Science.gov

Sample records for spectroscopic thermodynamic microscopic

  1. On thermodynamic and microscopic reversibility

    SciTech Connect

    Crooks, Gavin E.

    2011-07-12

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

  2. Microscopic Models for Chemical Thermodynamics

    NASA Astrophysics Data System (ADS)

    Malyshev, V. A.

    2005-06-01

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

  3. Single nanoparticle tracking spectroscopic microscope

    DOEpatents

    Yang, Haw; Cang, Hu; Xu, Cangshan; Wong, Chung M.

    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.

  4. 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.

  5. The Second Law of Thermodynamics at the Microscopic Scale

    NASA Astrophysics Data System (ADS)

    Josset, Thibaut

    2017-09-01

    In quantum statistical mechanics, equilibrium states have been shown to be the typical states for a system that is entangled with its environment, suggesting a possible identification between thermodynamic and von Neumann entropies. In this paper, we investigate how the relaxation toward equilibrium is made possible through interactions that do not lead to significant exchange of energy, and argue for the validity of the second law of thermodynamics at the microscopic scale.

  6. Quantitative Thermodynamic Analyses of Spectroscopic Titration Curves§

    PubMed Central

    Bujalowski, Wlodzimierz; Jezewska, Maria J.

    2014-01-01

    Elucidation of ligand - macromolecule interactions requires detailed knowledge of energetics of the formed complexes. Spectroscopic methods are most commonly used in characterizing molecular interactions in solution. The methods do not require large quantities of material and most importantly, do not perturb the studied reactions. However, spectroscopic methods absolutely require the determination of the relationship between the observed signal and the degree of binding in order to obtain meaningful interaction parameters. In other words, the meaningful, thermodynamic interaction parameters can be only determined if the relationship between the observed signal and the degree of binding is determined and not assumed, based on an ad hoc model of the relationship. The approaches discussed here allow an experimenter to quantitatively determine the degree of binding and the free ligand concentration, i.e., they enable to construct thermodynamic binding isotherms in a model-independent fashion. PMID:25284889

  7. Spectroscopic and Microscopic Study of Peroxyformic Pulping of Agave Waste.

    PubMed

    Hernández-Hernández, Hilda M; Chanona-Pérez, Jorge J; Vega, Alberto; Ligero, Pablo; Farrera-Rebollo, Reynold R; Mendoza-Pérez, Jorge A; Calderón-Domínguez, Georgina; Vera, Norma Güemes

    2016-10-01

    The peroxyformic process is based on the action of a carboxylic acid (mainly formic acid) and the corresponding peroxyacid. The influences of processing time (60-180 min), formic acid concentration (80-95%), temperature (60-80°C), and hydrogen peroxide concentration (2-4%) on peroxyformic pulping of agave leaves were studied by surface response methodology using a face-centered factorial design. Empirical models were obtained for the prediction of yield, κ number (KN) and pulp viscosity as functions of the aforementioned variables. Mathematical optimization enabled us to select a set of operational variables that produced the best fractionation of the material with the following results: pulp yield (26.9%), KN (3.6), and pulp viscosity (777 mL/g). Furthermore, this work allowed the description and evaluation of changes to the agave fibers during the fractionation process using different microscopic and spectroscopic techniques, and provided a comprehensive and qualitative view of the phenomena occurring in the delignification of agave fibers. The use of confocal and scanning electron microscopy provided a detailed understanding of the microstructural changes to the lignin and cellulose in the fibers throughout the process, whereas Raman spectroscopy and X-ray diffraction analysis indicated that cellulose in the pulp after treatment was mainly of type I.

  8. 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.

  9. 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…

  10. 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…

  11. Microscopic diagonal entropy and its connection to basic thermodynamic relations

    SciTech Connect

    Polkovnikov, Anatoli

    2011-02-15

    We define a diagonal entropy (d-entropy) for an arbitrary Hamiltonian system as S{sub d}=-{Sigma}{sub n{rho}nn}ln{rho}{sub nn} with the sum taken over the basis of instantaneous energy states. In equilibrium this entropy coincides with the conventional von Neumann entropy S{sub n} = -Tr{rho} ln {rho}. However, in contrast to S{sub n}, the d-entropy is not conserved in time in closed Hamiltonian systems. If the system is initially in stationary state then in accord with the second law of thermodynamics the d-entropy can only increase or stay the same. We also show that the d-entropy can be expressed through the energy distribution function and thus it is measurable, at least in principle. Under very generic assumptions of the locality of the Hamiltonian and non-integrability the d-entropy becomes a unique function of the average energy in large systems and automatically satisfies the fundamental thermodynamic relation. This relation reduces to the first law of thermodynamics for quasi-static processes. The d-entropy is also automatically conserved for adiabatic processes. We illustrate our results with explicit examples and show that S{sub d} behaves consistently with expectations from thermodynamics.

  12. Protein conjugation with PAMAM nanoparticles: Microscopic and thermodynamic analysis.

    PubMed

    Chanphai, P; Froehlich, E; Mandeville, J S; Tajmir-Riahi, H A

    2017-02-01

    PAMAM dendrimers form strong protein conjugates that are used in drug delivery systems. We report the thermodynamic and binding analysis of polyamidoamine (PAMAM-G4) conjugation with human serum albumin (HSA), bovine serum albumin (BSA) and milk beta-lactoglobulin (b-LG) in aqueous solution at physiological pH. Hydrophobicity played a major role in PAMAM-protein interactions with more hydrophobic b-LG forming stronger polymer-protein conjugates. Thermodynamic parameters showed PAMAM-protein bindings occur via hydrophobic and H-bonding contacts for b-LG, while van der waals and H-bonding interactions prevail in HSA and BSA-polymer conjugates. The protein loading efficacy was 45-55%. PAMAM complexation induced major alterations of protein conformation. TEM images show major polymer morphological changes upon protein conjugation.

  13. 3D-Mössbauer spectroscopic microscope for mc-Si solar cell evaluation

    NASA Astrophysics Data System (ADS)

    Ino, Y.; Soejima, H.; Hayakawa, K.; Yukihira, K.; Tanaka, K.; Fujita, H.; Watanabe, T.; Ogai, K.; Moriguchi, K.; Harada, Y.; Yoshida, Y.

    2016-12-01

    A 3D-Mössbauer Spectroscopic Microscope is developed to evaluate Fe impurities in multi-crystalline Si solar cells, which combines the Mössbauer spectroscopic microscope with a scanning electron microscope (SEM), an electron beam induced current (EBIC), an electron backscatter diffraction (EBSD), and an electron energy analyzer (HV-CSA). In addition, a new moving-coil-actuator with a liner encoder of 100 nm-resolution is incorporated for the operations with both a constant velocity and a constant acceleration mode successfully with the same precision as that obtained by the conventional transducers. Furthermore, a new multi-capillary X-ray lens is designed to achieve a γ-ray spot size less than 100 μm in diameter. The new microscope provides us to investigate the space correlation between Fe impurities and the lattice defects such as grain boundaries in multi-crystalline Si solar cells.

  14. Conformational contribution to thermodynamics of binding in protein-peptide complexes through microscopic simulation.

    PubMed

    Das, Amit; Chakrabarti, J; Ghosh, Mahua

    2013-03-19

    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.

  15. Microscope objective based 4π spectroscopic tissue scattering goniometry

    PubMed Central

    Simmons, Z. J.; Rogers, J. D.

    2017-01-01

    The measurement of optical scattering as a function of angle, goniometry, can provide a wealth of information about tissue. The goniometry technique described here measures the intensity profile at the pupil planes of two microscope objectives with a scattering sample between them. The maximum observable scattering angle is extended by employing off-axis illumination. This configuration permits several advantages including: i) rapid measurement of scattering into 4π sr to characterize the entire scattering phase function in isotropic tissue, ii) sensitivity to axially asymmetric scattering from anisotropic fibrous tissue, iii) selective interrogation of small regions within spatially inhomogenous tissue, iv) concurrent measurement of scattering coefficient μs, and v) measurement of wavelength dependent scattering properties via spectrally tunable source. The instrument is validated by comparing measurements of microsphere suspensions to the Mie scattering solution. Instrument capabilities are demonstrated with samples of rat brain and mouse eye tissues. PMID:28856053

  16. Spectroscopic and thermodynamic properties of L-ornithine monohydrochloride

    SciTech Connect

    Raja, M. Dinesh; Kumar, C. Maria Ashok; Arulmozhi, S.; Madhavan, J.

    2015-06-24

    L-Ornithine Monohydrochloride (LOMHCL) has been investigated with the help of B3LYP density functional theory with 6-31 G (d, p) basis set. Fourier transform infrared and Fourier transform Raman spectra is to identify the various functional groups. The theoretical frequencies showed very good agreement with experimental values. On the basis of the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between standard heat capacities (C) standard entropies (S), and standard enthalpy changes (H) and temperatures. Second harmonic generation (SHG) efficiency of the grown crystal has been studied.

  17. Calculation of the thermodynamic properties of fuel-vapor species from spectroscopic data

    SciTech Connect

    Green, D.W.

    1980-09-01

    Measured spectroscopic data, estimated molecular parameters, and a densty-of-states model for electronic structure have been used to calculate thermodynamic functions for gaseous ThO, ThO/sub 2/, UO, UO/sub 2/, UO/sub 3/, PuO, and PuO/sub 2/. Various methods for estimating parameters have been considered and numerically evaluated. The sensitivity of the calculated thermodynamic functions to molecular parameters has been examined quantitatively. New values of the standard enthalpies of formation at 298.15/sup 0/K have been derived from the best available ..delta..G/sup 0//sub f/ equations and the calculated thermodynamic functions. Estimates of the uncertainties have been made for measured and estimated data as well as for various mathematical and physical approximations. Tables of the thermodynamic functions to 6000/sup 0/K are recommended for gaseous thorium, uranium, and plutonium oxides.

  18. Spectroscopic and thermodynamic properties of Debaryomyces hansenii UFV-1 alpha-galactosidases.

    PubMed

    Viana, Pollyanna A; Rezende, Sebastião T; Meza, Andreia N; Gomide, Felipe T F; Nagem, Ronaldo A P; Santos, Alexandre M C; Santoro, Marcelo M; Guimarães, Valéria M

    2010-04-01

    Spectroscopic and thermodynamic properties were determined for Debaryomyces hansenii UFV-1 extracellular and intracellular alpha-galactosidases. alpha-Galactosidases showed similar secondary structure compositions (alpha-helix, beta-sheet parallel and beta-turn). Effects of pH and temperature on the structure of alpha-galactosidases were investigated using circular dichroism spectroscopy. It was more pronounced at low pH. Microcalorimetry was employed for the determination of thermodynamic parameters. Immediate thermal denaturation reversibility was not observed for alpha-galactosidases; it occurred as a thermodynamically driven process. Extracellular alpha-galactosidase, at pH 5.5, showed lower T(m) when compared to the intracellular enzyme. The CD and DSC data suggest that D. hansenii alpha-galactosidases have different behaviors although they possess some similar secondary structures. Copyright 2010 Elsevier B.V. All rights reserved.

  19. Proton Spectroscopic Factors Deduced from Helium-3 Global Phenomenological and Microscopic Optical Model Potentials

    NASA Astrophysics Data System (ADS)

    Jenny, Lee; Pang, Dan-Yang; Han, Yin-Lu; B. Tsang, M.

    2014-09-01

    Global phenomenological GDP08 and microscopic helium-3 optical model potentials have been recently derived. We evaluate these two potential sets by comparing the elastic scattering data of 25 MeV 3He on 16O, 18O, 19F, 23Na, 24Mg, 25Mg, 26Mg, 27Al, 28Si, 30Si, 31P, 32S, 34S, 35Cl, 37Cl, and 39K isotopes. Using the deuteron angular distributions calculated with the distorted wave Born approximation model, we extract the ground-state proton spectroscopic factors from (3He, d) reactions on the same set of nuclei. The extracted proton spectroscopic factors are compared with the large-basis shell-model calculations.

  20. Improving the connection between the microscopic and macroscopic approaches to thermodynamics in high school

    NASA Astrophysics Data System (ADS)

    Malgieri, Massimiliano; Onorato, Pasquale; Valentini, Anna; De Ambrosis, Anna

    2016-11-01

    In this article we discuss a teaching learning sequence on basic thermodynamics, spanning the first and second principle, and the concepts of irreversibility and entropy, intended for use in secondary school. With respect to previous works we emphasise the importance of discussing the compatibility between the time reversal symmetry of Newton’s laws and the irreversibility embodied in the second principle of thermodynamics in order to completely exploit the possibility of connecting the microscopic and macroscopic perspectives. The sequence was tested in an Italian secondary school, and the results obtained from a questionnaire which combines several test items used in previous studies at university level are consistently comparable with or better than those reported for undergraduate students on the same questions over a range of topics. Thus, our work suggests that the microscopic approach is a viable option for the teaching of thermodynamics at the secondary school level; and the understanding of macroscopic concepts is not impaired, but possibly enhanced, by the adoption of such a teaching strategy.

  1. Grasping the second law of thermodynamics at university: The consistency of macroscopic and microscopic explanations

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    [This paper is part of the Focused Collection on Upper Division Physics Courses.] 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 =4 8 ) focusing on the macroscopic and microscopic features of the second law concerned with heat transfer processes. The data analysis was based on a qualitative content analysis where students' responses to the macroscopic- and microscopic-level items were categorized to provide insight into the consistency of the students' ideas; if students relied on the same idea at both levels, they ended up in the same category at both levels, and their use of the second law was consistent. The most essential finding is that a majority of students, 52%-69% depending on the physical system under evaluation, used the second law of thermodynamics consistently at macroscopic and microscopic levels; approximately 40% of the students used it correctly in terms of physics while others relied on erroneous ideas, such as the idea of conserving entropy. The most common inconsistency harbored by 10%-15% of the students (depending on the physical system under evaluation) was students' tendency to consider the number of accessible microstates to remain constant even if the entropy was stated to increase in a similar process; other inconsistencies were only seen in the answers of a few students. In order to address the observed inconsistencies, we would suggest that lecturers should utilize tasks that challenge students to evaluate phenomena at macroscopic and microscopic levels concurrently and tasks that would guide students in their search for contradictions in their thinking.

  2. Simultaneous microscopic measurements of thermal and spectroscopic fields of a phase change material

    NASA Astrophysics Data System (ADS)

    Romano, M.; Ryu, M.; Morikawa, J.; Batsale, J. C.; Pradere, C.

    2016-05-01

    In this paper, simultaneous microscopic measurements of thermal and spectroscopic fields of a paraffin wax n-alkane phase change material are reported. Measurements collected using an original set-up are presented and discussed with emphasis on the ability to perform simultaneous characterization of the system when the proposed imaging process is used. Finally, this work reveals that the infrared wavelength contains two sets of important information. Furthermore, this versatile and flexible technique is well adapted to characterize many systems in which the mass and heat transfers effects are coupled.

  3. Thermodynamic analysis of liquid bridge for fixed volume in atomic force microscope

    NASA Astrophysics Data System (ADS)

    Wei, Zheng; He, MengFu; Zhao, WenBin; Li, Yang

    2013-10-01

    In ambient condition, capillary forces are the major contributors to the adhesive forces between the tip of an atomic force microscope (AFM) and the sample. In general, capillary forces are thought to be related to water film thickness, contact time and relative humidity and so on. In this paper, an original analysis regarding the liquid bridge, based on the surface and interface thermodynamic theory, is proposed. The cases covered in the study include the capillary forces and temperature of liquid bridge for quickly drawn liquid bridge, and for nonvolatile liquid bridge. The study results show that variation in temperature may occur in the liquid bridge when it is stretched.

  4. Spectroscopic and microscopic characterization of biosensor surfaces with protein/amino-organosilane/silicon structure.

    PubMed

    Awsiuk, K; Bernasik, A; Kitsara, M; Budkowski, A; Petrou, P; Kakabakos, S; Prauzner-Bechcicki, S; Rysz, J; Raptis, I

    2012-02-01

    Composition and structure of biorecognition protein layers created on silicon substrates modified with amino-organosilanes determine the sensitivity and specificity of silicon based biosensing devices. In the present work, diverse spectroscopic and microscopic methods were applied to characterize model biosensor surfaces, formed on Si(3)N(4) or SiO(2) by modification with (3-aminopropyl)triethoxysilane, coating with rabbit gamma-globulins (IgGs) through physical adsorption, blocking with bovine serum albumin (BSA) and specific binding of an anti-rabbit IgG antibody. In addition, silanized substrates with directly adsorbed BSA or anti-rabbit IgG antibody were examined as reference surfaces. The protein/amino-organosilane/silicon structure of all surfaces was confirmed by X-ray photoelectron spectroscopy. Homogeneity of protein coverage was verified with near-field scanning optical microscope, working in reflection and fluorescence mode. Surface coverage with proteins was determined with angle-resolved XPS using a previously established bilayer approach. Inner structure of protein layers was examined with atomic force microscopy. Vertical arrangement of carbon functional groups was revealed by high resolution ARXPS. Combined spectroscopic and microscopic data reveal the complex character of interactions with the immobilized IgG molecules during blocking with BSA and immunoreaction with anti-IgG antibody. Within experimental error, neither surface coverage nor lateral structural scales of protein layer (provided by Fourier and auto-correlation analysis of topographic and phase images) increase during blocking procedure. On the other hand, coverage and all structural measures rise considerably after immunoreaction. In addition, it was found that polar functional groups orient towards substrate for all protein layers, independently of coverage, prior to and after both blocking and specific binding.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Thermodynamic and Spectroscopic Studies of Lanthanides(III) Complexation with Polyamines in Dimethyl Sulfoxide

    SciTech Connect

    Di Bernardo, Plinio; Zanonato, Pier Luigi; Melchior, Andrea; Portanova, Roberto; Tolazzi, Marilena; Choppin, Gregory R.; Wang, Zheming

    2008-01-01

    The thermodynamic parameters of complexation of Ln(III) cations with tris(2-aminoethyl)amine (tren) and tetraethylenepentamine (tetren) were determined in dimethyl sulfoxide (DMSO) by potentiometry and calorimetry. The excitation and emission spectra and luminescence decay constants of Eu3+ and Tb3+ complexed by tren and tetren, as well as those of the same lanthanides(III) complexed with diethylenetriamine (dien) and triethylenetetramine (trien), were also obtained in the same solvent. The combination of thermodynamic and spectroscopic data showed that, in the 1:1 complexes, all nitrogens of the ligands bound to the lanthanides except in the case of tren, in which only pendant N bound. For the larger ligands (trien, tren, tetren) in the higher complexes (ML2), there was less complete binding by available donors, presumably due to steric crowding. FT-IR studies were carried out in an acetonitrile/DMSO mixture, suitably chosen in order to follow the changes in the primary solvation sphere of lanthanide(III) due to complexation of amine ligands. Results show that the mean number of molecules of DMSO removed from the inner coordination sphere of lanthanides(III) is lower than ligand denticity and that the coordination number of the metal ions increases with amine complexation from ~8 to ~10. Independently of the number and structure of the amines, linear trends, similar for all lanthanides, were obtained by plotting the values of ΔGj°, ΔHj° and TΔSj° for the complexation of ethylenediamine (en), dien, trien, tren and tetren as a function of the number of amine metal-coordinated nitrogen atoms. The main factors on which the thermodynamic functions of lanthanide(III) complexation reactions in DMSO depend are discussed.

  11. Development of Conductive Boron-Doped Diamond Electrode: A microscopic, Spectroscopic, and Voltammetric Study

    PubMed Central

    Bennet, Kevin E.; Lee, Kendall H.; Kruchowski, James N.; Chang, Su-Youne; Marsh, Michael P.; Orsow, Alexander A. Van; Paez, Aurelio; Manciu, Felicia S.

    2013-01-01

    Building on diamond characteristics such as hardness, chemical inertness and low electron emission threshold voltage, the current microscopic, spectroscopic and voltammetric investigations are directed towards improving the properties of electrode coating materials for their future use in clinical studies of deep brain stimulation via fast-scan cyclic voltammetry (FSCV). In this study we combine the capabilities of confocal Raman mapping in providing detailed and accurate analysis of local distributions of material constituents in a series of boron-doped polycrystalline diamond films grown by chemical vapor deposition, with information from the more conventional techniques of scanning electron microscopy (SEM) and infrared absorption spectroscopy. Although SEM images show a uniform distribution of film crystallites, they have the limitation of being unable to differentiate the distribution of boron in the diamond. Values of 1018–1021 atoms/cm3 of boron content have been estimated from the absorption coefficient of the 1290 cm−1 infrared absorption band and from the 500 cm−1 Raman vibration. The observed accumulation of boron atoms and carbon sp2 impurities at the grain boundaries suggests that very high doping levels do not necessarily contribute to improvement of the material’s conductivity, corroborating with voltammetric data. FSCV results also indicate an enhanced stability of analyte detection. PMID:28788420

  12. Development of Conductive Boron-Doped Diamond Electrode: A microscopic, Spectroscopic, and Voltammetric Study.

    PubMed

    Bennet, Kevin E; Lee, Kendall H; Kruchowski, James N; Chang, Su-Youne; Marsh, Michael P; Van Orsow, Alexander A; Paez, Aurelio; Manciu, Felicia S

    2013-12-06

    Building on diamond characteristics such as hardness, chemical inertness and low electron emission threshold voltage, the current microscopic, spectroscopic and voltammetric investigations are directed towards improving the properties of electrode coating materials for their future use in clinical studies of deep brain stimulation via fast-scan cyclic voltammetry (FSCV). In this study we combine the capabilities of confocal Raman mapping in providing detailed and accurate analysis of local distributions of material constituents in a series of boron-doped polycrystalline diamond films grown by chemical vapor deposition, with information from the more conventional techniques of scanning electron microscopy (SEM) and infrared absorption spectroscopy. Although SEM images show a uniform distribution of film crystallites, they have the limitation of being unable to differentiate the distribution of boron in the diamond. Values of 10(18)-10(21) atoms/cm³ of boron content have been estimated from the absorption coefficient of the 1290 cm(-1) infrared absorption band and from the 500 cm(-1) Raman vibration. The observed accumulation of boron atoms and carbon sp² impurities at the grain boundaries suggests that very high doping levels do not necessarily contribute to improvement of the material's conductivity, corroborating with voltammetric data. FSCV results also indicate an enhanced stability of analyte detection.

  13. Thermodynamic response functions of fluids: A microscopic approach based on NpT Monte Carlo

    NASA Astrophysics Data System (ADS)

    Piñeiro, Manuel M.; Cerdeiriña, Claudio A.; Medeiros, Milton

    2008-07-01

    On the basis of NpT Monte Carlo simulations, a detailed analysis on the microscopic origins of some specific features of thermodynamic response functions of fluids is performed. Specifically, the residual isobaric heat capacity Cpres, the isobaric thermal expansivity αp, and the isothermal compressibility κT for Lennard-Jones methane and optimized potential for liquid simulations (OPLS) methanol have been determined via standard techniques. For the former, data along the liquid, gas, and supercritical regions are presented, while a wide temperature range at a single supercritical pressure is covered for the latter. They have been obtained by computing the various pairwise fluctuations contributing to each property. Attention is mainly focused on isothermal and isobaric maxima found for both Cpres and αp, which have been rationalized at a molecular level using qualitative arguments. It is encountered that maxima emerge as a natural consequence of the destruction of fluid structure as temperature is increased or as pressure is decreased. The results for Lennard-Jones methane reveal the competition of energetic and volumetric effects, while those for OPLS methanol evidence that hydrogen-bonding is dominant as energetic effects are concerned. Further discussion on previous results and alternative approaches using equations of state as well as on closely related topics such as "maxima and critical phenomena" is included.

  14. 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.

  15. 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

  16. 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).

  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.

  18. 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.

  19. Spectroscopic and thermodynamic comparisons of Escherichia coli DNA photolyase and Vibrio cholerae cryptochrome 1.

    PubMed

    Sokolowsky, Kathleen; Newton, Maire; Lucero, Carlos; Wertheim, Bradley; Freedman, Jaryd; Cortazar, Frank; Czochor, Jennifer; Schelvis, Johannes P M; Gindt, Yvonne M

    2010-05-27

    Escherichia coli DNA photolyase and cryptochrome 1 isolated from Vibrio cholerae, a member of the CRY-DASH family, are directly compared using a variety of experimental methods including UV-vis and Raman spectroscopy, reduction potential measurements, and isothermal titration calorimetry. The semiquinone form of the cryptochrome has an absorption spectrum that is red-shifted from that of the photolyase, but the Raman spectrum indicates that the FAD binding pocket is similar to that of photolyase. The FADH(-)/FADH* reduction potential of the cryptochrome is significantly higher than that of the photolyase at 164 mV vs NHE, but it also increases upon substrate binding (to 195 mV vs NHE), an increase similar to what is observed in photolyase. The FADH(-)/FADH* reduction potential for both proteins was found to be insensitive to ATP binding. Isothermal titration calorimetry found that photolyase binds tighter to substrate (K(A) approximately 10(5) M(-1) for photolyase and approximately 10(4) M(-1) for cryptochrome 1), and the binding constants for both proteins were slightly sensitive to oxidation state. Based upon this work, it appears that this cryptochrome has significant spectroscopic and electrochemical similarities to CPD photolyase. The thermodynamic cycle of the enzymatic repair in the context of this work is discussed.

  20. Mechanism of Arsenic Adsorption on Magnetite Nanoparticles from Water: Thermodynamic and Spectroscopic Studies.

    PubMed

    Liu, Cheng-Hua; Chuang, Ya-Hui; Chen, Tsan-Yao; Tian, Yuan; Li, Hui; Wang, Ming-Kuang; Zhang, Wei

    2015-07-07

    Removal of arsenic (As) from water supplies is needed to reduce As exposure through drinking water and food consumption in many regions of the world. Magnetite nanoparticles (MNPs) are promising and novel adsorbents for As removal because of their great adsorption capacity for As and easy separation. This study aimed to investigate the adsorption mechanism of arsenate, As(V), and arsenite, As(III), on MNPs by macroscopic adsorption experiments in combination with thermodynamic calculation and microspectroscopic characterization using synchrotron-radiation-based X-ray absorption spectroscopy (XAS) and X-ray photoelectron spectroscopy (XPS). Adsorption reactions are favorable endothermic processes as evidenced by increased adsorption with increasing temperatures, and high positive enthalpy change. EXAFS spectra suggested predominant formation of bidentate binuclear corner-sharing complexes ((2)C) for As(V), and tridentate hexanuclear corner-sharing ((3)C) complexes for As(III) on MNP surfaces. The macroscopic and microscopic data conclusively identified the formation of inner-sphere complexes between As and MNP surfaces. More intriguingly, XANES and XPS results revealed complex redox transformation of the adsorbed As on MNPs exposed to air: Concomitant with the oxidation of MNPs, the oxidation of As(III) and MNPs was expected, but the observed As(V) reduction was surprising because of the role played by the reactive Fe(II).

  1. Quantum chemical calculations and spectroscopic measurements of spectroscopic and thermodynamic properties of given uranyl complexes in aqueous solutions with possible environmental and industrial applications

    NASA Astrophysics Data System (ADS)

    Višňak, Jakub; Sobek, Lukáš

    2016-11-01

    A brief introduction into computational methodology and preliminary results for spectroscopic (excitation energies, vibrational frequencies in ground and excited electronic states) and thermodynamic (stability constants, standard enthalpies and entropies of complexation reactions) properties of some 1:1, 1:2 and 1:3 uranyl sulphato- and selenato- complexes in aqueos solutions will be given. The relativistic effects are included via Effective Core Potential (ECP), electron correlation via (TD)DFT/B3LYP (dispersion interaction corrected) and solvation is described via explicit inclusion of one hydration sphere beyond the coordinated water molecules. We acknowledge limits of this approximate description - more accurate calculations (ranging from semi-phenomenological two-component spin-orbit coupling up to four-component Dirac-Coulomb-Breit hamiltonian) and Molecular Dynamics simulations are in preparation. The computational results are compared with the experimental results from Time-resolved Laser-induced Fluorescence Spectroscopy (TRLFS) and UV-VIS spectroscopic studies (including our original experimental research on this topic). In case of the TRLFS and UV-VIS speciation studies, the problem of complex solution spectra decomposition into individual components is ill-conditioned and hints from theoretical chemistry could be very important. Qualitative agreement between our quantum chemical calculations of the spectroscopic properties and experimental data was achieved. Possible applications for geochemical modelling (e.g. safety studies of nuclear waste repositories, modelling of a future mining site) and analytical chemical studies (including natural samples) are discussed.

  2. 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.

  3. Structural, spectroscopic, electronic, nonlinear optical and thermodynamic properties of a synthesized Schiff base compound: A combined experimental and theoretical approach

    NASA Astrophysics Data System (ADS)

    Gökce, Halil; Öztürk, Nuri; Kazıcı, Mehmet; Yörür Göreci, Çiğdem; Güneş, Serap

    2017-05-01

    A Schiff base compound, 2-[(1H-benzimidazol-2-ylimino)methyl]-4-bromophenol (BISB), was synthesized and its spectroscopic characterization was performed using experimental methods such as FT-IR, Raman, proton and carbon-13 NMR chemical shifts and UV-Vis. spectroscopies. Density functional theory (DFT/B3LYP/6-311G(d,p)) computations were used to investigate the optimized molecular geometry, conformational forms, harmonic vibrational wavenumbers, NMR chemical shifts, UV-Vis. spectroscopic parameters, natural bond orbital (NBO) analysis, HOMO-LUMO energies, nonlinear optical (NLO) properties, molecular electrostatic potential (MEP) map, atomic charges and thermodynamic properties of the BISB molecule. The assignments of vibrational modes were performed by means of potential energy distribution (PED) using VEDA4 program. The NBO analysis was used to investigate intramolecular hyrogen bonding (Osbnd H⋯N), bond species, hyperconjugation interactions and intramolecular charge transfers (ICTs). Considering the computed HOMO and LUMO energies, the quantum molecular descriptors such as ionization potential (I), electron affinity (A), chemical hardness (η), chemical softness (ζ), electronegativity (χ), chemical potential (μ) and electrophilicity index (ω) parameters were investigated for the BISB molecule. DFT computations were also performed to determine the dipole moment (μ), the mean polarizability (α), the anisotropy of the polarizability (Δα) and the first hyperpolarizability (β0) values. The recorded experimental spectroscopic results are in a good harmony with the computed data.

  4. 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.

  5. 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.

  6. Microscopic theories of model macromolecular fluids and fullerenes: The role of thermodynamic consistency

    NASA Astrophysics Data System (ADS)

    Caccamo, Carlo; Pellicane, Giuseppe

    2002-09-01

    We investigate the accuracy of two well-known integral equation theories (IETs) of the fluid state, namely, the modified hypernetted chain (MHNC) approximation and the hybridized mean spherical approximation (HMSA), as applied to systems characterized by short-range interactions. The theoretical approaches are implemented by enforcing their thermodynamic consistency according to two different strategies: in one case the equality of the isothermal compressibility, as calculated via the virial and fluctuation routes from structure to thermodynamics, is imposed ["local" consistency (LC)] in the other case the equality of the pressure as calculated either via the two previous routes, or via the virial and the energy routes, is imposed ["global" consistency (GC)]. We show that for the class of potentials at issue the GC is in general considerably more accurate than the LC. We document this result by investigating the performances of the MHNC and the HMSA, as applied to the calculation of the thermodynamic and structural properties of the hard-core Yukawa (HCY) potential, the Derjaguin-Landau-Vervey-Overbeek (DLVO) potential and the Girifalco potential for fullerenes. The obtained results are then compared with Monte Carlo simulation data, that we also produce for the same model systems. As far as the HCY potential is concerned, the investigation covers a range of the Yukawa inverse decay length, z, spanning from z=1.8 when the interaction mimics the Lennard-Jones 12-6 potential, to z=7 when the potential mimics the "effective" short range interaction between globular proteins in a highly charge-screened aqueous solution. IETs are then applied to the DLVO potential with charge and Hamaker constant values which fit the dynamical interaction factor of lysozyme in a solution of high ionic strength, and to the Girifalco potential with parameters appropriate to model C60 and C70. It emerges from the present study that the GC is able to provide Helmholtz free energies and

  7. Quasi-lattice model for the thermodynamic properties and microscopic structure of molten Fe-Si alloy

    NASA Astrophysics Data System (ADS)

    Kumar, A.; Jha, I. S.; Singh, B. P.

    2011-12-01

    The quasi-lattice model has been used to study the concentration dependant thermodynamic properties and microscopic structure of Fe-Si alloys in molten state. We have determined the free energy of mixing, excess entropy of mixing, the concentration-concentration structure factor in long wavelength limit [SCC(0)] and the Warren-Cowley short range order parameter (α1) of Fe-Si liquid alloy at 1873 K. The observed asymmetry in the properties of mixing of Fe-Si alloy in molten state is successfully explained on the basis of the quasi-lattice model. The analysis suggests that the Fe2Si complexes are most likely to exist in the liquid state and are strongly interacting in nature. The theoretical analysis suggests that the pairwise interaction energies between the species depend considerably on temperature and the alloy is more ordered towards Fe rich region.

  8. Molecular modeling of imidazolium-based [Tf2N-] ionic liquids: microscopic structure, thermodynamic and dynamic properties, and segmental dynamics.

    PubMed

    Logotheti, Georgia-Evangelia; Ramos, Javier; Economou, Ioannis G

    2009-05-21

    The microscopic structure, thermodynamic properties, local segmental dynamics, and self-diffusion coefficients of three ionic liquids (ILs) with a common anion, namely, the bis(trifluoromethylsulfonyl) imide ([Tf2N-]), and imidazolium-based cations that differ in the alkyl tail length, namely, the 1-butyl-3-methylimidazolium ([C4mim+]), the 1-hexyl-3-methylimidazolium ([C6mim+]), and the 1-octyl-3-methylimidazolium ([C8mim+]), are calculated over the temperature range of 298.15-333.15 K and pressure range of 0.1-60 MPa. Quantum calculations based on density functional theory are performed on isolated ion pairs, and minimum energy conformers are identified. Electronic density results are used to estimate the electrostatic potential of a molecular force field that is used subsequently for long molecular dynamics (MD) simulations of bulk ILs. Thermodynamic properties calculated from MD are shown to be in excellent agreement for the bulk density and good agreement for derivative properties when compared to experimental data. The new force field is an improvement over earlier ones for the same ILs. The microscopic structure as expressed through the radial distribution function is thoroughly calculated, and it is shown that the bulk structure characteristics are very similar to those obtained from the quantum calculations on isolated ion pairs. The segmental dynamics expressed in terms of bond and torsion angle decorrelation is shown to assume a broad range of characteristic times. Molecular segments in the alkyl tail of the cations are significantly faster than segments in the vicinity of the imidazolium ring. Finally, the new force field predicts accurately the self-diffusion coefficients of the cations and the anions over the entire temperature range examined, thus confirming its validity for a broad range of physical properties.

  9. Second harmonic microscopic imaging and spectroscopic characterization in prostate pathological tissue.

    PubMed

    Huang, Yanyue; Zhuang, Zhengfei

    2014-01-01

    Second harmonic microscopic imaging and spectroscopy technology has become a powerful tool for biomedical studies, especially in cancer research. In this paper, second harmonic generation in benign prostatic hyperplasia (BPH) and prostate cancer (PC) tissues in mouse model (C57BL6) have been reported. Excitated samples with different wavelength near-infrared laser from 780 to 850 nm we found that second harmonic signals from BPH nuclei stronger than that from PC, and a wavelength sensitivity was also observed in this experiment. Providing useful help for prostate malignancy diagnosis and identifying tissue components on clinic. © 2013 Wiley Periodicals, Inc.

  10. Structures, spectroscopic and thermodynamic properties of U₂On (n = 0 ∼ 2, 4) molecules: a density functional theory study.

    PubMed

    Li, Peng; Niu, Wen-Xia; Gao, Tao; Wang, Fan; Jia, Ting-Ting; Meng, Da-Qiao; Li, Gan

    2013-12-01

    The equilibrium structures, spectroscopic and thermodynamic parameters [entropy (S), internal energy (E), heat capacity (C p)] of U₂, U₂O, U₂O₂ and U₂O₄ uranium oxide molecules were investigated systematically using density functional theory (DFT). Our computations indicated that the ground electronic state of U₂ is the septet state and the equilibrium bond length is 2.194 Å; the ground electronic state of U₂O and U₂O₂ were found to be X³Φ and X³Σ(g) with stable C(∞v) and D(∞h) linear structures, respectively. The bridge-bonded structure with D(2h) symmetry and X³B₁(g) state is the most stable configuration for the U₂O₄ molecule. Mulliken population analyses show that U atoms always lose electrons to become the donor and O atoms always obtain electrons as the acceptor. Molecular orbital analyses demonstrated that the frontier orbitals of the title molecules were contributed mostly by 5f atomic orbitals of U atoms. Vibrational frequencies analyses indicate that the maximum absorption peaks stem from the stretching mode of U-O bonds in U₂O, U₂O₂ and U₂O₄. In addition, thermodynamic data of U₂O(n) (n = 0 ∼ 4) molecules at elevated temperatures of 293.0 K to 393.0 K was predicted.

  11. New fluorescence reactions in DNA cytochemistry. 2. Microscopic and spectroscopic studies on fluorescent aluminum complexes

    SciTech Connect

    Del Castillo, P.; Llorente, A.R.; Gomez, A.; Gosalvez, J.; Goyanes, V.J.; Stockert, J.C. )

    1990-02-01

    Metal-dye complexes are widely applied in light microscopic techniques for chromatin staining (e.g., hematoxylin and carmine), but fluorescent complexes between phosphate-binding cations and suitable ligands have been little used. Preformed and postformed Al complexes with different anionic dyes induced strong and selective fluorescence reactions in nuclei from chicken blood smears, frozen sections, paraffin-embedded sections and Epon-embedded sections of mouse and rat tissues, mitotic chromosomes, meiotic chromosomes and kinetoplasts of Trypanosoma cruzi epimastigotes. The DNA-dependent fluorescence of these structures showed a very low fading rate. The emission colors were related to the ligand. The most suitable compounds for forming fluorescent Al chelates were 8-hydroxyquinoline, morin, nuclear fast red and purpurin. Staining with diluted carmine solutions and InCl3 mordanting, followed by 8-hydroxyquinoline, also induced chromatin fluorescence. After treating isolated mouse chromosomes with the preformed complex Al-nuclear fast red, x-ray microanalysis indicated a P:Al:dye binding ratio of about 40:15:1. The selectivity, stability and easy formation of these fluorescent Al complexes are obvious advantages for their use as new cytochemical probes in cytologic studies.

  12. 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

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

    SciTech Connect

    Fang, Yurui; Zhang, Zhenglong; Sun, Mengtao

    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 × 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.

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

    NASA Astrophysics Data System (ADS)

    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.

  15. 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.

  16. New Evidences of Key Factors Involved in "Silent Stones" Etiopathogenesis and Trace Elements: Microscopic, Spectroscopic, and Biochemical Approach.

    PubMed

    Cavalu, Simona; Popa, Adriana; Bratu, Ioan; Borodi, Gheorghe; Maghiar, Adrian

    2015-12-01

    The knowledge of the key factors involved in etiopathogenesis of the gallstone disease requires chemical, structural, and elemental composition analysis. The application of different complementary analytical techniques, both microscopic and spectroscopic, are aimed to provide a more comprehensive determination of the gallbladder calculi ultrastructure and trace element identification. High sensitivity techniques such as electron microscopy (SEM), Fourier transform infrared (FTIR), electron paramagnetic resonance (EPR) spectroscopy, and X-ray diffraction (XRD) along with biochemical analysis are used in a new attempt to investigate various factors which play a regulatory role in the pathogenesis of gallstones. The microstructure of different types of gallbladder stones has specific characteristics which are related to the elemental composition. The binding of metal ions with bile salts and bilirubin plays important roles in gallstone formation as revealed by FTIR spectrum of calcium bilirubinate complex in pigment gallstones. The EPR results demonstrated the generation of bilirubin free radicals and variation of its electronic structure and conjugation system in the skeleton of bilirubin molecule during complex formation. EPR spectra of pigment gallstones demonstrate the coexistence of four paramagnetic centers including stable bilirubin free radical, Mn2+, Cu2+, and Fe3+ with distinct magnetic parameters and well-resolved hyperfine structure in the case of Mn2+ ions. The result confirms a macromolecular network structure with proteins and the formation of bilirubin-coordinated polymer. Bilirubin and bilirubinate free radical complexes may play an important role in pigment gallstone formation.

  17. 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.

  18. Macromolecular competition titration method accessing thermodynamics of the unmodified macromolecule-ligand interactions through spectroscopic titrations of fluorescent analogs.

    PubMed

    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.

  19. 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

  20. 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.

  1. Thermodynamic and spectroscopic study of Al(3+) interaction with glycine, l-cysteine and tranexamic acid in aqueous solution.

    PubMed

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

    2017-08-08

    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 M2L2(OH)2 species for Gly, ML, M2L 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 pL0.5 empiric parameter. For Gly, Cys and Tranex, pL0.5=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.

  2. 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 (ΔGp and ΔGb). PMID:25243216

  3. Redox, thermodynamic and spectroscopic of some transition metal complexes containing heterocyclic Schiff base ligands

    NASA Astrophysics Data System (ADS)

    Abu-Hussen, Azza A. A.; Linert, Wolfgang

    2009-09-01

    Complexes of two series of Schiff base ligands, H 2L a and H 2L b derived from the reaction of 2,6-diacetyl pyridine with semicarbazide, H 2L a and thiosemicarbazide, H 2L b, with the metal ions, Co(II), Ni(II), Cu(II), VO(IV) and UO 2(VI) have been prepared. The ligands are characterized by elemental analysis, IR, UV-vis and 1H NMR. The structures of the complexes are investigated with the IR, UV-vis, X-band ESR spectra, 1H NMR and thermal gravimetric analysis as well as conductivity and magnetic moment measurements. The IR-spectra reveal the presence of variable modes of chelation for the investigated ligands. A variety of binuclear or mononuclear complexes were obtained with the two ligands in tri-, tetra or pentadentate forms. The bonding sites are the pyridine nitrogen, two azomethine nitrogen atoms and ketonic oxygen in case of H 2L a or sulphur atoms in case of H 2L b. The Coats-Redfern equation has been used to calculate the kinetic and thermodynamic parameters for the different thermal decomposition steps of some complexes. Cyclic voltammograms of Co(II) and Ni(II) show quasi-reversible peaks. The redox properties and the nature of the electro-active species of the complexes have been characterized.

  4. Thermodynamic, spectroscopic, and computational studies of lanthanide complexation with Diethylenetriaminepentaacetic acide: temperature effect and coordination modes

    SciTech Connect

    Guoxin Tian; Leigh R. Martin; Zhiyong Zhang; Linfeng Rao

    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 consistent 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.

  5. Redox, thermodynamic and spectroscopic of some transition metal complexes containing heterocyclic Schiff base ligands.

    PubMed

    Abu-Hussen, Azza A A; Linert, Wolfgang

    2009-09-15

    Complexes of two series of Schiff base ligands, H(2)L(a) and H(2)L(b) derived from the reaction of 2,6-diacetyl pyridine with semicarbazide, H(2)L(a) and thiosemicarbazide, H(2)L(b), with the metal ions, Co(II), Ni(II), Cu(II), VO(IV) and UO(2)(VI) have been prepared. The ligands are characterized by elemental analysis, IR, UV-vis and (1)H NMR. The structures of the complexes are investigated with the IR, UV-vis, X-band ESR spectra, (1)H NMR and thermal gravimetric analysis as well as conductivity and magnetic moment measurements. The IR-spectra reveal the presence of variable modes of chelation for the investigated ligands. A variety of binuclear or mononuclear complexes were obtained with the two ligands in tri-, tetra or pentadentate forms. The bonding sites are the pyridine nitrogen, two azomethine nitrogen atoms and ketonic oxygen in case of H(2)L(a) or sulphur atoms in case of H(2)L(b). The Coats-Redfern equation has been used to calculate the kinetic and thermodynamic parameters for the different thermal decomposition steps of some complexes. Cyclic voltammograms of Co(II) and Ni(II) show quasi-reversible peaks. The redox properties and the nature of the electro-active species of the complexes have been characterized.

  6. 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.

  7. Conformational stability, spectroscopic (FT-IR & FT-Raman), HOMO-LUMO, NBO and thermodynamic function of 4-(trifloromethoxy) phenol.

    PubMed

    Balachandran, V; Murugan, M; Karpagam, V; Karnan, M; Ilango, G

    2014-09-15

    FT-IR and FT-Raman spectra of 4-(trifloromethoxy) phenol (4TFMP) have been recorded in the regions 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The total energy calculations of 4TFMP were tried for the possible conformers. The molecular structure, geometry optimization, vibrational frequencies were obtained by the DFT level of theory (B3LYP) with the standard basis sets 6-31+G(d) and 6-311++G(d,p). The harmonic frequencies were calculated and the scaled values were compared with experimental FT-IR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The chemical parameters were calculated from the HOMO and LUMO values. Molecular electrostatic potential (MEP) were calculated and analyzed. The thermodynamic functions (heat capacity, entropy, enthalpy) from spectroscopic data by statistical methods were obtained for the range of temperature 100-1000 K. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2017-11-05

    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 10(3)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. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Kinetic, spectroscopic and thermodynamic characterization of the Mycobacterium tuberculosis adrenodoxin reductase homologue FprA.

    PubMed Central

    McLean, Kirsty J; Scrutton, Nigel S; Munro, Andrew W

    2003-01-01

    adrenodoxin reductase (-274 mV). Our data provide a thermodynamic and transient kinetic framework for catalysis by FprA, and complement recent spectrophotometric and steady-state studies of the enzyme [Fischer, Raimondi, Aliverti and Zanetti (2002) Eur. J. Biochem. 269, 3005-3013]. PMID:12614197

  10. Spectroscopic and thermodynamic studies of light harvesting perylenediimide derivative - zinc porphyrin complex in aqueous media.

    PubMed

    El-Refaey, Ahmed; Shaban, Shaban Y; El-Kemary, Maged; El-Khouly, Mohamed E

    2017-11-05

    Self-assembly of perylene derivative such as N,N'-bis(2(trimethylammonium iodide) ethylene)perylene-3,4,9,10-tetracarboxyldiimide (TAIPDI) can produce one-dimensional form (1D) in an aqueous media. The ability of one-dimensional TAIPDI to form light harvesting complex with water-soluble zinc porphyrin (ZnTPPS4) via the π-π and electrostatic interactions has been described. Owing to electronic interactions between the π-systems, the complex formation is accompanied by pronounced absorption spectral changes in the UV/Vis absorption bands. The formation constant of the ZnTPPS4-TAIPDI complex has been determined as 2.60×10(4)M(-1) suggests a moderately stable complex. The steady-state fluorescence measurements exhibited fluorescence quenching of both the singlet TAIPDI and ZnTPPS4 because of the electron transfer process from the electron-donating ZnTPPS4 to the electron-accepting TAIPDI. Based on the picosecond time-resolved fluorescence, the rate and quantum yield of the electron transfer were found to be 2.47×10(10)s(-1) and 0.99, respectively, indicating fast and efficient electron transfer. The thermodynamic parameters of the complex formation have been determined from the stopped-flow measurements. The interaction between ZnTPPS4 and TAIPDI occurs in two steps, a fast and reversible step followed by a slow and irreversible one. The activation parameters for the complex formation (ΔH(#)=22±5kJmol(-1) and ΔS(#)=-123±18JK(-1)mol(-1)), (ΔH(#)=133±4kJmol(-1) and ΔS(#)=167±13Jmol(-1)K(-1)) were determined from variable temperature studies for the "on" and the "off" of the first step and ΔS(#)=246±37.89Jmol(-1)K(-1) and ΔH(#)=130±11kJmol(-1) for the second step. The negative and positive ΔS(#) values found for the interaction reactions are consistent with an associative interaction for the first step followed by dissociative mechanism for both the "off" and the second step. Copyright © 2017. Published by Elsevier B.V.

  11. 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

  12. Spectroscopic investigation on kinetics, thermodynamics and mechanism for electron transfer reaction of iron(III) complex with sulphur centered radical in stimulated biological system.

    PubMed

    Deepalakshmi, S; Sivalingam, A; Kannadasan, T; Subramaniam, P; Sivakumar, P; Brahadeesh, S T

    2014-04-24

    Electron transfer reactions of biological organic sulphides with several metal ions to generate sulphide radical cations are a great concern in biochemical process. To understand the mechanism, a stimulated biological system having model compounds, iron(III)-bipyridyl complex with thio-diglycolic acid (TDGA) was investigated. Spectroscopic study reveals the kinetics and thermodynamics of the reaction in aqueous perchloric acid medium. The reaction follows first and fractional order of 0.412 with respect to [Fe(bpy)3](3+) and TDGA, respectively. The oxidation is insensitive to variation in [H(+)] but slightly decreases with increase in ionic strength ([I]). Addition of acrylamide, a radical scavenger has no effect on the rate of the reaction. The high negative value of ΔS(#) (-74.3±1.09 J K(-1) mol(-1)) indicates the complex formed has a definite orientation higher than the reactants. Based on the above results, a suitable reaction mechanism for this reaction is proposed.

  13. Quest for Environmentally-Benign Ligands for Actinide Separations: Thermodynamic, Spectroscopic, and Structural Characterization of U(VI) Complexes with Oxa-Diamide and Related Ligands

    SciTech Connect

    Advanced Light Source; Tian, Guoxin; Rao, Linfeng; Teat, Simon J.; Liu, Guokui

    2009-01-05

    Complexation of U(VI) with N,N,N{prime},N{prime}-tetramethyl-3-oxa-glutaramide (TMOGA) and N,N-dimethyl-3-oxa-glutaramic acid (DMOGA) was studied in comparison with their dicarboxylate analog, oxydiacetic acid (ODA). Thermodynamic parameters, including stability constants, enthalpy and entropy of complexation, were determined by spectrophotometry, potentiometry and calorimetry. Single-crystal X-ray diffractometry, EXAFS spectroscopy, FT-IR absorption and laser-induced luminescence spectroscopy were used to obtain structural information on the U(VI) complexes. Like ODA, TMOGA and DMOGA form tridentate U(VI) complexes, with three oxygen atoms (the amide, ether and/or carboxylate oxygen) coordinating to the linear UO{sub 2}{sup 2+} cation via the equatorial plane. The stability constants, enthalpy and entropy of complexation all decrease in the order ODA > DMOGA > TMOGA, showing that the complexation is entropy driven and the substitution of a carboxylate group with an amide group reduces the strength of complexation with U(VI) due to the decrease in the entropy of complexation. The trend in the thermodynamic stability of the complexes correlates very well with the structural and spectroscopic data obtained by single crystal XRD, FT-IR and laser-induced luminescence spectroscopy.

  14. 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 (Ka) 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 MH2L+). Time-resolved fluorescence studies of Eu-(EDDAG-DA) solutions (at varying pH) identified a constant inner-sphere hydration number ofmore » 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

  15. The effects of organic solvents on the folding pathway and associated thermodynamics of proteins: a microscopic view.

    PubMed

    Yu, Yuqi; Wang, Jinan; Shao, Qiang; Shi, Jiye; Zhu, Weiliang

    2016-01-18

    Protein folding is subject to the effects of solvation environment. A variety of organic solvents are used as additives for in vitro refolding of denatured proteins. Examination of the solvent effects on protein folding could be of fundamental importance to understand the molecular interactions in determining protein structure. This article investigated the folding of α-helix and β-hairpin structures in water and the solutions of two representative refolding additives (methanol (MeOH) and 1-Ethyl-3-methylimidazolium chloride (EMIM-Cl) ionic liquid) using REMD simulations. For both α-helix and β-hairpin in MeOH/water solution or α-helix in EMIM-Cl/water solution, the transient structures along the folding pathway are consistent with the counterparts in water but the relative statistical weights are changed, leading to the decrease in the overall folding free energy barrier. Accordingly, MeOH promotes the folding of both α-helix and β-hairpin but EMIM-Cl ionic liquid only promotes the folding of α-helix, consistent with experimental observations. The present study reveals for the first time the trivial effects on folding route but significant effects on folding thermodynamics from MeOH and EMIM-Cl, explaining the function of protein refolding additives and testifying the validity of the folding mechanism revealed by in vitro protein folding study using refolding additives.

  16. Structural Analysis of Crystalline R(+)-α-Lipoic Acid-α-cyclodextrin Complex Based on Microscopic and Spectroscopic Studies.

    PubMed

    Ikuta, Naoko; Endo, Takatsugu; Hosomi, Shota; Setou, Keita; Tanaka, Shiori; Ogawa, Noriko; Yamamoto, Hiromitsu; Mizukami, Tomoyuki; Arai, Shoji; Okuno, Masayuki; Takahashi, Kenji; Terao, Keiji; Matsugo, Seiichi

    2015-10-16

    R(+)-α-lipoic acid (RALA) is a naturally-occurring substance, and its protein-bound form plays significant role in the energy metabolism in the mitochondria. RALA is vulnerable to a variety of physical stimuli, including heat and UV light, which prompted us to study the stability of its complexes with cyclodextrins (CDs). In this study, we have prepared and purified a crystalline RALA-αCD complex and evaluated its properties in the solid state. The results of ¹H NMR and PXRD analyses indicated that the crystalline RALA-αCD complex is a channel type complex with a molar ratio of 2:3 (RALA:α-CD). Attenuated total reflection/Fourier transform infrared analysis of the complex showed the shift of the C=O stretching vibration of RALA due to the formation of the RALA-αCD complex. Raman spectroscopic analysis revealed the significant weakness of the S-S and C-S stretching vibrations of RALA in the RALA-αCD complex implying that the dithiolane ring of RALA is almost enclosed in glucose ring of α-CD. Extent of this effect was dependent on the direction of the excitation laser to the hexagonal morphology of the crystal. Solid-state NMR analysis allowed for the chemical shift of the C=O peak to be precisely determined. These results suggested that RALA was positioned in the α-CD cavity with its 1,2-dithiolane ring orientated perpendicular to the plane of the α-CD ring.

  17. Structural Analysis of Crystalline R(+)-α-Lipoic Acid-α-cyclodextrin Complex Based on Microscopic and Spectroscopic Studies

    PubMed Central

    Ikuta, Naoko; Endo, Takatsugu; Hosomi, Shota; Setou, Keita; Tanaka, Shiori; Ogawa, Noriko; Yamamoto, Hiromitsu; Mizukami, Tomoyuki; Arai, Shoji; Okuno, Masayuki; Takahashi, Kenji; Terao, Keiji; Matsugo, Seiichi

    2015-01-01

    R(+)-α-lipoic acid (RALA) is a naturally-occurring substance, and its protein-bound form plays significant role in the energy metabolism in the mitochondria. RALA is vulnerable to a variety of physical stimuli, including heat and UV light, which prompted us to study the stability of its complexes with cyclodextrins (CDs). In this study, we have prepared and purified a crystalline RALA-αCD complex and evaluated its properties in the solid state. The results of 1H NMR and PXRD analyses indicated that the crystalline RALA-αCD complex is a channel type complex with a molar ratio of 2:3 (RALA:α-CD). Attenuated total reflection/Fourier transform infrared analysis of the complex showed the shift of the C=O stretching vibration of RALA due to the formation of the RALA-αCD complex. Raman spectroscopic analysis revealed the significant weakness of the S–S and C–S stretching vibrations of RALA in the RALA-αCD complex implying that the dithiolane ring of RALA is almost enclosed in glucose ring of α-CD. Extent of this effect was dependent on the direction of the excitation laser to the hexagonal morphology of the crystal. Solid-state NMR analysis allowed for the chemical shift of the C=O peak to be precisely determined. These results suggested that RALA was positioned in the α-CD cavity with its 1,2-dithiolane ring orientated perpendicular to the plane of the α-CD ring. PMID:26501268

  18. Arsenic removal by perilla leaf biochar in aqueous solutions and groundwater: An integrated spectroscopic and microscopic examination.

    PubMed

    Niazi, Nabeel Khan; Bibi, Irshad; Shahid, Muhammad; Ok, Yong Sik; Burton, Edward D; Wang, Hailong; Shaheen, Sabry M; Rinklebe, Jörg; Lüttge, Andreas

    2017-09-28

    In this study, we examined the removal of arsenite (As(III)) and arsenate (As(V)) by perilla leaf-derived biochars produced at 300 and 700 °C (referred as BC300 and BC700) in aqueous environments. Results revealed that the Langmuir isotherm model provided the best fit for As(III) and As(V) sorption, with the sorption affinity following the order: BC700-As(III) > BC700-As(V) > BC300-As(III) > BC300-As(V) (QL = 3.85-11.01 mg g(-1)). In general, As removal decreased (76-60%) with increasing pH from 7 to 10 except for the BC700-As(III) system, where notably higher As removal (88-90%) occurred at pH from 7 to 9. Surface functional moieties contributed to As sequestration by the biochars examined here. However, significantly higher surface area and aromaticity of BC700 favored a greater As removal compared to BC300, suggesting that surface complexation/precipitation dominated As removal by BC700. Arsenic K-edge X-ray absorption near edge structure (XANES) spectroscopy demonstrated that up to 64% of the added As(V) was reduced to As(III) in BC700- and BC300-As(V) sorption experiments, and in As(III) sorption experiments, partial oxidation of As(III) to As(V) occurred (37-39%). However, XANES spectroscopy was limited to precisely quantify As binding with sulfur species as As2S3-like phase. Both biochars efficiently removed As from natural As-contaminated groundwater (As: 23-190 μg L(-1); n = 12) despite in the presence of co-occurring anions (e.g., CO3(2-), PO4(3-), SO4(2-)) with the highest levels of As removal observed for BC700 (97-100%). Overall, this study highlights that perilla leaf biochars, notably BC700, possessed the greatest ability to remove As from solution and groundwater (drinking water). Significantly, the integrated spectroscopic techniques advanced our understanding to examine complex redox transformation of As(III)/As(V) with biochar, which are crucial to determine fate of As on biochar in aquatic environments. Copyright © 2017

  19. In situ characterization and analysis of Salmonella biofilm formation under meat processing environments using a combined microscopic and spectroscopic approach.

    PubMed

    Wang, Huhu; Ding, Shijie; Wang, Guangyu; Xu, Xinglian; Zhou, Guanghong

    2013-11-01

    Salmonella biofilm on food-contact surfaces present on food processing facilities may serve as a source of cross-contamination. In our work, biofilm formation by multi-strains of meat-borne Salmonella incubated at 20 °C, as well as the composition and distribution of extracellular polymeric substances (EPS), were investigated in situ by combining confocal laser scanning microscopy (CLSM), scanning electron microscope (SEM), attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) and Raman spectroscopy. A standard laboratory culture medium (tryptic soy broth, TSB) was used and compared with an actual meat substrate (meat thawing-loss broth, MTLB). The results indicated that Salmonella grown in both media were able to form biofilms on stainless steel surfaces via building a three-dimensional structure with multilayers of cells. Although the number of biofilm cells grown in MTLB was less than that in TSB, the cell numbers in MTLB was adequate to form a steady and mature biofilm. Salmonella grown in MTLB showed "cloud-shaped" morphology in the mature biofilm, whereas when grown in TSB appeared "reticular-shaped". The ATR-FTIR and Raman analysis revealed a completely different chemical composition between biofilms and the corresponding planktonic cells, and some important differences in biofilms grown in MTLB and in TSB. Importantly, our findings suggested that the progress towards a mature Salmonella biofilm on stainless steel surfaces may be associated with the production of the EPS matrix, mainly consisting of polysaccharides and proteins, which may serve as useful markers of biofilm formation. Our work indicated that a combination of these non-destructive techniques provided new insights into the formation of Salmonella biofilm matrix. © 2013.

  20. Scanning tunneling spectroscopic evidence for a magnetic field-revealed microscopic order in the high-TC superconductor YBa2Cu3O7-δ

    NASA Astrophysics Data System (ADS)

    Beyer, A. D.; Grinolds, M. S.; Teague, M. L.; Yeh, N.-C.; Tajima, S.

    2009-03-01

    We present spatially resolved scanning tunneling spectroscopic measurements of YBa2Cu3O7-δ as a function of magnetic field and at T<microscopic order. Ref.: Beyer, et.al. [arxiv:0808.3016].

  1. Influence of Galloyl Moiety in Interaction of Epicatechin with Bovine Serum Albumin: A Spectroscopic and Thermodynamic Characterization

    PubMed Central

    Pal, Sandip; Saha, Chabita; Hossain, Maidul; Dey, Subrata Kumar; Kumar, Gopinatha Suresh

    2012-01-01

    The health benefits stemming from green tea are well known, but the exact mechanism of its biological activity is not elucidated. Epicatechin (EC) and epicatechin gallate (ECG) are two dietary catechins ubiquitously present in green tea. Serum albumins functionally carry these catechins through the circulatory system and eliminate reactive oxygen species (ROS) induced injury. In the present study ECG is observed to have higher antioxidant activity; which is attributed to the presence of galloyl moiety. The binding affinity of these catechins to bovine serum albumin (BSA) will govern the efficacy of their biological activity. EC and ECG bind with BSA with binding constants 1.0×106 M−1 and 6.6×107 M−1, respectively. Changes in secondary structure of BSA on interaction with EC and ECG have been identified by circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. Thermodynamic characterization reveals the binding process to be exothermic, spontaneous and entropy driven. Mixed binding forces (hydrophobic, electrostatic and hydrogen bonding) exist between ECG and BSA. Binding site for EC is primarily site-II in sub-domain IIIA of BSA and for ECG; it is site-I in sub-domain IIA. ECG with its high antioxidant activity accompanied by high affinity for BSA could be a model in drug designing. PMID:22916242

  2. Caffeic acid binds to the minor groove of calf thymus DNA: A multi-spectroscopic, thermodynamics and molecular modelling study.

    PubMed

    Sarwar, Tarique; Ishqi, Hassan Mubarak; Rehman, Sayeed Ur; Husain, Mohammed Amir; Rahman, Yusra; Tabish, Mohammad

    2017-05-01

    Caffeic acid (CA) is a plant polyphenol which acts as an antioxidant and has various pharmacological effects. DNA is one of the major cellular targets of therapeutic molecules. Thus, studying the interaction of small molecules with DNA is of great importance. In the current article, we have studied the mode of binding of CA with calf thymus DNA (Ct-DNA) using a series of biophysical techniques. Formation of complex between CA and Ct-DNA is ascertained by analyzing the UV-vis absorbance and fluorescence emission spectra of CA upon successive addition of Ct-DNA. Binding constants of CA with Ct-DNA obtained using multiple experiments was in the order of 103 M-1 which is consistent with known groove binders. Analysis of thermodynamic parameters suggest that hydrogen bonding and van der Waal's forces played major role in the binding process. Competitive displacement studies confirmed that CA binds to the minor groove of Ct-DNA. These observations were further validated by KI quenching experiment, DNA melting studies, CD and viscosity measurements. In silico molecular docking further provided insight into the mode of binding of CA with Ct-DNA. Through in vitro experiments and in silico molecular docking studies, it was concluded that CA binds to the minor groove of Ct-DNA. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Spectroscopic studies on the thermodynamic and thermal denaturation of the ct-DNA binding of methylene blue

    NASA Astrophysics Data System (ADS)

    Mudasir; Wahyuni, Endang Tri; Tjahjono, Daryono H.; Yoshioka, Naoki; Inoue, Hidenari

    2010-10-01

    The ct-DNA binding properties of methylene blue (MB) including binding constant, thermodynamic parameter and thermal denaturation ( Tm) have been systematically studied by spectrophotometric method. The binding of MB to ct-DNA is quite strong as indicated by remarkable hypochromicity, red shift and equilibrium binding constant ( Kb). Van't Hoff plot of 1/ T versus ln Kb suggests that the MB dye binds exothermically to ct-DNA which is characterized by large negative enthalpy and entropy changes. According to polyelectrolyte theory, the charge release ( Z) when ct-DNA interacts with MB is +1.09 which corresponds very well to the one positive charge carried by the MB dye. The Kb at a low concentration of salt is dominated by electrostatic interaction (90%) while that at a high concentration of salt is mostly controlled by non-electrostatic process (85%). However, the stabilization of the DNA binding event in both cases is governed by non-electrostatic process. A moderate stabilization of double helix ct-DNA occurs when the MB dye binds to ct-DNA as indicated by the increase in Tm of ct-DNA of about 5.5 °C in the presence of MB. This suggests that MB dye possibly binds to ct-DNA via electrostatic and intercalation modes.

  4. Spectroscopic studies on the thermodynamic and thermal denaturation of the ct-DNA binding of methylene blue.

    PubMed

    Mudasir; Wahyuni, Endang Tri; Tjahjono, Daryono H; Yoshioka, Naoki; Inoue, Hidenari

    2010-10-01

    The ct-DNA binding properties of methylene blue (MB) including binding constant, thermodynamic parameter and thermal denaturation (T(m)) have been systematically studied by spectrophotometric method. The binding of MB to ct-DNA is quite strong as indicated by remarkable hypochromicity, red shift and equilibrium binding constant (K(b)). Van't Hoff plot of 1/T versus lnK(b) suggests that the MB dye binds exothermically to ct-DNA which is characterized by large negative enthalpy and entropy changes. According to polyelectrolyte theory, the charge release (Z) when ct-DNA interacts with MB is +1.09 which corresponds very well to the one positive charge carried by the MB dye. The K(b) at a low concentration of salt is dominated by electrostatic interaction (90%) while that at a high concentration of salt is mostly controlled by non-electrostatic process (85%). However, the stabilization of the DNA binding event in both cases is governed by non-electrostatic process. A moderate stabilization of double helix ct-DNA occurs when the MB dye binds to ct-DNA as indicated by the increase in T(m) of ct-DNA of about 5.5 degrees C in the presence of MB. This suggests that MB dye possibly binds to ct-DNA via electrostatic and intercalation modes.

  5. Influence of galloyl moiety in interaction of epicatechin with bovine serum albumin: a spectroscopic and thermodynamic characterization.

    PubMed

    Pal, Sandip; Saha, Chabita; Hossain, Maidul; Dey, Subrata Kumar; Kumar, Gopinatha Suresh

    2012-01-01

    The health benefits stemming from green tea are well known, but the exact mechanism of its biological activity is not elucidated. Epicatechin (EC) and epicatechin gallate (ECG) are two dietary catechins ubiquitously present in green tea. Serum albumins functionally carry these catechins through the circulatory system and eliminate reactive oxygen species (ROS) induced injury. In the present study ECG is observed to have higher antioxidant activity; which is attributed to the presence of galloyl moiety. The binding affinity of these catechins to bovine serum albumin (BSA) will govern the efficacy of their biological activity. EC and ECG bind with BSA with binding constants 1.0 × 10(6) M(-1) and 6.6 × 10(7) M(-1), respectively. Changes in secondary structure of BSA on interaction with EC and ECG have been identified by circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. Thermodynamic characterization reveals the binding process to be exothermic, spontaneous and entropy driven. Mixed binding forces (hydrophobic, electrostatic and hydrogen bonding) exist between ECG and BSA. Binding site for EC is primarily site-II in sub-domain IIIA of BSA and for ECG; it is site-I in sub-domain IIA. ECG with its high antioxidant activity accompanied by high affinity for BSA could be a model in drug designing.

  6. Binding of λ-carrageenan (a food additive) to almond cystatin: An insight involving spectroscopic and thermodynamic approach.

    PubMed

    Siddiqui, Azad Alam; Feroz, Anna; Khaki, Peerzada Shariq Shaheen; Bano, Bilqees

    2017-05-01

    Carrageenan is a high molecular weight linear sulphated polysaccharide, primarily used in food industry as gelling, thickening, and stabilizing agent. Almond milk prepared from almonds is low in fat, but high in antioxidants, energy, proteins, lipids and fibre. Purified almond cystatin was incubated with increasing concentrations of carrageenan at 25°C for different time interval and significant loss in inhibitory activity was observed. Interaction between carrageenan and cystatin resulted in complex formation as depicted by the decrease in fluorescence intensity with increase in the concentration of carrageenan. Stern-volmer analysis of fluorescence quenching data showed binding constant to be 1.84±0.20×10(4)M(-1) and number of binding sites close to unity. These results were further confirmed by supporting results obtained in UV-vis spectroscopy. FTIR analysis shows significant shift in the peak intensity and this change clearly depict change in the structure of cystatin from that of α helix to β-sheet. CD spectra further confirmed the structural transition of the cystatin from α helix to β-sheet structure on interaction with increased concentrations of carrageenan. The contributing thermodynamic parameters were determined by ITC. The negative ΔH° and positive TΔS° values suggest involvement of electrostatic forces and hydrophobic interaction in the formation of the λ-carrageenan-cystatin complex.

  7. Spectroscopic (FT-IR and FT-Raman) studies, NBO, HOMO-LUMO, NMR analyses and thermodynamics functions of 5-bromo-2-methoxybenzaldehyde

    NASA Astrophysics Data System (ADS)

    Balachandran, V.; Santhi, G.; Karpagam, V.

    2013-04-01

    The (FT-IR and FT-Raman) spectral properties of 5-bromo-2-methoxybenzaldehyde (BMB) are studied using density functional theory (DFT) employing B3LYP/6-311++G (d) and B3LYP/6-311++G (d, p) levels of theory. There are four conformers, C1, C2, C3, and C4 for this molecule. The computational results diagnose the most stable conformer of BMB as the C1 form. The optimized geometrical parameters obtained by B3LYP/6-311++G (d, p) method show good agreement with experimental X-ray data. A study on the electronic properties, such as HOMO and LUMO energies, is performed. The isotropic chemical shift computed by 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the BMB calculated using the gauge invariant atomic orbital (GIAO) method also shows good agreement with experimental observations. The MEP surface reflects the chemical reactivity of a molecule. The thermodynamic functions (heat capacity, internal heat energy, Gibbs energy and entropy) from spectroscopic data by statistical methods were obtained for the range of temperature 100-1000 K. The energetic behavior of the compound in different solvent medium (water, ethanol, and methanol) was examined by applying polarizable continuum model (PCM). The complete molecular orbital simulations and theoretical UV-visible spectra carried out in this study yield better understanding of charge delocalization pattern and stability of the title molecules to a greater extent.

  8. Incoherent superconductivity well above {T}_{{\\rm{c}}} in high-{T}_{{\\rm{c}}} cuprates—harmonizing the spectroscopic and thermodynamic data

    NASA Astrophysics Data System (ADS)

    Storey, J. G.

    2017-07-01

    Cuprate superconductors have long been known to exhibit an energy gap that persists high above the superconducting transition temperature ({T}{{c}}). Debate has continued now for decades as to whether it is a precursor superconducting gap or a pseudogap arising from some competing correlation. Failure to resolve this has arguably delayed explaining the origins of superconductivity in these highly complex materials. Here we effectively settle the question by calculating a variety of thermodynamic and spectroscopic properties, exploring the effect of a temperature-dependent pair-breaking term in the self-energy in the presence of pairing interactions that persist well above {T}{{c}}. We start by fitting the detailed temperature-dependence of the electronic specific heat and immediately can explain its hitherto puzzling field dependence. Taking this same combination of pairing temperature and pair-breaking scattering we are then able to simultaneously describe in detail the unusual temperature and field dependence of the superfluid density, tunneling, Raman and optical spectra, which otherwise defy explanation in terms a superconducting gap that closes conventionally at {T}{{c}}. These findings demonstrate that the gap above {T}{{c}} in the overdoped regime likely originates from incoherent superconducting correlations, and is distinct from the competing-order ‘pseudogap’ that appears at lower doping.

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

    PubMed

    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

    2014-08-07

    Efforts have been made to elucidate the origin of d(0) 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.

  10. Coordination and Thermodynamics of Trivalent Curium with Malonate at Increased Temperatures: A Spectroscopic and Quantum Chemical Study.

    PubMed

    Skerencak-Frech, Andrej; Trumm, Michael; Fröhlich, Daniel R; Panak, Petra J

    2017-09-05

    The complexation of Cm(III) with malonate is studied by time-resolved laser fluorescence spectroscopy (TRLFS) in the temperature range from 25 to 90 °C. Three complexes ([Cm(Mal)n](3-2n), n = 1, 2, 3) are identified and their molar fractions are determined as a function of the ligand concentration, the ionic strength, and the temperature. A general shift of the chemical equilibrium toward higher complexes with increasing temperature is observed, with the [CmMal3](3-) complex forming only at T > 40 °C. The conditional stability constants (log K'n(T)) are calculated and extrapolated to Im = 0 with the specific ion interaction theory (SIT). The log Kn(0)(T) values increase by 0.25 to 0.5 logarithmic unit in the studied temperature range. The temperature dependency of the log K°n(T) is fitted by the integrated Van't Hoff equation, yielding the thermodynamic functions ΔrH°m and ΔrS°m. The results show positive reaction enthalpies and entropies for each complexation step. While the ΔrH°n values are constant within their error range, the ΔrS°n values decrease successively with each ligand added. To explain this effect, quantum chemical calculations of binding energies and bond lengths of the different Cm(III) malonate species are performed. The results show that malonate is capable of stabilizing its end-on coordination mode to some extent by forming hydrogen bonds to first-shell water molecules. As a result, an equilibrium between side-on and end-on coordinated malonate ligands is present, with the latter becoming more pronounced for the higher complexes due to steric reasons.

  11. Thermodynamics and Mechanisms of the Interactions between Ultrasmall Fluorescent Gold Nanoclusters and Human Serum Albumin, γ-Globulins, and Transferrin: A Spectroscopic Approach.

    PubMed

    Yin, Miao-Miao; Dong, Ping; Chen, Wen-Qi; Xu, Shi-Ping; Yang, Li-Yun; Jiang, Feng-Lei; Liu, Yi

    2017-05-30

    Noble metal nanoclusters (NCs) show great promise as nanoprobes for bioanalysis and cellular imaging in biological applications due to ultrasmall size, good photophysical properties, and excellent biocompatibility. In order to achieve a comprehensive understanding of possible biological implications, a series of spectroscopic measurements were conducted under different temperatures to investigate the interactions of Au NCs (∼1.7 nm) with three model plasmatic proteins (human serum albumin (HSA), γ-globulins, and transferrin). It was found that the fluorescence quenching of HSA and γ-globulins triggered by Au NCs was due to dynamic quenching mechanism, while the fluorescence quenching of transferrin by Au NCs was a result of the formation of a Au NC-transferrin complex. The apparent association constants of the Au NCs bound to HSA, γ-globulins, and transferrin demonstrated no obvious difference. Thermodynamic studies demonstrated that the interaction between Au NCs and HSA (or γ-globulins) was driven by hydrophobic forces, while the electrostatic interactions played predominant roles in the adsorption process for transferrin. Furthermore, it was proven that Au NCs had no obvious interference in the secondary structures of these three kinds of proteins. In turn, these three proteins had a minor effect on the fluorescence intensity of Au NCs, which made fluorescent Au NCs promising in biological applications owing to their chemical and photophysical stability. In addition, by comparing the interactions of small molecules, Au NCs, and large nanomaterials with serum albumin, it was found that the binding constants were gradually increased with the increase of particle size. This work has elucidated the interaction mechanisms between nanoclusters and proteins, and shed light on a new interaction mode different from the protein corona on the surface of nanoparticles, which will highly contribute to the better design and applications of fluorescent nanoclusters.

  12. Comparative study of an osazone based ligand and its palladium(II) complex with human serum albumin: A spectroscopic, thermodynamic and molecular docking approach.

    PubMed

    Bandyopadhyay, Nirmalya; Pradhan, Ankur Bikash; Das, Suman; Naskar, Jnan Prakash

    2017-08-01

    An osazone based ligand, hexane-3,4-dione-bis(2'-phenylhydrazone) (LH2), was synthesized by 1:2M Schiff base condensation of 3,4-hexanedione and phenylhydrazine in dehydrated methanol. Its palladium(II) complex (1) has also been synthesized. LH2 and 1 have thoroughly been characterized by several spectroscopic and analytical means. DFT optimized structure of 1 shows that it is a monomeric Pd(II) complex having 'N2Cl2' coordination chromophore. Our BVS analysis also satisfactorily reproduces the oxidation number of the palladium center. 1 shows irreversible Pd(II)/Pd(I) reduction in its CV in methanol. 1 is three-fold more emissive than LH2. This enhanced emission has also been supported by time correlated single photon counting (TCSPC) measurements at room temperature. Human serum albumin (HSA) binding aspects of both LH2 and 1 have been investigated through various biophysical techniques. The binding constants as determined from Benesi-Hilderbrand plot using the absorbance spectral analyses were found respectively to be 1.18×10(5) and 4.38×10(4)M(-1) for LH2 and 1. The experimental findings confirm that both are good HSA binders. The thermodynamic parameters (∆G°, ∆H° and ∆S°) have also been evaluated by isothermal titration calorimetric (ITC) experiments. These parameters indicate that the binding processes are spontaneous both for LH2 and 1. Molecular docking analyses reveal that both LH2 and 1 reside in domain-I of HSA. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Effect of steric hindrance on carbon dioxide absorption into new amine solutions: thermodynamic and spectroscopic verification through solubility and NMR analysis.

    PubMed

    Park, Jung-Yeon; Yoon, Sang Jun; Lee, Huen

    2003-04-15

    Acid gas absorption technology is of great importance in these days for the prevention of global warming and the resulting worldwide climate change. More efficient process design and development for the removal of acid gases has become important, together with the development of new absorbents as one of urgent areas of research in addressing global-warming problems. In the present work, aqueous solutions of 2-amino-2-hydroxymethyl-1,3-propanediol (AHPD), a sterically hindered amine, has been examined as a potential CO2 absorbent and compared with the most commonly used absorbent, monoethanolamine (MEA) solution, through equilibrium solubility measurements and 13C NMR spectroscopic analyses. The solubilities of CO2 in aqueous 10 mass % AHPD solutions were higher than those in aqueous 10 mass % MEA solutions above 4 kPa at 298.15 K, but below 4 kPa, the solubility behavior appeared to be the opposite. The solubility difference between these two solutions increased with the CO2 partial pressures above the crossover pressure. Equilibrated CO2-MEA-H2O and CO2-AHPD-H2O solutions at various CO2 partal pressures ranging from 0.01 to 3000 kPa were analyzed by 13C NMR spectroscopy to provide a more microscopic understanding of the reaction mechanisms in the two solutions. In the CO2-amine-H2O solutions, amine reacted with CO2 to form mainly the protonated amine (AMH+), bicarbonate ion (HCO3-), and carbamate anion (AMCO2-), where the quantitative ratio of bicarbonate ion to carbamate anion strongly influenced the CO2 loading in the amine solutions. A profusion of bicarbonate ions, but a very small amount of carbamate anions, was identified in the CO2-AHPD-H2O solution, whereas a considerable amount of carbamate anions was formed in the CO2-MEA-H2O solution. AHPD contains more hydroxyl groups than nonhindered MEA, and hence, the chemical shifts in its 13C NMR spectra were strongly influenced by the solution pH values. In contrast, MEA appeared to be insensitive to pH. The

  14. 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

  15. First-principles calculation of thermodynamic stability of acids and bases under pH environment: A microscopic pH theory

    NASA Astrophysics Data System (ADS)

    Kim, Yong-Hyun; Kim, Kwiseon; Zhang, S. B.

    2012-04-01

    Despite being one of the most important thermodynamic variables, pH has yet to be incorporated into first-principles thermodynamics to calculate stability of acidic and basic solutes in aqueous solutions. By treating the solutes as defects in homogeneous liquids, we formulate a first-principles approach to calculate their formation energies under proton chemical potential, or pH, based on explicit molecular dynamics. The method draws analogy to first-principle calculations of defect formation energies under electron chemical potential, or Fermi energy, in semiconductors. From this, we propose a simple pictorial representation of the general theory of acid-base chemistry. By performing first-principles molecular dynamics of liquid water models with solutes, we apply the formulation to calculate formation energies of various neutral and charged solutes such as H+, OH-, NH3, NH4+, HCOOH, and HCOO- in water. The deduced auto-dissociation constant of water and the difference in the pKa values of NH3 and HCOOH show good agreement with known experimental values. Our first-principles approach can be further extended and applied to other bio- and electro-chemical molecules such as amino acids and redox reaction couples that could exist in aqueous environments to understand their thermodynamic stability.

  16. First-Principles Calculation of Thermodynamic Stability of Acids and Bases under pH Environment: A Microscopic pH Theory

    SciTech Connect

    Kim, Y. H.; Kim, K.; Zhang, S. B.

    2012-04-07

    Despite being one of the most important thermodynamic variables, pH has yet to be incorporated into first-principles thermodynamics to calculate stability of acidic and basic solutes in aqueous solutions. By treating the solutes as defects in homogeneous liquids, we formulate a first-principles approach to calculate their formation energies under proton chemical potential, or pH, based on explicit molecular dynamics. The method draws analogy to first-principle calculations of defect formation energies under electron chemical potential, or Fermi energy, in semiconductors. From this, we propose a simple pictorial representation of the general theory of acid-base chemistry. By performing first-principles molecular dynamics of liquid water models with solutes, we apply the formulation to calculate formation energies of various neutral and charged solutes such as H{sup +}, OH{sup -}, NH{sub 3}, NH{sub 4}{sup +}, HCOOH, and HCOO{sup -} in water. The deduced auto-dissociation constant of water and the difference in the pKa values of NH{sub 3} and HCOOH show good agreement with known experimental values. Our first-principles approach can be further extended and applied to other bio- and electro-chemical molecules such as amino acids and redox reaction couples that could exist in aqueous environments to understand their thermodynamic stability.

  17. First-principles calculation of thermodynamic stability of acids and bases under pH environment: a microscopic pH theory.

    PubMed

    Kim, Yong-Hyun; Kim, Kwiseon; Zhang, S B

    2012-04-07

    Despite being one of the most important thermodynamic variables, pH has yet to be incorporated into first-principles thermodynamics to calculate stability of acidic and basic solutes in aqueous solutions. By treating the solutes as defects in homogeneous liquids, we formulate a first-principles approach to calculate their formation energies under proton chemical potential, or pH, based on explicit molecular dynamics. The method draws analogy to first-principle calculations of defect formation energies under electron chemical potential, or Fermi energy, in semiconductors. From this, we propose a simple pictorial representation of the general theory of acid-base chemistry. By performing first-principles molecular dynamics of liquid water models with solutes, we apply the formulation to calculate formation energies of various neutral and charged solutes such as H(+), OH(-), NH(3), NH(4)(+), HCOOH, and HCOO(-) in water. The deduced auto-dissociation constant of water and the difference in the pKa values of NH(3) and HCOOH show good agreement with known experimental values. Our first-principles approach can be further extended and applied to other bio- and electro-chemical molecules such as amino acids and redox reaction couples that could exist in aqueous environments to understand their thermodynamic stability.

  18. Spectroscopic and microscopic studies of self-assembled nc-Si/a-SiC thin films grown by low pressure high density spontaneous plasma processing.

    PubMed

    Das, Debajyoti; Kar, Debjit

    2014-12-14

    In view of suitable applications in the window layer of nc-Si p-i-n solar cells in superstrate configuration, the growth of nc-Si/a-SiC composite films was studied, considering the trade-off relation between individual characteristics of its a-SiC component to provide a wide optical-gap and electrically conducting nc-Si component to simultaneously retain enough crystalline linkages to facilitate proper crystallization to the i-nc-Si absorber-layer during its subsequent growth. Self-assembled nc-Si/a-SiC thin films were spontaneously grown by low-pressure planar inductively coupled plasma CVD, operating in electromagnetic mode, providing high atomic-H density. Spectroscopic simulations of ellipsometry and Raman data, and systematic chemical and structural analysis by XPS, TEM, SEM and AFM were performed. Corresponding to optimized inclusion of C essentially incorporated as Si-C bonds in the network, the optical-gap of the a-SiC component widened, void fraction including the incubation layer thickness reduced. While the bulk crystallinity decreased only marginally, Si-ncs diminished in size with narrower distribution and increased number density. With enhanced C-incorporation, formation of C-C bonds in abundance deteriorates the Si continuous bonding network and persuades growth of an amorphous dominated silicon-carbon heterostructure containing high-density tiny Si-ncs. Stimulated nanocrystallization identified in the Si-network, induced by a limited amount of carbon incorporation, makes the material most suitable for applications in nc-Si solar cells. The novelty of the present work is to enable spontaneous growth of self-assembled superior quality nc-Si/a-SiC thin films and simultaneous spectroscopic simulation-based optimization of properties for utilization in devices.

  19. Thermodynamic and kinetic characterisation of individual haems in multicentre cytochromes c3.

    PubMed

    Paquete, Catarina M; Turner, David L; Louro, Ricardo O; Xavier, António V; Catarino, Teresa

    2007-09-01

    The characterisation of individual centres in multihaem proteins is difficult due to the similarities in the redox and spectroscopic properties of the centres. NMR has been used successfully to distinguish redox centres and allow the determination of the microscopic thermodynamic parameters in several multihaem cytochromes c(3) isolated from different sulphate-reducing bacteria. In this article we show that it is also possible to discriminate the kinetic properties of individual centres in multihaem proteins, if the complete microscopic thermodynamic characterisation is available and the system displays fast intramolecular equilibration in the time scale of the kinetic experiment. The deconvolution of the kinetic traces using a model of thermodynamic control provides a reference rate constant for each haem that does not depend on driving force and can be related to structural factors. The thermodynamic characterisation of three tetrahaem cytochromes and their kinetics of reduction by sodium dithionite are reported in this paper. Thermodynamic and kinetic data were fitted simultaneously to a model to obtain microscopic reduction potentials, haem-haem and haem-proton interacting potentials, and reference rate constants for the haems. The kinetic information obtained for these cytochromes and recently published data for other multihaem cytochromes is discussed with respect to the structural factors that determine the reference rates. The accessibility for the reducing agent seems to play an important role in controlling the kinetic rates, although is clearly not the only factor.

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

    SciTech Connect

    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 (Ka) 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 MH2L+). Time-resolved fluorescence studies of Eu-(EDDAG-DA) solutions (at varying pH) identified 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.

  1. Unexpected formation of a copper(II) 12-metallacrown-4 with (S)-glutamic-gamma-hydroxamic acid: a thermodynamic and spectroscopic study in aqueous solution.

    PubMed

    Tegoni, Matteo; Dallavalle, Francesco; Belosi, Barbara; Remelli, Maurizio

    2004-05-07

    The equilibria of copper(II) with (S)-glutamic-gamma-hydroxamic acid (H2L) were investigated in aqueous solution by different techniques: glass electrode potentiometry; calorimetry; VIS and CD spectrophotometry; and ES-MS. An unexpected pentacopper(II) 12-metallacrown-4 [Cu5L4H(-4)](2-) was detected, analogous to those well known formed by alpha- and beta-aminohydroxamic acids, but of lower stability. Another five species were found: [CuLH]+; [CuL2H2]; [Cu2L2]; [CuL2H]-; and [CuL2]2-. Their structures are proposed based on both spectroscopic and calorimetric data.

  2. Thermodynamic and spectroscopic speciation to explain the blackening process of hematite formed by atmospheric SO2 impact: the case of Marcus Lucretius House (Pompeii).

    PubMed

    Maguregui, Maite; Knuutinen, Ulla; Martínez-Arkarazo, Irantzu; Castro, Kepa; Madariaga, Juan M

    2011-05-01

    After many decades exposed to a polluted environment, in some areas of Marcus Lucretius House, there are clear signs that plasters and hematite pigments are suffering deterioration. In the exhaustive analysis of the black layer covering the red pigment hematite it was possible to identify magnetite (Fe(3)O(4)) as responsible for the black colour, which always appears in combination with gypsum. Thermodynamic modelling stated that the presence of gypsum as well as the transformation of hematite into magnetite is a consequence of the attack of atmospheric SO(2).

  3. Interactions fulvate-metal (Zn²⁺, Cu²⁺ and Fe²⁺): theoretical investigation of thermodynamic, structural and spectroscopic properties.

    PubMed

    Bertoli, Alexandre C; Garcia, Jerusa S; Trevisan, Marcello G; Ramalho, Teodorico C; Freitas, Matheus P

    2016-04-01

    The use of theoretical calculation to determine structural properties of fulvate-metal complex (zinc, copper and iron) is here related. The species were proposed in the ratio 1:1 and 2:1 for which the molecular structure was obtained through the semi-empirical method PM6. The calculation of thermodynamic stability ([Formula: see text]) predicted that the iron complex were more exo-energetic. Metallic ions were coordinated to the phtalate groups of the model-structure of fulvic acid Suwannee River and the calculations of vibrational frequencies suggested that hydrogen bonds may help on the stability of the complex formation.

  4. Characterization of the deterioration of bone black in the 17 th century Oranjezaal paintings using electron-microscopic and micro-spectroscopic imaging techniques

    NASA Astrophysics Data System (ADS)

    van Loon, Annelies; Boon, Jaap J.

    2004-10-01

    A whitish deterioration product was observed on the dark paint in a number of large-scale oil paintings that are part of the Oranjezaal interior decoration in the Royal Palace Huis ten Bosch (The Hague). The whitened areas of a painting by Pieter Soutman dating from 1648 were micro-sampled and compared with "healthy" black paint using different analytical imaging techniques. The dark paint was identified as bone black in linseed oil with a lead drier added. Microscopic images of the cross-section revealed a white top layer of 10-20 μm in the black paint layer. Imaging the cross-section surface with scanning electron microscopy with energy dispersive X-ray analysis (SEM-EDX) and specular reflection Fourier transform infrared (FTIR) showed homogeneous distributions of phosphate, phosphorus and calcium over the black and the white degraded bone black. X-ray diffraction (XRD) showed the presence of calcium phosphate hydrate (Ca 3(PO 4) 2· xH 2O), monetite (CaHPO 4) with possibly some poorly crystalline or amorphous hydroxyapatite (Ca 5(OH)(PO 4) 3). The EDX maps of lead and carbon, however, showed some discontinuity between the degraded and non-degraded bone black. There was an increase in the lead concentration in the white top layer, and a slight decrease of carbon. Transmission FTIR demonstrated that aromatic network polymers from the carbon black are markedly diminished in the white deterioration product. It is proposed that the carbonized organic matter in the bone black is vulnerable to photo bleaching in the presence of a lead catalyst under these circumstances.

  5. Comments to Irreversibility in Thermodynamics

    NASA Technical Reports Server (NTRS)

    Zak, M.

    1995-01-01

    The problem of irreversibility in thermodynamics was revisited and analyzed on the microscopic, stochastic, and macroscopic levels of description. It was demonstrated that Newtonian dynamics can be represented in the Reynolds form, a new phenomenological force with non-Lipschitz properties was introduced, and additional non- Lipschitz thermodynamical forces were incorporated into macroscopic models of transport phenomena.

  6. 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.

  7. Spectroscopic properties of Fe 2+ ions at tetragonal sites—Crystal field effects and microscopic modeling of spin Hamiltonian parameters for Fe 2+ ( S=2) ions in K 2FeF 4 and K 2ZnF 4

    NASA Astrophysics Data System (ADS)

    Rudowicz, C.; Piwowarska, D.

    2011-11-01

    Magnetic and spectroscopic properties of the planar antiferromagnet K 2FeF 4 are determined by the Fe 2+ ions at tetragonal sites. The two-dimensional easy-plane anisotropy exhibited by K 2FeF 4 is due to the zero field splitting (ZFS) terms arising from the orbital singlet ground state of Fe 2+ ions with the spin S=2. To provide insight into the single-ion magnetic anisotropy of K 2FeF 4, the crystal field theory and the microscopic spin Hamiltonian (MSH) approach based on the tensor method is adopted. Survey of available experimental data on the crystal field energy levels and free-ion parameters for Fe 2+ ions in K 2FeF 4 and related compounds is carried out to provide input for microscopic modeling of the ZFS parameters and the Zeeman electronic ones. The ZFS parameters are expressed in the extended Stevens notation and include contributions up to the fourth-order using as perturbation the spin-orbit and electronic spin-spin couplings within the tetragonal crystal field states of the ground 5D multiplet. Modeling of the ZFS parameters and the Zeeman electronic ones is carried out. Variation of these parameters is studied taking into account reasonable ranges of the microscopic ones, i.e. the spin-orbit and spin-spin coupling constants, and the energy level splittings, suitable for Fe 2+ ions in K 2FeF 4 and Fe 2+:K 2ZnF 4. Conversions between the ZFS parameters in the extended Stevens notation and the conventional ones are considered to enable comparison with the data of others. Comparative analysis of the MSH formulas derived earlier and our more complete ones indicates the importance of terms omitted earlier as well as the fourth-order ZFS parameters and the spin-spin coupling related contributions. The results may be useful also for Fe 2+ ions at axial symmetry sites in related systems, i.e. Fe:K 2MnF 4, Rb 2Co 1-xFe xF 4, Fe 2+:Rb 2CrCl 4, and Fe 2+:Rb 2ZnCl 4.

  8. Spectroscopic and thermodynamic study of charge transfer interaction between vitamin B 6 and p-chloranil in aqueous ethanol mixtures of varying composition

    NASA Astrophysics Data System (ADS)

    Datta, Kakali; Roy, Dalim Kumar; Mukherjee, Asok K.

    2008-07-01

    Charge transfer complexes of 1:1 stoichiometry have been found to form between vitamin B 6 (pyridoxine hydrochloride) and a series of electron acceptors including p-chloranil. Since vitamin B 6 is soluble in water while the electron acceptors are insoluble in water but soluble in ethanol, the medium chosen for study is water-ethanol mixture. From the trends in the CT absorption bands the vertical ionization potential of vitamin B 6 has been determined to be 8.12 eV. The enthalpy and entropy of formation of the complex between p-chloranil and vitamin B 6 have been determined by estimating the formation constant ( K) spectroscopically at four different temperatures in 75% ethanol-water mixture. Again, the magnitude of K has been found to decrease noticeably with decrease in dielectric constant of the medium (as the percentage of ethanol in the aqueous-ethanol mixture is increased). A plausible explanation for this has been given in terms of hydrolysis of pyridoxine hydrochloride.

  9. Amorphous SiO2 surface models: energetics of the dehydroxylation process, strain, ab initio atomistic thermodynamics and IR spectroscopic signatures.

    PubMed

    Comas-Vives, Aleix

    2016-03-14

    In this contribution, realistic amorphous SiO2 models of 2.1 × 2.1 nm with silanol densities ranging 1.1-7.2 OH per nm(2) are obtained by means of ab initio calculations via the dehydroxylation of a fully hydroxylated silica surface. The dehydroxyation process is considered to take place via direct condensation of adjacent silanol groups and silica migration steps. The latter reconstructions are needed in order to obtain highly dehydroxylated silica surfaces with favorable energetics and without the formation of defects. The obtained surface phase diagram of different silica models as a function of temperature and PH2O is able to correctly describe the silanol density under different conditions, and the IR spectroscopic signatures of the silanols are in qualitative agreement with the experiment. The amorphous silica models presented here have a high degree of heterogeneity as found from the big variability obtained in the energetics of the dehydroxylation steps. It was also found that the resulting average Si-O distance of the newly formed siloxane bridges serves as a descriptor of the strain introduced in the silica surface. All these factors can be crucial in order to simulate the activity of catalysts grafted onto silica with different silanol densities, especially the one containing ca. 1 OH per nm(2), which can serve as a model for the SiO2 surface pretreated under high vacuum and at 700 °C.

  10. Spectroscopic investigation (FTIR spectrum), NBO, HOMO-LUMO energies, NLO and thermodynamic properties of 8-Methyl-N-vanillyl-6-nonenamideby DFT methods

    NASA Astrophysics Data System (ADS)

    Sherin Percy Prema Leela, J.; Hemamalini, R.; Muthu, S.; Al-Saadi, Abdulaziz A.

    2015-07-01

    Capsicum a hill grown vegetable is also known as red pepper or chili pepper. Capsaicin(8-Methyl-N-vanillyl-6-nonenamide) is the active component in chili peppers, which is currently used in the treatment of osteoarthritis, psoriasis and cancer. Fourier transform infrared (FT-IR) spectrum of Capsaicin in the solid phase were recorded in the region 4000-400 cm-1 and analyzed. The vibrational frequencies of the title compound were obtained theoretically by DFT/B3LYP calculations employing the standard 6-311++G(d,p) basis set and were compared with Fourier transform infrared spectrum. Complete vibrational assignment analysis and correlation of the fundamental modes for the title compound were carried out. The vibrational harmonic frequencies were scaled using scale factor, yielding a good agreement between the experimentally recorded and the theoretically calculated values. Stability of the molecule arising from hyper conjugative interactions, charge delocalization and intra molecular hydrogen bond-like weak interaction has been analyzed using Natural bond orbital (NBO) analysis by using B3LYP/6-311++G(d,p) method. The results show that electron density (ED) in the σ∗ and π∗ antibonding orbitals and second-order delocalization energies E (2) confirm the occurrence of intra molecular charge transfer (ICT) within the molecule. The dipole moment (μ), polarizability (α) and the hyperpolarizability (β) values of the molecule has been computed. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures were calculated.

  11. Thermodynamic stability, spectroscopic identification, and gas storage capacity of CO2-CH4-N2 mixture gas hydrates: implications for landfill gas hydrates.

    PubMed

    Lee, Hyeong-Hoon; Ahn, Sook-Hyun; Nam, Byong-Uk; Kim, Byeong-Soo; Lee, Gang-Woo; Moon, Donghyun; Shin, Hyung Joon; Han, Kyu Won; Yoon, Ji-Ho

    2012-04-03

    Landfill gas (LFG), which is primarily composed of CH(4), CO(2), and N(2), is produced from the anaerobic digestion of organic materials. To investigate the feasibility of the storage and transportation of LFG via the formation of hydrate, we observed the phase equilibrium behavior of CO(2)-CH(4)-N(2) mixture hydrates. When the specific molar ratio of CO(2)/CH(4) was 40/55, the equilibrium dissociation pressures were gradually shifted to higher pressures and lower temperatures as the mole fraction of N(2) increased. X-ray diffraction revealed that the CO(2)-CH(4)-N(2) mixture hydrate prepared from the CO(2)/CH(4)/N(2) (40/55/5) gas mixture formed a structure I clathrate hydrate. A combination of Raman and solid-state (13)C NMR measurements provided detailed information regarding the cage occupancy of gas molecules trapped in the hydrate frameworks. The gas storage capacity of LFG hydrates was estimated from the experimental results for the hydrate formations under two-phase equilibrium conditions. We also confirmed that trace amounts of nonmethane organic compounds do not affect the cage occupancy of gas molecules or the thermodynamic stability of LFG hydrates.

  12. Spectroscopic investigation (FTIR spectrum), NBO, HOMO-LUMO energies, NLO and thermodynamic properties of 8-Methyl-N-vanillyl-6-nonenamideby DFT methods.

    PubMed

    Leela, J Sherin Percy Prema; Hemamalini, R; Muthu, S; Al-Saadi, Abdulaziz A

    2015-07-05

    Capsicum a hill grown vegetable is also known as red pepper or chili pepper. Capsaicin(8-Methyl-N-vanillyl-6-nonenamide) is the active component in chili peppers, which is currently used in the treatment of osteoarthritis, psoriasis and cancer. Fourier transform infrared (FT-IR) spectrum of Capsaicin in the solid phase were recorded in the region 4000-400 cm(-1) and analyzed. The vibrational frequencies of the title compound were obtained theoretically by DFT/B3LYP calculations employing the standard 6-311++G(d,p) basis set and were compared with Fourier transform infrared spectrum. Complete vibrational assignment analysis and correlation of the fundamental modes for the title compound were carried out. The vibrational harmonic frequencies were scaled using scale factor, yielding a good agreement between the experimentally recorded and the theoretically calculated values. Stability of the molecule arising from hyper conjugative interactions, charge delocalization and intra molecular hydrogen bond-like weak interaction has been analyzed using Natural bond orbital (NBO) analysis by using B3LYP/6-311++G(d,p) method. The results show that electron density (ED) in the σ∗ and π∗ antibonding orbitals and second-order delocalization energies E (2) confirm the occurrence of intra molecular charge transfer (ICT) within the molecule. The dipole moment (μ), polarizability (α) and the hyperpolarizability (β) values of the molecule has been computed. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures were calculated.

  13. Density functional theory, comparative vibrational spectroscopic studies, NBO, HOMO-LUMO analyses and thermodynamic functions of N-(bromomethyl)phthalimide and N-(chloromethyl)phthalimide

    NASA Astrophysics Data System (ADS)

    Balachandran, V.; Lalitha, S.; Rajeswari, S.

    2012-06-01

    Quantum mechanical calculations of energies, geometries, and vibrational wavenumbers of N-(bromomethyl)phthalimide and N-(chloromethyl)phthalimide are carried out using density functional theory (DFT/B3LYP) method with 6-31G and 6-311G(d,p) basis sets. The optimized geometrical parameters obtained by B3LYP method show good agreement with experimental data. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of N-(bromomethyl)phthalimide and N-(chloromethyl)phthalimide was also reported. The calculated HOMO and LUMO energies show that charge transfer occurs in the molecules. The thermodynamic functions of N-(bromomethyl)phthalimide and N-(chloromethyl)phthalimide have been performed at B3LYP/6-31G and B3LYP/6-311G(d,p) basis sets. The theoretical spectrograms for FT-IR and FT-Raman spectra of N-(bromomethyl)phthalimide and N-(chloromethyl)phthalimide have also been constructed.

  14. Topography of the combining region of a Thomsen-Friedenreich-antigen-specific lectin jacalin (Artocarpus integrifolia agglutinin). A thermodynamic and circular-dichroism spectroscopic study.

    PubMed Central

    Mahanta, S K; Sastry, M V; Surolia, A

    1990-01-01

    Thermodynamic analysis of carbohydrate binding by Artocarpus integrifolia (jackfruit) agglutinin (jacalin) shows that, among monosaccharides, Me alpha GalNAc (methyl-alpha-N-acetylgalactosamine) is the strongest binding ligand. Despite its strong affinity for Me alpha GalNAc and Me alpha Gal, the lectin binds very poorly when Gal and GalNAc are in alpha-linkage with other sugars such as in A- and B-blood-group trisaccharides, Gal alpha 1-3Gal and Gal alpha 1-4Gal. These binding properties are explained by considering the thermodynamic parameters in conjunction with the minimum energy conformations of these sugars. It binds to Gal beta 1-3GalNAc alpha Me with 2800-fold stronger affinity over Gal beta 1-3GalNAc beta Me. It does not bind to asialo-GM1 (monosialoganglioside) oligosaccharide. Moreover, it binds to Gal beta 1-3GalNAc alpha Ser, the authentic T (Thomsen-Friedenreich)-antigen, with about 2.5-fold greater affinity as compared with Gal beta 1-3GalNAc. Asialoglycophorin A was found to be about 169,333 times stronger an inhibitor than Gal beta 1-3GalNAc. The present study thus reveals the exquisite specificity of A. integrifolia lectin for the T-antigen. Appreciable binding of disaccharides Glc beta 1-3GalNAc and GlcNAc beta 1-3Gal and the very poor binding of beta-linked disaccharides, which instead of Gal and GalNAc contain other sugars at the reducing end, underscore the important contribution made by Gal and GalNAc at the reducing end for recognition by the lectin. The ligand-structure-dependent alterations of the c.d. spectrum in the tertiary structural region of the protein allows the placement of various sugar units in the combining region of the lectin. These studies suggest that the primary subsite (subsite A) can accommodate only Gal or GalNAc or alpha-linked Gal or GalNAc, whereas the secondary subsite (subsite B) can associate either with GalNAc beta Me or Gal beta Me. Considering these factors a likely arrangement for various disaccharides in the

  15. Femtosecond photoelectron point projection microscope

    SciTech Connect

    Quinonez, Erik; Handali, Jonathan; Barwick, Brett

    2013-10-15

    By utilizing a nanometer ultrafast electron source in a point projection microscope we demonstrate that images of nanoparticles with spatial resolutions of the order of 100 nanometers can be obtained. The duration of the emission process of the photoemitted electrons used to make images is shown to be of the order of 100 fs using an autocorrelation technique. The compact geometry of this photoelectron point projection microscope does not preclude its use as a simple ultrafast electron microscope, and we use simple analytic models to estimate temporal resolutions that can be expected when using it as a pump-probe ultrafast electron microscope. These models show a significant increase in temporal resolution when comparing to ultrafast electron microscopes based on conventional designs. We also model the microscopes spectroscopic abilities to capture ultrafast phenomena such as the photon induced near field effect.

  16. Possible extended forms of thermodynamic entropy

    NASA Astrophysics Data System (ADS)

    Sasa, Shin-ichi

    2014-01-01

    Thermodynamic entropy is determined by a heat measurement through the Clausius equality. The entropy then formalizes a fundamental limitation of operations by the second law of thermodynamics. The entropy is also expressed as the Shannon entropy of the microscopic degrees of freedom. Whenever an extension of thermodynamic entropy is attempted, we must pay special attention to how its three different aspects just mentioned are altered. In this paper, we discuss possible extensions of the thermodynamic entropy.

  17. 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.

  18. [Microscopic colitis].

    PubMed

    Bohr, Johan

    2002-02-11

    Microscopic colitis is an umbrella term for a newly described group of colitides, belonging to the inflammatory bowel diseases, which are only diagnosable by microscopic evaluation of a macroscopically normal colon mucosa. Collagenous colitis and lymphocytic colitis are the most common of these colitides. Microscopic colitis is characterised clinically by chronic non-bloody watery diarrhoea. Crampy abdominal pain, nocturnal diarrhoea, urgency, and initial weight loss are usual. Concomitant diseases of autoimmune origin and arthralgia are commonly seen. Treatment of microscopic colitis follows the guidelines for treatment of other inflammatory bowel diseases, but a substantial part of the patients with microscopic colitis enter spontaneous remission after some years. A minor part, however, have very troublesome symptoms and are almost refractory to treatment. Microscopic colitis has apparently no malignant potential.

  19. 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

  20. 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.

  1. Melt Structure and Properties: a Spectroscopic Perspective

    NASA Astrophysics Data System (ADS)

    Stebbins, J.

    2006-12-01

    Entropy, volume, and their P/T derivatives are at the heart of models of the thermodynamics of silicate melts and magmas. Quantitative characterization of glass structure is leading to important new insights into the links from "Microscopic to Macroscopic" that can at least guide interpretations of data and in some cases even have predictive power. A few recent examples will be discussed here. The often-large configurational components to heat capacities, thermal expansivities, and compressibilities of melts strongly indicate that structural changes with temperature and pressure are of key importance. At least some aspects of thermal increases in configurational (as opposed to vibrational) disorder are amenable to spectroscopic detection, either with in situ methods or on glasses with varying quench rates and thus varying fictive temperatures. In some systems, such changes are now clear, and can be shown to make significant contributions to properties. These include network cation coordination in systems such as borate liquids (BO4 to BO3 at higher T), and Al-Si disordering in aluminosilicates. In general, however, progress in this rich problem has only begun. It has long been suspected from thermodynamic analyses (and theoretical simulations) that configurational changes in melts play a key role in volume compression at high pressure, over and above that which can be expressed in "normal" equations of state or from those expected from bond compression and bending. Scattering and spectroscopic studies have revealed some of the important aspects of pressure-induced structural changes, but again we are just at the beginning of full understanding. For example, binary silicate glasses quenched from high-P melts clearly record some systematic increases in Si coordination, while aluminosilicates record systematic pressure and compositional (modifier cation field strength) effects on Al coordination in recovered samples with large, quenched-in density increases

  2. Microscopic Polyangiitis

    PubMed Central

    Chung, Sharon A.; Seo, Philip

    2010-01-01

    Synopsis In 1923, Friedrich Wohlwill described two patients with a “microscopic form of periarteritis nodosa”, which was distinct from classical polyarteritis nodosa. This disease, now known as microscopic polyangiitis (MPA), is a primary systemic vasculitis characterized by inflammation of the small-caliber blood vessels and the presence of circulating antineutrophil cytoplasmic antibodies (ANCA). Typically, microscopic polyangiitis presents with glomerulonephritis and pulmonary capillaritis, although involvement of the skin, nerves, and gastrointestinal tract is not uncommon. Treatment of MPA generally requires use of a cytotoxic agent (such as cyclophosphamide) in addition to high-dose glucocorticoids. Recent research has focused on identifying alternate treatment strategies that minimize or eliminate exposure to cytotoxic agents. This article will review the history, pathogenesis, clinical manifestations, and treatment of MPA. PMID:20688249

  3. 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.

  4. 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.

  5. Microscopic colitis.

    PubMed

    Delgado, Jorge; Delgado, Bertha; Fich, Alex; Odes, Shmuel

    2004-08-01

    Microscopic colitis is an idiopathic chronic inflammatory bowel disease presenting with watery diarrhea. While colonoscopy and radiology findings are normal, the colon shows striking pathologic findings, including lymphocytic colitis and collagenous colitis. The clinical course is usually benign with sustained remission. Recent medical evidence shows that bismuth and budesonide are effective treatments.

  6. Microscopic colitis

    PubMed Central

    Ianiro, Gianluca; Cammarota, Giovanni; Valerio, Luca; Annicchiarico, Brigida Eleonora; Milani, Alessandro; Siciliano, Massimo; Gasbarrini, Antonio

    2012-01-01

    Microscopic colitis may be defined as a clinical syndrome, of unknown etiology, consisting of chronic watery diarrhea, with no alterations in the large bowel at the endoscopic and radiologic evaluation. Therefore, a definitive diagnosis is only possible by histological analysis. The epidemiological impact of this disease has become increasingly clear in the last years, with most data coming from Western countries. Microscopic colitis includes two histological subtypes [collagenous colitis (CC) and lymphocytic colitis (LC)] with no differences in clinical presentation and management. Collagenous colitis is characterized by a thickening of the subepithelial collagen layer that is absent in LC. The main feature of LC is an increase of the density of intra-epithelial lymphocytes in the surface epithelium. A number of pathogenetic theories have been proposed over the years, involving the role of luminal agents, autoimmunity, eosinophils, genetics (human leukocyte antigen), biliary acids, infections, alterations of pericryptal fibroblasts, and drug intake; drugs like ticlopidine, carbamazepine or ranitidine are especially associated with the development of LC, while CC is more frequently linked to cimetidine, non-steroidal antiinflammatory drugs and lansoprazole. Microscopic colitis typically presents as chronic or intermittent watery diarrhea, that may be accompanied by symptoms such as abdominal pain, weight loss and incontinence. Recent evidence has added new pharmacological options for the treatment of microscopic colitis: the role of steroidal therapy, especially oral budesonide, has gained relevance, as well as immunosuppressive agents such as azathioprine and 6-mercaptopurine. The use of anti-tumor necrosis factor-α agents, infliximab and adalimumab, constitutes a new, interesting tool for the treatment of microscopic colitis, but larger, adequately designed studies are needed to confirm existing data. PMID:23180940

  7. Microscopic colitis.

    PubMed

    Ianiro, Gianluca; Cammarota, Giovanni; Valerio, Luca; Annicchiarico, Brigida Eleonora; Milani, Alessandro; Siciliano, Massimo; Gasbarrini, Antonio

    2012-11-21

    Microscopic colitis may be defined as a clinical syndrome, of unknown etiology, consisting of chronic watery diarrhea, with no alterations in the large bowel at the endoscopic and radiologic evaluation. Therefore, a definitive diagnosis is only possible by histological analysis. The epidemiological impact of this disease has become increasingly clear in the last years, with most data coming from Western countries. Microscopic colitis includes two histological subtypes [collagenous colitis (CC) and lymphocytic colitis (LC)] with no differences in clinical presentation and management. Collagenous colitis is characterized by a thickening of the subepithelial collagen layer that is absent in LC. The main feature of LC is an increase of the density of intra-epithelial lymphocytes in the surface epithelium. A number of pathogenetic theories have been proposed over the years, involving the role of luminal agents, autoimmunity, eosinophils, genetics (human leukocyte antigen), biliary acids, infections, alterations of pericryptal fibroblasts, and drug intake; drugs like ticlopidine, carbamazepine or ranitidine are especially associated with the development of LC, while CC is more frequently linked to cimetidine, non-steroidal antiinflammatory drugs and lansoprazole. Microscopic colitis typically presents as chronic or intermittent watery diarrhea, that may be accompanied by symptoms such as abdominal pain, weight loss and incontinence. Recent evidence has added new pharmacological options for the treatment of microscopic colitis: the role of steroidal therapy, especially oral budesonide, has gained relevance, as well as immunosuppressive agents such as azathioprine and 6-mercaptopurine. The use of anti-tumor necrosis factor-α agents, infliximab and adalimumab, constitutes a new, interesting tool for the treatment of microscopic colitis, but larger, adequately designed studies are needed to confirm existing data.

  8. Terahertz Microscope

    DTIC Science & Technology

    2010-05-01

    bases and bacterial spores , etc. Recently, biomolecular nanoparticles have been successfully imaged using a THz microscope by the group of Prof. Han...compounds, pharmaceutical materials, illegal drugs, amino acids, nuclei-bases and 30 bacterial spores , etc. THz waves can also penetrate through many...Am. B, vol. 7, pp. 2006-2015, 1990. 25. J. D. Joannopoulos, R. D. Meade, and J. N. Winn, Photonic Crystals: Molding the Flow of Light, Princeton U

  9. Thermodynamic holography

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    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.

  10. Nonequilibrium thermodynamics of nucleation

    SciTech Connect

    Schweizer, M.; Sagis, L. M. C.

    2014-12-14

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

  11. Nonequilibrium thermodynamics of nucleation.

    PubMed

    Schweizer, M; Sagis, L M C

    2014-12-14

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

  12. Nonequilibrium thermodynamics of nucleation

    NASA Astrophysics Data System (ADS)

    Schweizer, M.; Sagis, L. M. C.

    2014-12-01

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

  13. 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.

  14. 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))]-

    SciTech Connect

    Abergel, Rebecca J.; D'Aleo, Anthony; Ng Pak Leung, Clara; Shuh, David; Raymond, Kenneth

    2009-11-20

    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 mu s) and a quantum yield of 7.0percent 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 beta 110 = 20.2(2)) and to define the influence of the ligand scaffold on the stability and photophysical properties.

  15. Descriptive thermodynamics

    NASA Astrophysics Data System (ADS)

    Ford, David; Huntsman, Steven

    2006-06-01

    Thermodynamics (in concert with its sister discipline, statistical physics) can be regarded as a data reduction scheme based on partitioning a total system into a subsystem and a bath that weakly interact with each other. Whereas conventionally, the systems investigated require this form of data reduction in order to facilitate prediction, a different problem also occurs, in the context of communication networks, markets, etc. Such “empirically accessible” systems typically overwhelm observers with the sort of information that in the case of (say) a gas is effectively unobtainable. What is required for such complex interacting systems is not prediction (this may be impossible when humans besides the observer are responsible for the interactions) but rather, description as a route to understanding. Still, the need for a thermodynamical data reduction scheme remains. In this paper, we show how an empirical temperature can be computed for finite, empirically accessible systems, and further outline how this construction allows the age-old science of thermodynamics to be fruitfully applied to them.

  16. 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.

  17. Nanoscopic Thermodynamics.

    PubMed

    Qi, Weihong

    2016-09-20

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

  18. The Once and Future Second Law of Thermodynamics

    NASA Astrophysics Data System (ADS)

    Lloyd, Seth

    2008-08-01

    The second law of thermodynamics is a cornerstone of physics: together with its companion, the first law of thermodynamics, it is the support on which our scientific understanding of heat and the microscopic motion of atoms and molecules rests. Like Arthur, the once and future king (rex quondam, rex futurus), the second law is always with us, and always will be.

  19. Spectroscopic imaging in electron microscopy

    SciTech Connect

    Pennycook, Stephen J; Colliex, C.

    2012-01-01

    In the scanning transmission electron microscope, multiple signals can be simultaneously collected, including the transmitted and scattered electron signals (bright field and annular dark field or Z-contrast images), along with spectroscopic signals such as inelastically scattered electrons and emitted photons. In the last few years, the successful development of aberration correctors for the electron microscope has transformed the field of electron microscopy, opening up new possibilities for correlating structure to functionality. Aberration correction not only allows for enhanced structural resolution with incident probes into the sub-angstrom range, but can also provide greater probe currents to facilitate mapping of intrinsically weak spectroscopic signals at the nanoscale or even the atomic level. In this issue of MRS Bulletin, we illustrate the power of the new generation of electron microscopes with a combination of imaging and spectroscopy. We show the mapping of elemental distributions at atomic resolution and also the mapping of electronic and optical properties at unprecedented spatial resolution, with applications ranging from graphene to plasmonic nanostructures, and oxide interfaces to biology.

  20. Advances in thermodynamics

    SciTech Connect

    Sieniutycz, S. ); Salamon, P. )

    1990-01-01

    This book covers: nonequilibrium thermodynamics for solar energy applications; finite-time thermodynamics as applied to solar power conversion; thermodynamics and economics; exergy analysis; and an analysis of cumulative exergy consumption and exergy losses.

  1. Natural thermodynamics

    NASA Astrophysics Data System (ADS)

    Annila, Arto

    2016-02-01

    The principle of increasing entropy is derived from statistical physics of open systems assuming that quanta of actions, as undividable basic build blocks, embody everything. According to this tenet, all systems evolve from one state to another either by acquiring quanta from their surroundings or by discarding quanta to the surroundings in order to attain energetic balance in least time. These natural processes result in ubiquitous scale-free patterns: skewed distributions that accumulate in a sigmoid manner and hence span log-log scales mostly as straight lines. Moreover, the equation for least-time motions reveals that evolution is by nature a non-deterministic process. Although the obtained insight in thermodynamics from the notion of quanta in motion yields nothing new, it accentuates that contemporary comprehension is impaired when modeling evolution as a computable process by imposing conservation of energy and thereby ignoring that quantum of actions are the carriers of energy from the system to its surroundings.

  2. Thermodynamic investigation of interaction between [(η6-p-cymene) RuII(acetone-N4-phenylthiosemicarbazone)Cl]Cl anticancer drug and human serum albumin: spectroscopic and electrochemical studies.

    PubMed

    Huang, Shan; Zhu, Fawei; Qian, Quanquan; Xiao, Qi; Su, Wei

    2015-03-01

    In this contribution, the interaction between [(η (6)-p-cymene)Ru(II)(acetone-N (4)-phenylthiosemicarbazone)Cl]Cl (Ru-TSC) anticancer drug and human serum albumin (HSA) was investigated by spectroscopic and electrochemical techniques. The fluorescence spectra results indicated that Ru-TSC anticancer drug could quench the intrinsic fluorescence of HSA through dynamic quenching mode. The calculated corresponding activation energy of the interaction between Ru-TSC anticancer drug and HSA was 35.62 kJ mol(-1). The distance between HSA and Ru-TSC anticancer drug was obtained according to fluorescence resonance energy transfer. The results of synchronous fluorescence spectra, three-dimensional fluorescence spectra, Fourier transform infrared spectroscopy (FTIR) spectra, and circular dichroism (CD) spectra indicated that the microenvironment and the conformation of HSA were all changed in the presence of Ru-TSC anticancer drug. The results of cyclic voltammetry further validated the interaction between Ru-TSC and HSA. These results indicated that the biological activity of HSA was affected by Ru-TSC anticancer drug dramatically.

  3. Molecular structure, vibrational spectroscopic (FT-IR, FT-Raman), UV-vis spectra, first order hyperpolarizability, NBO analysis, HOMO and LUMO analysis, thermodynamic properties of benzophenone 2,4-dicarboxylic acid by ab initio HF and density functional method.

    PubMed

    Chaitanya, K

    2012-02-01

    The FT-IR (4000-450 cm(-1)) and FT-Raman spectra (3500-100 cm(-1)) of benzophenone 2,4-dicarboxylic acid (2,4-BDA) have been recorded in the condensed state. Density functional theory calculation with B3LYP/6-31G(d,p) basis set have been used to determine ground state molecular geometries (bond lengths and bond angles), harmonic vibrational frequencies, infrared intensities, Raman activities and bonding features of the title compounds. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the scaled quantum mechanical force field (SQMFF) methodology. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of 2,4-BDA is calculated using HF/6-31G(d,p) method on the finite-field approach. The stability of molecule has been analyzed by using NBO analysis. The calculated first hyperpolarizability shows that the molecule is an attractive molecule for future applications in non-linear optics. The calculated HOMO and LUMO energies show that charge transfer occurs within these molecules. Mulliken population analysis on atomic charges is also calculated. Because of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated. Finally, the UV-vis spectra and electronic absorption properties were explained and illustrated from the frontier molecular orbitals.

  4. Spectroscopic (FT-IR, FT-Raman, and UV-visible) and quantum chemical studies on molecular geometry, Frontier molecular orbitals, NBO, NLO and thermodynamic properties of 1-acetylindole.

    PubMed

    Shukla, Vikas K; Al-Abdullah, Ebtehal S; El-Emam, Ali A; Sachan, Alok K; Pathak, Shilendra K; Kumar, Amarendra; Prasad, Onkar; Bishnoi, Abha; Sinha, Leena

    2014-12-10

    Quantum chemical calculations of ground state energy, geometrical structure and vibrational wavenumbers of 1-acetylindole were carried out using density functional (DFT/B3LYP) method with 6-311++G(d,p) basis set. The FT-IR and FT-Raman spectra were recorded in the condensed state. The fundamental vibrational wavenumbers were calculated and a good correlation between experimental and scaled calculated wavenumbers has been accomplished. Electric dipole moment, polarizability and first static hyperpolarizability values of 1-acetylindole have been calculated at the same level of theory and basis set. The results show that the 1-acetylindole molecule possesses nonlinear optical (NLO) behavior with non-zero values. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-Visible spectrum of the molecule was recorded in the region 200-500nm and the electronic properties like HOMO and LUMO energies and composition were obtained using TD-DFT method. The calculated energies and oscillator strengths are in good correspondence with the experimental data. The thermodynamic properties of the compound under investigation were calculated at different temperatures. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. 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.

  6. 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.

  7. Stochastic approach to irreversible thermodynamics

    NASA Astrophysics Data System (ADS)

    Nicolis, Grégoire; De Decker, Yannick

    2017-10-01

    An extension of classical irreversible thermodynamics pioneered by Ilya Prigogine is developed, in which fluctuations of macroscopic observables accounting for microscopic-scale processes are incorporated. The contribution of the fluctuations to the entropy production is derived from a generalized entropy balance equation and expressed in terms of the fluctuating variables, via an extended local equilibrium Ansatz and in terms of the probability distributions of these variables. The approach is illustrated on reactive systems involving linear and nonlinear steps, and the role of the distance from equilibrium and of the nonlinearities is assessed.

  8. 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…

  9. 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…

  10. 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.

  11. TEAM Electron Microscope Animation

    SciTech Connect

    2012-01-01

    The TEAM Electron Microscope, a device that enables atomic-scale imaging in 3-D, has a rotating stage that can hold and position samples inside electron microscopes with unprecedented stability, position-control accuracy, and range of motion.The TEAM Stage makes one of the world's most powerful electron microscopes even better, and enables previously impossible experiments.

  12. Thermodynamic approach to creep and plasticity

    SciTech Connect

    Loefstedt, R.

    1997-06-01

    A solid subjected to a small load distorts rapidly in the manner predicted by elasticity theory. On a much longer time scale, the solid will creep. This dissipative motion is an important consideration in the engineering design of, for example, aircraft engines, but the macroscopic equations of motion describing this deformation are based on empirical observations. The principles of thermodynamics specify the dissipative fluxes appropriate to the classical equations of elasticity, which include one, unique to solids, which describes creep. The thermodynamic theory is presented, and the insights into the underlying microscopic mechanisms of creep, gleaned from the macroscopic formalism, are also discussed. {copyright} {ital 1997} {ital The American Physical Society}

  13. 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.

  14. 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.

  15. Spectroscopic and microscopic investigations of phthalocyanine aggregates on Gold(111)

    NASA Astrophysics Data System (ADS)

    Nishida, Krista Rachel Akiko

    Self-assembled organic pi systems are of interest because of their potential applications in light harvesting and electron transfer. Phthalocyanines (Pc) demonstrate desirable photonic and electronic properties, thus making them excellent candidates for functional nanostructures. The specific focus of this research has been the nanoscale aggregation of a metal-free organic dye, tetrasulfonic acid phthalocyanine (TSPc) and includes the use of UV-visible Spectroscopy, Resonance Light Scattering Spectroscopy (RLS), X-ray Photoelectron Spectroscopy (XPS), Atomic Force Microscopy (AFM) and ambient and ultra-high-vacuum Scanning Tunneling Microscopy (STM) and Scanning Tunneling Spectroscopy (STS). The UV-visible absorption studies show that TSPc aggregates upon dissolution in water and obeys Beer's Law within the concentration range of 10 -7M to 10-4M, indicating that TSPc concentration has no further effect on aggregation in aqueous solution. In addition, both ionic strength in NaCl and pH changes in the presence of NaOH, HCl or acetic acid (HAc) do affect aggregation. The RSL studies confirm these effects of pH only in the presence of HAc. The XPS studies show that the ratio of non-protonated to protonated nitrogens does not change with decreasing solution pH. STM images of TSPc deposited from pH<1 solutions reveal ordered branched web-like assemblies hundreds of nanometers in length, generally 2 nm tall and having variable widths. STM imaging shows TSPc aggregates decrease in order as pH increases. STM images of TSPc deposited from solutions with pH>10 show monolayer coverage of TSPc in salt form. High-resolution UHV-STM images of TSPc aggregates deposited from pH 0 solution on Au(111) reveal detailed coherent columnar architecture with the phthalocyanine macrocycles orientated parallel to the substrate surface. OMTS was used to identify the HOMO and LUMO of the TSPc aggregates and the results are contrasted with the same molecular states in unsubstituted metallated phthalocyanines (MPc). The positions of the filled and the empty states of the TSPc are comparable to those of other unsubstituted MPc's indicating that the electronegative sulfonate substituents have minimal effect on the electronic properties of the macrocycle. The HOMO-LUMO separation of TSPc is slightly above 2 eV, a value consistent with the literature assignments for the Pc ring band gap.

  16. 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

  17. Measuring Thermodynamic Length

    SciTech Connect

    Crooks, Gavin E

    2007-09-07

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

  18. Far-from-equilibrium measurements of thermodynamic length

    SciTech Connect

    Feng, Edward H.; Crooks, Gavin E.

    2008-11-05

    Thermodynamic length is a path function that generalizes the notion of length to the surface of thermodynamic states. Here, we show how to measure thermodynamic length in far-from-equilibrium experiments using the work fluctuation relations. For these microscopic systems, it proves necessary to define the thermodynamic length in terms of the Fisher information. Consequently, the thermodynamic length can be directly related to the magnitude of fluctuations about equilibrium. The work fluctuation relations link the work and the free energy change during an external perturbation on a system. We use this result to determine equilibrium averages at intermediate points of the protocol in which the system is out-of-equilibrium. This allows us to extend Bennett's method to determine the potential of mean force, as well as the thermodynamic length, in single molecule experiments.

  19. 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...

  20. 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...

  1. 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)

  2. Chemical thermodynamics: plenary review.

    NASA Astrophysics Data System (ADS)

    Fegley, B., Jr.

    1990-05-01

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

  3. 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.

  4. 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.

  5. Local detailed balance: a microscopic derivation

    NASA Astrophysics Data System (ADS)

    Bauer, M.; Cornu, F.

    2015-01-01

    Thermal contact is the archetype of non-equilibrium processes driven by constant non-equilibrium constraints when the latter are enforced by reservoirs exchanging conserved microscopic quantities. At a mesoscopic scale only the energies of the macroscopic bodies are accessible together with the configurations of the contact system. We consider a class of models where the contact system, as well as macroscopic bodies, have a finite number of possible configurations. The global system, with only discrete degrees of freedom, has no microscopic Hamiltonian dynamics, but it is shown that, if the microscopic dynamics is assumed to be deterministic and ergodic and to conserve energy according to some specific pattern, and if the mesoscopic evolution of the global system is approximated by a Markov process as closely as possible, then the mesoscopic transition rates obey three constraints. In the limit where macroscopic bodies can be considered as reservoirs at thermodynamic equilibrium (but with different intensive parameters), the mesoscopic transition rates turn into transition rates for the contact system and the third constraint becomes local detailed balance; the latter is generically expressed in terms of the microscopic exchange entropy variation, namely the opposite of the variation of the thermodynamic entropy of the reservoir involved in a given microscopic jump of the contact system configuration. For a finite-time evolution after contact has been switched on, we derive a fluctuation relation for the joint probability of the heat amounts received from the various reservoirs. The generalization to systems exchanging energy, volume and matter with several reservoirs, with a possible conservative external force acting on the contact system, is given explicitly.

  6. Conservation laws and symmetries in stochastic thermodynamics

    NASA Astrophysics Data System (ADS)

    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.

  7. 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.

  8. 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...

  9. 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)

  10. The Light Microscope.

    ERIC Educational Resources Information Center

    Baker, W. L.

    1995-01-01

    Describes the function of the various parts of the microscope and their integration in the formation of an optical image. Presents a procedure for setting up a microscope to obtain maximum resolution and contrast for each objective lens at all magnifications. (JRH)

  11. 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)

  12. Photography through the Microscope.

    ERIC Educational Resources Information Center

    McNeil, D. W.

    1992-01-01

    Describes how to illuminate and optically stain slides for microscope use and how to interface a 35mm camera with a microscope using an adaptor. Provides equipment descriptions and sources, details about illumination, image formation, darkfield adaptors, centerable filter adaptors, darkfield stops, rheinburg filters, and choosing specimens to…

  13. 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

  14. Atomic force microscopy of Precambrian microscopic fossils

    PubMed Central

    Kempe, André; Schopf, J. William; Altermann, Wladyslaw; Kudryavtsev, Anatoliy B.; Heckl, Wolfgang M.

    2002-01-01

    Atomic force microscopy (AFM) is a technique used routinely in material science to image substances at a submicron (including nm) scale. We apply this technique to analysis of the fine structure of organic-walled Precambrian fossils, microscopic sphaeromorph acritarchs (cysts of planktonic unicellular protists) permineralized in ≈650-million-year-old cherts of the Chichkan Formation of southern Kazakhstan. AFM images, backed by laser-Raman spectroscopic analysis of individual specimens, demonstrate that the walls of these petrified fossils are composed of stacked arrays of ≈200-nm-sized angular platelets of polycyclic aromatic kerogen. Together, AFM and laser-Raman spectroscopy provide means by which to elucidate the submicron-scale structure of individual microscopic fossils, investigate the geochemical maturation of ancient organic matter, and, potentially, distinguish true fossils from pseudofossils and probe the mechanisms of fossil preservation by silica permineralization. PMID:12089337

  15. Atomic force microscopy of Precambrian microscopic fossils.

    PubMed

    Kempe, André; Schopf, J William; Altermann, Wladyslaw; Kudryavtsev, Anatoliy B; Heckl, Wolfgang M

    2002-07-09

    Atomic force microscopy (AFM) is a technique used routinely in material science to image substances at a submicron (including nm) scale. We apply this technique to analysis of the fine structure of organic-walled Precambrian fossils, microscopic sphaeromorph acritarchs (cysts of planktonic unicellular protists) permineralized in approximately 650-million-year-old cherts of the Chichkan Formation of southern Kazakhstan. AFM images, backed by laser-Raman spectroscopic analysis of individual specimens, demonstrate that the walls of these petrified fossils are composed of stacked arrays of approximately 200-nm-sized angular platelets of polycyclic aromatic kerogen. Together, AFM and laser-Raman spectroscopy provide means by which to elucidate the submicron-scale structure of individual microscopic fossils, investigate the geochemical maturation of ancient organic matter, and, potentially, distinguish true fossils from pseudofossils and probe the mechanisms of fossil preservation by silica permineralization.

  16. 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.

  17. [Microscopic colitis: update 2014].

    PubMed

    Burgmann, Konstantin; Fraga, Montserrat; Schoepfer, Alain M; Yun, Pu

    2014-09-03

    Microscopic colitis, which includes lymphocytic colitis and collagenous colitis, represents a frequent cause of chronic watery diarrhea especially in the elderly population. Several medications, such as nonsteroidal antiinflammatory drugs, proton pump inhibitors or antidepressants, as well as cigarette smoking have been recognized as risk factors for microscopic colitis. The diagnosis of microscopic colitis is based on a macroscopically normal ileo-colonoscopy and several biopsies from the entire colon, which demonstrate the pathognomonic histopathologic findings. Therapy is mainly based on the use of budesonide. Other medications, such as mesalazine, cholestyramine and bismuth, have been evaluated as well but the evidence is less solid.

  18. 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.

  19. 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.

  20. 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

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

    SciTech Connect

    Sudheer, Tiwari, P.; Rai, V. N.; Srivastava, A. K.; Mukharjee, C.

    2015-06-24

    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.

  2. Thermodynamics of the alkaline transition in phytocyanins.

    PubMed

    Battistuzzi, Gianantonio; Bellei, Marzia; Dennison, Christopher; Di Rocco, Giulia; Sato, Katsuko; Sola, Marco; Yanagisawa, Sachiko

    2007-08-01

    The thermodynamics of the alkaline transition which influences the spectral and redox properties of the type 1 copper center in phytocyanins has been determined spectroscopically. The proteins investigated include Rhus vernicifera stellacyanin, cucumber basic protein and its Met89Gln variant, and umecyanin, the stellacyanin from horseradish roots, along with its Gln95Met variant. The changes in reaction enthalpy and entropy within the protein series show partial compensatory behavior. Thus, the reaction free energy change (hence the pK (a) value) is rather variable. This indicates that species-dependent differences in reaction thermodynamics, although containing an important contribution from changes in the hydrogen-bonding network of water molecules in the hydration sphere of the protein (which feature enthalpy-entropy compensation), are to a large extent protein-based. The data for axial ligand variants are consistent with the hypothesis of a copper-binding His as the deprotonating residue responsible for this transition.

  3. 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.

  4. Terrestrial Clay under Microscope

    NASA Image and Video Library

    2008-09-30

    A scanning electron microscope captured this image of terresterial soil containing a phyllosilicate mineral from Koua Bocca, Ivory Coast, West Africa. This soil shares some similarities with Martian soil scooped by NASA Phoenix Lander.

  5. Assessment of Petrological Microscopes.

    ERIC Educational Resources Information Center

    Mathison, Charter Innes

    1990-01-01

    Presented is a set of procedures designed to check the design, ergonomics, illumination, function, optics, accessory equipment, and image quality of a microscope being considered for purchase. Functions for use in a petrology or mineralogy laboratory are stressed. (CW)

  6. 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.

  7. Assessment of Petrological Microscopes.

    ERIC Educational Resources Information Center

    Mathison, Charter Innes

    1990-01-01

    Presented is a set of procedures designed to check the design, ergonomics, illumination, function, optics, accessory equipment, and image quality of a microscope being considered for purchase. Functions for use in a petrology or mineralogy laboratory are stressed. (CW)

  8. 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.

  9. Stochastic Thermodynamics of Learning

    NASA Astrophysics Data System (ADS)

    Goldt, Sebastian; Seifert, Udo

    2017-01-01

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

  10. Thermodynamics of Organic Compounds

    DTIC Science & Technology

    1981-01-01

    Organic Compounds by I A. Hossenlopp and D. W. Scott -- Journal of Chemical Thermodynamics , 13, No. 5, 405-414 (1981). t 1 I- i !I *1 I I ~ I [LI...National Bureau of Standards CINDAS Chemical Thermodynamics Division Purdue University Research Park Attn: Dr Stan Abramowitz Attn: Dr H H Li Mr David... Chemical Thermodynamics Division AFAOL/RJT (Dr 7 D Stull) Attn: Mr Donald D Wagman Wright-Patterson AFB, OH 45433 Washington, DC 20234 U.S. Army

  11. 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.

  12. Hypoxia in Microscopic Tumors

    PubMed Central

    Li, Xiao-Feng; O’Donoghue, Joseph A

    2008-01-01

    Tumor hypoxia has been commonly observed in a broad spectrum of primary solid malignancies. Hypoxia is associated with tumor progression, increased aggressiveness, enhanced metastatic potential and poor prognosis. Hypoxic tumor cells are resistant to radiotherapy and some forms of chemotherapy. Using an animal model, we recently showed that microscopic tumors less than 1 mm diameter were severely hypoxic. In this review, models and techniques for the study of hypoxia in microscopic tumors are discussed. PMID:18384940

  13. 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.

  14. [Stereo microscope, neglected tool].

    PubMed

    Gacek, Grzegorz

    2017-01-01

    Stereoscopes, in author opinion, are neglected tools in modern biology. This article shortly describes technical and application capabilities of the present stereomicroscopes. The two main types of stereomicroscope construction are depicted: Greenough microscope and Common Main Objective microscope. The technological breakthrough, asymmetrical optical design of stereomicroscopes, the Fusion Optics, is presented too. Because of very wide offer of a stereomicroscope platforms, illumination systems, software and imaging systems, the article contains also very useful factors to consider when selecting a stereomicroscope.

  15. Microscopic Theory of Fission

    SciTech Connect

    Younes, W.; Gogny, D.

    2008-04-17

    In recent years, the microscopic method has been applied to the notoriously difficult problem of nuclear fission with unprecedented success. In this paper, we discuss some of the achievements and promise of the microscopic method, as embodied in the Hartree-Fock method using the Gogny finite-range effective interaction, and beyond-mean-field extensions to the theory. The nascent program to describe induced fission observables using this approach at the Lawrence Livermore National Laboratory is presented.

  16. High-temperature thermodynamics.

    NASA Technical Reports Server (NTRS)

    Margrave, J. L.

    1967-01-01

    High temperature thermodynamics requiring species and phases identification, crystal structures, molecular geometries and vibrational, rotational and electronic energy levels and equilibrium constants

  17. Microscopic colitis: a review.

    PubMed

    Farrukh, A; Mayberry, J F

    2014-12-01

    In recent years, microscopic colitis has been increasingly diagnosed. This review was carried out to evaluate demographic factors for microscopic colitis and to perform a systematic assessment of available treatment options. Relevant publications up to December 2013 were identified following searches of PubMed and Google Scholar using the key words 'microscopic colitis', 'collagenous colitis' and 'lymphocytic colitis'. Two-hundred and forty-eight articles were identified. The term microscopic colitis includes lymphocytic colitis and collagenous colitis. Both have common clinical symptoms but are well defined histopathologically. The clinical course is usually benign, but serious complications, including death, may occur. A peak incidence from 60 to 70 years of age with a female preponderance is observed. Although most cases are idiopathic, associations with autoimmune disorders, such as coeliac disease and hypothyroidism, as well as with exposure to nonsteroidal anti-inflammatory drugs and proton-pump inhibitors, have been observed. The incidence and prevalence of microscopic colitis is rising and good-quality epidemiological research is needed. Treatment is currently largely based on anecdotal evidence and on results from limited clinical trials of budesonide. Long-term follow-up of these patients is not well established. The review synthesizes work on the definition of microscopic colitis and the relationship between collagenous and lymphocytic colitis. It reviews the international epidemiology and work on aetiology. In addition, it critically considers the efficacy of a range of treatments. Colorectal Disease © 2014 The Association of Coloproctology of Great Britain and Ireland.

  18. Spectroscopic studies of individual plasmon resonant nanoparticles

    NASA Astrophysics Data System (ADS)

    Mock, Jack J.; Smith, David R.; Barbic, Mladen; Oldenburg, Steven J.; Schultz, David A.; Schultz, Sheldon

    2003-11-01

    We present a detailed description of the apparatus and techniques that we have utilized in our experimental study of individual plas on resonant nanoparticles,along with a brief description of some major results. The apparatus consists of a spectroscopic system combined with a modified darkfield microscope, which enables the user to sequentially select individual resonant nanostructures in the microscopic field of view for spectroscopic study. Plasmon resonant nanostructures scatter light elastically,and typically have very large scattering cross-sections at their resonant optical wavelengths. In general, spectra can be obtained with acquisition times between .1 to 30 seconds,and color images can be captured using consumer digital color cameras. Spheres,tetrahedrons,and pentagonal platelets were fabricated using colloidal chemistry techniques. To produce highly anisotropic structures such as nanorods and "barbells", templates were used. Many of these nanostructures have been individually spectroscopically characterized,and their spectra correlated with their shape and size as determined by transmission electron icroscope (TEM). The unique shape,size, composition,and dielectric surroundings of the individual plasmon resonant nanostructures determine their plasmon resonant behavior. We will show how the composition of the substrate on which the particles are immobilized and the dielectric of the surrounding medium have a significant effect on the plasmon resonance of the individual particles.

  19. Microscopic theory of rubber elasticity.

    PubMed

    Oyerokun, Folusho T; Schweizer, Kenneth S

    2004-05-15

    A microscopic integral equation theory of elasticity in polymer liquids and networks is developed which addresses the nonclassical problem of the consequences of interchain repulsive interactions and packing correlations on mechanical response. The theory predicts strain induced softening, and a nonclassical intermolecular contribution to the linear modulus. The latter is of the same magnitude as the classical single chain entropy contribution at low polymer concentrations, but becomes much more important in the melt state, and dominant as the isotropic-nematic liquid crystal phase transition is approached. Comparison of the calculated stress-strain curve and induced nematic order parameter with computer simulations show good agreement. A nearly quadratic dependence of the linear elastic modulus on segmental concentration is found, as well as a novel fractional power law dependence on degree of polymerization. Quantitative comparison of the theory with experiments on polydimethylsiloxane networks are presented and good agreement is found. However, a nonzero modulus in the long chain limit is not predicted since quenched chemical crosslinks and trapped entanglements are not explicitly taken into account. The theory is generalizable to treat the structure, thermodynamics and mechanical response of nematic elastomers.

  20. Thermodynamics and bioenergetics.

    PubMed

    Demirel, Y; Sandler, S I

    2002-06-19

    Bioenergetics is concerned with the energy conservation and conversion processes in a living cell, particularly in the inner membrane of the mitochondrion. This review summarizes the role of thermodynamics in understanding the coupling between the chemical reactions and the transport of substances in bioenergetics. Thermodynamics has the advantages of identifying possible pathways, providing a measure of the efficiency of energy conversion, and of the coupling between various processes without requiring a detailed knowledge of the underlying mechanisms. In the last five decades, various new approaches in thermodynamics, non-equilibrium thermodynamics and network thermodynamics have been developed to understand the transport and rate processes in physical and biological systems. For systems not far from equilibrium the theory of linear non-equilibrium thermodynamics is used, while extended non-equilibrium thermodynamics is used for systems far away from equilibrium. All these approaches are based on the irreversible character of flows and forces of an open system. Here, linear non-equilibrium thermodynamics is mostly discussed as it is the most advanced. We also review attempts to incorporate the mechanisms of a process into some formulations of non-equilibrium thermodynamics. The formulation of linear non-equilibrium thermodynamics for facilitated transport and active transport, which represent the key processes of coupled phenomena of transport and chemical reactions, is also presented. The purpose of this review is to present an overview of the application of non-equilibrium thermodynamics to bioenergetics, and introduce the basic methods and equations that are used. However, the reader will have to consult the literature reference to see the details of the specific applications.

  1. Student Misconceptions in Thermodynamics.

    ERIC Educational Resources Information Center

    Granville, Mark F.

    1985-01-01

    Discusses misconceptions (in several thermodynamics statements) that seem to be particularly common among students who have finished a one-semester, junior-level course in chemical thermodynamics. When presented as true/false questions, these statements are usually judged true, although each requires at least one more condition to be satisfied.…

  2. Thermodynamics and Gravity,

    DTIC Science & Technology

    symmetry of the spacetime coordinates of the region in which the gravity field is located. The form of the laws of thermodynamics for matter located in a...gravity field is investigated by applying the broken spacetime symmetry forms of the first and second laws of thermodynamics. In a gravity field the

  3. The virtual microscope.

    PubMed

    Catalyürek, Umit; Beynon, Michael D; Chang, Chialin; Kurc, Tahsin; Sussman, Alan; Saltz, Joel

    2003-12-01

    We present the design and implementation of the Virtual Microscope, a software system employing a client/server architecture to provide a realistic emulation of a high power light microscope. The system provides a form of completely digital telepathology, allowing simultaneous access to archived digital slide images by multiple clients. The main problem the system targets is storing and processing the extremely large quantities of data required to represent a collection of slides. The Virtual Microscope client software runs on the end user's PC or workstation, while database software for storing, retrieving and processing the microscope image data runs on a parallel computer or on a set of workstations at one or more potentially remote sites. We have designed and implemented two versions of the data server software. One implementation is a customization of a database system framework that is optimized for a tightly coupled parallel machine with attached local disks. The second implementation is component-based, and has been designed to accommodate access to and processing of data in a distributed, heterogeneous environment. We also have developed caching client software, implemented in Java, to achieve good response time and portability across different computer platforms. The performance results presented show that the Virtual Microscope systems scales well, so that many clients can be adequately serviced by an appropriately configured data server.

  4. 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.

  5. 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…

  6. 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…

  7. Thermodynamic estimation: Ionic materials

    SciTech Connect

    Glasser, Leslie

    2013-10-15

    Thermodynamics establishes equilibrium relations among thermodynamic parameters (“properties”) and delineates the effects of variation of the thermodynamic functions (typically temperature and pressure) on those parameters. However, classical thermodynamics does not provide values for the necessary thermodynamic properties, which must be established by extra-thermodynamic means such as experiment, theoretical calculation, or empirical estimation. While many values may be found in the numerous collected tables in the literature, these are necessarily incomplete because either the experimental measurements have not been made or the materials may be hypothetical. The current paper presents a number of simple and relible estimation methods for thermodynamic properties, principally for ionic materials. The results may also be used as a check for obvious errors in published values. The estimation methods described are typically based on addition of properties of individual ions, or sums of properties of neutral ion groups (such as “double” salts, in the Simple Salt Approximation), or based upon correlations such as with formula unit volumes (Volume-Based Thermodynamics). - Graphical abstract: Thermodynamic properties of ionic materials may be readily estimated by summation of the properties of individual ions, by summation of the properties of ‘double salts’, and by correlation with formula volume. Such estimates may fill gaps in the literature, and may also be used as checks of published values. This simplicity arises from exploitation of the fact that repulsive energy terms are of short range and very similar across materials, while coulombic interactions provide a very large component of the attractive energy in ionic systems. Display Omitted - Highlights: • Estimation methods for thermodynamic properties of ionic materials are introduced. • Methods are based on summation of single ions, multiple salts, and correlations. • Heat capacity, entropy

  8. Integrated elastic microscope device

    NASA Astrophysics Data System (ADS)

    Lee, W. M.; Wright, D.; Watkins, R.; Cen, Zi

    2015-03-01

    The growing power of imaging and computing power of smartphones is creating the possibility of converting your smartphone into a high power pocket microscopy system. High quality miniature microscopy lenses attached to smartphone are typically made with glass or plastics that can only be produce at low cost with high volume. To revise the paradigm of microscope lenses, we devised a simple droplet lens fabrication technique that which produces low cost and high performance lens. Each lens is integrated into thin 3-D printed holder with complimentary light emitted diode (LEDs) that clips onto majority of smartphones. The integrated device converts a smartphone into a high power optical microscope/dermatoscope at around $2. This low cost device has wide application in a multitude of practical uses such as material inspection, dermascope and educational microscope.

  9. Electron microscope studies

    SciTech Connect

    Crewe, A.V.; Kapp, O.H.

    1992-07-01

    This is a report covering the research performed in the Crewe laboratory between 1964 and 1992. Because of limitations of space we have provided relatively brief summaries of the major research directions of the facility during these years. A complete bibliography has been included and we have referenced groups of pertinent publications at the beginning of each section. This report summarizes our efforts to develop better electron microscopes and chronicles many of the experimental programs, in materials science and biology, that acted both as a stimulus to better microscope design and also as a testing ground for many instrumental innovations.

  10. 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.

  11. 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.

  12. Making Art with Microscopes

    ERIC Educational Resources Information Center

    Benedis-Grab, Gregory

    2011-01-01

    Interdisciplinary teaching is a great way to focus on overarching concepts and help students make connections across disciplines. Historically, art and science have been connected disciplines. The botanical prints of the 18th and 19th centuries and early work with microscopes are two examples of a need for strong artistic skills in the science…

  13. Microscope on Mars

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This image taken at Meridiani Planum, Mars by the panoramic camera on the Mars Exploration Rover Opportunity shows the rover's microscopic imager (circular device in center), located on its instrument deployment device, or 'arm.' The image was acquired on the ninth martian day or sol of the rover's mission.

  14. Microscope on Mars

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This image taken at Meridiani Planum, Mars by the panoramic camera on the Mars Exploration Rover Opportunity shows the rover's microscopic imager (circular device in center), located on its instrument deployment device, or 'arm.' The image was acquired on the ninth martian day or sol of the rover's mission.

  15. Making Art with Microscopes

    ERIC Educational Resources Information Center

    Benedis-Grab, Gregory

    2011-01-01

    Interdisciplinary teaching is a great way to focus on overarching concepts and help students make connections across disciplines. Historically, art and science have been connected disciplines. The botanical prints of the 18th and 19th centuries and early work with microscopes are two examples of a need for strong artistic skills in the science…

  16. Wormholes and thermodynamics

    NASA Astrophysics Data System (ADS)

    González-Díaz, Pedro F.

    1996-07-01

    Hawking has recently pointed out that black holes cannot evaporate and disappear through wormholes because the entropy of a baby universe would not equal its size squared times some proportionality constant. In this report it is shown that multiply connected Euclidean wormhole spacetimes can be associated with nonlinear dynamic laws which are analogous to those of nonequilibrium thermodynamics, making plausible a full generalization of thermodynamics encompassing both nonequilibrium and gravitational effects. It is seen that both at equilibrium and out of it baby universe thermodynamics can provide the right relation between the size of the originating black hole and its entropy.

  17. Molecular structural investigation of adenosine using spectroscopic and quantum computational calculations

    NASA Astrophysics Data System (ADS)

    Bakkiyaraj, D.; Periandy, S.; Xavier, S.

    2016-09-01

    In this study; spectroscopic investigation of adenosine having clinical importance was studied computationally and obtained results were compared with experimental ones. In this scope, geometric optimization and conformational analysis were studied and vibrational spectroscopic properties were studied on the most stable form. NMR and TD-DFT studies on the title compound were conducted with its experimental data. In addition atomic charge distribution, NBO, frontier molecular analysis, thermodynamic analysis and hyperpolarization features were studied.

  18. 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.

  19. Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip?

    PubMed

    Geschwindner, Stefan; Ulander, Johan; Johansson, Patrik

    2015-08-27

    The use of ligand binding thermodynamics has been proposed as a potential success factor to accelerate drug discovery. However, despite the intuitive appeal of optimizing binding enthalpy, a number of factors complicate routine use of thermodynamic data. On a macroscopic level, a range of experimental parameters including temperature and buffer choice significantly influence the observed thermodynamic signatures. On a microscopic level, solute effects, structural flexibility, and cooperativity lead to nonlinear changes in enthalpy. This multifactorial character hides essential enthalpy contributions of intermolecular contacts, making them experimentally nonobservable. In this perspective, we present three case studies, reflect on some key factors affecting thermodynamic signatures, and investigate their relation to the hydrophobic effect, enthalpy-entropy compensation, lipophilic ligand efficiency, and promiscuity. The studies highlight that enthalpy and entropy cannot be used as direct end points but can together with calculations increase our understanding of ligand binding and identify interesting outliers that do not behave as expected.

  20. Turbopump thermodynamic cooling

    NASA Technical Reports Server (NTRS)

    Patten, T. C.; Mckee, H. B.

    1972-01-01

    System for cooling turbopumps used in cryogenic fluid storage facilities is described. Technique uses thermodynamic propellant vent to intercept pump heat at desired conditions. Cooling system uses hydrogen from outside source or residual hydrogen from cryogenic storage tank.

  1. Electrochemical thermodynamic measurement system

    DOEpatents

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

    2009-09-29

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

  2. Thermodynamics and Frozen Foods.

    ERIC Educational Resources Information Center

    Kerr, William L.; Reid, David S.

    1993-01-01

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

  3. Thermodynamics and Frozen Foods.

    ERIC Educational Resources Information Center

    Kerr, William L.; Reid, David S.

    1993-01-01

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

  4. 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.

  5. Thermodynamics in Fractional Calculus

    NASA Astrophysics Data System (ADS)

    Meilanov, R. P.; Magomedov, R. A.

    2014-11-01

    A generalization of thermodynamics in the formalism of fractional-order derivatives is given. Results of the traditional thermodynamics of Carnot, Clausius, and Helmholtz are obtained in the particular case where the exponent of a fractional-order derivative is equal to unity. A one-parametric "fractal" equation of state is obtained with account of the second virial coefficient. The application of the resulting equation of state in the case of the gas argon is considered.

  6. Thermodynamics of fractal universe

    NASA Astrophysics Data System (ADS)

    Sheykhi, Ahmad; Teimoori, Zeinab; Wang, Bin

    2013-01-01

    We investigate the thermodynamical properties of the apparent horizon in a fractal universe. We find that one can always rewrite the Friedmann equation of the fractal universe in the form of the entropy balance relation δQ=ThdSh, where δQ and Th are the energy flux and Unruh temperature seen by an accelerated observer just inside the apparent horizon. We find that the entropy Sh consists two terms, the first one which obeys the usual area law and the second part which is the entropy production term due to nonequilibrium thermodynamics of fractal universe. This shows that in a fractal universe, a treatment with nonequilibrium thermodynamics of spacetime may be needed. We also study the generalized second law of thermodynamics in the framework of fractal universe. When the temperature of the apparent horizon and the matter fields inside the horizon are equal, i.e. T=Th, the generalized second law of thermodynamics can be fulfilled provided the deceleration and the equation of state parameters ranges either as -1⩽q<0, -1⩽w<-1/3 or as q<-1, w<-1 which are consistent with recent observations. We also find that for Th=bT, with b<1, the GSL of thermodynamics can be secured in a fractal universe by suitably choosing the fractal parameter β.

  7. Acoustic imaging microscope

    DOEpatents

    Deason, Vance A.; Telschow, Kenneth L.

    2006-10-17

    An imaging system includes: an object wavefront source and an optical microscope objective all positioned to direct an object wavefront onto an area of a vibrating subject surface encompassed by a field of view of the microscope objective, and to direct a modulated object wavefront reflected from the encompassed surface area through a photorefractive material; and a reference wavefront source and at least one phase modulator all positioned to direct a reference wavefront through the phase modulator and to direct a modulated reference wavefront from the phase modulator through the photorefractive material to interfere with the modulated object wavefront. The photorefractive material has a composition and a position such that interference of the modulated object wavefront and modulated reference wavefront occurs within the photorefractive material, providing a full-field, real-time image signal of the encompassed surface area.

  8. Femtosecond scanning tunneling microscope

    SciTech Connect

    Taylor, A.J.; Donati, G.P.; Rodriguez, G.; Gosnell, T.R.; Trugman, S.A.; Some, D.I.

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). By combining scanning tunneling microscopy with ultrafast optical techniques we have developed a novel tool to probe phenomena on atomic time and length scales. We have built and characterized an ultrafast scanning tunneling microscope in terms of temporal resolution, sensitivity and dynamic range. Using a novel photoconductive low-temperature-grown GaAs tip, we have achieved a temporal resolution of 1.5 picoseconds and a spatial resolution of 10 nanometers. This scanning tunneling microscope has both cryogenic and ultra-high vacuum capabilities, enabling the study of a wide range of important scientific problems.

  9. Ion photon emission microscope

    DOEpatents

    Doyle, Barney L.

    2003-04-22

    An ion beam analysis system that creates microscopic multidimensional image maps of the effects of high energy ions from an unfocussed source upon a sample by correlating the exact entry point of an ion into a sample by projection imaging of the ion-induced photons emitted at that point with a signal from a detector that measures the interaction of that ion within the sample. The emitted photons are collected in the lens system of a conventional optical microscope, and projected on the image plane of a high resolution single photon position sensitive detector. Position signals from this photon detector are then correlated in time with electrical effects, including the malfunction of digital circuits, detected within the sample that were caused by the individual ion that created these photons initially.

  10. Electron microscope aperture system

    NASA Technical Reports Server (NTRS)

    Heinemann, K. (Inventor)

    1976-01-01

    An electron microscope including an electron source, a condenser lens having either a circular aperture for focusing a solid cone of electrons onto a specimen or an annular aperture for focusing a hollow cone of electrons onto the specimen, and an objective lens having an annular objective aperture, for focusing electrons passing through the specimen onto an image plane are described. The invention also entails a method of making the annular objective aperture using electron imaging, electrolytic deposition and ion etching techniques.

  11. Microscopic enteritis: Bucharest consensus.

    PubMed

    Rostami, Kamran; Aldulaimi, David; Holmes, Geoffrey; Johnson, Matt W; Robert, Marie; Srivastava, Amitabh; Fléjou, Jean-François; Sanders, David S; Volta, Umberto; Derakhshan, Mohammad H; Going, James J; Becheanu, Gabriel; Catassi, Carlo; Danciu, Mihai; Materacki, Luke; Ghafarzadegan, Kamran; Ishaq, Sauid; Rostami-Nejad, Mohammad; Peña, A Salvador; Bassotti, Gabrio; Marsh, Michael N; Villanacci, Vincenzo

    2015-03-07

    Microscopic enteritis (ME) is an inflammatory condition of the small bowel that leads to gastrointestinal symptoms, nutrient and micronutrient deficiency. It is characterised by microscopic or sub-microscopic abnormalities such as microvillus changes and enterocytic alterations in the absence of definite macroscopic changes using standard modern endoscopy. This work recognises a need to characterize disorders with microscopic and submicroscopic features, currently regarded as functional or non-specific entities, to obtain further understanding of their clinical relevance. The consensus working party reviewed statements about the aetiology, diagnosis and symptoms associated with ME and proposes an algorithm for its investigation and treatment. Following the 5(th) International Course in Digestive Pathology in Bucharest in November 2012, an international group of 21 interested pathologists and gastroenterologists formed a working party with a view to formulating a consensus statement on ME. A five-step agreement scale (from strong agreement to strong disagreement) was used to score 21 statements, independently. There was strong agreement on all statements about ME histology (95%-100%). Statements concerning diagnosis achieved 85% to 100% agreement. A statement on the management of ME elicited agreement from the lowest rate (60%) up to 100%. The remaining two categories showed general agreement between experts on clinical presentation (75%-95%) and pathogenesis (80%-90%) of ME. There was strong agreement on the histological definition of ME. Weaker agreement on management indicates a need for further investigations, better definitions and clinical trials to produce quality guidelines for management. This ME consensus is a step toward greater recognition of a significant entity affecting symptomatic patients previously labelled as non-specific or functional enteropathy.

  12. Microscopic enteritis: Bucharest consensus

    PubMed Central

    Rostami, Kamran; Aldulaimi, David; Holmes, Geoffrey; Johnson, Matt W; Robert, Marie; Srivastava, Amitabh; Fléjou, Jean-François; Sanders, David S; Volta, Umberto; Derakhshan, Mohammad H; Going, James J; Becheanu, Gabriel; Catassi, Carlo; Danciu, Mihai; Materacki, Luke; Ghafarzadegan, Kamran; Ishaq, Sauid; Rostami-Nejad, Mohammad; Peña, A Salvador; Bassotti, Gabrio; Marsh, Michael N; Villanacci, Vincenzo

    2015-01-01

    Microscopic enteritis (ME) is an inflammatory condition of the small bowel that leads to gastrointestinal symptoms, nutrient and micronutrient deficiency. It is characterised by microscopic or sub-microscopic abnormalities such as microvillus changes and enterocytic alterations in the absence of definite macroscopic changes using standard modern endoscopy. This work recognises a need to characterize disorders with microscopic and submicroscopic features, currently regarded as functional or non-specific entities, to obtain further understanding of their clinical relevance. The consensus working party reviewed statements about the aetiology, diagnosis and symptoms associated with ME and proposes an algorithm for its investigation and treatment. Following the 5th International Course in Digestive Pathology in Bucharest in November 2012, an international group of 21 interested pathologists and gastroenterologists formed a working party with a view to formulating a consensus statement on ME. A five-step agreement scale (from strong agreement to strong disagreement) was used to score 21 statements, independently. There was strong agreement on all statements about ME histology (95%-100%). Statements concerning diagnosis achieved 85% to 100% agreement. A statement on the management of ME elicited agreement from the lowest rate (60%) up to 100%. The remaining two categories showed general agreement between experts on clinical presentation (75%-95%) and pathogenesis (80%-90%) of ME. There was strong agreement on the histological definition of ME. Weaker agreement on management indicates a need for further investigations, better definitions and clinical trials to produce quality guidelines for management. This ME consensus is a step toward greater recognition of a significant entity affecting symptomatic patients previously labelled as non-specific or functional enteropathy. PMID:25759526

  13. Color Laser Microscope

    NASA Astrophysics Data System (ADS)

    Awamura, D.; Ode, T.; Yonezawa, M.

    1987-04-01

    A color laser microscope utilizing a new color laser imaging system has been developed for the visual inspection of semiconductors. The light source, produced by three lasers (Red; He-Ne, Green; Ar, Blue; He-Cd), is deflected horizontally by an AOD (Acoustic Optical Deflector) and vertically by a vibration mirror. The laser beam is focused in a small spot which is scanned over the sample at high speed. The light reflected back from the sample is reformed to contain linear information by returning to the original vibration mirror. The linear light is guided to the CCD image sensor where it is converted into a video signal. Individual CCD image sensors are used for each of the three R, G, or B color image signals. The confocal optical system with its laser light source yields a color TV monitor image with no flaring and a much sharper resolution than that of the conventional optical microscope. The AOD makes possible a high speed laser scan and a NTSC or PAL TV video signal is produced in real time without any video memory. Since the light source is composed of R, G, and B laser beams, color separation superior to that of white light illumination is achieved. Because of the photometric linearity of the image detector, the R, G, and B outputs of the system are most suitably used for hue analysis. The CCD linear image sensors in the optical system produce no geometrical distortion, and good color registration is available principally. The output signal can be used for high accuracy line width measuring. The many features of the color laser microscope make it ideally suited for the visual inspection of semiconductor processing. A number of these systems have already been installed in such a capacity. The Color Laser Microscope can also be a very useful tool for the fields of material engineering and biotechnology.

  14. Microscopic Image Inside 'Endurance'

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This magnified view of a rock surface inside 'Endurance Crater' combines four frames taken by the microscopic imager on NASA's Mars Exploration Rover Opportunity during the rover's 142nd martian day, or sol, on June 17, 2004. This patch of rock is in a region of contact between a layer of rock corresponding to bedrock that Opportunity examined earlier at 'Eagle Crater' and the next-lower layer. The area imaged is about 6 centimeters (2.4 inches) on each side.

  15. [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.

  16. Thermal Lens Microscope

    NASA Astrophysics Data System (ADS)

    Uchiyama, Kenji; Hibara, Akihide; Kimura, Hiroko; Sawada, Tsuguo; Kitamori, Takehiko

    2000-09-01

    We developed a novel laser microscope based on the thermal lens effect induced by a coaxial beam comprised of excitation and probe beams. The signal generation mechanism was confirmed to be an authentic thermal lens effect from the measurement of signal and phase dependences on optical configurations between the sample and the probe beam focus, and therefore, the thermal lens effect theory could be applied. Two-point spatial resolution was determined by the spot size of the excitation beam, not by the thermal diffusion length. Sensitivity was quite high, and the detection ability, evaluated using a submicron microparticle containing dye molecules, was 0.8 zmol/μm2, hence a distribution image of trace chemical species could be obtained quantitatively. In addition, analytes are not restricted to fluorescent species, therefore, the thermal lens microscope is a promising analytical microscope. A two-dimensional image of a histamine molecule distribution, which was produced in mast cells at the femtomole level in a human nasal mucous polyp, was obtained.

  17. 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.

  18. Virtual pinhole confocal microscope

    SciTech Connect

    George, J.S.; Rector, D.M.; Ranken, D.M.; Peterson, B.; Kesteron, J.

    1999-06-01

    Scanned confocal microscopes enhance imaging capabilities, providing improved contrast and image resolution in 3-D, but existing systems have significant technical shortcomings and are expensive. Researchers at Los Alamos National Laboratory have developed a novel approach--virtual pinhole confocal microscopy--that uses state of the art illumination, detection, and data processing technologies to produce an imager with a number of advantages: reduced cost, faster imaging, improved efficiency and sensitivity, improved reliability and much greater flexibility. Work at Los Alamos demonstrated proof of principle; prototype hardware and software have been used to demonstrate technical feasibility of several implementation strategies. The system uses high performance illumination, patterned in time and space. The authors have built functional confocal imagers using video display technologies (LCD or DLP) and novel scanner based on a micro-lens array. They have developed a prototype system for high performance data acquisition and processing, designed to support realtime confocal imaging. They have developed algorithms to reconstruct confocal images from a time series of spatially sub-sampled images; software development remains an area of active development. These advances allow the collection of high quality confocal images (in fluorescence, reflectance and transmission modes) with equipment that can inexpensively retrofit to existing microscopes. Planned future extensions to these technologies will significantly enhance capabilities for microscopic imaging in a variety of applications, including confocal endoscopy, and confocal spectral imaging.

  19. 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

  20. 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.

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

    PubMed

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

    2015-10-09

    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.

  2. 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.

  3. 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.

  4. 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.

  5. Microscopic molecular superfluid response: theory and simulations

    NASA Astrophysics Data System (ADS)

    Zeng, Tao; Roy, Pierre-Nicholas

    2014-04-01

    Since its discovery in 1938, superfluidity has been the subject of much investigation because it provides a unique example of a macroscopic manifestation of quantum mechanics. About 60 years later, scientists successfully observed this phenomenon in the microscopic world though the spectroscopic Andronikashvili experiment in helium nano-droplets. This reduction of scale suggests that not only helium but also para-H2 (pH2) can be a candidate for superfluidity. This expectation is based on the fact that the smaller number of neighbours and surface effects of a finite-size cluster may hinder solidification and promote a liquid-like phase. The first prediction of superfluidity in pH2 clusters was reported in 1991 based on quantum Monte Carlo simulations. The possible superfluidity of pH2 was later indirectly observed in a spectroscopic Andronikashvili experiment in 2000. Since then, a growing number of studies have appeared, and theoretical simulations have been playing a special role because they help guide and interpret experiments. In this review, we go over the theoretical studies of pH2 superfluid clusters since the experiment of 2000. We provide a historical perspective and introduce the basic theoretical formalism along with key experimental advances. We then present illustrative results of the theoretical studies and comment on the possible future developments in the field. We include sufficient theoretical details such that the review can serve as a guide for newcomers to the field.

  6. Microscopic theory of the lambda transition

    SciTech Connect

    Toyoda, T.

    1982-06-01

    Starting with a microscopic hamiltonian for a many-boson system with a hardcore interaction, the grand potential of the system, which contains the order-parameter of the lambda transition as one of the thermodynamical variables, is derived by making use of the finite temperature loop expansion. The divergence difficulty caused by the hardcore interaction is circumvented by the conventional field theoretic perturbation renormalization such that the chemical potential is renormalized instead of the conventional mass renormalization. The grand potential obtained consists of the superfluid part and the finite temperature elementary excitation part. The elementary excitation energy spectrum shows the Goldstone boson mode, namely, the photon, for the zero external field. A non-vanishing external field destroys such a Goldstone boson mode by causing an energy gap at zero momentum. The chemical potential and the critical temperature are also obtained for the weak coupling case. It is shown how the Bose-Einstein condensation is affected by the hardcore interaction.

  7. 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.

  8. 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.

  9. Light Microscopy Microscope Experiment

    NASA Image and Video Library

    2016-02-04

    Ground testing for the first confocal Light Microscopy Microscope (LMM) Experiment. Procter and Gamble is working with NASA Glenn scientists to prepare for a study that examines product stabilizers in a microgravity environment. The particles in the tube glow orange because they have been fluorescently tagged with a dye that reacts to green laser lights to allow construction of a 3D image point by point. The experiment, which will be sent to the ISS later this year, will help P&G develop improved product stabilizers to extend shelf life and develop more environmentally friendly packaging.

  10. Low frequency acoustic microscope

    DOEpatents

    Khuri-Yakub, Butrus T.

    1986-11-04

    A scanning acoustic microscope is disclosed for the detection and location of near surface flaws, inclusions or voids in a solid sample material. A focused beam of acoustic energy is directed at the sample with its focal plane at the subsurface flaw, inclusion or void location. The sample is scanned with the beam. Detected acoustic energy specularly reflected and mode converted at the surface of the sample and acoustic energy reflected by subsurface flaws, inclusions or voids at the focal plane are used for generating an interference signal which is processed and forms a signal indicative of the subsurface flaws, inclusions or voids.

  11. Nanosecond electron microscopes

    PubMed

    Bostanjoglo; Elschner; Mao; Nink; Weingartner

    2000-04-01

    Combining electron optics, fast electronics and pulsed lasers, a transmission and a photoelectron emission microscope were built, which visualize events in thin films and on surfaces with a time resolution of several nanoseconds. The high-speed electron microscopy is capable to track fast laser-induced processes in metals below the ablation threshold, which are difficult to detect by other imaging techniques. The material response to nano- and femtosecond laser pulses was found to be very different. It was dominated by thermo/chemocapillary flow and chemical reactions in the case of nanosecond pulses, and by mechanical deformations and non-thermal electron emission after a femtosecond pulse.

  12. Atomic Force Microscope

    SciTech Connect

    Day, R.D.; Russell, P.E.

    1988-12-01

    The Atomic Force Microscope (AFM) is a recently developed instrument that has achieved atomic resolution imaging of both conducting and non- conducting surfaces. Because the AFM is in the early stages of development, and because of the difficulty of building the instrument, it is currently in use in fewer than ten laboratories worldwide. It promises to be a valuable tool for obtaining information about engineering surfaces and aiding the .study of precision fabrication processes. This paper gives an overview of AFM technology and presents plans to build an instrument designed to look at engineering surfaces.

  13. Adirondack Under the Microscope

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This image was taken by the Mars Exploration Rover Spirit front hazard-identification camera after the rover's first post-egress drive on Mars Sunday, Jan. 15, 2004. Engineers drove the rover approximately 3 meters (10 feet) from the Columbia Memorial Station toward the first rock target, seen in the foreground. The football-sized rock was dubbed Adirondack because of its mountain-shaped appearance. Scientists have begun using the microscopic imager instrument at the end of the rover's robotic arm to examine the rock and understand how it formed.

  14. Adirondack Under the Microscope

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This image was taken by the Mars Exploration Rover Spirit front hazard-identification camera after the rover's first post-egress drive on Mars Sunday, Jan. 15, 2004. Engineers drove the rover approximately 3 meters (10 feet) from the Columbia Memorial Station toward the first rock target, seen in the foreground. The football-sized rock was dubbed Adirondack because of its mountain-shaped appearance. Scientists have begun using the microscopic imager instrument at the end of the rover's robotic arm to examine the rock and understand how it formed.

  15. Solid state optical microscope

    DOEpatents

    Young, I.T.

    1983-08-09

    A solid state optical microscope wherein wide-field and high-resolution images of an object are produced at a rapid rate by utilizing conventional optics with a charge-coupled photodiode array. A galvanometer scanning mirror, for scanning in one of two orthogonal directions is provided, while the charge-coupled photodiode array scans in the other orthogonal direction. Illumination light from the object is incident upon the photodiodes, creating packets of electrons (signals) which are representative of the illuminated object. The signals are then processed, stored in a memory, and finally displayed as a video signal. 2 figs.

  16. Solid state optical microscope

    DOEpatents

    Young, Ian T.

    1983-01-01

    A solid state optical microscope wherein wide-field and high-resolution images of an object are produced at a rapid rate by utilizing conventional optics with a charge-coupled photodiode array. A galvanometer scanning mirror, for scanning in one of two orthogonal directions is provided, while the charge-coupled photodiode array scans in the other orthogonal direction. Illumination light from the object is incident upon the photodiodes, creating packets of electrons (signals) which are representative of the illuminated object. The signals are then processed, stored in a memory, and finally displayed as a video signal.

  17. Thermodynamics of Nonadditive Systems.

    PubMed

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

    2015-06-12

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

  18. Thermodynamics "beyond" local equilibrium

    NASA Astrophysics Data System (ADS)

    Vilar, Jose; Rubi, Miguel

    2002-03-01

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

  19. Thermodynamics of catalytic nanoparticle morphology

    NASA Astrophysics Data System (ADS)

    Zwolak, Michael; Sharma, Renu; Lin, Pin Ann

    Metallic nanoparticles are an important class of industrial catalysts. The variability of their properties and the environment in which they act, from their chemical nature & surface modification to their dispersion and support, allows their performance to be optimized for many chemical processes useful in, e.g., energy applications and other areas. Their large surface area to volume ratio, as well as varying sizes and faceting, in particular, makes them an efficient source for catalytically active sites. These characteristics of nanoparticles - i.e., their morphology - can often display intriguing behavior as a catalytic process progresses. We develop a thermodynamic model of nanoparticle morphology, one that captures the competition of surface energy with other interactions, to predict structural changes during catalytic processes. Comparing the model to environmental transmission electron microscope images of nickel nanoparticles during carbon nanotube (and other product) growth demonstrates that nickel deformation in response to the nanotube growth is due to a favorable interaction with carbon. Moreover, this deformation is halted due to insufficient volume of the particles. We will discuss the factors that influence morphology and also how the model can be used to extract interaction strengths from experimental observations.

  20. Thermodynamics of graphene

    NASA Astrophysics Data System (ADS)

    Rusanov, A. I.

    2014-12-01

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

  1. Microscopic Tribotactic Walkers

    NASA Astrophysics Data System (ADS)

    Steimel, Joshua; Aragones, Juan; Alexander-Katz, Alfredo

    2014-03-01

    The translational motion of a rotating object near a surface is strongly dependent on the friction between the object and the surface. The process of friction is inherently directional and the friction coefficient can be anisotropic even in the absence of a net friction coefficient gradient. This is macroscopically observed in the ordering motif of some animal hair or scales and a microscopic analog can be imagined where the friction coefficient is determined by the strength and density of reversible bonds between a rotating object and the substrate. For high friction coefficients most of the rotational motion is converted into translational motion; conversely for low friction coefficients the object primarily rotates in place. We exploited this property to design and test a new class of motile system that displays tribotaxis, which is the process by which an object detects differences in the local friction coefficient and moves accordingly either to regions of higher or lower friction. These synthetic tribotactic microscopic walkers, composed of a pair of functionalized superparamagnetic beads, detect gradients in the spatial friction coefficient and migrate towards high friction areas when actuated in a random fashion. The effective friction between the walkers and the substrate is controlled by the local density of active receptors in the substrate. The tribotactic walkers also displayed trapping in high friction areas where the density of free receptors is higher.

  2. Forensic Scanning Electron Microscope

    NASA Astrophysics Data System (ADS)

    Keeley, R. H.

    1983-03-01

    The scanning electron microscope equipped with an x-ray spectrometer is a versatile instrument which has many uses in the investigation of crime and preparation of scientific evidence for the courts. Major applications include microscopy and analysis of very small fragments of paint, glass and other materials which may link an individual with a scene of crime, identification of firearms residues and examination of questioned documents. Although simultaneous observation and chemical analysis of the sample is the most important feature of the instrument, other modes of operation such as cathodoluminescence spectrometry, backscattered electron imaging and direct x-ray excitation are also exploited. Marks on two bullets or cartridge cases can be compared directly by sequential scanning with a single beam or electronic linkage of two instruments. Particles of primer residue deposited on the skin and clothing when a gun is fired can be collected on adhesive tape and identified by their morphology and elemental composition. It is also possible to differentiate between the primer residues of different types of ammunition. Bullets may be identified from the small fragments left behind as they pass through the body tissues. In the examination of questioned documents the scanning electron microscope is used to establish the order in which two intersecting ink lines were written and to detect traces of chemical markers added to the security inks on official documents.

  3. Electron microscope phase enhancement

    DOEpatents

    Jin, Jian; Glaeser, Robert M.

    2010-06-15

    A microfabricated electron phase shift element is used for modifying the phase characteristics of an electron beam passing though its center aperture, while not affecting the more divergent portion of an incident beam to selectively provide a ninety-degree phase shift to the unscattered beam in the back focal plan of the objective lens, in order to realize Zernike-type, in-focus phase contrast in an electron microscope. One application of the element is to increase the contrast of an electron microscope for viewing weakly scattering samples while in focus. Typical weakly scattering samples include biological samples such as macromolecules, or perhaps cells. Preliminary experimental images demonstrate that these devices do apply a ninety degree phase shift as expected. Electrostatic calculations have been used to determine that fringing fields in the region of the scattered electron beams will cause a negligible phase shift as long as the ratio of electrode length to the transverse feature-size aperture is about 5:1. Calculations are underway to determine the feasibility of aspect smaller aspect ratios of about 3:1 and about 2:1.

  4. Microscopic Rayleigh Droplet Beams

    NASA Astrophysics Data System (ADS)

    Doak, R. B.

    2005-11-01

    A periodically triggered Rayleigh Droplet Beam (RDB) delivers a perfectly linear and periodic stream of identical, monoenergetic droplets that are phase-locked to the trigger signal. The droplet diameter and spacing are easily adjusted of choice of nozzle diameter and trigger frequency. Any liquid of low viscosity may be emloyed as the beam fluid. Although the field of nanofluidics is expanding rapidly, little effort has yet been devoted to ``external flows'' such as RDB's. At ASU we have generated RDB's of water and methanol down to 2 microns in droplet diameter. Nozzle clogging is the sole impediment to smaller droplets. Microscopic Rayleigh droplet beams offer tremendous potential for fundamental physical measurements, fluid dynamics research, and nanofabrication. This talk will describe the apparatus and techniques used at ASU to generate RDB's (surprisingly simple and inexpensive), discuss the triboelectric phenomena that play a role (surprisingly significant), present some initial experimental fluid dynamics measurements, and briefly survey RDB applications. Our particular interest in RDB's is as microscopic transport systems to deliver hydrated, undenatured proteins into vacuum for structure determination via serial diffraction of x-rays or electrons. This may offer the first general method for structure determination of non-crystallizable proteins.

  5. Thermodynamics and evolutionary genetics

    NASA Astrophysics Data System (ADS)

    Müller, Ingo

    2010-03-01

    Thermodynamics and evolutionary genetics have something in common. Thus, the randomness of mutation of cells may be likened to the random thermal fluctuations in a gas. And the probabilistic nature of entropy in statistical thermodynamics can be carried over to a population of haploid and diploid cells without any conceptual change. The energetic potential wells in which the atoms of a liquid are caught correspond to selective advantages for some phenotype over others. Thus, the eventual stable state in a population comes about as a compromise in the universal competition between entropy and energy.

  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. Components in Chemical Thermodynamics

    NASA Astrophysics Data System (ADS)

    Alberty, Robert A.

    1995-09-01

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

  8. 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.

  9. 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.

  10. Thermodynamics of ABC transporters.

    PubMed

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

    2016-01-01

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

  11. Thermodynamics of lattice OCD

    SciTech Connect

    Matsuoka, H.

    1985-01-01

    The thermodynamic consequences of QCD are explored in the framework of lattice gauge theory. Attention is focused upon the nature of the chiral symmetry restoration transition at finite temperature and at finite baryon density, and possible strategies for identifying relevant thermodynamic phases are discussed. Some numerical results are presented on the chiral symmetry restoration in the SU(2) gauge theory at high baryon density. The results suggest that with T approx. = 110 MeV there is a second order restoration transition at the critical baryon density n/sub B//sup c/ approx. = 0.62 fm/sup -3/.

  12. Beyond Equilibrium Thermodynamics

    NASA Astrophysics Data System (ADS)

    Öttinger, Hans Christian

    2005-01-01

    Beyond Equilibrium Thermodynamics fills a niche in the market by providing a comprehensive introduction to a new, emerging topic in the field. The importance of non-equilibrium thermodynamics is addressed in order to fully understand how a system works, whether it is in a biological system like the brain or a system that develops plastic. In order to fully grasp the subject, the book clearly explains the physical concepts and mathematics involved, as well as presenting problems and solutions; over 200 exercises and answers are included. Engineers, scientists, and applied mathematicians can all use the book to address their problems in modelling, calculating, and understanding dynamic responses of materials.

  13. 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.

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

    SciTech Connect

    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.

  15. 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)

  16. 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)

  17. Anisotropic contrast optical microscope

    NASA Astrophysics Data System (ADS)

    Peev, D.; Hofmann, T.; Kananizadeh, N.; Beeram, S.; Rodriguez, E.; Wimer, S.; Rodenhausen, K. B.; Herzinger, C. M.; Kasputis, T.; Pfaunmiller, E.; Nguyen, A.; Korlacki, R.; Pannier, A.; Li, Y.; Schubert, E.; Hage, D.; Schubert, M.

    2016-11-01

    An optical microscope is described that reveals contrast in the Mueller matrix images of a thin, transparent, or semi-transparent specimen located within an anisotropic object plane (anisotropic filter). The specimen changes the anisotropy of the filter and thereby produces contrast within the Mueller matrix images. Here we use an anisotropic filter composed of a semi-transparent, nanostructured thin film with sub-wavelength thickness placed within the object plane. The sample is illuminated as in common optical microscopy but the light is modulated in its polarization using combinations of linear polarizers and phase plate (compensator) to control and analyze the state of polarization. Direct generalized ellipsometry data analysis approaches permit extraction of fundamental Mueller matrix object plane images dispensing with the need of Fourier expansion methods. Generalized ellipsometry model approaches are used for quantitative image analyses. These images are obtained from sets of multiple images obtained under various polarizer, analyzer, and compensator settings. Up to 16 independent Mueller matrix images can be obtained, while our current setup is limited to 11 images normalized by the unpolarized intensity. We demonstrate the anisotropic contrast optical microscope by measuring lithographically defined micro-patterned anisotropic filters, and we quantify the adsorption of an organic self-assembled monolayer film onto the anisotropic filter. Comparison with an isotropic glass slide demonstrates the image enhancement obtained by our method over microscopy without the use of an anisotropic filter. In our current instrument, we estimate the limit of detection for organic volumetric mass within the object plane of ≈49 fg within ≈7 × 7 μm2 object surface area. Compared to a quartz crystal microbalance with dissipation instrumentation, where contemporary limits require a total load of ≈500 pg for detection, the instrumentation demonstrated here improves

  18. Anisotropic contrast optical microscope.

    PubMed

    Peev, D; Hofmann, T; Kananizadeh, N; Beeram, S; Rodriguez, E; Wimer, S; Rodenhausen, K B; Herzinger, C M; Kasputis, T; Pfaunmiller, E; Nguyen, A; Korlacki, R; Pannier, A; Li, Y; Schubert, E; Hage, D; Schubert, M

    2016-11-01

    An optical microscope is described that reveals contrast in the Mueller matrix images of a thin, transparent, or semi-transparent specimen located within an anisotropic object plane (anisotropic filter). The specimen changes the anisotropy of the filter and thereby produces contrast within the Mueller matrix images. Here we use an anisotropic filter composed of a semi-transparent, nanostructured thin film with sub-wavelength thickness placed within the object plane. The sample is illuminated as in common optical microscopy but the light is modulated in its polarization using combinations of linear polarizers and phase plate (compensator) to control and analyze the state of polarization. Direct generalized ellipsometry data analysis approaches permit extraction of fundamental Mueller matrix object plane images dispensing with the need of Fourier expansion methods. Generalized ellipsometry model approaches are used for quantitative image analyses. These images are obtained from sets of multiple images obtained under various polarizer, analyzer, and compensator settings. Up to 16 independent Mueller matrix images can be obtained, while our current setup is limited to 11 images normalized by the unpolarized intensity. We demonstrate the anisotropic contrast optical microscope by measuring lithographically defined micro-patterned anisotropic filters, and we quantify the adsorption of an organic self-assembled monolayer film onto the anisotropic filter. Comparison with an isotropic glass slide demonstrates the image enhancement obtained by our method over microscopy without the use of an anisotropic filter. In our current instrument, we estimate the limit of detection for organic volumetric mass within the object plane of ≈49 fg within ≈7 × 7 μm(2) object surface area. Compared to a quartz crystal microbalance with dissipation instrumentation, where contemporary limits require a total load of ≈500 pg for detection, the instrumentation demonstrated here improves

  19. 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)

  20. A Hamiltonian approach to Thermodynamics

    SciTech Connect

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

    2016-10-15

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

  1. 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.

  2. On Teaching Thermodynamics

    ERIC Educational Resources Information Center

    Debbasch, F.

    2011-01-01

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

  3. Thermodynamics in dynamical spacetimes

    NASA Astrophysics Data System (ADS)

    Tresguerres, Romualdo

    2014-03-01

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

  4. Thermodynamics of liquid metal

    SciTech Connect

    Kushnirenko, A.N.

    1988-01-01

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

  5. Thermodynamics of Resource Recycling.

    ERIC Educational Resources Information Center

    Hauserman, W. B.

    1988-01-01

    Evaluates the overall economic efficiency of a closed resource cycle. Uses elementary thermodynamic definitions of overall thermal efficiency for determining an economically quantifiable basis. Selects aluminum for investigation and includes a value-entropy diagram for a closed aluminum cycle. (MVL)

  6. Thermodynamics with Design Problems.

    ERIC Educational Resources Information Center

    Cilento, E. V.; Sears, J. T.

    1983-01-01

    Discusses how basic thermodynamics concepts are integrated with design problems. Includes course goals, instructional strategies, and major advantages/disadvantages of the integrated design approach. Advantages include making subject more concrete, emphasizing interrelation of variables, and reinforcing concepts by use in design analysis; whereas…

  7. Program Computes Thermodynamic Functions

    NASA Technical Reports Server (NTRS)

    Mcbride, Bonnie J.; Gordon, Sanford

    1994-01-01

    PAC91 is latest in PAC (Properties and Coefficients) series. Two principal features are to provide means of (1) generating theoretical thermodynamic functions from molecular constants and (2) least-squares fitting of these functions to empirical equations. PAC91 written in FORTRAN 77 to be machine-independent.

  8. Thermodynamical Arguments against Evolution

    ERIC Educational Resources Information Center

    Rosenhouse, Jason

    2017-01-01

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

  9. Single molecules: Thermodynamic limits

    NASA Astrophysics Data System (ADS)

    Liphardt, Jan

    2012-09-01

    Technologies aimed at single-molecule resolution of non-equilibrium systems increasingly require sophisticated new ways of thinking about thermodynamics. An elegant extension to standard fluctuation theory grants access to the kinetic intermediate states of these systems -- as DNA-pulling experiments now demonstrate.

  10. On Teaching Thermodynamics

    ERIC Educational Resources Information Center

    Debbasch, F.

    2011-01-01

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

  11. Thermodynamics of Resource Recycling.

    ERIC Educational Resources Information Center

    Hauserman, W. B.

    1988-01-01

    Evaluates the overall economic efficiency of a closed resource cycle. Uses elementary thermodynamic definitions of overall thermal efficiency for determining an economically quantifiable basis. Selects aluminum for investigation and includes a value-entropy diagram for a closed aluminum cycle. (MVL)

  12. Thermodynamics of Dilute Solutions.

    ERIC Educational Resources Information Center

    Jancso, Gabor; Fenby, David V.

    1983-01-01

    Discusses principles and definitions related to the thermodynamics of dilute solutions. Topics considered include dilute solution, Gibbs-Duhem equation, reference systems (pure gases and gaseous mixtures, liquid mixtures, dilute solutions), real dilute solutions (focusing on solute and solvent), terminology, standard states, and reference systems.…

  13. Thermodynamically Correct Bioavailability Estimations

    DTIC Science & Technology

    1992-04-30

    6448 I 1. SWPPUMENTA* NOTIS lIa. OISTUAMJTiOAVAILAIILTY STATIMENT 121 OT REbT ostwosCo z I Approved for public release; distribution unlimited... research is to develop thermodynamically correct bioavailability estimations using chromatographic stationary phases as a model of the "interphase

  14. Thermodynamics of Organic Compounds

    DTIC Science & Technology

    1982-11-01

    95085 Washiagton, DC 20234 • . 4- Los Angeles, CA 90045 National Bureau of Standards CINDAS Chemical Thermodynamics Division Purdue University...Department of Energy Mackay School of Nines Bartlesville Energy Technology Attn: Prof Eugene Miller Center Reno, NV 89507 Attn: Mr William D Good

  15. Stochastic and Macroscopic Thermodynamics of Strongly Coupled Systems

    NASA Astrophysics Data System (ADS)

    Jarzynski, Christopher

    2017-01-01

    We develop a thermodynamic framework that describes a classical system of interest S that is strongly coupled to its thermal environment E . Within this framework, seven key thermodynamic quantities—internal energy, entropy, volume, enthalpy, Gibbs free energy, heat, and work—are defined microscopically. These quantities obey thermodynamic relations including both the first and second law, and they satisfy nonequilibrium fluctuation theorems. We additionally impose a macroscopic consistency condition: When S is large, the quantities defined within our framework scale up to their macroscopic counterparts. By satisfying this condition, we demonstrate that a unifying framework can be developed, which encompasses both stochastic thermodynamics at one end, and macroscopic thermodynamics at the other. A central element in our approach is a thermodynamic definition of the volume of the system of interest, which converges to the usual geometric definition when S is large. We also sketch an alternative framework that satisfies the same consistency conditions. The dynamics of the system and environment are modeled using Hamilton's equations in the full phase space.

  16. Mars Under the Microscope

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This magnified look at the martian soil near the Mars Exploration Rover Opportunity's landing site, Meridiani Planum, shows coarse grains sprinkled over a fine layer of sand. The image was captured by the rover's microscopic imager on the 10th day, or sol, of its mission. Scientists are intrigued by the spherical rocks, which can be formed by a variety of geologic processes, including cooling of molten lava droplets and accretion of concentric layers of material around a particle or 'seed.'

    The examined patch of soil is 3 centimeters (1.2 inches) across. The circular grain in the lower left corner is approximately 3 millimeters (.12 inches) across, or about the size of a sunflower seed.

  17. Imaging arrangement and microscope

    SciTech Connect

    Pertsinidis, Alexandros; Chu, Steven

    2015-12-15

    An embodiment of the present invention is an imaging arrangement that includes imaging optics, a fiducial light source, and a control system. In operation, the imaging optics separate light into first and second tight by wavelength and project the first and second light onto first and second areas within first and second detector regions, respectively. The imaging optics separate fiducial light from the fiducial light source into first and second fiducial light and project the first and second fiducial light onto third and fourth areas within the first and second detector regions, respectively. The control system adjusts alignment of the imaging optics so that the first and second fiducial light projected onto the first and second detector regions maintain relatively constant positions within the first and second detector regions, respectively. Another embodiment of the present invention is a microscope that includes the imaging arrangement.

  18. Embryos, microscopes, and society.

    PubMed

    Maienschein, Jane

    2016-06-01

    Embryos have different meanings for different people and in different contexts. Seen under the microscope, the biological embryo starts out as one cell and then becomes a bunch of cells. Gradually these divide and differentiate to make up the embryo, which in humans becomes a fetus at eight weeks, and then eventually a baby. At least, that happens in those cases that carry through normally and successfully. Yet a popular public perception imagines the embryo as already a little person in the very earliest stages of development, as if it were predictably to become an adult. In actuality, cells can combine, pull apart, and recombine in a variety of ways and still produce embryos, whereas most embryos never develop into adults at all. Biological embryos and popular imaginations of embryos diverge. This paper looks at some of the historical reasons for and social implications of that divergence.

  19. Visualizing the Microscopic World.

    PubMed

    Cerqueira, Nuno M F S A; Fernandes, Pedro A; Ramos, Maria João

    2017-08-09

    Visualization can be a motivating way of teaching students about the microscopic world. This can become even more exciting if the information is based on accurate computational results rather than on crude approximations that eventually might create unreal alternative perceptions. Here, we report on a VMD plug-in, named vmdMagazine, which can turn computational simulations into stunning high-impact video presentations, suitable for classes/lectures and even conferences. The software will help students/audience to understand atoms and molecules better and learn to like them. The present paper is meant to give a general idea of the software's potential, showing how it works and how it can be used for educational purposes. The software is freely available at: http://www.fc.up.pt/PortoBioComp/database/doku.php?id=vmdmagazine .

  20. Fermi Gas Microscope

    NASA Astrophysics Data System (ADS)

    Setiawan, Widagdo

    Recent advances in using microscopes in ultracold atom experiment have allowed experimenters for the first time to directly observe and manipulate individual atoms in individual lattice sites. This technique enhances our capability to simulate strongly correlated systems such as Mott insulator and high temperature superconductivity. Currently, all ultracold atom experiments with high resolution imaging capability use bosonic atoms. In this thesis, I present our progress towards creating the fermionic version of the microscope experiment which is more suitable for simulating real condensed matter systems. Lithium is ideal due to the existence of both fermionic and bosonic isotopes, its light mass, which means faster experiment time scales that suppresses many sources of technical noise, and also due to the existence of a broad Feshbach resonance, which can be used to tune the inter-particle interaction strength over a wide range from attractive, non-interacting, and repulsive interactions. A high numerical aperture objective will be used to image and manipulate the atoms with single lattice site resolution. This setup should allow us to implement the Hubbard hamiltonian which could describe interesting quantum phases such as antiferromagnetism, d-wave superfluidity, and high temperature superconductivity. I will also discuss the feasibility of the Raman sideband cooling method for cooling the atoms during the imaging process. We have also developed a new electronic control system to control the sequence of the experiment. This electronic system is very scalable in order to keep up with the increasing complexity of atomic physics experiments. Furthermore, the system is also designed to be more precise in order to keep up with the faster time scale of lithium experiment.

  1. Atomic Force Microscope Operation

    NASA Technical Reports Server (NTRS)

    2008-01-01

    [figure removed for brevity, see original site] Click on image for animation (large file)

    This animation is a scientific illustration of the operation of NASA's Phoenix Mars Lander's Atomic Force Microscope, or AFM. The AFM is part of Phoenix's Microscopy, Electrochemistry, and Conductivity Analyzer, or MECA.

    The AFM is used to image the smallest Martian particles using a very sharp tip at the end of one of eight beams.

    The beam of the AFM is set into vibration and brought up to the surface of a micromachined silicon substrate. The substrate has etched in it a series of pits, 5 micrometers deep, designed to hold the Martian dust particles.

    The microscope then maps the shape of particles in three dimensions by scanning them with the tip.

    At the end of the animation is a 3D representation of the AFM image of a particle that was part of a sample informally called 'Sorceress.' The sample was delivered to the AFM on the 38th Martian day, or sol, of the mission (July 2, 2008).

    The image shows four round pits, only 5 microns in depth, that were micromachined into the silicon substrate.

    A Martian particle only one micrometer, or one millionth of a meter, across is held in the upper left pit.

    The rounded particle shown at the highest magnification ever seen from another world is a particle of the dust that cloaks Mars. Such dust particles color the Martian sky pink, feed storms that regularly envelop the planet and produce Mars' distinctive red soil.

    The AFM was developed by a Swiss-led consortium, with Imperial College London producing the silicon substrate that holds sampled particles.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  2. Spectroscopic Modeling of Single Element Plasma

    SciTech Connect

    Ghomeishi, Mostafa; Yap, S. L.; Wong, C. S.; Saboohi, S.; Chan, L. S.

    2011-03-30

    A strategy for spectroscopic analysis of single element plasmas is through modeling. An experimental investigation or generation of a specified emission spectrum can be attempted based on the modeling results which are currently under investigating by many researchers in the world. In the emission spectroscopy, the K-shell emission is more interesting than emissions from other shells due to their unique EUV and SXR frequencies that can be applied in various scientific and industrial applications. Population information of our model is based on a steady state kinetic code which is calculated for a given electron temperature and an estimated electron density. Thus for each single element plasma it needs large amounts of experimental or theoretical database. Depending on the parameter of the plasma, theories based on local thermodynamic equilibrium (LTE) and non-LTE are considered. In the non-LTE case, the Corona model is used and the total absolute number densities are calculated based on the ion densities that are related to the electron density corresponds to the mean charge of the ions. The spectra generated by the model can then be compared with spectroscopic data obtained experimentally.

  3. Spectroscopic Low Coherence Interferometry

    NASA Astrophysics Data System (ADS)

    Bosschaart, Nienke; van Leeuwen, T. G.; Aalders, Maurice C.; Hermann, Boris; Drexler, Wolfgang; Faber, Dirk J.

    Low-coherence interferometry (LCI) allows high-resolution volumetric imaging of tissue morphology and provides localized optical properties that can be related to the physiological status of tissue. This chapter discusses the combination of spatial and spectroscopic information by means of spectroscopic OCT (sOCT) and low-coherence spectroscopy (LCS). We describe the theory behind these modalities for the assessment of spatially resolved optical absorption and (back)scattering coefficient spectra. These spectra can be used for the highly localized quantification of chromophore concentrations and assessment of tissue organization on (sub)cellular scales. This leads to a wealth of potential clinical applications, ranging from neonatology for the determination of billibrubin concentrations, to oncology for the optical assessment of the aggressiveness of a cancerous lesion.

  4. Cyclic Thermodynamics with Open Flow

    SciTech Connect

    Reid, R.S.; Ward, W.C.; Swift, G.W.

    1998-05-01

    Some general features of a new class of thermodynamic device combining a thermodynamic cycle with the externally applied steady flow of an open thermodynamic process are discussed and experimentally demonstrated in the context of a thermoacoustic refrigerator. {copyright} {ital 1998} {ital The American Physical Society}

  5. Spectroscopic Binary Stars

    NASA Astrophysics Data System (ADS)

    Batten, A.; Murdin, P.

    2000-11-01

    Historically, spectroscopic binary stars were binary systems whose nature was discovered by the changing DOPPLER EFFECT or shift of the spectral lines of one or both of the component stars. The observed Doppler shift is a combination of that produced by the constant RADIAL VELOCITY (i.e. line-of-sight velocity) of the center of mass of the whole system, and the variable shift resulting from the o...

  6. 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.

  7. Fourier transform infrared vibrational spectroscopic imaging: integrating microscopy and molecular recognition.

    PubMed

    Levin, Ira W; Bhargava, Rohit

    2005-01-01

    The recent development of Fourier transform infrared (FTIR) spectroscopic imaging has enhanced our capability to examine, on a microscopic scale, the spatial distribution of vibrational spectroscopic signatures of materials spanning the physical and biomedical disciplines. Recent activity in this emerging area has concentrated on instrumentation development, theoretical analyses to provide guidelines for imaging practice, novel data processing algorithms, and the introduction of the technique to new fields. To illustrate the impact and promise of this spectroscopic imaging methodology, we present fundamental principles of the technique in the context of FTIR spectroscopy and review new applications in various venues ranging from the physical chemistry of macromolecular systems to the detection of human disease.

  8. 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.

  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.

  10. 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.

  11. 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.

  12. 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.

  13. Contact symmetries and Hamiltonian thermodynamics

    SciTech Connect

    Bravetti, A.; Lopez-Monsalvo, C.S.; Nettel, F.

    2015-10-15

    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 Legendre 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.

  14. Athena microscopic Imager investigation

    USGS Publications Warehouse

    Herkenhoff, K. E.; Squyres, S. W.; Bell, J.F.; Maki, J.N.; Arneson, H.M.; Bertelsen, P.; Brown, D.I.; Collins, S.A.; Dingizian, A.; Elliott, S.T.; Goetz, W.; Hagerott, E.C.; Hayes, A.G.; Johnson, M.J.; Kirk, R.L.; McLennan, S.; Morris, R.V.; Scherr, L.M.; Schwochert, M.A.; Shiraishi, L.R.; Smith, G.H.; Soderblom, L.A.; Sohl-Dickstein, J. N.; Wadsworth, M.V.

    2003-01-01

    The Athena science payload on the Mars Exploration Rovers (MER) includes the Microscopic Imager (MI). The MI is a fixed-focus camera mounted on the end of an extendable instrument arm, the Instrument Deployment Device (IDD). The MI was designed to acquire images at a spatial resolution of 30 microns/pixel over a broad spectral range (400-700 nm). The MI uses the same electronics design as the other MER cameras but has optics that yield a field of view of 31 ?? 31 mm across a 1024 ?? 1024 pixel CCD image. The MI acquires images using only solar or skylight illumination of the target surface. A contact sensor is used to place the MI slightly closer to the target surface than its best focus distance (about 66 mm), allowing concave surfaces to be imaged in good focus. Coarse focusing (???2 mm precision) is achieved by moving the IDD away from a rock target after the contact sensor has been activated. The MI optics are protected from the Martian environment by a retractable dust cover. The dust cover includes a Kapton window that is tinted orange to restrict the spectral bandpass to 500-700 nm, allowing color information to be obtained by taking images with the dust cover open and closed. MI data will be used to place other MER instrument data in context and to aid in petrologic and geologic interpretations of rocks and soils on Mars. Copyright 2003 by the American Geophysical Union.

  15. 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.

  16. Statistical Thermodynamics of Biomembranes

    PubMed Central

    Devireddy, Ram V.

    2010-01-01

    An overview of the major issues involved in the statistical thermodynamic treatment of phospholipid membranes at the atomistic level is summarized: thermodynamic ensembles, initial configuration (or the physical system being modeled), force field representation as well as the representation of long-range interactions. This is followed by a description of the various ways that the simulated ensembles can be analyzed: area of the lipid, mass density profiles, radial distribution functions (RDFs), water orientation profile, Deuteurium order parameter, free energy profiles and void (pore) formation; with particular focus on the results obtained from our recent molecular dynamic (MD) simulations of phospholipids interacting with dimethylsulfoxide (Me2SO), a commonly used cryoprotective agent (CPA). PMID:19460363

  17. Thermodynamics of nuclear transport

    NASA Astrophysics Data System (ADS)

    Wang, Ching-Hao; Mehta, Pankaj; Elbaum, Michael

    Molecular transport across the nuclear envelope is important for eukaryotes for gene expression and signaling. Experimental studies have revealed that nuclear transport is inherently a nonequilibrium process and actively consumes energy. In this work we present a thermodynamics theory of nuclear transport for a major class of nuclear transporters that are mediated by the small GTPase Ran. We identify the molecular elements responsible for powering nuclear transport, which we term the ``Ran battery'' and find that the efficiency of transport, measured by the cargo nuclear localization ratio, is limited by competition between cargo molecules and RanGTP to bind transport receptors, as well as the amount of NTF2 (i.e. RanGDP carrier) available to circulate the energy flow. This picture complements our current understanding of nuclear transport by providing a comprehensive thermodynamics framework to decipher the underlying biochemical machinery. Pm and CHW were supported by a Simons Investigator in the Mathematical Modeling in Living Systems grant (to PM).

  18. THERMODYNAMICS AND SOLUBILITY OF (UxNp1-x)O2(am) SOLID SOLUTION IN THE CARBONATE SYSTEM

    SciTech Connect

    Rai, Dhanpat; Hess, Nancy J.; Yui, Mikazu; Felmy, Andrew R.; Moore, Dean A.

    2004-03-15

    ABSTRACT -The formation of a solid solution can significantly affect the solubility of a minor component. The objectives of this study were to determine the nature of U(IV) and Np(IV) solid solutions and their thermodynamic properties. For this purpose, co-precipitates of U(IV) and Np(IV) [(UxNp1-x )O2(am), with values for x of 0.95, 0.85, 0.50, 0.15, and 0.05] were prepared, characterized, and used to determine their solubility as a function of K2CO3 concentrations ranging from 1.0 m to 5.0 m in the presence of 0.01 m Na2S2O4 and 0.01 m KOH, and as a function of KHCO3 concentrations ranging from 0.1 m to 0.8 m in the presence of 0.01 m Na2S2O4. The solubility data show that the equilibrium in these systems is reached in <7 days, the solubility-controlling solids are amorphous, and that we were successful in maintaining U and Np in the tetravalent state. A scanning electron microscope equipped with energy dispersive spectrometry and x-ray absorption spectroscopic analyses of the solids indicated the equilibrated co-precipitates to be solid solutions. A close agreement between the thermodynamic predictions, assuming an ideal solid solution, and the experimental solubilities shows that U(IV) and Np(IV) form an ideal solid solution and that non-ideal solid solution behavior for this system can be ruled out.

  19. New distributions in thermodynamics

    NASA Astrophysics Data System (ADS)

    Maslov, V. P.

    2016-09-01

    A model of the equation of state for classical gases consisting of nonpolar molecules is constructed under the assumption that the spinodal, critical isochore, and second virial coefficients of the gas have been set. The corresponding thermodynamic distributions are determined. It is shown that the isotherms constructed in the framework of the proposed model coincide with the isotherms of the van der Waals model obtained on a different basis.

  20. Black Hole Thermodynamics

    NASA Astrophysics Data System (ADS)

    Israel, Werner

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

  1. Thermodynamics of Organic Compounds

    DTIC Science & Technology

    1979-01-01

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

  2. The design and performance of a mid-infrared FT-IR spectroscopic imaging system

    NASA Astrophysics Data System (ADS)

    Wright, N. A.; Crocombe, R. A.; Drapcho, D. L.; McCarthy, W. J.

    1998-06-01

    An integrated FT-IR spectroscopic imaging system is described. This consists of a step-scan FT-IR spectrometer, FT-IR microscope accessory and a 64×64 element MCT focal plane array, mounted on the microscope. Control of, and data acquisition from, both the spectrometer and the focal plane array is from a single PC. Typical data acquisition times for an 8 cm-1 resolution array are 1-4 minutes.

  3. 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.

  4. Thermodynamical Arguments Against Evolution

    NASA Astrophysics Data System (ADS)

    Rosenhouse, Jason

    2017-03-01

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

  5. Thermodynamics of barnase unfolding.

    PubMed

    Griko, Y V; Makhatadze, G I; Privalov, P L; Hartley, R W

    1994-04-01

    The thermodynamics of barnase denaturation has been studied calorimetrically over a broad range of temperature and pH. It is shown that in acidic solutions the heat denaturation of barnase is well approximated by a 2-state transition. The heat denaturation of barnase proceeds with a significant increase of heat capacity, which determines the temperature dependencies of the enthalpy and entropy of its denaturation. The partial specific heat capacity of denatured barnase is very close to that expected for the completely unfolded protein. The specific denaturation enthalpy value extrapolated to 130 degrees C is also close to the value expected for the full unfolding. Therefore, the calorimetrically determined thermodynamic characteristics of barnase denaturation can be considered as characteristics of its complete unfolding and can be correlated with structural features--the number of hydrogen bonds, extent of van der Waals contacts, and the surface areas of polar and nonpolar groups. Using this information and thermodynamic information on transfer of protein groups into water, the contribution of various factors to the stabilization of the native structure of barnase has been estimated. The main contributors to the stabilization of the native state of barnase appear to be intramolecular hydrogen bonds. The contributions of van der Waals interactions between nonpolar groups and those of hydration effects of these groups are not as large if considered separately, but the combination of these 2 factors, known as hydrophobic interactions, is of the same order of magnitude as the contribution of hydrogen bonding.

  6. Thermodynamical Arguments Against Evolution

    NASA Astrophysics Data System (ADS)

    Rosenhouse, Jason

    2017-02-01

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

  7. Raman spectroscopic biochemical mapping of tissues

    NASA Astrophysics Data System (ADS)

    Stone, Nicholas; Hart Prieto, Maria C.; Kendall, Catherine A.; Shetty, Geeta; Barr, Hugh

    2006-02-01

    Advances in technologies have brought us closer to routine spectroscopic diagnosis of early malignant disease. However, there is still a poor understanding of the carcinogenesis process. For example it is not known whether many cancers follow a logical sequence from dysplasia, to carcinoma in situ, to invasion. Biochemical tissue changes, triggered by genetic mutations, precede morphological and structural changes. These can be probed using Raman or FTIR microspectroscopy and the spectra analysed for biochemical constituents. Local microscopic distribution of various constituents can then be visualised. Raman mapping has been performed on a number of tissues including oesophagus, breast, bladder and prostate. The biochemical constituents have been calculated at each point using basis spectra and least squares analysis. The residual of the least squares fit indicates any unfit spectral components. The biochemical distribution will be compared with the defined histopathological boundaries. The distribution of nucleic acids, glycogen, actin, collagen I, III, IV, lipids and others appear to follow expected patterns.

  8. 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.

  9. Scientists View Battery Under Microscope

    SciTech Connect

    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.

  10. 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…

  11. 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

  12. 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…

  13. Scientists View Battery Under Microscope

    ScienceCinema

    None

    2016-07-12

    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.

  14. Microscopic anatomy: normal structure.

    PubMed

    King, Rosalind

    2013-01-01

    A peripheral nerve trunk is composed of nerve fascicles supported in a fibrous collagenous sheath and defined by concentric layers of cells (the perineurium) that separate the contents (the endoneurium) from its fibrous collagen support (the epineurium). In the endoneurium are myelinated and unmyelinated fibers that are axons combined with their supporting Schwann cells to provide physical and electrical connections with end-organs such as muscle fibers and sensory endings. Axons are tubular neuronal extensions with a cytoskeleton of neurotubules and tubulin along which organelles and proteins can travel between the neuronal cell body and the axon terminal. During development some axons enlarge and are covered by a chain of Schwann cells each associated with just one axon. As the axons grow in diameter, the Schwann cells wrap round them to produce a myelin sheath. This consists of many layers of compacted Schwann cell membrane plus some additional proteins. Adjacent myelin segments connect at highly specialized structures, the nodes of Ranvier. Myelin insulates the axon so that the nerve impulse can jump from one node to the next. The region adjacent to the node, the paranodal segment, is the site of myelin terminations on the axolemma. There are connections here between the Schwann cell and the axon via a complex chain of proteins. The Schwann cell cytoplasm in the adjacent segment, the juxtaparanode, contains most of the Schwann cell mitochondria. In addition to the node, continuity of myelin lamellae is broken at intervals along the internode by helical regions of decompaction known as Schmidt-Lanterman incisures; these are seen as paler conical segments in suitably stained microscopical preparations and provide a pathway between the adaxonal and abaxonal cytoplasm. Smaller axons without a myelin sheath conduct very much more slowly and have a more complex relationship with their supporting Schwann cells that has important implications for repair. Copyright

  15. T Tauri Spectroscopic Binaries

    NASA Astrophysics Data System (ADS)

    Dudorov, A. E.; Eretnova, O. V.

    2017-06-01

    The Hertzsprung-Russell diagram, the excess radius-age, and the eccentricity-period relations are constructed for double-lined spectroscopic T Tauri binaries. The masses and the ages of the classical T Tauri and the weak-line T Tauri stars are compared. All components of T Tauri stars have the excess radius in comparison with initial Main Sequence stars of corresponding mass. The younger the star the more excess radius it has. The overwhelming majority of close binaries (P<10d) have eccentricity near to zero. The fraction of quadruple systems in our sample are higher than for Main Sequence stars.

  16. Spectroscopic Studies of the Several Isomers of UO3

    SciTech Connect

    Sweet, Lucas E.; Reilly, Dallas D.; Abrecht, David G.; Buck, Edgar C.; Meier, David E.; Su, Yin-Fong; Brauer, Carolyn S.; Schwantes, Jon M.; Tonkyn, Russell G.; Szecsody, James E.; Blake, Thomas A.; Johnson, Timothy J.

    2013-09-26

    Uranium trioxide is known to adopt seven different structural forms. While these structural forms have been well characterized using x-ray or neutron diffraction techniques, little work has been done to characterize their spectroscopic properties, particularly of the pure phases. Since the structural isomers of UO3 all have similar thermodynamic stabilities and most tend to hydrolyze under open atmospheric conditions, mixtures of UO3 phases and the hydrolysis products are common. Much effort went into isolating pure phases of UO3. Utilizing x-ray diffraction as a sample identification check, UV/Vis/NIR spectroscopic signatures of α-UO3, β-UO3, γ-UO3 and UO2(OH)2 products were obtained. The spectra of the pure phases can now be used to characterize typical samples of UO3, which are often mixtures of isomers.

  17. Spectroscopic studies of protein folding: Linear and nonlinear methods

    PubMed Central

    Serrano, Arnaldo L; Waegele, Matthias M; Gai, Feng

    2012-01-01

    Although protein folding is a simple outcome of the underlying thermodynamics, arriving at a quantitative and predictive understanding of how proteins fold nevertheless poses huge challenges. Therefore, both advanced experimental and computational methods are continuously being developed and refined to probe and reveal the atomistic details of protein folding dynamics and mechanisms. Herein, we provide a concise review of recent developments in spectroscopic studies of protein folding, with a focus on new triggering and probing methods. In particular, we describe several laser-based techniques for triggering protein folding/unfolding on the picosecond and/or nanosecond timescales and various linear and nonlinear spectroscopic techniques for interrogating protein conformations, conformational transitions, and dynamics. PMID:22109973

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

    SciTech Connect

    Ikeda, Tatsuhiko N.; Sakumichi, Naoyuki; Polkovnikov, Anatoli; Ueda, Masahito

    2015-03-15

    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 without reference to the microscopic state of the system.

  19. Evaporation and instabilities of microscopic capillary bridges

    PubMed Central

    Maeda, Nobuo; Israelachvili, Jacob N.; Kohonen, Mika M.

    2003-01-01

    The formation and disappearance of liquid bridges between two surfaces can occur either through equilibrium or nonequilibrium processes. In the first instance, the bridge molecules are in thermodynamic equilibrium with the surrounding vapor medium. In the second, chemical potential gradients result in material transfer; mechanical instabilities, because of van der Waals force jumps on approach or a Rayleigh instability on rapid separation, may trigger irreversible film coalescence or bridge snapping. We have studied the growth and disappearance mechanisms of laterally microscopic liquid bridges of three hydrocarbon liquids in slit-like pores. At rapid slit-opening rates, the bridges rupture by means of a mechanical instability described by the Young–Laplace equation. Noncontinuum but apparently reversible behavior is observed when a bridge is held at nanoscopic surface separations H close to the thermodynamic equilibrium Kelvin length, 2rKcosθ, where rK is the Kelvin radius and θ is the contact angle. During the course of slow evaporation (at H > 2rKcosθ) and subsequent regrowth by capillary condensation (at H < 2rKcosθ), the refractive index of the bridge may vary continuously and reversibly between that of the bulk liquid and vapor. The evaporation process becomes irreversible only at the very final stage of evaporation, when the refractive index of the fluid attains virtually that of the vapor. Measured refractive index profiles and the time-dependence of evaporating neck diameters also seem to differ from predictions based on a continuum picture of bridge evaporation far from the critical point. We discuss these findings in terms of the probable density profiles in evolving liquid bridges. PMID:12538868

  20. Pressure and temperature induced high spin-low spin phase transition: Macroscopic and microscopic consideration

    NASA Astrophysics Data System (ADS)

    Levchenko, G.; Khristov, A.; Kuznetsova, V.; Shelest, V.

    2014-08-01

    The behavior under pressure of the high spin-low spin phase transition in the coordination compounds containing 3d ions is analyzed using thermodynamic and microscopic approaches. For thermodynamic approach the mean field model with interactions between spin-crossover molecules is considered. Microscopic model takes into account the interaction of d electrons of the transition metal ions with full symmetric distortions of the ligands. The relationship of the thermodynamic interaction parameters with microscopic ones is installed and shown how the quantum-mechanical interactions form the cooperativity of the system. Within the microscopic model the temperature and pressure dependences of the high spin fraction in 2-D compounds {Fe(3-Fpy)2[M(CN)4]} (M=Pd, Pt) are simulated and microscopic parameters are evaluated. It is concluded that different experimental behaviors of the temperature and pressure induced spin transitions are determined by different variations of the inelastic and elastic energies under pressure, and vibrational component of the free energy drives the ST equally with electronic part.

  1. Thermodynamic properties of Fe56,57

    NASA Astrophysics Data System (ADS)

    Algin, E.; Agvaanluvsan, U.; Guttormsen, M.; Larsen, A. C.; Mitchell, G. E.; Rekstad, J.; Schiller, A.; Siem, S.; Voinov, A.

    2008-11-01

    Nuclear level densities for Fe56,57 have been extracted from the primary γ-ray spectra using (3He,3He'γ) and (3He,αγ) reactions. Nuclear thermodynamic properties for Fe56 and Fe57 are investigated using the experimental level densities. These properties include entropy, Helmholtz free energy, caloric curves, chemical potential, and heat capacity. In particular, the breaking of Cooper pairs and single-quasiparticle entropy are discussed and shown to be important concepts for describing nuclear level density. Microscopic model calculations are performed for level densities of Fe56,57. The experimental and calculated level densities are compared. The average number of broken Cooper pairs and the parity distribution are extracted as a function of excitation energy for Fe56,57 from the model calculations.

  2. 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'.

  3. 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).

  4. Thermodynamics of Thermoelectric Materials

    NASA Astrophysics Data System (ADS)

    Doak, Jeff W.

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

  5. Thermodynamical interpretation of the geometrical variables associated with null surfaces

    NASA Astrophysics Data System (ADS)

    Chakraborty, Sumanta; Padmanabhan, T.

    2015-11-01

    The emergent gravity paradigm interprets gravitational field equations as describing the thermodynamic limit of the underlying statistical mechanics of microscopic degrees of freedom of the spacetime. The connection is established by attributing a heat density T s to the null surfaces where T is the appropriate Davies-Unruh temperature and s is the entropy density. The field equations can be obtained from a thermodynamic variational principle which extremizes the total heat density of all null surfaces. The explicit form of s determines the nature of the theory. We explore the consequences of this paradigm for an arbitrary null surface and highlight the thermodynamic significance of various geometrical quantities. In particular, we show that (a) a conserved current, associated with the time development vector in a natural fashion, has direct thermodynamic interpretation in all Lanczos-Lovelock models of gravity; (b) one can generalize the notion of gravitational momentum, introduced in T. Padmanabhan, [arXiv:1506.03814] to all Lanczos-Lovelock models of gravity such that the conservation of the total momentum leads to the relevant field equations; (c) the thermodynamic variational principle which leads to the field equations of gravity can also be expressed in terms of the gravitational momentum in all Lanczos-Lovelock models; and (d) three different projections of gravitational momentum related to an arbitrary null surface in the spacetime lead to three different equations, all of which have thermodynamic interpretation. The first one reduces to a Navier-Stokes equation for the transverse drift velocity. The second can be written as a thermodynamic identity T d S =d E +P d V . The third describes the time evolution of the null surface in terms of suitably defined surface and bulk degrees of freedom. The implications are discussed.

  6. 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.

  7. RNA Thermodynamic Structural Entropy

    PubMed Central

    Garcia-Martin, Juan Antonio; Clote, Peter

    2015-01-01

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

  8. RNA Thermodynamic Structural Entropy.

    PubMed

    Garcia-Martin, Juan Antonio; Clote, Peter

    2015-01-01

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

  9. Rotary thermodynamic apparatus and method

    SciTech Connect

    Kantor, F. W.

    1985-06-25

    A rotary inertial thermodynamic absorptive system which can be used as a gas-driven heat pump, a heat-flow-driven gas pump, or, in combination, a heat splitter for moving low-grade heat energy from a lower temperature source to a higher temperature heat sink. In one embodiment, an absorptive type rotary inertial thermodynamic device employs overspill/underspill barriers in its absorption and desorption chambers to achieve counterflow heat exchange therebetween and to ensure effective control of thermodynamic impedance.

  10. Dynamics versus thermodynamics

    NASA Astrophysics Data System (ADS)

    Berdichevsky, V. L.

    1991-05-01

    An effort is made to characterize the ways in which the approaches of statistical mechanics and thermodynamics can be useful in the study of the dynamic behavior of structures. This meditation proceeds through consideration of such wide-ranging and deliberately provocative questions as: 'What are to be considered values in a stress-distribution function?' and 'How many degrees-of-freedom has a beam?'; it then gives attention to the hierarchy of vibrations, the interaction of the mechanism of dissipation with invisible degrees of freedom, and a plausible view of vibrations for the case of small dissipation.

  11. Autonomous quantum thermodynamic machines

    NASA Astrophysics Data System (ADS)

    Tonner, Friedemann; Mahler, Günter

    2005-12-01

    We investigate the dynamics of a quantum system consisting of a single spin coupled to an oscillator and sandwiched between two thermal baths at different temperatures. By means of an adequately designed Lindblad equation, it is shown that this device can function as a thermodynamic machine exhibiting Carnot-type cycles. For the present model, this means that when run as a heat engine, coherent motion of the oscillator is amplified. Contrary to the quantum computer, such a machine has a quantum as well as a classical limit. Away from the classical limit, it asymptotically approaches a stationary transport scenario.

  12. Thermodynamics of Rubber Elasticity

    NASA Astrophysics Data System (ADS)

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

    2001-02-01

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

  13. Stochastic thermodynamics of resetting

    NASA Astrophysics Data System (ADS)

    Fuchs, Jaco; Goldt, Sebastian; Seifert, Udo

    2016-03-01

    Stochastic dynamics with random resetting leads to a non-equilibrium steady state. Here, we consider the thermodynamics of resetting by deriving the first and second law for resetting processes far from equilibrium. We identify the contributions to the entropy production of the system which arise due to resetting and show that they correspond to the rate with which information is either erased or created. Using Landauer's principle, we derive a bound on the amount of work that is required to maintain a resetting process. We discuss different regimes of resetting, including a Maxwell demon scenario where heat is extracted from a bath at constant temperature.

  14. Thermodynamics of Accelerating Black Holes

    NASA Astrophysics Data System (ADS)

    Appels, Michael; Gregory, Ruth; KubizÅák, David

    2016-09-01

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

  15. 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.

  16. Spectrophotometric, Fourier transform infrared spectroscopic and theoretical studies of the charge-transfer complexes between methyldopa [(S)-2 amino-3-(3,4-dihydroxyphenyl)-2-methyl propanoic acid] and the acceptors (chloranilic acid, o-chloranil and dichlorodicyanobenzoquinone) in acetonitrile and their thermodynamic properties

    NASA Astrophysics Data System (ADS)

    Sharma, K.; Sharma, S. P.; Lahiri, S. C.

    Methyldopa is a much used antihypertensive drug. It is the subject matter of study mostly for the determination and estimation of methyldopa in pharmaceutical properties. These considerations led us to study the charge-transfer interactions between methyldopa, a centrally acting antihypertensive agent of limited use with the known acceptors like o-chloranil (o-ClN), chloranilic acid (ClA) and dichlorodicyanobenzoquinone (DDQ). Methyldopa (MDP) formed beautifully colored complexes (having absorption maxima at 581 nm and 368 nm; 519 nm; 583.5 nm, 547 nm and 346 nm, respectively) with the acceptors mentioned before. The physico-chemical properties of the complexes were studied using UV-visible spectrophotometry and FTIR measurements. The composition, the accurate association constants and thermodynamics of the complexes were determined spectrophotometrically. Attempts were made to interpret the thermodynamics of complexes in terms of IDV, EAV and hνCT. Solid CT complexes between MDP + o-ClN, MDP + ClA and MDP + DDQ were prepared and FTIR spectra of the complexes were studied. The energies hνCT of the charge-transfer complexes and vertical ionization potential IDV of methyldopa were compared with the theoretical values of hνCT obtained from HOMO and LUMO of the donors and acceptors calculated using Density Function Theory utilizing different basis sets. The agreement between the results can be regarded to be reasonable. Oscillator strengths and dipole strengths of the complexes were determined theoretically and experimentally and the limitations of the calculations were outlined.

  17. A thermodynamic model of physical gels

    NASA Astrophysics Data System (ADS)

    An, Yonghao; Solis, Francisco J.; Jiang, Hanqing

    2010-12-01

    Physical gels are characterized by dynamic cross-links that are constantly created and broken, changing its state between solid and liquid under influence of environmental factors. This restructuring ability of physical gels makes them an important class of materials with many applications, such as in drug delivery. In this article, we present a thermodynamic model for physical gels that considers both the elastic properties of the network and the transient nature of the cross-links. The cross-links' reformation is captured through a connectivity tensor M at the microscopic level. The macroscopic quantities, such as the volume fraction of the monomer ϕ, number of monomers per cross-link s, and the number of cross-links per volume q, are defined by statistic averaging. A mean-field energy functional for the gel is constructed based on these variables. The equilibrium equations and the stress are obtained at the current state. We study the static thermodynamic properties of physical gels predicted by the model. We discuss the problems of un-constrained swelling and stress driven phase transitions of physical gels and describe the conditions under which these phenomena arise as functions of the bond activation energy Ea, polymer/solvent interaction parameter χ, and external stress p.

  18. 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

  19. Electronic absorption spectroscopic studies on charge-transfer interactions in a biologically important molecule: N, N'-dimethyl-4,4'-bipyridylium chloride (paraquat or methyl viologen) as an electron acceptor

    NASA Astrophysics Data System (ADS)

    Murthy, A. S. N.; Bhardwaj, A. P.

    The charge-transfer spectra of N, N'-dimethyl-4,4'-bipyridylium chloride (paraquat, PQ 2+) with a wide range of electron donors has been investigated and the thermodynamic data determined. An estimate of the empirical energy parameters has been made using the spectroscopic and thermodynamic data, using Mulliken's theory.

  20. Thermodynamics. [algebraic structure

    NASA Technical Reports Server (NTRS)

    Zeleznik, F. J.

    1976-01-01

    The fundamental structure of thermodynamics is purely algebraic, in the sense of atopological, and it is also independent of partitions, composite systems, the zeroth law, and entropy. The algebraic structure requires the notion of heat, but not the first law. It contains a precise definition of entropy and identifies it as a purely mathematical concept. It also permits the construction of an entropy function from heat measurements alone when appropriate conditions are satisfied. Topology is required only for a discussion of the continuity of thermodynamic properties, and then the weak topology is the relevant topology. The integrability of the differential form of the first law can be examined independently of Caratheodory's theorem and his inaccessibility axiom. Criteria are established by which one can determine when an integrating factor can be made intensive and the pseudopotential extensive and also an entropy. Finally, a realization of the first law is constructed which is suitable for all systems whether they are solids or fluids, whether they do or do not exhibit chemical reactions, and whether electromagnetic fields are or are not present.

  1. Thermodynamics of geothermal fluids

    SciTech Connect

    Rogers, P.S.Z.

    1981-03-01

    A model to predict the thermodynamic properties of geothermal brines, based on a minimum amount of experimental data on a few key systems, is tested. Volumetric properties of aqueous sodium chloride, taken from the literature, are represented by a parametric equation over the range 0 to 300{sup 0}C and 1 bar to 1 kbar. Density measurements at 20 bar needed to complete the volumetric description also are presented. The pressure dependence of activity and thermal properties, derived from the volumetric equation, can be used to complete an equation of state for sodium chloride solutions. A flow calorimeter, used to obtain heat capacity data at high temperatures and pressures, is described. Heat capacity measurements, from 30 to 200{sup 0}C and 1 bar to 200 bar, are used to derive values for the activity coefficient and other thermodynamic properties of sodium sulfate solutions as a function of temperature. Literature data on the solubility of gypsum in mixed electrolyte solutions have been used to evaluate model parameters for calculating gypsum solubility in seawater and natural brines. Predictions of strontium and barium sulfate solubility in seawater also are given.

  2. Thermodynamics of Error Correction

    NASA Astrophysics Data System (ADS)

    Sartori, Pablo; Pigolotti, Simone

    2015-10-01

    Information processing at the molecular scale is limited by thermal fluctuations. This can cause undesired consequences in copying information since thermal noise can lead to errors that can compromise the functionality of the copy. For example, a high error rate during DNA duplication can lead to cell death. Given the importance of accurate copying at the molecular scale, it is fundamental to understand its thermodynamic features. In this paper, we derive a universal expression for the copy error as a function of entropy production and work dissipated by the system during wrong incorporations. Its derivation is based on the second law of thermodynamics; hence, its validity is independent of the details of the molecular machinery, be it any polymerase or artificial copying device. Using this expression, we find that information can be copied in three different regimes. In two of them, work is dissipated to either increase or decrease the error. In the third regime, the protocol extracts work while correcting errors, reminiscent of a Maxwell demon. As a case study, we apply our framework to study a copy protocol assisted by kinetic proofreading, and show that it can operate in any of these three regimes. We finally show that, for any effective proofreading scheme, error reduction is limited by the chemical driving of the proofreading reaction.

  3. 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…

  4. 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…

  5. Adirondack Under the Microscope-2

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This overhead look at the martian rock dubbed Adirondack was captured by the Mars Exploration Rover Spirit's panoramic camera. It shows the approximate region where the rover's microscopic imager began its first close-up inspection.

  6. Microscopic derivation of discrete hydrodynamics.

    PubMed

    Español, Pep; Anero, Jesús G; Zúñiga, Ignacio

    2009-12-28

    By using the standard theory of coarse graining based on Zwanzig's projection operator, we derive the dynamic equations for discrete hydrodynamic variables. These hydrodynamic variables are defined in terms of the Delaunay triangulation. The resulting microscopically derived equations can be understood, a posteriori, as a discretization on an arbitrary irregular grid of the Navier-Stokes equations. The microscopic derivation provides a set of discrete equations that exactly conserves mass, momentum, and energy and the dissipative part of the dynamics produces strict entropy increase. In addition, the microscopic derivation provides a practical implementation of thermal fluctuations in a way that the fluctuation-dissipation theorem is satisfied exactly. This paper points toward a close connection between coarse-graining procedures from microscopic dynamics and discretization schemes for partial differential equations.

  7. Microscopic Procedures for Plant Meiosis.

    ERIC Educational Resources Information Center

    Braselton, James P.

    1997-01-01

    Describes laboratory techniques designed to familiarize students with meiosis and how microscopic preparations of meiosis are made. These techniques require the use of fresh or fixed flowers. Contains 18 references. (DDR)

  8. Recent Athena Microscopic Imager Results

    NASA Astrophysics Data System (ADS)

    Herkenhoff, K. E.; Ashley, J. W.; Johnson, J. R.; Parker, T. J.; Athena Science Team

    2012-03-01

    The Mars Exploration Rover Opportunity arrived at the rim of Endeavour Crater in August 2011. This presentation summarizes Opportunity Microscopic Imager observations of ejecta, bedrock, a gypsum vein, and other materials in the crater rim rocks.

  9. Adirondack Under the Microscope-2

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This overhead look at the martian rock dubbed Adirondack was captured by the Mars Exploration Rover Spirit's panoramic camera. It shows the approximate region where the rover's microscopic imager began its first close-up inspection.

  10. Mars Life? - Microscopic Tubular Structures

    NASA Image and Video Library

    1996-08-09

    This electron microscope image shows tubular structures of likely Martian origin. These structures are very similar in size and shape to extremely tiny microfossils found in some Earth rocks. http://photojournal.jpl.nasa.gov/catalog/PIA00287

  11. Microscopic Procedures for Plant Meiosis.

    ERIC Educational Resources Information Center

    Braselton, James P.

    1997-01-01

    Describes laboratory techniques designed to familiarize students with meiosis and how microscopic preparations of meiosis are made. These techniques require the use of fresh or fixed flowers. Contains 18 references. (DDR)

  12. Magnetic Resonance Force Microscope Development

    SciTech Connect

    Hammel, P.C.; Zhang, Z.; Suh, B.J.; Roukes, M.L.; Midzor, M.; Wigen, P.E.; Childress, J.R.

    1999-06-03

    Our objectives were to develop the Magnetic Resonance Force Microscope (MRFM) into an instrument capable of scientific studies of buried structures in technologically and scientifically important electronic materials such as magnetic multilayer materials. This work resulted in the successful demonstration of MRFM-detected ferromagnetic resonance (FMR) as a microscopic characterization tool for thin magnetic films. Strong FMR spectra obtained from microscopic Co thin films (500 and 1000 angstroms thick and 40 x 200 microns in lateral extent) allowed us to observe variations in sample inhomogeneity and magnetic anisotropy field. We demonstrated lateral imaging in microscopic FMR for the first time using a novel approach employing a spatially selective local field generated by a small magnetically polarized spherical crystallite of yttrium iron garnet. These successful applications of the MRFM in materials studies provided the basis for our successful proposal to DOE/BES to employ the MRF M in studies of buried interfaces in magnetic materials.

  13. (Center of excellence: Microlaser microscope)

    SciTech Connect

    Webb, R.H.

    1992-01-01

    This Center-of-Excellence grant has two components: development of an imaging system based on microlaser arrays forms a central project among a group of laser diagnostic and therapeutic efforts primarily funded outside the grant. In these first 8 months we have set up the Microlaser Microscope using small microlaser arrays. We have emphasized the basics of microlaser handling and electronic addressing and the optics of the microscope. Details of electronics and optics given here will be used in the larger arrays which should be available soon. After a description of the central Microlaser Microscope project, we touch briefly on the other projects of the Center, which have been outstandingly fruitful this year. Publications are necessarily concerned with the smaller projects, since the Microlaser Microscope is in its early stages.

  14. 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.

  15. HIGH TEMPERATURE MICROSCOPE AND FURNACE

    DOEpatents

    Olson, D.M.

    1961-01-31

    A high-temperature microscope is offered. It has a reflecting optic situated above a molten specimen in a furnace and reflecting the image of the same downward through an inert optic member in the floor of the furnace, a plurality of spaced reflecting plane mirrors defining a reflecting path around the furnace, a standard microscope supported in the path of and forming the end terminus of the light path.

  16. Taking Photographs with a Microscope

    PubMed Central

    Maude, Richard J.; Koh, Gavin C. K. W.; Silamut, Kamolrat

    2008-01-01

    We describe a simple, economical, and highly practical technique for taking digital photographs of specimens visualized through a light microscope. Most models of light microscope and compact digital camera, and even some cameraphones, can be used. The technique is quick to learn and can easily be performed in a resource-poor setting. It can be used to assist with diagnosis in remote areas and can be extremely useful for teaching. PMID:18784246

  17. Taking photographs with a microscope.

    PubMed

    Maude, Richard J; Koh, Gavin C K W; Silamut, Kamolrat

    2008-09-01

    We describe a simple, economical, and highly practical technique for taking digital photographs of specimens visualized through a light microscope. Most models of light microscope and compact digital camera, and even some cameraphones, can be used. The technique is quick to learn and can easily be performed in a resource-poor setting. It can be used to assist with diagnosis in remote areas and can be extremely useful for teaching.

  18. [MICROSCOPIC COLITIS: THE CLINICAL CASE].

    PubMed

    Kulygina, Y A; Skalinskaya, M I; Ageeva, T A

    2015-01-01

    During past years incidence and prevalence of microscopic colitis (MC) have increased, that is possible caused to the improvement of knowledge of doctors about the disease. This article contain modern views on epidemiology, diagnostic and variant of microscopic colitis treatment. A typical clinical picture of MC in the form of recurrent a watery diarrhea, with the absence of pathologic changes at roentgenologic and endoscopic investigations is described with the example of a clinical case.

  19. Nucleation in the presence of slow microscopic dynamics.

    PubMed

    Sear, Richard P

    2008-06-07

    Nucleation of a new thermodynamic phase is often a slow process due to the need to overcome a high free-energy barrier. However, there are other sources of slow dynamics; for example, at high densities/low temperatures, the movement of individual molecules or spins may be slow. Here, we study nucleation in a simple phenomenological model that has this type of slow microscopic dynamics. We do this to better understand how the two sources of slow dynamics interact. We find that as nucleation is intrinsically slow, only very slow microscopic dynamics strongly affect how nucleation occurs. The composition of the nucleus at the top of the nucleation barrier is much less sensitive to slow microscopic dynamics than is the composition of the nucleus once it is postcritical. However, slow dynamics affects not only the rate but also the pathway, which no longer goes over the saddle point in the free energy. We also find that the slow microscopic dynamics can cause sampling problems in an algorithm developed to calculate nucleation rates, and so cause it to predict the rate incorrectly.

  20. STM-SQUID probe microscope

    NASA Astrophysics Data System (ADS)

    Hayashi, Tadayuki; Tachiki, Minoru; Itozaki, Hideo

    2007-11-01

    We have developed a STM-SQUID probe microscope. A high TC SQUID probe microscope was combined with a scanning tunneling microscope for investigation of samples at room temperature in air. A high permeability probe needle was used as a magnetic flux guide to improve the spatial resolution. The probe with tip radius of less than 100 nm was prepared by microelectropolishing. The probe was also used as a scanning tunneling microscope tip. Topography of the sample surface could be measured by the scanning tunneling microscope with high spatial resolution prior to observation by SQUID microscopy. The SQUID probe microscope image could be observed while keeping the distance from the sample surface to the probe tip constant. We observed a topographic image and a magnetic image of Ni fine pattern and also a magnetically recorded hard disk. Furthermore we have investigated a sample vibration method of the static magnetic field emanating from a sample with the aim of achieving a higher signal-to-noise (S/N) ratio.

  1. Single-wavelength STED microscope

    NASA Astrophysics Data System (ADS)

    Baer, Stephen C.

    2011-03-01

    The zero-point STED microscope (US Pat. 5,866,911)1 was the first far-field microscope to overcome the diffraction limit, but optimally it requires two expensive synchronized short-pulsed lasers. Replacing the synchronized pulsed lasers with CW lasers had been proposed to reduce costs1, but this seriously reduced resolution compared to a similarly powered pulsed STED microscope. A recent theoretical and experimental study (Nat. Methods 4, 915 (2007))3 argued that CW STED has better resolution than previously believed, but there appear to be flaws in the theory sufficient to raise questions about its reported experimental confirmation. We describe an alternative approach to reducing cost of the STED microscope while preserving resolution. A portion of the beam from a femtosecond pulsed laser of a wavelength able to excite fluorescence by multiphoton absorption, is passed through a long optical fiber to stretch the pulses to reduce their peak power so they can no longer excite but can quench by stimulated emission. The stretched pulses are shaped into a doughnut profile and then recombined with the first beam for interaction with the specimen. With suitable fluorophores, this instrument should be able to match the resolution performance of the pulsed laser STED microscope using separate lasers. Particularly when added to an existing multiphoton microscope, such performance should be achievable at extremely low added cost.

  2. Maximum entropy production rate in quantum thermodynamics

    NASA Astrophysics Data System (ADS)

    Beretta, Gian Paolo

    2010-06-01

    In the framework of the recent quest for well-behaved nonlinear extensions of the traditional Schrödinger-von Neumann unitary dynamics that could provide fundamental explanations of recent experimental evidence of loss of quantum coherence at the microscopic level, a recent paper [Gheorghiu-Svirschevski 2001 Phys. Rev. A 63 054102] reproposes the nonlinear equation of motion proposed by the present author [see Beretta G P 1987 Found. Phys. 17 365 and references therein] for quantum (thermo)dynamics of a single isolated indivisible constituent system, such as a single particle, qubit, qudit, spin or atomic system, or a Bose-Einstein or Fermi-Dirac field. As already proved, such nonlinear dynamics entails a fundamental unifying microscopic proof and extension of Onsager's reciprocity and Callen's fluctuation-dissipation relations to all nonequilibrium states, close and far from thermodynamic equilibrium. In this paper we propose a brief but self-contained review of the main results already proved, including the explicit geometrical construction of the equation of motion from the steepest-entropy-ascent ansatz and its exact mathematical and conceptual equivalence with the maximal-entropy-generation variational-principle formulation presented in Gheorghiu-Svirschevski S 2001 Phys. Rev. A 63 022105. Moreover, we show how it can be extended to the case of a composite system to obtain the general form of the equation of motion, consistent with the demanding requirements of strong separability and of compatibility with general thermodynamics principles. The irreversible term in the equation of motion describes the spontaneous attraction of the state operator in the direction of steepest entropy ascent, thus implementing the maximum entropy production principle in quantum theory. The time rate at which the path of steepest entropy ascent is followed has so far been left unspecified. As a step towards the identification of such rate, here we propose a possible, well

  3. Automated markerless full field hard x-ray microscopic tomography at sub-50nm 3-dimension spatial resolution

    SciTech Connect

    Wang J.; Yu-chen Chen, K.; Yuan, W.; Tkachuk, A.; Erdonmez, C.

    2012-04-04

    A full field transmission x-ray microscope (TXM) has been developed and commissioned at the National Synchrotron Light Source at Brookhaven National Laboratory. The capabilities we developed in auto-tomography, local tomography, and spectroscopic imaging that overcome many of the limitations and difficulties in existing transmission x-ray microscopes are described and experimentally demonstrated. Sub-50 nm resolution in 3-dimension (3D) with markerless automated tomography has been achieved. These capabilities open up scientific opportunities in many research fields.

  4. Automated markerless full field hard x-ray microscopic tomography at sub-50 nm 3-dimension spatial resolution

    SciTech Connect

    Wang Jun; Karen Chen Yuchen; Yuan Qingxi; Tkachuk, Andrei; Hornberger, Benjamin; Feser, Michael; Erdonmez, Can

    2012-04-02

    A full field transmission x-ray microscope (TXM) has been developed and commissioned at the National Synchrotron Light Source at Brookhaven National Laboratory. The capabilities we developed in auto-tomography, local tomography, and spectroscopic imaging that overcome many of the limitations and difficulties in existing transmission x-ray microscopes are described and experimentally demonstrated. Sub-50 nm resolution in 3-dimension (3D) with markerless automated tomography has been achieved. These capabilities open up scientific opportunities in many research fields.

  5. Ch. 33 Modeling: Computational Thermodynamics

    SciTech Connect

    Besmann, Theodore M

    2012-01-01

    This chapter considers methods and techniques for computational modeling for nuclear materials with a focus on fuels. The basic concepts for chemical thermodynamics are described and various current models for complex crystalline and liquid phases are illustrated. Also included are descriptions of available databases for use in chemical thermodynamic studies and commercial codes for performing complex equilibrium calculations.

  6. 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)

  7. 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)

  8. 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…

  9. 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…

  10. Thermodynamic analysis of conductive filaments

    SciTech Connect

    Karpov, V.; Niraula, D.; Karpov, I.

    2016-08-29

    We present a thermodynamic theory of the conductive filament growth and dissolution in random access memory describing the observed features of their current-voltage (IV) characteristics. Our theory is based on the self-consisted Fokker-Planck approach reducing the filament kinetics to its thermodynamics. Expressing the observed IV features through material parameters, our results pave a way to device improvements.

  11. Thermodynamics and Spontaneity

    NASA Astrophysics Data System (ADS)

    Ochs, Raymond S.

    1996-10-01

    Despite the importance of thermodynamics as the foundation of chemistry, most students emerge from introductory courses with only a dim understanding of this subject. Generally students recognize that the information is significant, yet do not assimilate it into later studies, especially in applied fields such as biology and biochemistry. A clear sense of the problem is reflected in a number of other contributions to this Journal (e.g., 1 - 6). Most (1 - 4, 6) recommend increased rigor in derivation of equations. This may appeal to students in advanced courses in chemical thermodynamics, but not to most. A few other suggestions are to introduce the subject earlier in general chemistry courses (2) or to provide innovative ways to visualize reaction changes (3). I suggest that the problem lies at another level entirely: the meanings of the terms are not clear. Recently, MacNeal (7) introduced the concept of mathsemantics, the joining of mathematics with a deep understanding of the sense (semantics) in which it operates. For example, the author argues that not only can we add apples and oranges (yielding total fruit), but that anything less than such a synthesis is trivial. Mathematics is hard, not because of the actual mathematical part of the problem but because of the semantics. As discussed thoroughly by Weinburg (8), the very names we affix to ideas dominate how we think about them. A similar reorientation would benefit chemical education. By way of example, the word "spontaneous" is widely used in thermodynamics, presumably because the word is familiar and assists understanding of this subject. In the following, I will provide evidence that this word has contributed more to the obfuscation of chemical ideas than it has helped elucidate them. Literature Cited 1. Redlich, O. J. Chem. Educ. 1975, 52, 374 - 376. 2. Bergquist, W.; Heikkinen, H. J. Chem. Educ. 1990, 67, 1000 - 1003. 3. Macomber, R. S. J. Chem. Educ. 1994, 71, 311 - 312. 4. Sanchez, K. S.; Vergenz, R

  12. Thermodynamics of the Earth

    NASA Astrophysics Data System (ADS)

    Stacey, Frank D.

    2010-04-01

    Applications of elementary thermodynamic principles to the dynamics of the Earth lead to robust, quantitative conclusions about the tectonic effects that arise from convection. The grand pattern of motion conveys deep heat to the surface, generating mechanical energy with a thermodynamic efficiency corresponding to that of a Carnot engine operating over the adiabatic temperature gradient between the heat source and sink. Referred to the total heat flux derived from the Earth's silicate mantle, the efficiency is 24% and the power generated, 7.7 × 1012 W, causes all the material deformation apparent as plate tectonics and the consequent geological processes. About 3.5% of this is released in seismic zones but little more than 0.2% as seismic waves. Even major earthquakes are only localized hiccups in this motion. Complications that arise from mineral phase transitions can be used to illuminate details of the motion. There are two superimposed patterns of convection, plate subduction and deep mantle plumes, driven by sources of buoyancy, negative and positive respectively, at the top and bottom of the mantle. The patterns of motion are controlled by the viscosity contrasts (>104 : 1) at these boundaries and are self-selected as the least dissipative mechanisms of heat transfer for convection in a body with very strong viscosity variation. Both are subjects of the thermodynamic efficiency argument. Convection also drives the motion in the fluid outer core that generates the geomagnetic field, although in that case there is an important energy contribution by compositional separation, as light solute is rejected by the solidifying inner core and mixed into the outer core, a process referred to as compositional convection. Uncertainty persists over the core energy balance because thermal conduction is a drain on core energy that has been a subject of diverse estimates, with attendant debate over the need for radiogenic heat in the core. The geophysical approach to

  13. Approximating the detection limit of an infrared spectroscopic imaging microscope operating in an attenuated total reflection (ATR) modality: theoretical and empirical results for an instrument using a linear array detector and a 1.5 millimeter germanium hemisphere internal reflection element.

    PubMed

    Lanzarotta, Adam

    2015-01-01

    Theoretical and empirical detection limits have been estimated for aripiprazole (analyte) in alpha lactose monohydrate (matrix model pharmaceutical formulation) using a micro-attenuated total reflection Fourier transform infrared (ATR FT-IR) spectroscopic imaging instrument equipped with a linear array detector and a 1.5 mm germanium hemisphere internal reflection element (IRE). The instrument yielded a theoretical detection limit of 0.0035% (35 parts per million (ppm)) when operating under diffraction-limited conditions, which was 49 times lower than what was achieved with a traditional macro-ATR instrument operating under practical conditions (0.17%, 1700 ppm). However, these results may not be achievable for most analyses because the detection limits will be particle size limited, rather than diffraction limited, for mixtures with average particle diameters greater than 8.3 μm (most pharmaceutical samples). For example, a theoretical detection limit of 0.028% (280 ppm) was calculated for an experiment operating under particle size-limited conditions where the average particle size was 23.4 μm. These conditions yielded a detection limit of 0.022% (220 ppm) when measured empirically, which was close to the theoretical value and only eight times lower than that of a faster, more simplistic macro-ATR instrument. Considering the longer data acquisition and processing times characteristic of the micro-ATR imaging approach (minutes or even hours versus seconds), the cost-benefit ratio may not often be favorable for the analysis of analytes in matrices that exhibit only a few overlapping absorptions (low-interfering matrices such as alpha lactose monohydrate) using this technique compared to what can be achieved using macro-ATR. However, the advantage was significant for detecting analytes in more complex matrices (those that exhibited several overlapping absorptions with the analyte) because the detection limit of the macro-ATR approach was highly formulation

  14. Thermodynamic mixing properties and behavior of almandine-spessartine solid solutions

    NASA Astrophysics Data System (ADS)

    Dachs, Edgar; Geiger, Charles A.; Benisek, Artur; Grodzicki, Michael

    2014-01-01

    The heat capacity, Cp, of five solid-solution members of the almandine(Alm)-spessartine(Sps) binary, consisting of three synthetic polycrystalline and two natural single-crystal samples, was measured in the temperature range between 2 and 300 K using relaxation calorimetry and between 282 and 764 K using DSC methods. All garnets exhibit a λ-type heat-capacity anomaly at low temperatures resulting from a paramagnetic to antiferromagnetic phase transition. The temperature of the magnetic transition in Fe-rich garnets occurs between those of the two end-members (i.e. 9.2 K for almandine and 6.2 K for spessartine), but lies at lower values between 3.5 and 4.5 K for more Sps-rich compositions with XMngrt>0.5. The calorimetric entropy at 298 K shows mechanical-mixture behavior for Sps-rich garnets and a slight possible negative deviation from such behavior for Alm-rich compositions. At the 2σ level all data are, however, consistent with ideal mixing behavior and the Margules entropy interaction parameter, WS,FeMngrt, is zero for the Alm-Sps binary. Thermodynamic analysis of published high P and T phase-equilibrium Fe-Mn exchange experiments between garnet and ilmenite shows that the excess Gibbs free energy of mixing, ΔGex, for Fe-Mn in garnet is positive and asymmetric towards spessartine. Margules enthalpy interaction parameters of WH,FeMngrt=4170±518 J/cationṡmol and WH,MnFe=1221±588 J/cationṡmol are derived giving a maximum of ΔGex≈0.7 kJ/cationṡmol at XMngrt≈0.6. ΔHex obtained using autocorrelation analysis of published IR spectra of Alm-Sps solid solutions is in reasonable agreement with that derived from phase-equilibrium and calorimetry data. Previous diffraction and spectroscopic results on Alm-Sps garnets and quantum mechanical calculations made on almandine are used to interpret the macroscopic thermodynamic behavior from a microscopic basis. The relevance of the new garnet Fe-Mn mixing model for petrological calculations is demonstrated by

  15. 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

  16. Thermodynamic cost of acquiring information.

    PubMed

    Micadei, Kaonan; Serra, Roberto M; Céleri, Lucas C

    2013-12-01

    Connections between information theory and thermodynamics have proven to be very useful to establish bounding limits for physical processes. Ideas such as Landauer's erasure principle and information-assisted work extraction have greatly contributed not only to broadening our understanding about the fundamental limits imposed by nature, but also paving the way for practical implementations of information-processing devices. The intricate information-thermodynamics relation also entails a fundamental limit on parameter estimation, establishing a thermodynamic cost for information acquisition. We show that the amount of information that can be encoded in a physical system by means of a unitary process is limited by the dissipated work during the implementation of the process. This includes a thermodynamic tradeoff for information acquisition. Likewise, the information acquisition process is ultimately limited by the second law of thermodynamics. This tradeoff for information acquisition may find applications in several areas of knowledge.

  17. Layer-by-layer and intrinsic analysis of molecular and thermodynamic properties across soft interfaces

    SciTech Connect

    Sega, Marcello; Jedlovszky, Pál

    2015-09-21

    Interfaces are ubiquitous objects, whose thermodynamic behavior we only recently started to understand at the microscopic detail. Here, we borrow concepts from the techniques of surface identification and intrinsic analysis, to provide a complementary point of view on the density, stress, energy, and free energy distribution across liquid (“soft”) interfaces by analyzing the respective contributions coming from successive layers.

  18. Layer-by-layer and intrinsic analysis of molecular and thermodynamic properties across soft interfaces

    NASA Astrophysics Data System (ADS)

    Sega, Marcello; Fábián, Balázs; Jedlovszky, Pál

    2015-09-01

    Interfaces are ubiquitous objects, whose thermodynamic behavior we only recently started to understand at the microscopic detail. Here, we borrow concepts from the techniques of surface identification and intrinsic analysis, to provide a complementary point of view on the density, stress, energy, and free energy distribution across liquid ("soft") interfaces by analyzing the respective contributions coming from successive layers.

  19. Cooling by Thermodynamic Induction

    NASA Astrophysics Data System (ADS)

    Patitsas, S. N.

    2017-03-01

    A method is described for cooling conductive channels to below ambient temperature. The thermodynamic induction principle dictates that the electrically biased channel will cool if the electrical conductance decreases with temperature. The extent of this cooling is calculated in detail for both cases of ballistic and conventional transport with specific calculations for carbon nanotubes and conventional metals, followed by discussions for semiconductors, graphene, and metal-insulator transition systems. A theorem is established for ballistic transport stating that net cooling is not possible. For conventional transport, net cooling is possible over a broad temperature range, with the range being size-dependent. A temperature clamping scheme for establishing a metastable nonequilibrium stationary state is detailed and followed with discussion of possible applications to on-chip thermoelectric cooling in integrated circuitry and quantum computer systems.

  20. Geometry of thermodynamic control.

    PubMed

    Zulkowski, Patrick R; Sivak, David A; Crooks, Gavin E; DeWeese, Michael R

    2012-10-01

    A deeper understanding of nonequilibrium phenomena is needed to reveal the principles governing natural and synthetic molecular machines. Recent work has shown that when a thermodynamic system is driven from equilibrium then, in the linear response regime, the space of controllable parameters has a Riemannian geometry induced by a generalized friction tensor. We exploit this geometric insight to construct closed-form expressions for minimal-dissipation protocols for a particle diffusing in a one-dimensional harmonic potential, where the spring constant, inverse temperature, and trap location are adjusted simultaneously. These optimal protocols are geodesics on the Riemannian manifold and reveal that this simple model has a surprisingly rich geometry. We test these optimal protocols via a numerical implementation of the Fokker-Planck equation and demonstrate that the friction tensor arises naturally from a first-order expansion in temporal derivatives of the control parameters, without appealing directly to linear response theory.

  1. Modern problems of thermodynamics

    NASA Astrophysics Data System (ADS)

    Novikov, I. I.

    2012-12-01

    The role of energy and methods of its saving for the development of human society and life are analyzed. The importance of future use of space energy flows and energy of water and air oceans is emphasized. The authors consider the idea of the unit for production of electric energy and pure substances using sodium chloride which reserves are limitless on the planet. Looking retrospectively at the development of power engineering from the elementary fire to modern electric power station, we see that the used method of heat production, namely by direct interaction of fuel and oxidizer, is the simplest. However, it may be possible to combust coal, i.e., carbon in salt melt, for instance, sodium chloride that would be more rational and efficient. If the stated problems are solved positively, we would master all energy properties of the substance; and this is the main problem of thermodynamics being one of the sciences on energy.

  2. Thermodynamics and cement science

    SciTech Connect

    Damidot, D.; Lothenbach, B.; Herfort, D.; Glasser, F.P.

    2011-07-15

    Thermodynamics applied to cement science has proved to be very valuable. One of the most striking findings has been the extent to which the hydrate phases, with one conspicuous exception, achieve equilibrium. The important exception is the persistence of amorphous C-S-H which is metastable with respect to crystalline calcium silicate hydrates. Nevertheless C-S-H can be included in the scope of calculations. As a consequence, from comparison of calculation and experiment, it appears that kinetics is not necessarily an insuperable barrier to engineering the phase composition of a hydrated Portland cement. Also the sensitivity of the mineralogy of the AFm and AFt phase compositions to the presence of calcite and to temperature has been reported. This knowledge gives a powerful incentive to develop links between the mineralogy and engineering properties of hydrated cement paste and, of course, anticipates improvements in its performance leading to decreasing the environmental impacts of cement production.

  3. Cooling by Thermodynamic Induction

    NASA Astrophysics Data System (ADS)

    Patitsas, S. N.

    2016-11-01

    A method is described for cooling conductive channels to below ambient temperature. The thermodynamic induction principle dictates that the electrically biased channel will cool if the electrical conductance decreases with temperature. The extent of this cooling is calculated in detail for both cases of ballistic and conventional transport with specific calculations for carbon nanotubes and conventional metals, followed by discussions for semiconductors, graphene, and metal-insulator transition systems. A theorem is established for ballistic transport stating that net cooling is not possible. For conventional transport, net cooling is possible over a broad temperature range, with the range being size-dependent. A temperature clamping scheme for establishing a metastable nonequilibrium stationary state is detailed and followed with discussion of possible applications to on-chip thermoelectric cooling in integrated circuitry and quantum computer systems.

  4. Thermodynamics of Protein Aggregation

    NASA Astrophysics Data System (ADS)

    Osborne, Kenneth L.; Barz, Bogdan; Bachmann, Michael; Strodel, Birgit

    Amyloid protein aggregation characterizes many neurodegenerative disorders, including Alzheimer's, Parkinson's, and Creutz- feldt-Jakob disease. Evidence suggests that amyloid aggregates may share similar aggregation pathways, implying simulation of full-length amyloid proteins is not necessary for understanding amyloid formation. In this study we simulate GNNQQNY, the N-terminal prion-determining domain of the yeast protein Sup35 to investigate the thermodynamics of structural transitions during aggregation. We use a coarse-grained model with replica-exchange molecular dynamics to investigate the association of 3-, 6-, and 12-chain GNNQQNY systems and we determine the aggregation pathway by studying aggregation states of GN- NQQNY. We find that the aggregation of the hydrophilic GNNQQNY sequence is mainly driven by H-bond formation, leading to the formation of /3-sheets from the very beginning of the assembly process. Condensation (aggregation) and ordering take place simultaneously, which is underpinned by the occurrence of a single heat capacity peak only.

  5. Thermodynamics of anisotropic branes

    NASA Astrophysics Data System (ADS)

    Ávila, Daniel; Fernández, Daniel; Patiño, Leonardo; Trancanelli, Diego

    2016-11-01

    We study the thermodynamics of flavor D7-branes embedded in an anisotropic black brane solution of type IIB supergravity. The flavor branes undergo a phase transition between a `Minkowski embedding', in which they lie outside of the horizon, and a `black hole embedding', in which they fall into the horizon. This transition depends on the black hole temperature, its degree of anisotropy, and the mass of the flavor degrees of freedom. It happens either at a critical temperature or at a critical anisotropy. A general lesson we learn from this analysis is that the anisotropy, in this particular realization, induces similar effects as the temperature. In particular, increasing the anisotropy bends the branes more and more into the horizon. Moreover, we observe that the transition becomes smoother for higher anisotropies.

  6. Sand Compositional Analysis Using a Combined Geological and Spectroscopic Approach

    NASA Astrophysics Data System (ADS)

    Smith, Molly Elizabeth

    Many minerals, such as calcite and magnetite, show diagnostic overtone and combination bands in the 350-2500 nm window. Sand, though an important unconsolidated material with great abundance on the Earth's surface, is largely overlooked in spectroscopic studies. Over 100 sand samples were analyzed through traditional microscopic methods and compared to spectral reflectance collected via an ASD Spectroradiometer. Multiple methods were chosen to compare spectroscopic data to sand composition and grain size: 1) existing spectral indices, 2) continuum removal, 3) derivative analysis, and 4) correlation analysis. Particular focus was given to carbonate content. Results from derivative and correlation analysis showed strong correlations in the 2180-2240 nm and 2300-2360 nm windows to carbonate content. Proposed here is the Normalized Difference Carbonate Sand Index (NDCSI), which showed Pearson correlations of r=-0.78 for light-colored samples and r=-0.77 for all samples used. This index is viable for use with carbonate-rich sands.

  7. Thermodynamic aspects of vitrification.

    PubMed

    Wowk, Brian

    2010-02-01

    Vitrification is a process in which a liquid begins to behave as a solid during cooling without any substantial change in molecular arrangement or thermodynamic state variables. The physical phenomenon of vitrification is relevant to both cryopreservation by freezing, in which cells survive in glass between ice crystals, and cryopreservation by vitrification in which a whole sample is vitrified. The change from liquid to solid behavior is called the glass transition. It is coincident with liquid viscosity reaching 10(13) Poise during cooling, which corresponds to a shear stress relaxation time of several minutes. The glass transition can be understood on a molecular level as a loss of rotational and translational degrees of freedom over a particular measurement timescale, leaving only bond vibration within a fixed molecular structure. Reduced freedom of molecular movement results in decreased heat capacity and thermal expansivity in glass relative to the liquid state. In cryoprotectant solutions, the change from liquid to solid properties happens over a approximately 10 degrees C temperature interval centered on a glass transition temperature, typically near -120 degrees C (+/-10 degrees C) for solutions used for vitrification. Loss of freedom to quickly rearrange molecular position causes liquids to depart from thermodynamic equilibrium as they turn into a glass during vitrification. Residual molecular mobility below the glass transition temperature allows glass to very slowly contract, release heat, and decrease entropy during relaxation toward equilibrium. Although diffusion is practically non-existent below the glass transition temperature, small local movements of molecules related to relaxation have consequences for cryobiology. In particular, ice nucleation in supercooled vitrification solutions occurs at remarkable speed until at least 15 degrees C below the glass transition temperature. Copyright 2009 Elsevier Inc. All rights reserved.

  8. [Neoplasms and medical thermodynamics].

    PubMed

    Klimek, Rudolf

    2003-09-01

    Oncology--just as every field of medicine that deals with etiology, diagnostics, pathomechanism and treatment of diseases--is only a part of the general human knowledge, whose all significant achievements must be used to protect human health. This pursuit has as its object not only the benefits form practical discoveries (L. Pasteur, W.C. Roentgen, P. Curie and M. Skłodowska-Curie, V. Schally etc.), but also theoretical generalizations (A. Einstein, W.K. Heisenberg and I. Prigogine). Unfortunately it is the lack and/or slow adaptation of that information, that is responsible for the still unsatisfactory progress in clinical oncology. Responsibility rests not only with oncologists, but primarily with editors of medical journals and textbooks, who have a moral duty to follow the entire general knowledge, especially in the field of the basic research. On the basis of an analysis of the contents of the Polish oncology textbooks and materials from the specialist conferences in gynaecologic oncology, they were found to: 1. Omit the current, particularly domestic literature, 2. Contain mostly works, whose conclusions are textbook information, 3. Rarely include studies in the area of medical thermodynamics, 4. Attempt to explain the effects of the modern technologies, e.g. fotodynamics or nanotechnology using theoretical generalizations which are inadequate for them, and 5. Disregard the rule primum non nocere not only in prevention but even in the treatment of neoplasms. Neoplastic disease has many conditionings and types because of the unique identity of the neoplasms which cause it and which are caused by universal and natural phenomena of the self-organizing dissipative structures. It requires not only early diagnosing but also causative treatment already in the precancerous states, which are better detected by modern methods based on the quantum thermodynamics (lasers, fotodynamics, nuclear magnetic resonance, genetic nanotechnology etc.).

  9. Thermodynamics of feldspathoid solutions

    NASA Astrophysics Data System (ADS)

    Sack, Richard O.; Ghiorso, Mark S.

    We have developed models for the thermody-namic properties of nephelines, kalsilites, and leucites in the simple system NaAlSiO4-KAlSiO4-Ca0.5AlSiO4-SiO2-H2O that are consistent with all known constraints on subsolidus equilibria and thermodynamic properties, and have integrated them into the existing MELTS software package. The model for nepheline is formulated for the simplifying assumptions that (1) a molecular mixing-type approximation describes changes in the configurational entropy associated with the coupled exchange substitutions □Si?NaAl and □Ca? Na2 and that (2) Na+ and K+ display long-range non-convergent ordering between a large cation and the three small cation sites in the Na4Al4Si4O16 formula unit. Notable features of the model include the prediction that the mineral tetrakalsilite (``panunzite'', sensu stricto) results from anti-ordering of Na and K between the large cation and the three small cation sites in the nepheline structure at high temperatures, an average dT/dP slope of about 55°/kbar for the reaction over the temperature and pressure ranges 800-1050 °C and 500-5000 bars, roughly symmetric (i.e. quadratic) solution behavior of the K-Na substitution along joins between fully ordered components in nepheline, and large positive Gibbs energies for the nepheline reciprocal reactions and and for the leucite reciprocal reaction

  10. Diffusion and thermodynamic equilibrium under pressure variations

    NASA Astrophysics Data System (ADS)

    Moulas, Evangelos; Tajčmanová, Lucie; Vrijmoed, Johannes; Podladchikov, Yuri

    2015-04-01

    Pressure is one of the most fundamental variables in mineral thermodynamics. In that respect, pressure-sensitive mineral reactions provide an important constraint on pressure under which the rock was developed. One implicit assumption when interpreting such pressure estimates is that the state-of-stress is close to hydrostatic, homogeneous and that the differential stress is negligible. Recent spectroscopic data from the mineral scale documenting pressure variations do not support this assumption. In addition to observations, mechanical models (numerical and analytical) suggest that rocks can develop and maintain heterogeneous pressure distributions at geological time scales. The recently developed unconventional barometry explains chemical zoning in minerals as a result of a pressure variation. We focus to apply the unconventional barometry in cases where chemical zoning in minerals cannot be explained by sluggish kinetics. In that respect, the unconventional barometry offers an alternative view of the chemical zoning which is consistent with thermodynamic equilibrium. However, to distinguish between a pressure-controlled chemical zoning and a zoning reflecting an incomplete chemical reaction is still challenging, especially for multicomponent systems. In this contribution, different types of chemical zoning are discussed. We investigate plagioclase rims around kyanite from an amphibolitized eclogite from Rhodope Metamorphic Complex (Greece-Bulgaria) as a case study and compare them with similar published textures from the Bohemian Massif. Mineral microstructures and phase equilibrium suggest that both rocks experienced near-isothermal decompression at high (>700C) temperatures. However, several distinct microstructural features suggest the development and/or the decay of mechanically maintained heterogeneous pressure distributions. We discuss our results and interpretations based on phase-equilibrium modeling, unconventional barometry and diffusion modeling under

  11. Spectroscopic classification of supernova candidates

    NASA Astrophysics Data System (ADS)

    Hodgkin, S. T.; Hall, A.; Fraser, M.; Campbell, H.; Wyrzykowski, L.; Kostrzewa-Rutkowska, Z.; Pietro, N.

    2014-09-01

    We report the spectroscopic classification of four supernovae at the 2.5m Isaac Newton Telescope on La Palma, using the Intermediate Dispersion Spectrograph and the R300V grating (3500-8000 Ang; ~6 Ang resolution).

  12. Spectroscopic Detection of Pathogens

    SciTech Connect

    ALAM,M. KATHLEEN; TIMLIN,JERILYN A.; MARTIN,LAURA E.; HJELLE,DRIAN; LYONS,RICK; GARRISON,KRISTIN

    2000-11-01

    The goal of this LDRD Research project was to provide a preliminary examination of the use of infrared spectroscopy as a tool to detect the changes in cell cultures upon activation by an infectious agent. Due to a late arrival of funding, only 5 months were available to transfer and setup equipment at UTTM,develop cell culture lines, test methods of in-situ activation and collect kinetic data from activated cells. Using attenuated total reflectance (ATR) as a sampling method, live cell cultures were examined prior to and after activation. Spectroscopic data were collected from cells immediately after activation in situ and, in many cases for five successive hours. Additional data were collected from cells activated within a test tube (pre-activated), in both transmission mode as well as in ATR mode. Changes in the infrared data were apparent in the transmission data collected from the pre-activated cells as well in some of the pre-activated ATR data. Changes in the in-situ activated spectral data were only occasionally present due to (1) the limited time cells were studied and (2) incomplete activation. Comparison of preliminary data to infrared bands reported in the literature suggests the primary changes seen are due an increase in ribonucleic acid (RNA) production. This work will be continued as part of a 3 year DARPA grant.

  13. Spectroscopic optical coherence elastography.

    PubMed

    Adie, Steven G; Liang, Xing; Kennedy, Brendan F; John, Renu; Sampson, David D; Boppart, Stephen A

    2010-12-06

    We present an optical technique to image the frequency-dependent complex mechanical response of a viscoelastic sample. Three-dimensional hyperspectral data, comprising two-dimensional B-mode images and a third dimension corresponding to vibration frequency, were acquired from samples undergoing external mechanical excitation in the audio-frequency range. We describe the optical coherence tomography (OCT) signal when vibration is applied to a sample and detail the processing and acquisition techniques used to extract the local complex mechanical response from three-dimensional data that, due to a wide range of vibration frequencies, possess a wide range of sample velocities. We demonstrate frequency-dependent contrast of the displacement amplitude and phase of a silicone phantom containing inclusions of higher stiffness. Measurements of an ex vivo tumor margin demonstrate distinct spectra between adipose and tumor regions, and images of displacement amplitude and phase demonstrated spatially-resolved contrast. Contrast was also observed in displacement amplitude and phase images of a rat muscle sample. These results represent the first demonstration of mechanical spectroscopy based on B-mode OCT imaging. Spectroscopic optical coherence elastography (S-OCE) provides a high-resolution imaging capability for the detection of tissue pathologies that are characterized by a frequency-dependent viscoelastic response.

  14. 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.

  15. 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.

  16. X-ray spectroscopic application of Cr /Sc periodic multilayers

    NASA Astrophysics Data System (ADS)

    Le Guen, K.; Maury, H.; André, J.-M.; Jonnard, P.; Hardouin, A.; Delmotte, F.; Ravet-Krill, M.-F.

    2007-12-01

    The use of Cr /Sc multilayer interferential mirrors (MIMs) in optical systems such as x-ray microscopes or telescopes have been reported for the water window (between C K- and O K-absorption edges). However, their possibilities in spectroscopic application have never been described in the literature. The purpose of the paper is to report for the first time on the performances of Cr /Sc MIMs as Bragg dispersive devices for the analysis in wavelength dispersive spectrometry of samples containing N or Sc atoms. The possibility to distinguish the chemical state of the emitting N or Sc atoms is evidenced by using Johan-type and double-crystal spectrometers.

  17. Multivariate Chemical Image Fusion of Vibrational Spectroscopic Imaging Modalities.

    PubMed

    Gowen, Aoife A; Dorrepaal, Ronan M

    2016-07-02

    Chemical image fusion refers to the combination of chemical images from different modalities for improved characterisation of a sample. Challenges associated with existing approaches include: difficulties with imaging the same sample area or having identical pixels across microscopic modalities, lack of prior knowledge of sample composition and lack of knowledge regarding correlation between modalities for a given sample. In addition, the multivariate structure of chemical images is often overlooked when fusion is carried out. We address these challenges by proposing a framework for multivariate chemical image fusion of vibrational spectroscopic imaging modalities, demonstrating the approach for image registration, fusion and resolution enhancement of chemical images obtained with IR and Raman microscopy.

  18. An entanglement-enhanced microscope.

    PubMed

    Ono, Takafumi; Okamoto, Ryo; Takeuchi, Shigeki

    2013-01-01

    Among the applications of optical phase measurement, the differential interference contrast microscope is widely used for the evaluation of opaque materials or biological tissues. However, the signal-to-noise ratio for a given light intensity is limited by the standard quantum limit, which is critical for measurements where the probe light intensity is limited to avoid damaging the sample. The standard quantum limit can only be beaten by using N quantum correlated particles, with an improvement factor of √N. Here we report the demonstration of an entanglement-enhanced microscope, which is a confocal-type differential interference contrast microscope where an entangled photon pair (N=2) source is used for illumination. An image of a Q shape carved in relief on the glass surface is obtained with better visibility than with a classical light source. The signal-to-noise ratio is 1.35±0.12 times better than that limited by the standard quantum limit.

  19. Ergonomic microscope comfort and control.

    PubMed

    Thomas, Elizabeth Anne

    2011-03-01

    Microscope use in the inspection phase of computer chip manufacturing is a major cause of worker discomfort and injury. A two-phase ergonomics project to reduce employee fatigue and discomfort was planned, implemented, and evaluated in a microscope user environment within a high-technology manufacturing environment. Total Quality Management methodology and tools were employed by a multidisciplinary team led by an occupational health nurse practitioner to accomplish the project goals. A multifaceted approach including equipment changes, administrative changes, and focused training for behavior changes achieved the desired reduction in reports of fatigue and discomfort among microscope users. Occupational health nurses are ideal candidates to lead teams to accomplish meaningful health and safety goals consistent with corporate quality initiatives and strategic objectives. Copyright 2011, SLACK Incorporated.

  20. Microscopic characterization of peptide nanostructures.

    PubMed

    Mammadov, Rashad; Tekinay, Ayse B; Dana, Aykutlu; Guler, Mustafa O

    2012-02-01

    Peptide-based nanomaterials have been utilized for various applications from regenerative medicine to electronics since they provide several advantages including easy synthesis methods, numerous routes for functionalization and biomimicry of secondary structures of proteins which leads to design of self-assembling peptide molecules to form nanostructures. Microscopic characterization at nanoscale is critical to understand processes directing peptide molecules to self-assemble and identify structure-function relationship of the nanostructures. Here, fundamental studies in microscopic characterization of peptide nanostructures are discussed to provide insights in widely used microscopy tools. In this review, we will encompass characterization studies of peptide nanostructures with modern microscopes, such as TEM, SEM, AFM, and advanced optical microscopy techniques. We will also mention specimen preparation methods and describe interpretation of the images.

  1. Scanning thermal-conductivity microscope

    NASA Astrophysics Data System (ADS)

    Sarid, Dror; McCarthy, Brendan; Grover, Ranjan

    2006-02-01

    This article describes a novel implementation of an atomic force microscope that can map thermal-conductivity features across a sample with a high spatial resolution. The microscope employs a single-sided, metal-coated cantilever, which acts as a bimetallic strip together with a heating laser whose beam is focused on the cantilever's free end, on the opposite side of its tip. Subtracting the topography obtained by the unheated and heated cantilevers yields a map of thermal conductivity across the surface of a sample. The article presents (a) the theory of operation of the microscope and (b) the experimental results obtained on a silicon sample with oxide features, showing good agreement between the two.

  2. Microscope and method of use

    SciTech Connect

    Bongianni, W.L.

    1981-08-18

    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.

  3. 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.

  4. 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.

  5. Macroscopic-microscopic mass models

    SciTech Connect

    Nix, J.R.; Moller, P.

    1995-07-01

    We discuss recent developments in macroscopic-microscopic mass models, including the 1992 finite-range droplet model, the 1992 extended- Thomas-Fermi Strutinsky-integral model, and the 1994 Thomas-Fermi model, with particular emphasis on how well they extrapolate to new regions of nuclei. We also address what recent developments in macroscopic-microscopic mass models are teaching us about such physically relevant issues as the nuclear curvature energy, a new congruence energy arising from a greater-than-average overlap of neutron and proton wave functions, the nuclear incompressibility coefficient, and the coulomb redistribution energy arising from a central density depression. We conclude with a brief discussion of the recently discovered rock of metastable superheavy nuclei near {sup 272}110 that had been correctly predicted by macroscopic-microscopic models, along with a possible new tack for reaching an island near {sup 290}110 beyond our present horizon.

  6. Mosaic of Commemorative Microscope Substrate

    NASA Technical Reports Server (NTRS)

    2008-01-01

    Written by electron beam lithography in the Microdevices Laboratory of NASA's Jet Propulsion Laboratory, this Optical Microscope substrate helps the Phoenix Mars Mission science team learn how to assemble individual microscope images into a mosaic by aligning rows of text.

    Each line is about 0.1 millimeter tall, the average thickness of a human hair. Except for the Mogensen twins, the names are of babies born and team members lost during the original development of MECA (the Microscopy, Electrochemistry and Conductivity Analyzer) for the canceled 2001 Mars lander mission. The plaque also acknowledges the MECA 2001 principal investigator, now retired.

    This image was taken by the MECA Optical Microscope on Sol 111, or the 111th day of the Phoenix mission (Sept. 16, 2008).

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by JPL, Pasadena, Calif. Spacecraft development was by Lockheed Martin Space Systems, Denver.

  7. Mosaic of Commemorative Microscope Substrate

    NASA Technical Reports Server (NTRS)

    2008-01-01

    Written by electron beam lithography in the Microdevices Laboratory of NASA's Jet Propulsion Laboratory, this Optical Microscope substrate helps the Phoenix Mars Mission science team learn how to assemble individual microscope images into a mosaic by aligning rows of text.

    Each line is about 0.1 millimeter tall, the average thickness of a human hair. Except for the Mogensen twins, the names are of babies born and team members lost during the original development of MECA (the Microscopy, Electrochemistry and Conductivity Analyzer) for the canceled 2001 Mars lander mission. The plaque also acknowledges the MECA 2001 principal investigator, now retired.

    This image was taken by the MECA Optical Microscope on Sol 111, or the 111th day of the Phoenix mission (Sept. 16, 2008).

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by JPL, Pasadena, Calif. Spacecraft development was by Lockheed Martin Space Systems, Denver.

  8. Sample holder support for microscopes

    NASA Technical Reports Server (NTRS)

    Berry, Anthony (Inventor); Nerren, Billy H. (Inventor)

    1991-01-01

    A sample filter holder is disclosed for use with a microscope for holding the filter in a planar condition on the stage of the microscope so that automatic focusing of the microscope can be performed on particle samples dispersed on the filter. The holder includes a base having a well that communicates with an inlet port which is connected to a suction pump. A screen assembly is positioned within the well. The screen assembly includes a disk having a screen positioned on its top surface and secured to the disk at the peripheral edge of the screen. Small bores allow the outer surface of the screen to communicate with the well. The filter is placed on the screen and is held in a flat disposition by the suction forces.

  9. 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.

  10. Microscopic Materials on a Magnet

    NASA Technical Reports Server (NTRS)

    2008-01-01

    These images show a comparison of the weak magnet OM7 from the Optical Microscope on NASA's Phoenix Mars Lander before (left) and after (right) soil deposition.

    The microscope took the left image during Phoenix's Sol 15 (June 10, 2008) and the right image during Sol 21 (Jun 16, 2008).

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  11. Advanced Microscopic Integrated Thermocouple Arrays

    NASA Technical Reports Server (NTRS)

    Pettigrew, Penny J.

    1999-01-01

    The purpose of this research is to develop and refine a technique for making microscopic thermocouple arrays for use in measuring the temperature gradient across a solid-liquid interface during the solidification process. Current thermocouple technology does not allow for real-time measurements across the interface due to the prohibitive size of available thermocouples. Microscopic thermocouple arrays will offer a much greater accuracy and resolution of temperature measurements across the solid-liquid interface which will lead to a better characterization of the solidification process and interface reaction which affect the properties of the resulting material.

  12. Microscopic Materials on a Magnet

    NASA Technical Reports Server (NTRS)

    2008-01-01

    These images show a comparison of the weak magnet OM7 from the Optical Microscope on NASA's Phoenix Mars Lander before (left) and after (right) soil deposition.

    The microscope took the left image during Phoenix's Sol 15 (June 10, 2008) and the right image during Sol 21 (Jun 16, 2008).

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  13. Long working distance interference microscope

    DOEpatents

    Sinclair, Michael B.; DeBoer, Maarten P.; Smith, Norman F.

    2004-04-13

    Disclosed is a long working distance interference microscope suitable for three-dimensional imaging and metrology of MEMS devices and test structures on a standard microelectronics probe station. The long working distance of 10-30 mm allows standard probes or probe cards to be used. This enables nanometer-scale 3-D height profiles of MEMS test structures to be acquired across an entire wafer. A well-matched pair of reference/sample objectives is not required, significantly reducing the cost of this microscope, as compared to a Linnik microinterferometer.

  14. Actinide Thermodynamics at Elevated Temperatures

    SciTech Connect

    Friese, Judah I.; Rao, Linfeng; Xia, Yuanxian; Bachelor, Paula P.; Tian, Guoxin

    2007-11-16

    The postclosure chemical environment in the proposed Yucca Mountain repository is expected to experience elevated temperatures. Predicting migration of actinides is possible if sufficient, reliable thermodynamic data on hydrolysis and complexation are available for these temperatures. Data are scarce and scattered for 25 degrees C, and nonexistent for elevated temperatures. This collaborative project between LBNL and PNNL collects thermodynamic data at elevated temperatures on actinide complexes with inorganic ligands that may be present in Yucca Mountain. The ligands include hydroxide, fluoride, sulfate, phosphate and carbonate. Thermodynamic parameters of complexation, including stability constants, enthalpy, entropy and heat capacity of complexation, are measured with a variety of techniques including solvent extraction, potentiometry, spectrophotometry and calorimetry

  15. Computing Thermodynamic And Transport Properties

    NASA Technical Reports Server (NTRS)

    Mcbride, B.; Gordon, Sanford

    1993-01-01

    CET89 calculates compositions in chemical equilibrium and properties of mixtures of any chemical system for which thermodynamic data available. Provides following options: obtains chemical-equilibrium compositions and corresponding thermodynamic mixture properties for assigned thermodynamic states; calculates dilute-gas transport properties of complex chemical mixtures; obtains Chapman-Jouguet detonation properties for gaseous mixtures; calculates properties of incident and reflected shocks in terms of assigned velocities; and calculates theoretical performance of rocket for both equilibrium and frozen compositions during expansion. Rocket performance based on optional models of finite or infinite area combustor.

  16. Stochastic thermodynamics of information processing

    NASA Astrophysics Data System (ADS)

    Cardoso Barato, Andre

    2015-03-01

    We consider two recent advancements on theoretical aspects of thermodynamics of information processing. First we show that the theory of stochastic thermodynamics can be generalized to include information reservoirs. These reservoirs can be seen as a sequence of bits which has its Shannon entropy changed due to the interaction with the system. Second we discuss bipartite systems, which provide a convenient description of Maxwell's demon. Analyzing a special class of bipartite systems we show that they can be used to study cellular information processing, allowing for the definition of an entropic rate that quantifies how much a cell learns about a fluctuating external environment and that is bounded by the thermodynamic entropy production.

  17. Thermodynamic Metrics and Optimal Paths

    SciTech Connect

    Sivak, David; Crooks, Gavin

    2012-05-08

    A fundamental problem in modern thermodynamics is how a molecular-scale machine performs useful work, while operating away from thermal equilibrium without excessive dissipation. To this end, we derive a friction tensor that induces a Riemannian manifold on the space of thermodynamic states. Within the linear-response regime, this metric structure controls the dissipation of finite-time transformations, and bestows optimal protocols with many useful properties. We discuss the connection to the existing thermodynamic length formalism, and demonstrate the utility of this metric by solving for optimal control parameter protocols in a simple nonequilibrium model.

  18. 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.

  19. Computing Thermodynamic And Transport Properties

    NASA Technical Reports Server (NTRS)

    Mcbride, B.; Gordon, Sanford

    1993-01-01

    CET89 calculates compositions in chemical equilibrium and properties of mixtures of any chemical system for which thermodynamic data available. Provides following options: obtains chemical-equilibrium compositions and corresponding thermodynamic mixture properties for assigned thermodynamic states; calculates dilute-gas transport properties of complex chemical mixtures; obtains Chapman-Jouguet detonation properties for gaseous mixtures; calculates properties of incident and reflected shocks in terms of assigned velocities; and calculates theoretical performance of rocket for both equilibrium and frozen compositions during expansion. Rocket performance based on optional models of finite or infinite area combustor.

  20. 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

  1. 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.

  2. Rotating black hole thermodynamics with a particle probe

    SciTech Connect

    Gwak, Bogeun; Lee, Bum-Hoon

    2011-10-15

    The thermodynamics of Myers-Perry black holes in general dimensions are studied using a particle probe. When undergoing particle absorption, the changes of the entropy and irreducible mass are shown to be dependent on the particle radial momentum. The black hole thermodynamic behaviors are dependent on dimensionality for specific rotations. For a 4-dimensional Kerr black hole, its black hole properties are maintained for any particle absorption. 5-dimensional black holes can avoid a naked ring singularity by absorbing a particle in specific momenta ranges. Black holes over 6 dimensions become ultraspinning black holes through a specific form of particle absorption. The microscopical changes are interpreted in limited cases of Myers-Perry black holes using Kerr/CFT correspondence. We systematically describe the black hole properties changed by particle absorption in all dimensions.

  3. Thermodynamic phase transitions in a frustrated magnetic metamaterial.

    PubMed

    Anghinolfi, L; Luetkens, H; Perron, J; Flokstra, M G; Sendetskyi, O; Suter, A; Prokscha, T; Derlet, P M; Lee, S L; Heyderman, L J

    2015-09-21

    Materials with interacting magnetic degrees of freedom display a rich variety of magnetic behaviour that can lead to novel collective equilibrium and out-of-equilibrium phenomena. In equilibrium, thermodynamic phases appear with the associated phase transitions providing a characteristic signature of the underlying collective behaviour. Here we create a thermally active artificial kagome spin ice that is made up of a large array of dipolar interacting nanomagnets and undergoes phase transitions predicted by microscopic theory. We use low energy muon spectroscopy to probe the dynamic behaviour of the interacting nanomagnets and observe peaks in the muon relaxation rate that can be identified with the critical temperatures of the predicted phase transitions. This provides experimental evidence that a frustrated magnetic metamaterial can be engineered to admit thermodynamic phases.

  4. Fisher information and the thermodynamics of scale-invariant systems

    NASA Astrophysics Data System (ADS)

    Hernando, A.; Vesperinas, C.; Plastino, A.

    2010-02-01

    We present a thermodynamic formulation for scale-invariant systems based on the minimization with constraints of the Fisher information measure. In such a way a clear analogy between these systems’ thermal properties and those of gases and fluids is seen to emerge in a natural fashion. We focus our attention on the non-interacting scenario, speaking thus of scale-free ideal gases (SFIGs) and present some empirical evidences regarding such disparate systems as electoral results, city populations and total citations in Physics journals, that seem to indicate that SFIGs do exist. We also illustrate the way in which Zipf’s law can be understood in a thermodynamical context as the surface of a finite system. Finally, we derive an equivalent microscopic description of our systems which totally agrees with previous numerical simulations found in the literature.

  5. Third law of thermodynamics for the dissipative cyclotron motion

    SciTech Connect

    Kumar, Jishad

    2013-11-15

    We derive the heat capacity and the entropy of an exactly solvable model of a charged particle in the combined presence of a uniform homogeneous magnetic field and a finite dissipative quantum heat bath consisting of non interacting harmonic oscillators. The quantities are calculated from the reduced partition function of the damped system which is calculated using the imaginary time functional integral method within the framework of the well known microscopic system-plus-bath model. Unlike the typical choice of an ohmic spectral density of the bath oscillators, we consider the quantum heat bath is having a spectral density corresponding to a thermal harmonic noise. Subsequently we analyse the specific heat and entropy at low and high temperatures. The specific heat and the entropy obtained satisfy the third law of thermodynamics. The heat capacity vanishes as the temperature approaches its absolute zero value, as predicted by the third law of thermodynamics, and satisfies the classical equipartition theorem at high temperatures.

  6. Structural fluctuation of proteins induced by thermodynamic perturbation

    SciTech Connect

    Hirata, Fumio; Akasaka, Kazuyuki

    2015-01-28

    A theory to describe structural fluctuations of protein induced by thermodynamic perturbations, pressure, temperature, and denaturant, is proposed. The theory is formulated based on the three methods in the statistical mechanics: the generalized Langevin theory, the linear response theory, and the three dimensional interaction site model (3D-RISM) theory. The theory clarifies how the change in thermodynamic conditions, or a macroscopic perturbation, induces the conformational fluctuation, which is a microscopic property. The theoretical results are applied, on the conceptual basis, to explain the experimental finding by Akasaka et al., concerning the NMR experiment which states that the conformational change induced by pressure corresponds to structural fluctuations occurring in the ambient condition. A method to evaluate the structural fluctuation induced by pressure is also suggested by means of the 3D-RISM and the site-site Kirkwood-Buff theories.

  7. Thermodynamic product formula for a Taub–NUT black hole

    SciTech Connect

    Pradhan, P.

    2016-01-15

    We derive various important thermodynamic relations of the inner and outer horizons in the background of the Taub–NUT (Newman–Unti–Tamburino) black hole in four-dimensional Lorentzian geometry. We compare these properties with the properties of the Reissner–Nordström black hole. We compute the area product, area sum, area subtraction, and area division of black hole horizons. We show that they all are not universal quantities. Based on these relations, we compute the area bound of all horizons. From the area bound, we derive an entropy bound and an irreducible mass bound for both horizons. We further study the stability of such black holes by computing the specific heat for both horizons. It is shown that due to the negative specific heat, the black hole is thermodynamically unstable. All these calculations might be helpful in understanding the nature of the black hole entropy (both interior and exterior) at the microscopic level.

  8. 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.

  9. Geometric microcanonical thermodynamics for systems with first integrals.

    PubMed

    Franzosi, Roberto

    2012-05-01

    In the general case of a many-body Hamiltonian system described by an autonomous Hamiltonian H and with K ≥ 0 independent conserved quantities, we derive the microcanonical thermodynamics. Using simple approach, based on differential geometry, we derive the microcanonical entropy and the derivatives of the entropy with respect to the conserved quantities. In such a way, we show that all the thermodynamical quantities, such as the temperature, the chemical potential, and the specific heat, are measured as a microcanonical average of the appropriate microscopic dynamical functions that we have explicitly derived. Our method applies also in the case of nonseparable Hamiltonians, where the usual definition of kinetic temperature, derived by the virial theorem, does not apply.

  10. Imaging spectroscopic analysis at the Advanced Light Source

    SciTech Connect

    MacDowell, A. A.; Warwick, T.; Anders, S.; Lamble, G.M.; Martin, M.C.; McKinney, W.R.; Padmore, H.A.

    1999-05-12

    One of the major advances at the high brightness third generation synchrotrons is the dramatic improvement of imaging capability. There is a large multi-disciplinary effort underway at the ALS to develop imaging X-ray, UV and Infra-red spectroscopic analysis on a spatial scale from. a few microns to 10nm. These developments make use of light that varies in energy from 6meV to 15KeV. Imaging and spectroscopy are finding applications in surface science, bulk materials analysis, semiconductor structures, particulate contaminants, magnetic thin films, biology and environmental science. This article is an overview and status report from the developers of some of these techniques at the ALS. The following table lists all the currently available microscopes at the. ALS. This article will describe some of the microscopes and some of the early applications.

  11. [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.

  12. Thermodynamical string fragmentation

    NASA Astrophysics Data System (ADS)

    Fischer, Nadine; Sjöstrand, Torbjörn

    2017-01-01

    The observation of heavy-ion-like behaviour in pp collisions at the LHC suggests that more physics mechanisms are at play than traditionally assumed. The introduction e.g. of quark-gluon plasma or colour rope formation can describe several of the observations, but as of yet there is no established paradigm. In this article we study a few possible modifications to the Pythia event generator, which describes a wealth of data but fails for a number of recent observations. Firstly, we present a new model for generating the transverse momentum of hadrons during the string fragmentation process, inspired by thermodynamics, where heavier hadrons naturally are suppressed in rate but obtain a higher average transverse momentum. Secondly, close-packing of strings is taken into account by making the temperature or string tension environment-dependent. Thirdly, a simple model for hadron rescattering is added. The effect of these modifications is studied, individually and taken together, and compared with data mainly from the LHC. While some improvements can be noted, it turns out to be nontrivial to obtain effects as big as required, and further work is called for.

  13. A thermodynamic self-consistent theory of asymmetric hard-core Yukawa mixtures

    NASA Astrophysics Data System (ADS)

    Pellicane, Giuseppe; Caccamo, Carlo

    2016-10-01

    We perform structural and thermodynamic calculations in the framework of the modified hypernetted chain (MHNC) integral equation closure to the Ornstein-Zernike equation for binary mixtures of size-different particles interacting with hard-core Yukawa pair potentials. We use the Percus-Yevick (PY) bridge functions of a binary mixture of hard-sphere (HSM) particles. The hard-sphere diameters of the PY bridge functions of the HSM system are adjusted so to achieve thermodynamic consistency between the virial and compressibility equations of state. We show the benefit of thermodynamic consistency by comparing the MHNC results with the available computer simulation data reported in the literature, and we demonstrate that the self-consistent thermodynamic theory provides a better reproduction of the simulation data over other microscopic theories.

  14. Switch on Micro*scope!

    ERIC Educational Resources Information Center

    Roland, Sarah; Bahr, Michele; Olendzenski, Lorraine; Patterson, David J.

    2005-01-01

    Scientists at the Marine Biological Laboratory in Woods Hole, Massachusetts, have created micro*scope, a free, searchable knowledge environment for exploring the microbial world. Microbiology can easily be incorporated into the curriculum, because microbial communities are easy to access. Organisms grow quickly, making certain arrays of…

  15. Curriculum Guidelines for Microscopic Anatomy.

    ERIC Educational Resources Information Center

    Journal of Dental Education, 1993

    1993-01-01

    The American Association of Dental Schools' guidelines for curricula in microscopic anatomy offer an overview of the histology curriculum, note primary educational goals, outline specific content for general and oral histology, suggest prerequisites, and make recommendations for sequencing. Appropriate faculty and facilities are also suggested.…

  16. High-resolution electron microscope

    NASA Technical Reports Server (NTRS)

    Nathan, R.

    1977-01-01

    Employing scanning transmission electron microscope as interferometer, relative phases of diffraction maximums can be determined by analysis of dark field images. Synthetic aperture technique and Fourier-transform computer processing of amplitude and phase information provide high resolution images at approximately one angstrom.

  17. Nature Study with the Microscope.

    ERIC Educational Resources Information Center

    Sollberger, Dwight E.

    1991-01-01

    Identifies specific instruction difficulties, potential problems, solutions, and activities for successful use of microscopes in the classroom. Procedures are outlined for guiding students in creating their own slides with monocotyledon and dicotyledon stems, fern spores, stomata, lichens, and red onions. (MCO)

  18. Chasing Meteors With a Microscope.

    ERIC Educational Resources Information Center

    Jones, Richard C.

    1993-01-01

    Describes types of meteors and micrometeorites that enter the Earth's atmosphere. Presents an activity where students collect micrometeorites with a strip of tape in an undisturbed outdoor area. After 24 hours, they examine the tape by sandwiching it between 2 glass slides and view through a microscope at 100X. (PR)

  19. Switch on Micro*scope!

    ERIC Educational Resources Information Center

    Roland, Sarah; Bahr, Michele; Olendzenski, Lorraine; Patterson, David J.

    2005-01-01

    Scientists at the Marine Biological Laboratory in Woods Hole, Massachusetts, have created micro*scope, a free, searchable knowledge environment for exploring the microbial world. Microbiology can easily be incorporated into the curriculum, because microbial communities are easy to access. Organisms grow quickly, making certain arrays of…

  20. Nature Study with the Microscope.

    ERIC Educational Resources Information Center

    Sollberger, Dwight E.

    1991-01-01

    Identifies specific instruction difficulties, potential problems, solutions, and activities for successful use of microscopes in the classroom. Procedures are outlined for guiding students in creating their own slides with monocotyledon and dicotyledon stems, fern spores, stomata, lichens, and red onions. (MCO)

  1. Chasing Meteors With a Microscope.

    ERIC Educational Resources Information Center

    Jones, Richard C.

    1993-01-01

    Describes types of meteors and micrometeorites that enter the Earth's atmosphere. Presents an activity where students collect micrometeorites with a strip of tape in an undisturbed outdoor area. After 24 hours, they examine the tape by sandwiching it between 2 glass slides and view through a microscope at 100X. (PR)

  2. The Biggest Microscopic Image Ever

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This is a mosaic of four individual frames taken by the microscopic imager that have been very carefully stitched together to reveal the entire 5-centimeter-diameter (almost 2-inch) hole left on the rock dubbed 'Humphrey.' The holes were created by the Mars Exploration Rover Spirit's rock abrasion tool. The mosaic, created on March 7, 2004, is the first of its kind of an abraded surface on Mars, and gave scientists their first ever microscopic imager view of the entire drilled area. While it is easy for the panoramic camera and the navigation cameras to fit an area this size into their field of view, the microscopic imager can only capture a portion of the ground area with each image.

    Scientists are interested in many of the small features on 'Humphrey' uncovered by the rock abrasion tool and made visible by the microscopic imager. The sinuous veins within the rock could be evidence that water was trickling through the material while it was deep underground, whereas the dark 'age spots' in the center of the hole may be crystals of the mineral olivine.

  3. Scanning tunneling microscope nanoetching method

    DOEpatents

    Li, Yun-Zhong; Reifenberger, Ronald G.; Andres, Ronald P.

    1990-01-01

    A method is described for forming uniform nanometer sized depressions on the surface of a conducting substrate. A tunneling tip is used to apply tunneling current density sufficient to vaporize a localized area of the substrate surface. The resulting depressions or craters in the substrate surface can be formed in information encoding patterns readable with a scanning tunneling microscope.

  4. Curriculum Guidelines for Microscopic Anatomy.

    ERIC Educational Resources Information Center

    Journal of Dental Education, 1993

    1993-01-01

    The American Association of Dental Schools' guidelines for curricula in microscopic anatomy offer an overview of the histology curriculum, note primary educational goals, outline specific content for general and oral histology, suggest prerequisites, and make recommendations for sequencing. Appropriate faculty and facilities are also suggested.…

  5. 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.

  6. The Biggest Microscopic Image Ever

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This is a mosaic of four individual frames taken by the microscopic imager that have been very carefully stitched together to reveal the entire 5-centimeter-diameter (almost 2-inch) hole left on the rock dubbed 'Humphrey.' The holes were created by the Mars Exploration Rover Spirit's rock abrasion tool. The mosaic, created on March 7, 2004, is the first of its kind of an abraded surface on Mars, and gave scientists their first ever microscopic imager view of the entire drilled area. While it is easy for the panoramic camera and the navigation cameras to fit an area this size into their field of view, the microscopic imager can only capture a portion of the ground area with each image.

    Scientists are interested in many of the small features on 'Humphrey' uncovered by the rock abrasion tool and made visible by the microscopic imager. The sinuous veins within the rock could be evidence that water was trickling through the material while it was deep underground, whereas the dark 'age spots' in the center of the hole may be crystals of the mineral olivine.

  7. Program calculation of thermodynamic properties

    NASA Astrophysics Data System (ADS)

    Gill, Walter; Filho, Fernando Fachini; Ribeirodeoliveira, Ronaldo

    1986-12-01

    The determination of the thermodynamic properties are examined through the basic equations such as: state equation (Beattie-Bridgeman Form), saturation pressure equation, specific heat constant pressure or constant volume equation, and specific volume or density of liquid equation.

  8. 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.

  9. Thermodynamic black di-rings

    SciTech Connect

    Iguchi, Hideo; Mishima, Takashi

    2010-10-15

    Previously the five dimensional S{sup 1}-rotating black rings have been superposed in a concentric way by some solitonic methods, and regular systems of two S{sup 1}-rotating black rings were constructed by the authors and then Evslin and Krishnan (we called these solutions 'black di-rings'). In this place we show some characteristics of the solutions of five dimensional black di-rings, especially in thermodynamic equilibrium. After the summary of the di-ring expressions and their physical quantities, first we comment on the equivalence of the two different solution sets of the black di-rings. Then the existence of thermodynamic black di-rings is shown, in which both isothermality and isorotation between the inner black ring and the outer black ring are realized. We also give detailed analysis of peculiar properties of the thermodynamic black di-ring including discussion about a certain kind of thermodynamic stability (instability) of the system.

  10. Thermodynamic limit for isokinetic thermostats

    NASA Astrophysics Data System (ADS)

    Gallavotti, G.; Presutti, E.

    2010-05-01

    Thermostat models in space dimension d =1,2,3 for nonequilibrium statistical mechanics are considered and it is shown that, in the thermodynamic limit, the motions of frictionless thermostats and isokinetic thermostats coincide.

  11. Review of selenium thermodynamic data

    NASA Astrophysics Data System (ADS)

    Cowan, C. E.

    1988-02-01

    This report assesses the accuracy and completeness of available thermodynamic data on selenium. A review of experimental methods from published literature on selenium thermodynamic data focused on chemical reactions responsible for the formation of both aqueous complexes and solid phases of selenate, selenite, and selenide. The reviewer selected best data values, based on the methods used for estimating thermodynamic data. After inclusion of these values into the MINTEQ model, a validation study evaluated model performance for selenite and selenide solid phases. Lack of selenate data precluded model validation for this compound. The review furnished data on 22 aqueous complexes of selenite, 15 of selenide, and 17 of selenate, as well as 21 solid phases of selenite, 20 of selenide and 8 of selenate. These data proved inadequate to represent the formation of species in the solid phase. The validation study gave inconclusive predictions of selenite and selenide solubility and could not be used to assess the accuracy or completeness of the thermodynamic data.

  12. 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

  13. Thermodynamics of Asymptotically Conical Geometries.

    PubMed

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

    2015-06-12

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

  14. Thermodynamic and relativistic uncertainty relations

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  15. Thermodynamic geometry, phase transitions, and the Widom line.

    PubMed

    Ruppeiner, G; Sahay, A; Sarkar, T; Sengupta, G

    2012-11-01

    A microscopic characterization, based on the thermodynamic curvature R, is proposed for first-order liquid-gas phase transitions. Near the critical point, where R is proportional to the correlation volume ξ(3), we propose that R takes the same value in the coexisting phases. This proposal allows a determination of the liquid-gas coexistence curve with no use of the problematic Maxwell equal area construction. Furthermore, |R| ~ ξ(3) allows a direct determination of the Widom line in the supercritical regime. We illustrate with input from the van der Waals model and the National Institute of Standards and Technology Chemistry WebBook.

  16. Spectroscopic studies of cryogenic fluids: Benzene in propane

    NASA Astrophysics Data System (ADS)

    Nowak, R.; Bernstein, E. R.

    1987-03-01

    Energy shifts and bandwidths for the 1B2u↔1A1g optical absorption and emission transitions of benzene dissolved in propane are presented as a function of pressure, temperature, and density. Both absorption and emission spectra exhibit shifts to lower energy as a function of density, whereas no shifts are observed if density is kept constant and temperature and pressure are varied simultaneously. Density is thus the fundamental microscopic parameter for energy shifts of optical transitions. The emission half-width is a linear function of both temperature and pressure but the absorption half-width is dependent only upon pressure. These results are interpreted qualitatively in terms of changes occurring in the intermolecular potentials of the ground and excited states. Both changes in shape of and separation between the ground and excited state potentials are considered as a function of density. Classical dielectric (Onsager-Böttcher), microscopic dielectric (Wertheim) and microscopic quantum statistical mechanical (Schweizer-Chandler) theories of solvent effects on solute electronic spectra are compared with the experimental results. Calculations suggest limited applicability of dielectric theories but good agreement between experiment and microscopic theory. The results demonstrate the usefulness of cryogenic solutions for high pressure, low temperature spectroscopic studies of liquids.

  17. Simulating Metabolism with Statistical Thermodynamics

    SciTech Connect

    Cannon, William R.

    2014-08-04

    Kinetic probabilities of state are usually based on empirical measurements, while thermodynamic state probabilities are based on the assumption that chemical species are distributed to according to a multinomial Boltzmann distribution. While the use of kinetic simulations is desirable, obtaining all the mass action rate constants necessary to carry out kinetic simulations is an overwhelming challenge. Here, the kinetic probability of a state is compared in depth to the thermodynamic probability of a state for sets of coupled reactions. The entropic and energetic contributions to thermodynamic stable states are described and compared to entropic and energetic contributions of kinetic steady states. It is shown that many kinetic steady states are possible for a system of coupled reactions depending on the relative values of the mass action rate constants, but only one of these corresponds to a thermodynamically stable state. Furthermore, the thermodynamic stable state corresponds to a minimum free energy state. The use of thermodynamic simulations of state to model metabolic processes is attractive, since metabolite levels and energy requirements of pathways can be evaluated using only standard free energies of formation as parameters in the probability distribution. In chemical physics, the assumption of a Boltzmann distribution is the basis of transition state theory for modeling transitory species. Application to stable species, such as those found in metabolic processes, is a less severe assumption that would enable the use of simulations of state.

  18. General computational spectroscopic framework applied to Z-pinch dynamic hohlraum K-shell argon spectra

    SciTech Connect

    Adams, M L; Sinars, D B; Scott, H A

    2005-01-10

    We describe a general computational spectroscopic framework for interpreting observed spectra. The framework compares synthetic spectra with measured spectra, then optimizes the agreement using the Dakota toolkit to minimize a merit function that incorporates established spectroscopic techniques. We generate synthetic spectra using the self-consistent nonlocal thermodynamic equilibrium atomic kinetics and radiative transfer code Cretin, relativistic atomic structure and cross section data from Hullac, and detailed spectral line shapes from Totalb. We test the capabilities of both our synthetic spectra model and general spectroscopic framework by analyzing a K-shell argon spectrum from a Z-pinch dynamic hohlraum inertial confinement fusion capsule implosion experiment. The framework obtains close agreement between an experimental spectrum measured by a time integrated focusing spectrometer and the optimal synthetic spectrum. The synthetic spectra show that considering the spatial extent of the capsule and including the effects of optically thick resonance lines significantly affects the interpretation of measured spectra.

  19. Spectroscopic fingerprint of phase-incoherent superconductivity in the cuprate pseudogap state [corrected].

    PubMed

    Lee, Jhinhwan; Fujita, K; Schmidt, A R; Kim, Chung Koo; Eisaki, H; Uchida, S; Davis, J C

    2009-08-28

    A possible explanation for the existence of the cuprate "pseudogap" state is that it is a d-wave superconductor without quantum phase rigidity. Transport and thermodynamic studies provide compelling evidence that supports this proposal, but few spectroscopic explorations of it have been made. One spectroscopic signature of d-wave superconductivity is the particle-hole symmetric "octet" of dispersive Bogoliubov quasiparticle interference modulations. Here we report on this octet's evolution from low temperatures to well into the underdoped pseudogap regime. No pronounced changes occur in the octet phenomenology at the superconductor's critical temperature Tc, and it survives up to at least temperature T approximately 1.5 Tc. In this pseudogap regime, we observe the detailed phenomenology that was theoretically predicted for quasiparticle interference in a phase-incoherent d-wave superconductor. Thus, our results not only provide spectroscopic evidence to confirm and extend the transport and thermodynamics studies, but they also open the way for spectroscopic explorations of phase fluctuation rates, their effects on the Fermi arc, and the fundamental source of the phase fluctuations that suppress superconductivity in underdoped cuprates.

  20. Thermodynamics of firms' growth

    PubMed Central

    Zambrano, Eduardo; Hernando, Alberto; Hernando, Ricardo; Plastino, Angelo

    2015-01-01

    The distribution of firms' growth and firms' sizes is a topic under intense scrutiny. In this paper, we show that a thermodynamic model based on the maximum entropy principle, with dynamical prior information, can be constructed that adequately describes the dynamics and distribution of firms' growth. Our theoretical framework is tested against a comprehensive database of Spanish firms, which covers, to a very large extent, Spain's economic activity, with a total of 1 155 142 firms evolving along a full decade. We show that the empirical exponent of Pareto's law, a rule often observed in the rank distribution of large-size firms, is explained by the capacity of economic system for creating/destroying firms, and that can be used to measure the health of a capitalist-based economy. Indeed, our model predicts that when the exponent is larger than 1, creation of firms is favoured; when it is smaller than 1, destruction of firms is favoured instead; and when it equals 1 (matching Zipf's law), the system is in a full macroeconomic equilibrium, entailing ‘free’ creation and/or destruction of firms. For medium and smaller firm sizes, the dynamical regime changes, the whole distribution can no longer be fitted to a single simple analytical form and numerical prediction is required. Our model constitutes the basis for a full predictive framework regarding the economic evolution of an ensemble of firms. Such a structure can be potentially used to develop simulations and test hypothetical scenarios, such as economic crisis or the response to specific policy measures. PMID:26510828

  1. Microscopic meaning of grand potential resulting from combinatorial approach to a general system of particles

    NASA Astrophysics Data System (ADS)

    Fronczak, Agata

    2012-10-01

    We present an alternative approach to the problem of interacting fluids, which we believe may provide important insights into microscopic mechanisms that lead to the occurrence of phase transitions. The approach exploits enumerative properties and combinatorial meaning of Bell polynomials. We derive the exact formula for the probability of a general system of N particles at temperature T to consist of k weakly coupled clusters of various sizes. We also show that the grand potential of the system may be considered the exponential generating function for the number of internal states (thermodynamic probability) of these clusters. The microscopic interpretation of the grand potential is surprising, especially if one recalls that until now only the thermodynamic meaning of this free energy was known. We also derive an approximated expression for the density of states.

  2. Statistical thermodynamics of charge-stabilized colloids

    NASA Astrophysics Data System (ADS)

    Torres Valderrama, A.

    2008-06-01

    This thesis is a theoretical study of equilibrium statistical thermodynamic properties of colloidal systems in which electrostatic interactions play a dominant role, namely, charge-stabilized colloidal suspensions. Such systems are fluids consisting of a mixture of a large number of mesoscopic particles and microscopic ions which interact via the Coulomb force, suspended in a molecular fluid. Quantum statistical mechanics is essential to fully understand the properties and stability of such systems. A less fundamental but for many purposes, sufficient description, is provided by classical statistical mechanics. In such approximation the system is considered as composed of a great number of charged classical particles with additional hard-core repulsions. The kinetic energy or momentum integrals become independent Gaussians, and hence their contribution to the free energy can be trivially evaluated. The contribution of the potential energy to the free energy on the other hand, depends upon the configuration of all the particles and becomes highly non-trivial due to the long-range character of the Coulomb force and the extremely different length scales involved in the problem. Using the microscopic model described above, we focus on the calculation of equilibrium thermodynamic properties (response functions), correlations (structure factors), and mechanical properties (forces and stresses), which can be measured in experiments and computed by Monte Carlo simulations. This thesis is divided into three parts. In part I, comprising chapters 2 and 3, we focus on finite-thickness effects in colloidal platelets and rigid planar membranes. In chapter 2 we study electrolyte-mediated interactions between two of such colloidal objects. Several aspects of these interactions are considered including the nature (attractive or repulsive) of the force between the objects, the osmotic properties for different types of surfaces and image charge effects. In part II, which includes

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

    SciTech Connect

    Liu, Shi-Yu; Liu, Shiyang; Li, De-Jun; Wang, Sanwu; Guo, Jing; Shen, Yaogen

    2015-02-14

    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 sustained 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.

  4. 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.

  5. 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

  6. Thermodynamic analysis of biogenic and synthetic polyamines conjugation with PAMAM-G4 nanoparticles.

    PubMed

    Chanphai, P; Tajmir-Riahi, H A

    2016-02-01

    We report the thermodynamic analysis of the bindings of poly(amidoamine) (PAMAM-G4) nanoparticles with biogenic polyamines spermine (spm), spermidine (spmd) and synthetic polyamines 3,7,11,15-tetrazaheptadecane·4HCl (BE-333) in aqueous solution at physiological conditions. Multiple spectroscopic methods, thermodynamic parameters and molecular modelling were used to analyse polyamine bindings to PAMAM dendrimers. Thermodynamic parameters ΔS, ΔH and ΔG parameters showed that polyamines bind polymer through H-bonding and van der Waals contacts with biogenic polyamines form more stable conjugates than synthetic polyamines. Modelling showed that polyamines are located at the surface of PAMAM with the free binding energy of -3.56 (spermine), -3.88 (spermidine) and -3.13 kcal/mol (BE-333), indicating spontaneous polyamine-polymer interaction at room temperature.

  7. Hyperbaric Hydrothermal Atomic Force Microscope

    DOEpatents

    Knauss, Kevin G.; Boro, Carl O.; Higgins, Steven R.; Eggleston, Carrick M.

    2003-07-01

    A hyperbaric hydrothermal atomic force microscope (AFM) is provided to image solid surfaces in fluids, either liquid or gas, at pressures greater than normal atmospheric pressure. The sample can be heated and its surface imaged in aqueous solution at temperatures greater than 100.degree. C. with less than 1 nm vertical resolution. A gas pressurized microscope base chamber houses the stepper motor and piezoelectric scanner. A chemically inert, flexible membrane separates this base chamber from the sample cell environment and constrains a high temperature, pressurized liquid or gas in the sample cell while allowing movement of the scanner. The sample cell is designed for continuous flow of liquid or gas through the sample environment.

  8. Differential magnetic force microscope imaging.

    PubMed

    Wang, Ying; Wang, Zuobin; Liu, Jinyun; Hou, Liwei

    2015-01-01

    This paper presents a method for differential magnetic force microscope imaging based on a two-pass scanning procedure to extract differential magnetic forces and eliminate or significantly reduce background forces with reversed tip magnetization. In the work, the difference of two scanned images with reversed tip magnetization was used to express the local magnetic forces. The magnetic sample was first scanned with a low lift distance between the MFM tip and the sample surface, and the magnetization direction of the probe was then changed after the first scan to perform the second scan. The differential magnetic force image was obtained through the subtraction of the two images from the two scans. The theoretical and experimental results have shown that the proposed method for differential magnetic force microscope imaging is able to reduce the effect of background or environment interference forces, and offers an improved image contrast and signal to noise ratio (SNR). © Wiley Periodicals, Inc.

  9. Nanocarpets for Trapping Microscopic Particles

    NASA Technical Reports Server (NTRS)

    Noca, Flavio; Chen, Fei; Hunt, Brian; Bronikowski, Michael; Hoenk, Michael; Kowalczyk, Robert; Choi, Daniel

    2004-01-01

    Nanocarpets that is, carpets of carbon nanotubes are undergoing development as means of trapping microscopic particles for scientific analysis. Examples of such particles include inorganic particles, pollen, bacteria, and spores. Nanocarpets can be characterized as scaled-down versions of ordinary macroscopic floor carpets, which trap dust and other particulate matter, albeit not purposefully. Nanocarpets can also be characterized as mimicking both the structure and the particle-trapping behavior of ciliated lung epithelia, the carbon nanotubes being analogous to cilia. Carbon nanotubes can easily be chemically functionalized for selective trapping of specific particles of interest. One could, alternatively, use such other three-dimensionally-structured materials as aerogels and activated carbon for the purposeful trapping of microscopic particles. However, nanocarpets offer important advantages over these alternative materials: (1) Nanocarpets are amenable to nonintrusive probing by optical means; and (2) Nanocarpets offer greater surface-to-volume ratios.

  10. Shear Brillouin light scattering microscope

    PubMed Central

    Kim, Moonseok; Besner, Sebastien; Ramier, Antoine; Kwok, Sheldon J. J.; An, Jeesoo; Scarcelli, Giuliano; Yun, Seok Hyun

    2016-01-01

    Brillouin spectroscopy has been used to characterize shear acoustic phonons in materials. However, conventional instruments had slow acquisition times over 10 min per 1 mW of input optical power, and they required two objective lenses to form a 90° scattering geometry necessary for polarization coupling by shear phonons. Here, we demonstrate a confocal Brillouin microscope capable of detecting both shear and longitudinal phonons with improved speeds and with a single objective lens. Brillouin scattering spectra were measured from polycarbonate, fused quartz, and borosilicate in 1-10 s at an optical power level of 10 mW. The elastic constants, phonon mean free path and the ratio of the Pockels coefficients were determined at microscopic resolution. PMID:26832263

  11. Mars Life? - Microscopic Tubular Structures

    NASA Technical Reports Server (NTRS)

    1996-01-01

    This electron microscope image shows tubular structures of likely Martian origin. These structures are very similar in size and shape to extremely tiny microfossils found in some Earth rocks. This photograph is part of a report by a NASA research team published in the Aug. 16, 1996, issue of the journal Science. A two-year investigation by the 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.

  12. Hyperbaric hydrothermal atomic force microscope

    DOEpatents

    Knauss, Kevin G.; Boro, Carl O.; Higgins, Steven R.; Eggleston, Carrick M.

    2002-01-01

    A hyperbaric hydrothermal atomic force microscope (AFM) is provided to image solid surfaces in fluids, either liquid or gas, at pressures greater than normal atmospheric pressure. The sample can be heated and its surface imaged in aqueous solution at temperatures greater than 100.degree. C. with less than 1 nm vertical resolution. A gas pressurized microscope base chamber houses the stepper motor and piezoelectric scanner. A chemically inert, flexible membrane separates this base chamber from the sample cell environment and constrains a high temperature, pressurized liquid or gas in the sample cell while allowing movement of the scanner. The sample cell is designed for continuous flow of liquid or gas through the sample environment.

  13. Apparatus Would Stain Microscope Slides

    NASA Technical Reports Server (NTRS)

    Breeding, James D.

    1993-01-01

    Proposed apparatus meters specific amounts of fluid out of containers at specific times to stain microscope slides. Intended specifically for semiautomated staining of microbiological and hematological samples in microgravity, leakproof apparatus used in other environments in which technicians have little time to allocate to staining procedures and/or exposure to toxic staining agents or to micro-organisms to be stained hazardous. Apparatus adapted to perform almost any staining procedure and accommodates multiple staining reagents, useful for small or remote clinical laboratories.

  14. Microscopic Description of Scission Configurations

    SciTech Connect

    Dubray, N.; Goutte, H.; Berger, J. F.

    2007-02-26

    Properties of 226Th, 256Fm, 258Fm and 260Fm nuclei in the scission region are described using a full-microscopic Hartree-Fock-Bogoliubov approach with the effective Gogny nucleon-nucleon interaction. In a first step, the Potential Energy Surfaces are computed in the (q 20, q30) plane, the scission lines are found, fulfilling a given criterion on the density in the nuclear neck. Finally a few properties of the fragments along this line are presented.

  15. Apparatus Would Stain Microscope Slides

    NASA Technical Reports Server (NTRS)

    Breeding, James D.

    1993-01-01

    Proposed apparatus meters specific amounts of fluid out of containers at specific times to stain microscope slides. Intended specifically for semiautomated staining of microbiological and hematological samples in microgravity, leakproof apparatus used in other environments in which technicians have little time to allocate to staining procedures and/or exposure to toxic staining agents or to micro-organisms to be stained hazardous. Apparatus adapted to perform almost any staining procedure and accommodates multiple staining reagents, useful for small or remote clinical laboratories.

  16. Optical Analysis of Microscope Images

    NASA Astrophysics Data System (ADS)

    Biles, Jonathan R.

    Microscope images were analyzed with coherent and incoherent light using analog optical techniques. These techniques were found to be useful for analyzing large numbers of nonsymbolic, statistical microscope images. In the first part phase coherent transparencies having 20-100 human multiple myeloma nuclei were simultaneously photographed at 100 power magnification using high resolution holographic film developed to high contrast. An optical transform was obtained by focussing the laser onto each nuclear image and allowing the diffracted light to propagate onto a one dimensional photosensor array. This method reduced the data to the position of the first two intensity minima and the intensity of successive maxima. These values were utilized to estimate the four most important cancer detection clues of nuclear size, shape, darkness, and chromatin texture. In the second part, the geometric and holographic methods of phase incoherent optical processing were investigated for pattern recognition of real-time, diffuse microscope images. The theory and implementation of these processors was discussed in view of their mutual problems of dimness, image bias, and detector resolution. The dimness problem was solved by either using a holographic correlator or a speckle free laser microscope. The latter was built using a spinning tilted mirror which caused the speckle to change so quickly that it averaged out during the exposure. To solve the bias problem low image bias templates were generated by four techniques: microphotography of samples, creation of typical shapes by computer graphics editor, transmission holography of photoplates of samples, and by spatially coherent color image bias removal. The first of these templates was used to perform correlations with bacteria images. The aperture bias was successfully removed from the correlation with a video frame subtractor. To overcome the limited detector resolution it is necessary to discover some analog nonlinear intensity

  17. One-Angstrom microscope update

    SciTech Connect

    O'Keefe, Michael A.

    1999-04-04

    The One-Angstrom Microscope project has attained its goal, and is now producing images down to 1 Angstrom resolution. We have demonstrated transmission electron microscopy of defect structures down to a resolution of 1.1 Angstrom, with evidence that 0.89 Angstrom will be possible. This level of resolution will soon be made available to all those NCEM users who have a requirement for sub-Angstrom resolution.

  18. 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.

  19. Duties to Extraterrestrial Microscopic Organisms

    NASA Astrophysics Data System (ADS)

    Cockell, C. S.

    Formulating a normative axiology for the treatment of extraterrestrial microscopic organisms, should they ever be found, requires an extension of environmental ethics to beyond the Earth. Using an ethical framework for the treatment of terrestrial micro-organisms, this paper elaborates a similar ethic for the treatment of extraterrestrial microscopic organisms. An ethic of `teloempathy' allows for the moral considerability of any organism that has `interests', based on rudimentary qualities of conativism, and therefore allows for an identical treatment of all life, related or not related to life on Earth. Although, according to this ethic, individual extraterrestrial microscopic organisms have a good of their own and even `rights', at this level the ethic can only be theoretical, allowing for the inevitable destruction of many individual organisms during the course of human exploratory missions, similarly to the daily destruction of microbes by humans on Earth. A holistic teloempathy, an operative ethic, not only provides a framework for human exploration, but it also has important implications for planetary protection and proposals to implement planetary-scale atmospheric alterations on other bodies. Even prior to the discovery of extraterrestrial life, or the discovery of a complete absence of such life, this exercise yields important insights into the moral philosophy that guides our treatment of terrestrial micro-organisms.

  20. Compact Microscope Imaging System Developed

    NASA Technical Reports Server (NTRS)

    McDowell, Mark

    2001-01-01

    The Compact Microscope Imaging System (CMIS) is a diagnostic tool with intelligent controls for use in space, industrial, medical, and security applications. The CMIS can be used in situ with a minimum amount of user intervention. This system, which was developed at the NASA Glenn Research Center, can scan, find areas of interest, focus, and acquire images automatically. Large numbers of multiple cell experiments require microscopy for in situ observations; this is only feasible with compact microscope systems. CMIS is a miniature machine vision system that combines intelligent image processing with remote control capabilities. The software also has a user-friendly interface that can be used independently of the hardware for post-experiment analysis. CMIS has potential commercial uses in the automated online inspection of precision parts, medical imaging, security industry (examination of currency in automated teller machines and fingerprint identification in secure entry locks), environmental industry (automated examination of soil/water samples), biomedical field (automated blood/cell analysis), and microscopy community. CMIS will improve research in several ways: It will expand the capabilities of MSD experiments utilizing microscope technology. It may be used in lunar and Martian experiments (Rover Robot). Because of its reduced size, it will enable experiments that were not feasible previously. It may be incorporated into existing shuttle orbiter and space station experiments, including glove-box-sized experiments as well as ground-based experiments.