    Downing, Kenneth H.

    1999-01-01

    In order to improve the performance of a CCD camera on a high voltage electron microscope, an electron decelerator is inserted between the microscope column and the CCD. This arrangement optimizes the interaction of the electron beam with the scintillator of the CCD camera while retaining optimization of the microscope optics and of the interaction of the beam with the specimen. Changing the electron beam energy between the specimen and camera allows both to be optimized.

  5. Information thermodynamics of near-equilibrium computation

    NASA Astrophysics Data System (ADS)

    Prokopenko, Mikhail; Einav, Itai

    2015-06-01

    In studying fundamental physical limits and properties of computational processes, one is faced with the challenges of interpreting primitive information-processing functions through well-defined information-theoretic as well as thermodynamic quantities. In particular, transfer entropy, characterizing the function of computational transmission and its predictability, is known to peak near critical regimes. We focus on a thermodynamic interpretation of transfer entropy aiming to explain the underlying critical behavior by associating information flows intrinsic to computational transmission with particular physical fluxes. Specifically, in isothermal systems near thermodynamic equilibrium, the gradient of the average transfer entropy is shown to be dynamically related to Fisher information and the curvature of system's entropy. This relationship explicitly connects the predictability, sensitivity, and uncertainty of computational processes intrinsic to complex systems and allows us to consider thermodynamic interpretations of several important extreme cases and trade-offs.

  6. Spectroscopic studies on the interaction of bovine serum albumin with surfactants and apigenin

    NASA Astrophysics Data System (ADS)

    Zhao, Xu-Na; Liu, Yi; Niu, Li-Yuan; Zhao, Chen-Ping

    The binding of apigenin (Ap) to bovine serum albumin (BSA) has been studied using the methods of fluorescence spectroscopy and UV-vis absorption spectroscopy. The spectroscopic analysis of the quenching mechanism indicates that the quenching constants are inversely correlated with the temperatures and the quenching process could result from a static interaction. The type of interaction force was discussed and the binding site of Ap was in site I (subdomain IIA) of BSA. The thermodynamic parameters ΔH and ΔS are -42.02 kJ mol-1 and -48.31 J mol-1 K-1, respectively and the negative ΔG implying that the binding interaction was spontaneous. The distance r between BSA and Ap was calculated according to Förster's theory and the value is 3.44 nm. The synchronous and three-dimensional fluorescence spectra show that the binding of Ap to BSA could lead to the changes in the conformation and microenvironment of BSA. At the same time, the effects of ionic surfactants on the interaction of Ap and BSA have also been investigated.

  7. Spectroscopic Study of the Binding of Netropsin and Hoechst 33258 to Nucleic Acids

    NASA Astrophysics Data System (ADS)

    Vardevanyan, P. O.; Parsadanyan, M. A.; Antonyan, A. P.; Sahakyan, V. G.

    2018-05-01

    The interaction of groove binding compounds — peptide antibiotic (polyamide) netropsin and fluorescent dye (bisbenzimidazole) Hoechst 33258 — with the double-stranded DNA and synthetic double-stranded polynucleotide poly(rA)-poly(rU) has been studied by spectrophotometry. Absorption spectra of these ligand complexes with nucleic acids have been obtained. Spectral changes at the complexation of individual ligands with the mentioned nucleic acids reveal the similarity of binding of each of these ligands with both DNA and RNA. Based on the spectroscopic measurements, the binding parameters of netropsin and Hoechst 33258 binding to DNA and poly(rA)-poly(rU) - K and n, as well as the thermodynamic parameters ΔS, ΔG, and ΔH have been determined. It was found that the binding of Hoechst 33258 to both nucleic acids is accompanied by a positive change in enthalpy, while in the case of netropsin the change in enthalpy is negative. Moreover, the contribution of entropy to the formation of the complexes is more pronounced in the case of Hoechst 33258.

  8. The discovery of thermodynamics

    NASA Astrophysics Data System (ADS)

    Weinberger, Peter

    2013-07-01

    Based on the idea that a scientific journal is also an "agora" (Greek: market place) for the exchange of ideas and scientific concepts, the history of thermodynamics between 1800 and 1910 as documented in the Philosophical Magazine Archives is uncovered. Famous scientists such as Joule, Thomson (Lord Kelvin), Clausius, Maxwell or Boltzmann shared this forum. Not always in the most friendly manner. It is interesting to find out, how difficult it was to describe in a scientific (mathematical) language a phenomenon like "heat", to see, how long it took to arrive at one of the fundamental principles in physics: entropy. Scientific progress started from the simple rule of Boyle and Mariotte dating from the late eighteenth century and arrived in the twentieth century with the concept of probabilities. Thermodynamics was the driving intellectual force behind the industrial revolution, behind the enormous social changes caused by this revolution. The history of thermodynamics is a fascinating story, which also gives insights into the mechanism that seem to govern science.

  9. Concentration dependent switch in the kinetic pathway of lysozyme fibrillation: Spectroscopic and microscopic analysis

    NASA Astrophysics Data System (ADS)

    Kiran Kumar, E.; Prasad, Deepak Kumar; Prakash Prabhu, N.

    2017-08-01

    Formation of amyloid fibrils is found to be a general tendency of many proteins. Investigating the kinetic mechanisms and structural features of the intermediates and the final fibrillar state is essential to understand their role in amyloid diseases. Lysozyme, a notable model protein for amyloidogenic studies, readily formed fibrils in vitro at neutral pH in the presence of urea. It, however, showed two different kinetic pathways under varying urea concentrations when probed with thioflavin T (ThT) fluorescence. In 2 M urea, lysozyme followed a nucleation-dependent fibril formation pathway which was not altered by varying the protein concentration from 2 mg/ml to 8 mg/ml. In 4 M urea, the protein exhibited concentration dependent change in the mechanism. At lower protein concentrations, lysozyme formed fibrils without any detectable nuclei (nucleation-independent polymerization pathway). When the concentration of the protein was increased above 3 mg/ml, the protein followed nucleation-dependent polymerization pathway as observed in the case of 2 M urea condition. This was further verified using microscopic images of the fibrils. The kinetic parameters such as lag time, elongation rate, and fibrillation half-time, which were derived from ThT fluorescence changes, showed linear dependency against the initial protein concentration suggested that under the nucleation-dependent pathway conditions, the protein followed primary-nucleation mechanism without any significant secondary nucleation events. The results also suggested that the differences in the initial protein conformation might alter the mechanism of fibrillation; however, at the higher protein concentrations lysozyme shifted to nucleation-dependent pathway.

  10. Characterising protein, salt and water interactions with combined vibrational spectroscopic techniques.

    PubMed

    Perisic, Nebojsa; Afseth, Nils Kristian; Ofstad, Ragni; Hassani, Sahar; Kohler, Achim

    2013-05-01

    In this paper a combination of NIR spectroscopy and FTIR and Raman microspectroscopy was used to elucidate the effects of different salts (NaCl, KCl and MgSO(4)) on structural proteins and their hydration in muscle tissue. Multivariate multi-block technique Consensus Principal Component Analysis enabled integration of different vibrational spectroscopic techniques: macroscopic information obtained by NIR spectroscopy is directly related to microscopic information obtained by FTIR and Raman microspectroscopy. Changes in protein secondary structure observed at different concentrations of salts were linked to changes in protein hydration affinity. The evidence for this was given by connecting the underlying FTIR bands of the amide I region (1700-1600 cm(-1)) and the water region (3500-3000 cm(-1)) with water vibrations obtained by NIR spectroscopy. In addition, Raman microspectroscopy demonstrated that different cations affected structures of aromatic amino acid residues differently, which indicates that cation-π interactions play an important role in determination of the final structure of protein molecules. Copyright © 2012 Elsevier Ltd. All rights reserved.

  11. Dual Raman-Brillouin spectroscopic investigation of plant stress response and development

    NASA Astrophysics Data System (ADS)

    Coker, Zachary; Troyanova-Wood, Maria; Marble, Kassie; Yakovlev, Vladislav

    2018-03-01

    Raman and Brillouin spectroscopy are powerful tools for non-invasive and non-destructive investigations of material chemical and mechanical properties. In this study, we use a newly developed custom-built dual Raman-Brillouin microspectroscopy instrument to build on previous works studying in-vivo stress response of live plants using only a Raman spectroscopy system. This dual Raman-Brillouin spectroscopy system is capable of fast simultaneous spectra acquisition from single-point locations. Shifts and changes in a samples Brillouin spectrum indicate a change in the physical characteristics of the sample, namely mechano-elasticity; in measuring this change, we can establish a relationship between the mechanical properties of a sample and known stress response agents, such as reactive oxygen species and other chemical constituents as indicated by peaks in the Raman spectra of the same acquisition point. Simultaneous application of these spectroscopic techniques offers great promise for future development and applications in agricultural and biological studies and can help to improve our understanding of mechanochemical changes of plants and other biological samples in response to environmental and chemically induced stresses at microscopic or cellular level.

  12. The metallicity of M4: Accurate spectroscopic fundamental parameters for four giants

    NASA Technical Reports Server (NTRS)

    Drake, J. J.; Smith, V. V.; Suntzeff, N. B.

    1994-01-01

    High-quality spectra, covering the wavelength range 5480 to 7080 A, have been obtained for four giant stars in the intermediate-metallicity CN-bimodal globular cluster M4 (NGC 6121). We have employed a model atmosphere analysis that is entirely independent from cluster parameters, such as distance, age, and reddening, in order to derive accurate values for the stellar parameters effective temperature, surface gravity, and microturbulence, and for the abundance of iron relative to the Sun, (Fe/H), and of calcium, Ca/H, for each of the four stars. Detailed radiative transfer and statistical equilibrium calculations carried out for iron and calcium suggest that departures from local thermodynamic equilibrium are not significant for the purposes of our analysis. The spectroscopically derived effective temperatures for our program stars are hotter by about 200 K than existing photometric calibrations suggest. We conclude that this is due partly to the uncertain reddening of M4 and to the existing photometric temperature calibration for red giants being too cool by about 100 K. Comparison of our spectroscopic and existing photometric temperatures supports the prognosis of a significant east-west gradient in the reddening across M4. Our derived iron abundances are slightly higher than previous high-resolution studies suggested; the differences are most probably due to the different temperature scale and choice of microturbulent velocities adopted by earlier workers. The resulting value for the metallicity of M4 is (Fe/H )(sub M4) = -1.05 + or - 0.15. Based on this result, we suggest that metallicities derived in previous high-dispersion globular cluster abundance analyses could be too low by 0.2 to 0.3 dex. Our calcium abundances suggest an enhancement of calcium, an alpha element, over iron, relative to the Sun, in M4 of (Ca/H) = 0.23.

  13. The role of thermodynamics in biochemical engineering

    NASA Astrophysics Data System (ADS)

    von Stockar, Urs

    2013-09-01

    This article is an adapted version of the introductory chapter of a book whose publication is imminent. It bears the title "Biothermodynamics - The role of thermodynamics in biochemical engineering." The aim of the paper is to give a very short overview of the state of biothermodynamics in an engineering context as reflected in this book. Seen from this perspective, biothermodynamics may be subdivided according to the scale used to formalize the description of the biological system into three large areas: (i) biomolecular thermodynamics (most fundamental scale), (ii) thermodynamics of metabolism (intermediary scale), and (iii) whole-cell thermodynamics ("black-box" description of living entities). In each of these subareas, the main available theoretical approaches and the current and the potential applications are discussed. Biomolecular thermodynamics (i) is especially well developed and is obviously highly pertinent for the development of downstream processing. Its use ought to be encouraged as much as possible. The subarea of thermodynamics of live cells (iii), although scarcely applied in practice, is also expected to enhance bioprocess research and development, particularly in predicting culture performances, for understanding the driving forces for cellular growth, and in developing, monitoring, and controlling cellular cultures. Finally, there is no question that thermodynamic analysis of cellular metabolism (ii) is a promising tool for systems biology and for many other applications, but quite a large research effort is still needed before it may be put to practical use.

  14. Statistical thermodynamics of clustered populations.

    PubMed

    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.

  15. Development of Thermodynamic Conceptual Evaluation

    NASA Astrophysics Data System (ADS)

    Talaeb, P.; Wattanakasiwich, P.

    2010-07-01

    This research aims to develop a test for assessing student understanding of fundamental principles in thermodynamics. Misconceptions found from previous physics education research were used to develop the test. Its topics include heat and temperature, the zeroth and the first law of thermodynamics, and the thermodynamics processes. The content validity was analyzed by three physics experts. Then the test was administered to freshmen, sophomores and juniors majored in physics in order to determine item difficulties and item discrimination of the test. A few items were eliminated from the test. Finally, the test will be administered to students taking Physics I course in order to evaluate the effectiveness of Interactive Lecture Demonstrations that will be used for the first time at Chiang Mai University.

  16. Mars Life? - Microscopic Tubular Structures

    NASA Technical Reports Server (NTRS)

    1996-01-01

    This electron microscope image shows extremely tiny tubular structures that are possible microscopic fossils of bacteria-like organisms that may have lived on Mars more than 3.6 billion years ago. A two-year investigation by a NASA research team found organic molecules, mineral features characteristic of biological activity and possible microscopic fossils such as these inside of an ancient Martian rock that fell to Earth as a meteorite. The largest possible fossils are less than 1/100th the diameter of a human hair in size while most are ten times smaller. The fossil-like structures were found in carbonate minerals formed along pre-existing fractures in the meteorite in a fashion similar to the way fossils occur in limestone on Earth, although on a microscopic scale.

  17. Size- and shape-dependent surface thermodynamic properties of nanocrystals

    NASA Astrophysics Data System (ADS)

    Fu, Qingshan; Xue, Yongqiang; Cui, Zixiang

    2018-05-01

    As the fundamental properties, the surface thermodynamic properties of nanocrystals play a key role in the physical and chemical changes. However, it remains ambiguous about the quantitative influence regularities of size and shape on the surface thermodynamic properties of nanocrystals. Thus by introducing interface variables into the Gibbs energy and combining Young-Laplace equation, relations between the surface thermodynamic properties (surface Gibbs energy, surface enthalpy, surface entropy, surface energy and surface heat capacity), respectively, and size of nanocrystals with different shapes were derived. Theoretical estimations of the orders of the surface thermodynamic properties of nanocrystals agree with available experimental values. Calculated results of the surface thermodynamic properties of Au, Bi and Al nanocrystals suggest that when r > 10 nm, the surface thermodynamic properties linearly vary with the reciprocal of particle size, and when r < 10 nm, the effect of particle size on the surface thermodynamic properties becomes greater and deviates from linear variation. For nanocrystals with identical equivalent diameter, the more the shape deviates from sphere, the larger the surface thermodynamic properties (absolute value) are.

  18. Cantera and Cantera Electrolyte Thermodynamics Objects

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    John Hewson, Harry Moffat

    Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. It is a multi-organizational effort to create and formulate high quality 0D and 1D constitutive modeling tools for reactive transport codes.Institutions involved with the effort include Sandia, MIT, Colorado School of Mines, U. Texas, NASA, and Oak Ridge National Labs. Specific to Sandia's contributions, the Cantera Electrolyte Thermo Objects (CETO) packages is comprised of add-on routines for Cantera that handle electrolyte thermochemistry and reactions within the overall Cantera package. Cantera is a C++ Cal Tech code that handles gas phase species transport, reaction,more » and thermodynamics. With this addition, Cantera can be extended to handle problems involving liquid phase reactions and transport in electrolyte systems, and phase equilibrium problemsinvolving concentrated electrolytes and gas/solid phases. A full treatment of molten salt thermodynamics and transport has also been implemented in CETO. The routines themselves consist of .cpp and .h files containing C++ objects that are derived from parent Cantera objects representing thermodynamic functions. They are linked unto the main Cantera libraries when requested by the user. As an addendum to the main thermodynamics objects, several utility applications are provided. The first is multiphase Gibbs free energy minimizer based on the vcs algorithm, called vcs_cantera. This code allows for the calculation of thermodynamic equilibrium in multiple phases at constant temperature and pressure. Note, a similar code capability exists already in Cantera. This version follows the same algorithm, but gas a different code-base starting point, and is used as a research tool for algorithm development. The second program, cttables, prints out tables of thermodynamic and kinetic information for thermodynamic and kinetic objects within Cantera. This program serves as a "Get the

  19. Mechanics, Waves and Thermodynamics

    NASA Astrophysics Data System (ADS)

    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.

  20. Thermodynamics of micellization from heat-capacity measurements.

    PubMed

    Šarac, Bojan; Bešter-Rogač, Marija; Lah, Jurij

    2014-06-23

    Differential scanning calorimetry (DSC), the most important technique for studying the thermodynamics of structural transitions of biological macromolecules, is seldom used in quantitative thermodynamic studies of surfactant micellization/demicellization. The reason for this could be ascribed to an insufficient understanding of the temperature dependence of the heat capacity of surfactant solutions (DSC data) in terms of thermodynamics, which leads to problems with the design of experiments and interpretation of the output signals. We address these issues by careful design of DSC experiments performed with solutions of ionic and nonionic surfactants at various surfactant concentrations, and individual and global mass-action model analysis of the obtained DSC data. Our approach leads to reliable thermodynamic parameters of micellization for all types of surfactants, comparable with those obtained by using isothermal titration calorimetry (ITC). In summary, we demonstrate that DSC can be successfully used as an independent method to obtain temperature-dependent thermodynamic parameters for micellization. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. An Experimental Determination of Thermodynamic Values

    ERIC Educational Resources Information Center

    Antony, Erling; Muccianti, Christine; Vogel, Tracy

    2012-01-01

    Measurements have been added to an old demonstration of chemical equilibria allowing the determination of thermodynamic constants. The experiment allows the students an opportunity to merge qualitative observations associated with Le Chatelier's principle and thermodynamic calculations using graphical techniques. (Contains 4 figures.)

  2. Irreversible thermodynamics of Poisson processes with reaction.

    PubMed

    Méndez, V; Fort, J

    1999-11-01

    A kinetic model is derived to study the successive movements of particles, described by a Poisson process, as well as their generation. The irreversible thermodynamics of this system is also studied from the kinetic model. This makes it possible to evaluate the differences between thermodynamical quantities computed exactly and up to second-order. Such differences determine the range of validity of the second-order approximation to extended irreversible thermodynamics.

  3. Predictive thermodynamics for ionic solids and liquids.

    PubMed

    Glasser, Leslie; Jenkins, H Donald Brooke

    2016-08-21

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

  4. Scanning Microscopes Using X Rays and Microchannels

    NASA Technical Reports Server (NTRS)

    Wang, Yu

    2003-01-01

    Scanning microscopes that would be based on microchannel filters and advanced electronic image sensors and that utilize x-ray illumination have been proposed. Because the finest resolution attainable in a microscope is determined by the wavelength of the illumination, the xray illumination in the proposed microscopes would make it possible, in principle, to achieve resolutions of the order of nanometers about a thousand times as fine as the resolution of a visible-light microscope. Heretofore, it has been necessary to use scanning electron microscopes to obtain such fine resolution. In comparison with scanning electron microscopes, the proposed microscopes would likely be smaller, less massive, and less expensive. Moreover, unlike in scanning electron microscopes, it would not be necessary to place specimens under vacuum. The proposed microscopes are closely related to the ones described in several prior NASA Tech Briefs articles; namely, Miniature Microscope Without Lenses (NPO-20218), NASA Tech Briefs, Vol. 22, No. 8 (August 1998), page 43; and Reflective Variants of Miniature Microscope Without Lenses (NPO-20610), NASA Tech Briefs, Vol. 26, No. 9 (September 2002) page 6a. In all of these microscopes, the basic principle of design and operation is the same: The focusing optics of a conventional visible-light microscope are replaced by a combination of a microchannel filter and a charge-coupled-device (CCD) image detector. A microchannel plate containing parallel, microscopic-cross-section holes much longer than they are wide is placed between a specimen and an image sensor, which is typically the CCD. The microchannel plate must be made of a material that absorbs the illuminating radiation reflected or scattered from the specimen. The microchannels must be positioned and dimensioned so that each one is registered with a pixel on the image sensor. Because most of the radiation incident on the microchannel walls becomes absorbed, the radiation that reaches the

  5. Thermal, spectroscopic, and ab initio structural characterization of carprofen polymorphs.

    PubMed

    Bruni, Giovanna; Gozzo, Fabia; Capsoni, Doretta; Bini, Marcella; Macchi, Piero; Simoncic, Petra; Berbenni, Vittorio; Milanese, Chiara; Girella, Alessandro; Ferrari, Stefania; Marini, Amedeo

    2011-06-01

    Commercial and recrystallized polycrystalline samples of carprofen, a nonsteroidal anti-inflammatory drug, were studied by thermal, spectroscopic, and structural techniques. Our investigations demonstrated that recrystallized sample, stable at room temperature (RT), is a single polymorphic form of carprofen (polymorph I) that undergoes an isostructural polymorphic transformation by heating (polymorph II). Polymorph II remains then metastable at ambient conditions. Commercial sample is instead a mixture of polymorphs I and II. The thermodynamic relationships between the two polymorphs were determined through the construction of an energy/temperature diagram. The ab initio structural determination performed on synchrotron X-Ray powder diffraction patterns recorded at RT on both polymorphs allowed us to elucidate, for the first time, their crystal structure. Both crystallize in the monoclinic space group type P2(1) /c, and the unit cell similarity index and the volumetric isostructurality index indicate that the temperature-induced polymorphic transformation I → II is isostructural. Polymorphs I and II are conformational polymorphs, sharing a very similar hydrogen bond network, but with different conformation of the propanoic skeleton, which produces two different packing. The small conformational change agrees with the low value of transition enthalpy obtained by differential scanning calorimetry measurements and the small internal energy computed with density functional methods. Copyright © 2011 Wiley-Liss, Inc.

  6. Simulating Metabolism with Statistical Thermodynamics

    PubMed Central

    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. PMID:25089525

  7. Simulating metabolism with statistical thermodynamics.

    PubMed

    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.

  8. Binding thermodynamics discriminates fragments from druglike compounds: a thermodynamic description of fragment-based drug discovery.

    PubMed

    Williams, Glyn; Ferenczy, György G; Ulander, Johan; Keserű, György M

    2017-04-01

    Small is beautiful - reducing the size and complexity of chemical starting points for drug design allows better sampling of chemical space, reveals the most energetically important interactions within protein-binding sites and can lead to improvements in the physicochemical properties of the final drug. The impact of fragment-based drug discovery (FBDD) on recent drug discovery projects and our improved knowledge of the structural and thermodynamic details of ligand binding has prompted us to explore the relationships between ligand-binding thermodynamics and FBDD. Information on binding thermodynamics can give insights into the contributions to protein-ligand interactions and could therefore be used to prioritise compounds with a high degree of specificity in forming key interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Using Rubber-Elastic Material-Ideal Gas Analogies To Teach Introductory Thermodynamics. Part II: The Laws of Thermodynamics.

    ERIC Educational Resources Information Center

    Smith, Brent

    2002-01-01

    Describes the laws of thermodynamics as a supplement to an introductory thermodynamics undergraduate course. Uses rubber-elastic materials (REM) which have strong analogies to the concept of ideal gas. Provides examples of the analogies between ideal gas and REM and mathematical analogies. (YDS)

  10. Two-state thermodynamics and the possibility of a liquid-liquid phase transition in supercooled TIP4P/2005 water

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Singh, Rakesh S.; Debenedetti, Pablo G.; Biddle, John W.

    Water shows intriguing thermodynamic and dynamic anomalies in the supercooled liquid state. One possible explanation of the origin of these anomalies lies in the existence of a metastable liquid-liquid phase transition (LLPT) between two (high and low density) forms of water. While the anomalies are observed in experiments on bulk and confined water and by computer simulation studies of different water-like models, the existence of a LLPT in water is still debated. Unambiguous experimental proof of the existence of a LLPT in bulk supercooled water is hampered by fast ice nucleation which is a precursor of the hypothesized LLPT. Moreover,more » the hypothesized LLPT, being metastable, in principle cannot exist in the thermodynamic limit (infinite size, infinite time). Therefore, computer simulations of water models are crucial for exploring the possibility of the metastable LLPT and the nature of the anomalies. In this work, we present new simulation results in the NVT ensemble for one of the most accurate classical molecular models of water, TIP4P/2005. To describe the computed properties and explore the possibility of a LLPT, we have applied two-structure thermodynamics, viewing water as a non-ideal mixture of two interconvertible local structures (“states”). The results suggest the presence of a liquid-liquid critical point and are consistent with the existence of a LLPT in this model for the simulated length and time scales. We have compared the behavior of TIP4P/2005 with other popular water-like models, namely, mW and ST2, and with real water, all of which are well described by two-state thermodynamics. In view of the current debate involving different studies of TIP4P/2005, we discuss consequences of metastability and finite size in observing the liquid-liquid separation. We also address the relationship between the phenomenological order parameter of two-structure thermodynamics and the microscopic nature of the low-density structure.« less

  11. Spectroscopic studies of the interaction mechanisms between mono-caffeoylquinic acids and transferrin

    NASA Astrophysics Data System (ADS)

    Guan, Yanqing; Dong, Jing; Chen, Shizhong; Liu, Meixian; Wang, Daidong; Zhang, Xiaotian; Wang, Hong; Lin, Zongtao

    2017-06-01

    Transferrin (Tf) is an important protein responsible for circulating and transporting iron into cytoplasm. Tf can be taken into cells through endocytosis mediated by Tf receptor, which usually overexpresses in cancer cells. The Tf-Tf receptor pathway opens a possible avenue for novel targeted cancer therapy by utilizing Tf-binding active compounds. Among which, anti-cancer active caffeoylquinic acids (CQAs) were recently found to be promising Tf-binders by our group. For better understanding the anti-cancer activities of CQAs, it is important to unveil the binding mechanisms between CQAs and Tf. In this study, the fluorescence quenching, surface plasmon resonance (SPR), circular dichroism (CD) and molecular docking were used to investigate the interactions between CQA and Tf. The results showed that the calculated apparent association constants of interactions between 1-, 3-, 4- and 5-CQA and Tf at 298 K were 7.97 × 105 M- 1, 4.36 × 107 M- 1, 6.58 × 105 M- 1 and 4.42 × 106 M- 1, respectively. The thermodynamic parameters indicated that the interaction between 1-, 3-, 5-CQA and Tf is due to H-bonding, and electrostatic interactions were likely involved in the binding of 4-CQA and Tf. The CD results indicated that bindings of 1-CQA, 4-CQA and 5-CQA with Tf resulted in more stretched β-turn and random coil translated from β-sheet. In contrast, 3-CQA led to more stable a-helix conformation. Molecular docking studies of CQAs with Tf further displayed that CQAs were able to interact with residues near Fe3 + binding site. The spectroscopic studies revealed the action mechanisms, thermodynamics and interacting forces between CQAs and Tf, and thus are helpful for future design and discovery of Tf-binders for targeted cancer therapy applying Tf-Tf receptor pathway.

  12. Development of an ultrasound microscope combined with optical microscope for multiparametric characterization of a single cell.

    PubMed

    Arakawa, Mototaka; Shikama, Joe; Yoshida, Koki; Nagaoka, Ryo; Kobayashi, Kazuto; Saijo, Yoshifumi

    2015-09-01

    Biomechanics of the cell has been gathering much attention because it affects the pathological status in atherosclerosis and cancer. In the present study, an ultrasound microscope system combined with optical microscope for characterization of a single cell with multiple ultrasound parameters was developed. The central frequency of the transducer was 375 MHz and the scan area was 80 × 80 μm with up to 200 × 200 sampling points. An inverted optical microscope was incorporated in the design of the system, allowing for simultaneous optical observations of cultured cells. Two-dimensional mapping of multiple ultrasound parameters, such as sound speed, attenuation, and acoustic impedance, as well as the thickness, density, and bulk modulus of specimen/cell under investigation, etc., was realized by the system. Sound speed and thickness of a 3T3-L1 fibroblast cell were successfully obtained by the system. The ultrasound microscope system combined with optical microscope further enhances our understanding of cellular biomechanics.

  13. Imaging Schwarzschild multilayer X-ray microscope

    NASA Technical Reports Server (NTRS)

    Hoover, Richard B.; Baker, Phillip C.; Shealy, David L.; Core, David B.; Walker, Arthur B. C., Jr.; Barbee, Troy W., Jr.; Kerstetter, Ted

    1993-01-01

    We have designed, analyzed, fabricated, and tested Schwarzschild multilayer X-ray microscopes. These instruments use flow-polished Zerodur mirror substrates which have been coated with multilayers optimized for maximum reflectivity at normal incidence at 135 A. They are being developed as prototypes for the Water Window Imaging X-Ray Microscope. Ultrasmooth mirror sets of hemlite grade sapphire have been fabricated and they are now being coated with multilayers to reflect soft X-rays at 38 A, within the biologically important 'water window'. In this paper, we discuss the fabrication of the microscope optics and structural components as well as the mounting of the optics and assembly of the microscopes. We also describe the optical alignment, interferometric and visible light testing of the microscopes, present interferometrically measured performance data, and provide the first results of optical imaging tests.

  14. Handbook of Basic Atomic Spectroscopic Data

    National Institute of Standards and Technology Data Gateway

    SRD 108 Handbook of Basic Atomic Spectroscopic Data (Web, free access)   This handbook provides a selection of the most important and frequently used atomic spectroscopic data. The compilation includes data for the neutral and singly-ionized atoms of all elements hydrogen through einsteinium (Z = 1-99). The wavelengths, intensities, and spectrum assignments are given for each element, and the data for the approximately 12,000 lines of all elements are also collected into a single table.

  15. Mars Life? - Microscopic Tubular Structures

    NASA Image and Video Library

    1996-08-09

    This electron microscope image shows extremely tiny tubular structures that are possible microscopic fossils of bacteria-like organisms that may have lived on Mars more than 3.6 billion years ago. http://photojournal.jpl.nasa.gov/catalog/PIA00285

  16. Q: How do Microscopes Work?

    ERIC Educational Resources Information Center

    Zimov, Sarah

    2004-01-01

    Microscopes allow scientists to examine everyday objects in extraordinary ways. They provide high-resolution images that show objects in fine detail. This brief article describes the many types of microscopes and how they are used in different scientific venues.

  17. Thermodynamics of Small Alkali Metal Halide Cluster Ions: Comparison of Classical Molecular Simulations with Experiment and Quantum Chemistry

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Vlcek, Lukas; Uhlik, Filip; Moucka, Filip

    We evaluate the ability of selected classical molecular models to describe the thermodynamic and structural aspects of gas-phase hydration of alkali halide ions and the formation of small water clusters. To understand the effect of many-body interactions (polarization) and charge penetration effects on the accuracy of a force field, we perform Monte Carlo simulations with three rigid water models using different functional forms to account for these effects: (i) point charge non-polarizable SPC/E, (ii) Drude point charge polarizable SWM4- DP, and (iii) Drude Gaussian charge polarizable BK3. Model predictions are compared with experimental Gibbs free energies and enthalpies of ionmore » hydration, and with microscopic structural properties obtained from quantum DFT calculations. We find that all three models provide comparable predictions for pure water clusters and cation hydration, but differ significantly in their description of anion hydration. None of the investigated classical force fields can consistently and quantitatively reproduce the experimental gas phase hydration thermodynamics. The outcome of this study highlights the relation between the functional form that describes the effective intermolecular interactions and the accuracy of the resulting ion hydration properties.« less

  18. On the importance of image formation optics in the design of infrared spectroscopic imaging systems

    PubMed Central

    Mayerich, David; van Dijk, Thomas; Walsh, Michael; Schulmerich, Matthew; Carney, P. Scott

    2014-01-01

    Infrared spectroscopic imaging provides micron-scale spatial resolution with molecular contrast. While recent work demonstrates that sample morphology affects the recorded spectrum, considerably less attention has been focused on the effects of the optics, including the condenser and objective. This analysis is extremely important, since it will be possible to understand effects on recorded data and provides insight for reducing optical effects through rigorous microscope design. Here, we present a theoretical description and experimental results that demonstrate the effects of commonly-employed cassegranian optics on recorded spectra. We first combine an explicit model of image formation and a method for quantifying and visualizing the deviations in recorded spectra as a function of microscope optics. We then verify these simulations with measurements obtained from spatially heterogeneous samples. The deviation of the computed spectrum from the ideal case is quantified via a map which we call a deviation map. The deviation map is obtained as a function of optical elements by systematic simulations. Examination of deviation maps demonstrates that the optimal optical configuration for minimal deviation is contrary to prevailing practice in which throughput is maximized for an instrument without a sample. This report should be helpful for understanding recorded spectra as a function of the optics, the analytical limits of recorded data determined by the optical design, and potential routes for optimization of imaging systems. PMID:24936526

  19. On the importance of image formation optics in the design of infrared spectroscopic imaging systems.

    PubMed

    Mayerich, David; van Dijk, Thomas; Walsh, Michael J; Schulmerich, Matthew V; Carney, P Scott; Bhargava, Rohit

    2014-08-21

    Infrared spectroscopic imaging provides micron-scale spatial resolution with molecular contrast. While recent work demonstrates that sample morphology affects the recorded spectrum, considerably less attention has been focused on the effects of the optics, including the condenser and objective. This analysis is extremely important, since it will be possible to understand effects on recorded data and provides insight for reducing optical effects through rigorous microscope design. Here, we present a theoretical description and experimental results that demonstrate the effects of commonly-employed cassegranian optics on recorded spectra. We first combine an explicit model of image formation and a method for quantifying and visualizing the deviations in recorded spectra as a function of microscope optics. We then verify these simulations with measurements obtained from spatially heterogeneous samples. The deviation of the computed spectrum from the ideal case is quantified via a map which we call a deviation map. The deviation map is obtained as a function of optical elements by systematic simulations. Examination of deviation maps demonstrates that the optimal optical configuration for minimal deviation is contrary to prevailing practice in which throughput is maximized for an instrument without a sample. This report should be helpful for understanding recorded spectra as a function of the optics, the analytical limits of recorded data determined by the optical design, and potential routes for optimization of imaging systems.

  20. Simulated pressure denaturation thermodynamics of ubiquitin.

    PubMed

    Ploetz, Elizabeth A; Smith, Paul E

    2017-12-01

    Simulations of protein thermodynamics are generally difficult to perform and provide limited information. It is desirable to increase the degree of detail provided by simulation and thereby the potential insight into the thermodynamic properties of proteins. In this study, we outline how to analyze simulation trajectories to decompose conformation-specific, parameter free, thermodynamically defined protein volumes into residue-based contributions. The total volumes are obtained using established methods from Fluctuation Solution Theory, while the volume decomposition is new and is performed using a simple proximity method. Native and fully extended ubiquitin are used as the test conformations. Changes in the protein volumes are then followed as a function of pressure, allowing for conformation-specific protein compressibility values to also be obtained. Residue volume and compressibility values indicate significant contributions to protein denaturation thermodynamics from nonpolar and coil residues, together with a general negative compressibility exhibited by acidic residues. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Geometry and Thermodynamics: Exploring the Internal Energy Landscape

    ERIC Educational Resources Information Center

    Hantsaridou, A. P.; Polatoglou, H. M.

    2006-01-01

    If we look into the past we will discover that the teachers of thermodynamics were always trying to interpret an important part of their science by using geometry. The relation between geometry and thermodynamics is of great interest and importance in teaching thermodynamics. This article examines the way undergraduate students of thermodynamics…

  2. Thermodynamic, spectroscopic, and computational studies of lanthanide complexation with Diethylenetriaminepentaacetic acide: temperature effect and coordination modes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Guoxin Tian; Leigh R. Martin; Zhiyong Zhang

    2011-04-01

    Stability constants of two DTPA (diethylenetriaminepentaacetic acid) complexes with lanthanides (ML2- and MHL-, where M stands for Nd and Eu and L stands for diethylenetriaminepentaacetate) at 10, 25, 40, 55, and 70 degrees C were determined by potentiometry, absorption spectrophotometry, and luminescence spectroscopy. The enthalpies of complexation at 25 degrees C were determined by microcalorimetry. Thermodynamic data show that the complexation of Nd3þ and Eu3þ with DTPA is weakened at higher temperatures, a 10-fold decrease in the stability constants of ML2- and MHL- as the temperature is increased from 10 to 70 degrees C. The effect of temperature is consistentmore » with the exothermic enthalpy of complexation directly measured by microcalorimetry. Results by luminescence spectroscopy and density functional theory (DFT) calculations suggest that DTPA is octa-dentate in both the EuL2- and EuHL- complexes and, for the first time, the coordination mode in the EuHL- complex was clarified by integration of the experimental data and DFT calculations. In the EuHL- complex, the Eu is coordinated by an octa-dentate H(DTPA) ligand and a water molecule, and the protonation occurs on the oxygen of a carboxylate group.« less

  3. Stories to Make Thermodynamics and Related Subjects More Palatable

    NASA Astrophysics Data System (ADS)

    Bartell, Lawrence S.

    2001-08-01

    A collection of vignettes either recounting the personalities of some of the architects of thermodynamics or noting steps and missteps in the development of thermodynamics and the kinetic theory is combined with a set of stories illustrating thermodynamic principles. These offerings turned out to be much more easily remembered by students and were more effective in conveying certain points than a direct, unadorned exposition of thermodynamic laws and applications. For one thing, the stories kept the students awake and receptive to ideas. Students had invariably entered the class having heard horror stories about how tedious and impossibly difficult thermodynamics courses are.

  4. Quantum thermodynamics: a nonequilibrium Green's function approach.

    PubMed

    Esposito, Massimiliano; Ochoa, Maicol A; Galperin, Michael

    2015-02-27

    We establish the foundations of a nonequilibrium theory of quantum thermodynamics for noninteracting open quantum systems strongly coupled to their reservoirs within the framework of the nonequilibrium Green's functions. The energy of the system and its coupling to the reservoirs are controlled by a slow external time-dependent force treated to first order beyond the quasistatic limit. We derive the four basic laws of thermodynamics and characterize reversible transformations. Stochastic thermodynamics is recovered in the weak coupling limit.

  5. Thermodynamic-ensemble independence of solvation free energy.

    PubMed

    Chong, Song-Ho; Ham, Sihyun

    2015-02-10

    Solvation free energy is the fundamental thermodynamic quantity in solution chemistry. Recently, it has been suggested that the partial molar volume correction is necessary to convert the solvation free energy determined in different thermodynamic ensembles. Here, we demonstrate ensemble-independence of the solvation free energy on general thermodynamic grounds. Theoretical estimates of the solvation free energy based on the canonical or grand-canonical ensemble are pertinent to experiments carried out under constant pressure without any conversion.

  6. Evaluation of the microscopic distribution of florfenicol in feed pellets for salmon by Fourier Transform infrared imaging and multivariate analysis.

    PubMed

    Bastidas, Camila Y; von Plessing, Carlos; Troncoso, José; Del P Castillo, Rosario

    2018-04-15

    Fourier Transform infrared imaging and multivariate analysis were used to identify, at the microscopic level, the presence of florfenicol (FF), a heavily-used antibiotic in the salmon industry, supplied to fishes in feed pellets for the treatment of salmonid rickettsial septicemia (SRS). The FF distribution was evaluated using Principal Component Analysis (PCA) and Augmented Multivariate Curve Resolution with Alternating Least Squares (augmented MCR-ALS) on the spectra obtained from images with pixel sizes of 6.25 μm × 6.25 μm and 1.56 μm × 1.56 μm, in different zones of feed pellets. Since the concentration of the drug was 3.44 mg FF/g pellet, this is the first report showing the powerful ability of the used of spectroscopic techniques and multivariate analysis, especially the augmented MCR-ALS, to describe the FF distribution in both the surface and inner parts of feed pellets at low concentration, in a complex matrix and at the microscopic level. The results allow monitoring the incorporation of the drug into the feed pellets. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. Quantum thermodynamics of nanoscale steady states far from equilibrium

    NASA Astrophysics Data System (ADS)

    Taniguchi, Nobuhiko

    2018-04-01

    We develop an exact quantum thermodynamic description for a noninteracting nanoscale steady state that couples strongly with multiple reservoirs. We demonstrate that there exists a steady-state extension of the thermodynamic function that correctly accounts for the multiterminal Landauer-Büttiker formula of quantum transport of charge, energy, or heat via the nonequilibrium thermodynamic relations. Its explicit form is obtained for a single bosonic or fermionic level in the wide-band limit, and corresponding thermodynamic forces (affinities) are identified. Nonlinear generalization of the Onsager reciprocity relations are derived. We suggest that the steady-state thermodynamic function is also capable of characterizing the heat current fluctuations of the critical transport where the thermal fluctuations dominate. Also, the suggested nonequilibrium steady-state thermodynamic relations seemingly persist for a spin-degenerate single level with local interaction.

  8. On thermodynamical inconsistency of isotherm equations: Gibbs's thermodynamics.

    PubMed

    Tóth, József

    2003-06-01

    It has been proven that all isotherm equations which include the expression 1-Theta contradict the exact Gibbs thermodynamics. These contradictions have been discussed in detail in the case of the Langmuir (L) equation applied to gas/solid (G/S), solid/liquid (S/L), and gas/liquid (G/L) interfaces. In G/S adsorption the L equation can theoretically be applied only at low equilibrium pressures on condition that vg > vs . vg is the molar volume of the adsorbed amount in the gas phase and vs is the same in the Gibbs phase. In S/L and G/L adsorption the L equation is practically applicable only in the domain of very low concentrations. The cause of these contradictions (inconsistencies) is that Gibbs thermodynamics takes excess adsorbed amounts into account; however, the L and other isotherm equations calculate with the absolute adsorbed amount. The two amounts may be practically equal to each other when the limiting conditions mentioned above are fulfilled. It is also discussed how these inconsistent isotherm equations can be transformed into consistent ones.

  9. Occupational concerns associated with regular use of microscope.

    PubMed

    Jain, Garima; Shetty, Pushparaja

    2014-08-01

    Microscope work can be strenuous both to the visual system and the musculoskeletal system. Lack of awareness or indifference towards health issues may result in microscope users becoming victim to many occupational hazards. Our objective was to understand the occupational problems associated with regular use of microscope, awareness regarding the hazards, attitude and practice of microscope users towards the problems and preventive strategies. a questionnaire based survey done on 50 professionals and technicians who used microscope regularly in pathology, microbiology, hematology and cytology laboratories. Sixty two percent of subjects declared that they were suffering from musculoskeletal problems, most common locations being neck and back. Maximum prevalence of musculoskeletal problems was noted in those using microscope for 11-15 years and for more than 30 h/week. Sixty two percent of subjects were aware of workplace ergonomics. Fifty six percent of microscope users took regular short breaks for stretching exercises and 58% took visual breaks every 15-30 min in between microscope use sessions. As many as 94% subjects reported some form of visual problem. Fourty four percent of microscope users felt stressed with long working hours on microscope. The most common occupational concerns of microscope users were musculoskeletal problems of neck and back regions, eye fatigue, aggravation of ametropia, headache, stress due to long working hours and anxiety during or after microscope use. There is an immediate need for increasing awareness about the various occupational hazards and their irreversible effects to prevent them.

  10. Introduction to the special issue: Thermodynamic aspects of cryobiology.

    PubMed

    Elliott, Janet A W

    2010-02-01

    This brief paper introduces the subject of thermodynamics and the papers of the special issue on thermodynamic aspects of cryobiology. Thermodynamic terminology is defined for the non-specialist. Copyright 2009 Elsevier Inc. All rights reserved.

  11. Microscopic Polyangiitis

    MedlinePlus

    ... but possess sufficient differences as to justify separate classifications. Who gets Microscopic Polyangiitis? A typical patient MPA can affect individuals from all ethnic backgrounds and any age group. In the United States, the typical MPA patient ...

  12. Strain broadening of the 1042-nm zero phonon line of the NV- center in diamond: A promising spectroscopic tool for defect tomography

    NASA Astrophysics Data System (ADS)

    Biktagirov, T. B.; Smirnov, A. N.; Davydov, V. Yu.; Doherty, M. W.; Alkauskas, A.; Gibson, B. C.; Soltamov, V. A.

    2017-08-01

    The negatively charged nitrogen-vacancy (NV-) center in diamond is a promising candidate for many quantum applications. Here, we examine the splitting and broadening of the center's infrared (IR) zero-phonon line (ZPL). We develop a model for these effects that accounts for the strain induced by photodependent microscopic distributions of defects. We apply this model to interpret observed variations of the IR ZPL shape with temperature and photoexcitation conditions. We identify an anomalous temperature-dependent broadening mechanism and that defects other than the substitutional nitrogen center significantly contribute to strain broadening. The former conclusion suggests the presence of a strong Jahn-Teller effect in the center's singlet levels and the latter indicates that major sources of broadening are yet to be identified. These conclusions have important implications for the understanding of the center and the engineering of diamond quantum devices. Finally, we propose that, once the major sources of broadening are identified, the IR ZPL has the potential to be a sensitive spectroscopic tool for probing microscopic strain fields and performing defect tomography.

  13. Thermodynamic universality of quantum Carnot engines

    DOE PAGES

    Gardas, Bartłomiej; Deffner, Sebastian

    2015-10-12

    The Carnot statement of the second law of thermodynamics poses an upper limit on the efficiency of all heat engines. Recently, it has been studied whether generic quantum features such as coherence and quantum entanglement could allow for quantum devices with efficiencies larger than the Carnot efficiency. The present study shows that this is not permitted by the laws of thermodynamic —independent of the model. We will show that rather the definition of heat has to be modified to account for the thermodynamic cost of maintaining non-Gibbsian equilibrium states. As a result, our theoretical findings are illustrated for two experimentallymore » relevant examples.« less

  14. Universalities of thermodynamic signatures in topological phases

    PubMed Central

    Kempkes, S. N.; Quelle, A.; Smith, C. Morais

    2016-01-01

    Topological insulators (superconductors) are materials that host symmetry-protected metallic edge states in an insulating (superconducting) bulk. Although they are well understood, a thermodynamic description of these materials remained elusive, firstly because the edges yield a non-extensive contribution to the thermodynamic potential, and secondly because topological field theories involve non-local order parameters, and cannot be captured by the Ginzburg-Landau formalism. Recently, this challenge has been overcome: by using Hill thermodynamics to describe the Bernevig-Hughes-Zhang model in two dimensions, it was shown that at the topological phase transition the thermodynamic potential does not scale extensively due to boundary effects. Here, we extend this approach to different topological models in various dimensions (the Kitaev chain and Su-Schrieffer-Heeger model in one dimension, the Kane-Mele model in two dimensions and the Bernevig-Hughes-Zhang model in three dimensions) at zero temperature. Surprisingly, all models exhibit the same universal behavior in the order of the topological-phase transition, depending on the dimension. Moreover, we derive the topological phase diagram at finite temperature using this thermodynamic description, and show that it displays a good agreement with the one calculated from the Uhlmann phase. Our work reveals unexpected universalities and opens the path to a thermodynamic description of systems with a non-local order parameter. PMID:27929041

  15. Universalities of thermodynamic signatures in topological phases.

    PubMed

    Kempkes, S N; Quelle, A; Smith, C Morais

    2016-12-08

    Topological insulators (superconductors) are materials that host symmetry-protected metallic edge states in an insulating (superconducting) bulk. Although they are well understood, a thermodynamic description of these materials remained elusive, firstly because the edges yield a non-extensive contribution to the thermodynamic potential, and secondly because topological field theories involve non-local order parameters, and cannot be captured by the Ginzburg-Landau formalism. Recently, this challenge has been overcome: by using Hill thermodynamics to describe the Bernevig-Hughes-Zhang model in two dimensions, it was shown that at the topological phase transition the thermodynamic potential does not scale extensively due to boundary effects. Here, we extend this approach to different topological models in various dimensions (the Kitaev chain and Su-Schrieffer-Heeger model in one dimension, the Kane-Mele model in two dimensions and the Bernevig-Hughes-Zhang model in three dimensions) at zero temperature. Surprisingly, all models exhibit the same universal behavior in the order of the topological-phase transition, depending on the dimension. Moreover, we derive the topological phase diagram at finite temperature using this thermodynamic description, and show that it displays a good agreement with the one calculated from the Uhlmann phase. Our work reveals unexpected universalities and opens the path to a thermodynamic description of systems with a non-local order parameter.

  16. A Vector Representation for Thermodynamic Relationships

    ERIC Educational Resources Information Center

    Pogliani, Lionello

    2006-01-01

    The existing vector formalism method for thermodynamic relationship maintains tractability and uses accessible mathematics, which can be seen as a diverting and entertaining step into the mathematical formalism of thermodynamics and as an elementary application of matrix algebra. The method is based on ideas and operations apt to improve the…

  17. 21 CFR 884.6190 - Assisted reproductive microscopes and microscope accessories.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES OBSTETRICAL AND GYNECOLOGICAL DEVICES Assisted Reproduction... or embryos. Variations of microscopes and accessories used for these purposes would include phase...

  18. Infrared microscope inspection apparatus

    DOEpatents

    Forman, S.E.; Caunt, J.W.

    1985-02-26

    Apparatus and system for inspecting infrared transparents, such as an array of photovoltaic modules containing silicon solar cells, includes an infrared microscope, at least three sources of infrared light placed around and having their axes intersect the center of the object field and means for sending the reflected light through the microscope. The apparatus is adapted to be mounted on an X-Y translator positioned adjacent the object surface. 4 figs.

  19. Infrared microscope inspection apparatus

    DOEpatents

    Forman, Steven E.; Caunt, James W.

    1985-02-26

    Apparatus and system for inspecting infrared transparents, such as an array of photovoltaic modules containing silicon solar cells, includes an infrared microscope, at least three sources of infrared light placed around and having their axes intersect the center of the object field and means for sending the reflected light through the microscope. The apparatus is adapted to be mounted on an X-Y translator positioned adjacent the object surface.

  20. Spectroscopic characterization of effective components anthraquinones in Chinese medicinal herbs binding with serum albumins

    NASA Astrophysics Data System (ADS)

    Bi, Shuyun; Song, Daqian; Kan, Yuhe; Xu, Dong; Tian, Yuan; Zhou, Xin; Zhang, Hanqi

    2005-11-01

    The interactions of serum albumins such as human serum albumin (HSA) and bovine serum albumin (BSA) with emodin, rhein, aloe-emodin and aloin were assessed employing fluorescence quenching and absorption spectroscopic techniques. The results obtained revealed that there are relatively strong binding affinity for the four anthraquinones with HSA and BSA and the binding constants for the interactions of anthraquinones with HSA or BSA at 20 °C were obtained. Anthraquinone-albumin interactions were studied at different temperatures and in the presence of some metal ions. And the competition binding of anthraquinones with serum albumins was also discussed. The Stern-Volmer curves suggested that the quenching occurring in the reactions was the static quenching process. The binding distances and transfer efficiencies for each binding reactions were calculated according to the Föster theory of non-radiation energy transfer. Using thermodynamic equations, the main action forces of these reactions were also obtained. The reasons of the different binding affinities for different anthraquinone-albumin reactions were probed from the point of view of molecular structures.

  1. Quantum thermodynamics with local control

    NASA Astrophysics Data System (ADS)

    Lekscha, J.; Wilming, H.; Eisert, J.; Gallego, R.

    2018-02-01

    We investigate the limitations that emerge in thermodynamic tasks as a result of having local control only over the components of a thermal machine. These limitations are particularly relevant for devices composed of interacting many-body systems. Specifically, we study protocols of work extraction that employ a many-body system as a working medium whose evolution can be driven by tuning the on-site Hamiltonian terms. This provides a restricted set of thermodynamic operations, giving rise to alternative bounds for the performance of engines. Our findings show that those limitations in control render it, in general, impossible to reach Carnot efficiency; in its extreme ramification it can even forbid to reach a finite efficiency or finite work per particle. We focus on the one-dimensional Ising model in the thermodynamic limit as a case study. We show that in the limit of strong interactions the ferromagnetic case becomes useless for work extraction, while the antiferromagnetic case improves its performance with the strength of the couplings, reaching Carnot in the limit of arbitrary strong interactions. Our results provide a promising connection between the study of quantum control and thermodynamics and introduce a more realistic set of physical operations well suited to capture current experimental scenarios.

  2. Synthesis, spectroscopic, thermal and antimicrobial investigations of charge-transfer complexes formed from the drug procaine hydrochloride with quinol, picric acid and TCNQ

    NASA Astrophysics Data System (ADS)

    Adam, Abdel Majid A.

    2012-12-01

    Intermolecular charge-transfer or proton-transfer complexes between the drug procaine hydrochloride (PC-HCl) as a donor and quinol (QL), picric acid (PA) or 7,7',8,8'-tetracyanoquinodimethane (TCNQ) as a π-acceptor have been synthesized and spectroscopically studied in methanol at room temperature. Based on elemental analyses and photometric titrations, the stoichiometry of the complexes (donor:acceptor molar ratios) was determined to be 1:1 for all three complexes. The formation constant (KCT), molar extinction coefficient (ɛCT) and other spectroscopic data have been determined using the Benesi-Hildebrand method and its modifications. The newly synthesized CT complexes have been characterized via elemental analysis, IR, Raman, 1H NMR, and electronic absorption spectroscopy. The morphological features of these complexes were investigated using scanning electron microscopy (SEM), and the sharp, well-defined Bragg reflections at specific 2θ angles have been identified from the powder X-ray diffraction patterns. Thermogravimetric analyses (TGAs) and kinetic thermodynamic parameters were also used to investigate the thermal stability of the synthesized solid CT complexes. Finally, the CT complexes were screened for their antibacterial and antifungal activities against various bacterial and fungal strains, and only the complex obtained using picric acid exhibited moderate antibacterial activity against all of the tested strains.

  3. Thermodynamics of quantum information scrambling

    NASA Astrophysics Data System (ADS)

    Campisi, Michele; Goold, John

    2017-06-01

    Scrambling of quantum information can conveniently be quantified by so-called out-of-time-order correlators (OTOCs), i.e., correlators of the type <[Wτ,V ] †[Wτ,V ] > , whose measurements present a formidable experimental challenge. Here we report on a method for the measurement of OTOCs based on the so-called two-point measurement scheme developed in the field of nonequilibrium quantum thermodynamics. The scheme is of broader applicability than methods employed in current experiments and provides a clear-cut interpretation of quantum information scrambling in terms of nonequilibrium fluctuations of thermodynamic quantities, such as work and heat. Furthermore, we provide a numerical example on a spin chain which highlights the utility of our thermodynamic approach when understanding the differences between integrable and ergodic behaviors. We also discuss how the method can be used to extend the reach of current experiments.

  4. Fast and Adaptive Auto-focusing Microscope

    NASA Astrophysics Data System (ADS)

    Obara, Takeshi; Igarashi, Yasunobu; Hashimoto, Koichi

    Optical microscopes are widely used in biological and medical researches. By using the microscope, we can observe cellular movements including intracellular ions and molecules tagged with fluorescent dyes at a high magnification. However, a freely motile cell easily escapes from a 3D field of view of the typical microscope. Therefore, we propose a novel auto-focusing algorithm and develop a auto-focusing and tracking microscope. XYZ positions of a microscopic stage are feedback controlled to focus and track the cell automatically. A bright-field image is used to estimate a cellular position. XY centroids are used to estimate XY positions of the tracked cell. To estimate Z position, we use a diffraction pattern around the cell membrane. This estimation method is so-called Depth from Diffraction (DFDi). However, this method is not robust for individual differences between cells because the diffraction pattern depends on each cellular shape. Therefore, in this study, we propose a real-time correction of DFDi by using 2D Laplacian of an intracellular area as a goodness of the focus. To evaluate the performance of our developed algorithm and microscope, we auto-focus and track a freely moving paramecium. In this experimental result, the paramecium is auto-focused and kept inside the scope of the microscope during 45s. The evaluated focal error is within 5µm, while a length and a thickness of the paramecium are about 200µm and 50µm, respectively.

  5. Infrared spectroscopy and spectroscopic imaging in forensic science.

    PubMed

    Ewing, Andrew V; Kazarian, Sergei G

    2017-01-16

    Infrared spectroscopy and spectroscopic imaging, are robust, label free and inherently non-destructive methods with a high chemical specificity and sensitivity that are frequently employed in forensic science research and practices. This review aims to discuss the applications and recent developments of these methodologies in this field. Furthermore, the use of recently emerged Fourier transform infrared (FT-IR) spectroscopic imaging in transmission, external reflection and Attenuated Total Reflection (ATR) modes are summarised with relevance and potential for forensic science applications. This spectroscopic imaging approach provides the opportunity to obtain the chemical composition of fingermarks and information about possible contaminants deposited at a crime scene. Research that demonstrates the great potential of these techniques for analysis of fingerprint residues, explosive materials and counterfeit drugs will be reviewed. The implications of this research for the examination of different materials are considered, along with an outlook of possible future research avenues for the application of vibrational spectroscopic methods to the analysis of forensic samples.

  6. Thermodynamics of charged Lovelock: AdS black holes

    NASA Astrophysics Data System (ADS)

    Prasobh, C. B.; Suresh, Jishnu; Kuriakose, V. C.

    2016-04-01

    We investigate the thermodynamic behavior of maximally symmetric charged, asymptotically AdS black hole solutions of Lovelock gravity. We explore the thermodynamic stability of such solutions by the ordinary method of calculating the specific heat of the black holes and investigating its divergences which signal second-order phase transitions between black hole states. We then utilize the methods of thermodynamic geometry of black hole spacetimes in order to explain the origin of these points of divergence. We calculate the curvature scalar corresponding to a Legendre-invariant thermodynamic metric of these spacetimes and find that the divergences in the black hole specific heat correspond to singularities in the thermodynamic phase space. We also calculate the area spectrum for large black holes in the model by applying the Bohr-Sommerfeld quantization to the adiabatic invariant calculated for the spacetime.

  7. Thermodynamics of hairy black holes in Lovelock gravity

    NASA Astrophysics Data System (ADS)

    Hennigar, Robie A.; Tjoa, Erickson; Mann, Robert B.

    2017-02-01

    We perform a thorough study of the thermodynamic properties of a class of Lovelock black holes with conformal scalar hair arising from coupling of a real scalar field to the dimensionally extended Euler densities. We study the linearized equations of motion of the theory and describe constraints under which the theory is free from ghosts/tachyons. We then consider, within the context of black hole chemistry, the thermodynamics of the hairy black holes in the Gauss-Bonnet and cubic Lovelock theories. We clarify the connection between isolated critical points and thermodynamic singularities, finding a one parameter family of these critical points which occur for well-defined thermodynamic parameters. We also report on a number of novel results, including `virtual triple points' and the first example of a `λ-line' — a line of second order phase transitions — in black hole thermodynamics.

  8. Stochastic approach to equilibrium and nonequilibrium thermodynamics.

    PubMed

    Tomé, Tânia; de Oliveira, Mário J

    2015-04-01

    We develop the stochastic approach to thermodynamics based on stochastic dynamics, which can be discrete (master equation) and continuous (Fokker-Planck equation), and on two assumptions concerning entropy. The first is the definition of entropy itself and the second the definition of entropy production rate, which is non-negative and vanishes in thermodynamic equilibrium. Based on these assumptions, we study interacting systems with many degrees of freedom in equilibrium or out of thermodynamic equilibrium and how the macroscopic laws are derived from the stochastic dynamics. These studies include the quasiequilibrium processes; the convexity of the equilibrium surface; the monotonic time behavior of thermodynamic potentials, including entropy; the bilinear form of the entropy production rate; the Onsager coefficients and reciprocal relations; and the nonequilibrium steady states of chemical reactions.

  9. Thermodynamics sheds light on black hole dynamics

    NASA Astrophysics Data System (ADS)

    Cárdenas, Marcela; Julié, Félix-Louis; Deruelle, Nathalie

    2018-06-01

    We propose to unify two a priori distinct aspects of black hole physics: their thermodynamics, and their description as point particles, which is an essential starting point in the post-Newtonian approach to their dynamics. We will find that, when reducing a black hole to a point particle endowed with its specific effective mass, one in fact describes a black hole satisfying the first law of thermodynamics, such that its global charges, and hence its entropy, remain constant. This gives a thermodynamical interpretation of its effective mass, thus opening a promising synergy between black hole thermodynamics and the analytical approaches to the two-body problems in gravity theories. To illustrate this relationship, the Einstein-Maxwell-dilaton theory, which contains simple examples of asympotically flat, hairy black hole solutions, will serve as a laboratory.

  10. Evaluation of a completely robotized neurosurgical operating microscope.

    PubMed

    Kantelhardt, Sven R; Finke, Markus; Schweikard, Achim; Giese, Alf

    2013-01-01

    Operating microscopes are essential for most neurosurgical procedures. Modern robot-assisted controls offer new possibilities, combining the advantages of conventional and automated systems. We evaluated the prototype of a completely robotized operating microscope with an integrated optical coherence tomography module. A standard operating microscope was fitted with motors and control instruments, with the manual control mode and balance preserved. In the robot mode, the microscope was steered by a remote control that could be fixed to a surgical instrument. External encoders and accelerometers tracked microscope movements. The microscope was additionally fitted with an optical coherence tomography-scanning module. The robotized microscope was tested on model systems. It could be freely positioned, without forcing the surgeon to take the hands from the instruments or avert the eyes from the oculars. Positioning error was about 1 mm, and vibration faded in 1 second. Tracking of microscope movements, combined with an autofocus function, allowed determination of the focus position within the 3-dimensional space. This constituted a second loop of navigation independent from conventional infrared reflector-based techniques. In the robot mode, automated optical coherence tomography scanning of large surface areas was feasible. The prototype of a robotized optical coherence tomography-integrated operating microscope combines the advantages of a conventional manually controlled operating microscope with a remote-controlled positioning aid and a self-navigating microscope system that performs automated positioning tasks such as surface scans. This demonstrates that, in the future, operating microscopes may be used to acquire intraoperative spatial data, volume changes, and structural data of brain or brain tumor tissue.

  11. Miniaturized integration of a fluorescence microscope.

    PubMed

    Ghosh, Kunal K; Burns, Laurie D; Cocker, Eric D; Nimmerjahn, Axel; Ziv, Yaniv; Gamal, Abbas El; Schnitzer, Mark J

    2011-09-11

    The light microscope is traditionally an instrument of substantial size and expense. Its miniaturized integration would enable many new applications based on mass-producible, tiny microscopes. Key prospective usages include brain imaging in behaving animals for relating cellular dynamics to animal behavior. Here we introduce a miniature (1.9 g) integrated fluorescence microscope made from mass-producible parts, including a semiconductor light source and sensor. This device enables high-speed cellular imaging across ∼0.5 mm2 areas in active mice. This capability allowed concurrent tracking of Ca2+ spiking in >200 Purkinje neurons across nine cerebellar microzones. During mouse locomotion, individual microzones exhibited large-scale, synchronized Ca2+ spiking. This is a mesoscopic neural dynamic missed by prior techniques for studying the brain at other length scales. Overall, the integrated microscope is a potentially transformative technology that permits distribution to many animals and enables diverse usages, such as portable diagnostics or microscope arrays for large-scale screens.

  12. Miniaturized integration of a fluorescence microscope

    PubMed Central

    Ghosh, Kunal K.; Burns, Laurie D.; Cocker, Eric D.; Nimmerjahn, Axel; Ziv, Yaniv; Gamal, Abbas El; Schnitzer, Mark J.

    2013-01-01

    The light microscope is traditionally an instrument of substantial size and expense. Its miniaturized integration would enable many new applications based on mass-producible, tiny microscopes. Key prospective usages include brain imaging in behaving animals towards relating cellular dynamics to animal behavior. Here we introduce a miniature (1.9 g) integrated fluorescence microscope made from mass-producible parts, including semiconductor light source and sensor. This device enables high-speed cellular-level imaging across ∼0.5 mm2 areas in active mice. This capability allowed concurrent tracking of Ca2+ spiking in >200 Purkinje neurons across nine cerebellar microzones. During mouse locomotion, individual microzones exhibited large-scale, synchronized Ca2+ spiking. This is a mesoscopic neural dynamic missed by prior techniques for studying the brain at other length scales. Overall, the integrated microscope is a potentially transformative technology that permits distribution to many animals and enables diverse usages, such as portable diagnostics or microscope arrays for large-scale screens. PMID:21909102

  13. Immunocytochemistry by electron spectroscopic imaging using well defined boronated monovalent antibody fragments.

    PubMed

    Kessels, M M; Qualmann, B; Sierralta, W D

    1996-01-01

    Contributing to the rapidly developing field of immunoelectron microscopy a new kind of markers has been created. The element boron, incorporated as very stable carborane clusters into different kinds of peptides, served as a marker detectable by electron spectroscopic imaging (ESI)--an electron microscopic technique with high-resolution potential. Covalently linked immunoreagents conspicuous by the small size of both antigen recognizing part and marker moiety are accessible by using peptide concepts for label construction and their conjugation with Fab' fragments. Due to a specific labeling of the free thiol groups of the Fab' fragments, the antigen binding capacity was not affected by the attachment of the markers and the resulting immunoprobes exhibited an elongated shape with the antigen combining site and the label located at opposite ends. The labeling densities observed with these reagents were found to be significantly higher than those obtained by using conventional colloidal gold methods. Combined with digital image processing and analysis systems, boron-based ESI proved to be a powerful approach in ultrastructural immunocytochemistry employing pre- and post-embedding methods.

  14. Virtual microscopes in podiatric medical education.

    PubMed

    Becker, John H

    2006-01-01

    In many medical schools, microscopes are being replaced as teaching tools by computers with software that emulates the use of a light microscope. This article chronicles the adoption of "virtual microscopes" by a podiatric medical school and presents the results of educational research on the effectiveness of this adoption in a histology course. If the trend toward virtual microscopy in education continues, many 21st-century physicians will not be trained to operate a light microscope. The replacement of old technologies by new is discussed. The fundamental question is whether all podiatric physicians should be trained in the use of a particular tool or only those who are likely to use it in their own practice.

  15. The current status of microscopical hair comparisons.

    PubMed

    Rowe, W F

    2001-12-08

    Although the microscopical comparison of human hairs has been accepted in courts of law for over a century, recent advances in DNA technology have called this type of forensic examination into question. In a number of cases, post-conviction DNA testing has exonerated defendants who were convicted in part on the results of microscopical hair comparisons. A federal judge has held a Daubert hearing on the microscopical comparison of human hairs and has concluded that this type of examination does not meet the criteria for admission of scientific evidence in federal courts. A review of the available scientific literature on microscopical hair comparisons (including studies conducted by the Royal Canadian Mounted Police and the Federal Bureau of Investigation) leads to three conclusions: (1) microscopical comparisons of human hairs can yield scientifically defensible conclusions that can contribute to criminal investigations and criminal prosecutions, (2) the reliability of microscopical hair comparisons is strongly affected by the training of the forensic hair examiner, (3) forensic hair examiners cannot offer estimates of the probability of a match of a questioned hair with a hair from a randomly selected person. In order for microscopical hair examinations to survive challenges under the U.S. Supreme Court's Daubert decision, hair microscopists must be better trained and undergo frequent proficiency testing. More research on the error rates of microscopical hair comparisons should be undertaken, and guidelines for the permissible interpretations of such comparisons should be established. Until these issues have been addressed and satisfactorily resolved, microscopical hair comparisons should be regarded by law enforcement agencies and courts of law as merely presumptive in nature, and all microscopical hair comparisons should be confirmed by nuclear DNA profiling or mitochondrial DNA sequencing.

  16. Understanding the Thermodynamics of Biological Order

    ERIC Educational Resources Information Center

    Peterson, Jacob

    2012-01-01

    By growth in size and complexity (i.e., changing from more probable to less probable states), plants and animals appear to defy the second law of thermodynamics. The usual explanation describes the input of nutrient and sunlight energy into open thermodynamic systems. However, energy input alone does not address the ability to organize and create…

  17. IMIS: An intelligence microscope imaging system

    NASA Technical Reports Server (NTRS)

    Caputo, Michael; Hunter, Norwood; Taylor, Gerald

    1994-01-01

    Until recently microscope users in space relied on traditional microscopy techniques that required manual operation of the microscope and recording of observations in the form of written notes, drawings, or photographs. This method was time consuming and required the return of film and drawings from space for analysis. No real-time data analysis was possible. Advances in digital and video technologies along with recent developments in article intelligence will allow future space microscopists to have a choice of three additional modes of microscopy: remote coaching, remote control, and automation. Remote coaching requires manual operations of the microscope with instructions given by two-way audio/video transmission during critical phases of the experiment. When using the remote mode of microscopy, the Principal Investigator controls the microscope from the ground. The automated mode employs artificial intelligence to control microscope functions and is the only mode that can be operated in the other three modes as well. The purpose of this presentation is to discuss the advantages and disadvantages of the four modes of of microscopy and how the IMIS, a proposed intelligent microscope imaging system, can be used as a model for developing and testing concepts, operating procedures, and equipment design of specifications required to provide a comprehensive microscopy/imaging capability onboard Space Station Freedom.

  18. Water window imaging x ray microscope

    NASA Technical Reports Server (NTRS)

    Hoover, Richard B. (Inventor)

    1992-01-01

    A high resolution x ray microscope for imaging microscopic structures within biological specimens has an optical system including a highly polished primary and secondary mirror coated with identical multilayer coatings, the mirrors acting at normal incidence. The coatings have a high reflectivity in the narrow wave bandpass between 23.3 and 43.7 angstroms and have low reflectivity outside of this range. The primary mirror has a spherical concave surface and the secondary mirror has a spherical convex surface. The radii of the mirrors are concentric about a common center of curvature on the optical axis of the microscope extending from the object focal plane to the image focal plane. The primary mirror has an annular configuration with a central aperture and the secondary mirror is positioned between the primary mirror and the center of curvature for reflecting radiation through the aperture to a detector. An x ray filter is mounted at the stage end of the microscope, and film sensitive to x rays in the desired band width is mounted in a camera at the image plane of the optical system. The microscope is mounted within a vacuum chamber for minimizing the absorption of x rays in air from a source through the microscope.

  19. Thermodynamics of a periodically driven qubit

    NASA Astrophysics Data System (ADS)

    Donvil, Brecht

    2018-04-01

    We present a new approach to the open system dynamics of a periodically driven qubit in contact with a temperature bath. We are specifically interested in the thermodynamics of the qubit. It is well known that by combining the Markovian approximation with Floquet theory it is possible to derive a stochastic Schrödinger equation in for the state of the qubit. We follow here a different approach. We use Floquet theory to embed the time-non autonomous qubit dynamics into time-autonomous yet infinite dimensional dynamics. We refer to the resulting infinite dimensional system as the dressed-qubit. Using the Markovian approximation we derive the stochastic Schrödinger equation for the dressed-qubit. The advantage of our approach is that the jump operators are ladder operators of the Hamiltonian. This simplifies the formulation of the thermodynamics. We use the thermodynamics of the infinite dimensional system to recover the thermodynamical description for the driven qubit. We compare our results with the existing literature and recover the known results.

  20. Microscopic Analysis of Activated Sludge. Training Manual.

    ERIC Educational Resources Information Center

    Office of Water Program Operations (EPA), Cincinnati, OH. National Training and Operational Technology Center.

    This training manual presents material on the use of a compound microscope to analyze microscope communities, present in wastewater treatment processes, for operational control. Course topics include: sampling techniques, sample handling, laboratory analysis, identification of organisms, data interpretation, and use of the compound microscope.…

  1. Universality of P - V criticality in horizon thermodynamics

    NASA Astrophysics Data System (ADS)

    Hansen, Devin; Kubizňák, David; Mann, Robert B.

    2017-01-01

    We study P - V criticality of black holes in Lovelock gravities in the context of horizon thermodynamics. The corresponding first law of horizon thermodynamics emerges as one of the Einstein-Lovelock equations and assumes the universal (independent of matter content) form δ E = T δ S - P δ V , where P is identified with the total pressure of all matter in the spacetime (including a cosmological constant Λ if present). We compare this approach to recent advances in extended phase space thermodynamics of asymptotically AdS black holes where the `standard' first law of black hole thermodynamics is extended to include a pressure-volume term, where the pressure is entirely due to the (variable) cosmological constant. We show that both approaches are quite different in interpretation. Provided there is sufficient non-linearity in the gravitational sector, we find that horizon thermodynamics admits the same interesting black hole phase behaviour seen in the extended case, such as a Hawking-Page transition, Van der Waals like behaviour, and the presence of a triple point. We also formulate the Smarr formula in horizon thermodynamics and discuss the interpretation of the quantity E appearing in the horizon first law.

  2. Thimble microscope system

    NASA Astrophysics Data System (ADS)

    Kamal, Tahseen; Rubinstein, Jaden; Watkins, Rachel; Cen, Zijian; Kong, Gary; Lee, W. M.

    2016-12-01

    Wearable computing devices, e.g. Google Glass, Smart watch, embodies the new human design frontier, where technology interfaces seamlessly with human gestures. During examination of any subject in the field (clinic, surgery, agriculture, field survey, water collection), our sensory peripherals (touch and vision) often go hand-in-hand. The sensitivity and maneuverability of the human fingers are guided with tight distribution of biological nerve cells, which perform fine motor manipulation over a range of complex surfaces that is often out of sight. Our sight (or naked vision), on the other hand, is generally restricted to line of sight that is ill-suited to view around corner. Hence, conventional imaging methods are often resort to complex light guide designs (periscope, endoscopes etc) to navigate over obstructed surfaces. Using modular design strategies, we constructed a prototype miniature microscope system that is incorporated onto a wearable fixture (thimble). This unique platform allows users to maneuver around a sample and take high resolution microscopic images. In this paper, we provide an exposition of methods to achieve a thimble microscopy; microscope lens fabrication, thimble design, integration of miniature camera and liquid crystal display.

  3. Optical constants of electroplated gold from spectroscopic ellipsometry

    NASA Astrophysics Data System (ADS)

    Synowicki, R. A.; Herzinger, Craig M.; Hall, James T.; Malingowski, Andrew

    2017-11-01

    The optical constants of an opaque electroplated gold film (Laser Gold from Epner Technology Inc.), were determined by spectroscopic ellipsometry at room temperature over the spectral range from 0.142 μm in the vacuum ultraviolet to 36 μm in the infrared (photon energy range 0.034-8.75 eV). Data from two separate ellipsometer instruments covering different spectral ranges were analyzed simultaneously. The optical constants n&k or ε1&ε2 were determined by fitting an oscillator dispersion model combining Drude, Gaussian, and Sellmeier dispersion functions to the experimental Ψ and Δ data. The data were analyzed using both an ideal bulk substrate model and a simple overlayer model to account for surface roughness. Including the optical surface roughness layer improved ellipsometric data fits in the UV, and using a separate Drude function for the surface layer improved fits in the infrared. The surface roughness was also characterized using an Atomic Force Microscope. Using an oscillator dispersion model for the optical constants determined in this work allows for more realistic extrapolation to longer infrared wavelengths. Extending optical constants out to 50 μm and beyond is important for calibrating far-infrared reflectance measurements. Applications include understanding the thermal performance of cryogenic space-based instruments, such as the James Webb Space Telescope (JWST).

  4. Spin microscope based on optically detected magnetic resonance

    DOEpatents

    Berman, Gennady P [Los Alamos, NM; Chernobrod, Boris M [Los Alamos, NM

    2010-06-29

    The invention relates to scanning magnetic microscope which has a photoluminescent nanoprobe implanted in the tip apex of an atomic force microscope (AFM), a scanning tunneling microscope (STM) or a near-field scanning optical microscope (NSOM) and exhibits optically detected magnetic resonance (ODMR) in the vicinity of unpaired electron spins or nuclear magnetic moments in the sample material. The described spin microscope has demonstrated nanoscale lateral resolution and single spin sensitivity for the AFM and STM embodiments.

  5. Spin microscope based on optically detected magnetic resonance

    DOEpatents

    Berman, Gennady P.; Chernobrod, Boris M.

    2009-11-10

    The invention relates to scanning magnetic microscope which has a photoluminescent nanoprobe implanted in the tip apex of an atomic force microscope (AFM), a scanning tunneling microscope (STM) or a near-field scanning optical microscope (NSOM) and exhibits optically detected magnetic resonance (ODMR) in the vicinity of impaired electron spins or nuclear magnetic moments in the sample material. The described spin microscope has demonstrated nanoscale lateral resolution and single spin sensitivity for the AFM and STM embodiments.

  6. Spin microscope based on optically detected magnetic resonance

    DOEpatents

    Berman, Gennady P.; Chernobrod, Boris M.

    2007-12-11

    The invention relates to scanning magnetic microscope which has a photoluminescent nanoprobe implanted in the tip apex of an atomic force microscope (AFM), a scanning tunneling microscope (STM) or a near-field scanning optical microscope (NSOM) and exhibits optically detected magnetic resonance (ODMR) in the vicinity of unpaired electron spins or nuclear magnetic moments in the sample material. The described spin microscope has demonstrated nanoscale lateral resolution and single spin sensitivity for the AFM and STM embodiments.

  7. Spin microscope based on optically detected magnetic resonance

    DOEpatents

    Berman, Gennady P [Los Alamos, NM; Chernobrod, Boris M [Los Alamos, NM

    2010-07-13

    The invention relates to scanning magnetic microscope which has a photoluminescent nanoprobe implanted in the tip apex of an atomic force microscope (AFM), a scanning tunneling microscope (STM) or a near-field scanning optical microscope (NSOM) and exhibits optically detected magnetic resonance (ODMR) in the vicinity of unpaired electron spins or nuclear magnetic moments in the sample material. The described spin microscope has demonstrated nanoscale lateral resolution and single spin sensitivity for the AFM and STM embodiments.

  8. Spin microscope based on optically detected magnetic resonance

    DOEpatents

    Berman, Gennady P [Los Alamos, NM; Chernobrod, Boris M [Los Alamos, NM

    2009-10-27

    The invention relates to scanning magnetic microscope which has a photoluminescent nanoprobe implanted in the tip apex of an atomic force microscope (AFM), a scanning tunneling microscope (STM) or a near-field scanning optical microscope (NSOM) and exhibits optically detected magnetic resonance (ODMR) in the vicinity of unpaired electron spins or nuclear magnetic moments in the sample material. The described spin microscope has demonstrated nanoscale lateral resolution and single spin sensitivity for the AFM and STM embodiments.

  9. Nanoantenna-Enhanced Infrared Spectroscopic Chemical Imaging.

    PubMed

    Kühner, Lucca; Hentschel, Mario; Zschieschang, Ute; Klauk, Hagen; Vogt, Jochen; Huck, Christian; Giessen, Harald; Neubrech, Frank

    2017-05-26

    Spectroscopic infrared chemical imaging is ideally suited for label-free and spatially resolved characterization of molecular species, but often suffers from low infrared absorption cross sections. Here, we overcome this limitation by utilizing confined electromagnetic near-fields of resonantly excited plasmonic nanoantennas, which enhance the molecular absorption by orders of magnitude. In the experiments, we evaporate microstructured chemical patterns of C 60 and pentacene with nanometer thickness on top of homogeneous arrays of tailored nanoantennas. Broadband mid-infrared spectra containing plasmonic and vibrational information were acquired with diffraction-limited resolution using a two-dimensional focal plane array detector. Evaluating the enhanced infrared absorption at the respective frequencies, spatially resolved chemical images were obtained. In these chemical images, the microstructured chemical patterns are only visible if nanoantennas are used. This confirms the superior performance of our approach over conventional spectroscopic infrared imaging. In addition to the improved sensitivity, our technique provides chemical selectivity, which would not be available with plasmonic imaging that is based on refractive index sensing. To extend the accessible spectral bandwidth of nanoantenna-enhanced spectroscopic imaging, we employed nanostructures with dual-band resonances, providing broadband plasmonic enhancement and sensitivity. Our results demonstrate the potential of nanoantenna-enhanced spectroscopic infrared chemical imaging for spatially resolved characterization of organic layers with thicknesses of several nanometers. This is of potential interest for medical applications which are currently hampered by state-of-art infrared techniques, e.g., for distinguishing cancerous from healthy tissues.

  10. Using the Antenna Effect as a Spectroscopic Tool; Photophysics and Solution Thermodynamics of the Model Luminescent Hydroxypyridonate Complex [EuIII(3,4,3-LI(1,2-HOPO))]-

    PubMed Central

    Abergel, Rebecca J.; D'Aléo, Anthony; Leung, Clara Ng Pak; Shuh, David K.; Raymond, Kenneth N.

    2009-01-01

    While widely used in bioassays, the spectrofluorimetric method described here uses the antenna effect as a tool to probe the thermodynamic parameters of ligands that sensitize lanthanide luminescence. The Eu3+ coordination chemistry, solution thermodynamic stability and photophysical properties of the spermine-based hydroxypyridonate octadentate chelator 3,4,3-LI(1,2-HOPO) are reported. The complex [EuIII(3,4,3-LI(1,2-HOPO))]- luminesces with a long lifetime (805 μs) and a quantum yield of 7.0% in aqueous solution, at pH 7.4. These remarkable optical properties were exploited to determine the high (and proton-independent) stability of the complex (log β110 = 20.2(2)) and to define the influence of the ligand scaffold on the stability and photophysical properties. PMID:19902920

  11. Thermodynamic characterization of networks using graph polynomials

    NASA Astrophysics Data System (ADS)

    Ye, Cheng; Comin, César H.; Peron, Thomas K. DM.; Silva, Filipi N.; Rodrigues, Francisco A.; Costa, Luciano da F.; Torsello, Andrea; Hancock, Edwin R.

    2015-09-01

    In this paper, we present a method for characterizing the evolution of time-varying complex networks by adopting a thermodynamic representation of network structure computed from a polynomial (or algebraic) characterization of graph structure. Commencing from a representation of graph structure based on a characteristic polynomial computed from the normalized Laplacian matrix, we show how the polynomial is linked to the Boltzmann partition function of a network. This allows us to compute a number of thermodynamic quantities for the network, including the average energy and entropy. Assuming that the system does not change volume, we can also compute the temperature, defined as the rate of change of entropy with energy. All three thermodynamic variables can be approximated using low-order Taylor series that can be computed using the traces of powers of the Laplacian matrix, avoiding explicit computation of the normalized Laplacian spectrum. These polynomial approximations allow a smoothed representation of the evolution of networks to be constructed in the thermodynamic space spanned by entropy, energy, and temperature. We show how these thermodynamic variables can be computed in terms of simple network characteristics, e.g., the total number of nodes and node degree statistics for nodes connected by edges. We apply the resulting thermodynamic characterization to real-world time-varying networks representing complex systems in the financial and biological domains. The study demonstrates that the method provides an efficient tool for detecting abrupt changes and characterizing different stages in network evolution.

  12. Thermodynamic power of non-Markovianity

    PubMed Central

    Bylicka, Bogna; Tukiainen, Mikko; Chruściński, Dariusz; Piilo, Jyrki; Maniscalco, Sabrina

    2016-01-01

    The natural framework to discuss thermodynamics at the quantum level is the theory of open quantum systems. Memory effects arising from strong system-environment correlations may lead to information back-flow, that is non-Markovian behaviour. The relation between non-Markovianity and quantum thermodynamics has been until now largely unexplored. Here we show by means of Landauer’s principle that memory effects control the amount of work extraction by erasure in presence of realistic environments. PMID:27323947

  13. Dirac structures in nonequilibrium thermodynamics

    NASA Astrophysics Data System (ADS)

    Gay-Balmaz, François; Yoshimura, Hiroaki

    2018-01-01

    Dirac structures are geometric objects that generalize both Poisson structures and presymplectic structures on manifolds. They naturally appear in the formulation of constrained mechanical systems. In this paper, we show that the evolution equations for nonequilibrium thermodynamics admit an intrinsic formulation in terms of Dirac structures, both on the Lagrangian and the Hamiltonian settings. In the absence of irreversible processes, these Dirac structures reduce to canonical Dirac structures associated with canonical symplectic forms on phase spaces. Our geometric formulation of nonequilibrium thermodynamic thus consistently extends the geometric formulation of mechanics, to which it reduces in the absence of irreversible processes. The Dirac structures are associated with the variational formulation of nonequilibrium thermodynamics developed in the work of Gay-Balmaz and Yoshimura, J. Geom. Phys. 111, 169-193 (2017a) and are induced from a nonlinear nonholonomic constraint given by the expression of the entropy production of the system.

  14. Friction Force: From Mechanics to Thermodynamics

    ERIC Educational Resources Information Center

    Ferrari, Christian; Gruber, Christian

    2010-01-01

    We study some mechanical problems in which a friction force is acting on a system. Using the fundamental concepts of state, time evolution and energy conservation, we explain how to extend Newtonian mechanics to thermodynamics. We arrive at the two laws of thermodynamics and then apply them to investigate the time evolution and heat transfer of…

  15. Critical behavior and microscopic structure of charged AdS black holes via an alternative phase space

    NASA Astrophysics Data System (ADS)

    Dehyadegari, Amin; Sheykhi, Ahmad; Montakhab, Afshin

    2017-05-01

    It has been argued that charged Anti-de Sitter (AdS) black holes have similar thermodynamic behavior as the Van der Waals fluid system, provided one treats the cosmological constant as a thermodynamic variable (pressure) in an extended phase space. In this paper, we disclose the deep connection between charged AdS black holes and Van der Waals fluid system from an alternative point of view. We consider the mass of an AdS black hole as a function of square of the charge Q2 instead of the standard Q, i.e. M = M (S ,Q2 , P). We first justify such a change of view mathematically and then ask if a phase transition can occur as a function of Q2 for fixed P. Therefore, we write the equation of state as Q2 =Q2 (T , Ψ) where Ψ (conjugate of Q2) is the inverse of the specific volume, Ψ = 1 / v. This allows us to complete the analogy of charged AdS black holes with Van der Waals fluid system and derive the phase transition as well as critical exponents of the system. We identify a thermodynamic instability in this new picture with real analogy to Van der Waals fluid with physically relevant Maxwell construction. We therefore study the critical behavior of isotherms in Q2- Ψ diagram and deduce all the critical exponents of the system and determine that the system exhibits a small-large black hole phase transition at the critical point (Tc , Qc2 ,Ψc). This alternative view is important as one can imagine such a change for a given single black hole i.e. acquiring charge which induces the phase transition. Finally, we disclose the microscopic properties of charged AdS black holes by using thermodynamic geometry. Interestingly, we find that scalar curvature has a gap between small and large black holes, and this gap becomes exceedingly large as one moves away from the critical point along the transition line. Therefore, we are able to attribute the sudden enlargement of the black hole to the strong repulsive nature of the internal constituents at the phase transition.

  16. Considerations on non equilibrium thermodynamics of interactions

    NASA Astrophysics Data System (ADS)

    Lucia, Umberto

    2016-04-01

    Nature can be considered the ;first; engineer! For scientists and engineers, dynamics and evolution of complex systems are not easy to predict. A fundamental approach to study complex system is thermodynamics. But, the result is the origin of too many schools of thermodynamics with a consequent difficulty in communication between thermodynamicists and other scientists and, also, among themselves. The solution is to obtain a unified approach based on the fundamentals of physics. Here we suggest a possible unification of the schools of thermodynamics starting from two fundamental concepts of physics, interaction and flows.

  17. Thermodynamics and kinetics of binary nucleation in ideal-gas mixtures.

    PubMed

    Alekseechkin, Nikolay V

    2015-08-07

    The nonisothermal single-component theory of droplet nucleation [N. V. Alekseechkin, Physica A 412, 186 (2014)] is extended to binary case; the droplet volume V, composition x, and temperature T are the variables of the theory. An approach based on macroscopic kinetics (in contrast to the standard microscopic model of nucleation operating with the probabilities of monomer attachment and detachment) is developed for the droplet evolution and results in the derived droplet motion equations in the space (V, x, T)—equations for V̇≡dV/dt, ẋ, and Ṫ. The work W(V, x, T) of the droplet formation is obtained in the vicinity of the saddle point as a quadratic form with diagonal matrix. Also, the problem of generalizing the single-component Kelvin equation for the equilibrium vapor pressure to binary case is solved; it is presented here as a problem of integrability of a Pfaffian equation. The equation for Ṫ is shown to be the first law of thermodynamics for the droplet, which is a consequence of Onsager's reciprocal relations and the linked-fluxes concept. As an example of ideal solution for demonstrative numerical calculations, the o-xylene-m-xylene system is employed. Both nonisothermal and enrichment effects are shown to exist; the mean steady-state overheat of droplets and their mean steady-state enrichment are calculated with the help of the 3D distribution function. Some qualitative peculiarities of the nucleation thermodynamics and kinetics in the water-sulfuric acid system are considered in the model of regular solution. It is shown that there is a small kinetic parameter in the theory due to the small amount of the acid in the vapor and, as a consequence, the nucleation process is isothermal.

  18. Analysis of the Spectroscopic Aspects of Cationic Dye Basic Orange 21.

    PubMed

    Eizig, Zehavit; Major, Dan T; Kasdan, Harvey L; Afrimzon, Elena; Zurgil, Naomi; Sobolev, Maria; Deutsch, Mordechai

    2015-09-24

    Spectroscopic properties of cationic dye basic orange 21 (BO21) in solutions, in solids, and within leukocytes were examined. Results obtained with solutions indicate that influence of variables such as pH, viscosity, salt composition, and various proteins on the absorption spectrum of BO21 is negligible. However, in the presence of heparin, a blue shift (484-465 nm) is observed, which is attributed to the aggregation of BO21 on the polyanion. Applying density functional theory demonstrates that in aqueous solutions (a) the formation of BO21 oligomers is thermodynamically favorable, they are oriented in an antiparallel dipolar arrangement, and their binding energies are lower than those of parallel dipolar arrangements, (b) association between BO21 aggregates and heparin is highly favorable, and (c) the blue shift is due to the mixing of π → π* transitions caused by BO21 molecule stacking. However, when embedded in basophils, the absorption spectra of intracellular BO21 is extremely red-shifted, with two peaks (at 505 and 550 nm) found to be attributed to BO21 and the BO21-heparin complex, respectively, which are intracellularly hosted in nonaqueous environments. Initial evidence of the ability to differentiate between leukocyte types by BO21 is presented.

  19. Examples for Non-Ideal Solution Thermodynamics Study

    ERIC Educational Resources Information Center

    David, Carl W.

    2004-01-01

    A mathematical model of a non-ideal solution is presented, where it is shown how and where the non-ideality manifests itself in the standard thermodynamics tableau. Examples related to the non-ideal solution thermodynamics study are also included.

  20. Microscopic diffusion processes measured in living planarians

    DOE PAGES

    Mamontov, Eugene

    2018-03-08

    Living planarian flatworms were probed using quasielastic neutron scattering to measure, on the pico-to-nanosecond time scale and nanometer length scale, microscopic diffusion of water and cell constituents in the planarians. Measurable microscopic diffusivities were surprisingly well defined in such a complex system as living animals. The overall variation in the microscopic diffusivity of cell constituents was found to be far lower than the variation in the microscopic diffusivity of water in planarians in a temperature range of 284.5 to 304.1K.

  1. Microscopic diffusion processes measured in living planarians

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mamontov, Eugene

    Living planarian flatworms were probed using quasielastic neutron scattering to measure, on the pico-to-nanosecond time scale and nanometer length scale, microscopic diffusion of water and cell constituents in the planarians. Measurable microscopic diffusivities were surprisingly well defined in such a complex system as living animals. The overall variation in the microscopic diffusivity of cell constituents was found to be far lower than the variation in the microscopic diffusivity of water in planarians in a temperature range of 284.5 to 304.1K.

  2. Multidimensional custom-made non-linear microscope: from ex-vivo to in-vivo imaging

    NASA Astrophysics Data System (ADS)

    Cicchi, R.; Sacconi, L.; Jasaitis, A.; O'Connor, R. P.; Massi, D.; Sestini, S.; de Giorgi, V.; Lotti, T.; Pavone, F. S.

    2008-09-01

    We have built a custom-made multidimensional non-linear microscope equipped with a combination of several non-linear laser imaging techniques involving fluorescence lifetime, multispectral two-photon and second-harmonic generation imaging. The optical system was mounted on a vertical honeycomb breadboard in an upright configuration, using two galvo-mirrors relayed by two spherical mirrors as scanners. A double detection system working in non-descanning mode has allowed both photon counting and a proportional regime. This experimental setup offering high spatial (micrometric) and temporal (sub-nanosecond) resolution has been used to image both ex-vivo and in-vivo biological samples, including cells, tissues, and living animals. Multidimensional imaging was used to spectroscopically characterize human skin lesions, as malignant melanoma and naevi. Moreover, two-color detection of two photon excited fluorescence was applied to in-vivo imaging of living mice intact neocortex, as well as to induce neuronal microlesions by femtosecond laser burning. The presented applications demonstrate the capability of the instrument to be used in a wide range of biological and biomedical studies.

  3. The Latest in Handheld Microscopes

    ERIC Educational Resources Information Center

    Wighting, Mervyn J.; Lucking, Robert A.; Christmann, Edwin P.

    2004-01-01

    Around 1590, Zacharias Jansenn of Holland invented the microscope. Jansenn, an eyeglass maker by trade, experimented with lenses and discovered that things appeared closer with combinations of lenses. Over the past 400 years, several refinements to microscopes have occurred, making it possible to magnify objects between 200 and 1,500 times their…

  4. Thermodynamic understanding of Sn whisker growth on the Cu surface in Cu(top)-Sn(bottom) bilayer system upon room temperature aging

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Huang, Lin; Jian, Wei; Lin, Bing

    2015-06-07

    Sn whiskers are observed by scanning electron microscope on the Cu surface in Cu(top)-Sn(bottom) bilayer system upon room temperature aging. Only Cu{sub 6}Sn{sub 5} phase appears in the X-ray diffraction patterns and no Sn element is detected in the Cu sublayer by scanning transmission electron microscopy. Based on the interfacial thermodynamics, the intermetallic Cu{sub 6}Sn{sub 5} compound phase may form directly at the Sn grain boundary. Driven by the stress gradient during the formation of Cu{sub 6}Sn{sub 5} compound at Sn grain boundaries, Sn atoms segregate onto the Cu surface and accumulate to form Sn whisker.

  5. The optics of microscope image formation.

    PubMed

    Wolf, David E

    2013-01-01

    Although geometric optics gives a good understanding of how the microscope works, it fails in one critical area, which is explaining the origin of microscope resolution. To accomplish this, one must consider the microscope from the viewpoint of physical optics. This chapter describes the theory of the microscope-relating resolution to the highest spatial frequency that a microscope can collect. The chapter illustrates how Huygens' principle or construction can be used to explain the propagation of a plane wave. It is shown that this limit increases with increasing numerical aperture (NA). As a corollary to this, resolution increases with decreasing wavelength because of how NA depends on wavelength. The resolution is higher for blue light than red light. Resolution is dependent on contrast, and the higher the contrast, the higher the resolution. This last point relates to issues of signal-to-noise and dynamic range. The use of video and new digital cameras has necessitated redefining classical limits such as those of Rayleigh's criterion. Copyright © 2007 Elsevier Inc. All rights reserved.

  6. Viscoplasticity: A thermodynamic formulation

    NASA Technical Reports Server (NTRS)

    Freed, A. D.; Chaboche, J. L.

    1989-01-01

    A thermodynamic foundation using the concept of internal state variables is given for a general theory of viscoplasticity, as it applies to initially isotropic materials. Three fundamental internal state variables are admitted. They are: a tensor valued back stress for kinematic effects, and the scalar valued drag and yield strengths for isotropic effects. All three are considered to phenomenologically evolve according to competitive processes between strain hardening, strain induced dynamic recovery, and time induced static recovery. Within this phenomenological framework, a thermodynamically admissible set of evolution equations is put forth. This theory allows each of the three fundamental internal variables to be composed as a sum of independently evolving constituents.

  7. Science 101: How Does an Electron Microscope Work?

    ERIC Educational Resources Information Center

    Robertson, Bill

    2013-01-01

    Contrary to popular opinion, electron microscopes are not used to look at electrons. They are used to look for structure in things that are too small to observe with an optical microscope, or to obtain images that are magnified much more than is obtainable with an optical microscope. To understand how electron microscopes work, it will help to go…

  8. Thermodynamic and transport properties of gaseous tetrafluoromethane in chemical equilibrium

    NASA Technical Reports Server (NTRS)

    Hunt, J. L.; Boney, L. R.

    1973-01-01

    Equations and in computer code are presented for the thermodynamic and transport properties of gaseous, undissociated tetrafluoromethane (CF4) in chemical equilibrium. The computer code calculates the thermodynamic and transport properties of CF4 when given any two of five thermodynamic variables (entropy, temperature, volume, pressure, and enthalpy). Equilibrium thermodynamic and transport property data are tabulated and pressure-enthalpy diagrams are presented.

  9. Thermodynamic geometry for a non-extensive ideal gas

    NASA Astrophysics Data System (ADS)

    López, J. L.; Obregón, O.; Torres-Arenas, J.

    2018-05-01

    A generalized entropy arising in the context of superstatistics is applied to an ideal gas. The curvature scalar associated to the thermodynamic space generated by this modified entropy is calculated using two formalisms of the geometric approach to thermodynamics. By means of the curvature/interaction hypothesis of the geometric approach to thermodynamic geometry it is found that as a consequence of considering a generalized statistics, an effective interaction arises but the interaction is not enough to generate a phase transition. This generalized entropy seems to be relevant in confinement or in systems with not so many degrees of freedom, so it could be interesting to use such entropies to characterize the thermodynamics of small systems.

  10. The microscope in the hatchery

    USGS Publications Warehouse

    Fish, F.F.

    1935-01-01

    Without the aid of the microscope, it is safe to assume that fish Culture would now stand exactly where it did seventy-five years ago when methods of artificial fertilization were first applied. It is also safe to assume that the results from fish culture would be as unsatisfactory as they were at that time when the fishery resources were steadily declining in spite of the increased liberation of advanced fry from the hatcheries. During the past few years the microscope has saved millions of fish in our hatcheries which otherwise would have been sacrificed to disease. Moreover, the microscope has permitted all of the recent work in selective breeding, nutritional requirements, and disease control. This work marks most of the progress fish culture has made during the past twenty-five years. This progress forms the first definite step away from the old system of hatching and distributing fish, a system which was founded by the ancient Chinese. The microscope has been the key which enabled the fish culturist to solve the riddle of success which has stood, unanswered, for 2,500 years.

  11. Thermodynamics of Computational Copying in Biochemical Systems

    NASA Astrophysics Data System (ADS)

    Ouldridge, Thomas E.; Govern, Christopher C.; ten Wolde, Pieter Rein

    2017-04-01

    Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that, as in computation, a canonical biochemical readout network generates correlations; extracting no work from these correlations sets a lower bound on dissipation. For general input, the biochemical network cannot reach this bound, even with arbitrarily slow reactions or weak thermodynamic driving. It faces an accuracy-dissipation trade-off that is qualitatively distinct from and worse than implied by the bound, and more complex steady-state copy processes cannot perform better. Nonetheless, the cost remains close to the thermodynamic bound unless accuracy is extremely high. Additionally, we show that biomolecular reactions could be used in thermodynamically optimal devices under exogenous manipulation of chemical fuels, suggesting an experimental system for testing computational thermodynamics.

  12. The application of thermodynamic and spectroscopic techniques to adhesion in the polyimide/Ti 6-4 and polyphenylquinoxaline/Ti 6-4 systems

    NASA Technical Reports Server (NTRS)

    Dias, S.; Wightman, J. P.

    1984-01-01

    The results of calorimetric measurements of Ti adherend surfaces are presented. The measurements were carried out after several chemical pretreatments and after fracture of several lap shear samples aged at high temperature. The exact composition of the Ti samples was Ti(6 percent Al-4 percent V). The adhesives used were polyimides and polyphenylquinoxalines (PPQ). Each chemical pretreatment was accompanied by a unique spectroscopic feature which was characterized by XPS, SEM, and specular reflectance infrared spectroscopy. The energetics of the interaction between primer solutions and the Ti adherend were evaluated by microcalorimetry. Changes in the structure of the surface oxide layer upon heating of the adherend were deduced from immersion temperatures of the PI and PPQ solutions. The XPS and SEM data are given is a table.

  13. Microscope and method of use

    DOEpatents

    Bongianni, Wayne L.

    1984-01-01

    A method and apparatus for electronically focusing and electronically scanning microscopic specimens are given. In the invention, visual images of even moving, living, opaque specimens can be acoustically obtained and viewed with virtually no time needed for processing (i.e., real time processing is used). And planar samples are not required. The specimens (if planar) need not be moved during scanning, although it will be desirable and possible to move or rotate nonplanar specimens (e.g., laser fusion targets) against the lens of the apparatus. No coupling fluid is needed, so specimens need not be wetted. A phase acoustic microscope is also made from the basic microscope components together with electronic mixers.

  14. Microscope and method of use

    DOEpatents

    Bongianni, W.L.

    1984-04-17

    A method and apparatus for electronically focusing and electronically scanning microscopic specimens are given. In the invention, visual images of even moving, living, opaque specimens can be acoustically obtained and viewed with virtually no time needed for processing (i.e., real time processing is used). And planar samples are not required. The specimens (if planar) need not be moved during scanning, although it will be desirable and possible to move or rotate nonplanar specimens (e.g., laser fusion targets) against the lens of the apparatus. No coupling fluid is needed, so specimens need not be wetted. A phase acoustic microscope is also made from the basic microscope components together with electronic mixers. 7 figs.

  15. Handy Microscopic Close-Range Videogrammetry

    NASA Astrophysics Data System (ADS)

    Esmaeili, F.; Ebadi, H.

    2017-09-01

    The modeling of small-scale objects is used in different applications such as medicine, industry, and cultural heritage. The capability of modeling small-scale objects using imaging with the help of hand USB digital microscopes and use of videogrammetry techniques has been implemented and evaluated in this paper. Use of this equipment and convergent imaging of the environment for modeling, provides an appropriate set of images for generation of three-dimensional models. The results of the measurements made with the help of a microscope micrometer calibration ruler have demonstrated that self-calibration of a hand camera-microscope set can help obtain a three-dimensional detail extraction precision of about 0.1 millimeters on small-scale environments.

  16. Predicting RNA pseudoknot folding thermodynamics

    PubMed Central

    Cao, Song; Chen, Shi-Jie

    2006-01-01

    Based on the experimentally determined atomic coordinates for RNA helices and the self-avoiding walks of the P (phosphate) and C4 (carbon) atoms in the diamond lattice for the polynucleotide loop conformations, we derive a set of conformational entropy parameters for RNA pseudoknots. Based on the entropy parameters, we develop a folding thermodynamics model that enables us to compute the sequence-specific RNA pseudoknot folding free energy landscape and thermodynamics. The model is validated through extensive experimental tests both for the native structures and for the folding thermodynamics. The model predicts strong sequence-dependent helix-loop competitions in the pseudoknot stability and the resultant conformational switches between different hairpin and pseudoknot structures. For instance, for the pseudoknot domain of human telomerase RNA, a native-like and a misfolded hairpin intermediates are found to coexist on the (equilibrium) folding pathways, and the interplay between the stabilities of these intermediates causes the conformational switch that may underlie a human telomerase disease. PMID:16709732

  17. Methane on Mars: Thermodynamic Equilibrium and Photochemical Calculations

    NASA Technical Reports Server (NTRS)

    Levine, J. S.; Summers, M. E.; Ewell, M.

    2010-01-01

    The detection of methane (CH4) in the atmosphere of Mars by Mars Express and Earth-based spectroscopy is very surprising, very puzzling, and very intriguing. On Earth, about 90% of atmospheric ozone is produced by living systems. A major question concerning methane on Mars is its origin - biological or geological. Thermodynamic equilibrium calculations indicated that methane cannot be produced by atmospheric chemical/photochemical reactions. Thermodynamic equilibrium calculations for three gases, methane, ammonia (NH3) and nitrous oxide (N2O) in the Earth s atmosphere are summarized in Table 1. The calculations indicate that these three gases should not exist in the Earth s atmosphere. Yet they do, with methane, ammonia and nitrous oxide enhanced 139, 50 and 12 orders of magnitude above their calculated thermodynamic equilibrium concentration due to the impact of life! Thermodynamic equilibrium calculations have been performed for the same three gases in the atmosphere of Mars based on the assumed composition of the Mars atmosphere shown in Table 2. The calculated thermodynamic equilibrium concentrations of the same three gases in the atmosphere of Mars is shown in Table 3. Clearly, based on thermodynamic equilibrium calculations, methane should not be present in the atmosphere of Mars, but it is in concentrations approaching 30 ppbv from three distinct regions on Mars.

  18. Transformations between Extensive and Intensive Versions of Thermodynamic Relationships

    ERIC Educational Resources Information Center

    Eberhart, James G.

    2010-01-01

    Most thermodynamic properties are either extensive (e.g., volume, energy, entropy, amount, etc.) or intensive (e.g., temperature, pressure, chemical potential, mole fraction, etc.). By the same token most of the mathematical relationships in thermodynamics can be written in extensive or intensive form. The basic laws of thermodynamics are usually…

  19. Studies on the interaction of apigenin with calf thymus DNA by spectroscopic methods

    NASA Astrophysics Data System (ADS)

    Zhang, Shufang; Sun, Xuejun; Kong, Rongmei; Xu, Mingming

    2015-02-01

    The interaction between apigenin and calf thymus deoxyribonucleic acid (ctDNA) in a pH 7.4 Tris-HCl buffer solution was investigated by UV-Vis spectroscopy, fluorescence spectroscopy, DNA melting techniques, and viscosity measurements. It was found that apigenin molecules could intercalate into the base pairs of DNA, forming a apigenin-DNA complex with a binding constant of K310K = 6.4 × 104 L mol-1. The thermodynamic parameters enthalpy change (ΔH), entropy change (ΔS) and Gibbs free energy (ΔG) were calculated to be 7.36 × 104 J mol-1, 329 J K-1 mol-1 and -2.84 × 104 J mol-1 at 310 K, respectively. Hydrophobic interaction was the predominant intermolecular force in stabilizing the apigenin-DNA complex. Thermal denaturation study suggested that the stabilization of the ctDNA helix was increased when the apigenin binding to ctDNA as indicated by the increase in thermal denaturation temperature of ctDNA at around 5.0 °C in the presence of apigenin. Spectroscopic techniques together with melting techniques and viscosity determination provided evidences of intercalation mode of binding for the interaction between apigenin and ctDNA.

  20. Molecular structure and spectroscopic characterization of Carbamazepine with experimental techniques and DFT quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Suhasini, M.; Sailatha, E.; Gunasekaran, S.; Ramkumaar, G. R.

    2015-04-01

    A systematic vibrational spectroscopic assignment and analysis of Carbamazepine has been carried out by using FT-IR, FT-Raman and UV spectral data. The vibrational analysis were aided by electronic structure calculations - ab initio (RHF) and hybrid density functional methods (B3LYP) performed with standard basis set 6-31G(d,p). Molecular equilibrium geometries, electronic energies, natural bond order analysis, harmonic vibrational frequencies and IR intensities have been computed. A detailed interpretation of the vibrational spectra of the molecule has been made on the basis of the calculated Potential Energy Distribution (PED) by VEDA program. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λmax were determined by HF/6-311++G(d,p) Time-Dependent method. The thermodynamic functions of the title molecule were also performed using the RHF and DFT methods. The restricted Hartree-Fock and density functional theory-based nuclear magnetic resonance (NMR) calculation procedure was also performed, and it was used for assigning the 13C and 1H NMR chemical shifts of Carbamazepine.

  1. Spectroscopic characterization of low dose rate brachytherapy sources

    NASA Astrophysics Data System (ADS)

    Beach, Stephen M.

    The low dose rate (LDR) brachytherapy seeds employed in permanent radioactive-source implant treatments usually use one of two radionuclides, 125I or 103Pd. The theoretically expected source spectroscopic output from these sources can be obtained via Monte Carlo calculation based upon seed dimensions and materials as well as the bare-source photon emissions for that specific radionuclide. However the discrepancies resulting from inconsistent manufacturing of sources in comparison to each other within model groups and simplified Monte Carlo calculational geometries ultimately result in undesirably large uncertainties in the Monte Carlo calculated values. This dissertation describes experimentally attained spectroscopic outputs of the clinically used brachytherapy sources in air and in liquid water. Such knowledge can then be applied to characterize these sources by a more fundamental and metro logically-pure classification, that of energy-based dosimetry. The spectroscopic results contained within this dissertation can be utilized in the verification and benchmarking of Monte Carlo calculational models of these brachytherapy sources. This body of work was undertaken to establish a usable spectroscopy system and analysis methods for the meaningful study of LDR brachytherapy seeds. The development of a correction algorithm and the analysis of the resultant spectroscopic measurements are presented. The characterization of the spectrometer and the subsequent deconvolution of the measured spectrum to obtain the true spectrum free of any perturbations caused by the spectrometer itself is an important contribution of this work. The approach of spectroscopic deconvolution that was applied in this work is derived in detail and it is applied to the physical measurements. In addition, the spectroscopically based analogs to the LDR dosimetry parameters that are currently employed are detailed, as well as the development of the theory and measurement methods to arrive at these

  2. A Comparative Study of Microscopic Images Captured by a Box Type Digital Camera Versus a Standard Microscopic Photography Camera Unit

    PubMed Central

    Desai, Nandini J.; Gupta, B. D.; Patel, Pratik Narendrabhai

    2014-01-01

    Introduction: Obtaining images of slides viewed by a microscope can be invaluable for both diagnosis and teaching.They can be transferred among technologically-advanced hospitals for further consultation and evaluation. But a standard microscopic photography camera unit (MPCU)(MIPS-Microscopic Image projection System) is costly and not available in resource poor settings. The aim of our endeavour was to find a comparable and cheaper alternative method for photomicrography. Materials and Methods: We used a NIKON Coolpix S6150 camera (box type digital camera) with Olympus CH20i microscope and a fluorescent microscope for the purpose of this study. Results: We got comparable results for capturing images of light microscopy, but the results were not as satisfactory for fluorescent microscopy. Conclusion: A box type digital camera is a comparable, less expensive and convenient alternative to microscopic photography camera unit. PMID:25478350

  3. Microscope sterility during spine surgery.

    PubMed

    Bible, Jesse E; O'Neill, Kevin R; Crosby, Colin G; Schoenecker, Jonathan G; McGirt, Matthew J; Devin, Clinton J

    2012-04-01

    Prospective study. Assess the contamination rates of sterile microscope drapes after spine surgery. The use of the operating microscope has become more prevalent in certain spine procedures, providing superior magnification, visualization, and illumination of the operative field. However, it may represent an additional source of bacterial contamination and increase the risk of developing a postoperative infection. This study included 25 surgical spine cases performed by a single spine surgeon that required the use of the operative microscope. Sterile culture swabs were used to obtain samples from 7 defined locations on the microscope drape after its use during the operation. The undraped technician's console was sampled in each case as a positive control, and an additional 25 microscope drapes were swabbed immediately after they were applied to the microscope to obtain negative controls. Swab samples were assessed for bacterial growth on 5% sheep blood Columbia agar plates using a semiquantitative technique. No growth was observed on any of the 25 negative control drapes. In contrast, 100% of preoperative and 96% of postoperative positive controls demonstrated obvious contamination. In the postoperative group, all 7 sites of evaluation were found to be contaminated with rates of 12% to 44%. Four of the 7 evaluated locations were found to have significant contamination rates compared with negative controls, including the shafts of the optic eyepieces on the main surgeon side (24%, P = 0.022), "forehead" portion on both the main surgeon (24%, P = 0.022) and assistant sides (28%, P = 0.010), and "overhead" portion of the drape (44%, P = 0.0002). Bacterial contamination of the operative microscope was found to be significant after spine surgery. Contamination was more common around the optic eyepieces, likely due to inadvertent touching of unsterile portions. Similarly, all regions above the eyepieces also have a propensity for contamination because of unknown contact

  4. Miniature self-contained vacuum compatible electronic imaging microscope

    DOEpatents

    Naulleau, Patrick P.; Batson, Phillip J.; Denham, Paul E.; Jones, Michael S.

    2001-01-01

    A vacuum compatible CCD-based microscopic camera with an integrated illuminator. The camera can provide video or still feed from the microscope contained within a vacuum chamber. Activation of an optional integral illuminator can provide light to illuminate the microscope subject. The microscope camera comprises a housing with a objective port, modified objective, beam-splitter, CCD camera, and LED illuminator.

  5. Thermodynamics, Life, the Universe and Everything

    NASA Astrophysics Data System (ADS)

    Neswald, Elizabeth

    2015-01-01

    The laws of thermodynamics were developed in the first half of the nineteenth century to describe processes governing the working of steam engines. The mechanical equivalent of heat, which quantified the relationship between heat and motion, enabled the quantification and comparison of all energy transformation processes. The energy laws and the mechanical equivalent of heat quickly moved out of the narrower field of physics to form the basis of a cosmic narrative that began with stellar evolution and continued to universal heat death. Newer physiological theories turned to the energy laws to explain life processes, energy and entropy were integrated into theories of biological evolution and degeneration, and economists and cultural theorists turned to thermodynamics to explore both the limits of natural resources and economic expansion and the contradictions of industrial modernity. This paper discusses the career of thermodynamics as an explanatory model and cultural commonplace in the late nineteenth and early twentieth centuries, and the different scientific, religious, and social perspectives that could be expressed through this model. Connected through the entropy law intimately to irreversible processes and time, thermodynamics provided an arena to debate which way the world was going.

  6. Thermodynamically Feasible Kinetic Models of Reaction Networks

    PubMed Central

    Ederer, Michael; Gilles, Ernst Dieter

    2007-01-01

    The dynamics of biological reaction networks are strongly constrained by thermodynamics. An holistic understanding of their behavior and regulation requires mathematical models that observe these constraints. However, kinetic models may easily violate the constraints imposed by the principle of detailed balance, if no special care is taken. Detailed balance demands that in thermodynamic equilibrium all fluxes vanish. We introduce a thermodynamic-kinetic modeling (TKM) formalism that adapts the concepts of potentials and forces from irreversible thermodynamics to kinetic modeling. In the proposed formalism, the thermokinetic potential of a compound is proportional to its concentration. The proportionality factor is a compound-specific parameter called capacity. The thermokinetic force of a reaction is a function of the potentials. Every reaction has a resistance that is the ratio of thermokinetic force and reaction rate. For mass-action type kinetics, the resistances are constant. Since it relies on the thermodynamic concept of potentials and forces, the TKM formalism structurally observes detailed balance for all values of capacities and resistances. Thus, it provides an easy way to formulate physically feasible, kinetic models of biological reaction networks. The TKM formalism is useful for modeling large biological networks that are subject to many detailed balance relations. PMID:17208985

  7. Dissipative open systems theory as a foundation for the thermodynamics of linear systems.

    PubMed

    Delvenne, Jean-Charles; Sandberg, Henrik

    2017-03-06

    In this paper, we advocate the use of open dynamical systems, i.e. systems sharing input and output variables with their environment, and the dissipativity theory initiated by Jan Willems as models of thermodynamical systems, at the microscopic and macroscopic level alike. We take linear systems as a study case, where we show how to derive a global Lyapunov function to analyse networks of interconnected systems. We define a suitable notion of dynamic non-equilibrium temperature that allows us to derive a discrete Fourier law ruling the exchange of heat between lumped, discrete-space systems, enriched with the Maxwell-Cattaneo correction. We complete these results by a brief recall of the steps that allow complete derivation of the dissipation and fluctuation in macroscopic systems (i.e. at the level of probability distributions) from lossless and deterministic systems.This article is part of the themed issue 'Horizons of cybernetical physics'. © 2017 The Author(s).

  8. Spectroscopic wear detector

    NASA Technical Reports Server (NTRS)

    Madzsar, George C. (Inventor)

    1993-01-01

    The elemental composition of a material exposed to hot gases and subjected to wear is determined. Atoms of an elemental species not appearing in this material are implanted in a surface at a depth based on the maximum allowable wear. The exhaust gases are spectroscopically monitored to determine the exposure of these atoms when the maximum allowable wear is reached.

  9. Thermodynamic and structural signatures of water-driven methane-methane attraction in coarse-grained mW water.

    PubMed

    Song, Bin; Molinero, Valeria

    2013-08-07

    Hydrophobic interactions are responsible for water-driven processes such as protein folding and self-assembly of biomolecules. Microscopic theories and molecular simulations have been used to study association of a pair of methanes in water, the paradigmatic example of hydrophobic attraction, and determined that entropy is the driving force for the association of the methane pair, while the enthalpy disfavors it. An open question is to which extent coarse-grained water models can still produce correct thermodynamic and structural signatures of hydrophobic interaction. In this work, we investigate the hydrophobic interaction between a methane pair in water at temperatures from 260 to 340 K through molecular dynamics simulations with the coarse-grained monatomic water model mW. We find that the coarse-grained model correctly represents the free energy of association of the methane pair, the temperature dependence of free energy, and the positive change in entropy and enthalpy upon association. We investigate the relationship between thermodynamic signatures and structural order of water through the analysis of the spatial distribution of the density, energy, and tetrahedral order parameter Qt of water. The simulations reveal an enhancement of tetrahedral order in the region between the first and second hydration shells of the methane molecules. The increase in tetrahedral order, however, is far from what would be expected for a clathrate-like or ice-like shell around the solutes. This work shows that the mW water model reproduces the key signatures of hydrophobic interaction without long ranged electrostatics or the need to be re-parameterized for different thermodynamic states. These characteristics, and its hundred-fold increase in efficiency with respect to atomistic models, make mW a promising water model for studying water-driven hydrophobic processes in more complex systems.

  10. Thermodynamic efficiency of learning a rule in neural networks

    NASA Astrophysics Data System (ADS)

    Goldt, Sebastian; Seifert, Udo

    2017-11-01

    Biological systems have to build models from their sensory input data that allow them to efficiently process previously unseen inputs. Here, we study a neural network learning a binary classification rule for these inputs from examples provided by a teacher. We analyse the ability of the network to apply the rule to new inputs, that is to generalise from past experience. Using stochastic thermodynamics, we show that the thermodynamic costs of the learning process provide an upper bound on the amount of information that the network is able to learn from its teacher for both batch and online learning. This allows us to introduce a thermodynamic efficiency of learning. We analytically compute the dynamics and the efficiency of a noisy neural network performing online learning in the thermodynamic limit. In particular, we analyse three popular learning algorithms, namely Hebbian, Perceptron and AdaTron learning. Our work extends the methods of stochastic thermodynamics to a new type of learning problem and might form a suitable basis for investigating the thermodynamics of decision-making.

  11. SPECTROSCOPIC ORBITS FOR 15 LATE-TYPE STARS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Willmarth, Daryl W.; Abt, Helmut A.; Fekel, Francis C.

    2016-08-01

    Spectroscopic orbital elements are determined for 15 stars with periods from 8 to 6528 days with six orbits computed for the first time. Improved astrometric orbits are computed for two stars and one new orbit is derived. Visual orbits were previously determined for four stars, four stars are members of multiple systems, and five stars have Hipparcos “G” designations or have been resolved by speckle interferometry. For the nine binaries with previous spectroscopic orbits, we determine improved or comparable elements. For HD 28271 and HD 200790, our spectroscopic results support the conclusions of previous authors that the large values of their massmore » functions and lack of detectable secondary spectrum argue for the secondary in each case being a pair of low-mass dwarfs. The orbits given here may be useful in combination with future interferometric and Gaia satellite observations.« less

  12. The thermodynamic scale of inorganic crystalline metastability

    PubMed Central

    Sun, Wenhao; Dacek, Stephen T.; Ong, Shyue Ping; Hautier, Geoffroy; Jain, Anubhav; Richards, William D.; Gamst, Anthony C.; Persson, Kristin A.; Ceder, Gerbrand

    2016-01-01

    The space of metastable materials offers promising new design opportunities for next-generation technological materials, such as complex oxides, semiconductors, pharmaceuticals, steels, and beyond. Although metastable phases are ubiquitous in both nature and technology, only a heuristic understanding of their underlying thermodynamics exists. We report a large-scale data-mining study of the Materials Project, a high-throughput database of density functional theory–calculated energetics of Inorganic Crystal Structure Database structures, to explicitly quantify the thermodynamic scale of metastability for 29,902 observed inorganic crystalline phases. We reveal the influence of chemistry and composition on the accessible thermodynamic range of crystalline metastability for polymorphic and phase-separating compounds, yielding new physical insights that can guide the design of novel metastable materials. We further assert that not all low-energy metastable compounds can necessarily be synthesized, and propose a principle of ‘remnant metastability’—that observable metastable crystalline phases are generally remnants of thermodynamic conditions where they were once the lowest free-energy phase. PMID:28138514

  13. Designs for a quantum electron microscope.

    PubMed

    Kruit, P; Hobbs, R G; Kim, C-S; Yang, Y; Manfrinato, V R; Hammer, J; Thomas, S; Weber, P; Klopfer, B; Kohstall, C; Juffmann, T; Kasevich, M A; Hommelhoff, P; Berggren, K K

    2016-05-01

    One of the astounding consequences of quantum mechanics is that it allows the detection of a target using an incident probe, with only a low probability of interaction of the probe and the target. This 'quantum weirdness' could be applied in the field of electron microscopy to generate images of beam-sensitive specimens with substantially reduced damage to the specimen. A reduction of beam-induced damage to specimens is especially of great importance if it can enable imaging of biological specimens with atomic resolution. Following a recent suggestion that interaction-free measurements are possible with electrons, we now analyze the difficulties of actually building an atomic resolution interaction-free electron microscope, or "quantum electron microscope". A quantum electron microscope would require a number of unique components not found in conventional transmission electron microscopes. These components include a coherent electron beam-splitter or two-state-coupler, and a resonator structure to allow each electron to interrogate the specimen multiple times, thus supporting high success probabilities for interaction-free detection of the specimen. Different system designs are presented here, which are based on four different choices of two-state-couplers: a thin crystal, a grating mirror, a standing light wave and an electro-dynamical pseudopotential. Challenges for the detailed electron optical design are identified as future directions for development. While it is concluded that it should be possible to build an atomic resolution quantum electron microscope, we have also identified a number of hurdles to the development of such a microscope and further theoretical investigations that will be required to enable a complete interpretation of the images produced by such a microscope. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  14. Breakup effects on alpha spectroscopic factors of 16O

    NASA Astrophysics Data System (ADS)

    Adhikari, S.; Basu, C.; Sugathan, P.; Jhinghan, A.; Behera, B. R.; Saneesh, N.; Kaur, G.; Thakur, M.; Mahajan, R.; Dubey, R.; Mitra, A. K.

    2017-01-01

    The triton angular distribution for the 12C(7Li,t)16O* reaction is measured at 20 MeV, populating discrete states of 16O. Continuum discretized coupled reaction channel calculations are used to to extract the alpha spectroscopic properties of 16O states instead of the distorted wave born approximation theory to include the effects of breakup on the transfer process. The alpha reduced width, spectroscopic factors and the asymptotic normalization constant (ANC) of 16O states are extracted. The error in the spectroscopic factor is about 35% and in that of the ANC about 27%.

  15. Mars Life? - Microscopic Egg-shaped Structures

    NASA Image and Video Library

    1996-08-09

    This electron microscope image shows egg-shaped structures, some of which may be possible microscopic fossils of Martian origin as discussed by NASA research published in the Aug. 16, 1996. http://photojournal.jpl.nasa.gov/catalog/PIA00286

  16. Scientists View Battery Under Microscope

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    None

    2015-04-10

    PNNL researchers use a special microscope setup that shows the inside of a battery as it charges and discharges. This battery-watching microscope is located at EMSL, DOE's Environmental Molecular Sciences Laboratory that resides at PNNL. Researchers the world over can visit EMSL and use special instruments like this, many of which are the only one of their kind available to scientists.

  17. Scientists View Battery Under Microscope

    ScienceCinema

    None

    2018-01-16

    PNNL researchers use a special microscope setup that shows the inside of a battery as it charges and discharges. This battery-watching microscope is located at EMSL, DOE's Environmental Molecular Sciences Laboratory that resides at PNNL. Researchers the world over can visit EMSL and use special instruments like this, many of which are the only one of their kind available to scientists.

  18. Review of spectroscopic parameters for upper atmospheric measurements

    NASA Technical Reports Server (NTRS)

    Smith, M. A. H. (Editor)

    1985-01-01

    The workshop included communication of spectroscopic data requirements for the planned upper atmosphere research satellite (UARS) mission, review of the status of currently available spectroscopic parameters, and recommendation of additional studies. The objectives were accomplished and resulted in a series of general and specific recommendations for laboratory spectroscopy research to meet the needs of UARS and other atmospheric remote sensing programs.

  19. Theoretical Studies of Small-System Thermodynamics in Energetic Materials

    DTIC Science & Technology

    2016-01-06

    SECURITY CLASSIFICATION OF: This is a comprehensive theoretical research program to investigate the fundamental principles of small-system thermodynamics ...a.k.a. nanothermodynamics). The proposed work is motivated by our desire to better understand the fundamental dynamics and thermodynamics of...for Public Release; Distribution Unlimited Final Report: Theoretical Studies of Small-System Thermodynamics in Energetic Materials The views, opinions

  20. Nonequilibrium thermodynamics of dilute polymer solutions in flow.

    PubMed

    Latinwo, Folarin; Hsiao, Kai-Wen; Schroeder, Charles M

    2014-11-07

    Modern materials processing applications and technologies often occur far from equilibrium. To this end, the processing of complex materials such as polymer melts and nanocomposites generally occurs under strong deformations and flows, conditions under which equilibrium thermodynamics does not apply. As a result, the ability to determine the nonequilibrium thermodynamic properties of polymeric materials from measurable quantities such as heat and work is a major challenge in the field. Here, we use work relations to show that nonequilibrium thermodynamic quantities such as free energy and entropy can be determined for dilute polymer solutions in flow. In this way, we determine the thermodynamic properties of DNA molecules in strong flows using a combination of simulations, kinetic theory, and single molecule experiments. We show that it is possible to calculate polymer relaxation timescales purely from polymer stretching dynamics in flow. We further observe a thermodynamic equivalence between nonequilibrium and equilibrium steady-states for polymeric systems. In this way, our results provide an improved understanding of the energetics of flowing polymer solutions.

  1. Mars Life? - Microscopic Egg-shaped Structures

    NASA Technical Reports Server (NTRS)

    1996-01-01

    This electron microscope image shows egg-shaped structures, some of which may be possible microscopic fossils of Martian origin as discussed by NASA research published in the Aug. 16, 1996, issue of the journal Science. A two-year investigation found organic molecules, mineral features characteristic of biological activity and possible microscopic fossils such as these inside of an ancient Martian rock that fell to Earth as a meteorite. The largest possible fossils are less than 1/100th the diameter of a human hair in size while most are ten times smaller.

  2. T.D.S. spectroscopic databank for spherical tops: DOS version

    NASA Astrophysics Data System (ADS)

    Tyuterev, V. G.; Babikov, Yu. L.; Tashkun, S. A.; Perevalov, V. I.; Nikitin, A.; Champion, J.-P.; Wenger, C.; Pierre, C.; Pierre, G.; Hilico, J.-C.; Loete, M.

    1994-10-01

    T.D.S. (Traitement de Donnees Spectroscopiques or Tomsk-Dijon-Spectroscopy project) is a computer package concerned with high resolution spectroscopy of spherical top molecules like CH4, CF4, SiH4, SiF4, SnH4, GeH4, SF6, etc. T.D.S. contains information, fundamental spectroscopic data (energies, transition moments, spectroscopic constants) recovered from comprehensive modeling and simultaneous fitting of experimental spectra, and associated software written in C. The T.D.S. goal is to provide an access to all available information on vibration-rotation molecular states and transitions including various spectroscopic processes (Stark, Raman, etc.) under extended conditions based on extrapolations of laboratory measurements using validated theoretical models. Applications for T.D.S. may include: education/training in molecular physics, quantum chemistry, laser physics; spectroscopic applications (analysis, laser spectroscopy, atmospheric optics, optical standards, spectroscopic atlases); applications to environment studies and atmospheric physics (remote sensing); data supply for specific databases; and to photochemistry (laser excitation, multiphoton processes). The reported DOS-version is designed for IBM and compatible personal computers.

  3. Molecular structural property and potential energy dependence on nonequilibrium-thermodynamic state point of liquid n-hexadecane under shear.

    PubMed

    Tseng, Huan-Chang; Chang, Rong-Yeu; Wu, Jiann-Shing

    2011-01-28

    Extensive computer experiments have been conducted in order to shed light on the macroscopic shear flow behavior of liquid n-hexadecane fluid under isobaric-isothermal conditions through the nonequilibrium molecular dynamic methodology. With respect to shear rates, the accompanying variations in structural properties of the fluid span the microscopic range of understanding from the intrinsic to extrinsic characteristics. As drawn from the average value of bond length and bond angle, the distribution of dihedral angle, and the radius distribution function of intramolecular and intermolecular van der Waals distances, these intrinsic structures change with hardness, except in the situation of extreme shear rates. The shear-induced variation of thermodynamic state curve along with the shear rate studied is shown to consist of both the quasiequilibrium state plateau and the nonequilibrium-thermodynamic state slope. Significantly, the occurrence of nonequilibrium-thermodynamic state behavior is attributed to variations in molecular potential energies, which include bond stretching, bond bending, bond torsion, and intra- and intermolecular van der Waals interactions. To unfold the physical representation of extrinsic structural deformation, under the aggressive influence of a shear flow field, the molecular dimension and appearance can be directly described via the squared radius of gyration and the sphericity angle, R(g)(2) and ϕ, respectively. In addition, a specific orientational order S(x) defines the alignment of the molecules with the flow direction of the x-axis. As a result, at low shear rates, the overall molecules are slightly stretched and shaped in a manner that is increasingly ellipsoidal. Simultaneously, there is an obvious enhancement in the order. In contrast to high shear rates, the molecules spontaneously shrink themselves with a decreased value of R(g)(2), while their shape and order barely vary with an infinite value of ϕ and S(x). It is important to

  4. Teaching Differentials in Thermodynamics Using Spatial Visualization

    ERIC Educational Resources Information Center

    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…

  5. Detonation Jet Engine. Part 1--Thermodynamic Cycle

    ERIC Educational Resources Information Center

    Bulat, Pavel V.; Volkov, Konstantin N.

    2016-01-01

    We present the most relevant works on jet engine design that utilize thermodynamic cycle of detonative combustion. The efficiency advantages of thermodynamic detonative combustion cycle over Humphrey combustion cycle at constant volume and Brayton combustion cycle at constant pressure were demonstrated. An ideal Ficket-Jacobs detonation cycle, and…

  6. Understanding Product Optimization: Kinetic versus Thermodynamic Control.

    ERIC Educational Resources Information Center

    Lin, King-Chuen

    1988-01-01

    Discusses the concept of kinetic versus thermodynamic control of reactions. Explains on the undergraduate level (1) the role of kinetic and thermodynamic control in kinetic equations, (2) the influence of concentration and temperature upon the reaction, and (3) the application of factors one and two to synthetic chemistry. (MVL)

  7. Canonical fluid thermodynamics

    NASA Technical Reports Server (NTRS)

    Schmid, L. A.

    1972-01-01

    The space-time integral of the thermodynamic pressure plays the role of the thermodynamic potential for compressible, adiabatic flow in the sense that the pressure integral for stable flow is less than for all slightly different flows. This stability criterion can be converted into a variational minimum principle by requiring the molar free-enthalpy and the temperature, which are the arguments of the pressure function, to be generalized velocities, that is, the proper-time derivatives of scalar spare-time functions which are generalized coordinates in the canonical formalism. In a fluid context, proper-time differentiation must be expressed in terms of three independent quantities that specify the fluid velocity. This can be done in several ways, all of which lead to different variants (canonical transformations) of the same constraint-free action integral whose Euler-Lagrange equations are just the well-known equations of motion for adiabatic compressible flow.

  8. Thermodynamics with pressure and volume under charged particle absorption

    NASA Astrophysics Data System (ADS)

    Gwak, Bogeun

    2017-11-01

    We investigate the variation of the charged anti-de Sitter black hole under charged particle absorption by considering thermodynamic volume. When the energy of the particle is considered to contribute to the internal energy of the black hole, the variation exactly corresponds to the prediction of the first law of thermodynamics. Nevertheless, we find the decrease of the Bekenstein-Hawking entropy for extremal and near-extremal black holes under the absorption, which is an irreversible process. This violation of the second law of thermodynamics is only found when considering thermodynamic volume. We test the weak cosmic censorship conjecture affected by the violation. Fortunately, the conjecture is still valid, but extremal and near-extremal black holes do not change their configurations when any particle enters the black hole. This result is quite different from the case in which thermodynamic volume is not considered.

  9. Biochemical thermodynamics: applications of Mathematica.

    PubMed

    Alberty, Robert A

    2006-01-01

    The most efficient way to store thermodynamic data on enzyme-catalyzed reactions is to use matrices of species properties. Since equilibrium in enzyme-catalyzed reactions is reached at specified pH values, the thermodynamics of the reactions is discussed in terms of transformed thermodynamic properties. These transformed thermodynamic properties are complicated functions of temperature, pH, and ionic strength that can be calculated from the matrices of species values. The most important of these transformed thermodynamic properties is the standard transformed Gibbs energy of formation of a reactant (sum of species). It is the most important because when this function of temperature, pH, and ionic strength is known, all the other standard transformed properties can be calculated by taking partial derivatives. The species database in this package contains data matrices for 199 reactants. For 94 of these reactants, standard enthalpies of formation of species are known, and so standard transformed Gibbs energies, standard transformed enthalpies, standard transformed entropies, and average numbers of hydrogen atoms can be calculated as functions of temperature, pH, and ionic strength. For reactions between these 94 reactants, the changes in these properties can be calculated over a range of temperatures, pHs, and ionic strengths, and so can apparent equilibrium constants. For the other 105 reactants, only standard transformed Gibbs energies of formation and average numbers of hydrogen atoms at 298.15 K can be calculated. The loading of this package provides functions of pH and ionic strength at 298.15 K for standard transformed Gibbs energies of formation and average numbers of hydrogen atoms for 199 reactants. It also provides functions of temperature, pH, and ionic strength for the standard transformed Gibbs energies of formation, standard transformed enthalpies of formation, standard transformed entropies of formation, and average numbers of hydrogen atoms for 94

  10. Shearing interference microscope for step-height measurements.

    PubMed

    Trịnh, Hưng-Xuân; Lin, Shyh-Tsong; Chen, Liang-Chia; Yeh, Sheng-Lih; Chen, Chin-Sheng; Hoang, Hong-Hai

    2017-05-01

    A shearing interference microscope using a Savart prism as the shear plate is proposed for inspecting step-heights. Where the light beam propagates through the Savart prism and microscopic system to illuminate the sample, it then turns back to re-pass through the Savart prism and microscopic system to generate a shearing interference pattern on the camera. Two measurement modes, phase-shifting and phase-scanning, can be utilized to determine the depths of the step-heights on the sample. The first mode, which employs a narrowband source, is based on the five-step phase-shifting algorithm and has a measurement range of a quarter-wavelength. The second mode, which adopts a broadband source, is based on peak-intensity identification technology and has a measurement range up to a few micrometres. This paper is to introduce the configuration and measurement theory of this microscope, perform a setup used to implement it, and present the experimental results from the uses of the setup. The results not only verify the validity but also confirm the high measurement repeatability of the proposed microscope. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

  11. Thermodynamics of rock forming crystalline solutions

    NASA Technical Reports Server (NTRS)

    Saxena, S. K.

    1971-01-01

    Analysis of phase diagrams and cation distributions within crystalline solutions as means of obtaining thermodynamic data on rock forming crystalline solutions is discussed along with some aspects of partitioning of elements in coexisting phases. Crystalline solutions, components in a silicate mineral, and chemical potentials of these components were defined. Examples were given for calculating thermodynamic mixing functions in the CaW04-SrW04, olivine-chloride solution, and orthopyroxene systems.

  12. Microscopical and functional aspects of calcium-transport and deposition in terrestrial isopods.

    PubMed

    Ziegler, Andreas; Fabritius, Helge; Hagedorn, Monica

    2005-01-01

    Terrestrial isopods (Crustacea) are excellent model organisms to study epithelial calcium-transport and the regulation of biomineralization processes. They molt frequently and resorb cuticular CaCO(3) before the molt to prevent excessive loss of Ca(2+) ions when the old cuticle is shed. The resorbed mineral is stored in CaCO(3) deposits within the ecdysial gap of the first four anterior sternites. After the molt, the deposits are quickly resorbed to mineralise the posterior part of the new cuticle. The deposits contain numerous small spherules composed of an organic matrix and amorphous CaCO(3), which has a high solubility and, therefore, facilitates quick mobilization of Ca(2+) and HCO(3)(-) ions. During the formation and resorption of the deposits large amounts of Ca(2+), HCO(3)(-) and H(+) are transported across the anterior sternal epithelial cells. Within the last years, various light and electron microscopical techniques have been used to characterize the CaCO(3) deposits and the cellular mechanisms involved in biomineralization. The work on the CaCO(3) deposits includes studies on the ultrastructure of the deposits, the sequence of events during deposit formation and dissolution, and the mineral composition of the sternal deposits. The differentiation of the anterior sternal epithelial cells and the mechanisms of epithelial ion transport required for the mineralization and demineralisation of the deposits was studied using various analytical light and electron microscopical techniques including polarized light microscopy, immunocytochemistry, electron microprobe analysis, electron energy loss spectroscopy and electron spectroscopic imaging. Comparative analysis of deposit morphology and the differentiation of the sternal epithelia provide information on the evolution of CaCO(3) deposit formation in relation to the degree of adaptation to terrestrial environments.

  13. Thermodynamic properties of pressurized PH3 superconductor

    NASA Astrophysics Data System (ADS)

    Koka, S.; Rao, G. Venugopal

    2018-05-01

    The paper presents the superconducting thermodynamic functions determined for pressurized phosphorus trihydride (PH3). In particular, free energy difference ΔF, thermodynamic critical field Hc, specific heat etc. have been calculated using analytical expressions. The calculations were performed in the frame work of the strong-coupling formalism. The obtained dimensionless parameters: RΔ ≡ 2Δ(0)/kBTc, RC ≡ ΔC(Tc)/CN(Tc) and RH≡TcCN(Tc)/Hc2(0) are 4.05, 1.96 and 0.156 respectively, which significantly differ from the values arising from the BCS theory of superconductivity. The thermodynamic properties strongly depend on the depairing electron correlations and retardation effects.

  14. Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

    PubMed Central

    Flamholz, Avi; Reznik, Ed; Liebermeister, Wolfram; Milo, Ron

    2014-01-01

    In metabolism research, thermodynamics is usually used to determine the directionality of a reaction or the feasibility of a pathway. However, the relationship between thermodynamic potentials and fluxes is not limited to questions of directionality: thermodynamics also affects the kinetics of reactions through the flux-force relationship, which states that the logarithm of the ratio between the forward and reverse fluxes is directly proportional to the change in Gibbs energy due to a reaction (ΔrG′). Accordingly, if an enzyme catalyzes a reaction with a ΔrG′ of -5.7 kJ/mol then the forward flux will be roughly ten times the reverse flux. As ΔrG′ approaches equilibrium (ΔrG′ = 0 kJ/mol), exponentially more enzyme counterproductively catalyzes the reverse reaction, reducing the net rate at which the reaction proceeds. Thus, the enzyme level required to achieve a given flux increases dramatically near equilibrium. Here, we develop a framework for quantifying the degree to which pathways suffer these thermodynamic limitations on flux. For each pathway, we calculate a single thermodynamically-derived metric (the Max-min Driving Force, MDF), which enables objective ranking of pathways by the degree to which their flux is constrained by low thermodynamic driving force. Our framework accounts for the effect of pH, ionic strength and metabolite concentration ranges and allows us to quantify how alterations to the pathway structure affect the pathway's thermodynamics. Applying this methodology to pathways of central metabolism sheds light on some of their features, including metabolic bypasses (e.g., fermentation pathways bypassing substrate-level phosphorylation), substrate channeling (e.g., of oxaloacetate from malate dehydrogenase to citrate synthase), and use of alternative cofactors (e.g., quinone as an electron acceptor instead of NAD). The methods presented here place another arrow in metabolic engineers' quiver, providing a simple means of evaluating

  15. Thermodynamics: A Stirling effort

    NASA Astrophysics Data System (ADS)

    Horowitz, Jordan M.; Parrondo, Juan M. R.

    2012-02-01

    The realization of a single-particle Stirling engine pushes thermodynamics into stochastic territory where fluctuations dominate, and points towards a better understanding of energy transduction at the microscale.

  16. Understanding First Law of Thermodynamics through Activities

    ERIC Educational Resources Information Center

    Pathare, Shirish; Huli, Saurabhee; Ladage, Savita; Pradhan, H. C.

    2018-01-01

    The first law of thermodynamics involves several types of energies and many studies have shown that students lack awareness of them. They have difficulties in applying the law to different thermodynamic processes. These observations were confirmed in our pilot studies, carried out with students from undergraduate colleges across the whole of…

  17. van Leeuwenhoek microscopes-where are they now?

    PubMed

    Robertson, Lesley A

    2015-05-01

    When Antonie van Leeuwenhoek died, he left over 500 simple microscopes, aalkijkers (an adaption of his microscope to allow the examination of blood circulation in the tails of small eels) and lenses, yet now there are only 10 microscopes with a claim to being authentic, one possible aalkijker and six lenses. He made microscopes with more than one lens, and possibly three forms of the aalkijker. This paper attempts to establish exactly what he left and trace the fate of some of the others using the earliest possible documents and publications. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Spectroscopic detection

    DOEpatents

    Woskov, Paul P.; Hadidi, Kamal

    2003-01-01

    In embodiments, spectroscopic monitor monitors modulated light signals to detect low levels of contaminants and other compounds in the presence of background interference. The monitor uses a spectrometer that includes a transmissive modulator capable of causing different frequency ranges to move onto and off of the detector. The different ranges can include those with the desired signal and those selected to subtract background contributions from those with the desired signal. Embodiments of the system are particularly useful for monitoring metal concentrations in combustion effluent.

  19. Measuring the Thermodynamics of the Alloy/Scale Interface

    NASA Technical Reports Server (NTRS)

    Copland, Evan

    2004-01-01

    A method is proposed for the direct measurement of the thermodynamic properties of the alloy and oxide compound at the alloy/scale interface observed during steady-state oxidation. The thermodynamic properties of the alloy/scale interface define the driving force for solid-state transport in the alloy and oxide compound. Accurate knowledge of thermodynamic properties of the interface will advance our understanding of oxidation behavior. The method is based on the concept of local equilibrium and assumes that an alloy+scale equilibrium very closely approximates the alloy/scale interface observed during steady-state oxidation. The thermodynamics activities of this alloy+scale equilibrium are measured directly by Knudsen effusion-cell mass spectrometer (KEMS) using the vapor pressure technique. The theory and some practical considerations of this method are discussed in terms of beta-NiAl oxidation.

  20. Modeling the Non-Equilibrium Process of the Chemical Adsorption of Ammonia on GaN(0001) Reconstructed Surfaces Based on Steepest-Entropy-Ascent Quantum Thermodynamics.

    PubMed

    Kusaba, Akira; Li, Guanchen; von Spakovsky, Michael R; Kangawa, Yoshihiro; Kakimoto, Koichi

    2017-08-15

    Clearly understanding elementary growth processes that depend on surface reconstruction is essential to controlling vapor-phase epitaxy more precisely. In this study, ammonia chemical adsorption on GaN(0001) reconstructed surfaces under metalorganic vapor phase epitaxy (MOVPE) conditions (3Ga-H and N ad -H + Ga-H on a 2 × 2 unit cell) is investigated using steepest-entropy-ascent quantum thermodynamics (SEAQT). SEAQT is a thermodynamic-ensemble based, first-principles framework that can predict the behavior of non-equilibrium processes, even those far from equilibrium where the state evolution is a combination of reversible and irreversible dynamics. SEAQT is an ideal choice to handle this problem on a first-principles basis since the chemical adsorption process starts from a highly non-equilibrium state. A result of the analysis shows that the probability of adsorption on 3Ga-H is significantly higher than that on N ad -H + Ga-H. Additionally, the growth temperature dependence of these adsorption probabilities and the temperature increase due to the heat of reaction is determined. The non-equilibrium thermodynamic modeling applied can lead to better control of the MOVPE process through the selection of preferable reconstructed surfaces. The modeling also demonstrates the efficacy of DFT-SEAQT coupling for determining detailed non-equilibrium process characteristics with a much smaller computational burden than would be entailed with mechanics-based, microscopic-mesoscopic approaches.