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Sample records for bence jones proteins

  1. Bence-Jones protein - quantitative

    Science.gov (United States)

    Immunoglobulin light chains - urine; Urine Bence-Jones protein ... Bence-Jones proteins are a part of regular antibodies called light chains. These proteins are not normally in urine. Sometimes, when ...

  2. Clinical applications of immunofixation: a more sensitive technique for the detection of Bence Jones protein.

    OpenAIRE

    Whicher, J T; Hawkins, L.; Higginson, J.

    1980-01-01

    Immunofixation in agarose gel has been compared with agarose electrophoresis for the detection of Bence Jones protein in urine. The technique has a sensitivity between five and 10 times greater than electrophoresis and allows the identification of multiple Bence Jones proteins and Bence Jones proteins with fast mobility in the presence of other urinary proteins. In four out of 12 patients studied, Bence Jones protein was undetectable by electrophoresis of 300 times concentrated urine but was ...

  3. 21 CFR 866.5150 - Bence-Jones proteins immunological test system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Bence-Jones proteins immunological test system. 866.5150 Section 866.5150 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... bone marrow cells), leukemia (cancer of the blood-forming organs), and lymphoma (cancer of the...

  4. Nephrotoxicity of Bence-Jones proteins: correlation with endocytosis by BHK cells and intracellular movement

    Directory of Open Access Journals (Sweden)

    Ana Lucia Nicastri

    2001-06-01

    Full Text Available The aim of this investigation was to evaluate the endocytosis of two Bence-Jones proteins by renal cells in order to elucidate the interference of their physical and chemical characteristics on nephrotoxicity. Bence-Jones proteins (AK and GL were purified and isolated from the urine of two patients with multiple myeloma. The isotype of both proteins was characterised as being human monoclonal lambda light chain. The AK protein presented mainly an Ip>7.0, a high content of galactose and a low amount of sialic acid molecules. On the other hand, the GL protein presented a single band with an Ip of 4.3, a higher level of sialic acid and a reduced amount of galactose, in comparison with the AK protein. Baby Hamster Kidney (BHK cells were maintained in culture in bottles at 37ºC, using DMEM culture media supplemented with 10% of calf serum with a pH of 7.4. Once the monolayer was observed to be confluent, the BHK cells were incubated with the two proteins, dissolved in a serum-free medium for 1, 5, 15, 30, 60 minutes and 24 hours. Control cells were established omitting the incubation with Bence-Jones proteins, but maintaining all of the other conditions. After, this the cells were washed, trypsinised, centrifuged and fixed in a solution of 4% paraformaldehyde and 0.5% glutaraldehyde on a 0.1 M, pH 7.4 phosphate buffer. Cells were processed for immunocytochemical reactions by using protein A coupled with colloidal gold and further silver enhancement. Semi-thin sections of the pellets were obtained and submitted to the cytochemical reactions. Detection of labelling was made by using light microscopy. It was observed that GL protein tended to be directed towards a perinuclear position, whereas the AK protein tended to suffer lysosomal deviation, suggesting that there is a direct contribution of physical and chemical characteristics on intracellular direction taken by Bence-Jones proteins.O objetivo deste trabalho foi avaliar a endocitose de duas prote

  5. Nephrotoxicity of Bence-Jones proteins: interference in renal epithelial cell acidification

    Directory of Open Access Journals (Sweden)

    Nicastri A.L.

    2002-01-01

    Full Text Available The aim of the present study was to evaluate the acidification of the endosome-lysosome system of renal epithelial cells after endocytosis of two human immunoglobulin lambda light chains (Bence-Jones proteins, BJP obtained from patients with multiple myeloma. Renal epithelial cell handling of two BJP (neutral and acidic BJP was evaluated by rhodamine fluorescence. Renal cells (MDCK were maintained in culture and, when confluent, were incubated with rhodamine-labeled BJP for different periods of time. Photos were obtained with a fluorescence microscope (Axiolab-Zeiss. Labeling density was determined on slides with a densitometer (Shimadzu Dual-Wavelength Flying-Spot Scanner CS9000. Endocytosis of neutral and acidic BJP was correlated with acidic intracellular compartment distribution using acridine orange labeling. We compared the pattern of distribution after incubation of native neutral and acidic BJP and after complete deglycosylation of BJP by periodate oxidation. The subsequent alteration of pI converted neutral BJP to acidic BJP. There was a significant accumulation of neutral BJP in endocytic structures, reduced lysosomal acidification, and a diffuse pattern of acidification. This pattern was reversed after total deglycosylation and subsequent alteration of the pI to an acidic BJP. We conclude that the physicochemical characteristics of BJP interfere with intracellular acidification, possibly explaining the strong nephrotoxicity of neutral BJP. Lysosomal acidification is fundamental for adequate protein processing and catabolism.

  6. The renal and hepatic distribution of Bence Jones proteins depends on glycosylation: a scintigraphic study in rats.

    Science.gov (United States)

    Prado, M J; Nicastri, A L; Costa, P L; Rockman, T; Tersariol, I L; Nader, H B; Barros, R T; Prado, E B

    1997-07-01

    The aim of the present study was to evaluate renal and liver distribution of two monoclonal immunoglobulin light chains. The chains were purified individually from the urine of patients with multiple myeloma and characterized as lambda light chains with a molecular mass of 28 kDa. They were named BJg (high amount of galactose residues exposed) and BJs (sialic acid residues exposed) on the basis of carbohydrate content. A scintigraphic study was performed on male Wistar rats weighing 250 g for 60 min after i.v. administration of 1 mg of each protein (7.4 MBq), as the intact proteins and also after carbohydrate oxidation. Images were obtained with a Siemens gamma camera with a high-resolution collimator and processed with a MicroDelta system. Hepatic and renal distribution were established and are reported as percent of injected dose. Liver uptake of BJg was significantly higher than liver uptake of BJs (94.3 vs 81.4%) (P hepatic accumulation of both proteins and consequently a higher renal overload. The tissue distribution of periodate-treated BJg was similar to that of native BJs: 82.7 vs 81.4% in the liver and 17.3 vs 18.6% in the kidneys. These observations indicate the important role of sugar residues of Bence Jones proteins for their recognition by specific membrane receptors, which leads to differential tissue accumulation and possible toxicity. PMID:9361711

  7. The renal and hepatic distribution of Bence Jones proteins depends on glycosylation: a scintigraphic study in rats

    Directory of Open Access Journals (Sweden)

    M.J.B.A. Prado

    1997-07-01

    Full Text Available The aim of the present study was to evaluate renal and liver distribution of two monoclonal immunoglobulin light chains. The chains were purified individually from the urine of patients with multiple myeloma and characterized as lambda light chains with a molecular mass of 28 kDa. They were named BJg (high amount of galactose residues exposed and BJs (sialic acid residues exposed on the basis of carbohydrate content. A scintigraphic study was performed on male Wistar rats weighing 250 g for 60 min after iv administration of 1 mg of each protein (7.4 MBq, as the intact proteins and also after carbohydrate oxidation. Images were obtained with a Siemens gamma camera with a high-resolution collimator and processed with a MicroDelta system. Hepatic and renal distribution were established and are reported as percent of injected dose. Liver uptake of BJg was significantly higher than liver uptake of BJs (94.3 vs 81.4% (P<0.05. This contributed to its greater removal from the intravascular compartment, and consequently lower kidney accumulation of BJg in comparison to BJs (5.7 vs 18.6% (P<0.05. After carbohydrate oxidation, there was a decrease in hepatic accumulation of both proteins and consequently a higher renal overload. The tissue distribution of periodate-treated BJg was similar to that of native BJs: 82.7 vs 81.4% in the liver and 17.3 vs 18.6% in the kidneys. These observations indicate the important role of sugar residues of Bence Jones proteins for their recognition by specific membrane receptors, which leads to differential tissue accumulation and possible toxicity

  8. The renal and hepatic distribution of Bence Jones proteins depends on glycosylation: a scintigraphic study in rats

    OpenAIRE

    M.J.B.A. Prado; A.L. Nicastri; P.L.A. Costa; T. Rockman; Tersariol, I.L.S.; Nader, H B; R.T. Barros; E.B.A. Prado

    1997-01-01

    The aim of the present study was to evaluate renal and liver distribution of two monoclonal immunoglobulin light chains. The chains were purified individually from the urine of patients with multiple myeloma and characterized as lambda light chains with a molecular mass of 28 kDa. They were named BJg (high amount of galactose residues exposed) and BJs (sialic acid residues exposed) on the basis of carbohydrate content. A scintigraphic study was performed on male Wistar rats weighing 250 g for...

  9. Daniel Jones

    DEFF Research Database (Denmark)

    from the original phonetic transcription to the conventional orthography). Much unpublished work, ranging from lecture notes on the sound systems of French, Spanish and Italian, to hitherto unpublished details of Jones' dealings with celebrities such as George Bernard Shaw and the Poet Laureate Robert...... underrated, impact on the American structuralist school. This eight volume collection makes available the first editions of Jones' standard books, i.e. The Pronunciation of English (1909), An English Pronouncing Dictionary (1917) and An Outline of English Phonetics (1918). In addition, Jones' crucial...... pioneering works, now out of print for many decades, are made easily accessible to scholars once again. Numerous articles encompassing a variety of phonetic/phonological topics, for example, phonemic analysis, juncture, models of pronunciation, and historiography, are also included (converted where necessary...

  10. Analytical tools for solitons and periodic waves corresponding to phonons on Lennard-Jones lattices in helical proteins

    DEFF Research Database (Denmark)

    D'ovidio, Francesco; Bohr, Henrik; Lindgård, Per-Anker

    2005-01-01

    We study the propagation of solitons along the hydrogen bonds of an alpha helix. Modeling the hydrogen and peptide bonds with Lennard-Jones potentials, we show that the solitons can appear spontaneously and have long lifetimes. Remarkably, even if no explicit solution is known for the Lennard-Jon....... The soliton phenomena described in the simulations of alpha helices may help to explain recent x-ray experiments on long alpha helices in Rhodopsin where a long lifetime of the vibrational modes has been observed....

  11. Koltunud Indiana Jones / Kutt Kommel

    Index Scriptorium Estoniae

    Kommel, Kutt

    2008-01-01

    Steven Spielbergi neljas Indiana Jones'i film Harrison Fordiga nimiosas "Indiana Jones ja kristallpealuu kuningriik" ("Indiana Jones and the Kingdom of the Crystal Skull") : Ameerika Ühendriigid 2008

  12. Jones' instrument technology

    CERN Document Server

    Jones, Ernest Beachcroft; Kingham, Edward G; Radnai, Rudolf

    1985-01-01

    Jones' Instrument Technology, Volume 5: Automatic Instruments and Measuring Systems deals with general trends in automatic instruments and measuring systems. Specific examples are provided to illustrate the principles of such devices. A brief review of a considerable number of standards is undertaken, with emphasis on the IEC625 Interface System. Other relevant standards are reviewed, including the interface and backplane bus standards. This volume is comprised of seven chapters and begins with a short introduction to the principles of automatic measurements, classification of measuring system

  13. Indiana Jones ja kristallpealuu kuningriik / Jaanus Noormets

    Index Scriptorium Estoniae

    Noormets, Jaanus

    2008-01-01

    Steven Spielbergi neljas Indiana Jones'i film Harrison Fordiga nimiosas "Indiana Jones ja kristallpealuu kuningriik" ("Indiana Jones and the Kingdom of the Crystal Skull") : Ameerika Ühendriigid 2008

  14. Stabiilne Ashley Jones / Svea Suvi

    Index Scriptorium Estoniae

    Suvi, Svea

    2006-01-01

    Ameerika teleseriaali "Vaprad ja ilusad" ("The Bold and the Beautiful") osatäitja Ashley Jones (Bridget Forrester). Sama artikkel pealkirjaga "Uus Bridget" : Nädal, 30. jan. 2006, nr. 4, lk. 12 : ill

  15. Tagging, Encoding, and Jones Optimality

    DEFF Research Database (Denmark)

    Danvy, Olivier; López, Pablo Ernesto Martínes

    typed, however, residual programs are cluttered with type tags. To obtain the original source program, these tags must be removed. A number of sophisticated solutions have already been proposed. We observe, however, that with a simple representation shift, ordinary partial evaluation is already Jones...

  16. NMR Quantum Calculations of the Jones Polynomial

    CERN Document Server

    Marx, Raimund; Kauffman, Louis; Lomonaco, Samuel; Spörl, Andreas; Pomplun, Nikolas; Myers, John; Glaser, Steffen J

    2009-01-01

    The repertoire of problems theoretically solvable by a quantum computer recently expanded to include the approximate evaluation of knot invariants, specifically the Jones polynomial. The experimental implementation of this evaluation, however, involves many known experimental challenges. Here we present experimental results for a small-scale approximate evaluation of the Jones Polynomial by nuclear-magnetic resonance (NMR), in addition we show how to escape from the limitations of NMR approaches that employ pseudo pure states. Specifically, we use two spin 1/2 nuclei of natural abundance chloroform and apply a sequence of unitary transforms representing the Trefoil Knot, the Figure Eight Knot and the Borromean Rings. After measuring the state of the molecule in each case, we are able to estimate the value of the Jones Polynomial for each of the knots.

  17. Dow Jones tugevdab oma koostist / Virge Lahe

    Index Scriptorium Estoniae

    Lahe, Virge

    2008-01-01

    USA tööstusettevõtteid koondav indeks Dow Jones vahetab nimekirjast välja kaks firmat ning lisab finants- ja kütusesektori osakaalu suurendamiseks Bank of America ja Chevroni. Vt. samas: Dow Jonesi tööstuskeskmisse lisandumine pole aktsiatele tiibu andnud; Dow Jonesi tööstuskeskmine

  18. Reduction U(VI) using jones reductor

    International Nuclear Information System (INIS)

    Reduction of dissolved oxide uranium in sulfuric acid use of reductor Jones Zn (Hg) was carried out. The reduced uranium sulfate solution was analyzed its U(IV) by measuring its absorbance on 652 nm and compared to oxidation U(IV) solution with KMnO4 solution. It was found that the comparison was in a good agreement. However, measuring of absorbance of U(VI) solution on 429 nm result of oxidation U(IV) with KMnO4 solution was not change. (author)

  19. A new two-variable generalization of the Jones polynomial

    OpenAIRE

    Goundaroulis, Dimos; Lambropoulou, Sofia

    2016-01-01

    We present a new 2-variable generalization of the Jones polynomial that can be defined through the skein relation of the Jones polynomial. The well-definedness of this new generalization is proved algebraically. We also give a closed combinatorial formula for this new classical link invariant.

  20. Robert T. Jones, One of a Kind

    Science.gov (United States)

    Vincenti, Walter G.

    2005-01-01

    His contemporaries saw R.T. Jones as one of the notably creative aerodynamicists of the twentieth century. This essay reviews his remarkable life and career, including his years as a farm-country boy, college dropout, and fledgling airplane designer in Missouri, his time as an elevator operator and self-directed student in Washington, D.C., and his long professional career as an aerodynamicist at the Langley and Ames Aeronautical Laboratories and Stanford University. The focus in his career is on his fundamental discovery of the benefits of sweepback for the wings of high-speed airplanes. This includes speculation about his highly intuitive thought processes in arriving at his creative ideas. I also give an account of his work on blood flow and the mechanical heart, his avocational accomplishments as a maker of telescopes and violins, and his philosophical interest in human affairs.

  1. Obituary: Frank Culver Jones, 1932-2007

    Science.gov (United States)

    Ormes, Johnathan F.; Streitmatter, Robert E.

    2007-12-01

    Frank C. Jones, an emeritus theoretical physicist at NASA, died May 2, 2007 at age 74 after a struggle with a rare form of cancer. He died at his home in Silver Spring, Maryland, surrounded by his family. Frank was born July 30, 1932 in Fort Worth, Texas, the oldest of three boys. His parents were Kenneth Hugh and Nancy Culver Jones. Frank's father was a lawyer, and his grandfather was a Methodist minister. Frank graduated from Rice University in 1954 and earned a master's degree in 1955 and a doctorate in 1961, both in physics, from the University of Chicago. He did his graduate work with Prof. John Simpson. Dr. Jones began his professional career as an instructor in physics at Princeton University before joining NASA's Goddard Space Flight Center in 1963 as a National Research Council associate. He subsequently became a member of the Theory Division and the Laboratory for High Energy Astrophysics. His area of expertise was the origin, transport, and electromagnetic interactions of cosmic rays. His particular focus was the stochastic physics related to the diffusion of particles in random fields, plasma turbulence, and the shock acceleration of charged particles in collisionless plasmas. From 1993 to 1995, Frank was head of Goddard's Theoretical High Energy Astrophysics Office and continued to serve as Head of the Theory group. In 2003 he served as Acting Chief of the Laboratory for High Energy Astrophysics. He retired in 2005 and continued his affiliation with NASA as an emeritus scientist at Goddard until his death. As a youngster, Frank showed the signs of curiosity and initiative that indicated he might become an experimentalist. At the memorial service for Frank, his brother related the stories of how Frank had rigged a hidden microphone to play through the family television as his brother courted a young woman on the front porch swing, and how one of Frank's early chemistry experiments caused all the family silverware to turn black. Although Frank started

  2. Accurate Jones Matrix of the Practical Faraday Rotator

    Institute of Scientific and Technical Information of China (English)

    王林斗; 祝昇翔; 李玉峰; 邢文烈; 魏景芝

    2003-01-01

    The Jones matrix of practical Faraday rotators is often used in the engineering calculation of non-reciprocal optical field. Nevertheless, only the approximate Jones matrix of practical Faraday rotators has been presented by now. Based on the theory of polarized light, this paper presents the accurate Jones matrix of practical Faraday rotators. In addition, an experiment has been carried out to verify the validity of the accurate Jones matrix. This matrix accurately describes the optical characteristics of practical Faraday rotators, including rotation, loss and depolarization of the polarized light. The accurate Jones matrix can be used to obtain the accurate results for the practical Faraday rotator to transform the polarized light, which paves the way for the accurate analysis and calculation of practical Faraday rotators in relevant engineering applications.

  3. 77 FR 19718 - Dow Jones & Company, Inc., Dow Jones Content Services Including On-Site Workers From Aerotek, Inc...

    Science.gov (United States)

    2012-04-02

    ... Federal Register on February 8, 2012 (77 FR 6590). At the request of the New Jersey State agency, the... Employment and Training Administration Dow Jones & Company, Inc., Dow Jones Content Services Including On-Site Workers From Aerotek, Inc., Princeton, NJ; Amended Certification Regarding Eligibility To...

  4. Triangular dissections, aperiodic tilings and Jones algebras

    CERN Document Server

    Coquereaux, Robert

    1994-01-01

    The Brattelli diagram associated with a given bicolored Dynkin-Coxeter graph of type A_n determines planar fractal sets obtained by infinite dissections of a given triangle. All triangles appearing in the dissection process have angles that are multiples of \\pi/ (n+1). There are usually several possible infinite dissections compatible with a given n but a given one makes use of n/2 triangle types if n is even. Jones algebra with index [ 4 \\ \\cos^2{\\pi \\over n+1}]^{-1} (values of the discrete range) act naturally on vector spaces associated with those fractal sets. Triangles of a given type are always congruent at each step of the dissection process. In the particular case n=4, there are isometric and the whole structure lead, after proper inflation, to aperiodic Penrose tilings. The other "tilings" associated with other values of the index are discussed and shown to be encoded by equivalence classes of infinite sequences (with appropriate constraints) using only n/2 digits (if n is even) and generalizing the ...

  5. Chuck Jones lahkus, tema kangelased elavad edasi / Neeme Korv

    Index Scriptorium Estoniae

    Korv, Neeme, 1974-

    2002-01-01

    Suri Chuck Jones (1912-2002), kuulus USA animafilmirežissöör, kelle animasari "Tom & Jerry" on praegugi Eestis väga populaarne. Ta on loonud enam kui 300 animafilmi, saanud 3 Oscarit ning 1996. aastal ka elutöö Oscari. Eesti lapsed nägid nõukogude ajal esmakordselt Chuck Jones'i loomingut Raivo Järvi lastesaadetes "Laupäeval koos isaga"

  6. Differential diagnosis of plasma cell dyscrasias in rheumatological practice

    Directory of Open Access Journals (Sweden)

    V I Vasilyev

    2010-12-01

    Conclusion. Many clinical and laboratory manifestations of primary PCD and RD are similar and only the absence of classical laboratory markers of autoimmune disease, as well as the presence of serum monoclonal immunoglobulins and urinary Bence Jones protein suggest the presence of PCD, both primary PCDs and those with RD.

  7. Guts of surfaces and the colored Jones polynomial

    CERN Document Server

    Futer, David; Purcell, Jessica

    2013-01-01

    This monograph derives direct and concrete relations between colored Jones polynomials and the topology of incompressible spanning surfaces in knot and link complements. Under mild diagrammatic hypotheses, we prove that the growth of the degree of the colored Jones polynomials is a boundary slope of an essential surface in the knot complement. We show that certain coefficients of the polynomial measure how far this surface is from being a fiber for the knot; in particular, the surface is a fiber if and only if a particular coefficient vanishes. We also relate hyperbolic volume to colored Jones polynomials. Our method is to generalize the checkerboard decompositions of alternating knots. Under mild diagrammatic hypotheses, we show that these surfaces are essential, and obtain an ideal polyhedral decomposition of their complement. We use normal surface theory to relate the pieces of the JSJ decomposition of the  complement to the combinatorics of certain surface spines (state graphs). Since state graphs have p...

  8. The Dow-Jones,NASDAQ and the Standard & Poor Index

    Institute of Scientific and Technical Information of China (English)

    刘健平; 刘宏丽

    2000-01-01

    The Dow-Jones Industrial Average isthe most popular and best known measure ofstock prices on the New York Stock Ex-change.It is a list of the stocks of 30 majorAmerican companies.It is designed to showwhich directions stock prices are moving.Itis the one considered most important inworld money markets.Many investors mea-sure the health of all American stocks by theDow-Jones Industrial Average.It measuresthe average value of stocks sold on the New

  9. Imaginando Palmares: a obra de Gayl Jones Imagining Palmares: the work of Gayl Jones

    Directory of Open Access Journals (Sweden)

    Stelamaris Coser

    2005-12-01

    Full Text Available O longo poema narrativo Song for Anninho (1981, da escritora negra Gayl Jones (Estados Unidos, interfere na narrativa da história colonial brasileira ao resgatar a figura feminina na República de Palmares, reescrever a saga de resistência dos palmaristas do ponto de vista imaginário de uma mulher negra do século XVII e, através dela, reinventar o cotidiano, os amores, as disputas e os sonhos das pessoas comuns que integravam o quilombo. O texto reflete sobre a verdade histórica, o aspecto construído de documentos, as seleções e exclusões da linguagem, e a importância do relato oral para o conhecimento de vivências e identidades à margem da história oficial. Nessa versão especial, o relato dramático do sonho, da luta e da destruição do mais famoso quilombo brasileiro usa a imaginação literária para expandir a memória e os arquivos de um dos fatos mais importantes da história das Américas, contribuindo para estimular o diálogo interamericano e iluminar a diáspora africana no Brasil e no continente.The long narrative poem Song for Anninho (1981, written by black U.S. writer Gayl Jones, interferes in the narrative of Brazilian colonial history as it highlights the female presence in the Republic of Palmares, rewrites the tale of resistance from the point of view of a black woman in the 17th Century, and, through her, reinvents the everyday lives, loves, disputes, and dreams of common people in the quilombo. The text reflects about historical truth, the constructed character of documents, selections and exclusions in language, and the importance of oral accounts to give visibility to experiences and identities marginalized by official history. In this special version, the dramatic report of the dreams, struggles, and destruction of the most famous Brazilian quilombo uses literary imagination to expand the memory and the archives of one of the most important facts in the history of the Americas, contributing to stimulate

  10. Jones polynomials, volume, and essential knot surfaces: a survey

    OpenAIRE

    Futer, David; Kalfagianni, Efstratia; Purcell, Jessica S.

    2011-01-01

    This paper is a brief overview of recent results by the authors relating colored Jones polynomials to geometric topology. The proofs of these results appear in the papers [arXiv:1002.0256] and [arXiv:1108.3370], while this survey focuses on the main ideas and examples.

  11. Free energy of the Lennard-Jones solid

    NARCIS (Netherlands)

    Hoef, van der Martin A.

    2000-01-01

    We have determined a simple expression for the absolute Helmholtz free energy of the fcc Lennard-Jones solid from molecular dynamics simulations. The pressure and energy data from these simulations have been fitted to a simple functional form (18 parameters) for densities ranging from around 0.94–1.

  12. Rhodessa Jones: Saving Lives Through Song and Story

    OpenAIRE

    Johnson, Courtney D.

    2006-01-01

    On October 16, CSW and the Center for Performance Studies hosted an appearance by Rhodessa Jones as part of a weeklong series on African American performance, and her performance/discussion was a rousing and poignant exploration of the role of art in the transformation of both hearts and politics.

  13. Edward Burne-Jones' Heavenly Conception: A Biblical Cosmos

    Science.gov (United States)

    Cheney, L. D. G.

    2016-01-01

    Edward Burne-Jones was a Pre-Raphaelite artist and designer, who collaborated with William Morris on many decorative arts (stained glass windows, book illustrations, ceramic and tapestry designs). He was a founding partner in the firm Morris, Marshall, Faulkner & Company. Burne-Jones composed The Days of Creation between 1870 and 1876 for the Morris firm. These paintings were executed in gouache and gold paint, and cartoons were made for tile and in stained glass, for the Church of St. Editha at Tamworth in Staffordshire. Burne-Jones' creation was highly praised and elegantly described by Oscar Wilde: “The picture is divided into six compartments, each representing a day in the Creation of the World, under the symbol of an angel holding a crystal globe, within which is shown the work of a day.” This paper will examine how Burne-Jones visualized an unusual celestial creation where angels holding magical spheres unveil the divine manifestation for the creation of a terrestrial realm. He created a cosmic utopia of the natural world.

  14. Are there Psychological Barriers in the Dow-Jones Index?

    OpenAIRE

    Eduardo Ley; Hal R. Varian

    1994-01-01

    The popular press attaches particular significance to certain numerical values of the Dow-Jones index. These magic numbers are referred to as `resistance levels' or `psychological barriers.' We examine 38 years of closing values of this index to see if it is of any help in predicting future stock market returns.

  15. Cluster fusion algorithm: application to Lennard-Jones clusters

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    2008-01-01

    We present a new general theoretical framework for modelling the cluster structure and apply it to description of the Lennard-Jones clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing ...

  16. Cluster fusion algorithm: application to Lennard-Jones clusters

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    2006-01-01

    We present a new general theoretical framework for modelling the cluster structure and apply it to description of the Lennard-Jones clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing ...

  17. Public lecture | "Science and society" by Bob Jones | 22 May

    CERN Multimedia

    2014-01-01

    Public lecture: "Science and society: the impact of computing at CERN on society" by Bob Jones 22 May at 7.30 p.m. Globe of Science and Innovation Lecture in English, translated in French. Entrance free. Limited number of seats. Reservation essential: +41 22 767 76 76 or cern.reception@cern.ch

  18. Indiana Jones on tagasi ja näitab, kuidas käituda / Kristiina Davidjants

    Index Scriptorium Estoniae

    Davidjants, Kristiina, 1974-

    2008-01-01

    22 mail esilinastub Steven Spielbergi järjekordne Indiana Jones'i film, kaasstsenaristiks ja produtsendiks George Lucas ja Harrison Fordiga nimiosas "Indiana Jones ja kristallpealuu kuningriik" ("Indiana Jones and the Kingdom of the Crystal Skull"). Saaga varasemast kolmest filmist

  19. The Kauffman bracket and the Jones polynomial in quantum gravity

    International Nuclear Information System (INIS)

    In the loop representation the quantum states of gravity are given by knot invariants. From general arguments concerning the loop transform of the exponential of the Chern-Simons form, a certain expansion of the Kauffman bracket knot polynomial can be formally viewed as a solution of the Hamiltonian constraint with a cosmological constant in the loop representation. The Kauffman bracket is closely related to the Jones polynomial. In this paper the operation of the Hamiltonian on the power expansions of the Kauffman bracket and Jones polynomials is analyzed. It is explicitly shown that the Kauffman bracket is a formal solution of the Hamiltonian constraint to third order in the cosmological constant. We make use of the extended loop representation of quantum gravity where the analytic calculation can be thoroughly accomplished. Some peculiarities of the extended loop calculus are considered and the significance of the results to the case of the conventional loop representation is discussed. (orig.)

  20. Tubo de Lester-Jones: indicações e resultados Lester-Jones tube: indications and results

    Directory of Open Access Journals (Sweden)

    Walberto Passos Junior

    2004-12-01

    Full Text Available OBJETIVO: Avaliar as indicações, resultados e complicações advindas do seu uso. MÉTODOS: Avaliaram-se retrospectivamente 25 pacientes submetidos a 27 conjuntivorrinostomias com colocação de tubo de Lester-Jones. Foram estudados os dados do portador, a etiologia da afecção e as complicações que ocorreram no intra e no pós-operatório. Os dados foram avaliados segundo a freqüência de ocorrência. RESULTADOS: O tubo de Lester-Jones foi usado igualmente em ambos os sexos, mais em indivíduos abaixo dos 10 ou acima dos 50 anos de idade. As causas mais freqüentes para utilização foram a idiopática ou a agenesia congênita de pontos e canalículos. Houve melhora dos sintomas em 88% dos pacientes. Complicações ocorreram em 59,25% dos casos, dentre as quais: extrusão (40,74% e a migração (14,8% do tubo. CONCLUSÃO: Apesar das complicações observadas, o índice de cura com a utilização do tubo de Lester-Jones é alto, sendo boa opção para o tratamento das obstruções lacrimais altas.PURPOSE: To evaluate the results and the complications occurring with this procedure. METHODS: The authors retrospectively reviewed charts of 25 patients (27 lacrimal viers with upper lacrimal system obstruction who underwent conjunctivorhinostomy and Lester-Jones tube bypass. The patients were evaluated according to gender, causative factors and the com plications during and after surgery. The data were submitted to statistical analysis. RESULTS: The Lester-Jones bypass tube was used in both sexes and most frequently in patients under 10 or above 50 years. The most common obstructive factor was unknown and congenital agenesis. Eighty-eight per cent of the patients had no epiphora at the end of the treatment. Complications occurred in 59.25% of the patients, most of them related to tube extrusion (40.74% or migration (14.8%. The authors concluded that the Lester-Jones bypass tube is a good option to treat the upper lacrimal obstruction, in spite

  1. Environmental Groundwater Monitoring of Jones Creek Field, Niger Delta, Nigeria

    OpenAIRE

    Felix C. Ugbe

    2012-01-01

    Groundwater monitoring exercise was carried out in Jones Creek field of Western Niger Delta. The aim was to ascertain the groundwater status of the area where oil exploration has been carried out for over four decades. Ten boreholes were drilled to capture the ground water flow direction. Both in situ and laboratory analyses were conducted on the water samples to ascertain whether or not there is contamination. The status of the groundwater indicates that it meets WHO maximum permissible stan...

  2. Marine geophysics. By E.J.W. Jones

    Digital Repository Service at National Institute of Oceanography (India)

    Rao, D.G.

    at the National Institute of Oceanography, Goa, India, I read the book AMarine GeophysicsB written by Prof. E.J.W. Jones with great interest. I must place on record the author’s efforts to deal with all disciplines in marine geophysics fully covering basic... global positioning system, acoustic navigation and integrated navigation systems were also explained in order to optimize the advantages of each. This basic information is definitely useful to the budding re- searchers. Chapter 3 outlines different...

  3. Hopping in a supercooled binary Lennard-Jones liquid

    DEFF Research Database (Denmark)

    Schrøder, Thomas; Dyre, Jeppe

    1998-01-01

    A binary Lennard–Jones liquid has been investigated by molecular dynamics at equilibrium supercooled conditions. At the lowest temperature investigated, hopping is present in the system as indicated by a secondary peak in 4r2Gs(r,t), where Gs(r,t) is the van Hove self correlation function. To......", as often argued, and that the system has a single-peaked distribution of hopping-distances centered around the characteristic intermolecular distance....

  4. The homological content of the Jones representations at $q = -1$

    DEFF Research Database (Denmark)

    Egsgaard, Jens Kristian; Fuglede Jørgensen, Søren

    We generalize a discovery of Kasahara and show that the Jones representations of braid groups, when evaluated at $q = -1$, are related to the action on homology of a branched double cover of the underlying punctured disk. As an application, we prove for a large family of pseudo-Anosov mapping cla...... classes a conjecture put forward by Andersen, Masbaum, and Ueno by extending their original argument for the sphere with four marked points to our more general case....

  5. A Viola-Jones based hybrid face detection framework

    Science.gov (United States)

    Murphy, Thomas M.; Broussard, Randy; Schultz, Robert; Rakvic, Ryan; Ngo, Hau

    2013-12-01

    Improvements in face detection performance would benefit many applications. The OpenCV library implements a standard solution, the Viola-Jones detector, with a statistically boosted rejection cascade of binary classifiers. Empirical evidence has shown that Viola-Jones underdetects in some instances. This research shows that a truncated cascade augmented by a neural network could recover these undetected faces. A hybrid framework is constructed, with a truncated Viola-Jones cascade followed by an artificial neural network, used to refine the face decision. Optimally, a truncation stage that captured all faces and allowed the neural network to remove the false alarms is selected. A feedforward backpropagation network with one hidden layer is trained to discriminate faces based upon the thresholding (detection) values of intermediate stages of the full rejection cascade. A clustering algorithm is used as a precursor to the neural network, to group significant overlappings. Evaluated on the CMU/VASC Image Database, comparison with an unmodified OpenCV approach shows: (1) a 37% increase in detection rates if constrained by the requirement of no increase in false alarms, (2) a 48% increase in detection rates if some additional false alarms are tolerated, and (3) an 82% reduction in false alarms with no reduction in detection rates. These results demonstrate improved face detection and could address the need for such improvement in various applications.

  6. Quantum algorithms for virtual Jones polynomials via Thistlethwaite theorems

    Science.gov (United States)

    Vélez, Mario; Ospina, Juan

    2010-04-01

    Recently a quantum algorithm for the Jones polynomial of virtual links was proposed by Kauffman and Dye via the implementation of the virtual braid group in anyonic topological quantum computation when the virtual crossings are considered as generalized swap gates. Also recently, a mathematical method for the computation of the Jones polynomial of a given virtual link in terms of the relative Tuttle polynomial of its face (Tait) graph with some suitable variable substitutions was proposed by Diao and Hetyei. The method of Diao and Hetyei is offered as an alternative to the ribbon graph approach according to which the Tutte polynomial of a given virtual link is computed in terms of the Bollobás- Riordan polynomial of the corresponding ribbon graph. The method of Diao and Hetyei can be considered as an extension of the celebrated Thistlethwaite theorem according to which invariant polynomials for knots and links are derived from invariant polynomials for graphs. Starting from these ideas we propose a quantum algorithm for the Jones polynomial of a given virtual link in terms of the generalized Tutte polynomials by exploiting the Thistlethwaite theorem and the Kauffman algorithm . Our method is claimed as the quantum version of the Diao-Hetyei method. Possible supersymmetric implementations of our algortihm are discussed jointly with its formulations using topological quantum lambda calculus.

  7. Structure diagram of binary Lennard-Jones clusters

    Science.gov (United States)

    Mravlak, Marko; Kister, Thomas; Kraus, Tobias; Schilling, Tanja

    2016-07-01

    We analyze the structure diagram for binary clusters of Lennard-Jones particles by means of a global optimization approach for a large range of cluster sizes, compositions, and interaction energies and present a publicly accessible database of 180 000 minimal energy structures (http://softmattertheory.lu/clusters.html). We identify a variety of structures such as core-shell clusters, Janus clusters, and clusters in which the minority species is located at the vertices of icosahedra. Such clusters can be synthesized from nanoparticles in agglomeration experiments and used as building blocks in colloidal molecules or crystals. We discuss the factors that determine the formation of clusters with specific structures.

  8. The BQP-hardness of approximating the Jones polynomial

    Science.gov (United States)

    Aharonov, Dorit; Arad, Itai

    2011-03-01

    A celebrated important result due to Freedman et al (2002 Commun. Math. Phys. 227 605-22) states that providing additive approximations of the Jones polynomial at the kth root of unity, for constant k=5 and k>=7, is BQP-hard. Together with the algorithmic results of Aharonov et al (2005) and Freedman et al (2002 Commun. Math. Phys. 227 587-603), this gives perhaps the most natural BQP-complete problem known today and motivates further study of the topic. In this paper, we focus on the universality proof; we extend the result of Freedman et al (2002) to ks that grow polynomially with the number of strands and crossings in the link, thus extending the BQP-hardness of Jones polynomial approximations to all values to which the AJL algorithm applies (Aharonov et al 2005), proving that for all those values, the problems are BQP-complete. As a side benefit, we derive a fairly elementary proof of the Freedman et al density result, without referring to advanced results from Lie algebra representation theory, making this important result accessible to a wider audience in the computer science research community. We make use of two general lemmas we prove, the bridge lemma and the decoupling lemma, which provide tools for establishing the density of subgroups in SU(n). Those tools seem to be of independent interest in more general contexts of proving the quantum universality. Our result also implies a completely classical statement, that the multiplicative approximations of the Jones polynomial, at exactly the same values, are #P-hard, via a recent result due to Kuperberg (2009 arXiv:0908.0512). Since the first publication of those results in their preliminary form (Aharonov and Arad 2006 arXiv:quant-ph/0605181), the methods we present here have been used in several other contexts (Aharonov and Arad 2007 arXiv:quant-ph/0702008; Peter and Stephen 2008 Quantum Inf. Comput. 8 681). The present paper is an improved and extended version of the results presented by Aharonov and Arad

  9. Stereotype Threat Paradigm in Search of a Phenomenon: A Comment on Kellow and Jones's (2008) Study

    Science.gov (United States)

    Whaley, Arthur L.

    2009-01-01

    In a recent study, Kellow and Jones apply the stereotype threat paradigm to a sample of African American students attending an urban high school. The purpose of this commentary is to provide a conceptual and methodological critique of Kellow and Jones's study. Implications for the role of Black psychologists in evaluating research on African…

  10. Nucleation for Lennard-Jones Fluid by Density Functional Theory

    Institute of Scientific and Technical Information of China (English)

    FU Dong

    2005-01-01

    @@ A non-mean field density functional theory is employed to investigate the vapour-liquid nucleation. The excess Helmholtz free energy functional is formulated in terms of a local density approximation for short ranged repulsion and a density-gradient expansion for long-ranged attractions. An analytical expression for the direct correlation function of a Lennard-Jones fluid is utilized to take into account the effect of long-ranged attractions on intermolecular correlations. With the predicted bulk properties and surface tension as input, the nucleation properties including density profile, work of formation and number of particles at the reduced temperatures T* = 0.694 and 0.741 are inuestigated. The obtained number of particles in the critical nucleus agrees well with the simulation data.

  11. Vectorial polarization modes platform realized with Jones vectors in mathematica

    Science.gov (United States)

    Choi, Yong-Dae; Yun, Hee-Joong

    2015-09-01

    The fundamental concept in physics of polarization propagation of electromagnetic waves is newly understood to be a cardinal keyword in quantum cryptography transport technology and the Standard Model. Interactive visualization of the propagation mechanism of polarized electromagnetism in a medium with its helicity has received attention recently from scientists in the age of information and communication. This study presents a new dynamic polarization platform that presents the polarization modes of a transverse electromagnetic wave by using Jones vectors calculations in the symbolic program Mathematica to convert the state of polarization through the arrangement of the optical elements. The platform simulates a propagation process that satisfies Maxwell's two vector equations precisely with the vectorial nature of the electromagnetic wave.

  12. The Lennard-Jones melting line and isomorphism

    Science.gov (United States)

    Heyes, D. M.; Brańka, A. C.

    2015-12-01

    The location of the melting line (ML) of the Lennard-Jones (LJ) system and its associated physical properties are investigated using molecular dynamics computer simulation. The radial distribution function and the behavior of the repulsive and attractive parts of the potential energy indicate that the ML is not a single isomorph, but the isomorphic state evolves gradually with temperature, i.e., it is only "locally isomorphic." The state point dependence of the unitless isomorphic number, X ˜ , for a range of static and dynamical properties of the LJ system in the solid and fluid states, and for fluid argon, are also reported. The quantity X ˜ typically varies most with state point in the vicinity of the triple point and approaches a plateau in the high density (temperature) limit along the ML.

  13. More on the melting of Lennard-Jones clusters

    International Nuclear Information System (INIS)

    The melting of 13-atom clusters interacting via Lennard-Jones potentials has been revisited using molecular dynamics coupled to steepest descent quenches. A procedure was devised to account for the fraction of times the global and local minima of the potential energy surface are accessed during a long trajectory. This quantity presents a sigmoid shape. A phenomenological model of melting is given in terms of a correlated walk that maps the short time excursions among the global and local minima in configuration space. Comparison between the simulation results and the theoretical model shows that the melting transition is well described in terms of the temperature changes of the fraction of high energy minima accessed during the cluster trajectory. Cooperativity is clear from the S shape of this quantity, i.e., the access to a local minimum favours the access to other local minima. (orig.)

  14. Structure and dynamics of Lennard-Jones clusters with impurities

    International Nuclear Information System (INIS)

    Molecular dynamics simulations and Lennard-Jones potentials have been used to study binary mixed clusters. The low temperature structures, impurity solvation and the melting and freezing transitions for different values of the relative atomic size and interaction energy have been studied for A13B, A12B, A55B and A13B13 clusters. For A13B large impurities do not solvate even for high interaction energy. For A55B larger impurities remain on the surface for low interaction energies but solvate as the energy of interaction increases. The presence of the impurity very strongly affects the solid-liquid transition. Icosahedral structures remain as the minimum energy configurations for A13B13 clusters with atoms of the same size and different interaction energies. For A13B13 clusters with atoms of the same interaction energy and different size, smaller atoms go inside surrounded by the bigger surface atoms. (orig.)

  15. Freezing point depression in model Lennard-Jones solutions

    Science.gov (United States)

    Koschke, Konstantin; Jörg Limbach, Hans; Kremer, Kurt; Donadio, Davide

    2015-09-01

    Crystallisation of liquid solutions is of uttermost importance in a wide variety of processes in materials, atmospheric and food science. Depending on the type and concentration of solutes the freezing point shifts, thus allowing control on the thermodynamics of complex fluids. Here we investigate the basic principles of solute-induced freezing point depression by computing the melting temperature of a Lennard-Jones fluid with low concentrations of solutes, by means of equilibrium molecular dynamics simulations. The effect of solvophilic and weakly solvophobic solutes at low concentrations is analysed, scanning systematically the size and the concentration. We identify the range of parameters that produce deviations from the linear dependence of the freezing point on the molal concentration of solutes, expected for ideal solutions. Our simulations allow us also to link the shifts in coexistence temperature to the microscopic structure of the solutions.

  16. Water in the presence of inert Lennard-Jones obstacles

    Science.gov (United States)

    Kurtjak, Mario; Urbic, Tomaz

    2014-04-01

    Water confined by the presence of a 'sea' of inert obstacles was examined. In the article, freely mobile two-dimensional Mercedes-Benz (MB) water put to a disordered, but fixed, matrix of Lennard-Jones disks was studied by the Monte Carlo computer simulations. For the MB water molecules in the matrix of Lennard-Jones disks, we explored the structures, hydrogen-bond-network formation and thermodynamics as a function of temperature and size and density of matrix particles. We found that the structure of model water is perturbed by the presence of the obstacles. Density of confined water, which was in equilibrium with the bulk water, was smaller than the density of the bulk water and the temperature dependence of the density of absorbed water did not show the density anomaly in the studied temperature range. The behaviour observed as a consequence of confinement is similar to that of increasing temperature, which can for a matrix lead to a process similar to capillary evaporation. At the same occupancy of space, smaller matrix molecules cause higher destruction effect on the absorbed water molecules than the bigger ones. We have also tested the hypothesis that at low matrix densities the obstacles induce an increased ordering and 'hydrogen bonding' of the MB model molecules, relative to pure fluid, while at high densities the obstacles reduce MB water structuring, as they prevent the fluid to form good 'hydrogen-bonding' networks. However, for the size of matrix molecules similar to that of water, we did not observe this effect.

  17. Die sondeleer in die apologetiek van Dr. D. Martyn Lloyd-Jones / Johannes Louis Aucamp

    OpenAIRE

    Aucamp, Johannes Louis

    2004-01-01

    1. The central theoretical argument of this study is that Dr. D. Martyn Lloyd-Jones maintains a true and Biblical view of sin and that he sets off his view meaningfully and apologetically against unbiblical views regarding sin. The purpose of the study is to investigate Lloyd-Jones's view of sin and to indicate that it can at present be applied meaningfully and apologetically. 2. To develop and substantiate this argument, the following procedure has been followed: 2.1. Lloyd-Jones's the...

  18. Modified Kenneth Jones criteria for diagnosing tuberculous meningitis in children

    International Nuclear Information System (INIS)

    To evaluate accuracy of modified Kenneth Jones scoring criteria (MKJSC) as a screening tool to diagnose tuberculous meningitis in children. Study Design: Cross-sectional study. Place and Duration of Study: Paediatric Medicine, Unit-I, Bahawal Victoria Hospital, Bahawalpur, from May 2006 to March 2007. Methodology: A total of 100 children admitted through emergency in Paediatric Medicine, Unit-I, were included who were having fever and features suggestive of central nervous system (CNS) infection. Lumbar puncture was done in all patients after written consent. Findings of lumbar puncture were taken as gold standard for the diagnosis of TBM. MKJSC was applied on each patient and accuracy determined against the gold standard. Results: Out of 100 children, 47 were diagnosed as TBM on the basis of CSF results. All children had scored 0-7 or above according to MKJSC. A score 1-2, 3-4, 5-6 and 7 or more was obtained in 23, 25, 30 and 22 children respectively. Children who had scored 5 or more received ATT. Accuracy of MKJSC was calculated to be 91%. Conclusion: MKJSC is a simple and accurate tool to improve tuberculous meningitis case detection rate in children. (author)

  19. Metastable Lennard-Jones fluids. II. Thermal conductivity.

    Science.gov (United States)

    Baidakov, Vladimir G; Protsenko, Sergey P

    2014-06-01

    The method of equilibrium molecular dynamics with the use of the Green-Kubo formalism has been used to calculate the thermal conductivity λ in stable and metastable regions of a Lennard-Jones fluid. Calculations have been made in the range of reduced temperatures 0.4 ≤ T* = k(b)T/ε ≤ 2.0 and densities 0.01 ≤ ρ* = ρσ³ ≤ 1.2 on 15 isotherms for 234 states, 130 of which refer to metastable regions: superheated and supercooled liquids, supersaturated vapor. Equations have been built up which describe the dependence of the regular part of the thermal conductivity on temperature and density, and also on temperature and pressure. It has been found that in (p, T) variables in the region of a liquid-gas phase transition a family of lines of constant value of excess thermal conductivity Δλ = λ - λ0, where λ0 is the thermal conductivity of a dilute gas, has an envelope which coincides with the spinodal. Thus, at the approach to the spinodal of a superheated liquid and supersaturated vapor (∂Δλ/∂p)T → ∞, (∂Δλ/∂T)p → ∞. PMID:24908025

  20. Environmental Groundwater Monitoring of Jones Creek Field, Niger Delta, Nigeria

    Directory of Open Access Journals (Sweden)

    Felix C. Ugbe

    2012-05-01

    Full Text Available Groundwater monitoring exercise was carried out in Jones Creek field of Western Niger Delta. The aim was to ascertain the groundwater status of the area where oil exploration has been carried out for over four decades. Ten boreholes were drilled to capture the ground water flow direction. Both in situ and laboratory analyses were conducted on the water samples to ascertain whether or not there is contamination. The status of the groundwater indicates that it meets WHO maximum permissible standards acceptable for domestic purposes. The water is mildly acidic due to the gas flaring associated with exploitation activities. The water is devoid of contamination of oil and grease but has appreciably high iron content thereby requiring treatment to enhance groundwater quality for domestic purposes. The observed high TDS may be due to the incursion of saline water into the phreatic zone. The study establishes the fact that oil exploration and exploitation companies have over the years been adopting environmentally friendly strategies to conserve the prolific aquifer of the area.

  1. Diffusion Time-Scale Invariance, Markovization Processes and Memory Effects in Lennard-Jones Liquids

    OpenAIRE

    Yulmetyev, Renat M.; Mokshin, Anatolii V.; Hänggi, Peter

    2004-01-01

    We report the results of calculation of diffusion coefficients for Lennard-Jones liquids, based on the idea of time-scale invariance of relaxation processes in liquids. The results were compared with the molecular dynamics data for Lennard-Jones system and a good agreement of our theory with these data over a wide range of densities and temperatures was obtained. By calculations of the non-Markovity parameter we have estimated numerically statistical memory effects of diffusion in detail.

  2. Jones calculus modeling and analysis of the thermal distortion in a Ti:sapphire laser amplifier.

    Science.gov (United States)

    Cho, Seryeyohan; Jeong, Jihoon; Yu, Tae Jun

    2016-06-27

    The mathematical modeling of an anisotropic Ti:sapphire crystal with a significant thermal load is performed. The model is expressed by the differential Jones matrix. A thermally induced distortion in the chirped-pulse amplification process is shown by the solution of the differential Jones matrix. Using this model, the thermally distorted spatio-temporal laser beam shape is calculated for a high-power and high-repetition-rate Ti:sapphire amplifier. PMID:27410590

  3. Regulatory restrictions and energy: The impact of the Jones Act on spot gasoline prices

    International Nuclear Information System (INIS)

    The purpose of the present study is to estimate the effects of the Jones Act on spot gasoline prices. Although the Jones Act pertains to the domestic shipment of all types of goods, the present study will only focus on gasoline. The present study will use data obtained from the Energy Information Administration in order to determine if the price of gasoline declined during Jones Act waiver periods. Looking at daily prices, the results regarding the effects of the Jones Act on spot gasoline prices are mixed. When using a t-test, the results indicated either that there was no significant difference or that prices were actually higher during the waiver periods. When using a first-order autoregressive model, it was found that prices were lower during the 2005 waiver period but higher during the 2012 waiver. Given these inconclusive results, it is not possible to conclude that the Jones Act restrictions contribute to higher gasoline prices. - Highlights: • I examine the effect of the Jones Act on spot gasoline prices. • I use daily price data over a seven year period. • I find that the results are mixed. • For the Hurricane Katrina waiver, prices fell, but for the Hurricane Sandy waiver, prices rose

  4. Die Dag van die Here in As Silo kom van Hennie Jones

    Directory of Open Access Journals (Sweden)

    P. Verster

    1999-05-01

    Full Text Available The Day of the Lord in As Silo kom (When Silo comes by Hennie JonesAs Silo kom (When Silo comes by Hennie Jones is an important novel in view of the fact that biblical themes like those of the Messianic child and the Day of the Lord are incorporated in and dealt with extensively in the novel. The way in which the Day of the Lord is described in the Bible emphasizes that it will be a day of judgement for Israel and the other nations - a given that became a fixed concept for post-exilic prophets. The Day of the Lord, however, holds not only judgement but also salvation for Israel and the other nations. The question asked in this article is whether these functions of the Day of the Lord become clear enough in Jones' novel.

  5. Gingival Enlargement in a Case of Variant Jones Syndrome: a Case Report

    Science.gov (United States)

    DA, Roopa; Singh, Shinkhala; Gupta, Ira; Gopal, Saumiya

    2016-01-01

    Gingival enlargement can be caused by a variety of etiological factors like inflammation, drugs, and systemic diseases or can be presented as a part of a syndrome. One such syndrome is Jones Syndrome, which is associated with gingival enlargement and progressive hearing loss. We present here a case of fifteen-year-old boy with gingival enlargement, hearing loss, and generalized alveolar bone loss and diagnosed as Jones syndrome. The diagnosis was made based on history, clinical, radiographic, and histopathological findings. Gingival enlargement was surgically managed using gingivectomy and no recurrence was observed. The patient showed remarkable esthetical and functional improvement. PMID:26966711

  6. Investigation of the Role of Coordination Number in the Lennard-Jones-Devonshire Theory

    OpenAIRE

    Vakili-Nezhaad, Gholamreza

    2007-01-01

    The theory of Lennard-Jones-Devonshire (LJD) has been studied for more than six decades by many researchers. Recently, Magee and Wilding have shown that in addition to the critical point originally reported for the 12–6 Lennard-Jones potential, the model exhibits a further critical point. In the present work, the effect of coordination number on the pressure-volume-temperature behavior of systems represented by the LJD-based equation of state was investigated. It was found that by varying ...

  7. The SL_3 Jones polynomial of the trefoil: a case study of $q$-holonomic sequences

    OpenAIRE

    Garoufalidis, Stavros; Koutschan, Christoph

    2010-01-01

    The SL_3 colored Jones polynomial of the trefoil knot is a $q$-holonomic sequence of two variables with natural origin, namely quantum topology. The paper presents an explicit set of generators for the annihilator ideal of this $q$-holonomic sequence as a case study. On the one hand, our results are new and useful to quantum topology: this is the first example of a rank 2 Lie algebra computation concerning the colored Jones polynomial of a knot. On the other hand, this work illustrates the ap...

  8. OXYGEN TRANSFER EFFICIENCY SURVEYS AT THE JONES ISLAND TREATMENT PLANTS - 1985-1988

    Science.gov (United States)

    Ceramic plate diffusers were among the earliest forms of fine pore diffusers used for oxygen transfer in activated sludge treatment. They have been successfully used for over 60 years in the Jones Island West Plant of the Milwaukee Metropolitan Sewerage District and, since initia...

  9. Creative Imagination and Subjective Agency in Wynne-Jones' "The Maestro"

    Science.gov (United States)

    Cairns, Sue Ann

    2009-01-01

    The Canadian young adult novel "The Maestro" by Tim Wynne-Jones foregrounds the relationship between imagination and subjective agency. While Burl uses his imagination at the beginning to protect himself from his abusive father, his fantasies become dress rehearsals for small performances that allow him to try on new identities and exercise…

  10. On the Farrell-Jones Conjecture for higher algebraic K-theory

    OpenAIRE

    Bartels, A; Reich, H

    2003-01-01

    We prove the Farrell-Jones Isomorphism Conjecture about the algebraic K-theory of a group ring RG in the case where the group G is the fundamental group of a closed Riemannian manifold with strictly negative sectional curvature. The coefficient ring R is an arbitrary associative ring with unit and the result applies to all dimensions.

  11. Malaria and the Decline of Ancient Greece: Revisiting the Jones Hypothesis in an Era of Interdisciplinarity

    Science.gov (United States)

    Baron, Christopher; Hamlin, Christopher

    2015-01-01

    Between 1906 and 1909 the biologist Ronald Ross and the classicist W.H.S. Jones pioneered interdisciplinary research in biology and history in advancing the claim that malaria had been crucial in the decline of golden-age Greece (fourth century BCE). The idea had originated with Ross, winner of the Nobel Prize for demonstrating the importance of…

  12. The Representation of Latinos and the Use of Spanish: A Critical Content Analysis of "Skippyjon Jones"

    Science.gov (United States)

    Martínez-Roldan, Carmen M.

    2013-01-01

    This study illustrates the presence of Mock Spanish in some English-based picture books and the ways this usage misrepresents Latino people, language, and culture. The author conducted a critical content analysis of five Skippyjon Jones books. Her guiding question was, How is language used, particularly Spanish, in these English texts, and what…

  13. Enhancing Undergraduates' Capabilities through Team-Based Competitions: The Edward Jones Challenge

    Science.gov (United States)

    Umble, Elisabeth J.; Umble, Michael; Artz, Kendall

    2008-01-01

    The Edward Jones Company recently initiated financial sponsorship of team-based competitions in six undergraduate business core classes at Baylor University. The challenges were chosen to take place in an introductory freshman business class, Managerial Accounting, Principles of Marketing, Corporate Finance, Operations Management, and Strategic…

  14. "Armastuse retsepti" tippkokk Zeta Jones ei oska muna keeta / Triin Tael

    Index Scriptorium Estoniae

    Tael, Triin

    2007-01-01

    Scott Hicksi romantiline komöödiafilm "Armastuse retsept" ("No Reservations"), mille peaosas Walesist pärit näitlejanna Catherine Zeta Jones. Näitlejanna muljeid oma rolliks ettevalmistustest, mille hulka käis ka praktika pärisrestoranis

  15. Thermodynamic Perturbation Theory for Solid-Liquid Phase Transition of Lennard-Jones Model

    Institute of Scientific and Technical Information of China (English)

    ZHOUShi-Qi; ZHANGXiao-Qi

    2004-01-01

    Both a free volume approach for Helmholtz free energy and a theoretically-based fitted formula for radial distribution function (rdf) of hard sphere solid are employed to describe the Helmholtz free energy of Lennard-Jones solid in the framework of the first order thermodynamic perturbation theory, which also is employed for the uniform Lennard Jones fluid. The dividing of the Lennard-Jones potential follows from the INCA prescription, but the specification of the equivalent hard sphere diameter is determined by a simple iteration procedure devised originally for liquid state, but extended to solid state in the present study. Two hundred shells are used in the rdf to get an accurate perturbation term.The present approach is very accurate for the description of excess Helmholtz free energy of LJ solid, but shows some deviation from the simulation for excess Helmholtz free energy of uniform LJ fluid when the reduced temperature kT/ε is higher then 5. The present approach is satisfactory for description of solid-liquid phase transition of the Lennard-Jones model.

  16. Thermodynamic Perturbation Theory for Solid-Liquid Phase Transition of Lennard-Jones Model

    Institute of Scientific and Technical Information of China (English)

    ZHOU Shi-Qi; ZHANG Xiao-Qi

    2004-01-01

    Both a free volume approach for Helmholtz free energy and a theoretically-based fitted formula for radial distribution function (rdf) of hard sphere solid are employed to describe the Helmholtz free energy of Lennard-Jones solid in the framework of the first order thermodynamic perturbation theory, which also is employed for the uniform LennardJones fluid. The dividing of the Lennard-Jones potential follows from the WCA prescription, but the specification of the equivalent hard sphere diameter is determined by a simple iteration procedure devised originally for liquid state, but extended to solid state in the present study. Two hundred sheiks are used in the rdf to get an accurate perturbation term.The present approach is very accurate for the description of excess Helmholtz free energy of LJ solid, but shows some deviation from the simulation for excess Helmholtz free energy of uniform LJ fluid when the reduced temperature kT/ε is higher then 5. The present approach is satisfactory for description of solid-liquid phase transition of the Lennard-Jones model.

  17. The Game TV Plays: Or, Why an English Teacher Came to Hate Barnaby Jones.

    Science.gov (United States)

    Shaw, Patrick W.

    The message of current popular television shows in which the hero is, or appears to be, a dumb clod (e.g., Archie Bunker, Fred Sanford, Columbo, and Barnaby Jones), apparently is that corruption may be equated with articulation, wealth, and education, while virtue may be equated with poverty and, often, illiteracy. Unfortunately, the effect of…

  18. Käsitsi tegemise võlu / David Jones ; intervjueerinud Kai Lobjakas

    Index Scriptorium Estoniae

    Jones, David, 1953-

    2010-01-01

    10. Kohila keraamikasümpoosionil osalenud briti keraamik ja teoreetik David Jones endast, rakutehnikast, huvist põletamisega seonduvate teemade vastu, Kohila sümpoosioni raames tehtust, keraamika õpetamisest Inglismaal, käsitöö ja keraamika positsioonist praegu ja tulevikus jm.

  19. Fusion process of Lennard-Jones clusters: global minima and magic numbers formation

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    2004-01-01

    We present a new theoretical framework for modeling the fusion process of Lennard–Jones (LJ) clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing paths up to the cluster size of 150 atoms...

  20. Curvature Dependence of Interfacial Properties for Associating Lennard-Jones Fluids: A Density Functional Study

    Institute of Scientific and Technical Information of China (English)

    SUN Zong-Li; KANG Yan-Shuang

    2011-01-01

    Classical density functional theory is used to study the associating Lennard Jones fluids in contact with spherical hard wall of different curvature radii. The interfacial properties including contact density and fluid-solid interfacial tension are investigated. The influences of associating energy, curvature of hard wall and the bulk density of Huids on these properties are analyzed in detail. The results may provide helpful clues to understand the interfacial properties of other complex fluids.%@@ Classical density functional theory is used to study the associating Lennard Jones fluids in contact with spherical hard wall of different curvature radii.The interfacial properties including contact density and fluid-solid intcrfacial tension are investigated.The influences of associating energy, curvature of hard wall and the hulk density of fluids on these properties are analyzed in detail.The results may provide helpful clues to understand the interfacial properties of other complex fluids.

  1. Long range correction for multi-site Lennard-Jones models and planar interfaces

    CERN Document Server

    Werth, Stephan; Horsch, Martin; Vrabec, Jadran; Hasse, Hans

    2015-01-01

    A slab based long range correction approach for multi-site Lennard-Jones models is presented for systems with a planar film geometry that is based on the work by Janecek, J. Phys. Chem. B 110: 6264 (2006). It is efficient because it relies on a center-of-mass cutoff scheme and scales in terms of numerics almost perfectly with the molecule number. For validation, a series of simulations with the two-center Lennard-Jones model fluid, carbon dioxide and cyclohexane is carried out. The results of the present approach, a site-based long range correction and simulations without any long range correction are compared with respect to the saturated liquid density and the surface tension. The present simulation results exhibit only a weak dependence on the cutoff radius, indicating a high accuracy of the implemented long range correction.

  2. A Lennard-Jones embedded-atom potential and its application to the study of melting

    Institute of Scientific and Technical Information of China (English)

    王暾; 周富信; 刘曰武

    2002-01-01

    The nearest-neighbour Lennard-Jones potential from the embedded-atom method is extended to a form thatincludes more than nearest neighbours. The model has been applied to study melting with molecular dynamics. Thecalculated melting point, fractional volume change on melting, heat of fusion and linear coefficients of thermal expansionare in good agreement with experimental data. We have found that the second and third neighbours influence the meltingpoint distinctly.

  3. Effect of Energy Polydispersity on the Nature of Lennard-Jones Liquids

    OpenAIRE

    Ingebrigtsen, Trond S.; Tanaka, Hajime

    2016-01-01

    In the companion paper [T. S. Ingebrigtsen and H. Tanaka, J. Phys. Chem. B 119, 11052 (2015)] the effect of size polydispersity on the nature of Lennard-Jones (LJ) liquids, which represent most molecular liquids without hydrogen bonds, was studied. More specifically, it was shown that even highly size polydisperse LJ liquids are Roskilde-simple (RS) liquids. RS liquids are liquids with strong correlation between constant volume equilibrium fluctuations of virial and potential energy and are s...

  4. Designing for the future: a post-occupancy evaluation of the Peter Jones Learning Centre

    OpenAIRE

    Pizzuti-Ashby, Jacqueline Grace

    2013-01-01

    This exploratory study examines the Peter Jones Learning Centre’s (PJLC) transition from a quiet, autonomous interior to a learning commons model encouraging collaboration and socialization. Located at University of the Fraser Valley (UFV) in British Columbia, the PJLC has been revitalized to support new learning theories, in addition to providing a hub for students’ involvement and engagement on campus. Research in the planning, function, and utilization of non-formal learning environments i...

  5. PENDETEKSIAN BAGIAN TUBUH MANUSIA UNTUK FILTER PORNOGRAFI DENGAN METODE VIOLA-JONES

    Directory of Open Access Journals (Sweden)

    Benny Senjaya

    2012-05-01

    application. First, several parts of the human body are chosen to be detected as the data training using the Viola-Jones method. Then, another set of images (similar body parts but different images are run through the application to be recognized. The result shows 86.25% of successful detection. The failures are identified and show that the inputted data are completely different with the data training.

  6. Pressure-energy correlations and thermodynamic scaling in viscous Lennard-Jones liquids

    OpenAIRE

    Coslovich, D.; Roland, C. M.

    2008-01-01

    We use molecular dynamics simulation results on viscous binary Lennard-Jones mixtures to examine the correlation between the potential energy and the virial. In accord with a recent proposal [U. R. Pedersen et. al. Phys. Rev. Lett. 100, 015701 (2008)], the fluctuations in the two quantities are found to be strongly correlated, exhibiting a proportionality constant, Gamma, numerically equal to one-third the slope of an inverse power law approximation to the intermolecular potential function. T...

  7. DOF phase separation of the Lennard-Jones fcc(111) surface

    OpenAIRE

    Jayanthi, C. S.; Celestini, Franck; Ercolessi, Furio; Tosatti, Erio

    1999-01-01

    Recent lattice model calculations have suggested that a full-layered crystal surface may undergo, under canonical (particle-conserving) conditions, a preroughening-driven two-dimensional phase separation into two disordered flat (DOF) regions, of opposite order parameter. We have carried out extensive classical molecular dynamics (MD) simulations of the Lennard-Jones fcc(111) surface, to check whether these predictions are relevant or not for a realistic continuous system. Very long simulatio...

  8. Dynamics of an assembly of finite-size Lennard-Jones spheres

    International Nuclear Information System (INIS)

    The time-averaged Fourier spectra of the number density, velocity, and force fields are obtained numerically for an assembly of spherical particles interacting via the Lennard-Jones potential. The magnitude spectra determine the dominant wave numbers, and the phase difference between the Lennard-Jones force and number density spectra determines the nature of the particle dynamics. The latter is used to show that for every wave number k there is a critical frequency ωc(k), such that when ωc(k) the phase difference is π/2 and when ω approx-gt ωc(k) the phase difference is -π/2. The ratio of the frequency and the wave number at which the phase difference changes sign is used to define an effective sound speed for the particle system. The effective sound speed is shown to be a function of the dimensionless wave number, and is locally minimum at the same dimensionless wave numbers for which the static structure factor is minimum. It is also shown that the dynamical response of the particle system for waves with speeds greater than the effective sound speed is similar to the response of the hyperbolic systems of equations, and for waves with speeds smaller than the effective sound speed the response is similar to the response of the elliptic systems. The convection effects are shown to be of the same order of magnitude as the Lennard-Jones forces, and the change of type of the equations from hyperbolic to elliptic occurs when the magnitude of the convection term is comparable to the magnitude of the Lennard-Jones force term. It is also shown that the change of type cannot occur in a theory where the convection term is neglected. copyright 1996 The American Physical Society

  9. On the Farrell-Jones Conjecture for Waldhausen's $A$-theory

    OpenAIRE

    Enkelmann, Nils-Edvin; Lück, Wolfgang; Pieper, Malte; Ullmann, Mark; Winges, Christoph

    2016-01-01

    We prove the Farrell-Jones Conjecture for (non-connective) $A$-theory with coefficients and finite wreath products for hyperbolic groups, CAT(0)-groups, cocompact lattices in almost connected Lie groups and fundamental groups of manifolds of dimension less or equal to three. Moreover, we prove inheritance properties such as passing to subgroups, colimits of direct systems of groups, finite direct products and finite free products. These results hold also for Whitehead spectra and spectra of s...

  10. Towards identifying the world stock market cross-correlations: DAX versus Dow Jones

    OpenAIRE

    S. Drozdz; Gruemmer, F.; Ruf, F.; Speth, J.(Institut für Kernphysik, Forschungszentrum Jülich, Jülich, D-52425, Germany)

    2000-01-01

    Effects connected with the world globalization affect also the financial markets. On a way towards quantifying the related characteristics we study the financial empirical correlation matrix of the 60 companies which both the Deutsche Aktienindex (DAX) and the Dow Jones (DJ) industrial average comprised during the years 1990-1999. The time-dependence of the underlying cross-correlations is monitored using a time window of 60 trading days. Our study shows that if the time-zone delays are prope...

  11. The Dow Jones Industrial Average: Issues of Downward Bias and Increased Volatility

    OpenAIRE

    Mueller, Paul A.; Raj A. Padmaraj; Ralph C. St. John

    1999-01-01

    Does the method of divisor adjustment used for stock splits in the Dow Jones Industrial Average (DJIA) cause a downward bias in the averageÕs level and does this method of adjustment cause increased volatility in the average? To investigate these issues, two averages are created using DJIA stocks. One average is adjusted for stock splits through adjustment in the divisor. This method is identical to the DJIA method of adjustment. The other average makes adjustment for stock splits by adjustin...

  12. Deuterium-labeling method for the assignment of histidine nuclear magentic resonance peaks of proteins

    International Nuclear Information System (INIS)

    A tritium labelling method involving differential tritium exchange at the C-2 H position of histidines and 1H NMR of differentially deuterated proteins can be a general method for the assignment of the histidine NMR peaks. In the present report this method is modified by replacing the tritium with deuterium, which eliminates ambiguities arising from the tritium isotope effect. In the deuterium labelling method, differentially deuterated proteins are cleaved by trypsin into smaller peptides each containing a single histidine residue, which are separated by chromatography. The method was applied to the Bence Hones dimer Ak which contains two histidine residues in the constant domain of each of the light chains. The decay of the NMR peaks with time allowed the assignment of one peak to His189 and the other to His198

  13. Metastability, spectrum, and eigencurrents of the Lennard-Jones-38 network

    International Nuclear Information System (INIS)

    We develop computational tools for spectral analysis of stochastic networks representing energy landscapes of atomic and molecular clusters. Physical meaning and some properties of eigenvalues, left and right eigenvectors, and eigencurrents are discussed. We propose an approach to compute a collection of eigenpairs and corresponding eigencurrents describing the most important relaxation processes taking place in the system on its way to the equilibrium. It is suitable for large and complex stochastic networks where pairwise transition rates, given by the Arrhenius law, vary by orders of magnitude. The proposed methodology is applied to the network representing the Lennard-Jones-38 cluster created by Wales's group. Its energy landscape has a double funnel structure with a deep and narrow face-centered cubic funnel and a shallower and wider icosahedral funnel. However, the complete spectrum of the generator matrix of the Lennard-Jones-38 network has no appreciable spectral gap separating the eigenvalue corresponding to the escape from the icosahedral funnel. We provide a detailed description of the escape process from the icosahedral funnel using the eigencurrent and demonstrate a superexponential growth of the corresponding eigenvalue. The proposed spectral approach is compared to the methodology of the Transition Path Theory. Finally, we discuss whether the Lennard-Jones-38 cluster is metastable from the points of view of a mathematician and a chemical physicist, and make a connection with experimental works

  14. Metastability, spectrum, and eigencurrents of the Lennard-Jones-38 network

    Energy Technology Data Exchange (ETDEWEB)

    Cameron, Maria K., E-mail: cameron@math.umd.edu [Department of Mathematics, University of Maryland, College Park, Maryland 20742-4015 (United States)

    2014-11-14

    We develop computational tools for spectral analysis of stochastic networks representing energy landscapes of atomic and molecular clusters. Physical meaning and some properties of eigenvalues, left and right eigenvectors, and eigencurrents are discussed. We propose an approach to compute a collection of eigenpairs and corresponding eigencurrents describing the most important relaxation processes taking place in the system on its way to the equilibrium. It is suitable for large and complex stochastic networks where pairwise transition rates, given by the Arrhenius law, vary by orders of magnitude. The proposed methodology is applied to the network representing the Lennard-Jones-38 cluster created by Wales's group. Its energy landscape has a double funnel structure with a deep and narrow face-centered cubic funnel and a shallower and wider icosahedral funnel. However, the complete spectrum of the generator matrix of the Lennard-Jones-38 network has no appreciable spectral gap separating the eigenvalue corresponding to the escape from the icosahedral funnel. We provide a detailed description of the escape process from the icosahedral funnel using the eigencurrent and demonstrate a superexponential growth of the corresponding eigenvalue. The proposed spectral approach is compared to the methodology of the Transition Path Theory. Finally, we discuss whether the Lennard-Jones-38 cluster is metastable from the points of view of a mathematician and a chemical physicist, and make a connection with experimental works.

  15. Metastability, spectrum, and eigencurrents of the Lennard-Jones-38 network.

    Science.gov (United States)

    Cameron, Maria K

    2014-11-14

    We develop computational tools for spectral analysis of stochastic networks representing energy landscapes of atomic and molecular clusters. Physical meaning and some properties of eigenvalues, left and right eigenvectors, and eigencurrents are discussed. We propose an approach to compute a collection of eigenpairs and corresponding eigencurrents describing the most important relaxation processes taking place in the system on its way to the equilibrium. It is suitable for large and complex stochastic networks where pairwise transition rates, given by the Arrhenius law, vary by orders of magnitude. The proposed methodology is applied to the network representing the Lennard-Jones-38 cluster created by Wales's group. Its energy landscape has a double funnel structure with a deep and narrow face-centered cubic funnel and a shallower and wider icosahedral funnel. However, the complete spectrum of the generator matrix of the Lennard-Jones-38 network has no appreciable spectral gap separating the eigenvalue corresponding to the escape from the icosahedral funnel. We provide a detailed description of the escape process from the icosahedral funnel using the eigencurrent and demonstrate a superexponential growth of the corresponding eigenvalue. The proposed spectral approach is compared to the methodology of the Transition Path Theory. Finally, we discuss whether the Lennard-Jones-38 cluster is metastable from the points of view of a mathematician and a chemical physicist, and make a connection with experimental works. PMID:25399138

  16. Mainekas teadlane soovitab Eestil enam väliskapitali ligi meelitada / Simon Jones ; interv. Aleksei Günter

    Index Scriptorium Estoniae

    Jones, Simon

    2005-01-01

    Pärnus telekommunikatsiooni- ja infofoorumil viibiv innovatsiooniekspert vastab küsimustele, mis puudutavad tema hinnangut Eesti teadus- ja arendustegevusele, tehnoloogia kasutamist sotsiaalprobleemide lahendamisel ning Eesti varustamist tasuta internetiühendusega. Lisa: Simon Jones

  17. Volatility Transmission Between Dow Jones Stock Index And Emerging Islamic Stock Index: Case Of Subprime Financial Crises

    OpenAIRE

    Amir Saadaoui; Younes Boujelbene

    2015-01-01

    In the course of the recent global crisis, the stock shocks are distributed and transmitted from their homes in the developed stock market to emerging stock markets. By supporting the development of emerging stock markets, this study aims to see the transmission of volatility between the Dow Jones stock index and the Dow Jones emerging Islamic stock indiex. In this study we have divided the period into three, periods, before, during and after this crisis to demonstrate the resilience of the I...

  18. Evaluation of the American Heart Association 2015 revised Jones criteria versus existing guidelines

    Science.gov (United States)

    Kumar, Dinesh; Bhutia, Euden; Kumar, Pradeep; Shankar, Binoy; Juneja, Atul; Chandelia, Sudha

    2016-01-01

    Objectives To compare the diagnostic yield of acute rheumatic fever (ARF) by the American Heart Association/ American College of Cardiology (AHA/ACC) 2015 revised Jones criteria with the WHO 2004 and Australian guidelines 2012. Methods Retrospective observational study in 93 cases of suspected ARF admitted to the Division of Paediatric Cardiology between January 2012 and December 2014. WHO 2004, Australian guidelines and AHA/ACC 2015 Jones criteria were applied to assess definite and probable ARF. Results Of the 93 cases, 50 were diagnosed as the first episode of ARF and 43 as a recurrence of the condition. Subclinical carditis was a predominant presentation (38%) in the first episode group (p<0.01) whereas in the recurrence group carditis (88%) was the main presentation (p<0.01). Among the joint manifestations, the majority of patients in both the first episode group and the recurrence group presented with arthralgia. Of all the patients with suspected ARF (50), 34% of cases did not fulfil the standard Jones criteria 2004; however, 86% qualified as having ARF on applying the Australian and AHA/ACC 2015 criteria. Surprisingly in the recurrence group only 67% of the patients fulfilled AHA/ACC 2015 despite the modifications incorporated beyond WHO 2004; however, all the patients fulfilled the Australian guidelines either as definite (88.4%) or probable (11.6%). Inclusion of subclinical carditis, polyarthralgia and monoarthritis as major criteria influenced the diagnosis to definite ARF in 20%, 10% and 4% of patients, respectively. Conclusions The clinical manifestations of ARF, comprising subclinical carditis and arthralgia, are possibly milder in the Indian population; hence, inclusion of subclinical carditis, polyarthralgia and monoarthritis as major criteria in the newer guidelines has improved the diagnostic yield of ARF. In the absence of a gold standard for the diagnosis of ARF, it is not possible to comment on sensitivity and specificity. PMID:27326228

  19. Formation of global energy minimim structures in the growth process of Lennard-Jones clusters

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Koshelev, Andrey; Shutovich, Andrey; Solov'yov, Andrey V.; Greiner, Walter

    2003-01-01

    We present a new theoretical framework for modelling the cluster growing process. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing paths up to the cluster sizes of 150 atoms. We demonstrate...... that in this way all known global minimum structures of the Lennard-Jones (LJ) clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic numbers sequence for the clusters of noble gases atoms and compare...

  20. Exact numerical solution of the Schroedinger equation with the Lennard--Jones potential

    International Nuclear Information System (INIS)

    The series solution of a differential equation in an immediate neighborhood of an irregular singularity has a finite convergence radius. For the Lennard-Jones potential, devised as a model for Li+-He scattering, the convergence radius is so small that the repulsive potential is still extremely strong at a point near the convergence limit. Consequently, any standard numerical method cannot start from such a point. In the domain intermediate between the convergence limit of the series and the starting point of a standard numerical integration, the solution involves a part that varies rapidly. A special numerical method has been developed to deal with the solution in this domain

  1. The potential energy landscape in the Lennard-Jones binary mixture model

    International Nuclear Information System (INIS)

    The potential energy landscape in the Kob-Andersen Lennard-Jones binary mixture model has been studied carefully from the liquid down to the supercooled regime, from T = 2 down to 0.46. One thousand independent configurations along the time evolution locus have been examined at each temperature investigated. From the starting configuration, we searched for the nearest saddle (or quasi-saddle) and minimum of the potential energy. The vibrational densities of states for the starting and the two derived configurations have been evaluated. Besides the number of negative eigenvalues of the saddles other quantities show some signature of the approach of the dynamical arrest temperature

  2. Fairy tales? Marion Jones, C.J. Hunter and the framing of doping in American newspapers

    DEFF Research Database (Denmark)

    Pfister, Gertrud Ursula; Gems, Gerald

    2015-01-01

    convicted of doping. The material consists of sport reports about the 2000 Olympic Games in three American newspapers. These Games proved controversial due to the allegations and inquiries of the media (both national and international) regarding doping issues and the prominence of the American athletes...... under suspicion. At the same time, the 2000 Olympics can be considered a watershed in American anti-doping policy. The media portrayed Jones and Hunter as the Beauty and the Beast or Svengali and his victim, using a famous fairy tale and a well-known novel to capture attention, label the protagonists...

  3. Numerical simulation of pool boiling of a Lennard-Jones liquid

    KAUST Repository

    Inaoka, Hajime

    2013-09-01

    We performed a numerical simulation of pool boiling by a molecular dynamics model. In the simulation, a liquid composed of Lennard-Jones particles in a uniform gravitational field is heated by a heat source at the bottom of the system. The model successfully reproduces the change in regimes of boiling from nucleate boiling to film boiling with the increase of the heat source temperature. We present the pool boiling curve by the model, whose general behavior is consistent with those observed in experiments of pool boiling. © 2013 Elsevier B.V. All rights reserved.

  4. Kinetic non-optimality and vibrational stability of proteins

    OpenAIRE

    Cieplak, Marek; Hoang, Trinh Xuan

    2001-01-01

    Scaling of folding times in Go models of proteins and of decoy structures with the Lennard-Jones potentials in the native contacts reveal %robust power law trends when studied under optimal folding conditions. The power law exponent depends on the type of native geometry. Its value indicates lack of kinetic optimality in the model proteins. In proteins, mechanical and thermodynamic stabilities are correlated.

  5. In recognition of the retirement of Dr. Christopher T. Jones ; The Hon. Mike Rogers of Alabama in the House of Representatives

    OpenAIRE

    Rogers, Mike

    2012-01-01

    Jones graduated in 2010 from the Executive Leadership Program, Center for Homeland Defense and Security at the Naval Postgraduate School. Mr. ROGERS of Alabama. Mr. Speaker, I ask for the House’s attention today to honor Christopher T. Jones as he retires from the Center for Domestic Preparedness (CDP) in Anniston, Alabama. Dr. Jones joined the U.S. Department of Homeland Security’s Federal Emergency Management Agency (FEMA) as Superintendent for the CDP on August 3, 2008.

  6. The potential energy landscape for crystallisation of a Lennard-Jones fluid

    Science.gov (United States)

    de Souza, Vanessa K.; Wales, David J.

    2016-07-01

    Crystallisation pathways are explored by direct analysis of the potential energy landscape for a system of Lennard-Jones particles with periodic boundary conditions. A database of minima and transition states linking liquid and crystalline states is constructed using discrete path sampling and the entire potential energy landscape from liquid to crystal is visualised. We demonstrate that there is a strong negative correlation between the number of atoms in the largest crystalline cluster and the potential energy. In common with previous results we find a strong bias towards the growth of FCC rather than HCP clusters, despite a very small potential energy difference. We characterise three types of perfect crystals with very similar energies: pure FCC, pure HCP, and combinations of FCC and HCP layers. There are also many slightly defective crystalline structures. The effect of the simulation box is analysed for a supercell containing 864 atoms. There are low barriers between some of the different crystalline structures via pathways involving sliding layers, and many different defective structures with FCC layers stacked at an angle to the periodic box. Finally, we compare a binary Lennard-Jones system and visualise the potential energy landscape from supercooled liquid to crystal.

  7. A comparison of molecular dynamics and diffuse interface model predictions of Lennard-Jones fluid evaporation

    Energy Technology Data Exchange (ETDEWEB)

    Barbante, Paolo [Dipartimento di Matematica, Politecnico di Milano - Piazza Leonardo da Vinci 32 - 20133 Milano (Italy); Frezzotti, Aldo; Gibelli, Livio [Dipartimento di Scienze e Tecnologie Aerospaziali, Politecnico di Milano - Via La Masa 34 - 20156 Milano (Italy)

    2014-12-09

    The unsteady evaporation of a thin planar liquid film is studied by molecular dynamics simulations of Lennard-Jones fluid. The obtained results are compared with the predictions of a diffuse interface model in which capillary Korteweg contributions are added to hydrodynamic equations, in order to obtain a unified description of the liquid bulk, liquid-vapor interface and vapor region. Particular care has been taken in constructing a diffuse interface model matching the thermodynamic and transport properties of the Lennard-Jones fluid. The comparison of diffuse interface model and molecular dynamics results shows that, although good agreement is obtained in equilibrium conditions, remarkable deviations of diffuse interface model predictions from the reference molecular dynamics results are observed in the simulation of liquid film evaporation. It is also observed that molecular dynamics results are in good agreement with preliminary results obtained from a composite model which describes the liquid film by a standard hydrodynamic model and the vapor by the Boltzmann equation. The two mathematical model models are connected by kinetic boundary conditions assuming unit evaporation coefficient.

  8. Idiopathic gingival fibromatosis associated with progressive hearing loss: A nonfamilial variant of Jones syndrome

    Directory of Open Access Journals (Sweden)

    Bagavad Gita

    2014-01-01

    Full Text Available Gingival fibromatosis is characterized by gingival tissue overgrowth of a firm and fibrotic nature. The growth is slow and progressive and is drug-induced, idiopathic, or hereditary in etiology. It occurs isolated or frequently as a component of various syndromes. Our patient presented with the complaint of gingival enlargement associated with progressive deafness, characteristic of Jones syndrome. This case report is important and unique since it is the first known one to have a Jones syndrome-like presentation without a family history. A male patient aged 14 years reported with the chief complaint of swelling of gums and progressive hearing loss in both ears for the past one year. There was no family history or history of drug intake. Enlargement was generalized, fibrotic and bulbous, involving the free and attached gingiva, extending up to the middle 1/3 rd of the crown. Investigations such as pure tone audiogram, impedance audiometry, and Tone decay test concluded that there was severe right and moderate left sensorineural hearing loss. The case was diagnosed to be idiopathic, generalized gingival fibromatosis with progressive hearing loss. The gingival overgrowth was managed by gingivectomy and periodic review. The patient was advised to use high occlusion computer generated hearing aids for his deafness as it was not treatable by medicines or surgery. This unique case report once again emphasizes the heterogeneity of gingival fibromatosis, which can present in an atypical manner.

  9. Birefringence imaging of posterior eye by multi-functional Jones matrix optical coherence tomography.

    Science.gov (United States)

    Sugiyama, Satoshi; Hong, Young-Joo; Kasaragod, Deepa; Makita, Shuichi; Uematsu, Sato; Ikuno, Yasushi; Miura, Masahiro; Yasuno, Yoshiaki

    2015-12-01

    A clinical grade prototype of posterior multifunctional Jones matrix optical coherence tomography (JM-OCT) is presented. This JM-OCT visualized depth-localized birefringence in addition to conventional cumulative phase retardation imaging through local Jones matrix analysis. In addition, it simultaneously provides a sensitivity enhanced scattering OCT, a quantitative polarization uniformity contrast, and OCT-based angiography. The probe beam is at 1-μm wavelength band. The measurement speed and the depth-resolution were 100,000 A-lines/s, and 6.6 μm in tissue, respectively. Normal and pathologic eyes are examined and several clinical features are revealed, which includes high birefringence in the choroid and lamina cribrosa, and birefringent layered structure of the sclera. The theoretical details of the depth-localized birefringence imaging and conventional phase retardation imaging are formulated. This formulation indicates that the birefringence imaging correctly measures a depth-localized single-trip phase retardation of a tissue, while the conventional phase retardation can provide correct single-trip phase retardation only for some specific types of samples. PMID:26713208

  10. The fish and fisheries of Jones Bank and the wider Celtic Sea

    Science.gov (United States)

    Martinez, I.; Ellis, J. R.; Scott, B.; Tidd, A.

    2013-10-01

    The Celtic Sea is a diverse fishing ground that supports important commercial fisheries for a range of demersal fish, large and small-bodied pelagic fish and a variety of cephalopods and other shellfish. A regional overview of the main commercial fish stocks of the Celtic Sea and of the fish that occur in the vicinity of Jones Bank are provided through analyses of landings data from English and Welsh vessels, and from scientific trawl surveys. Dedicated smaller scale sampling via trawl surveys combined with baited cameras on and around the Jones Bank were also analysed to investigate the importance of sandbank habitats with attention paid to the differences in the species occurring on the top of the bank in comparison to adjacent off-bank habitats. Official landing statistics for UK (English and Welsh) vessels indicated that the predominant commercial demersal species in ICES Divisions VIIg,h (in terms of quantities landed) were anglerfish, megrim, pollack and skates (Rajidae). There were, however, regional differences in the distribution of fish and fisheries, and the area surrounding Jones Bank (ICES Rectangles 28E1 and 28E2) supports fisheries for megrim, anglerfish, skates, hake, ling and turbot, with otter trawl, gillnet and beam trawl the main gears used. Recent survey data collected with GOV (Grande Ouverture Verticale) trawl from the Celtic Sea (ICES Divisions VIIe-h, 2007-2010) were used to highlight the broad scale distribution of the main fish assemblages in the Celtic Sea. Analyses of the fish and cephalopod catches from these surveys indicated that there were four broad assemblages in the area, including (i) a region around the Cornwall (which will also be partly influenced by the necessity to use rockhopper ground gear on these rough grounds), (ii) the shallower regions of the north-western Celtic Sea (including parts of the Bristol Channel), (iii) the deeper parts of the outer shelf and (iv) the central Celtic Sea. These data also provided

  11. Mean spherical approximation for the Lennard-Jones-like two Yukawa model: Comparison against Monte Carlo data

    Directory of Open Access Journals (Sweden)

    A. Trokhymchuk

    2011-09-01

    Full Text Available Monte Carlo simulation studies are performed for the Lennard-Jones like two Yukawa (LJ2Y potential to show how properties of this model fluid depend on the replacement of the soft repulsion by the hard-core repulsion. Different distances for the positioning of hard core have been explored. We have found, that for temperatures that are slightly lower and slightly higher of the critical point temperature for the Lennard-Jones fluid, placing the hard core at distances that are shorter than zero-potential energy is well justified by thermodynamic properties that are practically the same as in original LJ2Y model without hard core. However, going to extreme conditions with the high temperature one should be careful since presence of the hard core provokes changes in the properties of the system. The later is extremely important when the mean spherical approximation (MSA theory is applied to treat the Lennard-Jones-like fluid.

  12. Distance fluctuation of a single molecule in Lennard-Jones liquid based on generalized Langevin equation and mode coupling theory

    Science.gov (United States)

    Li, Ping; Dong, Yunhong; Zhao, Nanrong; Hou, Zhonghuai

    2014-04-01

    Distance fluctuation of a single molecule, modeled as an idealized bead-spring chain, dissolved in a Lennard-Jones liquid is studied by using a multidimensional generalized Langevin equation, where the friction kernel ζ(t) is calculated from the kinetic mode coupling theory (MCT). Temporal behavior of the distance autocorrelation function shows three typical regimes of time dependence, starting with a constant, followed by a power law of t-α, and finally an exponential decay. Particular attentions are paid to the time span of the power law regime, which corresponds to anomalous subdiffusion behavior, and the MCT framework enables us to investigate thoroughly how this regime depends on microscopic details such as the bead-to-solvent mass ratio MR, chain spring frequency ω, and the chain length N. Interestingly, the exponent α is robust to be 1/2 against the change of these parameters, although the friction kernel ζ(t) shows nontrivial dependence on time. In addition, we find that the starting time of the power-law region t1 scales with Γ-1, with Γ = 4ω2/ζ0 where ζ0 is the zero-frequency friction which decreases rapidly with increasing bead mass. On the other hand, the ending time t2 is not sensitive to varying ω or ζ0, but it increases with N rapidly before it reaches a constant for N larger than some threshold value. Our work may provide a unified strategy starting from the microscopic level to understand the anomalous subdiffusive behavior regarding large scale conformational change of polymers or proteins.

  13. Algumas considerações sobre o termo afânise a partir de E. Jones e J. Lacan

    OpenAIRE

    Daniela Scheinkman Chatelard

    2001-01-01

    Em sua primeira parte, este artigo propõe-se a retomar e a desenvolver o termo afânise, tal como foi forjado por Ernest Jones. Na segunda parte, trata-se de acrescentar a importância dada por Jacques Lacan a este termo: do registro do puro desaparecimento do desejo, em sua relação com a castração, como foi sustentado por E. Jones, passamos ao registro do desaparecimento do sujeito, enquanto sujeito dividido e desejante. Para isso, recorremos ao exemplo do personagem literário, Hamlet, da trag...

  14. Gunfight at the NOT OK Corral: Reply to "High Noon for Microfinance" by Duvendack and Palmer-Jones (Uncut version).

    Science.gov (United States)

    Pitt, Mark M

    2012-01-01

    The paper "High Noon for Microfinance Impact Evaluations" by Duvendack and Palmer-Jones replicates the papers of Chemin (2008) and Pitt and Khandker (1998) that estimate the impact of microfinance in Bangladesh. My paper replicates the Duvendack and Palmer-Jones replication and finds so many serious errors in their code and misrepresentations of the methods described in their paper that I conclude that their results are spurious and provide no evidence about the validity of either the papers of Chemin or Pitt and Khandker or on the effectiveness of microfinance. PMID:24833807

  15. Re-sounding Radicalism: Echo in William Blake and the Chartist Poets Ernest Jones and Gerald Massey

    OpenAIRE

    Mccawley, Nichola Lee

    2012-01-01

    This thesis argues that William Blake’s poetry creates meaning through internal poetic echoes, and that these Blakean echoes re-sound in Ernest Jones and Gerald Massey’s Poetry. There is no demonstrable link between Blake and Chartism; this raises the question of how to account for poetic echoes that occur in the absence of a direct link. The thesis uses two complementary methodological strategies. The significance of the Blakean echoes in Jones and Massey’s work will be demonstrated through ...

  16. The Lion and the Lady Revisited: Another Look at the Firing of Mary L. Jones as Los Angeles Public Librarian in 1905.

    Science.gov (United States)

    Wiegand, Wayne A.

    1983-01-01

    Recounts events that led to the firing of Mary L. Jones, Director of Los Angeles Public Library (1905) and caught in public crossfire such figures as the mayor, city council, library board of directors, Charles Lummis (Jones's replacement), Susan B. Anthony, Anna Shaw, Herbert Putnam, and Melvil Dewey. (29 references) (EJS)

  17. Vapour-to-Liquid Nucleation in Associating Lennard-Jones Fluids with Multiple Association Sites

    Institute of Scientific and Technical Information of China (English)

    FU Dong; LIAO Tao

    2007-01-01

    The excess Helmholtz free energy functional for associating Lennard-Jones (LJ) fluid is formulated in terms of a weighted density approximation for short-ranged interactions and a Weeks Chandler-Andersen approximation for long-range attraction. Within the framework of density functional theory, phase equilibria, vapour-liquid surface tension and vapour-liquid nucleation properties including the density profile, work of formation, excess number of particles and critical supersaturation are investigated for associating LJ fluids with different numbers of association sites (M=1,2,3,4) per particle. The influences of association energy and association sites on phase equilibria, surface tension and vapour-liquid nucleation properties are discussed.

  18. Cavitation and crystallization in a metastable Lennard-Jones liquid at negative pressures and low temperatures.

    Science.gov (United States)

    Baidakov, Vladimir G; Bobrov, Konstantin S; Teterin, Aleksey S

    2011-08-01

    Molecular dynamics simulations have been used to investigate the kinetics of spontaneous cavitation and crystallization in a Lennard-Jones liquid at negative pressures in the temperature range where these processes compete with each other. The nucleation rate has been calculated in NVE and NpT ensembles by the method of mean lifetime and the transition interface sampling method with parallel path swapping. The data obtained have been used to determine in the framework of classical nucleation theory the value of the ratio of the solid-liquid and the liquid-void interfacial free energy for critical crystals and cavities and the values of their volumes at points where the cavitation rate of the liquid is equal to the rate of its crystallization. PMID:21823717

  19. Blueschist metamorphism in the Yreka-Fort Jones area, Klamath Mountains, California

    Science.gov (United States)

    Hotz, Preston E.

    1973-01-01

    Blueschist is plentiful in the Yreka-Fort Jones area, eastern Klamath Mountains, adjacent to a belt of serpentinite that marks the boundary between two fundamental lithologic units, an eastern belt of early Paleozoic sedimentary and metamorphic rocks, and a western greenstone-chert assemblage of late Paleozoic and Triassic(?) age. The blueschists, which contain lawsonite and glaucophane or crossite, occur with phyllitic quartzite and siliceous phyllite of the Stuart Fork Formation, which is overthrust northwestward on the greenstone-chert terrane. The blueschist facies metamorphism probably was synchronous with Middle and Late Jurassic metamorphism of the Stuart Fork Formation. The blueschist-serpentinite terrane possibly marks the site of collision between the eastern Klamath plate and an oceanic western Paleozoic and Triassic plate.

  20. A Jones matrix formalism for simulating 3D Polarised Light Imaging of brain tissue

    CERN Document Server

    Menzel, Miriam; De Raedt, Hans; Reckfort, Julia; Amunts, Katrin; Axer, Markus

    2015-01-01

    The neuroimaging technique 3D Polarised Light Imaging (3D-PLI) provides a high-resolution reconstruction of nerve fibres in human post-mortem brains. The orientations of the fibres are derived from birefringence measurements of histological brain sections assuming that the nerve fibres - consisting of an axon and a surrounding myelin sheath - are uniaxial birefringent and that the measured optic axis is oriented in direction of the nerve fibres (macroscopic model). Although experimental studies support this assumption, the molecular structure of the myelin sheath suggests that the birefringence of a nerve fibre can be described more precisely by multiple optic axes oriented radially around the fibre axis (microscopic model). In this paper, we compare the use of the macroscopic and the microscopic model for simulating 3D-PLI by means of the Jones matrix formalism. The simulations show that the macroscopic model ensures a reliable estimation of the fibre orientations as long as the polarimeter does not resolve ...

  1. Translation and cultural adaptation of the Jones Dependency Tool to Brazilian Portuguese

    Directory of Open Access Journals (Sweden)

    Karen Marchesan de Andrade

    2014-12-01

    Full Text Available Methodological study to translate and culturally adapt the Jones Dependency Tool (JDT to Portuguese. The translation and cultural adaptation method had four stages. First stage: translation of the original instrument from English to Portuguese. Second stage: content, cultural, semantic and conceptual equivalence in relation to the original instrument. Third stage: back-translation. Fourth stage: comparison of the translated and back-translated versions by a committee of specialists, resulting in the final version. In the Communication Domain, the original JDT measured pain using high, intermediate and low ranges, but the committee suggested replacing it with a visual analog scale. The translation and cultural adaptation of the JDT to Portuguese produced an instrument applicable to our reality. Studies need to be conducted to test the validity and reliability of the JDT in Brazilian Emergency Services. doi: 10.5216/ree.v16i4.22345.

  2. Myyntityön ja myynnin johtamisen kehittäminen, case Jack & Jones

    OpenAIRE

    Virranta, Heidi

    2014-01-01

    Tiivistelmä Myyntityö on entistä haastavampi ammatti. Pärjätäkseen kilpailussa yritys tarvitsee osaavan ja motivoituneen henkilöstön, joka haluaa aktiivisesti toimia myyntitavoitteiden saavuttamiseksi. Henkilöstön tueksi yritys tarvitsee osaavia esimiehiä, jotka myynnin johtamisen avulla saavat työntekijät tekemään parhaansa ja enemmän. Tässä opinnäytetyössä tutkittiin myyntityöhön vaikuttavia tekijöitä Kekäle Oy:n Jack & Jones-myymälöissä. Tutkimuksessa selvitettiin niin työntekijän...

  3. Phase diagram and universality of the Lennard-Jones gas-liquid system

    KAUST Repository

    Watanabe, Hiroshi

    2012-01-01

    The gas-liquid phase transition of the three-dimensional Lennard-Jones particles system is studied by molecular dynamics simulations. The gas and liquid densities in the coexisting state are determined with high accuracy. The critical point is determined by the block density analysis of the Binder parameter with the aid of the law of rectilinear diameter. From the critical behavior of the gas-liquid coexisting density, the critical exponent of the order parameter is estimated to be β = 0.3285(7). Surface tension is estimated from interface broadening behavior due to capillary waves. From the critical behavior of the surface tension, the critical exponent of the correlation length is estimated to be ν = 0.63(4). The obtained values of β and ν are consistent with those of the Ising universality class. © 2012 American Institute of Physics.

  4. Modelling of disjoining pressure for Lennard-Jones free thin films

    Science.gov (United States)

    Peng, Tiefeng; Gao, Xuechao; Li, Qibin; Yang, Siyuan; Tang, Qizhong

    2016-03-01

    Development of disjoining pressure was performed to study the symmetric, Lennard-Jones (LJ) free thin films using molecular modelling. A methodology rooted from film thermodynamics was established to derive the disjoining pressure isotherm (Π ‑ h), which is based on the surface tension at varied film thicknesses and can be viewed as a post-processing technique. The results showed that the disjoining pressure of LJ fluid is purely attractive. Compared with the complicated method reported previously, this methodology is demonstrated to be more convenient and readily applicable for other liquid films (e.g. water, aqueous thin films containing electrolyte or surfactants), meanwhile it can be applied at both low and high temperatures.

  5. Chemical diversity in the essential oil of Indian valerian (Valeriana jatamansi Jones).

    Science.gov (United States)

    Verma, Ram S; Verma, Rajesh K; Padalia, Rajendra C; Chauhan, Amit; Singh, Anand; Singh, Hemendra P

    2011-10-01

    To explore the diversity in the essential oil yield and composition of Valeriana jatamansi Jones (syn. V. wallichii DC) growing wild in Uttarakhand (Western Himalaya), 17 populations were collected from different locations and grown under similar conditions. Comparative results showed considerable variations in the essential oil yield and composition. The essential oil yield varied from 0.21 to 0.46% in the fresh roots and rhizomes of different populations of V. jatamansi. Analysis of the essential oils by GC (RI) and GC/MS and the subsequent classification by principal component analysis (PCA) resulted in six clusters with significant variations in their terpenoid composition. Major components in the essential oils of the different populations were patchouli alcohol (1; 13.4-66.7%), α-bulnesene (3; perfumery. PMID:22006721

  6. Mean-Spherical Approximation for the Lennard-Jones-like Two Yukawa Model: Comparison against Monte Carlo Data

    Czech Academy of Sciences Publication Activity Database

    Krejčí, J.; Nezbeda, Ivo; Melnyk, R.; Trokhymchuk, A.

    2011-01-01

    Roč. 14, č. 3 (2011), Article Number 33005. ISSN 1607-324X R&D Projects: GA AV ČR IAA400720710 Institutional research plan: CEZ:AV0Z40720504 Keywords : two Yukawa potential * Lennard-Jones fluid * mean-spherical approximation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.811, year: 2011

  7. Comment on Cross, Fine, Jones, and Walsh (2012): Good Therapeutic Services--Therapeutic Advocacy and Forensic Neutrality

    Science.gov (United States)

    Connell, Mary

    2012-01-01

    Cross, Fine, Jones, and Walsh (2012) provided a thoughtful review and critique of a book chapter describing the interview process at Child Advocacy Centers. They observed some of the ways that concerns raised in that chapter are being addressed and described revised guidelines that further clarify issues. Ongoing research and examination of the…

  8. From Epic to Novel——A Stylistic Study on the History of Tom Jones a Foundling

    Institute of Scientific and Technical Information of China (English)

    李潇雨

    2007-01-01

    This article takes Henry Fielding's novel Tom Jones as its object to make a textual analysis.It can be easily seen that novel as a literature type just derived from the process of breaking the narrative and aesthetic distance of traditional epic.

  9. Localized fluidity modes and the topology of the constant-potential-energy hypersurfaces of Lennard-Jones matter

    DEFF Research Database (Denmark)

    Cotterill, Rodney M J; Madsen, J.

    1986-01-01

    Sections of configuration space for Lennard-Jones matter were obtained by probing all the normal-mode energy profiles, following diagonalization of the dynamical matrix for a 240-particle system. For the crystal and sufficiently cold glass, these are single welled, whereas increasing numbers...

  10. Interatomic correlations moments of atoms in the two-dimensional hexagonal lattice by using Morse and Lenard-Jones potentials

    Science.gov (United States)

    Rodrigues, Clóves G.

    2016-06-01

    In this work we investigate the interatomic correlation moments in two-dimensional model of a weakly anharmonic crystal (i.e., not very high temperatures) with hexagonal lattice, using the Correlative Method of Unsymmetrized Self-Consistent Field (CUSF). The numerical results are obtained (and compared) by using the Morse and Lenard-Jones potentials.

  11. Excess entropy and crystallization in Stillinger-Weber and Lennard-Jones fluids

    Energy Technology Data Exchange (ETDEWEB)

    Dhabal, Debdas; Chakravarty, Charusita, E-mail: charus@chemistry.iitd.ac.in [Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016 (India); Nguyen, Andrew Huy; Molinero, Valeria [Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850 (United States); Singh, Murari [Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100 (Israel); Khatua, Prabir; Bandyopadhyay, Sanjoy [Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302 (India)

    2015-10-28

    Molecular dynamics simulations are used to contrast the supercooling and crystallization behaviour of monatomic liquids that exemplify the transition from simple to anomalous, tetrahedral liquids. As examples of simple fluids, we use the Lennard-Jones (LJ) liquid and a pair-dominated Stillinger-Weber liquid (SW{sub 16}). As examples of tetrahedral, water-like fluids, we use the Stillinger-Weber model with variable tetrahedrality parameterized for germanium (SW{sub 20}), silicon (SW{sub 21}), and water (SW{sub 23.15} or mW model). The thermodynamic response functions show clear qualitative differences between simple and water-like liquids. For simple liquids, the compressibility and the heat capacity remain small on isobaric cooling. The tetrahedral liquids in contrast show a very sharp rise in these two response functions as the lower limit of liquid-phase stability is reached. While the thermal expansivity decreases with temperature but never crosses zero in simple liquids, in all three tetrahedral liquids at the studied pressure, there is a temperature of maximum density below which thermal expansivity is negative. In contrast to the thermodynamic response functions, the excess entropy on isobaric cooling does not show qualitatively different features for simple and water-like liquids; however, the slope and curvature of the entropy-temperature plots reflect the heat capacity trends. Two trajectory-based computational estimation methods for the entropy and the heat capacity are compared for possible structural insights into supercooling, with the entropy obtained from thermodynamic integration. The two-phase thermodynamic estimator for the excess entropy proves to be fairly accurate in comparison to the excess entropy values obtained by thermodynamic integration, for all five Lennard-Jones and Stillinger-Weber liquids. The entropy estimator based on the multiparticle correlation expansion that accounts for both pair and triplet correlations, denoted by S{sub trip

  12. Excess entropy and crystallization in Stillinger-Weber and Lennard-Jones fluids

    International Nuclear Information System (INIS)

    Molecular dynamics simulations are used to contrast the supercooling and crystallization behaviour of monatomic liquids that exemplify the transition from simple to anomalous, tetrahedral liquids. As examples of simple fluids, we use the Lennard-Jones (LJ) liquid and a pair-dominated Stillinger-Weber liquid (SW16). As examples of tetrahedral, water-like fluids, we use the Stillinger-Weber model with variable tetrahedrality parameterized for germanium (SW20), silicon (SW21), and water (SW23.15 or mW model). The thermodynamic response functions show clear qualitative differences between simple and water-like liquids. For simple liquids, the compressibility and the heat capacity remain small on isobaric cooling. The tetrahedral liquids in contrast show a very sharp rise in these two response functions as the lower limit of liquid-phase stability is reached. While the thermal expansivity decreases with temperature but never crosses zero in simple liquids, in all three tetrahedral liquids at the studied pressure, there is a temperature of maximum density below which thermal expansivity is negative. In contrast to the thermodynamic response functions, the excess entropy on isobaric cooling does not show qualitatively different features for simple and water-like liquids; however, the slope and curvature of the entropy-temperature plots reflect the heat capacity trends. Two trajectory-based computational estimation methods for the entropy and the heat capacity are compared for possible structural insights into supercooling, with the entropy obtained from thermodynamic integration. The two-phase thermodynamic estimator for the excess entropy proves to be fairly accurate in comparison to the excess entropy values obtained by thermodynamic integration, for all five Lennard-Jones and Stillinger-Weber liquids. The entropy estimator based on the multiparticle correlation expansion that accounts for both pair and triplet correlations, denoted by Strip, is also studied. Strip is a

  13. Single-site Lennard-Jones models via polynomial chaos surrogates of Monte Carlo molecular simulation

    Science.gov (United States)

    Kadoura, Ahmad; Siripatana, Adil; Sun, Shuyu; Knio, Omar; Hoteit, Ibrahim

    2016-06-01

    In this work, two Polynomial Chaos (PC) surrogates were generated to reproduce Monte Carlo (MC) molecular simulation results of the canonical (single-phase) and the NVT-Gibbs (two-phase) ensembles for a system of normalized structureless Lennard-Jones (LJ) particles. The main advantage of such surrogates, once generated, is the capability of accurately computing the needed thermodynamic quantities in a few seconds, thus efficiently replacing the computationally expensive MC molecular simulations. Benefiting from the tremendous computational time reduction, the PC surrogates were used to conduct large-scale optimization in order to propose single-site LJ models for several simple molecules. Experimental data, a set of supercritical isotherms, and part of the two-phase envelope, of several pure components were used for tuning the LJ parameters (ɛ, σ). Based on the conducted optimization, excellent fit was obtained for different noble gases (Ar, Kr, and Xe) and other small molecules (CH4, N2, and CO). On the other hand, due to the simplicity of the LJ model used, dramatic deviations between simulation and experimental data were observed, especially in the two-phase region, for more complex molecules such as CO2 and C2 H6.

  14. Effect of Energy Polydispersity on the Nature of Lennard-Jones Liquids.

    Science.gov (United States)

    Ingebrigtsen, Trond S; Tanaka, Hajime

    2016-08-11

    In the companion paper [ Ingebrigtsen , T. S. ; Tanaka , H. J. Phys. Chem. B 2015 , 119 , 11052 ] the effect of size polydispersity on the nature of Lennard-Jones (LJ) liquids, which represent most molecular liquids without hydrogen bonds, was studied. More specifically, it was shown that even highly size polydisperse LJ liquids are Roskilde-simple (RS) liquids. RS liquids are liquids with strong correlation between constant volume equilibrium fluctuations of virial and potential energy and are simpler than other types of liquids. Moreover, it was shown that size polydisperse LJ liquids have isomorphs to a good approximation. Isomorphs are curves in the phase diagram of RS liquids along which structure, dynamics, and some thermodynamic quantities are invariant in dimensionless (reduced) units. In this paper, we study the effect of energy polydispersity on the nature of LJ liquids. We show that energy polydisperse LJ liquids are RS liquids. However, a tendency of particle segregation, which increases with the degree of polydispersity, leads to a loss of strong virial-potential energy correlation but is mitigated by increasing temperature and/or density. Isomorphs are a good approximation also for energy polydisperse LJ liquids, although particle-resolved quantities display a somewhat poorer scaling compared to the mean quantities along the isomorph. PMID:27434103

  15. The Lennard-Jones Potential Minimization Problem for Prion AGAAAAGA Amyloid Fibril Molecular Modeling

    CERN Document Server

    Zhang, Jiapu

    2011-01-01

    The simplified Lennard-Jones (LJ) potential minimization problem is minimize f(x)=4\\sum_{i=1}^N \\sum_{j=1,j

  16. A Hybrid Vehicle Detection Method Based on Viola-Jones and HOG + SVM from UAV Images.

    Science.gov (United States)

    Xu, Yongzheng; Yu, Guizhen; Wang, Yunpeng; Wu, Xinkai; Ma, Yalong

    2016-01-01

    A new hybrid vehicle detection scheme which integrates the Viola-Jones (V-J) and linear SVM classifier with HOG feature (HOG + SVM) methods is proposed for vehicle detection from low-altitude unmanned aerial vehicle (UAV) images. As both V-J and HOG + SVM are sensitive to on-road vehicles' in-plane rotation, the proposed scheme first adopts a roadway orientation adjustment method, which rotates each UAV image to align the roads with the horizontal direction so the original V-J or HOG + SVM method can be directly applied to achieve fast detection and high accuracy. To address the issue of descending detection speed for V-J and HOG + SVM, the proposed scheme further develops an adaptive switching strategy which sophistically integrates V-J and HOG + SVM methods based on their different descending trends of detection speed to improve detection efficiency. A comprehensive evaluation shows that the switching strategy, combined with the road orientation adjustment method, can significantly improve the efficiency and effectiveness of the vehicle detection from UAV images. The results also show that the proposed vehicle detection method is competitive compared with other existing vehicle detection methods. Furthermore, since the proposed vehicle detection method can be performed on videos captured from moving UAV platforms without the need of image registration or additional road database, it has great potentials of field applications. Future research will be focusing on expanding the current method for detecting other transportation modes such as buses, trucks, motors, bicycles, and pedestrians. PMID:27548179

  17. Collision frequency of Lennard-Jones fluids at high densities by equilibrium molecular dynamics simulation

    International Nuclear Information System (INIS)

    Arising from the inability of theoretical calculations to give accurate descriptions of (shear) viscosity in rare gases at high densities, we investigated the likely cause of discrepancy between theory and experiments. Molecular Dynamics simulations were performed to calculate transport coefficients and collision frequency of rare gases at high densities and different temperatures using a Lennard-Jones modelled pair potential. The results, when compared with experiments show an underestimation of the viscosity calculated through the Green-Kubo formalism, but in agreement with some other calculations performed by other groups. In the present work the origin of the underestimation is considered. Analyses of the transport coefficients show a very high collision frequency which suggests an atom may spend much less time in the neighbourhood of the fields of force of another atom and that the distribution in the systems studied adjusts itself to a nearly Maxwellian type which resulted in a locally and temporarily slowly varying temperature. We show that the time spent in the fields of force is so small compared with relaxation time thereby leading to a possible reduction in local velocity auto-correlation between atoms. (author)

  18. Factorizations for 3-rotations and polarization of the light in Mueller-Stokes an Jones formalisms

    CERN Document Server

    Red'kov, V M

    2008-01-01

    Formulas describing all 2-element and 3-element factorizations of arbitrary element of the groups SU(2) and SO(3,R) are derived. Six 2-element factorizations, $ (U_{2}U_{3}U'_{2}), (U_{3}U_{2}U'_{3}), (U_{3}U_{1}U'_{3}), (U_{1}U_{3}U'_{1}), (U_{1}U_{2}U'_{1}), (U_{2}U_{1}U'_{2})$, provide all possible way to define Euler type angles; and six 3-element ones, $ (U_{1}U_{2}U_{3}), (U_{1}U_{3}U'_{2}), (U_{2}U_{3}U_{1}), (U_{2}U_{1}U_{3}), (U_{3}U_{1}U_{2}), (U_{3}U_{2}U_{1})$ provide all possible ways to parameterize the unitary and orthogonal groups by three elementary angles. In thecontext the light polarization formalism of Stokes-Mueller vectors and Jones spinors, relations produced give a base to resolve arbitrary pure polarization rotators into all possible sets of elementary rotators of two or three constituents.

  19. Function after correction of a clawed great toe by a modified Robert Jones transfer.

    Science.gov (United States)

    Breusch, S J; Wenz, W; Döderlein, L

    2000-03-01

    We carried out a cross-sectional study in 51 patients (81 feet) with a clawed hallux in association with a cavus foot after a modified Robert Jones tendon transfer. The mean follow-up was 42 months (9 to 88). In all feet, concomitant procedures had been undertaken, such as extension osteotomy of the first metatarsal and transfer of the tendon of the peroneus longus to peroneus brevis, to correct the underlying foot deformity. All patients were evaluated clinically and radiologically. The overall rate of patient satisfaction was 86%. The deformity of the hallux was corrected in 80 feet. Catching of the big toe when walking barefoot, transfer lesions and metatarsalgia, hallux flexus, hallux limitus and asymptomatic nonunion of the interphalangeal joint were the most frequent complications. Hallux limitus was more likely when elevation of the first ray occurred (p = 0.012). Additional transfer of the tendon of peroneus longus to peroneus brevis was a significant risk factor for elevation of the first metatarsal (p hallux. PMID:10755436

  20. Nucleation of liquid droplets and voids in a stretched Lennard-Jones fcc crystal

    Energy Technology Data Exchange (ETDEWEB)

    Baidakov, Vladimir G., E-mail: baidakov@itp.uran.ru; Tipeev, Azat O. [Institute of Thermophysics, Ural Branch of the Russian Academy of Sciences, Amundsen Street 107a, 620016 Ekaterinburg (Russian Federation)

    2015-09-28

    The method of molecular dynamics simulation has been used to investigate the phase decay of a metastable Lennard-Jones face-centered cubic crystal at positive and negative pressures. It is shown that at high degrees of metastability, crystal decay proceeds through the spontaneous formation and growth of new-phase nuclei. It has been found that there exists a certain boundary temperature. Below this temperature, the crystal phase disintegrates as the result of formation of voids, and above, as a result of formation of liquid droplets. The boundary temperature corresponds to the temperature of cessation of a crystal–liquid phase equilibrium when the melting line comes in contact with the spinodal of the stretched liquid. The results of the simulations are interpreted in the framework of classical nucleation theory. The thermodynamics of phase transitions in solids has been examined with allowance for the elastic energy of stresses arising owing to the difference in the densities of the initial and the forming phases. As a result of the action of elastic forces, at negative pressures, the boundary of the limiting superheating (stretching) of a crystal approaches the spinodal, on which the isothermal bulk modulus of dilatation becomes equal to zero. At the boundary of the limiting superheating (stretching), the shape of liquid droplets and voids is close to the spherical one.

  1. Enhancement of the droplet nucleation in a dense supersaturated Lennard-Jones vapor

    Science.gov (United States)

    Zhukhovitskii, D. I.

    2016-05-01

    The vapor-liquid nucleation in a dense Lennard-Jones system is studied analytically and numerically. A solution of the nucleation kinetic equations, which includes the elementary processes of condensation/evaporation involving the lightest clusters, is obtained, and the nucleation rate is calculated. Based on the equation of state for the cluster vapor, the pre-exponential factor is obtained. The latter diverges as a spinodal is reached, which results in the nucleation enhancement. The work of critical cluster formation is calculated using the previously developed two-parameter model (TPM) of small clusters. A simple expression for the nucleation rate is deduced and it is shown that the work of cluster formation is reduced for a dense vapor. This results in the nucleation enhancement as well. To verify the TPM, a simulation is performed that mimics a steady-state nucleation experiments in the thermal diffusion cloud chamber. The nucleating vapor with and without a carrier gas is simulated using two different thermostats for the monomers and clusters. The TPM proves to match the simulation results of this work and of other studies.

  2. Single-site Lennard-Jones models via polynomial chaos surrogates of Monte Carlo molecular simulation

    KAUST Repository

    Kadoura, Ahmad

    2016-06-01

    In this work, two Polynomial Chaos (PC) surrogates were generated to reproduce Monte Carlo (MC) molecular simulation results of the canonical (single-phase) and the NVT-Gibbs (two-phase) ensembles for a system of normalized structureless Lennard-Jones (LJ) particles. The main advantage of such surrogates, once generated, is the capability of accurately computing the needed thermodynamic quantities in a few seconds, thus efficiently replacing the computationally expensive MC molecular simulations. Benefiting from the tremendous computational time reduction, the PC surrogates were used to conduct large-scale optimization in order to propose single-site LJ models for several simple molecules. Experimental data, a set of supercritical isotherms, and part of the two-phase envelope, of several pure components were used for tuning the LJ parameters (ε, σ). Based on the conducted optimization, excellent fit was obtained for different noble gases (Ar, Kr, and Xe) and other small molecules (CH4, N2, and CO). On the other hand, due to the simplicity of the LJ model used, dramatic deviations between simulation and experimental data were observed, especially in the two-phase region, for more complex molecules such as CO2 and C2 H6.

  3. A test of the mean density approximation for Lennard-Jones mixtures with large size ratios

    International Nuclear Information System (INIS)

    The mean density approximation for mixture radial distribution functions plays a central role in modern corresponding-states theories. This approximation is reasonably accurate for systems that do not differ widely in size and energy ratios and which are nearly equimolar. As the size ratio increases, however, or if one approaches an infinite dilution of one of the components, the approximation becomes progressively worse, especially for the small molecule pair. In an attempt to better understand and improve this approximation, isothermal molecular dynamics simulations have been performed on a series of Lennard-Jones mixtures. Thermodynamic properties, including the mixture radial distribution functions, have been obtained at seven compositions ranging from 5 to 95 mol%. In all cases the size ratio was fixed at two and three energy ratios were investigated, 22/ 11 =0.5, 1.0, and 1.5. The results of the simulations are compared with the mean density approximation and a modification to integrals evaluated with the mean density approximation is proposed

  4. Selected hydrogeologic and water-quality data from Jones Beach Island, Long Island, New York

    Science.gov (United States)

    Scorca, M.P.; Reilly, T.E.; Franke, O.L.

    1995-01-01

    A data-collection site was instrumented on Jones Beach Island, a barrier island south of Long Island, N.Y., to study local freshwater/ saltwater relations in the shallow ground-water system. A geologic test boring revealed about 88 feet of well-sorted glacial outwash sand above about 15 feet of Gardiners Clay, which directly overlies silty sand of the Magothy Formation. Tidal effects on water levels in Great South Bay, the upper glacial aquifer, and the Magothy aquifer were observed and quantified with a tidal gage in the bay and analog water-level recorders in the wells.Chloride concentrations in the upper Magothy aquifer were higher than expected--about 270 mg/L (milligrams per liter), and those in the upper glacial aquifer were 17,000 to 19,000 mg/L, about the same as in Great South Bay. Estimates of pressure and freshwater equivalent heads indicate that, at the data-collection site, freshwater is discharging upward from the Magothy aquifer into the salty upper glacial aquifer, but dilution by this freshwater is undetectable. The reason for the elevated chloride concentration in the Magothy aquifer cannot be determined from available hydrogeologic information.

  5. Theory of slope-dependent disjoining pressure with application to Lennard-Jones liquid films.

    Science.gov (United States)

    Yi, Taeil; Wong, Harris

    2007-09-15

    A liquid film of thickness hfilm thicknesses, it determines the stability and wettability of thin films. Current theory derived for uniform films gives Pi=Pi(h). This solution has been applied recently to non-uniform films and becomes unbounded near a contact line as h-->0. Consequently, many different effects have been considered to eliminate or circumvent this singularity. We present a mean-field theory of Pi that depends on the slope h(x) as well as the height h of the film. When this theory is implemented for Lennard-Jones liquid films, the new Pi=Pi(h,h(x)) is bounded near a contact line as h-->0. Thus, the singularity in Pi(h) is artificial because it results from extending a theory beyond its range of validity. We also show that the new Pi can capture all three regimes of drop behavior (complete wetting, partial wetting, and pseudo-partial wetting) without altering the signs of the long and short-range interactions. We find that a drop with a precursor film is linearly stable. PMID:17570389

  6. Spray flow-network flow transition of binary Lennard-Jones particle system

    KAUST Repository

    Inaoka, Hajime

    2010-07-01

    We simulate gas-liquid flows caused by rapid depressurization using a molecular dynamics model. The model consists of two types of Lennard-Jones particles, which we call liquid particles and gas particles. These two types of particles are distinguished by their mass and strength of interaction: a liquid particle has heavier mass and stronger interaction than a gas particle. By simulations with various initial number densities of these particles, we found that there is a transition from a spray flow to a network flow with an increase of the number density of the liquid particles. At the transition point, the size of the liquid droplets follows a power-law distribution, while it follows an exponential distribution when the number density of the liquid particles is lower than the critical value. The comparison between the transition of the model and that of models of percolation is discussed. The change of the average droplet size with the initial number density of the gas particles is also presented. © 2010 Elsevier B.V. All rights reserved.

  7. Fowler's approximation for the surface tension and surface energy of Lennard-Jones fluids revisited

    International Nuclear Information System (INIS)

    We present a detailed study of the validity of Fowler's approximation for calculating the surface tension and the surface energy of Lennard-Jones fluids. To do so, we consider three different explicit analytical expressions for the radial distribution function (RDF), including one proposed by our research group, together with very accurate expressions for the liquid and vapour densities, also proposed by our group. The calculation of the surface tension from the direct correlation function using both the Percus-Yevick and the hypernetted-chain approximations is also considered. Finally, our results are compared with those obtained by other authors by computer simulations or through relevant theoretical approximations. In particular, we consider the analytical expression proposed by Kalikmanov and Hofmans (1994 J. Phys.: Condens. Matter 6 2207-14) for the surface tension. Our results indicate that the values for the surface energy in Fowler's approximation obtained by other authors are adequate, and can be calculated from the RDF models. For the surface tension, however, the values considered as valid in previous works seem to be incorrect. The correct values can be obtained from our model for the RDF or from the Kalikmanov and Hofmans expression with suitable inputs

  8. Face Detection and Recognition Using Viola-Jones with PCA-LDA and Square Euclidean Distance

    Directory of Open Access Journals (Sweden)

    Nawaf Hazim Barnouti

    2016-05-01

    Full Text Available In this paper, an automatic face recognition system is proposed based on appearance-based features that focus on the entire face image rather than local facial features. The first step in face recognition system is face detection. Viola-Jones face detection method that capable of processing images extremely while achieving high detection rates is used. This method has the most impact in the 2000’s and known as the first object detection framework to provide relevant object detection that can run in real time. Feature extraction and dimension reduction method will be applied after face detection. Principal Component Analysis (PCA method is widely used in pattern recognition. Linear Discriminant Analysis (LDA method that used to overcome drawback the PCA has been successfully applied to face recognition. It is achieved by projecting the image onto the Eigenface space by PCA after that implementing pure LDA over it. Square Euclidean Distance (SED is used. The distance between two images is a major concern in pattern recognition. The distance between the vectors of two images leads to image similarity. The proposed method is tested on three databases (MUCT, Face94, and Grimace. Different number of training and testing images are used to evaluate the system performance and it show that increasing the number of training images will increase the recognition rate.

  9. Molecular Dynamics Simulation of the Lennard-Jones Polymers in a Good Solvent

    International Nuclear Information System (INIS)

    We carried out united-atom Langevin dynamics simulations of polymer's equilibrium state in a good solvent. Our primary goal was a pedagogical exposition of fundamental equilibrium properties of isolated polymers in dilutions with a model that contains many features of real materials. The polymer was chosen to be a three-dimensional chain of N identical beads (monomers) without internal structure. Each monomer interacted with its two neighbors by a harmonic potential, which modeled a chemical bond. Additionally all monomers within a chain were assumed to interact through the Lennard-Jones (LJ) potential. Interaction with solvent and with other polymers was introduced using Langevin forces. Analyzing internal energy per polymer and radius of gyration as function of temperature we observed a rapid globule to coil phase transition. Also we studied elastic properties of single polymer chain for temperatures below the transition and identified three regions with different elastic behavior. Typical chain lengths in our simulations ranged from 100 to 1000 monomers. The elaborated software package can easily be modified to study e.g. the effect of polymer stiffness on thermodynamic behavior. (author)

  10. Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems

    KAUST Repository

    Watanabe, H.

    2011-08-01

    Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also explained. A simple spatialdecomposition-based strategy is adopted for parallelization. By utilizing the developed code, benchmark simulations are performed on a HITACHI SR16000/J2 system consisting of IBM POWER6 processors which are 4.7 GHz at the National Institute for Fusion Science (NIFS) and an SGI Altix ICE 8400EX system consisting of Intel Xeon processors which are 2.93 GHz at the Institute for Solid State Physics (ISSP), the University of Tokyo. The parallelization efficiency of the largest run, consisting of 4.1 billion particles with 8192 MPI processes, is about 73% relative to that of the smallest run with 128 MPI processes at NIFS, and it is about 66% relative to that of the smallest run with 4 MPI processes at ISSP. The factors causing the parallel overhead are investigated. It is found that fluctuations of the execution time of each process degrade the parallel efficiency. These fluctuations may be due to the interference of the operating system, which is known as OS Jitter.

  11. Diagnostic accuracy of modified kenneth jones scoring criteria (mkjsc) in confirmed cases of tuberculosis in children

    International Nuclear Information System (INIS)

    Background: Tuberculosis (TB) is a granulomatous disease caused by Mycobacterium tuberculosis. The gold standard for the diagnosis of tuberculosis is detection of Mycobacterium tubercle bacilli. However, clinical scoring systems are most widely used for the diagnosis of TB in children. Objective: To determine the diagnostic accuracy of modified Kenneth Jones scoring criteria (MKJSC) in conformed cases of tuberculosis. Methodology: This cross-sectional comparative study was conducted in the department of Paediatrics, King Edward Medical University / Mayo Hospital, Lahore from January to June 2007. One hundred children below 15 years of age were enrolled. They were diagnosed as suspected cases of TB on the basis of fever and cough for more than 15 days. MKJSC was applied and each child was subjected to confirmatory test for TB. Results: There was an overall male preponderance of 54%. The mean age of study population was 1.8 +- 0.7 years. Out of 100 children, 66% were diagnosed as TB cases (23 with confirmatory tests and 43 with MKJSC of 5 or more). Sensitivity, specificity, positive and negative predictive value of MKJSC was 73.91%, 44.16%, 28.33%, and 85% respectively. Diagnostic accuracy of MKJSC was 51%. Conclusion: Present study does not support the hypothesis that MKJSC is a good alternative to confirmatory tests to diagnose tuberculosis in children. However, MKJSC is a simple tool, which can be applied to improve the case detection rate in the absence of sophisticated tests. (author)

  12. How long the singular value decomposed entropy predicts the stock market? - Evidence from the Dow Jones Industrial Average Index

    Science.gov (United States)

    Gu, Rongbao; Shao, Yanmin

    2016-07-01

    In this paper, a new concept of multi-scales singular value decomposition entropy based on DCCA cross correlation analysis is proposed and its predictive power for the Dow Jones Industrial Average Index is studied. Using Granger causality analysis with different time scales, it is found that, the singular value decomposition entropy has predictive power for the Dow Jones Industrial Average Index for period less than one month, but not for more than one month. This shows how long the singular value decomposition entropy predicts the stock market that extends Caraiani's result obtained in Caraiani (2014). On the other hand, the result also shows an essential characteristic of stock market as a chaotic dynamic system.

  13. Jenny Jones: “my vision for London is of a more sustainable, fairer and cleaner city”

    OpenAIRE

    Jones, Jenny

    2012-01-01

    Green Party candidate for London Mayor Jenny Jones details her proposals to encourage a 10:1 ratio of company pay, to boost contracts to smaller firms through her mayoral office and how Londoners could have a safer and healthier life in the city. This is the third in a three part series with the mayoral candidates, including Brian Paddick and Ken Livingstone, with an introduction by Tony Travers.

  14. Molecular Dynamics Simulations of DOPC Lipid Bilayers: The Effect of Lennard-Jones Parameters of Hydrocarbon Chains

    OpenAIRE

    Liu, Anping; Qi, Xiaoyang

    2012-01-01

    The current Chemistry at Harvard Molecular Mechanics (CHARMM) force field cannot accurately describe the properties of unsaturated phospholipid membranes. In this paper, a series of simulations was performed in which the Lennard-Jones (L-J) parameters of lipid acyl chains of dioleoylphosphatidylcholine (DOPC) were systematically adjusted. The results showed that adjustment of the L-J parameters in lipid acyl chains can significantly improve the current CHARMM force field. It was found that th...

  15. Book review: the Oxford handbook of creative industries edited by Candace Jones, Mark Lorenzen and Jonathan Sapsed

    OpenAIRE

    Jones, Candace; Lorenzen, Mark; Sapsed, Jonathan

    2016-01-01

    The creative industries are on the rise across the globe and their economic importance is also increasing. Through their new book, The Oxford Handbook of Creative Industries, editors Candace Jones, Mark Lorenzen and Jonathan Sapsed offer a collection of scholarly articles reflecting on this growing sector through a number of disciplinary lenses, including economics, public policy, management and law. Elisa Pannini finds this a useful read not only for scholars researching the field, but also ...

  16. Transport phenomena and microscopic structure in partially miscible binary fluids: A simulation study of the symmetrical Lennard-Jones mixture

    OpenAIRE

    Das, Subir K.; Horbach, Jürgen; Binder, Kurt

    2003-01-01

    Static and dynamic structure factors and various transport coefficients are computed for a Lennard-Jones model of a binary fluid (A,B) with a symmetrical miscibility gap, varying both temperature and relative concentration of the mixture. The model is first equilibrated by a semi-grandcanonical Monte Carlo method, choosing the temperature and chemical potential difference $\\Delta \\mu$ between the two species as the given independent variables. Varying for $\\Delta \\mu=0$ the temperature and pa...

  17. An entropy based analysis of the relationship between the DOW JONES Index and the TRNA Sentiment series

    OpenAIRE

    Allen, David; McAleer, Michael; Singh, Abhay

    2016-01-01

    textabstractThis paper features an analysis of the relationship between the DOW JONES Industrial Average Index (DJIA) and a sentiment news series using daily data obtained from the Thomson Reuters News Analytics (TRNA)1 provided by SIRCA (The Securities Industry Research Centre of the Asia Pacic). The recent growth in the availability of on-line financial news sources such as internet news and social media sources provides instantaneous access to financial news. Various commercial agencies ha...

  18. Analytical evaluation of third virial coefficient with Lennard-Jones (12-6) potential and its applications

    Science.gov (United States)

    Mamedov, Bahtiyar Akber; Somuncu, Elif

    2016-04-01

    An efficient analytical method to evaluate the third virial coefficient with Lennard-Jones (12-6) type potential is presented. Proposed approach is particularly suitable for analysis of various properties of three body systems. To conform the correctness of the calculation result, a comparison is given with the literature for NO2, SF6 and C2H2 molecules. Calculation results show that obtained formulae provide higher accuracy and efficiency than the proposed approaches in literature.

  19. Structures and autocorrelation functions of liquid Al and Mg modelled via Lennard-Jones potential from molecular dynamics simulation

    Indian Academy of Sciences (India)

    G A Adebayo; O Akinlade; L A Hussain

    2005-02-01

    The structures and autocorrelation functions of Al and Mg in the liquid state are investigated through the pair distribution function (), the diffusion coefficients as well as the shear viscosity via the Green{Kubo and Einstein relations. From the structure and the Enskog relation we determined the frequency of collisions of atoms in the first shell of () in the systems. We also discovered that the packing fraction of Lennard-Jones liquids should be approximately half the reduced density value. This approximation is accurate to within 99%. The temperature dependence of the pair distribution function and the atomic mean square displacement are investigated by performing simulations at various experimental temperatures and corresponding densities. The structures of the systems are affected by temperature via movements of atoms in the first minimum of (). The Lennard-Jones model shows that density dependence of the shear viscosity is in agreement with what is expected of simple liquids in the range of investigated temperatures and densities. In the gas limit, the Stoke-Einstein relation = B/2 is grossly overestimated by Lennard-Jones model. This could not be attributed to defficiencies in the model, as other investigators using first principle method could not obtain the gas limit of the Stoke-Einstein relation.

  20. Fire and EMS Districts, Jones County Fire Districts, Published in 2005, 1:4800 (1in=400ft) scale, Middle Georgia RC.

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This Fire and EMS Districts dataset, published at 1:4800 (1in=400ft) scale, was produced all or in part from Other information as of 2005. It is described as 'Jones...

  1. Clarifying hierarchical age-period-cohort models: A rejoinder to Bell and Jones.

    Science.gov (United States)

    Reither, Eric N; Land, Kenneth C; Jeon, Sun Y; Powers, Daniel A; Masters, Ryan K; Zheng, Hui; Hardy, Melissa A; Keyes, Katherine M; Fu, Qiang; Hanson, Heidi A; Smith, Ken R; Utz, Rebecca L; Yang, Y Claire

    2015-11-01

    Previously, Reither et al. (2015) demonstrated that hierarchical age-period-cohort (HAPC) models perform well when basic assumptions are satisfied. To contest this finding, Bell and Jones (2015) invent a data generating process (DGP) that borrows age, period and cohort effects from different equations in Reither et al. (2015). When HAPC models applied to data simulated from this DGP fail to recover the patterning of APC effects, B&J reiterate their view that these models provide "misleading evidence dressed up as science." Despite such strong words, B&J show no curiosity about their own simulated data--and therefore once again misapply HAPC models to data that violate important assumptions. In this response, we illustrate how a careful analyst could have used simple descriptive plots and model selection statistics to verify that (a) period effects are not present in these data, and (b) age and cohort effects are conflated. By accounting for the characteristics of B&J's artificial data structure, we successfully recover the "true" DGP through an appropriately specified model. We conclude that B&Js main contribution to science is to remind analysts that APC models will fail in the presence of exact algebraic effects (i.e., effects with no random/stochastic components), and when collinear temporal dimensions are included without taking special care in the modeling process. The expanded list of coauthors on this commentary represents an emerging consensus among APC scholars that B&J's essential strategy--testing HAPC models with data simulated from contrived DGPs that violate important assumptions--is not a productive way to advance the discussion about innovative APC methods in epidemiology and the social sciences. PMID:26277370

  2. A Hybrid Vehicle Detection Method Based on Viola-Jones and HOG + SVM from UAV Images

    Directory of Open Access Journals (Sweden)

    Yongzheng Xu

    2016-08-01

    Full Text Available A new hybrid vehicle detection scheme which integrates the Viola-Jones (V-J and linear SVM classifier with HOG feature (HOG + SVM methods is proposed for vehicle detection from low-altitude unmanned aerial vehicle (UAV images. As both V-J and HOG + SVM are sensitive to on-road vehicles’ in-plane rotation, the proposed scheme first adopts a roadway orientation adjustment method, which rotates each UAV image to align the roads with the horizontal direction so the original V-J or HOG + SVM method can be directly applied to achieve fast detection and high accuracy. To address the issue of descending detection speed for V-J and HOG + SVM, the proposed scheme further develops an adaptive switching strategy which sophistically integrates V-J and HOG + SVM methods based on their different descending trends of detection speed to improve detection efficiency. A comprehensive evaluation shows that the switching strategy, combined with the road orientation adjustment method, can significantly improve the efficiency and effectiveness of the vehicle detection from UAV images. The results also show that the proposed vehicle detection method is competitive compared with other existing vehicle detection methods. Furthermore, since the proposed vehicle detection method can be performed on videos captured from moving UAV platforms without the need of image registration or additional road database, it has great potentials of field applications. Future research will be focusing on expanding the current method for detecting other transportation modes such as buses, trucks, motors, bicycles, and pedestrians.

  3. Detecting macroeconomic phases in the Dow Jones Industrial Average time series

    Science.gov (United States)

    Wong, Jian Cheng; Lian, Heng; Cheong, Siew Ann

    2009-11-01

    In this paper, we perform statistical segmentation and clustering analysis of the Dow Jones Industrial Average (DJI) time series between January 1997 and August 2008. Modeling the index movements and log-index movements as stationary Gaussian processes, we find a total of 116 and 119 statistically stationary segments respectively. These can then be grouped into between five and seven clusters, each representing a different macroeconomic phase. The macroeconomic phases are distinguished primarily by their volatilities. We find that the US economy, as measured by the DJI, spends most of its time in a low-volatility phase and a high-volatility phase. The former can be roughly associated with economic expansion, while the latter contains the economic contraction phase in the standard economic cycle. Both phases are interrupted by a moderate-volatility market correction phase, but extremely-high-volatility market crashes are found mostly within the high-volatility phase. From the temporal distribution of various phases, we see a high-volatility phase from mid-1998 to mid-2003, and another starting mid-2007 (the current global financial crisis). Transitions from the low-volatility phase to the high-volatility phase are preceded by a series of precursor shocks, whereas the transition from the high-volatility phase to the low-volatility phase is preceded by a series of inverted shocks. The time scale for both types of transitions is about a year. We also identify the July 1997 Asian Financial Crisis to be the trigger for the mid-1998 transition, and an unnamed May 2006 market event related to corrections in the Chinese markets to be the trigger for the mid-2007 transition.

  4. Crystallization of Lennard-Jones nanodroplets: From near melting to deeply supercooled

    Science.gov (United States)

    Malek, Shahrazad M. A.; Morrow, Gregory P.; Saika-Voivod, Ivan

    2015-03-01

    We carry out molecular dynamics (MD) and Monte Carlo (MC) simulations to characterize nucleation in liquid clusters of 600 Lennard-Jones particles over a broad range of temperatures. We use the formalism of mean first-passage times to determine the rate and find that Classical Nucleation Theory (CNT) predicts the rate quite well, even when employing simple modelling of crystallite shape, chemical potential, surface tension, and particle attachment rate, down to the temperature where the droplet loses metastability and crystallization proceeds through growth-limited nucleation in an unequilibrated liquid. Below this crossover temperature, the nucleation rate is still predicted when MC simulations are used to directly calculate quantities required by CNT. Discrepancy in critical embryo sizes obtained from MD and MC arises when twinned structures with five-fold symmetry provide a competing free energy pathway out of the critical region. We find that crystallization begins with hcp-fcc stacked precritical nuclei and differentiation to various end structures occurs when these embryos become critical. We confirm that using the largest embryo in the system as a reaction coordinate is useful in determining the onset of growth-limited nucleation and show that it gives the same free energy barriers as the full cluster size distribution once the proper reference state is identified. We find that the bulk melting temperature controls the rate, even though the solid-liquid coexistence temperature for the droplet is significantly lower. The value of surface tension that renders close agreement between CNT and direct rate determination is significantly lower than what is expected for the bulk system.

  5. Liquid-liquid interfacial properties of a symmetrical Lennard-Jones binary mixture

    International Nuclear Information System (INIS)

    We determine the interfacial properties of a symmetrical binary mixture of equal-sized spherical Lennard-Jones molecules, σ11 = σ22, with the same dispersive energy between like species, ϵ11 = ϵ22, but different dispersive energies between unlike species low enough to induce phase separation. We use the extensions of the improved version of the inhomogeneous long-range corrections of Janecek [J. Phys. Chem. B 110, 6264 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] and Martínez-Ruiz et al. [J. Chem. Phys. 141, 184701 (2014)], to deal with the interaction energy and microscopic components of the pressure tensor. We perform Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of the symmetrical mixture with different cut-off distances rc and in combination with the inhomogeneous long-range corrections. The pressure tensor is obtained using the mechanical (virial) and thermodynamic route. The liquid-liquid interfacial tension is also evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the test-area methodology. This allows to check the validity of the recent extensions presented to deal with the contributions due to long-range corrections for intermolecular energy and pressure tensor in the case of binary mixtures that exhibit liquid-liquid immiscibility. In addition to the pressure tensor and the surface tension, we also obtain density profiles and coexistence densities and compositions as functions of pressure, at a given temperature. According to our results, the main effect of increasing the cut-off distance rc is to sharpen the liquid-liquid interface and to increase the width of the biphasic coexistence region. Particularly interesting is the presence of a relative minimum in the total density profiles of the symmetrical mixture. This minimum is related with a desorption of the molecules

  6. Liquid-liquid interfacial properties of a symmetrical Lennard-Jones binary mixture

    Energy Technology Data Exchange (ETDEWEB)

    Martínez-Ruiz, F. J.; Blas, F. J., E-mail: felipe@uhu.es [Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Física Aplicada, Universidad de Huelva, 21007 Huelva (Spain); Moreno-Ventas Bravo, A. I. [Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Geología, Universidad de Huelva, 21007 Huelva (Spain)

    2015-09-14

    We determine the interfacial properties of a symmetrical binary mixture of equal-sized spherical Lennard-Jones molecules, σ{sub 11} = σ{sub 22}, with the same dispersive energy between like species, ϵ{sub 11} = ϵ{sub 22}, but different dispersive energies between unlike species low enough to induce phase separation. We use the extensions of the improved version of the inhomogeneous long-range corrections of Janecek [J. Phys. Chem. B 110, 6264 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] and Martínez-Ruiz et al. [J. Chem. Phys. 141, 184701 (2014)], to deal with the interaction energy and microscopic components of the pressure tensor. We perform Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of the symmetrical mixture with different cut-off distances r{sub c} and in combination with the inhomogeneous long-range corrections. The pressure tensor is obtained using the mechanical (virial) and thermodynamic route. The liquid-liquid interfacial tension is also evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the test-area methodology. This allows to check the validity of the recent extensions presented to deal with the contributions due to long-range corrections for intermolecular energy and pressure tensor in the case of binary mixtures that exhibit liquid-liquid immiscibility. In addition to the pressure tensor and the surface tension, we also obtain density profiles and coexistence densities and compositions as functions of pressure, at a given temperature. According to our results, the main effect of increasing the cut-off distance r{sub c} is to sharpen the liquid-liquid interface and to increase the width of the biphasic coexistence region. Particularly interesting is the presence of a relative minimum in the total density profiles of the symmetrical mixture. This minimum is related

  7. Bold镙钉治疗Jones骨折%Treatment of 16 cases Jones fractures by open reduction and bold screw fixation

    Institute of Scientific and Technical Information of China (English)

    单宇; 蒋富贵; 张晓剑; 徐能

    2013-01-01

    Objective To evaluate the clinical effect of Bold screw fixation in the treatment of jones fracture.Method From March 2006 to May 2012,16 case of Jones fracture were treated by open reduction and Bold screw fixation.Result All the patients were obtained healing of bone reunion and followed up for 6~12 months,no residual pain and nonunion.According to Maryland foot scording system,9 cases were excellent,5 good,2 fair and the rate of excellent and good was 87.5 %.Conclusion Bold screw fixation is an effective therapy for Jones fracture of open reduction and it has the benefit of early exercise,no need to remove,fixed solid.%目的 探讨Bold螺钉内固定治疗Jones骨折的临床疗效.方法 2006年3月~2012年5月,采用切开复位Bold螺钉内固定治疗Jones骨折16例.结果 16例均获随访,随访时间6~12m,均获得骨性愈合,未残留疼痛或骨不愈合.按Maryland足部评分系统评分,优9例,良5例,可2例,优良率87.5%.结论 Bold螺钉治疗Jones骨折具有早期功能锻炼、无需取出、固定稳固等优点,是治疗Jones骨折的有效方法.

  8. Certain Equilibrium Properties of Gases and Gas Mixtures an Steeper lennard-Jones and Stockmayer Type Potentials

    Directory of Open Access Journals (Sweden)

    S. C. Saxena

    1967-04-01

    Full Text Available The discussion on second virial and zero pressure Joule-Thomson coefficients of non polar gases and gas mixtures is given on the Lennard Jones Type Potentials with the choice of the repulsive index as 12 and 18. These studies are also extended to polar gases and gas mixtures by including the electric dipole-dipole moment term in the two potentials. The tabulations are given for the (18-6-3 potential to enable computations of second virial and Joule-Thomson coefficients.

  9. Phase changes in 38 atom Lennard-Jones clusters; 1, A parallel tempering study in the canonical ensemble

    CERN Document Server

    Neirotti, J P; Freeman, D L; Doll, J D; Freeman, David L.

    2000-01-01

    The heat capacity and isomer distributions of the 38 atom Lennard-Jones cluster have been calculated in the canonical ensemble using parallel tempering Monte Carlo methods. A distinct region of temperature is identified that corresponds to equilibrium between the global minimum structure and the icosahedral basin of structures. This region of temperatures occurs below the melting peak of the heat capacity and is accompanied by a peak in the derivative of the heat capacity with temperature. Parallel tempering is shown to introduce correlations between results at different temperatures. A discussion is given that compares parallel tempering with other related approaches that ensure ergodic simulations.

  10. Density functional theory of inhomogeneous liquids. I. The liquid-vapor interface in Lennard-Jones fluids

    OpenAIRE

    Lutsko, James F.

    2007-01-01

    A simple model is proposed for the direct correlation function (DCF) for simple fluids consisting of a hard-core contribution, a simple parametrized core correction, and a mean-field tail. The model requires as input only the free energy of the homogeneous fluid, obtained, e.g., from thermodynamic perturbation theory. Comparison to the DCF obtained from simulation of a Lennard-Jones fluid shows this to be a surprisingly good approximation for a wide range of densities. The model is used to co...

  11. Measuring Student Attention with Face Detection: : Viola-Jones versus Multi-Block Local Binary Pattern using OpenCV

    OpenAIRE

    Eriksson, Josefine; Anna, Lindelöf

    2015-01-01

    The purpose of this study is to discuss and attempt to approach an answer to the question of how face detection could be used to measure attention in a lecture hall.The conclusion might help further studies in using face detection to provide teachers with tools which can be used to improve learning during lectures. Face detection in real time applications became possible in 2001 when Viola and Jones presented a new method several times faster than any previous attempt. In 2007 Liao et al. pre...

  12. Noise-immune complex correlation for vasculature imaging based on standard and Jones-matrix optical coherence tomography

    Science.gov (United States)

    Makita, Shuichi; Kurokawa, Kazuhiro; Hong, Young-Joo; Li, En; Miura, Masahiro; Yasuno, Yoshiaki

    2016-03-01

    A new optical coherence angiography (OCA) method, called correlation mapping OCA (cmOCA), is presented by using the SNR-corrected complex correlation. An SNR-correction theory for the complex correlation calculation is presented. The method also integrates a motion-artifact-removal method for the sample motion induced decorrelation artifact. The theory is further extended to compute more reliable correlation by using multi- channel OCT systems, such as Jones-matrix OCT. The high contrast vasculature imaging of in vivo human posterior eye has been obtained. Composite imaging of cmOCA and degree of polarization uniformity indicates abnormalities of vasculature and pigmented tissues simultaneously.

  13. Effect of gold nanoparticles on structure and dynamics of binary Lennard-Jones liquid: direct space analysis.

    Science.gov (United States)

    Separdar, L; Davatolhagh, S

    2013-02-01

    We investigate the static structure and diffusive dynamics of binary Lennard-Jones mixture upon supercooling in the presence of gold nanoparticle within the framework of the mode-coupling theory of the dynamic glass transition in the direct space by means of constant-NVT molecular dynamics simulations. It is found that the presence of gold nanoparticle causes the energy per particle and the pressure of this system to decrease with respect to the bulk binary Lennard-Jones mixture. Furthermore, the presence of nanoparticle has a direct effect on the liquid structure and causes the peaks of the radial distribution functions to become shorter with respect to the bulk binary Lennard-Jones liquid. The dynamics of the liquid at a given density is found to be consistent with the mode-coupling theory (MCT) predictions in a certain range at low temperatures. In accordance with the idealized MCT, the diffusion constants D(T) show a power-law behavior at low temperatures for both types of binary Lennard-Jones (BLJ) particles as well as the gold atoms comprising the nanoparticle. The mode-coupling crossover temperature T(c) is the same for all particle types; however, T(c)=0.4 is reduced with respect to that of the bulk BLJ liquid, and the γ exponent is found to depend on the particle type. The existence of the nanoparticle causes the short-time β-relaxation regime to shorten and the range of validity of the MCT shrinks with respect to the bulk BLJ. It is also found that at intermediate and low temperatures the curves of the mean-squared displacements (MSDs) versus tD(T) fall onto a master curve. The MSDs follow the master curve in an identical time range with the long-time α-relaxation regime of the mode-coupling theory. By obtaining the viscosity, it is observed that the Stokes-Einstein relation remains valid at high and intermediate temperatures but breaks down as the temperatures approach T(c) as a result of the cooperative motion or activated processes. PMID:23496514

  14. Effect of gold nanoparticles on structure and dynamics of binary Lennard-Jones liquid: Direct space analysis

    Science.gov (United States)

    Separdar, L.; Davatolhagh, S.

    2013-02-01

    We investigate the static structure and diffusive dynamics of binary Lennard-Jones mixture upon supercooling in the presence of gold nanoparticle within the framework of the mode-coupling theory of the dynamic glass transition in the direct space by means of constant-NVT molecular dynamics simulations. It is found that the presence of gold nanoparticle causes the energy per particle and the pressure of this system to decrease with respect to the bulk binary Lennard-Jones mixture. Furthermore, the presence of nanoparticle has a direct effect on the liquid structure and causes the peaks of the radial distribution functions to become shorter with respect to the bulk binary Lennard-Jones liquid. The dynamics of the liquid at a given density is found to be consistent with the mode-coupling theory (MCT) predictions in a certain range at low temperatures. In accordance with the idealized MCT, the diffusion constants D(T) show a power-law behavior at low temperatures for both types of binary Lennard-Jones (BLJ) particles as well as the gold atoms comprising the nanoparticle. The mode-coupling crossover temperature Tc is the same for all particle types; however, Tc=0.4 is reduced with respect to that of the bulk BLJ liquid, and the γ exponent is found to depend on the particle type. The existence of the nanoparticle causes the short-time β-relaxation regime to shorten and the range of validity of the MCT shrinks with respect to the bulk BLJ. It is also found that at intermediate and low temperatures the curves of the mean-squared displacements (MSDs) versus tD(T) fall onto a master curve. The MSDs follow the master curve in an identical time range with the long-time α-relaxation regime of the mode-coupling theory. By obtaining the viscosity, it is observed that the Stokes-Einstein relation remains valid at high and intermediate temperatures but breaks down as the temperatures approach Tc as a result of the cooperative motion or activated processes.

  15. Teaching computers to fold proteins

    DEFF Research Database (Denmark)

    Winther, Ole; Krogh, Anders Stærmose

    2004-01-01

    A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages...... which are estimated by (generalized ensemble) Monte Carlo. We test the learning algorithm on a Lennard-Jones (LJ) force field with a torsional angle degrees-of-freedom and a single-atom side-chain. In a test with 24 peptides of known structure, none folded correctly with the initial potential functions...

  16. High-accuracy calculations of sixteen collision integrals for Lennard-Jones (12–6) gases and their interpolation to parameterize neon, argon, and krypton

    International Nuclear Information System (INIS)

    The inverse problem of parameterizing intermolecular potentials given macroscopic transport and thermodynamic data is addressed. Procedures are developed to create arbitrary-precision algorithms for transport collision integrals, using the Lennard-Jones (12–6) potential as an example. Interpolation formulas are produced that compute these collision integrals to four-digit accuracy over the reduced-temperature range 0.3≤T⁎≤400, allowing very fast computation. Lennard-Jones parameters for neon, argon, and krypton are determined by simultaneously fitting the observed temperature dependences of their viscosities and second virial coefficients—one of the first times that a thermodynamic and a dynamic property have been used simultaneously for Lennard-Jones parameterization. In addition to matching viscosities and second virial coefficients within the bounds of experimental error, the determined Lennard-Jones parameters are also found to predict the thermal conductivity and self-diffusion coefficient accurately, supporting the value of the Lennard-Jones (12–6) potential for noble-gas transport-property correlation

  17. Volatility Transmission Between Dow Jones Stock Index And Emerging Islamic Stock Index: Case Of Subprime Financial Crises

    Directory of Open Access Journals (Sweden)

    Amir Saadaoui

    2015-02-01

    Full Text Available In the course of the recent global crisis, the stock shocks are distributed and transmitted from their homes in the developed stock market to emerging stock markets. By supporting the development of emerging stock markets, this study aims to see the transmission of volatility between the Dow Jones stock index and the Dow Jones emerging Islamic stock indiex. In this study we have divided the period into three, periods, before, during and after this crisis to demonstrate the resilience of the Islamic market index in response to the global financial crisis. Another aim of this study is to provide a new guide line for investors in emerging stock market before making investment decisions. The data are daily, going from 02/01/2005 until 31/12/2012. To measure the transmission we used bivariate BEKK-GARCH and DCC-GARCH model. The result shows that there is a transmission mainly during the crisis period which means that the crisis affects all the financial assets whether Islamic or not. The same result also shows the preference to invest in both Islamic and classical stock indexes since they are less risky.

  18. Flory-Huggins parameter χ, from binary mixtures of Lennard-Jones particles to block copolymer melts

    Energy Technology Data Exchange (ETDEWEB)

    Chremos, Alexandros, E-mail: achremos@imperial.ac.uk [Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Nikoubashman, Arash, E-mail: arashn@princeton.edu; Panagiotopoulos, Athanassios Z. [Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544 (United States)

    2014-02-07

    In this contribution, we develop a coarse-graining methodology for mapping specific block copolymer systems to bead-spring particle-based models. We map the constituent Kuhn segments to Lennard-Jones particles, and establish a semi-empirical correlation between the experimentally determined Flory-Huggins parameter χ and the interaction of the model potential. For these purposes, we have performed an extensive set of isobaric–isothermal Monte Carlo simulations of binary mixtures of Lennard-Jones particles with the same size but with asymmetric energetic parameters. The phase behavior of these monomeric mixtures is then extended to chains with finite sizes through theoretical considerations. Such a top-down coarse-graining approach is important from a computational point of view, since many characteristic features of block copolymer systems are on time and length scales which are still inaccessible through fully atomistic simulations. We demonstrate the applicability of our method for generating parameters by reproducing the morphology diagram of a specific diblock copolymer, namely, poly(styrene-b-methyl methacrylate), which has been extensively studied in experiments.

  19. Ternary and quaternary Lennard-Jones atomic clusters: The effects of atomic sizes on the compositions, geometries, and relative stability

    Energy Technology Data Exchange (ETDEWEB)

    Takeuchi, Hiroshi, E-mail: takehi@sci.hokudai.ac.jp

    2015-08-18

    Highlights: • Geometry optimization of ternary and quaternary Lennard-Jones clusters. • Elucidation of atomic compositions, growth sequence, and relative stability. • Pronounced effects of the atom-size difference on the features of the clusters. • High efficiency of atom-type conversions in the geometry optimization. - Abstract: Global-minimum geometries of ternary and quaternary Lennard-Jones clusters have been calculated with constraints on atomic compositions of the clusters. In the present study, the constraints were removed to obtain optimal compositions. The size ratios of the largest-sized atom to the smallest-sized one ranged from 1.1 to 1.6 whereas the depths of the interatomic potentials were constant. The heuristic method combined with the geometrical perturbations and atom-type conversion was used to search for the global minima of the clusters with up to 50 atoms. The smallest-sized and largest-sized atoms usually occupy cores and outer shells, respectively, and the atoms with intermediate sizes are often lacking. The size ratio has pronounced effects on the compositions, structures, and relative stability of the clusters.

  20. Ternary and quaternary Lennard-Jones atomic clusters: The effects of atomic sizes on the compositions, geometries, and relative stability

    International Nuclear Information System (INIS)

    Highlights: • Geometry optimization of ternary and quaternary Lennard-Jones clusters. • Elucidation of atomic compositions, growth sequence, and relative stability. • Pronounced effects of the atom-size difference on the features of the clusters. • High efficiency of atom-type conversions in the geometry optimization. - Abstract: Global-minimum geometries of ternary and quaternary Lennard-Jones clusters have been calculated with constraints on atomic compositions of the clusters. In the present study, the constraints were removed to obtain optimal compositions. The size ratios of the largest-sized atom to the smallest-sized one ranged from 1.1 to 1.6 whereas the depths of the interatomic potentials were constant. The heuristic method combined with the geometrical perturbations and atom-type conversion was used to search for the global minima of the clusters with up to 50 atoms. The smallest-sized and largest-sized atoms usually occupy cores and outer shells, respectively, and the atoms with intermediate sizes are often lacking. The size ratio has pronounced effects on the compositions, structures, and relative stability of the clusters

  1. Flory-Huggins parameter χ, from binary mixtures of Lennard-Jones particles to block copolymer melts

    Science.gov (United States)

    Chremos, Alexandros; Nikoubashman, Arash; Panagiotopoulos, Athanassios Z.

    2014-02-01

    In this contribution, we develop a coarse-graining methodology for mapping specific block copolymer systems to bead-spring particle-based models. We map the constituent Kuhn segments to Lennard-Jones particles, and establish a semi-empirical correlation between the experimentally determined Flory-Huggins parameter χ and the interaction of the model potential. For these purposes, we have performed an extensive set of isobaric-isothermal Monte Carlo simulations of binary mixtures of Lennard-Jones particles with the same size but with asymmetric energetic parameters. The phase behavior of these monomeric mixtures is then extended to chains with finite sizes through theoretical considerations. Such a top-down coarse-graining approach is important from a computational point of view, since many characteristic features of block copolymer systems are on time and length scales which are still inaccessible through fully atomistic simulations. We demonstrate the applicability of our method for generating parameters by reproducing the morphology diagram of a specific diblock copolymer, namely, poly(styrene-b-methyl methacrylate), which has been extensively studied in experiments.

  2. Mechanical Stretching of Proteins: Calmodulin and Titin

    OpenAIRE

    Cieplak, Marek

    2004-01-01

    Mechanical unfolding of several domains of calmodulin and titin is studied using a Go-like model with a realistic contact map and Lennard-Jones contact interactions. It is shown that this simple model captures the experimentally observed difference between the two proteins: titin is a spring that is tough and strong whereas calmodulin acts like a weak spring with featureless force-displacement curves. The difference is related to the dominance of the alpha secondary structures in the native s...

  3. Comparison between Utsu's and Vere-Jones' aftershocks model by means of a computer simulation based on the acceptance-rejection sampling of von Neumann

    Science.gov (United States)

    Reyes, J.; Morales-Esteban, A.; González, E.; Martínez-Álvarez, F.

    2016-07-01

    In this research, a new algorithm for generating a stochastic earthquake catalog is presented. The algorithm is based on the acceptance-rejection sampling of von Neumann. The result is a computer simulation of earthquakes based on the calculated statistical properties of each zone. Vere-Jones states that an earthquake sequence can be modeled as a series of random events. This is the model used in the proposed simulation. Contrariwise, Utsu indicates that the mainshocks are special geophysical events. The algorithm has been applied to zones of Chile, China, Spain, Japan, and the USA. This allows classifying the zones according to Vere-Jones' or Utsu's model. The results have been quantified relating the mainshock with the largest aftershock within the next 5 days (which has been named as Bath event). The results show that some zones fit Utsu's model and others Vere-Jones'. Finally, the fraction of seismic events that satisfy certain properties of magnitude and occurrence is analyzed.

  4. 李成、田爱平会见国际不锈钢论坛秘书长(ISSF)Jone Rowe

    Institute of Scientific and Technical Information of China (English)

    2013-01-01

    9月10日上午,中国特钢企业协会名誉会长、顾问李成、秘书长田爱平存北京会见了国际不锈钢论坛(ISSF)Jone Rowe。Jone Rowe首先对李成在第八届中国国际不锈钢大会上的发言表示赞成,他特别同意李成关于开拓不锈钢市场是我们不锈钢业界最重要的任务的观点。

  5. The Emperor Jones de Louis Gruenberg : le long voyage au cœur/corps de l’Autre race Louis Gruenberg’s Emperor Jones: The Long Journey into the Heart of the Other Race

    Directory of Open Access Journals (Sweden)

    Benoît Depardieu

    2009-11-01

    Full Text Available On January 7, 1933, two years before Gershwin’s Porgy and Bess, The Emperor Jones, composed by Louis Gruenberg in 1931, had its world premiere at the Metropolitan Opera of New York. Although Gruenberg’s opera looks like a mere musical adaptation of O’Neill’s acclaimed play, first performed in 1920, some alterations made by the composer allow to question its ambivalent reception by the audience and the critics. Apart from the singular choice of O’Neill’s play and Gruenberg’s special interest in African American music and vocal traditions, this paper analyses the influence of the Harlem Renaissance period and the fantasmatics of race, present in both the play and the opera, albeit exacerbated in the latter through the scopic enjoyment of the body of the black Other.

  6. Ann Conway-Jones, Gregory of Nyssa’s Tabernacle Imagery in its Jewish and Christian Contexts

    OpenAIRE

    Vinel, Françoise

    2016-01-01

    S’il fallait caractériser la perspective et la méthode définies par Ann Conway-Jones (ACJ) dans le premier chapitre du livre, on pourrait utiliser le titre des études publiées par Sarah Coakley sous le titre : Re-Thinking Gregory of Nyssa, paru en 2003 chez Blackwell à Oxford. Le renouvellement de l’approche de l’œuvre et de la pensée du Cappadocien passe par le refus ou du moins la critique de distinctions longtemps considérées comme opératoires (christianisme/platonisme, théologie/spiritual...

  7. Cluster growth mechanisms in Lennard-Jones fluids: A comparison between molecular dynamics and Brownian dynamics simulations

    Science.gov (United States)

    Jung, Jiyun; Lee, Jumin; Kim, Jun Soo

    2015-03-01

    We present a simulation study on the mechanisms of a phase separation in dilute fluids of Lennard-Jones (LJ) particles as a model of self-interacting molecules. Molecular dynamics (MD) and Brownian dynamics (BD) simulations of the LJ fluids are employed to model the condensation of a liquid droplet in the vapor phase and the mesoscopic aggregation in the solution phase, respectively. With emphasis on the cluster growth at late times well beyond the nucleation stage, we find that the growth mechanisms can be qualitatively different: cluster diffusion and coalescence in the MD simulations and Ostwald ripening in the BD simulations. We also show that the rates of the cluster growth have distinct scaling behaviors during cluster growth. This work suggests that in the solution phase the random Brownian nature of the solute dynamics may lead to the Ostwald ripening that is qualitatively different from the cluster coalescence in the vapor phase.

  8. Relation between calculated Lennard-Jones potential and thermal stability of Cu-based bulk metallic glasses

    International Nuclear Information System (INIS)

    Two metallic bulk glasses, Cu60Zr30Ti10 and Cu47Ti33Zr11Ni8Si1, with a diameter of 3 mm were prepared by copper mold casting method. Dilatometric measurement was carried out on the two glassy alloys to obtain information about the average nearest-neighbour distance r0 and the effective depth of pair potential V0. By assuming a Lennard-Jones potential, r0 and V0 were calculated to be 0.28 nm and 0.16 eV for Cu60Zr30Ti10 and 0.27 nm and 0.13 eV for Cu47Ti33Zr11Ni8Si1, respectively. It was found that the glassy alloy Cu60Zr30Ti10 was more stable than Cu47Ti33Zr11Ni8Si1 against heating from both experiment and calculation

  9. Diffusion in Lennard-Jones fluids using dual control volume grand canonical molecular dynamics simulation (DCV-GCMD)

    International Nuclear Information System (INIS)

    A new approach to calculating diffusivities, both transport as well as equilibrium, is presented. The dual control volume grand canonical molecular dynamics (or DCV-GCMD) method employs two local control volumes for chemical potential control via particle creation/destruction as in grand canonical Monte Carlo (GCMC) simulations. The control volumes are inserted in a standard NVT molecular dynamics simulation yielding a simulation with stochastic chemical potential control that may be thought of as a hybrid GCMC-MD approach. The geometrical control of the chemical potential enables a steady state chemical potential gradient to be established in the system. By measuring the density profile and flux, Fick's law is used to determine the diffusivity. An example calculation is presented for a simple Lennard-Jones system

  10. Perturbation approach for equation of state for hard-sphere and Lennard–Jones pure fluids

    Indian Academy of Sciences (India)

    S B Khasare; M S Deshpande

    2011-06-01

    In this paper we have established the equation of state (EOS) for liquids. The EOS was established for hard-sphere (HS) fluid along with Lennard–Jones (LJ) fluid incorporating perturbation techniques. The calculations are based on suitable axiomatic functional forms for surface tension $S_m (r )$, $r ≥ d/2$ with intermolecular separation , as a variable, and is an arbitrary real number (pole). The results for /ρ from the present EOS thus obtained are compared with Percus-Yevick (PY), scaled particle theory (SPT), and Carnahan–Starling (CS). In addition, we have found a simple EOS for the HS fluid in the region which represents the simulation data accurately. It is observed that, this EOS for HS gives, PY (pressure) for = 0, CS for = 4/5, whereas for = 1 it corresponds to SPT.

  11. Noise-immune complex correlation for optical coherence angiography based on standard and Jones matrix optical coherence tomography

    Science.gov (United States)

    Makita, Shuichi; Kurokawa, Kazuhiro; Hong, Young-Joo; Miura, Masahiro; Yasuno, Yoshiaki

    2016-01-01

    This paper describes a complex correlation mapping algorithm for optical coherence angiography (cmOCA). The proposed algorithm avoids the signal-to-noise ratio dependence and exhibits low noise in vasculature imaging. The complex correlation coefficient of the signals, rather than that of the measured data are estimated, and two-step averaging is introduced. Algorithms of motion artifact removal based on non perfusing tissue detection using correlation are developed. The algorithms are implemented with Jones-matrix OCT. Simultaneous imaging of pigmented tissue and vasculature is also achieved using degree of polarization uniformity imaging with cmOCA. An application of cmOCA to in vivo posterior human eyes is presented to demonstrate that high-contrast images of patients’ eyes can be obtained. PMID:27446673

  12. A simple water model in the presence of inert Lennard-Jones obstacles II: the hydrophobic effect

    Science.gov (United States)

    Kurtjak, Mario; Urbic, Tomaz

    2015-04-01

    Using Monte Carlo computer simulations, hydrophobic effect for a non-polar particle with the diameter of a water molecule was studied in water, confined within a disordered matrix. Freely mobile two-dimensional Mercedes-Benz water was put in a disordered, but fixed, matrix of Lennard-Jones disks. Influence of temperature and matrix properties on the thermodynamic quantities of a non-polar solute solvation was studied. The hydrophobic effect is changed by the presence of the obstacles. Smaller matrix particles change the solute-water structure and thermodynamics drastically, as it was also observed for the properties of pure confined water. The study is bringing new scientific important observations in understanding the role of hydrophobic forces under confinement.

  13. [Purpura: primary systemic amyloidosis manifestation].

    Science.gov (United States)

    Lestre, Sara; Gonçalves, Andreia; João, Alexandre; Ferreira, Ana; Apetato, Margarida

    2009-01-01

    Primary Systemic Amyloidosis (AL) is the most frequent form of systemic amyloidosis and its morbilility is associated with immunoglobulin light chains deposition in vital organs. The mucocutaneous manifestations occur in about 30-40% of the cases and are important in diagnostic suspicion, once they appear in early stages of disease. We report a 71-years-old female patient, with disseminated purpura and cutaneous fragility with 6 months of evolution, accompanied by recent complaints of dysphagy. The first laboratory evaluation didn't show any alterations. The histological and immunohistochemical study of subcutaneous abdominal fat and skin biopsy showed lambda type amyloid protein. In the systemic work-up, we highlight a proteinúria > 1g/24h with Bence Jones proteins and the presence of monoclonal immunoglobulin light chain (lambda type) in serum immunoelectrophoresis. With the diagnosis of primary systemic amyloidosis, treatment with prednisolone and melphalan was started. PMID:19686633

  14. The application of the global isomorphism to the surface tension of the liquid-vapor interface of the Lennard-Jones fluids

    OpenAIRE

    Kulinskii, Vladimir

    2012-01-01

    In this communication we show that the surface tension of the real fluids of the Lennard-Jones type can be obtained from the surface tension of the lattice gas (Ising model) on the basis of the global isomorphism approach developed earlier for the bulk properties.

  15. Ouincy Jones / Quincy Jones ; intervjueerinud Emil Wilbekin

    Index Scriptorium Estoniae

    Jones, Quincy, 1933-

    2009-01-01

    Endise jazzartisti ja preaguse muusikaärimehe, produtsendi Quincy Jonesi mõtteid tööst viieosalise dokumentaalfilmiga "Say it Loud: Black Music in America" , tööst Michael Jacksoniga ja muusikast

  16. Nodular liver lesions involving multiple myeloma: A case report and literature review

    Institute of Scientific and Technical Information of China (English)

    Xiao-Ning Wu; Xin-Yan Zhao; Ji-Dong Jia

    2009-01-01

    We report a case of a 62-year old woman admitted to our hospital for multiple nodular metastatic liver lesions found by ultrasonography in a regular medical examination. Routine laboratory tests were normal.PET-CT showed multiple bone lesions and nodular liver lesions. Liver biopsy revealed nodular infiltration of multiple myeloma with positive staining of kappa light chain. Further investigation of bone marrow aspiration, immunofixation and immunoelectrophoresis of serum protein, urine test for Bence-Jones protein,β2-microglobulin in serum and urine confirmed the diagnosis. The patient also coinfected with hepatitis C virus (HCV). With six cycles of chemotherapy with VAD schedule, she achieved complete remission. In this report, a literature review of liver lesions involving multiple myeloma is also provided.

  17. Gaussian approximation to single particle correlations at and below the picosecond scale for Lennard-Jones and nanoparticle fluids

    International Nuclear Information System (INIS)

    To describe short time (picosecond) and small scale (nanometre) transport in fluids, a Green's function approach was recently developed. This approach relies on an expansion of the distribution of single particle displacements around a Gaussian function, yielding an infinite series of correction terms. Applying a recent theorem (van Zon and Cohen 2006 J. Stat. Phys. 123 1–37) shows that for sufficiently small times the terms in this series become successively smaller, so that truncating the series near or at the Gaussian level might provide a good approximation. In this paper, we derive a theoretical estimate for the time scale at which truncating the series at or near the Gaussian level could be supposed to be accurate for equilibrium nanoscale systems. In order to numerically estimate this time scale, the coefficients for the first few terms in the series are determined in computer simulations for a Lennard-Jones (LJ) fluid, an isotopic LJ mixture and a suspension of a LJ-based model of nanoparticles in a LJ fluid. The results suggest that for LJ fluids an expansion around a Gaussian is accurate at time scales up to a picosecond, while for nanoparticles in suspension (a nanofluid), the characteristic time scale up to which the Gaussian is accurate becomes of the order of 5–10 ps. (invited article)

  18. Effect of the computational domain size and shape on the self-diffusion coefficient in a Lennard-Jones liquid

    Science.gov (United States)

    Kikugawa, Gota; Ando, Shotaro; Suzuki, Jo; Naruke, Yoichi; Nakano, Takeo; Ohara, Taku

    2015-01-01

    In the present study, molecular dynamics (MD) simulations on the monatomic Lennard-Jones liquid in a periodic boundary system were performed in order to elucidate the effect of the computational domain size and shape on the self-diffusion coefficient measured by the system. So far, the system size dependence in cubic computational domains has been intensively investigated and these studies showed that the diffusion coefficient depends linearly on the inverse of the system size, which is theoretically predicted based on the hydrodynamic interaction. We examined the system size effect not only in the cubic cell systems but also in rectangular cell systems which were created by changing one side length of the cubic cell with the system density kept constant. As a result, the diffusion coefficient in the direction perpendicular to the long side of the rectangular cell significantly increases more or less linearly with the side length. On the other hand, the diffusion coefficient in the direction along the long side is almost constant or slightly decreases. Consequently, anisotropy of the diffusion coefficient emerges in a rectangular cell with periodic boundary conditions even in a bulk liquid simulation. This unexpected result is of critical importance because rectangular fluid systems confined in nanospace, which are present in realistic nanoscale technologies, have been widely studied in recent MD simulations. In order to elucidate the underlying mechanism for this serious system shape effect on the diffusion property, the correlation structures of particle velocities were examined.

  19. O’Neill’s Treatment of Racism in All God’s Chillum Got Wings and the Emperor Jones

    Directory of Open Access Journals (Sweden)

    Asim Karim

    2011-07-01

    Full Text Available Society and culture of a particular place is governed by certain elements that have substantial impact on the very personality and behavior of people of that very place. These elements range from such micro ones as home and family to such macro ones as religious affiliation, ethnic and sectarian belongingness and economic conditions. The impact of these cultural elements could be substantially meaningful in developing healthy personality traits or regressive behavioral defects. American literature provides rich study of what could be the disturbing role of such factor as racial belongingness on personality and behavior. O’Neill treatment of racial factor did not develop into a set pattern in his long dramatic career and the consensus is that he predominantly followed stereotypic image of the white/black in American society. This study, however, evaluates specific impact of racism in personality/behavioral disintegration in All God Chillum Got wings and The Emperor Jones. Secondly it asserts that the peculiar psychic states as highlighted in All God’s Chillum in particular match similar states produced in his other plays not concerned with racism. Thus the treatment of personality regression here is in line with similar states in other plays.

  20. Simple cubic equation of state applied to hard-sphere, Lennard-Jones fluids, simple fluids and solids

    International Nuclear Information System (INIS)

    Based on the expansion and extension of the virial equation of state (EOS) of hard-sphere fluids solved by the Percus–Yevick integration equation, a universal cubic (UC) EOS is developed. The UC EOS is applied to model hard-sphere and Lennard-Jones (LJ) fluids, simple Ar and N2 liquids at low temperatures, and supercritical Ar and N2 fluids at high temperatures, as well as ten solids, respectively. The three parameters are determined for the hard-sphere fluid by fitting molecular dynamics (MD) simulation data of the third to eighth virial coefficients in the literature; for other fluids by fitting isothermal compression data; and for solids by using the Einstein model. The results show that the UC EOS gives better results than the Carnahan–Starling EOS for compressibility of hard-sphere fluids. The Helmholtz free energy and internal energy for LJ fluids are predicted and compared with MD simulation data. The calculated pressures for simple Ar and N2 liquids are compared with experimental data. The agreement is fairly good. Eight three-parameter EOSs are applied to describe isothermals of ten typical solids. It is shown that the UC EOS gives the best precision with correct behavior at high-pressure limitation. The UC EOS considering thermal effects is used to analytically evaluate the isobaric thermal expansivity and isothermal compressibility coefficients. The results are in good agreement with experimental data. (paper)

  1. Variability in Thermal response of Primed and Non‐primed Seeds of Squirreltail [Elymus elymoides (Raf.) Swezey and Elymus multisetus (J. G. Smith) M. E. Jones

    OpenAIRE

    HARDEGREE, STUART P.; Jones, Thomas A.; VACTOR, STEVEN S. VAN

    2002-01-01

    Bottlebrush squirreltail [Elymus elymoides (Raf.) Swezey = Sitanion hystrix (Nutt.) J. G. Smith] and big squirreltail [Elymus multisetus (J. G. Smith) M. E. Jones = Sitanion jubatum (J. G. Smith)] have a broad geographical distribution and have been identified as high priority species for restoration of degraded rangelands in the western United States. These rangelands exhibit high annual and seasonal variability in seedbed microclimate. The objective of this study was to examine variability ...

  2. The bulk viscosity of a symmetrical Lennard--Jones mixture above and at liquid--liquid coexistence: A computer simulation study

    OpenAIRE

    Das, Subir K.; Horbach, Jürgen; Binder, Kurt

    2004-01-01

    A Lennard--Jones model of a binary dense liquid (A,B) with a symmetrical miscibility gap is investigated by means of computer simulation methods. Semigrand--canonical Monte Carlo simulations yield the phase diagram in the $T$--$x$ plane ($T$: temperature, $x$: concentration of A or B particles) as well as equilibrated configurations at coexistence. Then Molecular Dynamics simulations use these configurations to determine static properties (isothermal compressibility $\\kappa_T$ and concentrati...

  3. Sequencing of folding events in Go-like proteins

    OpenAIRE

    Hoang, Trinh Xuan; Cieplak, Marek

    2000-01-01

    We have studied folding mechanisms of three small globular proteins: crambin (CRN), chymotrypsin inhibitor 2 (CI2) and the fyn Src Homology 3 domain (SH3) which are modelled by a Go-like Hamiltonian with the Lennard-Jones interactions. It is shown that folding is dominated by a well-defined sequencing of events as determined by establishment of particular contacts. The order of events depends primarily on the geometry of the native state. Variations in temperature, coupling strengths and visc...

  4. Scaling of Folding Properties in Go Models of Proteins

    OpenAIRE

    Cieplak, Marek; Xuan Hoang, Trinh

    2000-01-01

    Insights about scaling of folding properties of proteins are obtained bystudying folding in heteropolymers described by Go-like Hamiltonians. Bothlattice and continuum space models are considered. In the latter case, themonomer-monomer interactions correspond to the Lennard-Jones potential.Several statistical ensembles of the two- and three-dimensional targetnative conformations are considered. Among them are maximally compactconformations which are confined to a lattice and those which are o...

  5. Butterflies (Lepidoptera: Papilionoidea and Hesperoidea and other protected fauna of Jones Estate, a dying watershed in the Kumaon Himalaya, Uttarakhand, India

    Directory of Open Access Journals (Sweden)

    P. Smetacek

    2012-08-01

    Full Text Available Two hundred and forty three species of butterflies recorded from Jones Estate, Uttarakhand between 1951 and 2010 are reported. The ongoing rapid urbanization of Jones Estate micro-watershed will destroy the habitat of 49 species of wildlife protected under Indian law, as well as several species of narrow endemic moths and butterflies. The only known Indian habitat for the butterfly Lister’s Hairstreak Pamela dudgeoni will be destroyed. The effect on the water flow of both the Bhimtal and Sattal lake systems will clearly be adverse, as is evident from the drying up of Kua Tal and the reduced flow of perennial water springs during the dry season on the Estate. The undoubtedly negative effect of urbanization on these valuable fresh water resources will be irreversible in the long term. The trend can be reversed by extending protection to Jones Estate by re-declaring it a Green Belt of Bhimtal and by banning construction in the catchment area of Bhimtal lake, as has been done in Nainital and Mussoorie, both in Uttarakhand.

  6. Uncertain parameters of Jones-Wilkin-Lee equation of state for detonation pro ducts of explosive%炸药爆轰产物Jones-Wilkins-Lee状态方程不确定参数∗

    Institute of Scientific and Technical Information of China (English)

    王言金; 张树道; 李华; 周海兵

    2016-01-01

    Jones-Wilkins-Lee (JWL)状态方程是一种不显含化学反应、由实验方法确定参数的半经验状态方程,能比较精确地描述爆轰产物的膨胀驱动做功过程。在JWL状态方程中有多个未知(不确定)参数需要确定。传统的确定JWL状态方程参数的方法是“调参数”,人为因素影响较大,无法给出参数的不确定性信息。本文利用贝叶斯分析方法研究了炸药的不确定参数,该方法能够基于以往的认识、实验和模拟数据标定(calibration)不确定参数。在本文结果中,不确定参数的后验分布均值与文献结果相符合,基于参数标定结果的数值模拟90%置信区间完全包含实验数据。数值标定结果说明贝叶斯参数标定适用于确定样品炸药的JWL状态方程参数。特别是,在本文JWL状态方程参数标定过程中极大地减少了人为因素的影响。%Equation of state of detonation products possesses various types of mathematical expressions which describe the relation between pressure and volume. Jones-Wilkin-Lee (JWL) equation of state is a widely used equation of state of detonation products because of its simplicity in hydrodynamic calculations. The JWL equation of state may accurately describe the process of expansion drive of detonation products. The JWL equation of state contains parameters, and describe the relation among the volume, energy and pressure of detonation products. These parameters may be deter-mined by detonation experimental data and numerical method. Traditional numerical method is adjusting parameters based on experimental data and numerical experience. Obviously, artificial ingredient may affect the calibrating result in traditional method. This paper uses the Bayesian method to determine the unknown (uncertain) parameter of JWL equation of state for detonation products. The method can calibrate the uncertain parameters based on the known parameter information, the experimental and

  7. Effective protein-protein interaction from structure factor data of a lysozyme solution

    International Nuclear Information System (INIS)

    We report the determination of an effective protein-protein central potential for a lysozyme solution, obtained from the direct inversion of the total structure factor of the system, as extracted from small angle neutron scattering. The inversion scheme rests on a hypernetted-chain relationship between the effective potential and the structural functions, and is preliminarily tested for the case of a Lennard-Jones interaction. The characteristics of our potential are discussed in comparison with current models of effective interactions in complex fluids. The phase behavior predictions are also investigated

  8. Scaling relation and regime map of explosive gas–liquid flow of binary Lennard-Jones particle system

    KAUST Repository

    Inaoka, Hajime

    2012-02-01

    We study explosive gasliquid flows caused by rapid depressurization using a molecular dynamics model of Lennard-Jones particle systems. A unique feature of our model is that it consists of two types of particles: liquid particles, which tend to form liquid droplets, and gas particles, which remain supercritical gaseous states under the depressurization realized by simulations. The system has a pipe-like structure similar to the model of a shock tube. We observed physical quantities and flow regimes in systems with various combinations of initial particle number densities and initial temperatures. It is observed that a physical quantity Q, such as pressure, at position z measured along a pipe-like system at time t follows a scaling relation Q(z,t)=Q(zt) with a scaling function Q(ζ). A similar scaling relation holds for time evolution of flow regimes in a system. These scaling relations lead to a regime map of explosive flows in parameter spaces of local physical quantities. The validity of the scaling relations of physical quantities means that physics of equilibrium systems, such as an equation of state, is applicable to explosive flows in our simulations, though the explosive flows involve highly nonequilibrium processes. In other words, if the breaking of the scaling relations is observed, it means that the explosive flows cannot be fully described by physics of equilibrium systems. We show the possibility of breaking of the scaling relations and discuss its implications in the last section. © 2011 Elsevier B.V. All rights reserved.

  9. Clinical analysis of kidney impairement in multiple myeloma%多发性骨髓瘤肾脏损害的临床分析

    Institute of Scientific and Technical Information of China (English)

    保红云; 荣冬靖; 邱敏; 王丽

    2011-01-01

    Objective To investigate the clinical characteristics and the correlative factor of kidney lesion in multiple myeloma.Methods Retrospective analysis was performed on the clinical characteristics and laboratory data of 45 MM patients.Results The incidence of kidney lesion was 42.2%, the most common kidney lesion was chronic renal failure.There was a significant correlation between the quantity of bone marrow plasmacyte,β2 - microglobulin, urine Bence - Jones protein and renal functional lesion(P < 0.01 ).Anemia and bone lesion were correlated to kidney damage(P < 0.05).Conclusion Proliferation of bone marrow plasmacyte,β2 - microglobulin and urine Bence - Jones protein are main causes of kidney lesion in multiple myeloma.%目的探讨多发性骨髓瘤肾脏损害的临床特征及其发生的相关因素.方法 对多发性骨髓瘤患者肾脏损害的临床表现及实验室检查进行回顾性分析.结果 肾脏损害发生率42.2%,以慢性肾功能不全最常见.骨髓浆细胞数量、β2微球蛋白(β2-MG)及尿游离轻链与肾功能损害之间有显著相关性(P<0.01);贫血及多发性骨损害与肾功能损害之间有相关性(P<0.05).结论 骨髓浆细胞增殖、β2-MG及尿游离轻链可能是多发性骨髓瘤肾脏损害的主要原因.

  10. Immunological evidence of monoclonal gammopathy in North India: a hospital based study

    Directory of Open Access Journals (Sweden)

    Kalpana Singh

    2010-08-01

    Full Text Available Kalpana Singh1, Bhawna Singh2, Sarika Arora2, Alpana Saxena11Department of Biochemistry, Maulana Azad Medical College and LN Hospital, New Delhi, India; 2Department of Biochemistry, GB Pant Hospital, New Delhi, IndiaBackground: Monoclonal gammopathy of unknown significance (MGUS is a condition in which a paraprotein is found in the blood during standard laboratory tests. It is age-related and characterized by accumulation of bone marrow plasma cells derived from a single abnormal clone. The aim of this study was to investigate the pattern of MGUS in North Indian urban population.Methods: Serum and urine samples were collected from 320 suspected cases of gammopathy, were analyzed by sensitive immunological technique based protein electrophoresis followed by immunofixation for detection and type of monoclonal/polyclonal gammopathies. Twenty-five healthy subjects were included as controls.Results: Gammopathies were observed in 38 (11.88% patients. Out of these 7.5% were ¬monoclonal and 4.3% were polyclonal. Overall age of presentation of these monoclonal ¬gammopathies in both sexes was between 21 and 76 years. Gender-related ratio (men:women for these gammopathies was 1:1.18. Predominant heavy chain isotype was IgG (62.5% followed by IgA (37.5%. Among light chains, kappa (κ and lambda (λ chains appeared in 91.6% and 8.4% gammopathies respectively. Paraprotein fractions obtained were IgGκ (58.3%, IgGλ (4.16%, IgAκ (33.3%, and IgAλ (4.16% with 25% samples being positive for Bence Jones proteinuria.Conclusions: Clinical laboratories play an important role in confirming the immunological diagnosis of gammopathies. Determination of nature of paraproteinemia and its associated diseases calls for more extensive studies in India.Keywords: monoclonal gammopathy, immunoelectrophoresis, multiple myeloma, bence jones protein, immunoglobulins

  11. HYDRAULICS, Jones County, Iowa

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  12. HYDROLOGY, JONES COUNTY, USA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  13. TERRAIN, JONES COUNTY, IA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Terrain data, as defined in FEMA Guidelines and Specifications, Appendix N: Data Capture Standards, describes the digital topographic data that was used to create...

  14. FLOODPLAIN, JONES COUNTY, USA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — The Floodplain Mapping/Redelineation study deliverables depict and quantify the flood risks for the study area. The primary risk classifications used are the...

  15. Cooperativity and Contact Order in Protein Folding

    OpenAIRE

    Cieplak, Marek

    2004-01-01

    The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as in the absence of cooperativity. For a fixed native geometry, small changes in the effective contact map may affect the folding times in a chance way and to the extent that is comparable to the shift in the folding times due to cooperativity. The contact ord...

  16. Does Bridget Jones watch EastEnders or The Love Boat? Cultural and linguistic issues in the translation of chick-lit novels

    OpenAIRE

    Ilaria Parini

    2015-01-01

    Abstract - Chick lit is a genre comprised of books chiefly written by women for women. These books are mainly characterized by the tone, which is very confidential and personal, and often relies on the use of colloquial and slangy (and occasionally obscene) expressions, by the use of humour, and by the numerous references to popular culture. This paper aims at analyzing the strategies used in the Italian translation of one of the best-known examples of the genre, Helen Fielding’s Bridget Jone...

  17. La Chartreuse de Parme,Tom Jones et Vanity Fair : la représentation autoconsciente dans trois stades de développement

    OpenAIRE

    2007-01-01

    En résumé INTRODUCTION Pour ce mémoire j ai choisi trois uvres réalistes, notamment The History of Tom Jones, a Foundling publié par Henry Fielding en 1749, La Chartreuse de Parme de Stendhal (1839) et Vanity Fair, a novel without a hero de William Makepeace Thackeray qui est paru en feuilleton en 1847-48. Je me concentrerai sur la Chartreuse et me servirai d exemples des deux autres uvres pour mettre en relief celle de Stendhal. Stendhal et Fielding partageaient « le m...

  18. Accuracy of temperature-derivative of radial distribution function calculated under approximations in Ornstein-Zernike theory for one-component Lennard-Jones fluid

    Science.gov (United States)

    Miyata, Tatsuhiko; Miyazaki, Sanae

    2016-08-01

    The accuracy of the temperature derivative of radial distribution function obtained under hypernetted chain (HNC), Kovalenko-Hirata (KH), Percus-Yevick (PY) and Verlet-modified (VM) closure approximations is examined for one-component Lennard-Jones fluid. As relevant thermodynamic quantities, constant-volume heat capacity and thermal pressure coefficient are investigated in terms of their accuracy under the above four approximations. It is found that HNC and KH closures overestimate these quantities, whereas PY closure tends to underestimate them. VM closure predicts rather accurately the quantities. A significant cancellation is observed along the integration for the above quantities under HNC and KH closures, especially at high density state.

  19. Use of Multiple Methods to Estimate Walrus (Odobenus rosmarus rosmarus) Abundance in the Penny Strait-Lancaster Sound and West Jones Sound Stocks, Canada

    OpenAIRE

    Robert EA Stewart; Born, Erik W.; J Blair Dunn; William R Koski; Anna K Ryan

    2013-01-01

    Surveys to estimate walrus abundance at terrestrial haulout sites in the Penny Strait-Lancaster Sound (PS-LS) and West Jones Sound (WJS) stocks were conducted in 1977 and 1998-2009. The Minimum Counted Population (MCP) was similar in 1977 (565) to recent years (557) for the PS-LS stock. The MCP for the WJS stock was higher in recent surveys (404) than in 1977 (290). Regression analysis of MCP and density (number of walrus divided by number of haulouts surveyed) showed no significant trends ov...

  20. Strength of semiconductors, metals, and ceramics evaluated by a microscopic cleavage model with Morse-type and Lennard-Jones-type interaction

    International Nuclear Information System (INIS)

    An improved microscopic cleavage model, based on a Morse-type and Lennard-Jones-type interaction instead of the previously employed half-sine function, is used to determine the maximum cleavage strength for the brittle materials diamond, tungsten, molybdenum, silicon, GaAs, silica, and graphite. The results of both interaction potentials are in much better agreement with the theoretical strength values obtained by ab initio calculations for diamond, tungsten, molybdenum, and silicon than the previous model. Reasonable estimates of the intrinsic strength are presented for GaAs, silica, and graphite, where first principles values are not available

  1. Complete scaling makes differences along the critical isobar: Molecular dynamics simulations of Lennard-Jones fluid with finite-time scaling

    OpenAIRE

    Wang, Yankui; Liu, Ji; Xiao, Jiajie; Zhong, Fan

    2015-01-01

    We show that, along the critical isobar, the complete scaling results in a unique leading scaling qualitatively distinct to that arising from the simple and the revised scalings. This is verified by a complete-field finite-time scaling theory, which combines the complete scaling with finite-time scaling, and its application to the molecular dynamics simulations of the vapor-liquid critical point of a three-dimensional one-component Lennard-Jones fluid in an isobaric-isothermal ensemble with l...

  2. Folding of Proteins in Go Models with Angular Interactions

    OpenAIRE

    Cieplak, Marek; Hoang, Trinh Xuan

    2003-01-01

    Molecular dynamics studies of Go models of proteins with the 10-12 contact potential and the bond and dihedral angle terms indicate statistical similarities to other Go models, e.g. with the Lennard-Jones contact potentials. The folding times depend on the protein size as power laws with the exponents depending on the native structural classes. There is no dependence of the folding times on the relative contact order even though the folding scenarios are governed mostly by the contact order.

  3. Statistical analysis of earthquakes after the 1999 MW 7.7 Chi-Chi, Taiwan, earthquake based on a modified Reasenberg-Jones model

    Science.gov (United States)

    Chen, Yuh-Ing; Huang, Chi-Shen; Liu, Jann-Yenq

    2015-12-01

    We investigated the temporal-spatial hazard of the earthquakes after the 1999 September 21 MW = 7.7 Chi-Chi shock in a continental region of Taiwan. The Reasenberg-Jones (RJ) model (Reasenberg and Jones, 1989, 1994) that combines the frequency-magnitude distribution (Gutenberg and Richter, 1944) and time-decaying occurrence rate (Utsu et al., 1995) is conventionally employed for assessing the earthquake hazard after a large shock. However, it is found that the b values in the frequency-magnitude distribution of the earthquakes in the study region dramatically decreased from background values after the Chi-Chi shock, and then gradually increased up. The observation of a time-dependent frequency-magnitude distribution motivated us to propose a modified RJ model (MRJ) to assess the earthquake hazard. To see how the models perform on assessing short-term earthquake hazard, the RJ and MRJ models were separately used to sequentially forecast earthquakes in the study region. To depict the potential rupture area for future earthquakes, we further constructed relative hazard (RH) maps based on the two models. The Receiver Operating Characteristics (ROC) curves (Swets, 1988) finally demonstrated that the RH map based on the MRJ model was, in general, superior to the one based on the original RJ model for exploring the spatial hazard of earthquakes in a short time after the Chi-Chi shock.

  4. Communication: Studies of the Lennard-Jones fluid in 2, 3, and 4 dimensions highlight the need for a liquid-state 1/d expansion.

    Science.gov (United States)

    Costigliola, Lorenzo; Schrøder, Thomas B; Dyre, Jeppe C

    2016-06-21

    The recent theoretical prediction by Maimbourg and Kurchan [e-print arXiv:1603.05023 (2016)] that for regular pair-potential systems the virial potential-energy correlation coefficient increases towards unity as the dimension d goes to infinity is investigated for the standard 12-6 Lennard-Jones fluid. This is done by computer simulations for d = 2, 3, 4 going from the critical point along the critical isotherm/isochore to higher density/temperature. In both cases the virial potential-energy correlation coefficient increases significantly. For a given density and temperature relative to the critical point, with increasing number of dimension the Lennard-Jones system conforms better to the hidden-scale-invariance property characterized by high virial potential-energy correlations (a property that leads to the existence of isomorphs in the thermodynamic phase diagram, implying that it becomes effectively one-dimensional in regard to structure and dynamics). The present paper also gives the first numerical demonstration of isomorph invariance of structure and dynamics in four dimensions. Our findings emphasize the need for a universally applicable 1/d expansion in liquid-state theory; we conjecture that the systems known to obey hidden scale invariance in three dimensions are those for which the yet-to-be-developed 1/d expansion converges rapidly. PMID:27334147

  5. Virial series for inhomogeneous fluids applied to the Lennard-Jones wall-fluid surface tension at planar and curved walls

    Science.gov (United States)

    Urrutia, Ignacio; Paganini, Iván E.

    2016-05-01

    We formulate a straightforward scheme of statistical mechanics for inhomogeneous systems that includes the virial series in powers of the activity for the grand free energy and density distributions. There, cluster integrals formulated for inhomogeneous systems play a main role. We center on second order terms that were analyzed in the case of hard-wall confinement, focusing in planar, spherical, and cylindrical walls. Further analysis was devoted to the Lennard-Jones system and its generalization, the 2k-k potential. For these interaction potentials, the second cluster integral was evaluated analytically. We obtained the fluid-substrate surface tension at second order for the planar, spherical, and cylindrical confinement. Spherical and cylindrical cases were analyzed using a series expansion in the radius including higher order terms. We detected a lnR/R2 dependence of the surface tension for the standard Lennard-Jones system confined by spherical and cylindrical walls, no matter if particles are inside or outside of the hard walls. The analysis was extended to bending and Gaussian curvatures, where exact expressions were also obtained.

  6. Communication: Studies of the Lennard-Jones fluid in 2, 3, and 4 dimensions highlight the need for a liquid-state 1/d expansion

    Science.gov (United States)

    Costigliola, Lorenzo; Schrøder, Thomas B.; Dyre, Jeppe C.

    2016-06-01

    The recent theoretical prediction by Maimbourg and Kurchan [e-print arXiv:1603.05023 (2016)] that for regular pair-potential systems the virial potential-energy correlation coefficient increases towards unity as the dimension d goes to infinity is investigated for the standard 12-6 Lennard-Jones fluid. This is done by computer simulations for d = 2, 3, 4 going from the critical point along the critical isotherm/isochore to higher density/temperature. In both cases the virial potential-energy correlation coefficient increases significantly. For a given density and temperature relative to the critical point, with increasing number of dimension the Lennard-Jones system conforms better to the hidden-scale-invariance property characterized by high virial potential-energy correlations (a property that leads to the existence of isomorphs in the thermodynamic phase diagram, implying that it becomes effectively one-dimensional in regard to structure and dynamics). The present paper also gives the first numerical demonstration of isomorph invariance of structure and dynamics in four dimensions. Our findings emphasize the need for a universally applicable 1/d expansion in liquid-state theory; we conjecture that the systems known to obey hidden scale invariance in three dimensions are those for which the yet-to-be-developed 1/d expansion converges rapidly.

  7. Molecular dynamics of folding of secondary structures in Go-type models of proteins

    OpenAIRE

    Hoang, Trinh Xuan; Cieplak, Marek

    1999-01-01

    We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and a soft repulsion for the non-native contacts. The interactions are chosen to make the target secondary structure be the native state of the system. We provide a thorough equilibrium and kinetic characterization of the sequences through the molecular dynamic...

  8. Moore’s Law: The Life of Gordon Moore, Silicon Valley’s Quiet Revolutionary Arnold Thackray, David C. Brock, and Rachel Jones [Book Review

    Energy Technology Data Exchange (ETDEWEB)

    Devanathan, Ram

    2016-05-01

    Five decades ago, Gordon Moore, who would go on to co-found Intel Corporation, made a prescient observation about the exponential advance of semiconductor technology with a corresponding decrease in device cost. His prediction about the pace of doubling of the number of transistors in an integrated circuit came to be known eponymously as Moore’s law and has held true for 50 years. He also foresaw, way back in 1965, the development of home computers, electronic controls in automobiles, portable communications systems, and electronic wrist watches. Moore’s fascinating life, characterized by relentless innovation, charity and breathtaking humility, is the subject of this comprehensive authorized biography. The enthralling narrative is the product of collaboration between an academic (Thackray), a technology historian (Brock) and a journalist (Jones), and draws its material from numerous interviews, Moore’s meticulously maintained notes and professional records, personal papers, industry data, published volumes, and news accounts.

  9. Phase Equilibria and Plate-fluid Interfacial Tensions for Four-site Associating Lennard-Jones Fluids Confined in Slit Pores

    Institute of Scientific and Technical Information of China (English)

    FU Dong; YAN Shu-Mei; WANG Xue-Min

    2008-01-01

    The excess Helmholtz free energy functional for four-site associating Lennard-Jones(LJ)fluid was formulated in terms of a modified fundamental measure theory for short-ranged interactions and a first-order mean-spherical approximation theory for long-ranged attraction.Within the framework of density functional theory,the thermodynamic properties including the average density isotherms,density profiles and fractions of not bonded monomers characterizing the coexistences between gas-like and liquid-like phases for capillary condensation,phase equilibria and equilibrium plate-fluid interfacial tensions were investigated.The influences of association energy,fluid-solid interaction and pore width on the inhomogeneous behavior of four-site associating LJ fluids confined in slit pores were discussed.

  10. Optical Layout Analysis of Polarization Interference Imaging Spectrometer by Jones Calculus in View of both Optical Throughput and Interference Fringe Visibility

    Science.gov (United States)

    Zhang, Xuanni; Zhang, Chunmin

    2013-01-01

    A polarization interference imaging spectrometer based on Savart polariscope was presented. Its optical throughput was analyzed by Jones calculus. The throughput expression was given, and clearly showed that the optical throughput mainly depended on the intensity of incident light, transmissivity, refractive index and the layout of optical system. The simulation and analysis gave the optimum layout in view of both optical throughput and interference fringe visibility, and verified that the layout of our former design was optimum. The simulation showed that a small deviation from the optimum layout influenced interference fringe visibility little for the optimum one, but influenced severely for others, so a small deviation is admissible in the optimum, and this can mitigate the manufacture difficulty. These results pave the way for further research and engineering design.

  11. Accurate Monte Carlo simulations on FCC and HCP Lennard-Jones solids at very low temperatures and high reduced densities up to 1.30

    Science.gov (United States)

    Adidharma, Hertanto; Tan, Sugata P.

    2016-07-01

    Canonical Monte Carlo simulations on face-centered cubic (FCC) and hexagonal closed packed (HCP) Lennard-Jones (LJ) solids are conducted at very low temperatures (0.10 ≤ T∗ ≤ 1.20) and high densities (0.96 ≤ ρ∗ ≤ 1.30). A simple and robust method is introduced to determine whether or not the cutoff distance used in the simulation is large enough to provide accurate thermodynamic properties, which enables us to distinguish the properties of FCC from that of HCP LJ solids with confidence, despite their close similarities. Free-energy expressions derived from the simulation results are also proposed, not only to describe the properties of those individual structures but also the FCC-liquid, FCC-vapor, and FCC-HCP solid phase equilibria.

  12. Thermodynamic, Structural and Transport Properties of Lennard-Jones Liquid Systems. A Molecular Dynamics Simulations of Liquid Helium, Neon, Methane and Nitrogen

    Directory of Open Access Journals (Sweden)

    F. Ould Kadour

    2003-12-01

    Full Text Available Abstract: Molecular dynamics calculations are carried out in order to find the properties of Lennard Jones liquids in different state points of their phase diagram. The spherical shape and the stability of the helium, neon, methane and nitrogen make the liquids easily accessible to numerical simulation. Thermodynamic, structural, and transport properties are studied and compared with both experimental data and recent theoretical investigations. In the present work, up to 22 state points are covered, some of which are near or at the triple point. It will be shown that the classical approach leads to data that are in very good agreement with experiments and other types of calculations. At high temperatures and low densities, we observe a decrease in the uncertainties in the stress autocorrelation function by increasing the number of iterations.

  13. The Effectively Used Expressionistic Devices in The Emperor Jones%表现主义手法在《琼斯皇》中的应用

    Institute of Scientific and Technical Information of China (English)

    和伟

    2004-01-01

    本文从表现主义手法的角度对奥尼尔的进行了研究,着重探讨了表现主义手法在揭示剧中人物内心灵魂,挖掘人物的精神世界,展示其深刻的内心体验,及畸形心理形为中的体现.%This article inquires into how O' Neill uses expressionistic techniques to express Jones'inner world. The author points out the function of revealing the character's spirit, excavating the character's spiritual world, the character's profound experience and complicated abnormal psychology when O' Neill applies the symbology.

  14. Solitons on H bonds in proteins

    DEFF Research Database (Denmark)

    d'Ovidio, F.; Bohr, H.G.; Lindgård, Per-Anker

    2003-01-01

    A model for soliton dynamics on a hydrogen-bond network in helical proteins is proposed. It employs the formalism-of fully integrable Toda lattices in three dimensions which admit phonons as well as solitons along the hydrogen bonds of the helices. A simulation of the three-dimensional Toda lattice...... system shows that the solitons are spontaneously created and are stable and moving along the helix axis. A perturbation on one of the three H-bond lines forms solitons on the other H bonds as well. The robust solitary wave may explain very long-lived modes in the frequency range of 100 cm(-1) which are...... found in recent x-ray laser experiments. The dynamics parameters of the Toda lattice are in accordance with the usual Lennard-Jones parameters used for realistic H-bond potentials in proteins....

  15. Avaliação cefalométrica das alterações dentoesqueléticas de jovens com má oclusão de Classe II dentária tratados com distalizadores Jones jig Cephalometric evaluation of dentoskeletal changes in Class II young patients treated with Jones jig appliances

    Directory of Open Access Journals (Sweden)

    Mayara Paim Patel

    2009-06-01

    Full Text Available OBJETIVO: esta pesquisa objetivou avaliar cefalometricamente as alterações dentoesqueléticas de jovens com Classe II dentária tratados com o distalizador Jones jig. METODOLOGIA: foram avaliados 30 pacientes, sendo 15 de cada gênero, com média de idades iniciais de 13,63 anos; brasileiros, naturais da cidade de Bauru/SP, caracterizados por má oclusão de Classe II, 1ª e 2ª divisões de Angle sem comprometimento esquelético. Os jovens foram tratados com aparelho Jones jig a fim de distalizar os molares superiores a uma relação molar de "super Classe I"; sendo que esse dispositivo permaneceu, em média, por 0,55 anos. Ao final da sobrecorreção, os molares distalizados receberam um botão de Nance e, como ancoragem extrabucal, o aparelho extrabucal (AEB com tração média-alta, com o intuito de verticalizar e corrigir a angulação radicular dos molares distalizados. Foram realizadas telerradiografias em normal lateral inicial (T1 e pós-distalização (T2. As medidas cefalométricas foram submetidas ao teste t dependente de Student para avaliar as alterações de T1 para T2. RESULTADOS: com base nos resultados obtidos e a partir da metodologia empregada, observou-se alterações dentárias significativas, como a movimentação distal linear e angular, assim como a intrusão dos segundos e primeiros molares superiores no sentido vertical. Também se confirmou efeitos indesejáveis, como a perda de ancoragem refletida em mesialização, extrusão e angulação mesial dos segundos pré-molares, a protrusão dos incisivos superiores e o aumento do trespasse vertical e horizontal. Pode-se confirmar que certas movimentações dentárias promovem significativas alterações esqueléticas de estruturas localizadas à distância, ou seja, observou-se extrusão significativa dos segundos pré-molares superiores, o que resultou em rotação mandibular, aumento significativo da altura facial anteroinferior e protrusão do lábio inferior

  16. Thermal motion in proteins: Large effects on the time-averaged interaction energies

    Science.gov (United States)

    Goethe, Martin; Fita, Ignacio; Rubi, J. Miguel

    2016-03-01

    As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.

  17. A pressure consistent bridge correction of Kovalenko-Hirata closure in Ornstein-Zernike theory for Lennard-Jones fluids by apparently adjusting sigma parameter

    Science.gov (United States)

    Ebato, Yuki; Miyata, Tatsuhiko

    2016-05-01

    Ornstein-Zernike (OZ) integral equation theory is known to overestimate the excess internal energy, Uex, pressure through the virial route, Pv, and excess chemical potential, μex, for one-component Lennard-Jones (LJ) fluids under hypernetted chain (HNC) and Kovalenko-Hirata (KH) approximatons. As one of the bridge correction methods to improve the precision of these thermodynamic quantities, it was shown in our previous paper that the method to apparently adjust σ parameter in the LJ potential is effective [T. Miyata and Y. Ebato, J. Molec. Liquids. 217, 75 (2016)]. In our previous paper, we evaluated the actual variation in the σ parameter by using a fitting procedure to molecular dynamics (MD) results. In this article, we propose an alternative method to determine the actual variation in the σ parameter. The proposed method utilizes a condition that the virial and compressibility pressures coincide with each other. This method can correct OZ theory without a fitting procedure to MD results, and possesses characteristics of keeping a form of HNC and/or KH closure. We calculate the radial distribution function, pressure, excess internal energy, and excess chemical potential for one-component LJ fluids to check the performance of our proposed bridge function. We discuss the precision of these thermodynamic quantities by comparing with MD results. In addition, we also calculate a corrected gas-liquid coexistence curve based on a corrected KH-type closure and compare it with MD results.

  18. Examination of Electric Utility CEO Compensation 2000-2011 and its significance to Company Earnings, Company Revenue, Company Stock and the Dow Jones Utility Average

    Science.gov (United States)

    Labovitch, Andrew

    This dissertation examined electric utility CEO compensation during the years 2000 through 2011 for United States owned and operated companies. To determine the extent to which agency theory may apply to electric utility CEO compensation, this examination segmented the industry by four types of company financial metrics: revenue, earnings, stock price and the Dow Jones Utility Average; by five categories of CEO compensation: base salary, bonus, stock grants, all other compensation and total compensation; and by four categories of company size as measured by revenue: large, medium, small and the industry as a whole. Electric utility CEO compensation data was analyzed with the financial metrics to determine correlations. No type of compensation was highly correlated to any of the financial metrics for any size industry segment indicating that there was little agency. CEO compensation in large electric utility companies was higher than compensation in medium and smaller companies even though the CEOs at larger companies earned less per dollar of revenue and per dollar of earnings than their counterparts in smaller companies.

  19. Energy world governance. Review of the conference which was held at IFRI, 26 March 2009, with Tatsuo Masuda, Andre Mernier et Richard H. Jones

    International Nuclear Information System (INIS)

    The conference was related with some of the major questions concerning global energy governance today, the role of the different international organizations dealing with energy, the rules of the game between market and state players, the efforts to deal with climate change, and the integration of emerging countries in global energy governance, the roles of the different international organizations dealing with energy (will we see further fragmentation or more cooperation between them?). Tatsuo Masuda in his contribution discussed global energy governance from an oil perspective. Andre Mernier noted the particular nature of the Energy Charter, which, as it is founded upon an international treaty, is unlike other organizations in being legally binding. The legal basis of the organization means that agreements are especially powerful. Then Richard H. Jones underlined that last summer's volatility in oil markets, the ensuing financial and economic crisis, the major disruption in gas supplies to European markets this winter and the upcoming climate change negotiations have led to increasing calls for a stronger global dialogue on energy issues. This dialogue should deal with prices and investment, energy security and climate change

  20. Use of Multiple Methods to Estimate Walrus (Odobenus rosmarus rosmarus Abundance in the Penny Strait-Lancaster Sound and West Jones Sound Stocks, Canada

    Directory of Open Access Journals (Sweden)

    Robert EA Stewart

    2013-08-01

    Full Text Available Surveys to estimate walrus abundance at terrestrial haulout sites in the Penny Strait-Lancaster Sound (PS-LS and West Jones Sound (WJS stocks were conducted in 1977 and 1998-2009. The Minimum Counted Population (MCP was similar in 1977 (565 to recent years (557 for the PS-LS stock. The MCP for the WJS stock was higher in recent surveys (404 than in 1977 (290. Regression analysis of MCP and density (number of walrus divided by number of haulouts surveyed showed no significant trends over time. We also calculated bounded count estimates for comparison. Finally, we used broad-scale behavioural data to estimate the proportion of the total stock that could be considered countable, to produce two adjusted estimates. We selected recent surveys with good coverage and ignored adjusted estimates that were lower than MCP. For the PS-LS stock, the adjusted MCP (with 95% CL was 672 (575-768 and 727 (623-831 walrus in 2007 and 2009, respectively. For WJS, the best estimates were the adjusted MCP of 503 (473-534 in 2008 and the adjusted bounded count of 470 (297-1732 in 2009. While both stocks appear to have remained stable over three decades, differences in survey coverage and possible differences in walrus distribution make precise population estimation difficult.

  1. Impactos do Índice Dow Jones, Commodities e Câmbio sobre o Ibovespa: uma Análise do Efeito Contágio

    Directory of Open Access Journals (Sweden)

    Pedro Raffy Vartanian

    2012-07-01

    Full Text Available The purpose of this research is to evaluate the existence of contagion effects of the Dow Jones index, commodity prices and exchange rate on the trajectory of the Bovespa index in the period 1999-2010, and analyze the longterm relationships between the variables. The theoretical framework is based on contagion effect, which occurs in the spread of market disturbances from one country to another country as discussed by Dornbusch, Park and Claessens (2000, Pericoli and Sbracia (2003, and Forbes and Rigobon (2002, as well as in empirical studies such as Lamounier and Nogueira (2007, Tabak e Lima (2003, Groppo (2006 and Pimenta (2004, among others, complete with research of the impact on commodity prices in the stock market, as can be seen in Barr and Kantor (2002. For this purpose, a cointegration test from the procedure suggested by Johansen (1991 was applied, and a vector autoregression model (VAR, initially proposed by Sims (1980 and Sims (1986, with the causality/exogeneity Granger test, was utilized. The results of Johansen cointegration test did not indicate the existence of long-term relationships between the variables. As to short-term effects, the impulse response functions showed that the Brazilian stock market index reacts positively to shocks in commodity prices and the U.S. stock market, and it demonstrates a positive reaction to currency depreciation, which suggests presence of the contagion effect.

  2. First and Second-Phase Transitions of Gases at Isobaric Process; Lennard-Jones (9,6) Gases with a Hard Core

    Science.gov (United States)

    Matsumoto, Akira

    2014-12-01

    The thermodynamic functions for Lennard-Jones (9,6) gases with a hard core that are evaluated till the third virial coefficients, are investigated at an isobaric process. Some thermodynamic functions are analytically expressed as functions of intensive variables, temperature, and pressure. Some thermodynamic quantities for carbon dioxide are calculated numerically and drawn graphically. In critical states, the heat capacity diverges to infinity at the critical point while the Gibbs free energy, volume, enthalpy, and entropy are continuous at the critical point. In the coexistence of two phases, the boiling temperatures and the enthalpy changes of vaporization are obtained by numerical calculations for 20 substances. The Gibbs free energy indicates a polygonal line; entropy, volume, and enthalpy jump from the liquid to gaseous phase at the boiling point. The heat capacity does not diverge to infinity but shows a finite discrepancy at boiling point. This suggests that a first-order phase transition at the boiling point and a second-order phase transition may occur at the critical point.

  3. Power-law correlations in finance-related Google searches, and their cross-correlations with volatility and traded volume: Evidence from the Dow Jones Industrial components

    Science.gov (United States)

    Kristoufek, Ladislav

    2015-06-01

    We study power-law correlations properties of the Google search queries for Dow Jones Industrial Average (DJIA) component stocks. Examining the daily data of the searched terms with a combination of the rescaled range and rescaled variance tests together with the detrended fluctuation analysis, we show that the searches are in fact power-law correlated with Hurst exponents between 0.8 and 1.1. The general interest in the DJIA stocks is thus strongly persistent. We further reinvestigate the cross-correlation structure between the searches, traded volume and volatility of the component stocks using the detrended cross-correlation and detrending moving-average cross-correlation coefficients. Contrary to the universal power-law correlations structure of the related Google searches, the results suggest that there is no universal relationship between the online search queries and the analyzed financial measures. Even though we confirm positive correlation for a majority of pairs, there are several pairs with insignificant or even negative correlations. In addition, the correlations vary quite strongly across scales.

  4. Formerly utilized MED/AEC sites Remedial Action Program. Report of the decontamination of Jones Chemical Laboratory, Ryerson Physical Laboratory, and Eckhart Hall, the University of Chicago, Chicago, Illinois

    International Nuclear Information System (INIS)

    The US Department of Energy (DOE) has implemented a program to decontaminate radioactively contaminated sites that were formerly utilized by the Manhattan Engineer District (MED) and/or the Atomic Energy Commission (AEC) for activities that included handling of radioactive material. This program is referred to as the ''Formerly Utilized Sites Remedial Action Program'' (FUSRAP). Among these sites are Jones Chemical Laboratory, Ryerson Physical Laboratory, Kent Chemical Laboratory, and Eckhart Hall of The University of Chicago, Chicago, Illinois. Since 1977, the University of Chicago decontaminated Kent Chemical Laboratory as part of a facilities renovation program. All areas of Eckhart Hall, Ryerson Physical Laboratory, and Jones Chemical Laboratory that had been identified as contaminated in excess of current guidelines in the 1976-1977 surveys were decontaminated to levels where no contamination could be detected relative to natural backgrounds. All areas that required defacing to achieve this goal were restored to their original condition. The radiological evaluation of the sewer system, based primarily on the radiochemical analyses of sludge and water samples, indicated that the entire sewer system is potentially contaminated. While this evaluation was defined as part of this project, the decontamination of the sewer system was not included in the purview of this effort. The documentation included in this report substantiates the judgment that all contaminated areas identified in the earlier reports in the three structures included in the decontamination effort (Eckhart Hall, Ryerson Physical Laboratory, and Jones Chemical Laboratory) were cleaned to levels commensurate with release for unrestricted use

  5. Mechanical stretching of proteins: calmodulin and titin

    Science.gov (United States)

    Cieplak, Marek

    2005-07-01

    Mechanical unfolding of several domains of calmodulin and titin is studied using a Go-like model with a realistic contact map and Lennard-Jones contact interactions. It is shown that this simple model captures the experimentally observed difference between the two proteins: titin is a spring that is tough and strong whereas calmodulin acts like a weak spring with featureless force-displacement curves. The difference is related to the dominance of the α secondary structures in the native structure of calmodulin. The tandem arrangements of calmodulin unwind simultaneously in each domain whereas the domains in titin unravel in a serial fashion. The sequences of contact events during unravelling are correlated with the contact order, i.e., with the separation between contact making amino acids along the backbone in the native state. Temperature is found to affect stretching in a profound way.

  6. Tests of the Structure-Based Models of Proteins

    International Nuclear Information System (INIS)

    The structure-based models of proteins are defined through the condition that their ground state coincides with the native structure of the proteins. There are many variants of such models and they yield different properties. Optimal variants can be selected by making comparisons to experimental data on single-molecule stretching. Here, we discuss the 15 best performing variants and focus on fine tuning the selection process by adjusting the velocity of stretching to match the experimental conditions. The very best variant is found to correspond to the 10-12 potential in the native contacts with the energies modulated by the Miyazawa-Jernigan statistical potential and variable length parameters. The second best model incorporates the Lennard-Jones potential with uniform amplitudes. We then make a detailed comparison of the two models in which theoretical surveys of stretching properties of 7510 proteins were made previously. (authors)

  7. Protein Foods

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... the vegetarian proteins, whether they have carbohydrate. Best Protein Choices The best choices are: Plant-based proteins ...

  8. An analytical equation of state for describing isotropic-nematic phase equilibria of Lennard-Jones chain fluids with variable degree of molecular flexibility.

    Science.gov (United States)

    van Westen, Thijs; Oyarzún, Bernardo; Vlugt, Thijs J H; Gross, Joachim

    2015-06-28

    We develop an equation of state (EoS) for describing isotropic-nematic (IN) phase equilibria of Lennard-Jones (LJ) chain fluids. The EoS is developed by applying a second order Barker-Henderson perturbation theory to a reference fluid of hard chain molecules. The chain molecules consist of tangentially bonded spherical segments and are allowed to be fully flexible, partially flexible (rod-coil), or rigid linear. The hard-chain reference contribution to the EoS is obtained from a Vega-Lago rescaled Onsager theory. For the description of the (attractive) dispersion interactions between molecules, we adopt a segment-segment approach. We show that the perturbation contribution for describing these interactions can be divided into an "isotropic" part, which depends only implicitly on orientational ordering of molecules (through density), and an "anisotropic" part, for which an explicit dependence on orientational ordering is included (through an expansion in the nematic order parameter). The perturbation theory is used to study the effect of chain length, molecular flexibility, and attractive interactions on IN phase equilibria of pure LJ chain fluids. Theoretical results for the IN phase equilibrium of rigid linear LJ 10-mers are compared to results obtained from Monte Carlo simulations in the isobaric-isothermal (NPT) ensemble, and an expanded formulation of the Gibbs-ensemble. Our results show that the anisotropic contribution to the dispersion attractions is irrelevant for LJ chain fluids. Using the isotropic (density-dependent) contribution only (i.e., using a zeroth order expansion of the attractive Helmholtz energy contribution in the nematic order parameter), excellent agreement between theory and simulations is observed. These results suggest that an EoS contribution for describing the attractive part of the dispersion interactions in real LCs can be obtained from conventional theoretical approaches designed for isotropic fluids, such as a Perturbed

  9. A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution

    Science.gov (United States)

    Sumi, Tomonari; Maruyama, Yutaka; Mitsutake, Ayori; Koga, Kenichiro

    2016-06-01

    In the conventional classical density functional theory (DFT) for simple fluids, an ideal gas is usually chosen as the reference system because there is a one-to-one correspondence between the external field and the density distribution function, and the exact intrinsic free-energy functional is available for the ideal gas. In this case, the second-order density functional Taylor series expansion of the excess intrinsic free-energy functional provides the hypernetted-chain (HNC) approximation. Recently, it has been shown that the HNC approximation significantly overestimates the solvation free energy (SFE) for an infinitely dilute Lennard-Jones (LJ) solution, especially when the solute particles are several times larger than the solvent particles [T. Miyata and J. Thapa, Chem. Phys. Lett. 604, 122 (2014)]. In the present study, we propose a reference-modified density functional theory as a systematic approach to improve the SFE functional as well as the pair distribution functions. The second-order density functional Taylor series expansion for the excess part of the intrinsic free-energy functional in which a hard-sphere fluid is introduced as the reference system instead of an ideal gas is applied to the LJ pure and infinitely dilute solution systems and is proved to remarkably improve the drawbacks of the HNC approximation. Furthermore, the third-order density functional expansion approximation in which a factorization approximation is applied to the triplet direct correlation function is examined for the LJ systems. We also show that the third-order contribution can yield further refinements for both the pair distribution function and the excess chemical potential for the pure LJ liquids.

  10. Local pressure components and interfacial tension at a liquid-solid interface obtained by the perturbative method in the Lennard-Jones system

    International Nuclear Information System (INIS)

    A classical molecular dynamics simulation was conducted for a system composed of fluid molecules between two planar solid surfaces, and whose interactions are described by the 12-6 Lennard-Jones form. This paper presents a general description of the pressure components and interfacial tension at a fluid-solid interface obtained by the perturbative method on the basis of statistical thermodynamics, proposes a method to consider the pressure components tangential to an interface which are affected by interactions with solid atoms, and applies this method to the calculation system. The description of the perturbative method is extended to subsystems, and the local pressure components and interfacial tension at a liquid-solid interface are obtained and examined in one- and two-dimensions. The results are compared with those obtained by two alternative methods: (a) an evaluation of the intermolecular force acting on a plane, and (b) the conventional method based on the virial expression. The accuracy of the numerical results is examined through the comparison of the results obtained by each method. The calculated local pressure components and interfacial tension of the fluid at a liquid-solid interface agreed well with the results of the two alternative methods at each local position in one dimension. In two dimensions, the results showed a characteristic profile of the tangential pressure component which depended on the direction tangential to the liquid-solid interface, which agreed with that obtained by the evaluation of the intermolecular force acting on a plane in the present study. Such good agreement suggests that the perturbative method on the basis of statistical thermodynamics used in this study is valid to obtain the local pressure components and interfacial tension at a liquid-solid interface

  11. Spontaneous cavitation in a Lennard-Jones liquid: Molecular dynamics simulation and the van der Waals-Cahn-Hilliard gradient theory

    Science.gov (United States)

    Baidakov, Vladimir G.

    2016-02-01

    The process of bubble nucleation in a Lennard-Jones (LJ) liquid is studied by molecular dynamics (MD) simulation. The bubble nucleation rate J is determined by the mean life-time method at temperatures above that of the triple point in the region of negative pressures. The results of simulation are compared with classical nucleation theory (CNT) and modified classical nucleation theory (MCNT), in which the work of formation of a critical bubble is determined in the framework of the van der Waals-Cahn-Hilliard gradient theory (GT). It has been found that the values of J obtained in MD simulation systematically exceed the data of CNT, and this excess in the nucleation rate reaches 8-10 orders of magnitude close to the triple point temperature. The results of MCNT are in satisfactory agreement with the data of MD simulation. To describe the properties of vapor-phase nuclei in the framework of GT, an equation of state has been built up which describes stable, metastable and labile regions of LJ fluids. The surface tension of critical bubbles γ has been found from CNT and data of MD simulation as a function of the radius of curvature of the surface of tension R*. The dependence γ(R*) has also been calculated from GT. The Tolman length has been determined, which is negative and in modulus equal to ≈(0.1 - 0.2) σ. The paper discusses the applicability of the Tolman formula to the description of the properties of critical nuclei in nucleation.

  12. Development of a Jones vector based model for the measurement of a plasma current in a thermonuclear fusion reactor with a POTDR setup

    Science.gov (United States)

    Aerssens, M.; Gusarov, A.; Moreau, P.; Malard, P.; Massaut, V.; Mégret, P.; Wuilpart, M.

    2012-04-01

    Fibre optical current sensor (FOCS) is a promising alternative to inductive sensors for the measurement of the plasma current in future thermonuclear fusion reactors. Standard FOCS relies on the measurement of the state of polarisation (SOP) of light at the output of an optical bre surrounding a current. Because of the Faraday eect, magnetic eld induced by electrical current rotates the SOP of light travelling into the bre. According to the Ampere's theorem this rotation is proportional to the surrounded current. In future tokamaks like ITER and DEMO, the plasma current will be suciently high to generate a rotation of the SOP higher than 2 radians. These conditions may lead to uncertainties on the determination of the plasma current if no post processing is performed. In this paper we propose a solution with a Polarisation Optical Time Domain Re ectometer (POTDR) setup allowing both unambiguous plasma current measurement and also local magnetic eld measurements. This measurement is based on the assessment of the SOP rotation of the Rayleigh backscattered POTDR signal. Thanks to the presence of an input polarizer, SOP variations are converted into power uctuations that contain information about the distribution of the magnetic eld and therefore about the plasma current. Using the Jones formalism we have developed a model accounting for the modication of the SOP of light travelling into the optical bre and the evolution of the POTDR signal. In parallel experimental PODTR measurements have been performed on the Tore Supra tokamak situated at CEA Cadarache in France. A comparison between the models and the experimental results conrms the capability of the system to measure the plasma current and the local magnetic eld even if further data post processing are still required.

  13. Explicit expressions of self-diffusion coefficient, shear viscosity, and the Stokes-Einstein relation for binary mixtures of Lennard-Jones liquids

    International Nuclear Information System (INIS)

    Explicit expressions of the self-diffusion coefficient, Di, and shear viscosity, ηsv, are presented for Lennard-Jones (LJ) binary mixtures in the liquid states along the saturated vapor line. The variables necessary for the expressions were derived from dimensional analysis of the properties: atomic mass, number density, packing fraction, temperature, and the size and energy parameters used in the LJ potential. The unknown dependence of the properties on each variable was determined by molecular dynamics (MD) calculations for an equimolar mixture of Ar and Kr at the temperature of 140 K and density of 1676 kg m−3. The scaling equations obtained by multiplying all the single-variable dependences can well express Di and ηsv evaluated by the MD simulation for a whole range of compositions and temperatures without any significant coupling between the variables. The equation for Di can also explain the dual atomic-mass dependence, i.e., the average-mass and the individual-mass dependence; the latter accounts for the “isotope effect” on Di. The Stokes-Einstein (SE) relation obtained from these equations is fully consistent with the SE relation for pure LJ liquids and that for infinitely dilute solutions. The main differences from the original SE relation are the presence of dependence on the individual mass and on the individual energy parameter. In addition, the packing-fraction dependence turned out to bridge another gap between the present and original SE relations as well as unifying the SE relation between pure liquids and infinitely dilute solutions

  14. Explicit expressions of self-diffusion coefficient, shear viscosity, and the Stokes-Einstein relation for binary mixtures of Lennard-Jones liquids

    Energy Technology Data Exchange (ETDEWEB)

    Ohtori, Norikazu, E-mail: ohtori@chem.sc.niigata-u.ac.jp [Department of Chemistry, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181 (Japan); Ishii, Yoshiki [Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181 (Japan)

    2015-10-28

    Explicit expressions of the self-diffusion coefficient, D{sub i}, and shear viscosity, η{sub sv}, are presented for Lennard-Jones (LJ) binary mixtures in the liquid states along the saturated vapor line. The variables necessary for the expressions were derived from dimensional analysis of the properties: atomic mass, number density, packing fraction, temperature, and the size and energy parameters used in the LJ potential. The unknown dependence of the properties on each variable was determined by molecular dynamics (MD) calculations for an equimolar mixture of Ar and Kr at the temperature of 140 K and density of 1676 kg m{sup −3}. The scaling equations obtained by multiplying all the single-variable dependences can well express D{sub i} and η{sub sv} evaluated by the MD simulation for a whole range of compositions and temperatures without any significant coupling between the variables. The equation for D{sub i} can also explain the dual atomic-mass dependence, i.e., the average-mass and the individual-mass dependence; the latter accounts for the “isotope effect” on D{sub i}. The Stokes-Einstein (SE) relation obtained from these equations is fully consistent with the SE relation for pure LJ liquids and that for infinitely dilute solutions. The main differences from the original SE relation are the presence of dependence on the individual mass and on the individual energy parameter. In addition, the packing-fraction dependence turned out to bridge another gap between the present and original SE relations as well as unifying the SE relation between pure liquids and infinitely dilute solutions.

  15. Explicit expressions of self-diffusion coefficient, shear viscosity, and the Stokes-Einstein relation for binary mixtures of Lennard-Jones liquids

    Science.gov (United States)

    Ohtori, Norikazu; Ishii, Yoshiki

    2015-10-01

    Explicit expressions of the self-diffusion coefficient, Di, and shear viscosity, ηsv, are presented for Lennard-Jones (LJ) binary mixtures in the liquid states along the saturated vapor line. The variables necessary for the expressions were derived from dimensional analysis of the properties: atomic mass, number density, packing fraction, temperature, and the size and energy parameters used in the LJ potential. The unknown dependence of the properties on each variable was determined by molecular dynamics (MD) calculations for an equimolar mixture of Ar and Kr at the temperature of 140 K and density of 1676 kg m-3. The scaling equations obtained by multiplying all the single-variable dependences can well express Di and ηsv evaluated by the MD simulation for a whole range of compositions and temperatures without any significant coupling between the variables. The equation for Di can also explain the dual atomic-mass dependence, i.e., the average-mass and the individual-mass dependence; the latter accounts for the "isotope effect" on Di. The Stokes-Einstein (SE) relation obtained from these equations is fully consistent with the SE relation for pure LJ liquids and that for infinitely dilute solutions. The main differences from the original SE relation are the presence of dependence on the individual mass and on the individual energy parameter. In addition, the packing-fraction dependence turned out to bridge another gap between the present and original SE relations as well as unifying the SE relation between pure liquids and infinitely dilute solutions.

  16. Protein-protein interactions

    DEFF Research Database (Denmark)

    Byron, Olwyn; Vestergaard, Bente

    2015-01-01

    Responsive formation of protein:protein interaction (PPI) upon diverse stimuli is a fundament of cellular function. As a consequence, PPIs are complex, adaptive entities, and exist in structurally heterogeneous interplays defined by the energetic states of the free and complexed protomers. The...

  17. The value of Tc-99m MIBI scintigraphy in active disease and remission phase of multiple myeloma

    International Nuclear Information System (INIS)

    Background: 99m Tc methoxy isobutyl isonitrile (99m Tc -MIBI)has been proposed as a tumor seeking agent in malignant disease. The goal of this study is to evaluate the frequency distribution of the different patterns, intensity and extension of abnormal uptake identified in MIBI scan in relation with various clinical status of the patients diagnosed as a multiple myeloma. Methods: forty-three patients entered the study, including six patients with no prior treatment , 22 patients who received autologous bone morrow graft, and 15 patients with history of chemotherapy and radiotherapy. Plasma protein electrophoresis for monoclonal antibody, bone morrow biopsy and urine analysis for Bence-Jones protein has been carried out and standard criteria were used for diagnosis of active disease and remission phase for each patients. The extension of each lesion(E-score) on scintigraphy were categorized into E0-E3 by three nuclear physicians who were blinded to the patient's clinical condition. I-score was also obtained with comparing the intensity of the lesions with intensity of myocardial uptake and classified as I0-I3. Results: the sensitivity, specificity, positive predictive value and negative predictive value of 99m Tc -MIBI scan for determining active lesions and released cases were 69%, 100%, 100% and 60%, respectively. Nineteen patients were initially thought to be in remission phase, but scintigraphy was abnormal in 5 cases who were diagnosed as active myeloma later in the course of the study. There was a significant correlation between clinical status and pattern, intensity and extension of the abnormal uptake of 99m Tc -MIBI. Also a significant correlation between intensity and extension of the abnormal tracer uptake with serum monoclonal component and urine Bence-Jones protein was noted, however no correlation between blood hemo globulin and degree of extension in scintigraphy was seen. Conclusion: Our study suggests the pattern, extension and intensity of 99m Tc

  18. Effect of dispersive long-range corrections to the pressure tensor: The vapour-liquid interfacial properties of the Lennard-Jones system revisited

    International Nuclear Information System (INIS)

    We propose an extension of the improved version of the inhomogeneous long-range corrections of Janeček [J. Phys. Chem. B 110, 6264–6269 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] to account for the intermolecular potential energy of spherical, rigid, and flexible molecular systems, to deal with the contributions to the microscopic components of the pressure tensor due to the dispersive long-range corrections. We have performed Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of spherical Lennard-Jones molecules with different cutoff distances, rc = 2.5, 3, 4, and 5σ. In addition, we have also considered cutoff distances rc = 2.5 and 3σ in combination with the inhomogeneous long-range corrections proposed in this work. The normal and tangential microscopic components of the pressure tensor are obtained using the mechanical or virial route in combination with the recipe of Irving and Kirkwood, while the macroscopic components are calculated using the Volume Perturbation thermodynamic route proposed by de Miguel and Jackson [J. Chem. Phys. 125, 164109 (2006)]. The vapour-liquid interfacial tension is evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the Test-Area methodology. In addition to the pressure tensor and the surface tension, we also obtain density profiles, coexistence densities, vapour pressure, critical temperature and density, and interfacial thickness as functions of temperature, paying particular attention to the effect of the cutoff distance and the long-range corrections on these properties. According to our results, the main effect of increasing the cutoff distance (at fixed temperature) is to sharpen the vapour-liquid interface, to decrease the vapour pressure, and to increase the width of the biphasic coexistence region. As a result, the interfacial thickness

  19. Effect of dispersive long-range corrections to the pressure tensor: The vapour-liquid interfacial properties of the Lennard-Jones system revisited

    Energy Technology Data Exchange (ETDEWEB)

    Martínez-Ruiz, F. J.; Blas, F. J., E-mail: felipe@uhu.es [Departamento de Física Aplicada, Universidad de Huelva, 21071 Huelva (Spain); Centro de Investigación de Física Teórica y Matemática, Universidad de Huelva, 21071 Huelva (Spain); Mendiboure, B. [Laboratoire des Fluides Complexes et leurs Réservoirs, UMR5150, Université de Pau et des Pays de l’Adour, B. P. 1155, Pau Cedex 64014 (France); Moreno-Ventas Bravo, A. I. [Centro de Investigación de Física Teórica y Matemática, Universidad de Huelva, 21071 Huelva (Spain); Departamento de Geología, Facultad de Ciencias Experimentales, Universidad de Huelva, 21071 Huelva (Spain)

    2014-11-14

    We propose an extension of the improved version of the inhomogeneous long-range corrections of Janeček [J. Phys. Chem. B 110, 6264–6269 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] to account for the intermolecular potential energy of spherical, rigid, and flexible molecular systems, to deal with the contributions to the microscopic components of the pressure tensor due to the dispersive long-range corrections. We have performed Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of spherical Lennard-Jones molecules with different cutoff distances, r{sub c} = 2.5, 3, 4, and 5σ. In addition, we have also considered cutoff distances r{sub c} = 2.5 and 3σ in combination with the inhomogeneous long-range corrections proposed in this work. The normal and tangential microscopic components of the pressure tensor are obtained using the mechanical or virial route in combination with the recipe of Irving and Kirkwood, while the macroscopic components are calculated using the Volume Perturbation thermodynamic route proposed by de Miguel and Jackson [J. Chem. Phys. 125, 164109 (2006)]. The vapour-liquid interfacial tension is evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the Test-Area methodology. In addition to the pressure tensor and the surface tension, we also obtain density profiles, coexistence densities, vapour pressure, critical temperature and density, and interfacial thickness as functions of temperature, paying particular attention to the effect of the cutoff distance and the long-range corrections on these properties. According to our results, the main effect of increasing the cutoff distance (at fixed temperature) is to sharpen the vapour-liquid interface, to decrease the vapour pressure, and to increase the width of the biphasic coexistence region. As a result, the interfacial

  20. Energy world governance. Review of the conference which was held at IFRI, 26 March 2009, with Tatsuo Masuda, Andre Mernier et Richard H. Jones; La gouvernance mondiale de l'Energie - Resume de la conference qui a eu lieu a l'Ifri le 26 Mar 2009 autour de Tatsuo Masuda, Andre Mernier et Richard H. Jones

    Energy Technology Data Exchange (ETDEWEB)

    Schulke, Ch.

    2009-07-01

    The conference was related with some of the major questions concerning global energy governance today, the role of the different international organizations dealing with energy, the rules of the game between market and state players, the efforts to deal with climate change, and the integration of emerging countries in global energy governance, the roles of the different international organizations dealing with energy (will we see further fragmentation or more cooperation between them?). Tatsuo Masuda in his contribution discussed global energy governance from an oil perspective. Andre Mernier noted the particular nature of the Energy Charter, which, as it is founded upon an international treaty, is unlike other organizations in being legally binding. The legal basis of the organization means that agreements are especially powerful. Then Richard H. Jones underlined that last summer's volatility in oil markets, the ensuing financial and economic crisis, the major disruption in gas supplies to European markets this winter and the upcoming climate change negotiations have led to increasing calls for a stronger global dialogue on energy issues. This dialogue should deal with prices and investment, energy security and climate change

  1. Formerly Utilized MED/AEC Sites Remedial Action Program. Project management plan for the decontamination of Jones Laboratory, Ryerson Physical Laboratory, and Eckhart Hall, the University of Chicago, Chicago, Illinois

    International Nuclear Information System (INIS)

    The Department of Energy (DOE) has in place a plan for the decontamination and decommissioning of contaminated sites that had been formerly utilized by the Manhattan Engineering District (MED) and/or the Atomic Energy Commission. This plan is referred to as the Formerly Utilized Sites Remedial Action Program (FUSRAP). Among these sites are Jones Laboratory, Ryerson Physical Laboratory and Eckhart Hall of The University of Chicago at Chicago, Illinois. This document represents the Project Management Plan for the decontamination of these facilities. 13 references, 3 figures, 1 table

  2. Down-regulation of ATM Protein Sensitizes Human Prostate Cancer Cells to Radiation-induced Apoptosis*

    OpenAIRE

    Truman, Jean-Philip; Gueven, Nuri; Lavin, Martin; Leibel, Steven; Kolesnick, Richard; Fuks, Zvi; Haimovitz-Friedman, Adriana

    2005-01-01

    Treatment with the protein kinase C activator 12-O tetradecanoylphorbol 12-acetate (TPA) enables radiation-resistant LNCaP human prostate cancer cells to undergo radiation-induced apoptosis, mediated via activation of the enzyme ceramide synthase (CS) and de novo synthesis of the sphingolipid ceramide (Garzotto, M., Haimovitz-Friedman, A., Liao, W. C., White-Jones, M., Huryk, R., Heston, D. W. W., Cardon-Cardo, C., Kolesnick, R., and Fuks, Z. (1999) Cancer Res. 59, 5194-5201). Here, we show t...

  3. Complete remission achieved in a multiple myeloma patient with elevated serum KL-6 level by a combination regimen with bortezomib, cyclophosphamide, and dexamethasone.

    Science.gov (United States)

    Okuno, Yutaka; Nishimura, Nao; Nosaka, Kisato; Hata, Hiroyuki; Mitsuya, Hiroaki

    2014-04-01

    A 79-year-old woman suffering from double vision after a 4-year history of MGUS was referred to our hospital. MRI revealed that she had three intracranial plasmacytoma masses and one spinal plasmacytoma mass. Bone marrow aspirates showed 52.4% plasma cell infiltration and immunoelectrophoresis identified serum IgG-M protein, leading to a diagnosis of IgG-type multiple myeloma. IgG was elevated to 3,355 mg/dl and urine type Bence-Jones protein was positive. KL-6, a membrane-bound glycoprotein encoded by Mucin 1 and a marker of interstitial pneumonia, was also elevated to 1,409 mg/dl, but computed tomography of the lungs revealed no obvious pulmonary lesions. Previously reported studies showing that myeloma patients with elevated KL-6 might have a poor prognosis prompted us to treat this patient with a three-drug (bortezomib, cyclophosphamide, and dexamethasone: VCD) combination regimen. When 6 cycles of the regimen had been completed, no M-protein was detectable in her serum. Furthermore, κ free light chain had significantly decreased from 12,700 to 24.8 mg/l. In addition, (18)F-FDG PET/CT revealed reduced mass sizes and no (18)F-FDG uptakes by plasmacytomas. Thus, she was defined as having achieved a stringent complete remission (sCR). We therefore concluded that the VCD combination regimen was highly effective in this multiple myeloma patient with KL-6 elevation. PMID:24850459

  4. High incidence of intact or fragmented immunoglobulin in urine of patients with multiple myeloma.

    Science.gov (United States)

    Kraj, Maria; Kruk, Barbara; Lech-Marańda, Ewa; Warzocha, Krzysztof; Prochorec-Sobieszek, Monika

    2015-01-01

    In this prospective study we determined the incidence of intact/fragmented immunoglobulin and Bence Jones protein in urine immunofixation using Sebia reagents and HydrasysTM 2 apparatus and compared the results to concentrations of serum free light chains (FLC) assessed using Siemens BNTM II nephelometer and the immunoassay Freelite (Binding Site) in 289 patients with multiple myeloma at diagnosis. It was found that in one third of IgG, IgA and IgD myeloma patients, intact/fragmented immunoglobulin can be detected in urine and is connected with impaired renal function and reduced survival. Urine immunofixation detects monoclonal protein (FLC and intact/fragmented immunoglobulin) in 66-79% of IgG and IgA myeloma patients while serum FLC immunoassay detect it in 82-94% of IgG and IgA myeloma patients. However, the latter method is inadequate for detection of intact/fragmented immunoglobulin in urine. Serum FLC immunoassay and urine immunofixation are complementary methods in diagnosing and monitoring monoclonal protein in patients with myeloma. PMID:25860239

  5. Smoldering Multiple Myeloma

    Directory of Open Access Journals (Sweden)

    Minjie Gao

    2015-01-01

    Full Text Available Smoldering multiple myeloma (SMM is an asymptomatic precursor stage of multiple myeloma (MM characterized by clonal bone marrow plasma cells (BMPC ≥ 10% and/or M protein level ≥ 30 g/L in the absence of end organ damage. It represents an intermediate stage between monoclonal gammopathy of undetermined significance (MGUS and symptomatic MM. The risk of progression to symptomatic MM is not uniform, and several parameters have been reported to predict the risk of progression. These include the level of M protein and the percentage of BMPC, the proportion of immunophenotypically aberrant plasma cells, and the presence of immunoparesis, free light-chain (FLC ratio, peripheral blood plasma cells (PBPC, pattern of serum M protein evolution, abnormal magnetic resonance imaging (MRI, cytogenetic abnormalities, IgA isotype, and Bence Jones proteinuria. So far treatment is still not recommended for SMM, because several trials suggested that patients with SMM do not benefit from early treatment. However, the Mateos et al. trial showed a survival benefit after early treatment with lenalidomide plus dexamethasone in patients with high-risk SMM. This trial has prompted a reevaluation of early treatment in an asymptomatic patient population.

  6. Effect of Lysine Modification on the Stability and Cellular Binding of Human Amyloidogenic Light Chains

    Energy Technology Data Exchange (ETDEWEB)

    O' Neill, Hugh Michael [ORNL; Davern, Sandra M. [University of Tennessee Graduate School of Medicine; Murphy, Charles L. [University of Tennessee Graduate School of Medicine; Wall, Jonathan [ORNL; Deborah, Weiss T. [University of Tennessee Graduate School of Medicine; Solomon, Alan [ORNL

    2011-01-01

    AL amyloidosis is characterized by the pathologic deposition as fibrils of monoclonal light chains (i.e., Bence Jones proteins [BJPs]) in particular organs and tissues. This phenomenon has been attributed to the presence in amyloidogenic proteins of particular amino acids that cause these molecules to become unstable, as well as post-translational modifications and, in regard to the latter, we have investigated the effect of biotinylation of lysyl residues on cell binding. We utilized an experimental system designed to test if BJPs obtained from patients with AL amyloidosis or, as a control, multiple myeloma (MM), bound human fibroblasts and renal epithelial cells. As documented by fluorescent microscopy and ELISA, the amyloidogenic BJPs, as compared with MM components, bound preferentially and this reactivity increased significantly after chemical modification of their lysyl residues with sulfo-NHS-biotin. Further, based on tryptophan fluorescence and circular dichorism data, it was apparent that their conformation was altered, which we hypothesize exposed a binding site not accessible on the native protein. The results of our studies indicate that post-translational structural modifications of pathologic light chains can enhance their capacity for cellular interaction and thus may contribute to the pathogenesis of AL amyloidosis and multiple myeloma.

  7. : Protein flexibility

    OpenAIRE

    Bornot, Aurélie; Offmann, Bernard; De Brevern, Alexandre

    2007-01-01

    Protein structures and protein structural models are great tools to reach protein function and provide very relevant information for drug design. Nevertheless, protein structures are not rigid entities. Cutting-edge bioinformatics methods tend to take into account the flexibility of these macromolecules. We present new approaches used to define protein structure flexibility.

  8. Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins.

    Directory of Open Access Journals (Sweden)

    Yunxiang Sun

    Full Text Available Energetic frustration is becoming an important topic for understanding the mechanisms of protein folding, which is a long-standing big biological problem usually investigated by the free energy landscape theory. Despite the significant advances in probing the effects of folding frustrations on the overall features of protein folding pathways and folding intermediates, detailed characterizations of folding frustrations at an atomic or residue level are still lacking. In addition, how and to what extent folding frustrations interact with protein topology in determining folding mechanisms remains unclear. In this paper, we tried to understand energetic frustrations in the context of protein topology structures or native-contact networks by comparing the energetic frustrations of five homologous Im9 alpha-helix proteins that share very similar topology structures but have a single hydrophilic-to-hydrophobic mutual mutation. The folding simulations were performed using a coarse-grained Gō-like model, while non-native hydrophobic interactions were introduced as energetic frustrations using a Lennard-Jones potential function. Energetic frustrations were then examined at residue level based on φ-value analyses of the transition state ensemble structures and mapped back to native-contact networks. Our calculations show that energetic frustrations have highly heterogeneous influences on the folding of the four helices of the examined structures depending on the local environment of the frustration centers. Also, the closer the introduced frustration is to the center of the native-contact network, the larger the changes in the protein folding. Our findings add a new dimension to the understanding of protein folding the topology determination in that energetic frustrations works closely with native-contact networks to affect the protein folding.

  9. Total protein

    Science.gov (United States)

    The total protein test measures the total amount of two classes of proteins found in the fluid portion of your ... nutritional problems, kidney disease or liver disease . If total protein is abnormal, you will need to have more ...

  10. Clinical and radiological observations of multiple myeloma

    International Nuclear Information System (INIS)

    Multiple myeloma is a primary malignant tumor of bone marrow characterized by proliferation of cells arising from primitive marrow reticulum that resemble plasma cells. This one of common primary malignant neoplasm involving bone elements. Bone pain, soft tissue mass, low grade fever, anemia, neurologic symptom and renal insufficiency are the main clinical pictures. Authors present radiological and clinical findings of multiple myeloma in 10 cases of pathologically proved multiple myeloma. The results obtained are as follows; 1. In the age and sex distributions, all cases are over 45 years of age, and male to female is 7 : 3. 2. Clinical manifestations are bone pain, anemia, infection, weight loss, and bleeding. 3. Radiological findings are numerous punched out osteolytic lesions, generalized osteoporosis and osteolytic change, pathologic compression fractures, fracture only and osteoporosis, lytic and fractures.4. Laboratory findings are monoclonal gammopathy in serum-electrophoresis, proteinuria, anemia, elevated uric acid in serum, Bence-Jones protein in urine and albumin/ globulin ratio inverse in serum protein

  11. Interfacial Protein-Protein Associations

    OpenAIRE

    Langdon, Blake B.; Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

    2013-01-01

    While traditional models of protein adsorption focus primarily on direct protein-surface interactions, recent findings suggest that protein-protein interactions may play a central role. Using high-throughput intermolecular resonance energy transfer (RET) tracking, we directly observed dynamic, protein-protein associations of bovine serum albumin on poly(ethylene glycol) modified surfaces. The associations were heterogeneous and reversible, and associating molecules resided on the surface for ...

  12. Archive of Digitized Analog Boomer Seismic Reflection Data Collected from the Mississippi-Alabama-Florida Shelf During Cruises Onboard the R/V Kit Jones, June 1990 and July 1991

    Science.gov (United States)

    Sanford, Jordan M.; Harrison, Arnell S.; Wiese, Dana S.; Flocks, James G.

    2009-01-01

    In June of 1990 and July of 1991, the U.S. Geological Survey (USGS) conducted geophysical surveys to investigate the shallow geologic framework of the Mississippi-Alabama-Florida shelf in the northern Gulf of Mexico, from Mississippi Sound to the Florida Panhandle. Work was done onboard the Mississippi Mineral Resources Institute R/V Kit Jones as part of a project to study coastal erosion and offshore sand resources. This report is part of a series to digitally archive the legacy analog data collected from the Mississippi-Alabama SHelf (MASH). The MASH data rescue project is a cooperative effort by the USGS and the Minerals Management Service (MMS). This report serves as an archive of high-resolution scanned Tagged Image File Format (TIFF) and Graphics Interchange Format (GIF) images of the original boomer paper records, navigation files, trackline maps, Geographic Information System (GIS) files, cruise logs, and formal Federal Geographic Data Committee (FGDC) metadata.

  13. 5 June 2013 - European Union Ambassador to Switzerland and the Principality of Liechtenstein R. Jones in the ATLAS cavern with ATLAS Collaboration Deputy Spokesperson T. Wengler, in the LHC tunnel at Point 1 with Technology Department Head F. Bordry and signing the guest book with Director-General R. Heuer. Head of the EU Projects Office S. Stavrev present.

    CERN Multimedia

    Jean-Claude Gadmer

    2013-01-01

    5 June 2013 - European Union Ambassador to Switzerland and the Principality of Liechtenstein R. Jones in the ATLAS cavern with ATLAS Collaboration Deputy Spokesperson T. Wengler, in the LHC tunnel at Point 1 with Technology Department Head F. Bordry and signing the guest book with Director-General R. Heuer. Head of the EU Projects Office S. Stavrev present.

  14. Nasal septum extramedullary plasmacytoma

    Directory of Open Access Journals (Sweden)

    Belić Branislav

    2013-01-01

    Full Text Available Introduction. Plasmacytomas are malignant tumors characterized by abnormal monoclonal proliferation of plasma cells. They originate in either bone - solitary osseous plasmacytoma, or in soft tissue - extramedullary plasmacytoma (EMP. EMP represents less than 1% of all head and neck malignancies. Case report. We presented a case of EMP of the nasal septum in a 44-year-old male who had progressive difficulty in breathing through the nose and frequent heavy epistaxis on the right side. Nasal endoscopy showed dark red, soft, polypoid tumor in the last third of the right nasal cavity arising from the nasal septum. The biopsy showed that it was plasmacytoma. Bence Jones protein in the urine, serum electrophoresis, bone marrow biopsy, skeletal survey and other screening tests failed to detect multiple myeloma. This confirmed the diagnosis of EMP. The mass was completely removed via an endoscopic approach, and then, 4 week later, radiotherapy was conducted with a radiation dose of 50 Gray. No recurrence was noted in a 3-year follow- up period. Conclusion. EMP of the nasal cavity, being rare and having long natural history, represents a diagnostic and therapeutic challenge for any ear, nose and throat surgeon. Depending on the resectability of the lesion, a combined therapy is the accepted treatment.

  15. Report of a case of multiple myeloma

    International Nuclear Information System (INIS)

    This is a report of myeloma occurred in the left mandibular body and skull. 66-year-old patient was referred to our hospital with a complaint of painful swelling on the left mandibular body area. The author diagnosed it as a multiple myeloma by the clinical examination, radiographic findings, laboratory findings and the histopathological findings. The purpose of this reports to aid in the diagnosis of multiple myeloma and to differentiate it from malignant tumours. The Characteristic features are as follows: 1. In clinical examination, painful swallowing was observed in left mandibular body area. 2. In radiographic findings, radiograms showed relatively ill-defined radiolucency without sclerotic border in left mandibular body area. And also represented multiple punched-out radiolucency in the skull and pathologic fracture of vertebral body on lumbar 3 level. 3. In histopathologic findings, infiltration of abnormal plasma cells was observed. 4. In laboratory findings, decreasing of albumin/globulin ratio, hypercalcaemia, renal impairment was observed, but we could not find the Bence-Jones protein in urine.

  16. Total protein

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003483.htm Total protein To use the sharing features on this page, please enable JavaScript. The total protein test measures the total amount of two classes ...

  17. Protein Structure

    Science.gov (United States)

    Asmus, Elaine Garbarino

    2007-01-01

    Individual students model specific amino acids and then, through dehydration synthesis, a class of students models a protein. The students clearly learn amino acid structure, primary, secondary, tertiary, and quaternary structure in proteins and the nature of the bonds maintaining a protein's shape. This activity is fun, concrete, inexpensive and…

  18. Tau protein

    DEFF Research Database (Denmark)

    Frederiksen, Jette Lautrup Battistini; Kristensen, Kim; Bahl, Jmc;

    2011-01-01

    Background: Tau protein has been proposed as biomarker of axonal damage leading to irreversible neurological impairment in MS. CSF concentrations may be useful when determining risk of progression from ON to MS. Objective: To investigate the association between tau protein concentration and 14...... the Department of Neurology of Glostrup Hospital, University of Copenhagen, Denmark, were included. CSF samples were analysed for tau protein and 14-3-3 protein, and clinical and paraclinical information was obtained from medical records. Results: The study shows a significantly increased...... concentration of tau protein in CSF from patients with relapsing-remitting MS and patients monosymptomatic at onset who progressed to MS, but interestingly no increased tau protein concentration in monosymptomatic ON. The concentration of tau protein was significantly correlated to Expanded Disability Status...

  19. Protein politics

    OpenAIRE

    Vijver, Marike

    2005-01-01

    This study is part of the program of the interdisciplinary research group Profetas (protein foods, environment, technology and society). Profetas consists of technological, environmental and socio-economic research projects on protein food systems which result in the development of scenarios and strategies for guiding a shift towards a more plant protein based diet. The different research projects focus on the goal of identifying viable options for a more sustainable food system. Profetas aro...

  20. Principles of protein-protein interactions.

    OpenAIRE

    Jones, S; Thornton, J. M.

    1996-01-01

    This review examines protein complexes in the Brookhaven Protein Databank to gain a better understanding of the principles governing the interactions involved in protein-protein recognition. The factors that influence the formation of protein-protein complexes are explored in four different types of protein-protein complexes--homodimeric proteins, heterodimeric proteins, enzyme-inhibitor complexes, and antibody-protein complexes. The comparison between the complexes highlights differences tha...

  1. Use of polydispersity index as control parameter to study melting/freezing of Lennard-Jones system: Comparison among predictions of bifurcation theory with Lindemann criterion, inherent structure analysis and Hansen-Verlet rule

    Indian Academy of Sciences (India)

    Sarmistha Sarkar; Rajib Biswas; Partha Pratim Ray; Biman Bagchi

    2015-10-01

    Using polydispersity index as an additional order parameter we investigate freezing/melting transition of Lennard-Jones polydisperse systems (with Gaussian polydispersity in size), especially to gain insight into the origin of the terminal polydispersity. The average inherent structure (IS) energy and root mean square displacement (RMSD) of the solid before melting both exhibit quite similar polydispersity dependence including a discontinuity at solid-liquid transition point. Lindemann ratio, obtained from RMSD, is found to be dependent on temperature. At a given number density, there exists a value of polydispersity index (P) above which no crystalline solid is stable. This transition value of polydispersity (termed as transition polydispersity, P) is found to depend strongly on temperature, a feature missed in hard sphere model systems. Additionally, for a particular temperature when number density is increased, P shifts to higher values. This temperature and number density dependent value of P saturates surprisingly to a value which is found to be nearly the same for all temperatures, known as terminal polydispersity (TP). This value (TP ∼ 0.11) is in excellent agreement with the experimental value of 0.12, but differs from hard sphere transition where this limiting value is only 0.048. Terminal polydispersity (TP) thus has a quasiuniversal character. Interestingly, the bifurcation diagram obtained from non-linear integral equation theories of freezing seems to provide an explanation of the existence of unique terminal polydispersity in polydisperse systems. Global bond orientational order parameter is calculated to obtain further insights into mechanism for melting.

  2. Protein-Protein Interaction Databases

    DEFF Research Database (Denmark)

    Szklarczyk, Damian; Jensen, Lars Juhl

    2015-01-01

    of research are explored. Here we present an overview of the most widely used protein-protein interaction databases and the methods they employ to gather, combine, and predict interactions. We also point out the trade-off between comprehensiveness and accuracy and the main pitfall scientists have to be aware...

  3. Whey Protein

    Science.gov (United States)

    ... quality of life in people with mitochondrial diseases. Ovarian cysts (Polycystic ovarian syndrome). Early research suggests that taking ... weight, fat mass, and cholesterol in people with ovarian cysts. However, whey protein does not improve blood sugar ...

  4. Comment on "A praxis-oriented perspective of streamflow inference from stage observations – the method of Dottori et al. (2009 and the alternative of the Jones Formula, with the kinematic wave celerity computed on the looped rating curve" by Koussis (2009

    Directory of Open Access Journals (Sweden)

    A. D. Koussis

    2010-06-01

    Full Text Available The estimation of transient streamflow from stage measurements is indeed important and the study of Dottori, Martina and Todini (2009 (henceforth DMT is useful, however, DMT seem to miss certain of its practical aspects. The goal is to infer the discharge from measurements of the stage conveniently and with accuracy adequate for practical work. This comment addresses issues of the applicability of the DMT method in the field. DMT also advocate their method as a replacement of the widely used Jones Formula. The Jones Formula was modified by Thomas (Henderson, 1966 to include the temporal derivative of the depth, instead of the spatial one, to specifically allow discharge estimation from at-a-section stage observations. The outcome of the comparison is not surprising in view of this approximation. However, this discussion intends to show that, properly evaluated, the praxis-oriented Jones Formula, which did well in the tests, can perform better than DMT imply. It will be also documented that the DMT methodology relates to a known method for computing flood depth profiles.

  5. Protein Crystallization

    Science.gov (United States)

    Chernov, Alexander A.

    2005-01-01

    Nucleation, growth and perfection of protein crystals will be overviewed along with crystal mechanical properties. The knowledge is based on experiments using optical and force crystals behave similar to inorganic crystals, though with a difference in orders of magnitude in growing parameters. For example, the low incorporation rate of large biomolecules requires up to 100 times larger supersaturation to grow protein, rather than inorganic crystals. Nucleation is often poorly reproducible, partly because of turbulence accompanying the mixing of precipitant with protein solution. Light scattering reveals fluctuations of molecular cluster size, its growth, surface energies and increased clustering as protein ages. Growth most often occurs layer-by-layer resulting in faceted crystals. New molecular layer on crystal face is terminated by a step where molecular incorporation occurs. Quantitative data on the incorporation rate will be discussed. Rounded crystals with molecularly disordered interfaces will be explained. Defects in crystals compromise the x-ray diffraction resolution crucially needed to find the 3D atomic structure of biomolecules. The defects are immobile so that birth defects stay forever. All lattice defects known for inorganics are revealed in protein crystals. Contribution of molecular conformations to lattice disorder is important, but not studied. This contribution may be enhanced by stress field from other defects. Homologous impurities (e.g., dimers, acetylated molecules) are trapped more willingly by a growing crystal than foreign protein impurities. The trapped impurities induce internal stress eliminated in crystals exceeding a critical size (part of mni for ferritin, lysozyme). Lesser impurities are trapped from stagnant, as compared to the flowing, solution. Freezing may induce much more defects unless quickly amorphysizing intracrystalline water.

  6. Determination and Analysis of Oligosaccharides in Valeriana Jatamansii Jones and 5 Drugs for Gastrointestinal Diseases%中药马蹄香和5种治疗胃肠病药物中的低聚糖含量测定和分析

    Institute of Scientific and Technical Information of China (English)

    黄永坤; 潘媛; 张峻; 肖桦; 刘梅; 董坚

    2012-01-01

    目的 深入认识马蹄香和5种治疗胃肠病药物中的低聚糖成分.方法 应用戴安CS-3000离子色谱分析仪测定马蹄香散剂、蒙脱石散、盐酸小檗碱片、复方谷氨酰胺肠溶胶囊、参苓健脾胃颗粒和L-谷氨酰胺呱.仑酸钠颗粒6种治疗胃肠病药物中的10种低聚糖含量.结果 复方谷氨酰胺肠溶胶囊、马蹄香散剂和参苓健脾胃颗粒中含10种低聚糖量高.L-谷氨酰胺呱仑酸钠颗粒中没有检测出低聚糖.在单个的低聚糖含量中,半乳糖三糖的量在参苓健脾胃颗粒最高,其次为蒙脱石散和马蹄香散剂,毛蕊花糖的量在马蹄香散剂中最高,麦芽四至七糖的量在复方谷氨酰胺肠溶胶囊中较高.结论 马蹄香散剂、蒙脱石散、复方谷氨酰胺肠溶胶囊和参苓健脾胃颗粒中低聚糖含量高,毛蕊花糖在马蹄香散剂中含量最高.%Objective To investigate the effective agents in the Valeriana Jatamansii Jones and 5 drugs for treatment of viral enteritis. Methods The content of 10 oligosaccharides in 6 drugs including Valeriana Jatamansii Jones, Dictahedral Smectite Powder, Berberine Hydrochloride Tablets, Compound Glutamin Entersoluble capsule, Shenling Jianpiwei Keli, L-Glutamine and Sodium Gualenate Granules for gastroenteral diseases was determined by DIONEX CS- 3000 high performance liquid chromatography- iron analyzer in the study. Results The results showed 10 oligosaccharides were rich in the Compound Glutamin Entersoluble capsule, Valeriana Jatamansii Jones and Shenling Jianpiwei Keli. There was no oligosaccharides in the L- Glutamine and Sodium Gualenate Granules. There was higher content of the galactose in the Shenling Jianpiwei Keli, the Montmorillonite powder and Valeriana Jatamansii Jones, especially the galactose was rich in the Shenling Jianpiwei Keli. The verbascoses were rich in the Valeriana Jatamansii Jones. There were higher content of maltotetraose Dp4 and 7 in the Compound Glutamin Entersoluble

  7. Arabinogalactan proteins

    DEFF Research Database (Denmark)

    Knoch, Eva; Dilokpimol, Adiphol; Geshi, Naomi

    2014-01-01

    Arabinogalactan proteins (AGPs) are a highly diverse class of cell surface proteoglycans that are commonly found in most plant species. AGPs play important roles in many cellular processes during plant development, such as reproduction, cell proliferation, pattern formation and growth, and in plant...

  8. PRELIMINARY DFIRM DATABASE, JONES COUNTY, TEXAS, USA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — The Digital Flood Insurance Rate Map (DFIRM) Database depicts flood risk information and supporting data used to develop the risk data. The primary risk...

  9. Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks

    OpenAIRE

    Peng Liu; Lei Yang; Daming Shi; Xianglong Tang

    2015-01-01

    A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict protein-protein interactions associated with the complexes. The proposed method is adaptive to protein complexes with different structure, number, and size of nodes in a protein-protein interaction net...

  10. Polysaccharide-Protein Complexes in a Coarse-Grained Model.

    Science.gov (United States)

    Poma, Adolfo B; Chwastyk, Mateusz; Cieplak, Marek

    2015-09-10

    We construct two variants of coarse-grained models of three hexaoses: one based on the centers of mass of the monomers and the other associated with the C4 atoms. The latter is found to be better defined and more suitable for studying interactions with proteins described within α-C based models. We determine the corresponding effective stiffness constants through all-atom simulations and two statistical methods. One method is the Boltzmann inversion (BI) and the other, named energy-based (EB), involves direct monitoring of energies as a function of the variables that define the stiffness potentials. The two methods are generally consistent in their account of the stiffness. We find that the elastic constants differ between the hexaoses and are noticeably different from those determined for the crystalline cellulose Iβ. The nonbonded couplings through hydrogen bonds between different sugar molecules are modeled by the Lennard-Jones potentials and are found to be stronger than the hydrogen bonds in proteins. We observe that the EB method agrees with other theoretical and experimental determinations of the nonbonded parameters much better than BI. We then consider the hexaose-Man5B catalytic complexes and determine the contact energies between their the C4-α-C atoms. These interactions are found to be stronger than the proteinic hydrogen bonds: about four times as strong for cellohexaose and two times for mannohexaose. The fluctuational dynamics of the coarse-grained complexes are found to be compatible with previous all-atom studies by Bernardi et al. PMID:26291477

  11. Grafting of protein-protein binding sites

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A strategy for grafting protein-protein binding sites is described. Firstly, key interaction residues at the interface of ligand protein to be grafted are identified and suitable positions in scaffold protein for grafting these key residues are sought. Secondly, the scaffold proteins are superposed onto the ligand protein based on the corresponding Ca and Cb atoms. The complementarity between the scaffold protein and the receptor protein is evaluated and only matches with high score are accepted. The relative position between scaffold and receptor proteins is adjusted so that the interface has a reasonable packing density. Then the scaffold protein is mutated to corresponding residues in ligand protein at each candidate position. And the residues having bad steric contacts with the receptor proteins, or buried charged residues not involved in the formation of any salt bridge are mutated. Finally, the mutated scaffold protein in complex with receptor protein is co-minimized by Charmm. In addition, we deduce a scoring function to evaluate the affinity between mutated scaffold protein and receptor protein by statistical analysis of rigid binding data sets.

  12. Detecting overlapping protein complexes in protein-protein interaction networks

    OpenAIRE

    Nepusz, Tamás; Yu, Haiyuan; Paccanaro, Alberto

    2012-01-01

    We introduce clustering with overlapping neighborhood expansion (ClusterONE), a method for detecting potentially overlapping protein complexes from protein-protein interaction data. ClusterONE-derived complexes for several yeast data sets showed better correspondence with reference complexes in the Munich Information Center for Protein Sequence (MIPS) catalog and complexes derived from the Saccharomyces Genome Database (SGD) than the results of seven popular methods. The results also showed a...

  13. EDITORIAL: Precision proteins Precision proteins

    Science.gov (United States)

    Demming, Anna

    2010-06-01

    Since the birth of modern day medicine, during the times of Hippocrates in ancient Greece, the profession has developed from the rudimentary classification of disease into a rigorous science with an inspiring capability to treat and cure. Scientific methodology has distilled clinical diagnostic tools from the early arts of prognosis, which used to rely as much on revelation and prophecy, as intuition and judgement [1]. Over the past decade, research into the interactions between proteins and nanosystems has provided some ingenious and apt techniques for delving into the intricacies of anatomical systems. In vivo biosensing has emerged as a vibrant field of research, as much of medical diagnosis relies on the detection of substances or an imbalance in the chemicals in the body. The inherent properties of nanoscale structures, such as cantilevers, make them well suited to biosensing applications that demand the detection of molecules at very low concentrations. Measurable deflections in cantilevers functionalised with antibodies provide quantitative indicators of the presence of specific antigens when the two react. Such developments have roused mounting interest in the interactions of proteins with nanostructures, such as carbon nanotubes [3], which have demonstrated great potential as generic biomarkers. Plasmonic properties are also being exploited in sensing applications, such as the molecular sentinel recently devised by researchers in the US. The device uses the plasmonic properties of a silver nanoparticle linked to a Raman labelled hairpin DNA probe to signal changes in the probe geometry resulting from interactions with substances in the environment. Success stories so far include the detection of two specific genes associated with breast cancer [4]. A greater understanding of how RNA interference regulates gene expression has highlighted the potential of using this natural process as another agent for combating disease in personalized medicine. However, the

  14. New patterns of relapse in multiple myeloma: a case of "light chain escape" in which FLC predicted relapse earlier than urine and serum immunofixation.

    Science.gov (United States)

    Caldini, Anna; Nozzoli, Chiara; Terreni, Alessandro; Staderini, Michela; Berardi, Margherita; Biagioli, Tiziana; Brogi, Marco; Bosi, Alberto

    2016-06-01

    Multiple myeloma (MM) is characterized, in about 80% of cases, by the production of monoclonal intact immunoglobulin and more than 95% of them have elevated concentrations of involved (i.e. of the same class of intact immunoglobulin) free light chain (FLC). The introduction of novel therapeutic strategies has changed the natural history of the disease, leading to new manifestations of relapse. Light chain escape (LCE) is a pattern of relapse in which the FLC increase is not accompanied by a concomitant raise of the original monoclonal component (MC). Here we present a case of a 55-year-old man with an IgG kappa MM stage III diagnosed in September 2007. At presentation an IgG kappa MC and urine Bence Jones protein (BJP) kappa were present. Bone marrow biopsy (BMB) showed the presence of 80% monotypic kappa plasma cells (PCs). The patient received bortezomib, thalidomide, dexamethasone before undergoing a double autologous stem cell transplantation (ASCT) in October 2008 and April 2009. In May 2011 he relapsed showing the same pattern of presentation and treatment with lenalidomide and dexamethasone was started. ln May 2013 serum and urine immunofixation and FLC became negative. In September 2014, an increase of kappa FLC was observed, while serum and urine immunofixations remained negative until January 2015, when urine immunofixation became positive. Eventually, in February 2015, serum immunofixation revealed the presence of a free kappa MC. After a new BMB showing 80% of monotypic kappa PCs, a LCE relapse was diagnosed and the patient started the treatment with bendamustine, bortezomib and dexamethasone. In the present case, the increase of kappa FLC has indicated relapse 4 and 5 months earlier than urine and serum IFE, respectively. Our observation confirms that it is advisable to routinely perform FLC or BJP during follow up of MM patients undergoing ASCT and/or treatment with biological drugs to ensure that LCE is not missed. PMID:26581069

  15. Prevalence and type of monoclonal gammopathy of undetermined significance in an apparently healthy Nigerian population: a cross sectional study

    Directory of Open Access Journals (Sweden)

    Onwah A

    2012-06-01

    Full Text Available Abstract Background The prevalence of monoclonal gammopathy of undetermined significance (MGUS, a premalignant plasma-cell disorder has not been determined in our geographic area Nigeria. Methods A cross sectional survey was carried on apparently healthy Nigerians selected by multistage sampling technique from the cosmopolitan city of Lagos, Nigeria. Subjects enrolled into the study had 2-step screening for the presence, type and concentration of monoclonal band. Agarose-gel electrophoresis was performed on all serum samples, and any serum sample with a discrete band of monoclonal protein or thought to have a localized band was subjected to Immunofixation. Subjects were also evaluated for Bence jones proteinuria, haematological and biochemical parameters. Results Four hundred and ten subjects with a mean age of 45.68 ± 10.3 years, a median of 45.00 years and a range of 20 to 80 years were enrolled into the study. MGUS was identified in only one (0.24 percent of the 410 study subject. This subject was demonstrated to have a double monoclonal gammopathy; IgGλ at 16.9 g/L and IgAκ at 8.5 g/L. None of them including the sole subject with MGUS had a monoclonal urinary light chain. Conclusion Among residents of Lagos, Nigeria, MGUS was found in only 0.24% percent of apparently normal persons with a median age of 45 years. This suggests that MGUS which represents the earliest stage of monoclonal plasma/lymphoid cell proliferation is not a common finding in the relatively young population of Nigeria. Future epidemiologic studies dealing with plasma cell disorders in older people are required to carefully examine the relationship between environmental factors and prevalence of MGUS and its ultimate progression to MM.

  16. Protein Crystal Based Nanomaterials

    Science.gov (United States)

    Bell, Jeffrey A.; VanRoey, Patrick

    2001-01-01

    This is the final report on a NASA Grant. It concerns a description of work done, which includes: (1) Protein crystals cross-linked to form fibers; (2) Engineering of protein to favor crystallization; (3) Better knowledge-based potentials for protein-protein contacts; (4) Simulation of protein crystallization.

  17. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  18. Protein-protein complexation in bioluminescence

    OpenAIRE

    Titushin, Maxim S.; Feng, Yingang; Lee, John; Vysotski, Eugene S.; Liu, Zhi-jie

    2011-01-01

    In this review we summarize the progress made towards understanding the role of protein-protein interactions in the function of various bioluminescence systems of marine organisms, including bacteria, jellyfish and soft corals, with particular focus on methodology used to detect and characterize these interactions. In some bioluminescence systems, protein-protein interactions involve an “accessory protein” whereby a stored substrate is efficiently delivered to the bioluminescent enzyme lucife...

  19. Protein folding, protein homeostasis, and cancer

    Institute of Scientific and Technical Information of China (English)

    John H. Van Drie

    2011-01-01

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

  20. Protein-Protein Interaction Analysis by Docking

    OpenAIRE

    Stephan Ederer; Florian Fink; Wolfram Gronwald

    2009-01-01

    Based on a protein-protein docking approach we have developed a procedure to verify or falsify protein-protein interactions that were proposed by other methods such as yeast-2-hybrid assays. Our method currently utilizes intermolecular energies but can be expanded to incorporate additional terms such as amino acid based pair-potentials. We show some early results that demonstrate the general applicability of our approach.

  1. Protein-losing enteropathy

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/007338.htm Protein-losing enteropathy To use the sharing features on this page, please enable JavaScript. Protein-losing enteropathy is an abnormal loss of protein ...

  2. Protein and Heart Health

    Science.gov (United States)

    ... Recognition & Awards Healthy Workplace Food and Beverage Toolkit Protein and Heart Health Updated:May 5,2015 Protein ... said. What’s the harm in getting too much protein? The main problem is that often the extra ...

  3. SPIDer: Saccharomyces protein-protein interaction database

    Directory of Open Access Journals (Sweden)

    Li Zhenbo

    2006-12-01

    Full Text Available Abstract Background Since proteins perform their functions by interacting with one another and with other biomolecules, reconstructing a map of the protein-protein interactions of a cell, experimentally or computationally, is an important first step toward understanding cellular function and machinery of a proteome. Solely derived from the Gene Ontology (GO, we have defined an effective method of reconstructing a yeast protein interaction network by measuring relative specificity similarity (RSS between two GO terms. Description Based on the RSS method, here, we introduce a predicted Saccharomyces protein-protein interaction database called SPIDer. It houses a gold standard positive dataset (GSP with high confidence level that covered 79.2% of the high-quality interaction dataset. Our predicted protein-protein interaction network reconstructed from the GSPs consists of 92 257 interactions among 3600 proteins, and forms 23 connected components. It also provides general links to connect predicted protein-protein interactions with three other databases, DIP, BIND and MIPS. An Internet-based interface provides users with fast and convenient access to protein-protein interactions based on various search features (searching by protein information, GO term information or sequence similarity. In addition, the RSS value of two GO terms in the same ontology, and the inter-member interactions in a list of proteins of interest or in a protein complex could be retrieved. Furthermore, the database presents a user-friendly graphical interface which is created dynamically for visualizing an interaction sub-network. The database is accessible at http://cmb.bnu.edu.cn/SPIDer/index.html. Conclusion SPIDer is a public database server for protein-protein interactions based on the yeast genome. It provides a variety of search options and graphical visualization of an interaction network. In particular, it will be very useful for the study of inter-member interactions

  4. Fractura mandibular patológica por plasmocitoma intraóseo Pathological mandibular fracture due to intraosseous plasmacytoma

    Directory of Open Access Journals (Sweden)

    D. Antunes Freitas

    2012-06-01

    duct and rarely in the oral cavity. The search for a systemic disease is important in cases where the diagnosis is made. A case of a patient, a man of 73 years of age, residing in the rural village of Great Mogol, Minas Gerais (Brazil, Computed tomography showed irregular osteolytic hypodensity and resorption at the base of the left mandibular alveolar ridge. The lesion measuring 38.0 mm × 19.0 mm × 15.0 mm. On CT clearly shows the presence of pathological fracture of the left side. Needle aspiration was performed, where blood was obtained. Incisional biopsy was performed. The presumptive diagnosis was ameloblastoma. The biopsy specimen was sent for analysis anatomohistopatológica. Microscopy showed tumor cells composed of monomorphic cells with oval nuclei, large peripheral and eccentric, prominent nucleoli and basophilic cytoplasm, surrounded by scant stroma and infiltration of cancellous bone. The urine test was conducted specifically for the Bence-Jones protein, which was negative. The skull and chest radiographs were performed and showed no changes. He then completed a diagnosis of solitary plasmacytoma of the jaw. The patient is undergoing radiotherapy at the Oncology Department of Santa Casa de Misericordia. The patient had severe mucositis and changes in facial color as a result of radiotherapy.

  5. PIC: Protein Interactions Calculator

    OpenAIRE

    Tina, KG; Bhadra, R.; Srinivasan, N.

    2007-01-01

    Interactions within a protein structure and interactions between proteins in an assembly are essential considerations in understanding molecular basis of stability and functions of proteins and their complexes. There are several weak and strong interactions that render stability to a protein structure or an assembly. Protein Interactions Calculator (PIC) is a server which, given the coordinate set of 3D structure of a protein or an assembly, computes various interactions such as disulphide bo...

  6. Drugging Membrane Protein Interactions.

    Science.gov (United States)

    Yin, Hang; Flynn, Aaron D

    2016-07-11

    The majority of therapeutics target membrane proteins, accessible on the surface of cells, to alter cellular signaling. Cells use membrane proteins to transduce signals into cells, transport ions and molecules, bind cells to a surface or substrate, and catalyze reactions. Newly devised technologies allow us to drug conventionally "undruggable" regions of membrane proteins, enabling modulation of protein-protein, protein-lipid, and protein-nucleic acid interactions. In this review, we survey the state of the art of high-throughput screening and rational design in drug discovery, and we evaluate the advances in biological understanding and technological capacity that will drive pharmacotherapy forward against unorthodox membrane protein targets. PMID:26863923

  7. PREFACE: Protein protein interactions: principles and predictions

    Science.gov (United States)

    Nussinov, Ruth; Tsai, Chung-Jung

    2005-06-01

    Proteins are the `workhorses' of the cell. Their roles span functions as diverse as being molecular machines and signalling. They carry out catalytic reactions, transport, form viral capsids, traverse membranes and form regulated channels, transmit information from DNA to RNA, making possible the synthesis of new proteins, and they are responsible for the degradation of unnecessary proteins and nucleic acids. They are the vehicles of the immune response and are responsible for viral entry into the cell. Given their importance, considerable effort has been centered on the prediction of protein function. A prime way to do this is through identification of binding partners. If the function of at least one of the components with which the protein interacts is known, that should let us assign its function(s) and the pathway(s) in which it plays a role. This holds since the vast majority of their chores in the living cell involve protein-protein interactions. Hence, through the intricate network of these interactions we can map cellular pathways, their interconnectivities and their dynamic regulation. Their identification is at the heart of functional genomics; their prediction is crucial for drug discovery. Knowledge of the pathway, its topology, length, and dynamics may provide useful information for forecasting side effects. The goal of predicting protein-protein interactions is daunting. Some associations are obligatory, others are continuously forming and dissociating. In principle, from the physical standpoint, any two proteins can interact, but under what conditions and at which strength? The principles of protein-protein interactions are general: the non-covalent interactions of two proteins are largely the outcome of the hydrophobic effect, which drives the interactions. In addition, hydrogen bonds and electrostatic interactions play important roles. Thus, many of the interactions observed in vitro are the outcome of experimental overexpression. Protein disorder

  8. Protein sequence comparison and protein evolution

    Energy Technology Data Exchange (ETDEWEB)

    Pearson, W.R. [Univ. of Virginia, Charlottesville, VA (United States). Dept. of Biochemistry

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial examines how the information conserved during the evolution of a protein molecule can be used to infer reliably homology, and thus a shared proteinfold and possibly a shared active site or function. The authors start by reviewing a geological/evolutionary time scale. Next they look at the evolution of several protein families. During the tutorial, these families will be used to demonstrate that homologous protein ancestry can be inferred with confidence. They also examine different modes of protein evolution and consider some hypotheses that have been presented to explain the very earliest events in protein evolution. The next part of the tutorial will examine the technical aspects of protein sequence comparison. Both optimal and heuristic algorithms and their associated parameters that are used to characterize protein sequence similarities are discussed. Perhaps more importantly, they survey the statistics of local similarity scores, and how these statistics can both be used to improve the selectivity of a search and to evaluate the significance of a match. They them examine distantly related members of three protein families, the serine proteases, the glutathione transferases, and the G-protein-coupled receptors (GCRs). Finally, the discuss how sequence similarity can be used to examine internal repeated or mosaic structures in proteins.

  9. Prediction of Protein-Protein Interactions Using Protein Signature Profiling

    Institute of Scientific and Technical Information of China (English)

    Mahmood; A.; Mahdavi; Yen-Han; Lin

    2007-01-01

    Protein domains are conserved and functionally independent structures that play an important role in interactions among related proteins. Domain-domain inter- actions have been recently used to predict protein-protein interactions (PPI). In general, the interaction probability of a pair of domains is scored using a trained scoring function. Satisfying a threshold, the protein pairs carrying those domains are regarded as "interacting". In this study, the signature contents of proteins were utilized to predict PPI pairs in Saccharomyces cerevisiae, Caenorhabditis ele- gans, and Homo sapiens. Similarity between protein signature patterns was scored and PPI predictions were drawn based on the binary similarity scoring function. Results show that the true positive rate of prediction by the proposed approach is approximately 32% higher than that using the maximum likelihood estimation method when compared with a test set, resulting in 22% increase in the area un- der the receiver operating characteristic (ROC) curve. When proteins containing one or two signatures were removed, the sensitivity of the predicted PPI pairs in- creased significantly. The predicted PPI pairs are on average 11 times more likely to interact than the random selection at a confidence level of 0.95, and on aver- age 4 times better than those predicted by either phylogenetic profiling or gene expression profiling.

  10. Urine Protein and Urine Protein to Creatinine Ratio

    Science.gov (United States)

    ... limited. Home Visit Global Sites Search Help? Urine Protein and Urine Protein to Creatinine Ratio Share this page: Was this page helpful? Also known as: 24-Hour Urine Protein; Urine Total Protein; Urine Protein to Creatinine Ratio; ...

  11. Protein- protein interaction detection system using fluorescent protein microdomains

    Science.gov (United States)

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2010-02-23

    The invention provides a protein labeling and interaction detection system based on engineered fragments of fluorescent and chromophoric proteins that require fused interacting polypeptides to drive the association of the fragments, and further are soluble and stable, and do not change the solubility of polypeptides to which they are fused. In one embodiment, a test protein X is fused to a sixteen amino acid fragment of GFP (.beta.-strand 10, amino acids 198-214), engineered to not perturb fusion protein solubility. A second test protein Y is fused to a sixteen amino acid fragment of GFP (.beta.-strand 11, amino acids 215-230), engineered to not perturb fusion protein solubility. When X and Y interact, they bring the GFP strands into proximity, and are detected by complementation with a third GFP fragment consisting of GFP amino acids 1-198 (strands 1-9). When GFP strands 10 and 11 are held together by interaction of protein X and Y, they spontaneous association with GFP strands 1-9, resulting in structural complementation, folding, and concomitant GFP fluorescence.

  12. IGSF9 Family Proteins

    DEFF Research Database (Denmark)

    Hansen, Maria; Walmod, Peter Schledermann

    2013-01-01

    The Drosophila protein Turtle and the vertebrate proteins immunoglobulin superfamily (IgSF), member 9 (IGSF9/Dasm1) and IGSF9B are members of an evolutionarily ancient protein family. A bioinformatics analysis of the protein family revealed that invertebrates contain only a single IGSF9 family gene......, whereas vertebrates contain two to four genes. In cnidarians, the gene appears to encode a secreted protein, but transmembrane isoforms of the protein have also evolved, and in many species, alternative splicing facilitates the expression of both transmembrane and secreted isoforms. In most species, the...... longest isoforms of the proteins have the same general organization as the neural cell adhesion molecule family of cell adhesion molecule proteins, and like this family of proteins, IGSF9 family members are expressed in the nervous system. A review of the literature revealed that Drosophila Turtle...

  13. Surface Mediated Protein Disaggregation

    Science.gov (United States)

    Radhakrishna, Mithun; Kumar, Sanat K.

    2014-03-01

    Preventing protein aggregation is of both biological and industrial importance. Biologically these aggregates are known to cause amyloid type diseases like Alzheimer's and Parkinson's disease. Protein aggregation leads to reduced activity of the enzymes in industrial applications. Inter-protein interactions between the hydrophobic residues of the protein are known to be the major driving force for protein aggregation. In the current paper we show how surface chemistry and curvature can be tuned to mitigate these inter-protein interactions. Our results calculated in the framework of the Hydrophobic-Polar (HP) lattice model show that, inter-protein interactions can be drastically reduced by increasing the surface hydrophobicity to a critical value corresponding to the adsorption transition of the protein. At this value of surface hydrophobicity, proteins lose inter-protein contacts to gain surface contacts and thus the surface helps in reducing the inter-protein interactions. Further, we show that the adsorption of the proteins inside hydrophobic pores of optimal sizes are most efficient both in reducing inter-protein contacts and simultaneously retaining most of the native-contacts due to strong protein-surface interactions coupled with stabilization due to the confinement. Department of Energy (Grant No DE-FG02-11ER46811).

  14. Discover protein sequence signatures from protein-protein interaction data

    Directory of Open Access Journals (Sweden)

    Haasl Ryan J

    2005-11-01

    Full Text Available Abstract Background The development of high-throughput technologies such as yeast two-hybrid systems and mass spectrometry technologies has made it possible to generate large protein-protein interaction (PPI datasets. Mining these datasets for underlying biological knowledge has, however, remained a challenge. Results A total of 3108 sequence signatures were found, each of which was shared by a set of guest proteins interacting with one of 944 host proteins in Saccharomyces cerevisiae genome. Approximately 94% of these sequence signatures matched entries in InterPro member databases. We identified 84 distinct sequence signatures from the remaining 172 unknown signatures. The signature sharing information was then applied in predicting sub-cellular localization of yeast proteins and the novel signatures were used in identifying possible interacting sites. Conclusion We reported a method of PPI data mining that facilitated the discovery of novel sequence signatures using a large PPI dataset from S. cerevisiae genome as input. The fact that 94% of discovered signatures were known validated the ability of the approach to identify large numbers of signatures from PPI data. The significance of these discovered signatures was demonstrated by their application in predicting sub-cellular localizations and identifying potential interaction binding sites of yeast proteins.

  15. Polymer Directed Protein Assemblies

    Directory of Open Access Journals (Sweden)

    Patrick van Rijn

    2013-05-01

    Full Text Available Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e.g., virus particles. Viruses are a multi-protein assembly of which the morphology is dictated by poly-nucleotides namely RNA or DNA. This “biopolymer” directs the proteins and imposes limitations on the structure like the length or diameter of the particle. Not only do these bionanoparticles use polymer-directed self-assembly, also processes like amyloid formation are in a way a result of directed protein assembly by partial unfolded/misfolded biopolymers namely, polypeptides. The combination of proteins and synthetic polymers, inspired by the natural processes, are therefore regarded as a highly promising area of research. Directed protein assembly is versatile with respect to the possible interactions which brings together the protein and polymer, e.g., electrostatic, v.d. Waals forces or covalent conjugation, and possible combinations are numerous due to the large amounts of different polymers and proteins available. The protein-polymer interacting behavior and overall morphology is envisioned to aid in clarifying protein-protein interactions and are thought to entail some interesting new functions and properties which will ultimately lead to novel bio-hybrid materials.

  16. Reconciling the understanding of ‘hydrophobicity’ with physics-based models of proteins

    Science.gov (United States)

    Harris, Robert C.; Montgomery Pettitt, B.

    2016-03-01

    The idea that a ‘hydrophobic energy’ drives protein folding, aggregation, and binding by favoring the sequestration of bulky residues from water into the protein interior is widespread. The solvation free energies (Δ {{G}\\text{solv}} ) of small nonpolar solutes increase with surface area (A), and the free energies of creating macroscopic cavities in water increase linearly with A. These observations seem to imply that there is a hydrophobic component (Δ {{G}\\text{hyd}} ) of Δ {{G}\\text{solv}} that increases linearly with A, and this assumption is widely used in implicit solvent models. However, some explicit-solvent molecular dynamics studies appear to contradict these ideas. For example, one definition (Δ {{G}\\text{LJ}} ) of Δ {{G}\\text{hyd}} is that it is the free energy of turning on the Lennard-Jones (LJ) interactions between the solute and solvent. However, Δ {{G}\\text{LJ}} decreases with A for alanine and glycine peptides. Here we argue that these apparent contradictions can be reconciled by defining Δ {{G}\\text{hyd}} to be a near hard core insertion energy (Δ {{G}\\text{rep}} ), as in the partitioning proposed by Weeks, Chandler, and Andersen. However, recent results have shown that Δ {{G}\\text{rep}} is not a simple function of geometric properties of the molecule, such as A and the molecular volume, and that the free energy of turning on the attractive part of the LJ potential cannot be computed from first-order perturbation theory for proteins. The theories that have been developed from these assumptions to predict Δ {{G}\\text{hyd}} are therefore inadequate for proteins.

  17. Protein Dynamics in an RNA Binding Protein

    Science.gov (United States)

    Hall, Kathleen

    2006-03-01

    Using ^15N NMR relaxation measurements, analyzed with the Lipari-Szabo formalism, we have found that the human U1A RNA binding protein has ps-ns motions in those loops that make contact with RNA. Specific mutations can alter the extent and pattern of motions, and those proteins inevitably lose RNA binding affinity. Proteins with enhanced mobility of loops and termini presumably lose affinity due to increased conformational sampling by those parts of the protein that interact directly with RNA. There is an entropic penalty associated with locking down those elements upon RNA binding, in addition to a loss of binding efficiency caused by the increased number of conformations adopted by the protein. However, in addition to local conformational heterogeneity, analysis of molecular dynamics trajectories by Reorientational Eigenmode Dynamics reveals that loops of the wild type protein undergo correlated motions that link distal sites across the binding surface. Mutations that disrupt correlated motions result in weaker RNA binding, implying that there is a network of interactions across the surface of the protein. (KBH was a Postdoctoral Fellow with Al Redfield from 1985-1990). This work was supported by the NIH (to KBH) and NSF (SAS).

  18. Anisotropic Contributions to Protein-Protein Interactions.

    Science.gov (United States)

    Quang, Leigh J; Sandler, Stanley I; Lenhoff, Abraham M

    2014-02-11

    The anisotropy of shape and functionality of proteins complicates the prediction of protein-protein interactions. We examine the distribution of electrostatic and nonelectrostatic contributions to these interactions for two globular proteins, lysozyme and chymosin B, which differ in molecular weight by about a factor of 2. The interaction trends for these proteins are computed in terms of contributions to the osmotic second virial coefficient that are evaluated using atomistic models of the proteins. Our emphasis is on identifying the orientational configurations that contribute most strongly to the overall interactions due to high-complementarity interactions, and on calculating the effect of ionic strength on such interactions. The results emphasize the quantitative importance of several features of protein interactions, notably that despite differences in their frequency of occurrence, configurations differing appreciably in interaction energy can contribute meaningfully to overall interactions. However, relatively small effects due to charge anisotropy or specific hydration can affect the overall interaction significantly only if they contribute to strongly attractive configurations. The results emphasize the necessity of accounting for detailed anisotropy to capture actual experimental trends, and the sensitivity of even very detailed atomistic models to subtle solution contributions. PMID:26580057

  19. Protein Data Bank (PDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and...

  20. [Protein-losing enteropathy].

    Science.gov (United States)

    Amiot, A

    2015-07-01

    Protein-losing enteropathy is a rare syndrome of gastrointestinal protein loss. The primary causes can be classified into lymphatic leakage due to increased interstitial pressure and increased leakage of protein-rich fluids due to erosive or non-erosive gastrointestinal disorders. The diagnosis of protein-losing enteropathy should be considered in patients with chronic diarrhea and peripheral oedema. The diagnosis of protein-losing enteropathy is most commonly based on the determination of fecal alpha-1 antitrypsin clearance. Most protein-losing enteropathy cases are the result of either lymphatic obstruction or a variety of gastrointestinal disorders and cardiac diseases, while primary intestinal lymphangiectasia (Waldmann's disease) is less common. Treatment of protein-losing enteropathy targets the underlying disease but also includes dietary modification, such as high-protein and low-fat diet along with medium-chain triglyceride supplementation. PMID:25618488

  1. Protein (Cyanobacteria): 360792 [

    Lifescience Database Archive (English)

    Full Text Available YP_007146453.1 1117:17211 1161:2741 1162:3098 56106:1490 142864:1490 56107:1490 putative stress ... protein (general stress ... protein 26) Cylindrospermum stagnale PCC 7417 MTTS ...

  2. Hydrodynamic effects in proteins

    Science.gov (United States)

    Szymczak, Piotr; Cieplak, Marek

    2011-01-01

    Experimental and numerical results pertaining to flow-induced effects in proteins are reviewed. Special emphasis is placed on shear-induced unfolding and on the role of solvent mediated hydrodynamic interactions in the conformational transitions in proteins.

  3. Hydrodynamic effects in proteins

    Energy Technology Data Exchange (ETDEWEB)

    Szymczak, Piotr [Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Hoza 69, 00-681 Warsaw (Poland); Cieplak, Marek, E-mail: piotr.szymczak@fuw.edu.pl [Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, 02-668 Warsaw (Poland)

    2011-01-26

    Experimental and numerical results pertaining to flow-induced effects in proteins are reviewed. Special emphasis is placed on shear-induced unfolding and on the role of solvent mediated hydrodynamic interactions in the conformational transitions in proteins. (topical review)

  4. Protein electrophoresis - serum

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003540.htm Protein electrophoresis - serum To use the sharing features on ... JavaScript. This lab test measures the types of protein in the fluid (serum) part of a blood ...

  5. Protein: CAD [Trypanosomes Database

    Lifescience Database Archive (English)

    Full Text Available CAD carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotaseCAD trifunct ... ional protein carbamoylphosphate synthetase 2/aspartate transcarb ... amylase/dihydroorotasemultifunctional protein ... CAD H.sapiens 47458828 18105007 790 P27708 CAD_(ge ...

  6. Learning about Proteins

    Science.gov (United States)

    ... need from peanuts alone, but if you have peanut butter on whole-grain bread, you're set. Likewise, ... protein in a day: 2 tablespoons (15 milliliters) peanut butter (7 grams protein) 1 cup (240 milliliters) low- ...

  7. Electrophoretic Separation of Proteins

    OpenAIRE

    Chakavarti, Bulbul; Chakavarti, Deb

    2008-01-01

    Electrophoresis is used to separate complex mixtures of proteins (e.g., from cells, subcellular fractions, column fractions, or immunoprecipitates), to investigate subunit compositions, and to verify homogeneity of protein samples. It can also serve to purify proteins for use in further applications. In polyacrylamide gel electrophoresis, proteins migrate in response to an electrical field through pores in a polyacrylamide gel matrix; pore size decreases with increasing acrylamide concentrati...

  8. Simulations of protein folding

    International Nuclear Information System (INIS)

    We have developed a simple, phenomenological, Monte-Carlo code that predicts the three-dimensional structure of globular proteins from the DNA sequences that define them. We have applied this code to two small proteins, the villin headpiece (1VII) and colel rop (1ROP). Our code folds both proteins to within 5 A rms of their native structures

  9. Destabilized bioluminescent proteins

    Science.gov (United States)

    Allen, Michael S.; Rakesh, Gupta; Gary, Sayler S.

    2007-07-31

    Purified nucleic acids, vectors and cells containing a gene cassette encoding at least one modified bioluminescent protein, wherein the modification includes the addition of a peptide sequence. The duration of bioluminescence emitted by the modified bioluminescent protein is shorter than the duration of bioluminescence emitted by an unmodified form of the bioluminescent protein.

  10. Protein domain prediction

    NARCIS (Netherlands)

    Ingolfsson, Helgi; Yona, Golan

    2008-01-01

    Domains are considered to be the building blocks of protein structures. A protein can contain a single domain or multiple domains, each one typically associated with a specific function. The combination of domains determines the function of the protein, its subcellular localization and the interacti

  11. CSF total protein

    Science.gov (United States)

    CSF total protein is a test to determine the amount of protein in your spinal fluid, also called cerebrospinal fluid (CSF). ... The normal protein range varies from lab to lab, but is typically about 15 to 60 mg/dL. Note: mg/dL = ...

  12. Modeling Protein Domain Function

    Science.gov (United States)

    Baker, William P.; Jones, Carleton "Buck"; Hull, Elizabeth

    2007-01-01

    This simple but effective laboratory exercise helps students understand the concept of protein domain function. They use foam beads, Styrofoam craft balls, and pipe cleaners to explore how domains within protein active sites interact to form a functional protein. The activity allows students to gain content mastery and an understanding of the…

  13. Protein - Which is Best?

    Science.gov (United States)

    Hoffman, Jay R; Falvo, Michael J

    2004-09-01

    Protein intake that exceeds the recommended daily allowance is widely accepted for both endurance and power athletes. However, considering the variety of proteins that are available much less is known concerning the benefits of consuming one protein versus another. The purpose of this paper is to identify and analyze key factors in order to make responsible recommendations to both the general and athletic populations. Evaluation of a protein is fundamental in determining its appropriateness in the human diet. Proteins that are of inferior content and digestibility are important to recognize and restrict or limit in the diet. Similarly, such knowledge will provide an ability to identify proteins that provide the greatest benefit and should be consumed. The various techniques utilized to rate protein will be discussed. Traditionally, sources of dietary protein are seen as either being of animal or vegetable origin. Animal sources provide a complete source of protein (i.e. containing all essential amino acids), whereas vegetable sources generally lack one or more of the essential amino acids. Animal sources of dietary protein, despite providing a complete protein and numerous vitamins and minerals, have some health professionals concerned about the amount of saturated fat common in these foods compared to vegetable sources. The advent of processing techniques has shifted some of this attention and ignited the sports supplement marketplace with derivative products such as whey, casein and soy. Individually, these products vary in quality and applicability to certain populations. The benefits that these particular proteins possess are discussed. In addition, the impact that elevated protein consumption has on health and safety issues (i.e. bone health, renal function) are also reviewed. Key PointsHigher protein needs are seen in athletic populations.Animal proteins is an important source of protein, however potential health concerns do exist from a diet of protein

  14. Highly thermostable fluorescent proteins

    Science.gov (United States)

    Bradbury, Andrew M.; Waldo, Geoffrey S.; Kiss, Csaba

    2011-03-22

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  15. Protein hydration and dynamics

    International Nuclear Information System (INIS)

    Inelastic neutron scattering can measure the protein thermal fluctuations under the physiological aqueous environment, especially it is powerful to observe the low-energy protein dynamics in THz region, which are revealed theoretically to be coupled with solvations. Neutron enables the selective observation of protein and hydration water by deuteration. The complementary analysis with molecular dynamics simulation is also effective for the study of protein hydration. Some examples of the application toward the understanding of molecular basis of protein functions will be introduced. (author)

  16. Protein crystallization with paper

    Science.gov (United States)

    Matsuoka, Miki; Kakinouchi, Keisuke; Adachi, Hiroaki; Maruyama, Mihoko; Sugiyama, Shigeru; Sano, Satoshi; Yoshikawa, Hiroshi Y.; Takahashi, Yoshinori; Yoshimura, Masashi; Matsumura, Hiroyoshi; Murakami, Satoshi; Inoue, Tsuyoshi; Mori, Yusuke; Takano, Kazufumi

    2016-05-01

    We developed a new protein crystallization method that incorporates paper. A small piece of paper, such as facial tissue or KimWipes, was added to a drop of protein solution in the traditional sitting drop vapor diffusion technique, and protein crystals grew by incorporating paper. By this method, we achieved the growth of protein crystals with reducing osmotic shock. Because the technique is very simple and the materials are easy to obtain, this method will come into wide use for protein crystallization. In the future, it could be applied to nanoliter-scale crystallization screening on a paper sheet such as in inkjet printing.

  17. Protein and vegetarian diets.

    Science.gov (United States)

    Marsh, Kate A; Munn, Elizabeth A; Baines, Surinder K

    2013-08-19

    A vegetarian diet can easily meet human dietary protein requirements as long as energy needs are met and a variety of foods are eaten. Vegetarians should obtain protein from a variety of plant sources, including legumes, soy products, grains, nuts and seeds. Eggs and dairy products also provide protein for those following a lacto-ovo-vegetarian diet. There is no need to consciously combine different plant proteins at each meal as long as a variety of foods are eaten from day to day, because the human body maintains a pool of amino acids which can be used to complement dietary protein. The consumption of plant proteins rather than animal proteins by vegetarians may contribute to their reduced risk of chronic diseases such as diabetes and heart disease. PMID:25369930

  18. Protein kinesis: The dynamics of protein trafficking and stability

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-12-31

    The purpose of this conference is to provide a multidisciplinary forum for exchange of state-of-the-art information on protein kinesis. This volume contains abstracts of papers in the following areas: protein folding and modification in the endoplasmic reticulum; protein trafficking; protein translocation and folding; protein degradation; polarity; nuclear trafficking; membrane dynamics; and protein import into organelles.

  19. Protein Electrophoresis/Immunofixation Electrophoresis

    Science.gov (United States)

    ... be limited. Home Visit Global Sites Search Help? Protein Electrophoresis Immunofixation Electrophoresis Share this page: Was this page helpful? Also known as: Serum Protein Electrophoresis; Protein ELP; SPE; SPEP; Urine Protein Electrophoresis; ...

  20. Protein: FEB6 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FEB6 Photoresponse regulatory proteins HD1 SE1 Zinc finger protein HD1 Protein CONSTANS-like, Pr ... otein HEADING DATE 1, Protein PHOTOPERIOD SENSITIVITY ... 1 39947 Oryza sativa subsp. japonica 4340746 Q9FDX ...

  1. Identifying novel protein phenotype annotations by hybridizing protein-protein interactions and protein sequence similarities.

    Science.gov (United States)

    Chen, Lei; Zhang, Yu-Hang; Huang, Tao; Cai, Yu-Dong

    2016-04-01

    Studies of protein phenotypes represent a central challenge of modern genetics in the post-genome era because effective and accurate investigation of protein phenotypes is one of the most critical procedures to identify functional biological processes in microscale, which involves the analysis of multifactorial traits and has greatly contributed to the development of modern biology in the post genome era. Therefore, we have developed a novel computational method that identifies novel proteins associated with certain phenotypes in yeast based on the protein-protein interaction network. Unlike some existing network-based computational methods that identify the phenotype of a query protein based on its direct neighbors in the local network, the proposed method identifies novel candidate proteins for a certain phenotype by considering all annotated proteins with this phenotype on the global network using a shortest path (SP) algorithm. The identified proteins are further filtered using both a permutation test and their interactions and sequence similarities to annotated proteins. We compared our method with another widely used method called random walk with restart (RWR). The biological functions of proteins for each phenotype identified by our SP method and the RWR method were analyzed and compared. The results confirmed a large proportion of our novel protein phenotype annotation, and the RWR method showed a higher false positive rate than the SP method. Our method is equally effective for the prediction of proteins involving in all the eleven clustered yeast phenotypes with a quite low false positive rate. Considering the universality and generalizability of our supporting materials and computing strategies, our method can further be applied to study other organisms and the new functions we predicted can provide pertinent instructions for the further experimental verifications. PMID:26728152

  2. Development of the Knowledge-based & Empirical Combined Scoring Algorithm (KECSA) to Score Protein-Ligand Interactions

    Science.gov (United States)

    Zheng, Zheng

    2013-01-01

    We describe a novel knowledge-based protein-ligand scoring function that employs a new definition for the reference state, allowing us to relate a statistical potential to a Lennard-Jones (LJ) potential. In this way, the LJ potential parameters were generated from protein-ligand complex structural data contained in the PDB. Forty-nine types of atomic pairwise interactions were derived using this method, which we call the knowledge-based and empirical combined scoring algorithm (KECSA). Two validation benchmarks were introduced to test the performance of KECSA. The first validation benchmark included two test sets that address the training-set and enthalpy/entropy of KECSA The second validation benchmark suite included two large-scale and five small-scale test sets to compare the reproducibility of KECSA with respect to two empirical score functions previously developed in our laboratory (LISA and LISA+), as well as to other well-known scoring methods. Validation results illustrate that KECSA shows improved performance in all test sets when compared with other scoring methods especially in its ability to minimize the RMSE. LISA and LISA+ displayed similar performance using the correlation coefficient and Kendall τ as the metric of quality for some of the small test sets. Further pathways for improvement are discussed which would KECSA more sensitive to subtle changes in ligand structure. PMID:23560465

  3. Sensitizing properties of proteins

    DEFF Research Database (Denmark)

    Poulsen, Lars K.; Ladics, Gregory S; McClain, Scott;

    2014-01-01

    The scope of allergy risk is diverse considering the myriad ways in which protein allergenicity is affected by physiochemical characteristics of proteins. The complexity created by the matrices of foods and the variability of the human immune system add additional challenges to understanding the...... relationship between sensitization potential and allergy disease. To address these and other issues, an April 2012 international symposium was held in Prague, Czech Republic, to review and discuss the state-of-the-science of sensitizing properties of protein allergens. The symposium, organized by the Protein...... scientists from academia, government, and industry participated in the symposium. Experts provided overviews on known mechanisms by which proteins in food may cause sensitization, discussed experimental models to predict protein sensitizing potential, and explored whether such experimental techniques may be...

  4. NMR of unfolded proteins

    Indian Academy of Sciences (India)

    Amarnath Chtterjee; Ashutosh Kumar; Jeetender Chugh; Sudha Srivastava; Neel S Bhavesh; Ramakrishna V Hosur

    2005-01-01

    In the post-genomic era, as more and more genome sequences are becoming known and hectic efforts are underway to decode the information content in them, it is becoming increasingly evident that flexibility in proteins plays a crucial role in many of the biological functions. Many proteins have intrinsic disorder either wholly or in specific regions. It appears that this disorder may be important for regulatory functions of the proteins, on the one hand, and may help in directing the folding process to reach the compact native state, on the other. Nuclear magnetic resonance (NMR) has over the last two decades emerged as the sole, most powerful technique to help characterize these disordered protein systems. In this review, we first discuss the significance of disorder in proteins and then describe the recent developments in NMR methods for their characterization. A brief description of the results obtained on several disordered proteins is presented at the end.

  5. Computational Protein Design

    DEFF Research Database (Denmark)

    Johansson, Kristoffer Enøe

    to a central method that enables new developments. For example, novel enzymes with functions not found in natural proteins have been de novo designed to give enough activity for experimental optimization. This thesis presents the current state-of-the-art within computational design methods together......Proteins are the major functional group of molecules in biology. The impact of protein science on medicine and chemical productions is rapidly increasing. However, the greatest potential remains to be realized. The fi eld of protein design has advanced computational modeling from a tool of support...... with a novel method based on probability theory. With the aim of assembling a complete pipeline for protein design, this work touches upon several aspects of protein design. The presented work is the computational half of a design project where the other half is dedicated to the experimental part of...

  6. Protein Models Comparator

    CERN Document Server

    Widera, Paweł

    2011-01-01

    The process of comparison of computer generated protein structural models is an important element of protein structure prediction. It has many uses including model quality evaluation, selection of the final models from a large set of candidates or optimisation of parameters of energy functions used in template free modelling and refinement. Although many protein comparison methods are available online on numerous web servers, their ability to handle a large scale model comparison is often very limited. Most of the servers offer only a single pairwise structural comparison, and they usually do not provide a model-specific comparison with a fixed alignment between the models. To bridge the gap between the protein and model structure comparison we have developed the Protein Models Comparator (pm-cmp). To be able to deliver the scalability on demand and handle large comparison experiments the pm-cmp was implemented "in the cloud". Protein Models Comparator is a scalable web application for a fast distributed comp...

  7. Protein oxidation and peroxidation.

    Science.gov (United States)

    Davies, Michael J

    2016-04-01

    Proteins are major targets for radicals and two-electron oxidants in biological systems due to their abundance and high rate constants for reaction. With highly reactive radicals damage occurs at multiple side-chain and backbone sites. Less reactive species show greater selectivity with regard to the residues targeted and their spatial location. Modification can result in increased side-chain hydrophilicity, side-chain and backbone fragmentation, aggregation via covalent cross-linking or hydrophobic interactions, protein unfolding and altered conformation, altered interactions with biological partners and modified turnover. In the presence of O2, high yields of peroxyl radicals and peroxides (protein peroxidation) are formed; the latter account for up to 70% of the initial oxidant flux. Protein peroxides can oxidize both proteins and other targets. One-electron reduction results in additional radicals and chain reactions with alcohols and carbonyls as major products; the latter are commonly used markers of protein damage. Direct oxidation of cysteine (and less commonly) methionine residues is a major reaction; this is typically faster than with H2O2, and results in altered protein activity and function. Unlike H2O2, which is rapidly removed by protective enzymes, protein peroxides are only slowly removed, and catabolism is a major fate. Although turnover of modified proteins by proteasomal and lysosomal enzymes, and other proteases (e.g. mitochondrial Lon), can be efficient, protein hydroperoxides inhibit these pathways and this may contribute to the accumulation of modified proteins in cells. Available evidence supports an association between protein oxidation and multiple human pathologies, but whether this link is causal remains to be established. PMID:27026395

  8. Proteins at interfaces

    OpenAIRE

    Evers, Florian

    2011-01-01

    Protein adsorption is a fundamental and ubiquitous phenomenon, which has severe implications in the fields of biomaterials as well as bio- and nanotechnology, e.g., in drug delivery, biofouling, the biocompatibility of implants, food chemistry, and biosensors. Therefore, the mechanisms of protein adsorption and controlling the interfacial affinity of proteins have become intriguing and interdisciplinary research topics. In this work, X-ray and neutron reflectometry are the main...

  9. Protein-surfactant interactions

    OpenAIRE

    Valstar, Ank

    2000-01-01

    Protein-surfactant interactions in aqueous media have been investigated. The globular proteins lysozyme and bovine serum albumin (BSA) served as model proteins. Several ionic and non-ionic surfactants were used. Fluorescence probe measurements showed that at low sodium dodecyl sulfate (SDS) concentration (< 0.1 M) one micelle-like SDS cluster is bound to lysozyme. From dynamic light scattering (DLS) results it was observed that lysozyme in the complex does not correspond to the fully unfol...

  10. Pressure cryocooling protein crystals

    Science.gov (United States)

    Kim, Chae Un; Gruner, Sol M.

    2011-10-04

    Preparation of cryocooled protein crystal is provided by use of helium pressurizing and cryocooling to obtain cryocooled protein crystal allowing collection of high resolution data and by heavier noble gas (krypton or xenon) binding followed by helium pressurizing and cryocooling to obtain cryocooled protein crystal for collection of high resolution data and SAD phasing simultaneously. The helium pressurizing is carried out on crystal coated to prevent dehydration or on crystal grown in aqueous solution in a capillary.

  11. Biofilm Matrix Proteins

    OpenAIRE

    Fong, Jiunn N. C.; Yildiz, Fitnat H.

    2015-01-01

    Proteinaceous components of the biofilm matrix include secreted extracellular proteins, cell surface adhesins and protein subunits of cell appendages such as flagella and pili. Biofilm matrix proteins play diverse roles in biofilm formation and dissolution. They are involved in attaching cells to surfaces, stabilizing the biofilm matrix via interactions with exopolysaccharide and nucleic acid components, developing three-dimensional biofilm architectures, and dissolving biofilm matrix via enz...

  12. Ribosome-inactivating proteins

    OpenAIRE

    Walsh, Matthew J; Dodd, Jennifer E; Hautbergue, Guillaume M.

    2013-01-01

    Ribosome-inactivating proteins (RIPs) were first isolated over a century ago and have been shown to be catalytic toxins that irreversibly inactivate protein synthesis. Elucidation of atomic structures and molecular mechanism has revealed these proteins to be a diverse group subdivided into two classes. RIPs have been shown to exhibit RNA N-glycosidase activity and depurinate the 28S rRNA of the eukaryotic 60S ribosomal subunit. In this review, we compare archetypal RIP family members with oth...

  13. Trisulfides in Proteins

    DEFF Research Database (Denmark)

    Nielsen, Rasmus W.; Tachibana, Christine; Hansen, Niels Erik;

    2011-01-01

    post-translational modification, and the number of proteins in which a trisulfide has been unambiguously identified is small. Nevertheless, we believe that its prevalence may be underestimated, particularly with the increasing evidence for significant pools of sulfides in living tissues and their...... possible roles in cellular metabolism. This review focuses on examples of proteins that are known to contain a trisulfide bridge, and gives an overview of the chemistry of trisulfide formation, and the methods by which it is detected in proteins....

  14. Staining Proteins in Gels

    OpenAIRE

    Gallagher, Sean; Chakavarti, Deb

    2008-01-01

    Following separation by electrophoretic methods, proteins in a gel can be detected by several staining methods. This unit describes protocols for detecting proteins by four popular methods. Coomassie blue staining is an easy and rapid method. Silver staining, while more time consuming, is considerably more sensitive and can thus be used to detect smaller amounts of protein. Fluorescent staining is a popular alternative to traditional staining procedures, mainly because it is more sensitive th...

  15. Comparisons of the M1 genome segments and encoded μ2 proteins of different reovirus isolates

    Directory of Open Access Journals (Sweden)

    Arnold Michelle M

    2004-09-01

    Full Text Available Abstract Background The reovirus M1 genome segment encodes the μ2 protein, a structurally minor component of the viral core, which has been identified as a transcriptase cofactor, nucleoside and RNA triphosphatase, and microtubule-binding protein. The μ2 protein is the most poorly understood of the reovirus structural proteins. Genome segment sequences have been reported for 9 of the 10 genome segments for the 3 prototypic reoviruses type 1 Lang (T1L, type 2 Jones (T2J, and type 3 Dearing (T3D, but the M1 genome segment sequences for only T1L and T3D have been previously reported. For this study, we determined the M1 nucleotide and deduced μ2 amino acid sequences for T2J, nine other reovirus field isolates, and various T3D plaque-isolated clones from different laboratories. Results Determination of the T2J M1 sequence completes the analysis of all ten genome segments of that prototype. The T2J M1 sequence contained a 1 base pair deletion in the 3' non-translated region, compared to the T1L and T3D M1 sequences. The T2J M1 gene showed ~80% nucleotide homology, and the encoded μ2 protein showed ~71% amino acid identity, with the T1L and T3D M1 and μ2 sequences, respectively, making the T2J M1 gene and μ2 proteins amongst the most divergent of all reovirus genes and proteins. Comparisons of these newly determined M1 and μ2 sequences with newly determined M1 and μ2 sequences from nine additional field isolates and a variety of laboratory T3D clones identified conserved features and/or regions that provide clues about μ2 structure and function. Conclusions The findings suggest a model for the domain organization of μ2 and provide further evidence for a role of μ2 in viral RNA synthesis. The new sequences were also used to explore the basis for M1/μ2-determined differences in the morphology of viral factories in infected cells. The findings confirm the key role of Ser/Pro208 as a prevalent determinant of differences in factory morphology

  16. Acanthamoeba castellanii STAT protein.

    Science.gov (United States)

    Kicinska, Anna; Leluk, Jacek; Jarmuszkiewicz, Wieslawa

    2014-01-01

    STAT (signal transducers and activators of transcription) proteins are one of the important mediators of phosphotyrosine-regulated signaling in metazoan cells. We described the presence of STAT protein in a unicellular, free-living amoebae with a simple life cycle, Acanthamoeba castellanii. A. castellanii is the only, studied to date, Amoebozoan that does not belong to Mycetozoa but possesses STATs. A sequence of the A. castellanii STAT protein includes domains similar to those of the Dictyostelium STAT proteins: a coiled coil (characteristic for Dictyostelium STAT coiled coil), a STAT DNA-binding domain and a Src-homology domain. The search for protein sequences homologous to A. castellanii STAT revealed 17 additional sequences from lower eukaryotes. Interestingly, all of these sequences come from Amoebozoa organisms that belong to either Mycetozoa (slime molds) or Centramoebida. We showed that there are four separated clades within the slime mold STAT proteins. The A. castellanii STAT protein branches next to a group of STATc proteins from Mycetozoa. We also demonstrate that Amoebozoa form a distinct monophyletic lineage within the STAT protein world that is well separated from the other groups. PMID:25338074

  17. Acanthamoeba castellanii STAT protein.

    Directory of Open Access Journals (Sweden)

    Anna Kicinska

    Full Text Available STAT (signal transducers and activators of transcription proteins are one of the important mediators of phosphotyrosine-regulated signaling in metazoan cells. We described the presence of STAT protein in a unicellular, free-living amoebae with a simple life cycle, Acanthamoeba castellanii. A. castellanii is the only, studied to date, Amoebozoan that does not belong to Mycetozoa but possesses STATs. A sequence of the A. castellanii STAT protein includes domains similar to those of the Dictyostelium STAT proteins: a coiled coil (characteristic for Dictyostelium STAT coiled coil, a STAT DNA-binding domain and a Src-homology domain. The search for protein sequences homologous to A. castellanii STAT revealed 17 additional sequences from lower eukaryotes. Interestingly, all of these sequences come from Amoebozoa organisms that belong to either Mycetozoa (slime molds or Centramoebida. We showed that there are four separated clades within the slime mold STAT proteins. The A. castellanii STAT protein branches next to a group of STATc proteins from Mycetozoa. We also demonstrate that Amoebozoa form a distinct monophyletic lineage within the STAT protein world that is well separated from the other groups.

  18. Consensus protein design

    Science.gov (United States)

    Porebski, Benjamin T.; Buckle, Ashley M.

    2016-01-01

    A popular and successful strategy in semi-rational design of protein stability is the use of evolutionary information encapsulated in homologous protein sequences. Consensus design is based on the hypothesis that at a given position, the respective consensus amino acid contributes more than average to the stability of the protein than non-conserved amino acids. Here, we review the consensus design approach, its theoretical underpinnings, successes, limitations and challenges, as well as providing a detailed guide to its application in protein engineering. PMID:27274091

  19. Engineering therapeutic protein disaggregases

    Science.gov (United States)

    Shorter, James

    2016-01-01

    Therapeutic agents are urgently required to cure several common and fatal neurodegenerative disorders caused by protein misfolding and aggregation, including amyotrophic lateral sclerosis (ALS), Parkinson’s disease (PD), and Alzheimer’s disease (AD). Protein disaggregases that reverse protein misfolding and restore proteins to native structure, function, and localization could mitigate neurodegeneration by simultaneously reversing 1) any toxic gain of function of the misfolded form and 2) any loss of function due to misfolding. Potentiated variants of Hsp104, a hexameric AAA+ ATPase and protein disaggregase from yeast, have been engineered to robustly disaggregate misfolded proteins connected with ALS (e.g., TDP-43 and FUS) and PD (e.g., α-synuclein). However, Hsp104 has no metazoan homologue. Metazoa possess protein disaggregase systems distinct from Hsp104, including Hsp110, Hsp70, and Hsp40, as well as HtrA1, which might be harnessed to reverse deleterious protein misfolding. Nevertheless, vicissitudes of aging, environment, or genetics conspire to negate these disaggregase systems in neurodegenerative disease. Thus, engineering potentiated human protein disaggregases or isolating small-molecule enhancers of their activity could yield transformative therapeutics for ALS, PD, and AD. PMID:27255695

  20. Simulations of Protein Folding

    CERN Document Server

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

    2000-01-01

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

  1. Ultrafiltration of pegylated proteins

    Science.gov (United States)

    Molek, Jessica R.

    There is considerable clinical interest in the use of "second-generation" therapeutics produced by conjugation of a native protein with various polymers including polyethylene glycol (PEG). PEG--protein conjugates, so-called PEGylated proteins, can exhibit enhanced stability, half-life, and bioavailability. One of the challenges in the commercial production of PEGylated proteins is the purification required to remove unreacted polymer, native protein, and in many cases PEGylated proteins with nonoptimal degrees of conjugation. The overall objective of this thesis was to examine the use of ultrafiltration for the purification of PEGylated proteins. This included: (1) analysis of size-based separation of PEGylated proteins using conventional ultrafiltration membranes, (2) use of electrically-charged membranes to exploit differences in electrostatic interactions, and (3) examination of the effects of PEGylation on protein fouling. The experimental results were analyzed using appropriate theoretical models, with the underlying physical properties of the PEGylated proteins evaluated using size exclusion chromatography, capillary electrophoresis, dynamic light scattering, and reverse phase chromatography. PEGylated proteins were produced by covalent attachment of activated PEG to a protein via primary amines on the lysine residues. A simple model was developed for the reaction kinetics, which was used to explore the effect of reaction conditions and mode of operation on the distribution of PEGylated products. The effective size of the PEGylated proteins was evaluated using size exclusion chromatography, with appropriate correlations developed for the size in terms of the molecular weight of the native protein and attached PEG. The electrophoretic mobility of the PEGylated proteins were evaluated by capillary electrophoresis with the data in good agreement with a simple model accounting for the increase in protein size and the reduction in the number of protonated amine

  2. How Many Protein-Protein Interactions Types Exist in Nature?

    OpenAIRE

    Garma, Leonardo; Mukherjee, Srayanta; Mitra, Pralay; Zhang, Yang

    2012-01-01

    Protein quaternary structure universe” refers to the ensemble of all protein-protein complexes across all organisms in nature. The number of quaternary folds thus corresponds to the number of ways proteins physically interact with other proteins. This study focuses on answering two basic questions: Whether the number of protein-protein interactions is limited and, if yes, how many different quaternary folds exist in nature. By all-to-all sequence and structure comparisons, we grouped the pro...

  3. How Many Protein-Protein Interactions Types Exist in Nature?

    OpenAIRE

    Leonardo Garma; Srayanta Mukherjee; Pralay Mitra; Yang Zhang

    2012-01-01

    "Protein quaternary structure universe" refers to the ensemble of all protein-protein complexes across all organisms in nature. The number of quaternary folds thus corresponds to the number of ways proteins physically interact with other proteins. This study focuses on answering two basic questions: Whether the number of protein-protein interactions is limited and, if yes, how many different quaternary folds exist in nature. By all-to-all sequence and structure comparisons, we grouped the pro...

  4. Protein (Cyanobacteria): 286011 [

    Lifescience Database Archive (English)

    Full Text Available YP_007057271.1 1117:4890 1161:684 1185:224 373984:129 373994:129 histidine kinase,PAS ... domain-con ... taining protein,PAS ... domain-containing protein,histidine kinase,GAF dom ...

  5. Protein (Viridiplantae): 357488463 [

    Lifescience Database Archive (English)

    Full Text Available XP_003614519.1 33090:2423 35493:1202 131221:1202 3193:1202 58023:2056 78536:1595 58024:1595 3398 ... 938 3814:1938 163742:3028 3877:3028 3880:3028 Cyst nematode ... resistance protein-like protein Medicago truncatul ...

  6. Poxviral Ankyrin Proteins

    Directory of Open Access Journals (Sweden)

    Michael H. Herbert

    2015-02-01

    Full Text Available Multiple repeats of the ankyrin motif (ANK are ubiquitous throughout the kingdoms of life but are absent from most viruses. The main exception to this is the poxvirus family, and specifically the chordopoxviruses, with ANK repeat proteins present in all but three species from separate genera. The poxviral ANK repeat proteins belong to distinct orthologue groups spread over different species, and align well with the phylogeny of their genera. This distribution throughout the chordopoxviruses indicates these proteins were present in an ancestral vertebrate poxvirus, and have since undergone numerous duplication events. Most poxviral ANK repeat proteins contain an unusual topology of multiple ANK motifs starting at the N-terminus with a C-terminal poxviral homologue of the cellular F-box enabling interaction with the cellular SCF ubiquitin ligase complex. The subtle variations between ANK repeat proteins of individual poxviruses suggest an array of different substrates may be bound by these protein-protein interaction domains and, via the F-box, potentially directed to cellular ubiquitination pathways and possible degradation. Known interaction partners of several of these proteins indicate that the NF-κB coordinated anti-viral response is a key target, whilst some poxviral ANK repeat domains also have an F-box independent affect on viral host-range.

  7. Protein (Viridiplantae): 186478918 [

    Lifescience Database Archive (English)

    Full Text Available NP_001117362.1 33090:264 35493:490 131221:490 3193:490 58023:763 78536:5554 58024:5554 3398:5554 ... 88 3699:588 3700:588 980083:588 3701:588 3702:2514 StaR -like protein domain-containing protein Arabidopsis ...

  8. Protein (Viridiplantae): 145336153 [

    Lifescience Database Archive (English)

    Full Text Available NP_174031.2 33090:264 35493:490 131221:490 3193:490 58023:763 78536:5554 58024:5554 3398:5554 71 ... 88 3699:588 3700:588 980083:588 3701:588 3702:2514 StaR -like protein domain-containing protein Arabidopsis ...

  9. Protein (Viridiplantae): 186478920 [

    Lifescience Database Archive (English)

    Full Text Available NP_001117363.1 33090:264 35493:490 131221:490 3193:490 58023:763 78536:5554 58024:5554 3398:5554 ... 88 3699:588 3700:588 980083:588 3701:588 3702:2514 StaR -like protein domain-containing protein Arabidopsis ...

  10. Protein (Viridiplantae): 18396209 [

    Lifescience Database Archive (English)

    Full Text Available NP_564271.1 33090:264 35493:490 131221:490 3193:490 58023:763 78536:5554 58024:5554 3398:5554 71 ... 88 3699:588 3700:588 980083:588 3701:588 3702:2514 StaR -like protein domain-containing protein Arabidopsis ...

  11. Proteins in biomass streams

    NARCIS (Netherlands)

    Mulder, W.J.

    2010-01-01

    The focus of this study is to give an overview of traditional and new biomasses and biomass streams that contain proteins. When information was available, the differences in molecular structure and physical and chemical properties for the different proteins is given. For optimal biomass use, isolati

  12. Protein (Cyanobacteria): 187726 [

    Lifescience Database Archive (English)

    Full Text Available ZP_00515693.1 1117:3739 1118:294 263510:556 263511:556 165597:1102 Cobalamin synthesis ... protein/P ... 47K:Cobalamin synthesis ... protein/P47K Crocosphaera watsonii WH 8501 MHKIPVT ...

  13. Protein (Cyanobacteria): 187721 [

    Lifescience Database Archive (English)

    Full Text Available ZP_00515086.1 1117:3739 1118:294 263510:556 263511:556 165597:1102 Cobalamin synthesis ... protein/P ... 47K:Cobalamin synthesis ... protein/P47K Crocosphaera watsonii WH 8501 MSGINQQ ...

  14. Protein (Cyanobacteria): 187724 [

    Lifescience Database Archive (English)

    Full Text Available ZP_00514782.1 1117:3739 1118:294 263510:556 263511:556 165597:1102 Cobalamin synthesis ... protein/P ... 47K:Cobalamin synthesis ... protein/P47K Crocosphaera watsonii WH 8501 MQIVDKK ...

  15. Protein (Cyanobacteria): 187722 [

    Lifescience Database Archive (English)

    Full Text Available ZP_00515750.1 1117:3739 1118:294 263510:556 263511:556 165597:1102 Cobalamin synthesis ... protein/P ... 47K:Cobalamin synthesis ... protein/P47K Crocosphaera watsonii WH 8501 MTPLNFN ...

  16. Protein (Cyanobacteria): 187723 [

    Lifescience Database Archive (English)

    Full Text Available ZP_00515087.1 1117:3739 1118:294 263510:556 263511:556 165597:1102 Cobalamin synthesis ... protein/P ... 47K:Cobalamin synthesis ... protein/P47K Crocosphaera watsonii WH 8501 MTRLDFN ...

  17. Protein (Viridiplantae): 15240110 [

    Lifescience Database Archive (English)

    Full Text Available NP_201488.1 33090:325 35493:1944 131221:1944 3193:1944 58023:3713 78536:2650 58024:2650 3398:265 ... :1852 LOB domain-containing protein 36 (ASYMMETRIC LEAVES ... 2-like protein 1) Arabidopsis thaliana MASSSSPCAAC ...

  18. Protein (Viridiplantae): 357505877 [

    Lifescience Database Archive (English)

    Full Text Available XP_003623227.1 33090:2309 35493:2314 131221:2314 3193:2314 58023:1780 78536:1486 58024:1486 3398 ... 163742:9849 3877:9849 3880:9849 Cell cycle control crn ... (Crooked neck) protein-like protein Medicago trunc ...

  19. Protein (Viridiplantae): 357472389 [

    Lifescience Database Archive (English)

    Full Text Available XP_003606479.1 33090:29954 35493:20452 131221:20452 3193:20452 58023:15679 78536:15788 58024:157 ... 2228 163742:12813 3877:12813 3880:12813 Defects in morphology ... protein-like protein Medicago truncatula MAETSSSNN ...

  20. Protein (Viridiplantae): 357472385 [

    Lifescience Database Archive (English)

    Full Text Available XP_003606477.1 33090:29954 35493:20452 131221:20452 3193:20452 58023:15679 78536:15788 58024:157 ... 2228 163742:12813 3877:12813 3880:12813 Defects in morphology ... protein-like protein Medicago truncatula MAETSSSNN ...

  1. Protein (Viridiplantae): 357440307 [

    Lifescience Database Archive (English)

    Full Text Available XP_003590431.1 33090:29954 35493:20452 131221:20452 3193:20452 58023:15679 78536:15788 58024:157 ... 2228 163742:12813 3877:12813 3880:12813 Defects in morphology ... protein-like protein Medicago truncatula MAGTSSKIP ...

  2. Protein (Viridiplantae): 357444551 [

    Lifescience Database Archive (English)

    Full Text Available XP_003592553.1 33090:29954 35493:20452 131221:20452 3193:20452 58023:15679 78536:15788 58024:157 ... 2228 163742:12813 3877:12813 3880:12813 Defects in morphology ... protein-like protein Medicago truncatula MAGTSSKIP ...

  3. C-reactive protein

    Science.gov (United States)

    C-reactive protein (CRP) is produced by the liver. The level of CRP rises when there is inflammation throughout the body. It is one of a group of proteins called "acute phase reactants" that go up in response to inflammation. ...

  4. Protein (Viridiplantae): 18414878 [

    Lifescience Database Archive (English)

    Full Text Available NP_567527.1 33090:1722 35493:20777 131221:20777 3193:20777 58023:13588 78536:13546 58024:13546 3 ... 83:5979 3701:5979 3702:6150 Tryptophan RNA-binding attenuator ... protein-like protein Arabidopsis thaliana MAAPFFST ...

  5. Protein (Viridiplantae): 238480800 [

    Lifescience Database Archive (English)

    Full Text Available NP_001154247.1 33090:1722 35493:20777 131221:20777 3193:20777 58023:13588 78536:13546 58024:1354 ... 83:5979 3701:5979 3702:6150 Tryptophan RNA-binding attenuator ... protein-like protein Arabidopsis thaliana MAAPFFST ...

  6. Protein (Viridiplantae): 238480798 [

    Lifescience Database Archive (English)

    Full Text Available NP_001154246.1 33090:1722 35493:20777 131221:20777 3193:20777 58023:13588 78536:13546 58024:1354 ... 83:5979 3701:5979 3702:6150 Tryptophan RNA-binding attenuator ... protein-like protein Arabidopsis thaliana MAAPFFST ...

  7. Protein (Cyanobacteria): 305313 [

    Lifescience Database Archive (English)

    Full Text Available ZP_09781770.1 1117:5986 1150:1684 35823:2516 376219:684 Cytochrome b6-f complex iron -sulfur subu ... nit 1 (Rieske iron -sulfur protein 1) (Plastohydroquinone:plastocyanin ... oxidoreductase iron -sulfur protein 1) (ISP 1) (RISP 1) Arthrospira sp. ...

  8. Protein Attachment on Nanodiamonds.

    Science.gov (United States)

    Lin, Chung-Lun; Lin, Cheng-Huang; Chang, Huan-Cheng; Su, Meng-Chih

    2015-07-16

    A recent advance in nanotechnology is the scale-up production of small and nonaggregated diamond nanoparticles suitable for biological applications. Using detonation nanodiamonds (NDs) with an average diameter of ∼4 nm as the adsorbents, we have studied the static attachment of three proteins (myoglobin, bovine serum albumin, and insulin) onto the nanoparticles by optical spectroscopy, mass spectrometry, and dynamic light scattering, and electrophoretic zeta potential measurements. Results show that the protein surface coverage is predominantly determined by the competition between protein-protein and protein-ND interactions, giving each protein a unique and characteristic structural configuration in its own complex. Specifically, both myoglobin and bovine serum albumin show a Langmuir-type adsorption behavior, forming 1:1 complexes at saturation, whereas insulin folds into a tightly bound multimer before adsorption. The markedly different adsorption patterns appear to be independent of the protein concentration and are closely related to the affinity of the individual proteins for the NDs. The present study provides a fundamental understanding for the use of NDs as a platform for nanomedical drug delivery. PMID:25815400

  9. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model.

    Science.gov (United States)

    Debiec, Karl T; Cerutti, David S; Baker, Lewis R; Gronenborn, Angela M; Case, David A; Chong, Lillian T

    2016-08-01

    We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agreement with NMR relaxation rates, and maintains the expected conformational propensities of structured proteins/peptides, as well as disordered peptides-all on the microsecond (μs) time scale, which is a critical regime for drug design applications. These encouraging results demonstrate the power and robustness of our automated methods for deriving new force fields. All parameters described here and the mdgx program used to fit them are included in the AmberTools16 distribution. PMID:27399642

  10. Protein sequence databases.

    Science.gov (United States)

    Apweiler, Rolf; Bairoch, Amos; Wu, Cathy H

    2004-02-01

    A variety of protein sequence databases exist, ranging from simple sequence repositories, which store data with little or no manual intervention in the creation of the records, to expertly curated universal databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each sequence record. As the focus of researchers moves from the genome to the proteins encoded by it, these databases will play an even more important role as central comprehensive resources of protein information. Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium. PMID:15036160

  11. Manipulating and Visualizing Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Simon, Horst D.

    2003-12-05

    ProteinShop Gives Researchers a Hands-On Tool for Manipulating, Visualizing Protein Structures. The Human Genome Project and other biological research efforts are creating an avalanche of new data about the chemical makeup and genetic codes of living organisms. But in order to make sense of this raw data, researchers need software tools which let them explore and model data in a more intuitive fashion. With this in mind, researchers at Lawrence Berkeley National Laboratory and the University of California, Davis, have developed ProteinShop, a visualization and modeling program which allows researchers to manipulate protein structures with pinpoint control, guided in large part by their own biological and experimental instincts. Biologists have spent the last half century trying to unravel the ''protein folding problem,'' which refers to the way chains of amino acids physically fold themselves into three-dimensional proteins. This final shape, which resembles a crumpled ribbon or piece of origami, is what determines how the protein functions and translates genetic information. Understanding and modeling this geometrically complex formation is no easy matter. ProteinShop takes a given sequence of amino acids and uses visualization guides to help generate predictions about the secondary structures, identifying alpha helices and flat beta strands, and the coil regions that bind them. Once secondary structures are in place, researchers can twist and turn these pre-configurations until they come up with a number of possible tertiary structure conformations. In turn, these are fed into a computationally intensive optimization procedure that tries to find the final, three-dimensional protein structure. Most importantly, ProteinShop allows users to add human knowledge and intuition to the protein structure prediction process, thus bypassing bad configurations that would otherwise be fruitless for optimization. This saves compute cycles and accelerates

  12. MicroProteins

    DEFF Research Database (Denmark)

    Eguen, Teinai Ebimienere; Straub, Daniel; Graeff, Moritz;

    2015-01-01

    MicroProteins (miPs) are short, usually single-domain proteins that, in analogy to miRNAs, heterodimerize with their targets and exert a dominant-negative effect. Recent bioinformatic attempts to identify miPs have resulted in a list of potential miPs, many of which lack the defining...... characteristics of a miP. In this opinion article, we clearly state the characteristics of a miP as evidenced by known proteins that fit the definition; we explain why modulatory proteins misrepresented as miPs do not qualify as true miPs. We also discuss the evolutionary history of miPs, and how the miP concept...... can extend beyond transcription factors (TFs) to encompass different non-TF proteins that require dimerization for full function....

  13. The centrality of cancer proteins in human protein-protein interaction network: a revisit.

    Science.gov (United States)

    Xiong, Wei; Xie, Luyu; Zhou, Shuigeng; Liu, Hui; Guan, Jihong

    2014-01-01

    Topological analysis of protein-protein interaction (PPI) networks has been widely applied to the investigation on cancer mechanisms. However, there is still a debate on whether cancer proteins exhibit more topological centrality compared to the other proteins in the human PPI network. To resolve this debate, we first identified four sets of human proteins, and then mapped these proteins into the yeast PPI network by homologous genes. Finally, we compared these proteins' properties in human and yeast PPI networks. Experiments over two real datasets demonstrated that cancer proteins tend to have higher degree and smaller clustering coefficient than non-cancer proteins. Experimental results also validated that cancer proteins have larger betweenness centrality compared to the other proteins on the STRING dataset. However, on the BioGRID dataset, the average betweenness centrality of cancer proteins is larger than that of disease and control proteins, but smaller than that of essential proteins. PMID:24878726

  14. Protein oxidation in aquatic foods

    DEFF Research Database (Denmark)

    Baron, Caroline P.

    2014-01-01

    The chapter discusses general considerations about protein oxidation and reviews the mechanisms involved in protein oxidation and consequences of protein oxidation on fish proteins. It presents two case studies, the first deals with protein and lipid oxidation in frozen rainbow trout......, and the second with oxidation in salted herring. The mechanisms responsible for initiation of protein oxidation are unclear, but it is generally accepted that free radical species initiating lipid oxidation can also initiate protein oxidation. The chapter focuses on interaction between protein and lipid...... oxidation. The protein carbonyl group measurement is the widely used method for estimating protein oxidation in foods and has been used in fish muscle. The chapter also talks about the impact of protein oxidation on protein functionality, fish muscle texture, and food nutritional value. Protein oxidation...

  15. An Algorithm for Finding Functional Modules and Protein Complexes in Protein-Protein Interaction Networks

    OpenAIRE

    Guangyu Cui; Yu Chen; De-Shuang Huang; Kyungsook Han

    2008-01-01

    Biological processes are often performed by a group of proteins rather than by individual proteins, and proteins in a same biological group form a densely connected subgraph in a protein-protein interaction network. Therefore, finding a densely connected subgraph provides useful information to predict the function or protein complex of uncharacterized proteins in the highly connected subgraph. We have developed an efficient algorithm and program for finding cliques and near-cliques in a prote...

  16. Quantification of the Influence of Protein-Protein Interactions on Adsorbed Protein Structure and Bioactivity

    OpenAIRE

    Wei, Yang; Thyparambil, Aby A.; Latour, Robert A.

    2013-01-01

    While protein-surface interactions have been widely studied, relatively little is understood at this time regarding how protein-surface interaction effects are influenced by protein-protein interactions and how these effects combine with the internal stability of a protein to influence its adsorbed-state structure and bioactivity. The objectives of this study were to develop a method to study these combined effects under widely varying protein-protein interaction conditions using hen egg-whit...

  17. New approach for predicting protein-protein interactions

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ Protein-protein interactions (PPIs) are of vital importance for virtually all processes of a living cell. The study of these associations of protein molecules could improve people's understanding of diseases and provide basis for therapeutic approaches.

  18. Analysis of correlations between protein complex and protein-protein interaction and mRNA expression

    Institute of Scientific and Technical Information of China (English)

    CAI Lun; XUE Hong; LU Hongchao; ZHAO Yi; ZHU Xiaopeng; BU Dongbo; LING Lunjiang; CHEN Runsheng

    2003-01-01

    Protein-protein interaction is a physical interaction of two proteins in living cells. In budding yeast Saccharomyces cerevisiae, large-scale protein-protein interaction data have been obtained through high-throughput yeast two-hybrid systems (Y2H) and protein complex purification techniques based on mass-spectrometry. Here, we collect 11855 interactions between total 2617 proteins. Through seriate genome-wide mRNA expression data, similarity between two genes could be measured. Protein complex data can also be obtained publicly and can be translated to pair relationship that any two proteins can only exist in the same complex or not. Analysis of protein complex data, protein-protein interaction data and mRNA expression data can elucidate correlations between them. The results show that proteins that have interactions or similar expression patterns have a higher possibility to be in the same protein complex than randomized selected proteins, and proteins which have interactions and similar expression patterns are even more possible to exist in the same protein complex. The work indicates that comprehensive integration and analysis of public large-scale bioinformatical data, such as protein complex data, protein-protein interaction data and mRNA expression data, may help to uncover their relationships and common biological information underlying these data. The strategies described here may help to integrate and analyze other functional genomic and proteomic data, such as gene expression profiling, protein-localization mapping and large-scale phenotypic data, both in yeast and in other organisms.

  19. Piezoelectric allostery of protein.

    Science.gov (United States)

    Ohnuki, Jun; Sato, Takato; Takano, Mitsunori

    2016-07-01

    Allostery is indispensable for a protein to work, where a locally applied stimulus is transmitted to a distant part of the molecule. While the allostery due to chemical stimuli such as ligand binding has long been studied, the growing interest in mechanobiology prompts the study of the mechanically stimulated allostery, the physical mechanism of which has not been established. By molecular dynamics simulation of a motor protein myosin, we found that a locally applied mechanical stimulus induces electrostatic potential change at distant regions, just like the piezoelectricity. This novel allosteric mechanism, "piezoelectric allostery", should be of particularly high value for mechanosensor/transducer proteins. PMID:27575163

  20. Alpha Shapes and Proteins

    DEFF Research Database (Denmark)

    Winter, Pawel; Sterner, Henrik; Sterner, Peter

    We provide a unified description of (weighted) alpha shapes, beta shapes and the corresponding simplicialcomplexes. We discuss their applicability to various protein-related problems. We also discuss filtrations of alpha shapes and touch upon related persistence issues.We claim that the full...... potential of alpha-shapes and related geometrical constructs in protein-related problems yet remains to be realized and verified. We suggest parallel algorithms for (weighted) alpha shapes, and we argue that future use of filtrations and kinetic variants for larger proteins will need such implementation....

  1. Protein crystallography prescreen kit

    Science.gov (United States)

    Segelke, Brent W.; Krupka, Heike I.; Rupp, Bernhard

    2005-07-12

    A kit for prescreening protein concentration for crystallization includes a multiplicity of vials, a multiplicity of pre-selected reagents, and a multiplicity of sample plates. The reagents and a corresponding multiplicity of samples of the protein in solutions of varying concentrations are placed on sample plates. The sample plates containing the reagents and samples are incubated. After incubation the sample plates are examined to determine which of the sample concentrations are too low and which the sample concentrations are too high. The sample concentrations that are optimal for protein crystallization are selected and used.

  2. Human Protein Z.

    OpenAIRE

    Broze, G J; Miletich, J P

    1984-01-01

    Protein Z was purified from human plasma by a four-step procedure which included barium citrate adsorption, ammonium sulfate fractionation, DEAE-Sepharose chromatography, and blue agarose chromatography with a yield of 20%. It is a 62,000 mol wt protein with an extinction coefficient of 12.0. The concentration of Protein Z in pooled, citrated plasma is 2.2 micrograms/ml and its half-life in patients starting warfarin anticoagulation therapy is estimated to be less than 2.5 d. The NH2-terminal...

  3. Evolution of proteins.

    Science.gov (United States)

    Dayhoff, M. O.

    1971-01-01

    The amino acid sequences of proteins from living organisms are dealt with. The structure of proteins is first discussed; the variation in this structure from one biological group to another is illustrated by the first halves of the sequences of cytochrome c, and a phylogenetic tree is derived from the cytochrome c data. The relative geological times associated with the events of this tree are discussed. Errors which occur in the duplication of cells during the evolutionary process are examined. Particular attention is given to evolution of mutant proteins, globins, ferredoxin, and transfer ribonucleic acids (tRNA's). Finally, a general outline of biological evolution is presented.

  4. The characterisation and prediction of protein-protein interfaces.

    OpenAIRE

    Kabir, T.

    2004-01-01

    Understanding how proteins interact with each other is of fundamental importance and is one of the most important goals of molecular biology. In order to study the characteristics of protein-protein interaction sites datasets of non-homologous protein-complexes have been compiled. These datasets include 142 obligate homocomplexes, 20 obligate hetero-complexes, 20 enzyme-inhibitor complexes, 15 antibody-antigen complexes, and 10 signaling complexes. Overall, the protein-protein interfaces of o...

  5. Whey Protein- The Role of Protein Supplementation in Resistance Training

    OpenAIRE

    Zimmer, Raymond

    2005-01-01

    Adequate protein intake is an important concern for many athletes who are undergoing strength-training programs. Many athletes choose to take a protein supplement, such as whey protein, in order to help them build lean muscle mass more efficiently. But the benefit of very high levels of dietary protein in resistance training remains questionable. This paper examines the effectiveness of whey protein, and other forms of protein supplements, in helping athletes augment their muscle mass. A comp...

  6. Protein-protein interaction databases: keeping up with growing interactomes

    OpenAIRE

    Lehne Benjamin; Schlitt Thomas

    2009-01-01

    Abstract Over the past few years, the number of known protein-protein interactions has increased substantially. To make this information more readily available, a number of publicly available databases have set out to collect and store protein-protein interaction data. Protein-protein interactions have been retrieved from six major databases, integrated and the results compared. The six databases (the Biological General Repository for Interaction Datasets [BioGRID], the Molecular INTeraction ...

  7. The effect of protein-protein and protein-membrane interactions on membrane fouling in ultrafiltration

    NARCIS (Netherlands)

    Huisman, I.H.; Prádanos, P.; Hernández, A.

    2000-01-01

    It was studied how protein-protein and protein-membrane interactions influence the filtration performance during the ultrafiltration of protein solutions over polymeric membranes. This was done by measuring flux, streaming potential, and protein transmission during filtration of bovine serum albumin

  8. Polymers for Protein Conjugation

    Directory of Open Access Journals (Sweden)

    Gianfranco Pasut

    2014-01-01

    Full Text Available Polyethylene glycol (PEG at the moment is considered the leading polymer for protein conjugation in view of its unique properties, as well as to its low toxicity in humans, qualities which have been confirmed by its extensive use in clinical practice. Other polymers that are safe, biodegradable and custom-designed have, nevertheless, also been investigated as potential candidates for protein conjugation. This review will focus on natural polymers and synthetic linear polymers that have been used for protein delivery and the results associated with their use. Genetic fusion approaches for the preparation of protein-polypeptide conjugates will be also reviewed and compared with the best known chemical conjugation ones.

  9. Protein (Cyanobacteria): 292092 [

    Lifescience Database Archive (English)

    Full Text Available ZP_11392515.1 1117:5087 1150:2441 44887:135 864702:135 PAS ... domain type 3-containing protein,PAS ... STISDITSQKRTEAALQRSTARYENLASNIPGMIYQVVLETNGHFRFAYASPAS REIFGLEPEQLMKSAALGMTVIHPDDVVSFRQSIAQSAKTLQTQLGKLPK ...

  10. Protein turnover in sheep

    International Nuclear Information System (INIS)

    Considerable advances have been made in the knowledge of the mechanisms and control of synthesis and degradation of proteins in animal tissues during the last decade. Most of the work on the measurement of synthetic and degradative rates of the mixed protein fraction from tissues has been conducted in the rat. There have, unfortunately, been few publications describing results of protein turnover studies with ruminants. Consideration is given here to the techniques used to measure protein turnover, and some of the results obtained, particularly with sheep, are summarized. No attempt has been made to discuss directly the situation in parasitized animals; rather the aim is to provide background information which complements other work dealing with the effects of parasites on the nitrogen metabolism of ruminants. (author)

  11. Engineered Proteins for Bioelectrochemistry

    Science.gov (United States)

    Akram, Muhammad Safwan; Rehman, Jawad Ur; Hall, Elizabeth A. H.

    2014-06-01

    It is only in the past two decades that excellent protein engineering tools have begun to meet parallel advances in materials chemistry, nanofabrication, and electronics. This is revealing scenarios from which synthetic enzymes can emerge, which were previously impossible, as well as interfaces with novel electrode materials. That means the control of the protein structure, electron transport pathway, and electrode surface can usher us into a new era of bioelectrochemistry. This article reviews the principle of electron transfer (ET) and considers how its application at the electrode, within the protein, and at a redox group is directing key advances in the understanding of protein structure to create systems that exhibit better efficiency and unique bioelectrochemistry.

  12. Protein (Viridiplantae): 308813231 [

    Lifescience Database Archive (English)

    Full Text Available XP_003083922.1 33090:9527 3041:5078 1035538:3664 13792:3664 70447:4128 70448:5494 Protein requir ... ed for actin cytoskeleton organization ... and cell cycle progression (ISS) Ostreococcus taur ...

  13. Protein (Viridiplantae): 308808566 [

    Lifescience Database Archive (English)

    Full Text Available XP_003081593.1 33090:6182 3041:4098 1035538:2508 13792:2508 70447:3211 70448:4097 Mitochondrial ... inheritance and actin cytoskeleton organization ... protein (ISS) Ostreococcus tauri MPPKKPPPPPPDAKSYP ...

  14. The Pentapeptide Repeat Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Vetting,M.; Hegde, S.; Fajardo, J.; Fiser, A.; Roderick, S.; Takiff, H.; Blanchard, J.

    2006-01-01

    The Pentapeptide Repeat Protein (PRP) family has over 500 members in the prokaryotic and eukaryotic kingdoms. These proteins are composed of, or contain domains composed of, tandemly repeated amino acid sequences with a consensus sequence of [S, T,A, V][D, N][L, F]-[S, T,R][G]. The biochemical function of the vast majority of PRP family members is unknown. The three-dimensional structure of the first member of the PRP family was determined for the fluoroquinolone resistance protein (MfpA) from Mycobacterium tuberculosis. The structure revealed that the pentapeptide repeats encode the folding of a novel right-handed quadrilateral {beta}-helix. MfpA binds to DNA gyrase and inhibits its activity. The rod-shaped, dimeric protein exhibits remarkable size, shape and electrostatic similarity to DNA.

  15. Protein (Viridiplantae): 255084748 [

    Lifescience Database Archive (English)

    Full Text Available XP_002504805.1 33090:7862 3041:6362 1035538:5159 13792:5159 38832:5340 296587:5427 DUF1244/molyb ... denum cofactor synthesis ... fusion protein Micromonas sp. RCC299 MASTRTEIEAYAF ...

  16. Protein (Viridiplantae): 303283029 [

    Lifescience Database Archive (English)

    Full Text Available XP_003060806.1 33090:7862 3041:6362 1035538:5159 13792:5159 38832:5340 38833:5093 564608:5093 mo ... lybdenum cofactor synthesis ... protein Micromonas pusilla CCMP1545 MVDAQTTEKIEAYA ...

  17. Protein (Viridiplantae): 308812183 [

    Lifescience Database Archive (English)

    Full Text Available XP_003083399.1 33090:12970 3041:5897 1035538:4613 13792:4613 70447:1628 70448:5196 Glycosylphosp ... hatidylinositol anchor synthesis ... protein (ISS) Ostreococcus tauri MSARRASFQSRFNDSSQ ...

  18. Protein (Viridiplantae): 308810647 [

    Lifescience Database Archive (English)

    Full Text Available XP_003082632.1 33090:15674 3041:5296 1035538:3911 13792:3911 70447:3635 70448:4717 senescence-in ... ducible chloroplast stay-green ... protein (ISS) Ostreococcus tauri MDRATTSSRASTARTFH ...

  19. Protein (Viridiplantae): 308811905 [

    Lifescience Database Archive (English)

    Full Text Available XP_003083260.1 33090:255 3041:4962 1035538:3528 13792:3528 70447:3840 70448:5111 T08009 probable ... ribosomal protein L5-green ... alga (ISS) Ostreococcus tauri MGKRRQKRKSQSVAKTTAYQ ...

  20. Protein (Cyanobacteria): 28423 [

    Lifescience Database Archive (English)

    Full Text Available ZP_10226597.1 1117:517 1118:7626 1125:2051 1160279:627 Type 4 prepilin-like proteins leader ... pept ... ide-processing enzyme (Includes: Leader ... peptidase ; N-methyltransferase) Microcystis sp. T ...

  1. Protein (Cyanobacteria): 360784 [

    Lifescience Database Archive (English)

    Full Text Available YP_007097029.1 1117:17211 1118:17546 217161:1718 1173032:1718 1173020:1718 putative stress ... prote ... in (general stress ... protein 26) Chamaesiphon minutus PCC 6605 MANATENQ ...

  2. Protein (Cyanobacteria): 392180 [

    Lifescience Database Archive (English)

    Full Text Available ZP_07113914.1 1117:24513 1150:7038 1158:3915 272129:3709 Bifunctional protein birA (Includes: Biotin ... otin operon repressor; Biotin --(acetyl-CoA-carboxylase) synthetase (Biotin --prot ...

  3. Interactive protein manipulation

    Energy Technology Data Exchange (ETDEWEB)

    SNCrivelli@lbl.gov

    2003-07-01

    We describe an interactive visualization and modeling program for the creation of protein structures ''from scratch''. The input to our program is an amino acid sequence -decoded from a gene- and a sequence of predicted secondary structure types for each amino acid-provided by external structure prediction programs. Our program can be used in the set-up phase of a protein structure prediction process; the structures created with it serve as input for a subsequent global internal energy minimization, or another method of protein structure prediction. Our program supports basic visualization methods for protein structures, interactive manipulation based on inverse kinematics, and visualization guides to aid a user in creating ''good'' initial structures.

  4. Protein (Viridiplantae): 308811366 [

    Lifescience Database Archive (English)

    Full Text Available XP_003082991.1 33090:1951 3041:1340 1035538:592 13792:592 70447:610 70448:205 Transporter, ABC s ... uperfamily (Breast cancer ... resistance protein) (ISS), partial Ostreococcus ta ...

  5. Protein (Viridiplantae): 308810513 [

    Lifescience Database Archive (English)

    Full Text Available XP_003082565.1 33090:8864 3041:8803 1035538:7822 13792:7822 70447:3615 70448:4680 Predicted memb ... rane protein (associated with esophageal cancer ... in humans) (ISS) Ostreococcus tauri MTSSRKLCAFVRDA ...

  6. Protein (Viridiplantae): 308804289 [

    Lifescience Database Archive (English)

    Full Text Available XP_003079457.1 33090:1951 3041:1340 1035538:592 13792:592 70447:610 70448:205 Transporter, ABC s ... uperfamily (Breast cancer ... resistance protein) (ISS) Ostreococcus tauri MASRV ...

  7. Untying knots in proteins.

    Science.gov (United States)

    Sułkowska, Joanna I; Sułkowski, Piotr; Szymczak, Piotr; Cieplak, Marek

    2010-10-13

    A shoelace can be readily untied by pulling its ends rather than its loops. Attempting to untie a native knot in a protein can also succeed or fail depending on where one pulls. However, thermal fluctuations induced by the surrounding water affect conformations stochastically and may add to the uncertainty of the outcome. When the protein is pulled by the termini, the knot can only get tightened, and any attempt at untying results in failure. We show that, by pulling specific amino acids, one may easily retract a terminal segment of the backbone from the knotting loop and untangle the knot. At still other amino acids, the outcome of pulling can go either way. We study the dependence of the untying probability on the way the protein is grasped, the pulling speed, and the temperature. Elucidation of the mechanisms underlying this dependence is critical for a successful experimental realization of protein knot untying. PMID:20857930

  8. Protein (Viridiplantae): 308806666 [

    Lifescience Database Archive (English)

    Full Text Available XP_003080644.1 33090:21099 3041:5360 1035538:3986 13792:3986 70447:3049 70448:3532 COG3310: Unch ... aracterized protein conserved in bacteria ... (ISS) Ostreococcus tauri MRRTCASRNLARSPVAARERCRQMV ...

  9. Protein (Viridiplantae): 308803575 [

    Lifescience Database Archive (English)

    Full Text Available XP_003079100.1 33090:20519 3041:4460 1035538:2940 13792:2940 70447:2035 70448:2555 COG4399: Unch ... aracterized protein conserved in bacteria ... (ISS) Ostreococcus tauri MKALQRLVLRGSTDGVRPACERAMA ...

  10. Protein (Viridiplantae): 308804123 [

    Lifescience Database Archive (English)

    Full Text Available XP_003079374.1 33090:20519 3041:4460 1035538:2940 13792:2940 70447:2035 70448:2555 COG4399: Unch ... aracterized protein conserved in bacteria ... (ISS) Ostreococcus tauri MDSLATSRRRRLARAGAAIATALAL ...

  11. Protein (Viridiplantae): 255077633 [

    Lifescience Database Archive (English)

    Full Text Available XP_002502450.1 33090:20956 3041:5145 1035538:3740 13792:3740 38832:3722 296587:3525 isocitrate d ... ehydrogenase (NADP+), bacteria -like protein Micromonas sp. RCC299 MAAASAGGKIQAAPM ...

  12. Protein (Cyanobacteria): 228257 [

    Lifescience Database Archive (English)

    Full Text Available ZP_09784859.1 1117:4333 1150:1533 35823:3512 376219:3411 Protein ushA precursor (Includes: UDP-sugar ... ugar hydrolase (UDP-sugar ... pyrophosphatase) (UDP-sugar ... diphosphatase); 5'-nuc ...

  13. Protein folding and cosmology

    CERN Document Server

    González-Diáz, P F

    1997-01-01

    Protein denaturing induced by supercooling is interpreted as a process where some or all internal symmetries of the native protein are spontaneously broken. Hence, the free-energy potential corresponding to a folding-funnel landscape becomes temperature-dependent and describes a phase transition. The idea that deformed vortices could be produced in the transition induced by temperature quenching, from native proteins to unfolded conformations is discussed in terms of the Zurek mechanism that implements the analogy between vortices, created in the laboratory at low energy, and the cosmic strings which are thought to have been left after symmetry breaking phase transitions in the early universe. An experiment is proposed to test the above idea which generalizes the cosmological analogy to also encompass biological systems and push a step ahead the view that protein folding is a biological equivalent of the big bang.

  14. Protein (Viridiplantae): 308804764 [

    Lifescience Database Archive (English)

    Full Text Available XP_003079694.1 33090:24290 3041:9393 1035538:8433 13792:8433 70447:5209 70448:2928 probable memb ... rane protein YCR013c-yeast ... (ISS) Ostreococcus tauri MQLREVKERLRAYFSSSAATPGRTR ...

  15. Protein (Cyanobacteria): 338848 [

    Lifescience Database Archive (English)

    Full Text Available YP_007172477.1 1117:11758 1118:7408 13034:1671 292566:1671 13035:1671 cell envelope-related func ... tion transcriptional attenuator ... common domain protein Dactylococcopsis salina PCC ...

  16. Electron transfer in proteins

    DEFF Research Database (Denmark)

    Farver, O; Pecht, I

    1991-01-01

    Electron migration between and within proteins is one of the most prevalent forms of biological energy conversion processes. Electron transfer reactions take place between active centers such as transition metal ions or organic cofactors over considerable distances at fast rates and with remarkable...... specificity. The electron transfer is attained through weak electronic interaction between the active sites, so that considerable research efforts are centered on resolving the factors that control the rates of long-distance electron transfer reactions in proteins. These factors include (in addition to the......-containing proteins. These proteins serve almost exclusively in electron transfer reactions, and as it turns out, their metal coordination sites are endowed with properties uniquely optimized for their function....

  17. Protein Colloidal Aggregation Project

    Science.gov (United States)

    Oliva-Buisson, Yvette J. (Compiler)

    2014-01-01

    To investigate the pathways and kinetics of protein aggregation to allow accurate predictive modeling of the process and evaluation of potential inhibitors to prevalent diseases including cataract formation, chronic traumatic encephalopathy, Alzheimer's Disease, Parkinson's Disease and others.

  18. Interactive protein manipulation

    International Nuclear Information System (INIS)

    We describe an interactive visualization and modeling program for the creation of protein structures ''from scratch''. The input to our program is an amino acid sequence -decoded from a gene- and a sequence of predicted secondary structure types for each amino acid-provided by external structure prediction programs. Our program can be used in the set-up phase of a protein structure prediction process; the structures created with it serve as input for a subsequent global internal energy minimization, or another method of protein structure prediction. Our program supports basic visualization methods for protein structures, interactive manipulation based on inverse kinematics, and visualization guides to aid a user in creating ''good'' initial structures

  19. Egg protein hydrolysates

    NARCIS (Netherlands)

    Amerongen, van A.; Beelen, M.J.C.; Wolbers, L.A.M.; Gilst, van W.H.; Buikema, J.H.; Nelissen, J.W.P.M.

    2009-01-01

    The present invention provides egg-protein hydrolysates with DPP-IV inhibitory activity which are particularly suited for the treatment of diabetes. Particularly advantageous is to use hydrolysate of lysozyme for the treatment of diabetes.

  20. The Malignant Protein Puzzle.

    Science.gov (United States)

    Walker, Lary C; Jucker, Mathias

    2016-01-01

    When most people hear the words malignant and brain, cancer immediately comes to mind. But our authors argue that proteins can be malignant too, and can spread harmfully through the brain in neurodegenerative diseases that include Alzheimer's, Parkinson's, CTE, and ALS. Studying how proteins such as PrP, amyloid beta, tau, and others aggregate and spread, and kill brain cells, represents a crucial new frontier in neuroscience. PMID:27408676

  1. Fish protein hydrolysates

    Energy Technology Data Exchange (ETDEWEB)

    Mackie, I.M.

    1982-01-01

    Proteolytic enzymes now available in commercial quantities can be used to liquefy the fish and fish waste presently considered suitable for conversion to fish meal. The products obtained are readily dispersed or dissolved in water and have a high nutritional value. They have been satisfactorily used as substitutes for milk proteins in milk replacers for young animals. Further research is necessary on means of controlling the degree of hydrolysis to give protein preparations with acceptable functional properties as human food supplements. (Refs. 21).

  2. Recombinant Collagenlike Proteins

    Science.gov (United States)

    Fertala, Andzej

    2007-01-01

    A group of collagenlike recombinant proteins containing high densities of biologically active sites has been invented. The method used to express these proteins is similar to a method of expressing recombinant procollagens and collagens described in U. S. Patent 5,593,859, "Synthesis of human procollagens and collagens in recombinant DNA systems." Customized collagenous proteins are needed for biomedical applications. In particular, fibrillar collagens are attractive for production of matrices needed for tissue engineering and drug delivery. Prior to this invention, there was no way of producing customized collagenous proteins for these and other applications. Heretofore, collagenous proteins have been produced by use of such biological systems as yeasts, bacteria, and transgenic animals and plants. These products are normal collagens that can also be extracted from such sources as tendons, bones, and hides. These products cannot be made to consist only of biologically active, specific amino acid sequences that may be needed for specific applications. Prior to this invention, it had been established that fibrillar collagens consist of domains that are responsible for such processes as interaction with cells, binding of growth factors, and interaction with a number of structural proteins present in the extracellular matrix. A normal collagen consists of a sequence of domains that can be represented by a corresponding sequence of labels, e.g., D1D2D3D4. A collagenlike protein of the present invention contains regions of collagen II that contain multiples of a single domain (e.g., D1D1D1D1 or D4D4D4D4) chosen for its specific biological activity. By virtue of the multiplicity of the chosen domain, the density of sites having that specific biological activity is greater than it is in a normal collagen. A collagenlike protein according to this invention can thus be made to have properties that are necessary for tissue engineering.

  3. Untying Knots in Proteins

    OpenAIRE

    Sułkowska, Joanna I.; Sułkowski, Piotr; Szymczak, Piotr; Cieplak, Marek

    2010-01-01

    A shoelace can be readily untied by pulling its ends rather than its loops. Attempting to untie a native knot in a protein can also succeed or fail depending on where one pulls. However, thermal fluctuations induced by the surrounding water affect conformations stochastically and may add to the uncertainty of the outcome. When the protein is pulled by the termini, the knot can only get tightened, and any attempt at untying results in failure. We show that, by pulling specific amino acids, ...

  4. Digestibility of sorghum proteins.

    OpenAIRE

    Axtell, J D; Kirleis, A. W.; Hassen, M M; D'Croz Mason, N; Mertz, E T; Munck, L.

    1981-01-01

    Published information indicates that rice, maize, and wheat proteins are much more digestible in children than sorghum proteins are (66-81% compared with 46%). However, this digestibility difference cannot be demonstrated with the weanling rat, which gave digestibility values of 80% for cooked and 85% for uncooked sorghum gruels. Therefore, a search was made for a laboratory system sensitive to the digestibility differences between sorghum and other cereals. We found that porcine pepsin in vi...

  5. Identifying Unknown Proteins

    OpenAIRE

    Barker, Winona C.; Dayhoff, Margaret O.

    1983-01-01

    In this paper we discuss ways to identify a protein, both when its amino acid sequence is known and, particularly, prior to the determination of the complete sequence. If a similar sequence is in the Protein Sequence Database, an unknown may be identified on the basis of partial or ambiguous sequence data, or on the basis of amino acid composition. Identification in the early stages of structural determination can save time and scarce resources by preventing duplicate effort or by suggesting ...

  6. Proteins and their crystals

    Czech Academy of Sciences Publication Activity Database

    Kutá-Smatanová, Ivana; Hogg, T.; Hilgenfeld, R.; Grandori, R.; Carey, J.; Vácha, František; Štys, Dalibor

    2003-01-01

    Roč. 10, č. 1 (2003), s. 31-32. ISSN 1211-5894 R&D Projects: GA MŠk LN00A141; GA ČR GA206/00/D007 Institutional research plan: CEZ:AV0Z5051902; CEZ:MSM 123100001 Keywords : pokeweed antiviral protein * flavodoxin-like protein * PSII Subject RIV: EB - Genetics ; Molecular Biology

  7. Occupational protein contact dermatitis.

    Science.gov (United States)

    Barbaud, Annick; Poreaux, Claire; Penven, Emmanuelle; Waton, Julie

    2015-12-01

    Occupational contact dermatitis is generally caused by haptens but can also be induced by proteins causing mainly immunological contact urticaria (ICU); chronic hand eczema in the context of protein contact dermatitis (PCD). In a monocentric retrospective study, from our database, only 31 (0.41%) of patients with contact dermatitis had positive skin tests with proteins: 22 had occupational PCD, 3 had non-occupational PCD, 5 occupational ICU and 1 cook had a neutrophilic fixed food eruption (NFFE) due to fish. From these results and analysis of literature, the characteristics of PCD can be summarized as follows. It is a chronic eczematous dermatitis, possibly exacerbated by work, suggestive if associated with inflammatory perionyxix and immediate erythema with pruritis, to be investigated when the patient resumes work after a period of interruption. Prick tests with the suspected protein-containing material are essential, as patch tests have negative results. In case of multisensitisation revealed by prick tests, it is advisable to analyse IgE against recombinant allergens. A history of atopy, found in 56 to 68% of the patients, has to be checked for. Most of the cases are observed among food-handlers but PCD can also be due to non-edible plants, latex, hydrolysed proteins or animal proteins. Occupational exposure to proteins can thus lead to the development of ICU. Reflecting hypersensitivity to very low concentrations of allergens, investigating ICU therefore requires caution and prick tests should be performed with a diluted form of the causative protein-containing product. Causes are food, especially fruit peel, non-edible plants, cosmetic products, latex, animals. PMID:26242922

  8. Protein hydrolysates in sports nutrition

    Directory of Open Access Journals (Sweden)

    Manninen Anssi H

    2009-09-01

    Full Text Available Abstract It has been suggested that protein hydrolysates providing mainly di- and tripeptides are superior to intact (whole proteins and free amino acids in terms of skeletal muscle protein anabolism. This review provides a critical examination of protein hydrolysate studies conducted in healthy humans with special reference to sports nutrition. The effects of protein hydrolysate ingestion on blood amino acid levels, muscle protein anabolism, body composition, exercise performance and muscle glycogen resynthesis are discussed.

  9. Protein Functionality in Food Systems

    Institute of Scientific and Technical Information of China (English)

    WANG Panpan

    2010-01-01

    The structure,shape,color,smell and taste of food were decided by protein functionality.The utilization of protein will improve by changing the protein functionality.Protein functionality is also advantage to maintain and utilize the nutrition of food.This paper summarized the nature,classification,factors and prospect of protein functionality.It ccn provide a theoretical basis for application of protein in food industry.

  10. Protein Databases on the Internet

    OpenAIRE

    Xu, Dong

    2004-01-01

    Protein databases have become a crucial part of modern biology. Huge amounts of data for protein structures, functions, and particularly sequences are being generated. Searching databases is often the first step in the study of a new protein. Comparison between proteins or between protein families provides information about the relationship between proteins within a genome or across different species, and hence offers much more information than can be obtained by studying only an isolated pro...

  11. More protein in cereals?

    International Nuclear Information System (INIS)

    Ways in which the protein content of plant crops may be raised by the use of nuclear radiation are to be discussed at a symposium in Vienna in June next year, organized by the joint Food and Agriculture Organization/Agency Division of Atomic Energy in Food and Agriculture. Plant crops - especially cereal grains - are the basic food and protein source of most of the world's population, particularly in less-developed countries. But their natural protein content is low; increasing the quantity and nutritional quality of plant protein is potentially the most feasible way to combat widespread protein malnutrition. This improvement in seed stock can be achieved by plant breeding methods in which nuclear irradiation techniques are used to induce mutations in grain, and other isotopic techniques can be used to select only those mutants which have the desired properties. The scientists who attend the symposium will have an opportunity to review what mutation plant breeders have achieved, the application of nuclear techniques to screening for protein and amino-acid content and nutritional value, and isotopic methods which contribute to research in plant nutrition and physiology. (author)

  12. Stretching to Understand Proteins

    Science.gov (United States)

    Cieplak, Marek

    2007-03-01

    Mechanical stretching of single proteins has been studied experimentally for about 50 proteins yielding a variety of force patterns and values of the peak forces. We have performed a theoretical survey of 7749 proteins of known native structure and map out the landscape of possible dynamical behaviors unders stretching at constant speed. The model used is constructed based on the native geometry. It is solved by methods of molecular dynamics and validated by comparing the theoretical predictions to experimental results. We characterize the distribution of peak forces and on correlations with the system size and with the structure classification as characterized by the CATH scheme. We identify proteins with the biggest forces and show that they belong to few topology classes. We determine which protein segments act as mechanical clamps and show that, in most cases, they correspond to long stretches of parallel beta-strands, but other mechanisms are also possible. We then consider stretching by fluid flows. We show that unfolding induced by a uniform flow shows a richer behavior than that in the force clamp. The dynamics of unfolding is found to depend strongly on the selection of the amino acid, usually one of the termini, which is anchored. These features offer potentially wider diagnostic tools to investigate structure of proteins compared to experiments based on the atomic force microscopy.

  13. Inferring protein function by domain context similarities in protein-protein interaction networks

    OpenAIRE

    Sun Zhirong; Liu Ke; Chen Hu; Zhang Song

    2009-01-01

    Abstract Background Genome sequencing projects generate massive amounts of sequence data but there are still many proteins whose functions remain unknown. The availability of large scale protein-protein interaction data sets makes it possible to develop new function prediction methods based on protein-protein interaction (PPI) networks. Although several existing methods combine multiple information resources, there is no study that integrates protein domain information and PPI networks to pre...

  14. Achievement of hemodialysis discontinuation with lenalidomide and dexamethasone therapy in a refractory BJP-type multiple myeloma patient.

    Science.gov (United States)

    Uchida, Tomoyuki; Inoue, Morihiro; Hua, Jian; Hagihara, Masao

    2016-05-01

    A 63-year-old man with Bence Jones-κ multiple myeloma (MM) presented with renal impairment. First, we administered a bortezomib-containing regimen which is considered to be the first choice among therapeutic approaches for MM patients with renal failure. However, his condition was refractory to bortezomib, and the renal dysfunction worsened (creatinine 12.55mg/dl) necessitating the initiation of hemodialysis. Subsequently, we administered an adjusted dose of lenalidomide and dexamethasone. Dialysis could be discontinued after 3 cycles of lenalidomide therapy. After 4 cycles, he achieved a stringent complete response (sCR) with the creatinine level at 1.85mg/dl. This case suggests lenalidomide to be an effective drug for patients with multiple myeloma and renal impairment refractory to treatment with bortezomib. PMID:27263787

  15. ADSORPTION OF PROTEIN ON NANOPARTICLES

    Institute of Scientific and Technical Information of China (English)

    WU Qi

    1994-01-01

    The adsorption of protein on nanoparticles was studied by using dynamic light scattering to measure the hydrodynamic size of both pure protein and nanoparticles adsorbed with different amounts of protein. The thickness of the adsorbed protein layer increases as protein concentration, but decreases as the initial size of nanoparticles. After properly scaling the thickness with the initial diameter, we are able to fit all experimental data with a single master curve. Our experimental results suggest that the adsorbed proteins form a monolayeron the nanoparticle surface and the adsorbed protein molecules are attached to the particle surface at many points through a possible hydrogen-bonding. Our results also indicate that as protein concentration increases, the overall shape of the adsorbed protein molecule continuously changes from a flat layer on the particle surface to a stretched coil extended into water. During the change, the hydrodynamic volume of the adsorbed protein increases linearly with protein concentration.

  16. Measuring protein breakdown rate in individual proteins in vivo

    DEFF Research Database (Denmark)

    Holm, Lars; Kjaer, Michael

    2010-01-01

    To outline different approaches of how protein breakdown can be quantified and to present a new approach to determine the fractional breakdown rate of individual slow turnover proteins in vivo.......To outline different approaches of how protein breakdown can be quantified and to present a new approach to determine the fractional breakdown rate of individual slow turnover proteins in vivo....

  17. Histophilus somni Surface Proteins.

    Science.gov (United States)

    Corbeil, Lynette B

    2016-01-01

    The pathogen surface is usually the first site of interaction with the host. Histophilus somni was earlier thought to only have an outer membrane on its surface. Now it is known that the surface is composed of many virulence factors, including outer membrane proteins, lipooligosaccharide or endotoxin, a fibrillar network, and an exopolysaccharide. Outer membrane blebs, endotoxin, the fibrillar network, and the exopolysaccharide are also shed from the surface. This review will focus on the surface proteins of this pathogen that may colonize the mucosal surface of ruminants as a commensal or may cause pneumonia, septicemia, myocarditis, thrombotic meningoencephalitis, arthritis, and/or abortion. The major outer membrane protein has been well studied. Since its size and epitopes vary from strain to strain, it may be useful for typing strains. Iron-regulated OMPs have also received much attention because of their role in iron uptake for in vivo growth of H. somni. Other OMPs may be protective, based on passive immunization with monospecific antibodies and active immunization experiments. The surface and shed fibrillar network has been shown to be an immunoglobulin-binding protein in that it binds bovine IgG2 by the Fc portion. Two repeat domains (DR1 and DR2) have cytotoxic Fic motifs. Vaccine studies with recombinant DR2 are promising. Studies of the bacterial genome as well as comparison of surface proteins of different strains from the various H. somni syndromes and carrier states will be discussed and have provided much insight into pathogenesis and protection. PMID:26728061

  18. Biclonal gammopathy in multiple myeloma: a case report.

    Science.gov (United States)

    Bakta, I M; Sutarka, I N

    2000-05-01

    Monoclonal gammopathy is a group of B-cell disorders which result in the production of a specific and unique monoclonal immunoglobulin (M-component). Biclonal gammopathy is characterized by the simultaneous appearance of two different M-components. The incidence is about 1% of all monoclonal gammopathy. This paper reports on a 48-year-old male who had a chief complaint of back-pain beginning 7 months earlier. A physical examination was unremarkable, except for anemia and tenderness in the back. Hemoglobin was 5.4 g/dl, white blood cells 4.5 x 10(3)/microliter, platelets 157 x 10(3)/microliter, and reticulocytes 0.9%. Serum iron was 79 mg/dl, and total iron-binding capacity was 210 mg/dl. A blood smear showed the formation of rouleaux, but no plasma cells were found. Serum creatinine was 5.4 mg/dl, with a creatinine clearance of 18.1 ml/min. Serum electrolytes were normal except for serum calcium which was 14.4 mg/dl. The urinalysis showed strongly positive proteinuria (+2), with negative Bence Jones protein. Serum protein electrophoresis showed an increase and a spike pattern of beta-2 globulin (2.8 g/dl) and alpha-2 globulin (1.5 g/dl), with normal gamma globulin. By nephelometry technique, serum IgG was normal (1388 mg/dl), IgA was high (900 mg/dl), and IgM was also high (517 mg/dl). Advanced and extensive osteolytic lesions were found in the clavicle, ribs, skull, humerus, femur, and columna vertebralis. Plasma cells (myeloma cells) in bone marrow were 32%. The clinical diagnosis was multiple myeloma (biclonal gammopathy) stage IIIB (Durie and Salmon staging system). Clinical response was good after two series of conventional chemotherapy, with normal serum electrophoresis, decreasing serum creatinine and serum calcium. Based on the above data, the diagnosis of multiple myeloma with biclonal gammopathy was confirmed. This is a rare case with a combination of IgA and IgM M-components. PMID:10895208

  19. Ontology integration to identify protein complex in protein interaction networks

    OpenAIRE

    Yang Zhihao; Lin Hongfei; Xu Bo

    2011-01-01

    Abstract Background Protein complexes can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of protein complexes detection algorithms. Methods We have developed novel semantic similarity metho...

  20. Identifying Protein-Protein Interaction Sites Using Covering Algorithm

    OpenAIRE

    Jie Song; Jiaxing Cheng; Xiuquan Du

    2009-01-01

    Identification of protein-protein interface residues is crucial for structural biology. This paper proposes a covering algorithm for predicting protein-protein interface residues with features including protein sequence profile and residue accessible area. This method adequately utilizes the characters of a covering algorithm which have simple, lower complexity and high accuracy for high dimension data. The covering algorithm can achieve a comparable performance (69.62%, Complete dataset; 60....

  1. Protein-Protein Interaction Detection: Methods and Analysis

    OpenAIRE

    V. Srinivasa Rao; Srinivas, K.; Sujini, G. N.; G. N. Sunand Kumar

    2014-01-01

    Protein-protein interaction plays key role in predicting the protein function of target protein and drug ability of molecules. The majority of genes and proteins realize resulting phenotype functions as a set of interactions. The in vitro and in vivo methods like affinity purification, Y2H (yeast 2 hybrid), TAP (tandem affinity purification), and so forth have their own limitations like cost, time, and so forth, and the resultant data sets are noisy and have more false positives to annotate t...

  2. Protein Microarray On-Demand: A Novel Protein Microarray System

    OpenAIRE

    Chatterjee, Deb K.; Sitaraman, Kalavathy; Baptista, Cassio; Hartley, James; Hill, Thomas M.; David J. Munroe

    2008-01-01

    We describe a novel, simple and low-cost protein microarray strategy wherein the microarrays are generated by printing expression ready plasmid DNAs onto slides that can be converted into protein arrays on-demand. The printed expression plasmids serve dual purposes as they not only direct the synthesis of the protein of interest; they also serve to capture the newly synthesized proteins through a high affinity DNA-protein interaction. To accomplish this we have exploited the high-affinity bin...

  3. Polarizable protein packing

    KAUST Repository

    Ng, Albert H.

    2011-01-24

    To incorporate protein polarization effects within a protein combinatorial optimization framework, we decompose the polarizable force field AMOEBA into low order terms. Including terms up to the third-order provides a fair approximation to the full energy while maintaining tractability. We represent the polarizable packing problem for protein G as a hypergraph and solve for optimal rotamers with the FASTER combinatorial optimization algorithm. These approximate energy models can be improved to high accuracy [root mean square deviation (rmsd) < 1 kJ mol -1] via ridge regression. The resulting trained approximations are used to efficiently identify new, low-energy solutions. The approach is general and should allow combinatorial optimization of other many-body problems. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011 Copyright © 2011 Wiley Periodicals, Inc.

  4. Polarizable protein packing.

    Science.gov (United States)

    Ng, Albert H; Snow, Christopher D

    2011-05-01

    To incorporate protein polarization effects within a protein combinatorial optimization framework, we decompose the polarizable force field AMOEBA into low order terms. Including terms up to the third-order provides a fair approximation to the full energy while maintaining tractability. We represent the polarizable packing problem for protein G as a hypergraph and solve for optimal rotamers with the FASTER combinatorial optimization algorithm. These approximate energy models can be improved to high accuracy [root mean square deviation (rmsd) < 1 kJ mol(-1)] via ridge regression. The resulting trained approximations are used to efficiently identify new, low-energy solutions. The approach is general and should allow combinatorial optimization of other many-body problems. PMID:21264879

  5. Electron transfer in proteins.

    Science.gov (United States)

    Gray, H B; Winkler, J R

    1996-01-01

    Electron-transfer (ET) reactions are key steps in a diverse array of biological transformations ranging from photosynthesis to aerobic respiration. A powerful theoretical formalism has been developed that describes ET rates in terms of two parameters: the nuclear reorganization energy (lambda) and the electronic-coupling strength (HAB). Studies of ET reactions in ruthenium-modified proteins have probed lambda and HAB in several metalloproteins (cytochrome c, myoglobin, azurin). This work has shown that protein reorganization energies are sensitive to the medium surrounding the redox sites and that an aqueous environment, in particular, leads to large reorganization energies. Analyses of electronic-coupling strengths suggest that the efficiency of long-range ET depends on the protein secondary structure: beta sheets appear to mediate coupling more efficiently than alpha-helical structures, and hydrogen bonds play a critical role in both. PMID:8811189

  6. Accessory Proteins at ERES

    DEFF Research Database (Denmark)

    Klinkenberg, Rafael David

    proteins. Together these components co‐operate in cargo‐selection as well as forming, loading and releasing budding vesicles from specific regions on the membrane surface of the ER. Coat components furthermore convey vesicle targeting towards the Golgi. However, not much is known about the mechanisms that...... regulate the COPII assembly at the vesicle bud site. This thesis provides the first regulatory mechanism of COPII assembly in relation to ER‐membrane lipid‐signal recognition by the accessory protein p125A (Sec23IP). The aim of the project was to characterize p125A function by dissecting two main domains...... in the protein; a putative lipid‐associating domain termed the DDHD domain that is defined by the four amino acid motif that gives the domain its name; and a ubiquitously found domain termed Sterile α‐motif (SAM), which is mostly associated with oligomerization and polymerization. We first show, that...

  7. Sound of proteins

    DEFF Research Database (Denmark)

    2007-01-01

    In my group we work with Molecular Dynamics to model several different proteins and protein systems. We submit our modelled molecules to changes in temperature, changes in solvent composition and even external pulling forces. To analyze our simulation results we have so far used visual inspection...... and statistical analysis of the resulting molecular trajectories (as everybody else!). However, recently I started assigning a particular sound frequency to each amino acid in the protein, and by setting the amplitude of each frequency according to the movement amplitude we can "hear" whenever two aminoacids....... These are early days, and it still remains to be proven that this method has any advantage over other methods, but at least it is fun to do and the harmonies produced invoke an eerie sounding futuristic landscape...

  8. Ubiquitin domain proteins in disease

    DEFF Research Database (Denmark)

    Klausen, Louise Kjær; Schulze, Andrea; Seeger, Michael;

    2007-01-01

    The human genome encodes several ubiquitin-like (UBL) domain proteins (UDPs). Members of this protein family are involved in a variety of cellular functions and many are connected to the ubiquitin proteasome system, an essential pathway for protein degradation in eukaryotic cells. Despite their...... and cancer. Publication history: Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com)....

  9. SOY PROTEIN NANOPARTICLES AND NANOCOMPOSITES

    Science.gov (United States)

    Soy protein isolate (SPI) is obtained from soybean by removing soybean oil and soy carbohydrates. SPI contains more than 90% protein. Structurally, SPI is a globular protein and its aggregates in water consist of sphere-like protein particles. The number average aggregate size of SPI at pH=5.2 is...

  10. The Formation of Protein Structure

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1996-01-01

    Dynamically induced curvature owing to long-range excitations along the backbones of protein molecules with non-linear elastic properties may control the folding of proteins.......Dynamically induced curvature owing to long-range excitations along the backbones of protein molecules with non-linear elastic properties may control the folding of proteins....

  11. Vibrational spectroscopy of proteins

    International Nuclear Information System (INIS)

    Two important steps for the development of a biosensor are the immobilization of the biological component (e.g. protein) on a surface and the enhancement of the signal to improve the sensitivity of detection. To address these subjects, the present work describes Fourier transform infrared (FTIR) investigations of several proteins bound to the surface of an attenuated total reflection (ATR) crystal. Furthermore, new nanostructured surfaces for signal enhancement were developed for use in FTIR microscopy. The mitochondrial redox-protein cytochrome c oxidase (CcO) was incorporated into a protein-tethered bilayer lipid membrane (ptBLM) on an ATR crystal featuring a roughened two-layer gold surface for signal enhancement. Electrochemical excitation by periodic potential pulses at different modulation frequencies was followed by time-resolved FTIR spectroscopy. Phase sensitive detection was used for deconvolution of the IR spectra into vibrational components. A model based on protonation-dependent chemical reaction kinetics could be fitted to the time evolution of IR bands attributed to several different redox centers of the CcO. Further investigations involved the odorant binding protein 14 (OBP14) of the honey bee (Apis mellifera), which was studied using ATR-FTIR spectroscopy and circular dichroism. OBP14 was found to be thermally stable up to 45 °C, thus permitting the potential application of this protein for the fabrication of biosensors. Thermal denaturation measurements showed that odorant binding increases the thermal stability of the OBP-odorant complex. In another project, plasmonic nanostructures were fabricated that enhance the absorbance in FTIR microscopy measurements. The nanostructures are composed of an array of round-shaped insulator and gold discs on top of a continuous gold layer. Enhancement factors of up to ⁓125 could be observed with self-assembled monolayers of dodecanethiol molecules immobilized on the gold surface (author)

  12. Modeling Mercury in Proteins.

    Science.gov (United States)

    Parks, J M; Smith, J C

    2016-01-01

    Mercury (Hg) is a naturally occurring element that is released into the biosphere both by natural processes and anthropogenic activities. Although its reduced, elemental form Hg(0) is relatively nontoxic, other forms such as Hg(2+) and, in particular, its methylated form, methylmercury, are toxic, with deleterious effects on both ecosystems and humans. Microorganisms play important roles in the transformation of mercury in the environment. Inorganic Hg(2+) can be methylated by certain bacteria and archaea to form methylmercury. Conversely, bacteria also demethylate methylmercury and reduce Hg(2+) to relatively inert Hg(0). Transformations and toxicity occur as a result of mercury interacting with various proteins. Clearly, then, understanding the toxic effects of mercury and its cycling in the environment requires characterization of these interactions. Computational approaches are ideally suited to studies of mercury in proteins because they can provide a detailed molecular picture and circumvent issues associated with toxicity. Here, we describe computational methods for investigating and characterizing how mercury binds to proteins, how inter- and intraprotein transfer of mercury is orchestrated in biological systems, and how chemical reactions in proteins transform the metal. We describe quantum chemical analyses of aqueous Hg(II), which reveal critical factors that determine ligand-binding propensities. We then provide a perspective on how we used chemical reasoning to discover how microorganisms methylate mercury. We also highlight our combined computational and experimental studies of the proteins and enzymes of the mer operon, a suite of genes that confer mercury resistance in many bacteria. Lastly, we place work on mercury in proteins in the context of what is needed for a comprehensive multiscale model of environmental mercury cycling. PMID:27497164

  13. Mining protein structure data

    OpenAIRE

    Santos, José Carlos Almeida

    2006-01-01

    The principal topic of this work is the application of data mining techniques, in particular of machine learning, to the discovery of knowledge in a protein database. In the first chapter a general background is presented. Namely, in section 1.1 we overview the methodology of a Data Mining project and its main algorithms. In section 1.2 an introduction to the proteins and its supporting file formats is outlined. This chapter is concluded with section 1.3 which defines that main problem we...

  14. Protein-based ferrogels.

    Science.gov (United States)

    Mody, Puja; Hart, Cassidy; Romano, Siena; El-Magbri, Mariam; Esson, Moira M; Ibeh, Trisha; Knowlton, Elizabeth D; Zhang, Ming; Wagner, Michael J; Hartings, Matthew R

    2016-06-01

    We present a novel synthesis in which hemoglobin and Fe(2+) react, in the presence of KNO3 and KOH, to produce protein microgels that contain magnetic iron oxide nanoparticles. The synthesis results in microgels with polymer properties (denaturing and glass transition temperatures) that are consistent with the dried protein. The iron oxide nanoparticles that exhibit an average diameter of 22nm, are ferrimagnetic, and display properties consistent with Fe3O4. The multiple functional capabilities displayed by these materials: biocompatibility, magnetism, dye uptake and controlled release, and other properties archetypal of hydrogels, will make the magnetic hydrogels attractive for a number of biomedical applications. PMID:26901627

  15. Lipid-transfer proteins.

    Science.gov (United States)

    Ng, Tzi Bun; Cheung, Randy Chi Fai; Wong, Jack Ho; Ye, Xiujuan

    2012-01-01

    Lipid-transfer proteins (LTPs) are basic proteins found in abundance in higher plants. LTPs play lots of roles in plants such as participation in cutin formation, embryogenesis, defense reactions against phytopathogens, symbiosis, and the adaptation of plants to various environmental conditions. In addition, LTPs from field mustard and Chinese daffodil exhibit antiproliferative activity against human cancer cells. LTPs from chili pepper and coffee manifest inhibitory activity against fungi pathogenic to humans such as Candida species. The intent of this article is to review LTPs in the plant kingdom. PMID:23193591

  16. Chirality and Protein Folding

    OpenAIRE

    Kwiecinska, Joanna I.; Cieplak, Marek

    2004-01-01

    There are several simple criteria of folding to a native state in model proteins. One of them involves crossing of a threshold value of the RMSD distance away from the native state. Another checks whether all native contacts are established, i.e. whether the interacting amino acids come closer than some characteristic distance. We use Go-like models of proteins and show that such simple criteria may prompt one to declare folding even though fragments of the resulting conformations have a wron...

  17. Conformation Distributions in Adsorbed Proteins.

    Science.gov (United States)

    Meuse, Curtis W.; Hubbard, Joseph B.; Vrettos, John S.; Smith, Jackson R.; Cicerone, Marcus T.

    2007-03-01

    While the structural basis of protein function is well understood in the biopharmaceutical and biotechnology industries, few methods for the characterization and comparison of protein conformation distributions are available. New methods capable of measuring the stability of protein conformations and the integrity of protein-protein, protein-ligand and protein-surface interactions both in solution and on surfaces are needed to help the development of protein-based products. We are developing infrared spectroscopy methods for the characterization and comparison of molecular conformation distributions in monolayers and in solutions. We have extracted an order parameter describing the orientational and conformational variations of protein functional groups around the average molecular values from a single polarized spectrum. We will discuss the development of these methods and compare them to amide hydrogen/deuterium exchange methods for albumin in solution and on different polymer surfaces to show that our order parameter is related to protein stability.

  18. The Road Inventory of Jones Hole National Fish Hatchery

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — To determine the relative needs of the U.S. Fish and Wildlife Service, the Federal Highway Administration FHWA was asked to inventory all public access and...

  19. The Double Jones Birefringence in Magneto-electric Medium

    OpenAIRE

    Waqas Mahmood; Qing Zhao

    2014-01-01

    In this paper, the Maxwell’s equations for a tensorial magneto-electric (ME) medium are solved, which is an extension to the work on the uniaxial anisotropic nonmagnetic medium. The coefficients of the dielectric permittivity, magnetic permeability, and of the magneto-electric effect are considered as tensors. The polarization is shown lying in the plane of two perpendicular independent vectors, and the relationship for the transverse polarization is given. The propagation of an electromagnet...

  20. Idiosyncratic risk in the Dow Jones Eurostoxx50 Index

    Science.gov (United States)

    Daly, Kevin; Vo, Vinh

    2008-07-01

    Recent evidence by Campbell et al. [J.Y. Campbell, M. Lettau B.G. Malkiel, Y. Xu, Have individual stocks become more volatile? An empirical exploration of idiosyncratic risk, The Journal of Finance (February) (2001)] shows an increase in firm-level volatility and a decline of the correlation among stock returns in the US. In relation to the Euro-Area stock markets, we find that both aggregate firm-level volatility and average stock market correlation have trended upwards. We estimate a linear model of the market risk-return relationship nested in an EGARCH(1, 1)-M model for conditional second moments. We then show that traditional estimates of the conditional risk-return relationship, that use ex-post excess-returns as the conditioning information set, lead to joint tests of the theoretical model (usually the ICAPM) and of the Efficient Market Hypothesis in its strong form. To overcome this problem we propose alternative measures of expected market risk based on implied volatility extracted from traded option prices and we discuss the conditions under which implied volatility depends solely on expected risk. We then regress market excess-returns on lagged market implied variance computed from implied market volatility to estimate the relationship between expected market excess-returns and expected market risk.We investigate whether, as predicted by the ICAPM, the expected market risk is the main factor in explaining the market risk premium and the latter is independent of aggregate idiosyncratic risk.

  1. G Protein-coupled receptors

    OpenAIRE

    Ross, Elliott M.

    2014-01-01

    G protein-coupled receptors and heterotrimeric G proteins can diffuse laterally in the plasma membrane such that one receptor can catalyze the activation (GDP/GTP exchange) of multiple G proteins. In some cases, these processes are fast enough to support molecular signal amplification, where a single receptor maintains the activation of multiple G proteins at steady-state. Amplification in cells is probably highly regulated. It depends upon the identities of the G receptor and G protein - som...

  2. Protein stability, flexibility and function

    DEFF Research Database (Denmark)

    Teilum, Kaare; Olsen, Johan G; Kragelund, Birthe B

    2011-01-01

    Proteins rely on flexibility to respond to environmental changes, ligand binding and chemical modifications. Potentially, a perturbation that changes the flexibility of a protein may interfere with its function. Millions of mutations have been performed on thousands of proteins in quests for a...... data presented is it clear that there are specific sites (flexibility hotspots) in proteins that are important for both binding and stability. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches....

  3. Protein oxidation in aquatic foods

    DEFF Research Database (Denmark)

    Baron, Caroline P.

    oxidation. The protein carbonyl group measurement is the widely used method for estimating protein oxidation in foods and has been used in fish muscle. The chapter also talks about the impact of protein oxidation on protein functionality, fish muscle texture, and food nutritional value. Protein oxidation...... may not only induce quality losses but may be desirable in some type of foods, such as salted herring....

  4. Measuring protein breakdown in individual proteins in vivo

    DEFF Research Database (Denmark)

    Holm, Lars; Kjær, Michael

    2010-01-01

    PURPOSE OF REVIEW: To outline different approaches of how protein breakdown can be quantified and to present a new approach to determine the fractional breakdown rate of individual slow turnover proteins in vivo. RECENT FINDINGS: None of the available methods for determining protein breakdown can...... be used to determine the breakdown rate of specific proteins and, therefore, do not keep up to the preceding methodological demands in physiological research. A newly developed approach to determine the fractional breakdown rate of single proteins seems promising. Its conceptual advantage is that the...... proteins of interest are the site of measurement. Hence, the application initially demands the proteins to be labeled with stable isotopically labeled amino acids. Subsequently, the loss of label from the proteins will be dependent on the protein breakdown rate when no labeled amino acids are...

  5. Integral UBL domain proteins: a family of proteasome interacting proteins

    DEFF Research Database (Denmark)

    Hartmann-Petersen, Rasmus; Gordon, Colin

    2004-01-01

    The family of ubiquitin-like (UBL) domain proteins (UDPs) comprises a conserved group of proteins involved in a multitude of different cellular activities. However, recent studies on UBL-domain proteins indicate that these proteins appear to share a common property in their ability to interact with......-domain proteins catalyse the formation of ubiquitin-protein conjugates, whereas others appear to target ubiquitinated proteins for degradation and interact with chaperones. Hence, by binding to the 26S proteasome the UBL-domain proteins seem to tailor and direct the basic proteolytic functions of the particle to...... 26S proteasomes. The 26S proteasome is a multisubunit protease which is responsible for the majority of intracellular proteolysis in eukaryotic cells. Before degradation commences most proteins are first marked for destruction by being coupled to a chain of ubiquitin molecules. Some UBL...

  6. Interaction between plate make and protein in protein crystallisation screening.

    Directory of Open Access Journals (Sweden)

    Gordon J King

    Full Text Available BACKGROUND: Protein crystallisation screening involves the parallel testing of large numbers of candidate conditions with the aim of identifying conditions suitable as a starting point for the production of diffraction quality crystals. Generally, condition screening is performed in 96-well plates. While previous studies have examined the effects of protein construct, protein purity, or crystallisation condition ingredients on protein crystallisation, few have examined the effect of the crystallisation plate. METHODOLOGY/PRINCIPAL FINDINGS: We performed a statistically rigorous examination of protein crystallisation, and evaluated interactions between crystallisation success and plate row/column, different plates of same make, different plate makes and different proteins. From our analysis of protein crystallisation, we found a significant interaction between plate make and the specific protein being crystallised. CONCLUSIONS/SIGNIFICANCE: Protein crystal structure determination is the principal method for determining protein structure but is limited by the need to produce crystals of the protein under study. Many important proteins are difficult to crystallize, so that identification of factors that assist crystallisation could open up the structure determination of these more challenging targets. Our findings suggest that protein crystallisation success may be improved by matching a protein with its optimal plate make.

  7. HIV protein sequence hotspots for crosstalk with host hub proteins.

    Directory of Open Access Journals (Sweden)

    Mahdi Sarmady

    Full Text Available HIV proteins target host hub proteins for transient binding interactions. The presence of viral proteins in the infected cell results in out-competition of host proteins in their interaction with hub proteins, drastically affecting cell physiology. Functional genomics and interactome datasets can be used to quantify the sequence hotspots on the HIV proteome mediating interactions with host hub proteins. In this study, we used the HIV and human interactome databases to identify HIV targeted host hub proteins and their host binding partners (H2. We developed a high throughput computational procedure utilizing motif discovery algorithms on sets of protein sequences, including sequences of HIV and H2 proteins. We identified as HIV sequence hotspots those linear motifs that are highly conserved on HIV sequences and at the same time have a statistically enriched presence on the sequences of H2 proteins. The HIV protein motifs discovered in this study are expressed by subsets of H2 host proteins potentially outcompeted by HIV proteins. A large subset of these motifs is involved in cleavage, nuclear localization, phosphorylation, and transcription factor binding events. Many such motifs are clustered on an HIV sequence in the form of hotspots. The sequential positions of these hotspots are consistent with the curated literature on phenotype altering residue mutations, as well as with existing binding site data. The hotspot map produced in this study is the first global portrayal of HIV motifs involved in altering the host protein network at highly connected hub nodes.

  8. Characterization of Protein Complexes and Subcomplexes in Protein-Protein Interaction Databases

    OpenAIRE

    Nazar Zaki; Elfadil A. Mohamed; Antonio Mora

    2015-01-01

    The identification and characterization of protein complexes implicated in protein-protein interaction data are crucial to the understanding of the molecular events under normal and abnormal physiological conditions. This paper provides a novel characterization of subcomplexes in protein interaction databases, stressing definition and representation issues, quantification, biological validation, network metrics, motifs, modularity, and gene ontology (GO) terms. The paper introduces the concep...

  9. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    Directory of Open Access Journals (Sweden)

    Peiqiang Yu

    2007-01-01

    Full Text Available The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1 using the newly advanced synchrotron technology (S-FTIR as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2 revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3 prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4 obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  10. Transient protein-protein interactions visualized by solution NMR.

    Science.gov (United States)

    Liu, Zhu; Gong, Zhou; Dong, Xu; Tang, Chun

    2016-01-01

    Proteins interact with each other to establish their identities in cell. The affinities for the interactions span more than ten orders of magnitude, and KD values in μM-mM regimen are considered transient and are important in cell signaling. Solution NMR including diamagnetic and paramagnetic techniques has enabled atomic-resolution depictions of transient protein-protein interactions. Diamagnetic NMR allows characterization of protein complexes with KD values up to several mM, whereas ultraweak and fleeting complexes can be modeled with the use of paramagnetic NMR especially paramagnetic relaxation enhancement (PRE). When tackling ever-larger protein complexes, PRE can be particularly useful in providing long-range intermolecular distance restraints. As NMR measurements are averaged over the ensemble of complex structures, structural information for dynamic protein-protein interactions besides the stereospecific one can often be extracted. Herein the protein interaction dynamics are exemplified by encounter complexes, alternative binding modes, and coupled binding/folding of intrinsically disordered proteins. Further integration of NMR with other biophysical techniques should allow better visualization of transient protein-protein interactions. In particular, single-molecule data may facilitate the interpretation of ensemble-averaged NMR data. Though same structures of proteins and protein complexes were found in cell as in diluted solution, we anticipate that the dynamics of transient protein protein-protein interactions be different, which awaits awaits exploration by NMR. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions. PMID:25896389

  11. Protein (Viridiplantae): 308810769 [

    Lifescience Database Archive (English)

    Full Text Available XP_003082693.1 33090:1723 3041:2182 1035538:123 13792:123 70447:3706 70448:4753 K+-channel ERG a ... nd related proteins, contain PAS /PAC sensor domain (ISS) Ostreococcus tauri MHFNADL ...

  12. Protein (Viridiplantae): 308809165 [

    Lifescience Database Archive (English)

    Full Text Available XP_003081892.1 33090:2400 3041:801 1035538:331 13792:331 70447:681 70448:136 K+-channel ERG and ... related proteins, contain PAS /PAC sensor domain (ISS) Ostreococcus tauri MPSTAGM ...

  13. Protein (Viridiplantae): 357507515 [

    Lifescience Database Archive (English)

    Full Text Available XP_003624046.1 33090:6310 35493:7221 131221:7221 3193:7221 58023:3109 78536:1898 58024:1898 3398 ... 803:6139 3814:6139 163742:7708 3877:7708 3880:7708 Nematode ... resistance-like protein Medicago truncatula MTLPLA ...

  14. Protein (Viridiplantae): 225448363 [

    Lifescience Database Archive (English)

    Full Text Available XP_002268520.1 33090:30695 35493:21281 131221:21281 3193:21281 58023:14619 78536:14658 58024:146 ... 667:4453 3602:4453 3603:4453 29760:4453 PREDICTED: nematode ... resistance protein-like HSPRO2 isoform 1 Vitis vin ...

  15. Protein (Viridiplantae): 226529483 [

    Lifescience Database Archive (English)

    Full Text Available NP_001151109.1 33090:30695 35493:21281 131221:21281 3193:21281 58023:14619 78536:14658 58024:146 ... 0:6136 147369:6136 147429:6136 4575:6020 4577:6020 nematode -resistance protein Zea mays MATPDLSPVSPVRRDDKQCAPS ...

  16. Protein (Viridiplantae): 357125930 [

    Lifescience Database Archive (English)

    Full Text Available XP_003564642.1 33090:30695 35493:21281 131221:21281 3193:21281 58023:14619 78536:14658 58024:146 ... :4262 147385:4262 15367:4262 15368:4262 PREDICTED: nematode ... resistance protein-like HSPRO1-like Brachypodium d ...

  17. Protein (Viridiplantae): 356553794 [

    Lifescience Database Archive (English)

    Full Text Available XP_003545237.1 33090:30695 35493:21281 131221:21281 3193:21281 58023:14619 78536:14658 58024:146 ... 14:9870 163735:3769 3846:3769 3847:3769 PREDICTED: nematode ... resistance protein-like HSPRO2-like Glycine max MV ...

  18. Protein (Viridiplantae): 357492609 [

    Lifescience Database Archive (English)

    Full Text Available XP_003616593.1 33090:30695 35493:21281 131221:21281 3193:21281 58023:14619 78536:14658 58024:146 ... :9870 3814:9870 163742:15503 3877:15503 3880:15503 Nematode ... resistance HS1pro1 protein Medicago truncatula MVD ...

  19. Protein (Viridiplantae): 351726303 [

    Lifescience Database Archive (English)

    Full Text Available NP_001236610.1 33090:30695 35493:21281 131221:21281 3193:21281 58023:14619 78536:14658 58024:146 ... 803:9870 3814:9870 163735:3769 3846:3769 3847:3769 nematode ... resistance HS1pro1 protein Glycine max MVDLDWQTKMV ...

  20. Protein (Viridiplantae): 350537949 [

    Lifescience Database Archive (English)

    Full Text Available NP_001234063.1 33090:6270 35493:2337 131221:2337 3193:2337 58023:2583 78536:1868 58024:1868 3398 ... 4 424574:154 4107:154 49274:154 4081:154 root-knot nematode ... resistance protein Solanum lycopersicum MEKRKDIEEA ...