The Cutoff Level for Urine Protein in Urine Immunofixation Electrophoresis.

Science.gov (United States)

Ellidag, Hamit Yasar; Curek, Gulten; Eren, Esin; Aydin, Ozgur; Yilmaz, Necat

2015-01-01

Immunofixation electrophoresis (IFE) maintains its importance in diagnosing monoclonal gammopathies. In particular, urine IFE detects free light chains (FLC) in urine samples even at low concentrations and offers higher sensitivity compared to serum electrophoresis and serum IFE. The aim of the present study was to determine the place and significance of quantitative urinary protein measurement before IFE in interpreting the results of subsequent IFE and to determine the most appropriate protein concentrations for the appearance of bands. The records of a total of 600 patients, who underwent screening for Bence Jones proteinuria using IFE on 24-hour urine, were retrospectively reviewed. Urine IFE was performed using Helena SAS-I and SAS-I devices. The total protein concentration in the urine was quantitatively determined by the Pyrogallol red method, and the urine albumin level was determined using the immunoturbidimetric method. These analyses were measured on an Olympus/Beckmann AU5800. The evaluation of IFE results revealed that 311 patients had normal results, 108 patients had monoclonal bands, five patients had biclonal bands, 28 had polyclonal bands, and 148 patients had various degrees of proteinuria. ROC curves were created in order to determine the most appropriate urinary protein and albumin levels to observe bands in IFE. Accordingly, urine baseline protein level (mg/dL) showed the highest AUC value (cutoff value: 19.4 mg/dL, sensitivity: 92%, specificity: 98.2%, AUC: 0.972). The present study showed that quantitative protein measurement before IFE eliminated the disadvantages associated with the IFE method and its interpretation.

Free light chains of immunoglobulins in the diagnosis and prognosis of multiple myeloma

Directory of Open Access Journals (Sweden)

N. V. Lyubimova

2017-01-01

Full Text Available Background: Analysis of free light chains of immunoglobulins (FLC in the serum is an effective method in the diagnosis of multiple myeloma. Plasma cells produce two types of FLC: κand λ-FLC. FLC, which are not incorporated into monoclonal intact immunoglobulins, are released into circulation, and then are filtered and reabsorbed in kidneys depending on their molecular weight. Circulating FLC commonly form homodimers, known as Bence-Jones protein, which is a biomarker of Bence-Jones multiple myeloma. According to the international guidelines, the ratio κ/λ FLC is an important diagnostic criterion of multiple myeloma. Aim: To evaluate the diagnostic and prognostic value of serum FLC in multiple myeloma patients. Materials and methods: We examined 118 patients with multiple myeloma, admitted to the Department of Hemoblastosis Chemotherapy of N.N. Blokhin Russian Cancer Research Center from 2010 to 2016, and 68 healthy men and women. Serum concentrations of FLC were measured with an immunoturbidimetric method using the test-system Freelite Human Lambda and Freelite Human Kappa (Binding Site Inc.. Results: The levels of monoclonal κor λ-FLC in patients with G-, A-myeloma and Bence-Jones multiple myeloma were significantly higher than those in the control group (p < 0.005. The diagnostic sensitivity of quantification of FLC and their ratio was 87.3% and 89.8%, and in combination with the use of immune electrophoresis it was close to 100%. Analysis of progression free survival and overall survival showed significant differences (p < 0.04 between the groups of patients according their κ/λ FLC ratio. The basal value of κ/λ FLC ratio of less than 0.04 and more than 140 was a  predictor of unfavorable outcome. Conclusion: The inclusion of the determination of serum FLC into the assessment plan of patients with suspected monoclonal gammapathy makes it possible to increase diagnostic sensitivity of the available methods for paraprotein

Multiple Myeloma

African Journals Online (AJOL)

proteinuria was also a poor prognostic finding,. but only because of its association with renal failure. Patients with. Bence-Jones protcinur;a and normal renal ... chemotherapy. The mean time which elapsed before the criteria of response were achieved, was 7 months. Five ad- ditional patients who are at present being ...

Daniel Jones

DEFF Research Database (Denmark)

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...

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

The Jones Family's Culture of Literacy

Science.gov (United States)

Johnson, Amy Suzanne

2010-01-01

This article considers the uses of literacy within the Jones family (all names are pseudonyms), an African American family who lives in the rural South of the United States. Drawing on life history data with three women in the Jones family--Harriet Jones (grandmother), Sally Harris (mother), and Lola Harris (granddaughter)--the author traces how…

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-Jones...... potential, the solitons can be characterized analytically with a good quantitative agreement using formulas for a Toda potential with parameters fitted to the Lennard-Jones potential. We also discuss and show the robustness of the family of periodic solutions called cnoidal waves, corresponding to phonons...

Tagging, Encoding, and Jones Optimality

DEFF Research Database (Denmark)

Danvy, Olivier; López, Pablo Ernesto Martínes

2003-01-01

A partial evaluator is said to be Jones-optimal if the result of specializing a self-interpreter with respect to a source program is textually identical to the source program, modulo renaming. Jones optimality has already been obtained if the self-interpreter is untyped. If the selfinterpreter...... is 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...

Magnetoelectric Jones dichroism

International Nuclear Information System (INIS)

Andrews, D L; Daniels, G J; Stedman, G E

2003-01-01

Recent work on liquids has verified a novel magnetoelectrical birefringence predicted by Jones. Co-present static electric and magnetic fields generate a differential response to optical polarizations positively or negatively tilted against a plane orthogonal to the one containing the static field vectors. Reports indicated a dichroic counterpart; establishing its theory is the present aim. Results are trilinearly dependent on the irradiance, and the static electric and magnetic fields. For isotropic fluids a scalar quantifies propensity for Jones dichroism. In field-polarized fluids a second scalar also contributes; temperature dependence enables determination of both parameters. (letter to the editor)

Tagging, Encoding, and Jones Optimality

DEFF Research Database (Denmark)

Danvy, Olivier; Lopez, Pablo E. Martinez

2003-01-01

A partial evaluator is said to be Jones-optimal if the result of specializing a self-interpreter with respect to a source program is textually identical to the source program, modulo renaming. Jones optimality has already been obtained if the self-interpreter is untyped. If the selfinterpreter...... is 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......-optimal, modulo an encoding. The representation shift amounts to reading the type tags as constructors for higherorder abstract syntax. We substantiate our observation by considering a typed self-interpreter whose input syntax is higher-order. Specializing this interpreter with respect to a source program yields...

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

STS-98 Crew Interview: Tom Jones

Science.gov (United States)

2001-01-01

The STS-98 Mission Specialist Tom Jones is seen being interviewed. He answers questions about his inspiration to become an astronaut, his career path, and his training. He gives details on the mission's goals and significance, and the payload and hardware it brings to the International Space Station (ISS). Mr. Jones discusses his role in the mission's spacewalks and activities.

The Performance of Dow Jones Country Islamic Indexes Against Dow Jones Country Conventional Indexes in Asia and the Middle East : An Empirical Study of the Last Decade

OpenAIRE

Suharwardy, Zain

2013-01-01

This paper attempts to examine the performance of six countries spanning from Asia and the Middle East. Countries are selected from the Dow Jones Islamic Market Index and the focus is kept to only choose countries that have an active Dow Jones Islamic Market Country Index along with a parallel Dow Jones Conventional Country Index. Further break down is made by comparing the country performances to their respective Dow Jones regional index’s (Dow Jones Asia Index and the Dow Jones MENA) in ord...

Magnetoelectric Jones spectroscopy of alkali atoms

International Nuclear Information System (INIS)

Chernushkin, V V; Mironova, P V; Ovsiannikov, V D

2008-01-01

The Jones effect in a medium of free atoms exposed to static electric and magnetic fields is a useful tool for determining details of an atomic structure. For atoms in their nS ground states irradiated by a monochromatic wave in resonance with a single-photon transition to an n' D state, the bilinear Jones effect is not shaded by the quadratic Kerr and Cotton-Mouton effects, nor by the linear in magnetic field Faraday effect. The position and shape of the amplitude resonance may provide information on spectroscopic properties of atomic levels. We generalize equations for the Jones-effect amplitude to the case of a doublet structure of energy levels and calculate corresponding parameters for alkali atoms. General equations are derived for the amplitude dependence on the relative orientation of the static electric and magnetic fields and on the angle between the static field and the major axis of the wave polarization vector. These equations demonstrate explicitly that the three bilinear-in-static-fields optical birefringence effects-(i) the Jones birefringence (in parallel fields), (ii) the linear birefringence and (iii) the directional birefringence (the last two in perpendicular fields)-correspond to particular cases of the bilinear-in-static-fields correction to the amplitude of Rayleigh forward scattering

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

International Nuclear Information System (INIS)

Saghari, M.; Fallahi, B.; Eftekhari, M.; Irvani, M.; Izadyar, S.; Esmaili, J.; Beiki, D.; Fard, A.

2004-01-01

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 E 0 -E 3 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 I 0 -I 3 . 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

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

Phase diagram of a modified Lennard-Jones system

International Nuclear Information System (INIS)

Sakagami, Takahiro; Fuchizaki, Kazuhiro

2010-01-01

The well-known Lennard-Jones potential is modified in such a way that it smoothly vanishes at a certain distance. A system whose interparticle interaction is given by such a potential is referred to as a modified Lennard-Jones system, and is served as a standard system describing simple solids and fluids. A phase diagram is determined based on the free energies obtained through thermodynamic integration.

Forefoot Adduction Is a Risk Factor for Jones Fracture.

Science.gov (United States)

Fleischer, Adam E; Stack, Rebecca; Klein, Erin E; Baker, Jeffrey R; Weil, Lowell; Weil, Lowell Scott

Jones fractures are among the most common fractures of the foot; however, much remains unknown about their etiology. The purpose of the present study was to further examine the risk factors of forefoot and hindfoot alignment on Jones fractures using an epidemiologic study design. We used a retrospective, matched, case-control study design. Cases consisted of patients with acute, isolated Jones fractures confirmed on plain film radiographs seen at our institute from January 2009 to December 2013. Patients presenting with pain unrelated to metatarsal fractures served as controls. Controls were matched to cases by age (±2 years), gender, and year of presentation. Weightbearing foot radiographs were assessed for 13 angular relationships by a single rater. Conditional multivariable logistic regression was used to identify important risk factors. Fifty patients with acute Jones fractures and 200 controls were included. The only significant variables in the final multivariable model were the metatarsus adductus angle (odds ratio [OR] 1.16, 95% confidence interval [CI] 1.08 to 1.25) and fourth/fifth intermetatarsal angle (OR 0.69, 95% CI 0.57 to 0.83)-both measures of static forefoot adduction. The presence of metatarsus adductus (defined as >15°) on foot radiographs was associated with a 2.4 times greater risk of a Jones fracture (adjusted OR 2.4, 95% CI 1.2 to 4.8). We have concluded that the risk of Jones fracture increases with an adducted forefoot posture. In our population, which consisted primarily of patients presenting after a fall (10 of 50; 20%) or misstep/inversion injury (19 of 50; 38%), the hindfoot alignment appeared to be a less important factor. Copyright © 2017 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

Verina Morton Jones, MD.

Science.gov (United States)

Rishworth, Susan K

2012-01-01

The purpose of this historical article is to demonstrate, as the biography of Verina Morton Jones, MD, is uncovered, the difficulties inherent in researching original source material on the lives of 19th- and early 20th-century African American physicians as well as the great benefits derived from doing this research. The procedures used include basic archival research and close examination of published materials about her in the past, in conjunction with oral history. Original correspondence from Dr Morton Jones to her niece and nephew is used to illustrate events in her life and the thoughts and attitudes she expressed. Some of these thoughts and attitudes reflect those current situations in which African Americans found themselves, and others are quite unique, no doubt owing to her privileged position in the African American community. The principle conclusions reached include the great benefits derived from doing this kind of research, as difficult and time-consuming as that may be, with the enhanced knowledge and appreciation of the heritage of African American physicians, and insights into American social history during this period.

Topological quantum information, virtual Jones polynomials and Khovanov homology

International Nuclear Information System (INIS)

Kauffman, Louis H

2011-01-01

In this paper, we give a quantum statistical interpretation of the bracket polynomial state sum 〈K〉, the Jones polynomial V K (t) and virtual knot theory versions of the Jones polynomial, including the arrow polynomial. We use these quantum mechanical interpretations to give new quantum algorithms for these Jones polynomials. In those cases where the Khovanov homology is defined, the Hilbert space C(K) of our model is isomorphic with the chain complex for Khovanov homology with coefficients in the complex numbers. There is a natural unitary transformation U:C(K) → C(K) such that 〈K〉 = Trace(U), where 〈K〉 denotes the evaluation of the state sum model for the corresponding polynomial. We show that for the Khovanov boundary operator ∂:C(K) → C(K), we have the relationship ∂U + U∂ = 0. Consequently, the operator U acts on the Khovanov homology, and we obtain a direct relationship between the Khovanov homology and this quantum algorithm for the Jones polynomial. (paper)

A response to Dodds and Jones.

Science.gov (United States)

Purdy, Laura M

1989-01-01

In response to "Surrogacy and Autonomy," by Susan Dodds and Karen Jones in this issue of Bioethics, the author concedes that only a surrogacy practice stringently regulated by good counseling, escape clauses for pregnant women, and the prohibition of profit-making agencies will save women from exploitation, but she objects to singling out women for paternalistic "protection against themselves," and to defending women's autonomy to the extent of their right to behave in ways known to harm a fetus. Dodds and Jones' concerns about attitudes toward women, genetic bias, the concept of children as property, and the harm principle generated by surrogacy contracts are answered with arguments for why surrogacy should not be illegal.

Cluster fusion algorithm: application to Lennard-Jones clusters

DEFF Research Database (Denmark)

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

2006-01-01

paths up to the cluster size of 150 atoms. We demonstrate that in this way all known global minima structures of the Lennard-Jones 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 number sequence......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...... for the clusters of noble gas atoms and compare it with experimental observations. We report the striking correspondence of the peaks in the dependence of the second derivative of the binding energy per atom on cluster size calculated for the chain of the Lennard-Jones clusters based on the icosahedral symmetry...

Cluster fusion algorithm: application to Lennard-Jones clusters

DEFF Research Database (Denmark)

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

2008-01-01

paths up to the cluster size of 150 atoms. We demonstrate that in this way all known global minima structures of the Lennard-Jones 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 number sequence......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...... for the clusters of noble gas atoms and compare it with experimental observations. We report the striking correspondence of the peaks in the dependence of the second derivative of the binding energy per atom on cluster size calculated for the chain of the Lennard-Jones clusters based on the icosahedral symmetry...

Scaling of the dynamics of flexible Lennard-Jones chains

DEFF Research Database (Denmark)

Veldhorst, Arno; Dyre, Jeppe C.; Schrøder, Thomas

2015-01-01

The previous paper [A. A. Veldhorst et al., J. Chem. Phys. 141, 054904 (2014)] demonstrated that the isomorph theory explains the scaling properties of a liquid of flexible chains consisting of ten Lennard-Jones particles connected by rigid bonds. We here investigate the same model with harmonic......, dynamics, and the excess entropy are invariant. The Lennard-Jones chain liquid with harmonic bondsdoes have curves in the phase diagram along which the structure and dynamics are invariant. The excess entropy is not invariant on these curves, which we refer to as “pseudoisomorphs.” In particular......, this means that Rosenfeld’s excess-entropy scaling (the dynamics being a function of excess entropy only) does not apply for the Lennard-Jones chain with harmonic bonds...

Protein Structure Prediction by Protein Threading

Science.gov (United States)

Xu, Ying; Liu, Zhijie; Cai, Liming; Xu, Dong

The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on "the inverse protein folding problem" laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural environments defined in terms of solvent accessibility and protein secondary structure, the authors derived a simple and yet profoundly novel approach to assessing if a protein sequence fits well with a given protein structural fold. Their follow-up work (Elofsson et al., 1996; Fischer and Eisenberg, 1996; Fischer et al., 1996a,b) and the work by Jones, Taylor, and Thornton (Jones et al., 1992) on protein fold recognition led to the development of a new brand of powerful tools for protein structure prediction, which we now term "protein threading." These computational tools have played a key role in extending the utility of all the experimentally solved structures by X-ray crystallography and nuclear magnetic resonance (NMR), providing structural models and functional predictions for many of the proteins encoded in the hundreds of genomes that have been sequenced up to now.

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"

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...

Nuclear-magnetic-resonance quantum calculations of the Jones polynomial

International Nuclear Information System (INIS)

Marx, Raimund; Spoerl, Andreas; Pomplun, Nikolas; Schulte-Herbrueggen, Thomas; Glaser, Steffen J.; Fahmy, Amr; Kauffman, Louis; Lomonaco, Samuel; Myers, John M.

2010-01-01

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 pseudopure 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 nuclear spin state of the molecule in each case, we are able to estimate the value of the Jones polynomial for each of the knots.

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

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

Thermal conductivity of the Lennard-Jones chain fluid model.

Science.gov (United States)

Galliero, Guillaume; Boned, Christian

2009-12-01

Nonequilibrium molecular dynamics simulations have been performed to estimate, analyze, and correlate the thermal conductivity of a fluid composed of short Lennard-Jones chains (up to 16 segments) over a large range of thermodynamic conditions. It is shown that the dilute gas contribution to the thermal conductivity decreases when the chain length increases for a given temperature. In dense states, simulation results indicate that the residual thermal conductivity of the monomer increases strongly with density, but is weakly dependent on the temperature. Compared to the monomer value, it has been noted that the residual thermal conductivity of the chain was slightly decreasing with its length. Using these results, an empirical relation, including a contribution due to the critical enhancement, is proposed to provide an accurate estimation of the thermal conductivity of the Lennard-Jones chain fluid model (up to 16 segments) over the domain 0.8values of the Lennard-Jones chain fluid model merge on the same "universal" curve when plotted as a function of the excess entropy. Furthermore, it is shown that the reduced configurational thermal conductivity of the Lennard-Jones chain fluid model is approximately proportional to the reduced excess entropy for all fluid states and all chain lengths.

Symmetric webs, Jones-Wenzl recursions and q-Howe duality

DEFF Research Database (Denmark)

Rose, David; Tubbenhauer, Daniel

We define and study the category of symmetric sl2-webs. This category is a combinatorial description of the category of all finite dimensional quantum sl2-modules. Explicitly, we show that (the additive closure of) the symmetric sl2-spider is (braided monoidally) equivalent to the latter. Our mai...... tool is a quantum version of symmetric Howe duality. As a corollary of our construction, we provide new insight into Jones-Wenzl projectors and the colored Jones polynomials....

The Jones polynomial as a new invariant of topological fluid dynamics

International Nuclear Information System (INIS)

Ricca, Renzo L; Liu, Xin

2014-01-01

A new method based on the use of the Jones polynomial, a well-known topological invariant of knot theory, is introduced to tackle and quantify topological aspects of structural complexity of vortex tangles in ideal fluids. By re-writing the Jones polynomial in terms of helicity, the resulting polynomial becomes then function of knot topology and vortex circulation, providing thus a new invariant of topological fluid dynamics. Explicit computations of the Jones polynomial for some standard configurations, including the Whitehead link and the Borromean rings (whose linking numbers are zero), are presented for illustration. In the case of a homogeneous, isotropic tangle of vortex filaments with same circulation, the new Jones polynomial reduces to some simple algebraic expression, that can be easily computed by numerical methods. This shows that this technique may offer a new setting and a powerful tool to detect and compute topological complexity and to investigate relations with energy, by tackling fundamental aspects of turbulence research. (paper)

Prozone effect of serum IgE levels in a case of plasma cell leukemia

Directory of Open Access Journals (Sweden)

Talamo Giampaolo

2010-09-01

Full Text Available Abstract We describe a case of multiple myeloma (MM and secondary plasma cell leukemia (PCL secreting IgE-kappa immunoglobulin. To our knowledge, only 2 cases of IgE-producing secondary PCL have been reported in the medical literature. In our patient, the only tumor marker available for monitoring the therapeutic response to chemotherapy and allogeneic stem cell transplantation was the quantitative M component at serum protein electrophoresis (SPEP, because serum free light chains were in the normal range, Bence-Jones proteinuria was absent, and quantitative serum IgE levels provided inaccurate and erratic results, due to the prozone effect. This is a laboratory phenomenon that occurs when antigen excess interferes with antibody-based methods requiring immune complex formation for detection. It is important to recognize the presence of a prozone effect, because it can produce falsely normal results, and therefore it could lead clinicians to incorrect assessment of the response to therapy.

Prozone effect of serum IgE levels in a case of plasma cell leukemia.

Science.gov (United States)

Talamo, Giampaolo; Castellani, William; Dolloff, Nathan G

2010-09-10

We describe a case of multiple myeloma (MM) and secondary plasma cell leukemia (PCL) secreting IgE-kappa immunoglobulin. To our knowledge, only 2 cases of IgE-producing secondary PCL have been reported in the medical literature. In our patient, the only tumor marker available for monitoring the therapeutic response to chemotherapy and allogeneic stem cell transplantation was the quantitative M component at serum protein electrophoresis (SPEP), because serum free light chains were in the normal range, Bence-Jones proteinuria was absent, and quantitative serum IgE levels provided inaccurate and erratic results, due to the prozone effect. This is a laboratory phenomenon that occurs when antigen excess interferes with antibody-based methods requiring immune complex formation for detection. It is important to recognize the presence of a prozone effect, because it can produce falsely normal results, and therefore it could lead clinicians to incorrect assessment of the response to therapy.

A new approach to radiative transfer theory using Jones's vectors. I

International Nuclear Information System (INIS)

Fymat, A.L.; Vasudevan, R.

1975-01-01

Radiative transfer of partially polarized radiation in an anisotropically scattering, inhomogeneous atmosphere containing arbitrary polydispersion of particles is described using Jones's amplitude vectors and matrices. This novel approach exploits the close analogy between the quantum mechanical states of spin 1/2 systems and the polarization states of electromagnetic radiation described by Jones's vector, and draws on the methodology of such spin 1/2 systems. The complete equivalence between the transport equation for Jones's vectors and the classical radiative transfer equation for Stokes's intensity vectors is demonstrated in two independent ways after deriving the transport equations for the polarization coherency matrices and for the quaternions corresponding to the Jones's vectors. A compact operator formulation of the theory is provided, and used to derive the necessary equations for both a local and a global description of the transport of Jones's vectors. Lastly, the integro-differential equations for the amplitude reflection and transmission matrices are derived, and related to the usual corresponding equations. The present formulation is the most succinct and the most convenient one for both theoretical and experimental studies. It yields a simpler analysis than the classical formulation since it reduces by a factor of two the dimensionality of transfer problems. It preserves information on phases, and thus can be used directly across the entire electromagnetic spectrum without any further conversion into intensities. (Auth.)

JST Thesaurus Headwords and Synonyms: Bence‐Jonesタンパク質 [MeCab user dictionary for science technology term[Archive

Lifescience Database Archive (English)

Full Text Available MeCab user dictionary for science technology term Bence‐Jonesタンパク質 名詞 一般 * * * * Ｂｅ...ｎｃｅ‐Ｊｏｎｅｓ蛋白質 Ｂｅｎｃｅ‐Ｊｏｎｅｓタンパクシツ ビーイーエヌシーイー‐ジェイオーエヌイーエスタンパクシツ Thesaurus2015 200906056340129484 C LS19/LS33 UNKNOWN_2 Bence ‐ Jones タンパク質

Freezing of Lennard-Jones-type fluids

International Nuclear Information System (INIS)

Khrapak, Sergey A.; Chaudhuri, Manis; Morfill, Gregor E.

2011-01-01

We put forward an approximate method to locate the fluid-solid (freezing) phase transition in systems of classical particles interacting via a wide range of Lennard-Jones-type potentials. This method is based on the constancy of the properly normalized second derivative of the interaction potential (freezing indicator) along the freezing curve. As demonstrated recently it yields remarkably good agreement with previous numerical simulation studies of the conventional 12-6 Lennard-Jones (LJ) fluid [S.A.Khrapak, M.Chaudhuri, G.E.Morfill, Phys. Rev. B 134, 052101 (2010)]. In this paper, we test this approach using a wide range of the LJ-type potentials, including LJ n-6 and exp-6 models, and find that it remains sufficiently accurate and reliable in reproducing the corresponding freezing curves, down to the triple-point temperatures. One of the possible application of the method--estimation of the freezing conditions in complex (dusty) plasmas with ''tunable'' interactions--is briefly discussed.

A Lennard-Jones-like perspective on first order transitions in biological helices

DEFF Research Database (Denmark)

Oskolkov, Nikolay N.; Bohr, Jakob

2013-01-01

Helical structures with Lennard-Jones self-interactions are studied for optimal conformations. For this purpose, their self-energy is analyzed for extrema with respect to the geometric parameters of the helices. It is found that Lennard-Jones helices exhibit a first order phase transition from...

Not Fully Developed Turbulence in the Dow Jones Index

Science.gov (United States)

Trincado, Estrella; Vindel, Jose María

2013-08-01

The shape of the curves relating the scaling exponents of the structure functions to the order of these functions is shown to distinguish the Dow Jones index from other stock market indices. We conclude from the shape differences that the information-loss rate for the Dow Jones index is reduced at smaller time scales, while it grows for other indices. This anomaly is due to the construction of the index, in particular to its dependence on a single market parameter: price. Prices are subject to turbulence bursts, which act against full development of turbulence.

Birefringence of cellotape: Jones representation and experimental analysis

International Nuclear Information System (INIS)

Belendez, Augusto; Frances, Jorge; Neipp, Cristian; Fernandez, Elena

2010-01-01

In this paper, we analyse a simple experiment to study the effects of polarized light. A simple optical system composed of a polarizer, a retarder (cellotape) and an analyser is used to study the effect on the polarization state of the light which impinges on the setup. The optical system is characterized by means of a Jones matrix, and a simple procedure based on Jones vectors is used to obtain an expression for the intensity after the light passes through the optical system. The light intensity is measured by a photodetector and the expression obtained theoretically is experimentally validated. By fitting the experimental intensity data, the value of the retardation introduced by the retarder can also be obtained.

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

International Nuclear Information System (INIS)

Gius, Mark

2013-01-01

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

Estimating Depolarization with the Jones Matrix Quality Factor

Science.gov (United States)

Hilfiker, James N.; Hale, Jeffrey S.; Herzinger, Craig M.; Tiwald, Tom; Hong, Nina; Schöche, Stefan; Arwin, Hans

2017-11-01

Mueller matrix (MM) measurements offer the ability to quantify the depolarization capability of a sample. Depolarization can be estimated using terms such as the depolarization index or the average degree of polarization. However, these calculations require measurement of the complete MM. We propose an alternate depolarization metric, termed the Jones matrix quality factor, QJM, which does not require the complete MM. This metric provides a measure of how close, in a least-squares sense, a Jones matrix can be found to the measured Mueller matrix. We demonstrate and compare the use of QJM to other traditional calculations of depolarization for both isotropic and anisotropic depolarizing samples; including non-uniform coatings, anisotropic crystal substrates, and beetle cuticles that exhibit both depolarization and circular diattenuation.

Iodine-based contrast media, multiple myeloma and monoclonal gammopathies: literature review and ESUR Contrast Media Safety Committee guidelines.

Science.gov (United States)

Stacul, Fulvio; Bertolotto, Michele; Thomsen, Henrik S; Pozzato, Gabriele; Ugolini, Donatella; Bellin, Marie-France; Bongartz, Georg; Clement, Olivier; Heinz-Peer, Gertraud; van der Molen, Aart; Reimer, Peter; Webb, Judith A W

2018-02-01

Many radiologists and clinicians still consider multiple myeloma (MM) and monoclonal gammopathies (MG) a contraindication for using iodine-based contrast media. The ESUR Contrast Media Safety Committee performed a systematic review of the incidence of post-contrast acute kidney injury (PC-AKI) in these patients. A systematic search in Medline and Scopus databases was performed for renal function deterioration studies in patients with MM or MG following administration of iodine-based contrast media. Data collection and analysis were performed according to the PRISMA statement 2009. Eligibility criteria and methods of analysis were specified in advance. Cohort and case-control studies reporting changes in renal function were included. Thirteen studies were selected that reported 824 iodine-based contrast medium administrations in 642 patients with MM or MG, in which 12 unconfounded cases of PC-AKI were found (1.6 %). The majority of patients had intravenous urography with high osmolality ionic contrast media after preparatory dehydration and purgation. MM and MG alone are not risk factors for PC-AKI. However, the risk of PC-AKI may become significant in dehydrated patients with impaired renal function. Hypercalcaemia may increase the risk of kidney damage, and should be corrected before contrast medium administration. Assessment for Bence-Jones proteinuria is not necessary. • Monoclonal gammopathies including multiple myeloma are a large spectrum of disorders. • In monoclonal gammopathy with normal renal function, PC-AKI risk is not increased. • Renal function is often reduced in myeloma, increasing the risk of PC-AKI. • Correction of hypercalcaemia is necessary in myeloma before iodine-based contrast medium administration. • Bence-Jones proteinuria assessment in myeloma is unnecessary before iodine-based contrast medium administration.

Free energy of the Lennard-Jones solid

NARCIS (Netherlands)

Hoef, van der M.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

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.

Evaporation of Lennard-Jones clusters

International Nuclear Information System (INIS)

Roman, C.E.; Garzon, I.L.

1991-01-01

Extensive molecular dynamics simulations have been done to study the evaporation of a 13-atom Lennard-Jones cluster. The survival probability and the evaporative lifetime are calculated as a function of the cluster total energy from a classical trajectory analysis. The results are interpreted in terms of the RRK theory of unimolecular dissociation. The calculation of the binding energy of the evaporated species from the evaporation rate and the average kinetic energy release is discussed. (orig.)

Staging Henry Fielding: The Author-Narrator in Tom Jones On Screen

OpenAIRE

Løfaldli, Eli

2017-01-01

As recent adaptation theory has shown, classic-novel adaptation typically sets issues connected to authorship and literal and figurative ownership into play. This key feature of such adaptations is also central to the screen versions of Henry Fielding’s Tom Jones (1749). In much of Fielding’s fiction, the narrator, typically understood as an embodiment of Fielding himself, is a particularly prominent presence. The author-narrator in Tom Jones is no exception: not only is his presence strongly...

Phase diagram of power law and Lennard-Jones systems: Crystal phases

International Nuclear Information System (INIS)

Travesset, Alex

2014-01-01

An extensive characterization of the low temperature phase diagram of particles interacting with power law or Lennard-Jones potentials is provided from Lattice Dynamical Theory. For power law systems, only two lattice structures are stable for certain values of the exponent (or softness) (A15, body centered cube (bcc)) and two more (face centered cubic (fcc), hexagonal close packed (hcp)) are always stable. Among them, only the fcc and bcc are equilibrium states. For Lennard-Jones systems, the equilibrium states are either hcp or fcc, with a coexistence curve in pressure and temperature that shows reentrant behavior. The hcp solid never coexists with the liquid. In all cases analyzed, for both power law and Lennard-Jones potentials, the fcc crystal has higher entropy than the hcp. The role of anharmonic terms is thoroughly analyzed and a general thermodynamic integration to account for them is proposed

Magnetoelectric Jones birefringence and dichroism in a medium of free atoms

International Nuclear Information System (INIS)

Mironova, P V; Ovsiannikov, V D; Chernushkin, V V

2006-01-01

Theoretical treatment of the magnetoelectric Jones birefringence and dichroism is developed through the bilinearity in static electric and magnetic field dipole-forbidden corrections to the amplitude of Rayleigh scattering. In particular cases of orientation of the static fields relative to the polarization and wave vectors of monochromatic radiation, the amplitude determines corrections to the refractive index of atomic gas responsible for (i) the Jones birefringence and dichroism (ii) linear birefringence and dichroism and (iii) directional anisotropy for the monochromatic wave. The analytical equations and numerical data for the indicated corrections, calculated for alkaline-earth-like atoms, determine optimal conditions for observing the effects in vapours. For resonance on 1 D 2 state essential enhancement is discovered in the frequency dependence for the ratio of refractive index anisotropy of the Jones effect to the square-root product of corresponding anisotropies determining the Kerr and Cotton-Mouton effects

Prevalence of Jones Fracture Repair and Impact on Short-Term NFL Participation.

Science.gov (United States)

Tu, Leigh-Anne; Knapik, Derrick M; Sheehan, Joseph; Salata, Michael J; Voos, James E

2018-01-01

Elite American football athletes are at high risk for Jones fractures. Fixation is recommended to minimize nonunion and allow early return to play. The purpose of this investigation was to evaluate the prevalence of Jones fracture repair in athletes invited to the National Football League (NFL) Combine and the impact of fracture repair on short-term NFL participation compared to athletes with no history of repair. A total of 1311 athletes participating in the Combine from 2012 to 2015 were evaluated. Athletes with history of Jones fracture repair were identified. Athlete demographic information was collected while physical examination findings were recorded. Radiographs were evaluated to determine fixation type and the presence of nonunion. Future participation in the NFL was evaluated based on draft status, games played, and games started in the athlete's first season following the Combine. Fixation was performed for 41 Jones fractures in 40 athletes (3.1%). The highest prevalence was in defensive linemen (n = 10 athletes), with the greatest rate in tight ends (5.1%, n = 4 of 79 athletes). Intramedullary screw fixation was used for all fractures. Incomplete bony union was present in 3 (8%) fractures. Athletes with a history of repair were not at significant risk for going undrafted ( P = .61), playing ( P = .23), or starting ( P = .76) fewer NFL games compared to athletes with no history of repair during athletes' first NFL season. Athletes with a history of Jones fracture repair were not at significant risk of going undrafted or for diminished participation during their first season in the NFL. Level IV, case series.

Early Experience with the StopLoss Jones Tube.

Science.gov (United States)

Bagdonaite, Laura; Pearson, Andrew R

2015-06-01

Extrusion is the most common reason for failure after Jones tube placement. The StopLoss Jones tube (SLJT) is a new innovation in Jones tubes that incorporates a flexible silicone internal flange to resist extrusion. We present our early experience of using this new tube and associated introducer system. We retrospectively analysed the case notes of a single surgeon consecutive series of patients having SLJT placement from November 2011 to November 2013. 29 SLJTs were placed in 25 eyes of 19 patients. Tube follow-up ranged from 1-25 months (mean 10 months) with a total of 291 tube-months. The indications for SLJT placement were: previous LJT complications (52%), failed canalicular-DCR surgery (31%), primary placement for inoperable canalicular occlusion (14%) and patent non-functioning DCR (3%). Tube length ranged from 10-16 mm. The tube introducer system was simple and effective and there were no intra-operative complications. The tube extrusion rate was 0%. Complications occurred in 5 tubes: 1 was too long, and 4 others (14%) developed conjunctival overgrowth/medial tube migration. Patient satisfaction with the tube was: 86% fully satisfied, 10% was moderately satisfied, 3% not satisfied. The overall final surgical success rate at last follow-up was 92%. In this short follow-up initial study the SLJT is simple to use and has a high rate of success and patient satisfaction. The addition of the internal silicone flange appears to prevent the previously common problem of extrusion.

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

Return to Play and Performance After Jones Fracture in National Basketball Association Athletes

Science.gov (United States)

Begly, John P.; Guss, Michael; Ramme, Austin J.; Karia, Raj; Meislin, Robert J.

2015-01-01

Background: Basketball players are at risk for foot injuries, including Jones fractures. It is unknown how this injury affects the future play and performance of athletes. Hypothesis: National Basketball Association (NBA) players who sustain Jones fractures of the base of the fifth metatarsal have high rates of return to play and do not experience a decrease in performance on return to competition when compared with preinjury and with control-matched peers. Study Design: Retrospective cohort study. Level of Evidence: Level 5. Methods: Data on 26 elite basketball players with Jones fractures over 19 NBA seasons (1994-1995 to 2012-2013) were obtained from injury reports, press releases, player profiles, and online public databases. Variables included age, body mass index (BMI), player position, experience, and surgical treatment. Individual season statistics pre- and postinjury were collected. Twenty-six controls were identified by matched player position, age, and performance statistics. Results: The mean age at the time of injury was 24.8 years, mean BMI was 24.7 kg/m2, and the mean experience prior to injury was 4.1 NBA seasons. Return to previous level of competition was achieved by 85% of athletes. There was no change in player efficiency rating (PER) when pre- and postinjury performance was compared. When compared with controls, no decline in PER measured performance was identified. Conclusion: The majority of NBA players sustaining a Jones fracture return to their preinjury level of competition. These elite athletes demonstrate no decrease in performance on their return to play. Clinical Relevance: Jones fractures are well-studied injuries in terms of etiology, diagnosis, and management. However, the effect of these injuries on future performance of athletes is unknown. Using the findings of our study, orthopaedic surgeons may be better prepared to counsel and educate elite athletes who sustain a Jones fracture. PMID:26627111

Return to Play and Performance After Jones Fracture in National Basketball Association Athletes.

Science.gov (United States)

Begly, John P; Guss, Michael; Ramme, Austin J; Karia, Raj; Meislin, Robert J

2016-07-01

Basketball players are at risk for foot injuries, including Jones fractures. It is unknown how this injury affects the future play and performance of athletes. National Basketball Association (NBA) players who sustain Jones fractures of the base of the fifth metatarsal have high rates of return to play and do not experience a decrease in performance on return to competition when compared with preinjury and with control-matched peers. Retrospective cohort study. Level 5. Data on 26 elite basketball players with Jones fractures over 19 NBA seasons (1994-1995 to 2012-2013) were obtained from injury reports, press releases, player profiles, and online public databases. Variables included age, body mass index (BMI), player position, experience, and surgical treatment. Individual season statistics pre- and postinjury were collected. Twenty-six controls were identified by matched player position, age, and performance statistics. The mean age at the time of injury was 24.8 years, mean BMI was 24.7 kg/m(2), and the mean experience prior to injury was 4.1 NBA seasons. Return to previous level of competition was achieved by 85% of athletes. There was no change in player efficiency rating (PER) when pre- and postinjury performance was compared. When compared with controls, no decline in PER measured performance was identified. The majority of NBA players sustaining a Jones fracture return to their preinjury level of competition. These elite athletes demonstrate no decrease in performance on their return to play. Jones fractures are well-studied injuries in terms of etiology, diagnosis, and management. However, the effect of these injuries on future performance of athletes is unknown. Using the findings of our study, orthopaedic surgeons may be better prepared to counsel and educate elite athletes who sustain a Jones fracture. © 2015 The Author(s).

System of multifunctional Jones matrix tomography of phase anisotropy in diagnostics of endometriosis

Science.gov (United States)

Ushenko, V. O.; Koval, G. D.; Ushenko, Yu. O.; Pidkamin, L. Y.; Sidor, M. I.; Vanchuliak, O.; Motrich, A. V.; Gorsky, M. P.; Meglinskiy, I.

2017-09-01

The paper presents the results of Jones-matrix mapping of uterine wall histological sections with second-degree and third-degree endometriosis. The technique of experimental measurement of coordinate distributions of the modulus and phase values of Jones matrix elements is suggested. Within the statistical and cross-correlation approaches the modulus and phase maps of Jones matrix images of optically thin biological layers of polycrystalline films of plasma and cerebrospinal fluid are analyzed. A set of objective parameters (statistical and generalized correlation moments), which are the most sensitive to changes in the phase of anisotropy, associated with the features of polycrystalline structure of uterine wall histological sections with second-degree and third-degree endometriosis are determined.

Thermal decay of Lennard-Jones clusters

International Nuclear Information System (INIS)

Garzon, I.L.; Avalos-Borja, M.

1989-01-01

The decay mechanisms of argon clusters have been studied using molecular dynamics simulations and Lennard-Jones potentials. Heating up processes were applied to Ar 13 up to temperatures in the melting region. In this range of temperatures large fluctuations in the mean kinetic energy of the system are present and a sequential evaporation is observed. The thermal decay of these aggregates occurs in a time scale of nanoseconds. (orig.)

Equilibrium spherically curved two-dimensional Lennard-Jones systems

NARCIS (Netherlands)

Voogd, J.M.; Sloot, P.M.A.; van Dantzig, R.

2005-01-01

To learn about basic aspects of nano-scale spherical molecular shells during their formation, spherically curved two-dimensional N-particle Lennard-Jones systems are simulated, studying curvature evolution paths at zero-temperature. For many N-values (N < 800) equilibrium configu- rations are traced

E-tailing in Australia: A preliminary analysis of David Jones

Directory of Open Access Journals (Sweden)

Jun Xu

2017-06-01

Full Text Available Compared with other countries, especially China, United States, United Kingdom, Japan and Germany, Australiars online retail fall behind in terms of both its sale and percentage contribution to the total retail. This paper analyses David Jones, which is typical of large department store chains, and Australian e-tailing environment as a case study to identify enablers for and obstacle to the advancement of e-tailing in Australia. Based on the analysis, the paper provides David Jones with recommendations on internal improvement, supply chain, customer relationship, and adoption of emerging technologies. Future research will be conducted to investigate if the recommendations are also applicable for other Australian retailers.

Shelley Jones: Helping Ugandan girls stay in school | IDRC ...

International Development Research Centre (IDRC) Digital Library (Canada)

Shelley Jones with her Masters of Education students debating gender issues ... early pregnancies, limited family support, or educational gender discrimination.” ... Girls' Secondary Education in Uganda: Assessing Policy within the Women's ...

Do America's Schools Need a "Dow Jones Index"?

Science.gov (United States)

Guthrie, James W.

1994-01-01

Discusses America's fascination with measuring education. Discusses the advantages and disadvantages of a single composite indicator, akin to the Dow Jones Index, to measure educational productivity. Describes progress in the California State Education Department in developing a composite index to measure student performance. (SR)

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

Pendeteksian Bagian Tubuh Manusia untuk Filter Pornografi dengan Metode Viola-Jones

Directory of Open Access Journals (Sweden)

Benny Senjaya

2012-06-01

Full Text Available Information Technology does help people to get information promptly anytime and anywhere. Unfortunately, the information gathered from the Internet does not always come out positive. Some information can be destructive, such as porn images. To mitigate this problem, the study aims to create a desktop application that could detect parts of human body which can be expanded in the future to become an image filter application for pornography. The detection methodology in this study is Viola-Jones method which provides a complete framework for extracting and recognizing image features. A combination of Viola-Jones method with Haar-like features, integral image, boosting algorithm, and cascade classifier provide a robust detector for the 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.

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

International Nuclear Information System (INIS)

Singh, P.

1996-01-01

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 ω c (k), such that when ω c (k) the phase difference is π/2 and when ω approx-gt ω c (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

Molecular dynamics study of the hydration of Lennard-Jones solutes

International Nuclear Information System (INIS)

Geiger, A.; Rahman, A.; Stillinger, F.H.

1979-01-01

In order to clarify the nature of hydrophobic interactions in water, we have used the molecular dynamics simulation method to study a system comprising two Lennard-Jones solute particles and 214 water molecules. Although the solutes were placed initially in contact, forces in the system drive them slightly apart to permit formation of vertex-sharing solvent ''cages.'' Definite orientational preferences have been observed for water molecules in the first solvation layer around the Lennard-Jones solutes; these preferences are loosely reminiscent of structure in clathrates. Nevertheless, substantial local disorder is obviously present. The dynamical data show that translational and rotational motions of solvation--sheath water molecules are perceptibly slower (by at least 20%) than those in pure bulk water

Occurrence of pathotypes of Ascochyta pinodes (Jones in the Olsztyn district

Directory of Open Access Journals (Sweden)

Helena Furgał-Węgrzycka

2013-12-01

Full Text Available The causal agent of leaf and pods spot-pot of peas and field peas in the Olsztyn district was the fungus Ascochyta pinodes (Jones. Investigated isolates of A. pinoides different by macroscopic and microscopic features. From diseased leaves and pods of peas and field peas saprophytic fungi were also obtained. Among them Alternaria alternata, Cladosporium cladosporioides, Epicoccum purpurascens, Stemphylium botryosum, Sordaria fimicola and mycelia sterilia were dominant. In the study on the identification and distribution of pathotypes of A. pinodes (Jones six pathotypes were identified among which pathotypes 3 dominated. The identified pathotypes differed by macroscopic and microscopic features.

High and Crazy Niggers: Anti-Rationalism in Leroi Jones

Science.gov (United States)

Brown, Lloyd W.

1974-01-01

Suggests that the assumption that the theme of anti-rationalism in Jones is an attack on reason as such and that such a theme rests on an exclusive commitment to the irrational needs to be tested. (Author/AM)

75 FR 20802 - Safety Zone; New York Air Show at Jones Beach State Park, Atlantic Ocean off of Jones Beach...

Science.gov (United States)

2010-04-21

... meeting would be beneficial. If we determine that one would aid this rulemaking, we will hold one at a... to the shows, as well as providing additional time should they run over the scheduled period. The... running east along the shoreline of Jones Beach State Park to approximate position 40[deg]35'49'' N, 073...

Are there Long-Run Diversification Gains from the Dow Jones Islamic Finance Index?

OpenAIRE

Mehmet Balcilar; Charl Jooste; Shawkat Hammoudeh; Rangan Gupta; Vassilios Babalos

2014-01-01

We compare nonlinear cointegration tests with the standard cointegration tests in studying the relationship of the Dow Jones Islamic finance index with three other conventional equity market indices. Our results show that there is a long-run nonlinear cointegrating relationship between the Dow Jones Islamic stock market index and other conventional stock market indices. Our findings rely on a battery of standard tests as well as on the Bierens and Martins (2010) test that investigates time-va...

An index with improved diagnostic accuracy for the diagnosis of Crohn's disease derived from the Lennard-Jones criteria.

Science.gov (United States)

Reinisch, S; Schweiger, K; Pablik, E; Collet-Fenetrier, B; Peyrin-Biroulet, L; Alfaro, I; Panés, J; Moayyedi, P; Reinisch, W

2016-09-01

The Lennard-Jones criteria are considered the gold standard for diagnosing Crohn's disease (CD) and include the items granuloma, macroscopic discontinuity, transmural inflammation, fibrosis, lymphoid aggregates and discontinuous inflammation on histology. The criteria have never been subjected to a formal validation process. To develop a validated and improved diagnostic index based on the items of Lennard-Jones criteria. Included were 328 adult patients with long-standing CD (median disease duration 10 years) from three centres and classified as 'established', 'probable' or 'non-CD' by Lennard-Jones criteria at time of diagnosis. Controls were patients with ulcerative colitis (n = 170). The performance of each of the six diagnostic items of Lennard-Jones criteria was modelled by logistic regression and a new index based on stepwise backward selection and cut-offs was developed. The diagnostic value of the new index was analysed by comparing sensitivity, specificity and accuracy vs. Lennard-Jones criteria. By Lennard-Jones criteria 49% (n = 162) of CD patients would have been diagnosed as 'non-CD' at time of diagnosis (sensitivity/specificity/accuracy, 'established' CD: 0.34/0.99/0.67; 'probable' CD: 0.51/0.95/0.73). A new index was derived from granuloma, fibrosis, transmural inflammation and macroscopic discontinuity, but excluded lymphoid aggregates and discontinuous inflammation on histology. Our index provided improved diagnostic accuracy for 'established' and 'probable' CD (sensitivity/specificity/accuracy, 'established' CD: 0.45/1/0.72; 'probable' CD: 0.8/0.85/0.82), including the subgroup isolated colonic CD ('probable' CD, new index: 0.73/0.85/0.79; Lennard-Jones criteria: 0.43/0.95/0.69). We developed an index based on items of Lennard-Jones criteria providing improved diagnostic accuracy for the differential diagnosis between CD and UC. © 2016 John Wiley & Sons Ltd.

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

International Nuclear Information System (INIS)

Cameron, Maria K.

2014-01-01

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

Phase diagram of a Lennard-Jones solid

International Nuclear Information System (INIS)

Choi, Y.; Ree, T.; Ree, F.H.

1993-01-01

A phase diagram of a Lennard-Jones solid at kT/ε≥0.8 is constructed by our recent perturbation theory. It shows the stability of the face-centered-cubic phase except within a small pressure and temperature domain, where the hexagonal-close packed phase may occur. The theory predicts anharmonic contributions to the Helmholtz free energy (important to the crystal stability) in good agreement with Monte Carlo data

Volatility Transmission between Dow Jones Stock Index and Emerging Bond Index

Directory of Open Access Journals (Sweden)

Amir Saadaoui

2016-04-01

Full Text Available In this paper, we use a bivariate GARCH model to estimate simultaneously of the mean and the conditional variance between the Dow Jones stock index and some emerging bond indices. We used the DCC-GARCH model to graphically demonstrate the peaks of the volatility transmission. We examined this transmission using daily returns between July, 30, 2009 and January, 18, 2011 extracted from Datastream. Our results demonstrate that there is a significant transmission of shocks and volatility between the Dow Jones stock index and bond indices of the emerging countries. The results also confirm the idea that the crisis was transmitted from the United States to the emerging countries due to foreign investment made in these countries.

Scaling of the dynamics of flexible Lennard-Jones chains

DEFF Research Database (Denmark)

Veldhorst, Arno; Dyre, J. C.; Schrøder, Thomas

2014-01-01

functions of excess entropy) which has been observed in simulations of both molecular and polymeric systems. Doing molecular dynamics simulations of flexible Lennard-Jones chains (LJC) with rigid bonds, we here provide the first detailed test of the isomorph theory applied to flexible chain molecules. We...

Highlight: Dr David Butler-Jones on fighting pandemics | IDRC ...

International Development Research Centre (IDRC) Digital Library (Canada)

2016-04-15

Apr 15, 2016 ... In the context of developing countries, Butler-Jones drew attention to the importance of public healthcare teams of doctors and paramedics, data, and accreditation standards in identifying appropriate interventions. There is a need to explore the public-private nexus, traditional medicines, and public health ...

A note on Valeriana jatamansi Jones (Caprifoliaceae s.l.)

NARCIS (Netherlands)

Mabberley, D.J.; Noltie, H.J.

2014-01-01

The tangled arguments around the names of jatamansi drug plants are examined and the correct synonymies and typifications for Nardostachys jatamansi (D.Don) DC. and V. jatamansi Jones (both Caprifoliaceae s.l.) are provided. The conservation status of the former, and the need for further work on the

Marine geophysics. By E.J.W. Jones

Digital Repository Service at National Institute of Oceanography (India)

Rao, D.G.

.Earth-Science Reviews 52 2001 381–384 www.elsevier.comrlocaterearscirev Book reviews Marine Geophysics E.J.W. Jones, University College, London, UK, Wiley, Chichester, West Sussex PO19IUD, England, 1999, 466 pp. As a practicing marine geophysicist working... principles, theory, state-of-the-art instruments, latest techniques in data acquisition, processing and interpretation. The book contains 16 chapters, in which the author has done commendable job in presenting the best examples of case studies in critical...

Simulation of depositions of a Lennard-Jones cluster on a crystalline surface

International Nuclear Information System (INIS)

Saitoh, Kuniyasu; Hayakawa, Hisao

2009-01-01

Depositions of amorphous Lennard-Jones clusters on a crystalline surface are numerically investigated. From the results of the molecular dynamics simulation, we found that the deposited clusters exhibit a transition from multilayered adsorption to monolayered adsorption at a critical incident speed. Employing the energy conservation law, we can explain the behavior of the ratio of the number of atoms adsorbed on the substrate to the cluster size. The boundary shape of the deposited cluster depends strongly on the incident speed, and some unstable modes grow during the spread of the deposited cluster on the substrate. We also discuss the wettability between different Lennard-Jones atoms. (author)

RISM theory distribution functions for Lennard--Jones interaction site fluids

International Nuclear Information System (INIS)

Johnson, E.; Hazoume, R.P.

1978-01-01

Reference interaction site model (RISM) theory distribution functions for Lennard-Jones interaction site fluids are discussed. The comparison with computer simulation results suggests that these distribution functions are as accurate as RISM distribution functions for fused hard sphere molecular fluids

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.

Renal complications in multiple myeloma and related disorders: survivorship care plan of the International Myeloma Foundation Nurse Leadership Board.

Science.gov (United States)

Faiman, Beth M; Mangan, Patricia; Spong, Jacy; Tariman, Joseph D

2011-08-01

Kidney dysfunction is a common clinical feature of symptomatic multiple myeloma. Some degree of renal insufficiency or renal failure is present at diagnosis or will occur during the course of the disease and, if not reversed, will adversely affect overall survival and quality of life. Chronic insults to the kidneys from other illnesses, treatment, or multiple myeloma itself can further damage renal function and increase the risk for additional complications, such as anemia. Patients with multiple myeloma who have light chain (Bence Jones protein) proteinuria may experience renal failure or progress to end-stage renal disease (ESRD) and require dialysis because of light chain cast nephropathy. Kidney failure in patients with presumed multiple myeloma also may result from amyloidosis, light chain deposition disease, or acute tubular necrosis caused by nephrotoxic agents; therefore, identification of patients at risk for kidney damage is essential. The International Myeloma Foundation's Nurse Leadership Board has developed practice recommendations for screening renal function, identifying positive and negative contributing risk and environmental factors, selecting appropriate therapies and supportive care measures to decrease progression to ESRD, and enacting dialysis to reduce and manage renal complications in patients with multiple myeloma.

Highlight: Dr David Butler-Jones on fighting pandemics | CRDI ...

International Development Research Centre (IDRC) Digital Library (Canada)

15 avr. 2016 ... Dr David Butler-Jones, professor in the Faculty of Medicine at the University of Manitoba and former Chief Medical Health Officer of Canada, delivered a lecture on lessons learned from the 2009 flu pandemic in Canada. He also commented on India's draft National Health Policy 2015 at the India ...

Cephalometric effects of the Jones Jig appliance followed by fixed appliances in Class II malocclusion treatment.

Science.gov (United States)

Patel, Mayara Paim; Henriques, José Fernando Castanha; Freitas, Karina Maria Salvatore; Grec, Roberto Henrique da Costa

2014-01-01

The aim of this study was to cephalometrically assess the skeletal and dentoalveolar effects of Class II malocclusion treatment performed with the Jones Jig appliance followed by fixed appliances. The sample comprised 25 patients with Class II malocclusion treated with the Jones Jig appliance followed by fixed appliances, at a mean initial age of 12.90 years old. The mean time of the entire orthodontic treatment was 3.89 years. The distalization phase lasted for 0.85 years, after which the fixed appliance was used for 3.04 years. Cephalograms were used at initial (T1), post-distalization (T2) and final phases of treatment (T3). For intragroup comparison of the three phases evaluated, dependent ANOVA and Tukey tests were used. Jones Jig appliance did not interfere in the maxillary and mandibular component and did not change maxillomandibular relationship. Jones Jig appliance promoted distalization of first molars with anchorage loss, mesialization and significant extrusion of first and second premolars, as well as a significant increase in anterior face height at the end of treatment. The majority of adverse effects that occur during intraoral distalization are subsequently corrected during corrective mechanics. Buccal inclination and protrusion of mandibular incisors were identified. By the end of treatment, correction of overjet and overbite was observed. Jones Jig appliance promoted distalization of first molars with anchorage loss represented by significant mesial movement and extrusion of first and second premolars, in addition to a significant increase in anterior face height.

Shelley Jones — Aider les jeunes Ougandaises à poursuivre leurs ...

International Development Research Centre (IDRC) Digital Library (Canada)

18 nov. 2014 ... ... d'entre elles abandonnent l'école à cause de leur cycle menstruel. ... Shelley Jones with her Masters of Education students debating gender issues ... limité ou à la discrimination sexospécifique en matière d'éducation.

Analytic Debye-Grüneisen equation of state for a generalized Lennard-Jones solids

Institute of Scientific and Technical Information of China (English)

孙久勋; 吴强; 蔡灵仓; 经福谦

2003-01-01

The approximate method to treat the practical quantum anharmonic solids proposed by Hardy,Lacks and Shukla is reformulated with explicit physical meanings.It is shown that the quantum effect is important at low temperature,it can be treated in the harmonic framework; and the anharmonic effect is important at high temperature and tends to zero at low temperature,it can be treated by using a classical approximation.The alternative formulation is easier for various applications,and is applied to a Debye-Gruneisen solid with the generalized Lennard-Jones intermolecular interaction.The expressions for the Debye temperature and Gruneisen parameter as a function of volume are analytically derived.The analytic equation of state is applied to predict the thermodynamic properties of solid xenon at normal-pressure with the nearest-neighbour Lennard-Jones interaction,and is further applied to research the properties of solid xenon and krypton at high pressure by using an all-neighbour Lennard-Jones interaction.The theoretical results are in agreement with the experiments.

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

Directory of Open Access Journals (Sweden)

Daniela Scheinkman Chatelard

2001-12-01

Full Text Available 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 tragédia de Shakespeare.Some considerations about the aphanisis term from E. Jones and J. Lacan. The aim of the article in its first part is to retake and to develop the term aphanisis, such as forged by Ernest Jones. In its second part, the purpose is to add to this term the importance given by Jacques Lacan : from the register of the pure disappearing of desire in its relation to castration, as supported by Jones, we will pass on to the register of the disappearing of the subject, while in the form of a divided and desiring subject. Therefore, we will use the example of the literary character, Hamlet, taken from Shakespeare's tragedy.

The Kauffman bracket and the Jones polynomial in quantum gravity

International Nuclear Information System (INIS)

Griego, J.

1996-01-01

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.)

Binding energy of large icosahedral and cuboctahedral Lennard-Jones clusters

International Nuclear Information System (INIS)

Northby, J.A.; Xie, J.

1989-01-01

It is widely believed that the lowest energy configurations for small rare gas clusters have icosahedral symmetry. This contrasts with the bulk crystal structures which have cuboctahedral fcc symmetry. It is of interest to understand the transition between this finite and bulk behavior. To model this transition in rare gas clusters we have undertaken optimization studies within the Lennard-Jones pair potential model. Using a combination of Monte Carlo and Partan Search optimization methods, the lowest energy relaxed structures of Lennard-Jones clusters having icosahedral and cuboctahedral symmetry were found. Studies were performed for complete shell clusters ranging in size from one shell having 13 atoms to 14 shells having 10,179 atoms. It was found that the icosahedral structures are lower in energy than the cuboctahedral structures for cluster sizes having 13 shells or fewer. Additional studies were performed using the more accurate Aziz-Chen [HFD-C] pair potential parameterized for argon. The conclusions appear to be relatively insensitive to the form of the potential. (orig.)

"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

The impact of modifying the Jones Act on US coastal shipping.

Science.gov (United States)

2014-06-01

The study assesses exempt coastal shipping defined as exempted from the US-built stipulation of the : Jones Act, operating with functional crews and exempted from Harbor Maintenance Tax (HMT). The : study focuses on two research questions: (a) the im...

Density functional study of the pressure tensor for inhomogeneous Lennard—Jones fluids

International Nuclear Information System (INIS)

Sun Zong-Li; Liu Zhi-Cheng; Kang Yan-Shuang; Ma Heng-Xin; Kang Yan-Mei

2012-01-01

Based on classical density functional theory, an expression of the pressure tensor for inhomogeneous fluids is presented. This takes into account greater correlation between particles, especially for systems that are geometrically confined or involve an interface. The density and pressure components of Lennard-Jones fluids confined in hard and softened nano-cavities are calculated. A comparison between the results of this work and IK expression suggests that the agreement depends on temperature. The interfacial tension for hard sphere fluids agrees well with the Monte Carlo result when the bulk density is not too large. The results of the solid-fluid interfacial tension for Lennard—Jones fluids demonstrate that different types of external potentials modulate the interfacial tension in different manners. (condensed matter: structural, mechanical, and thermal properties)

Autonomic Neuropathy and Albuminocytologic Dissociation in Cerebrospinal Fluid As the Presenting Features of Primary Amyloidosis: A Case Report

Directory of Open Access Journals (Sweden)

Jingjing Li

2017-07-01

Full Text Available ObjectivePrimary amyloidosis is a disease with a poor prognosis and multi-organ involvement. Here, we report the clinical and pathological features of a patient with primary amyloidosis featuring autonomic neuropathy as the initial symptom and albuminocytologic dissociation in the cerebrospinal fluid (CSF.MethodsThe patient was a 60-year-old Chinese male with numbness, orthostatic hypotension, and gastrointestinal symptoms. For diagnosis, we performed an electromyogram (EMG, lumbar puncture, Bence Jones protein urine test, serum electrophoresis blood test, sural nerve and rectal membrane biopsies, transthyretin (TTR gene sequencing, and bone marrow puncture.ResultsCongo red staining of sural nerve and rectal membrane biopsies showed amyloid deposition and apple-green birefringence was visualized under polarized light microscopy. TTR gene sequencing showed no causative mutation. Following lumbar puncture, normal CSF cell counts and elevated CSF protein concentration (1,680 mg/L were detected. Bone marrow puncture showed that out of the total number of whole blood cells, 0.56% were abnormal plasma cells and that 87.4% of the total number of plasma cells were abnormal. EMG results showed mixed peripheral nerve damage predominately in the sensory nerve fibers.ConclusionObvious symptoms of neuropathy, particularly autonomic neuropathy, albuminocytologic dissociation, and organ function damage suggested a diagnosis of amyloidosis. In such patients, neurologists should use caution to differentiate between chronic inflammatory demyelinating polyneuropathy, primary amyloidosis, and familial amyloid neuropathy.

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...

C. Rick Jones Is IRPA Keynote Lecturer on Stakeholder Engagement

International Nuclear Information System (INIS)

Strom, Daniel J.

2008-01-01

At the recent IRPA 12 Conference in Buenos Aires, Argentina, C. Rick Jones gave the keynote lecture 'Stakeholder Engagement in Practice - Now Is the Time to Act' This was one of the very best talks at the conference, covering IRPA's draft 'Guiding Principles for Radiation Protection Professionals on Stakeholder Engagement'

The BQP-hardness of approximating the Jones polynomial

International Nuclear Information System (INIS)

Aharonov, Dorit; Arad, Itai

2011-01-01

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

The BQP-hardness of approximating the Jones polynomial

Energy Technology Data Exchange (ETDEWEB)

Aharonov, Dorit; Arad, Itai, E-mail: itaia@cs.huji.ac.il [Department of Computer Science and Engineering, Hebrew University, Jerusalem (Israel)

2011-03-15

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

Revised Jones Criteria For The Diagnosis of Acute Rheumatic Fever (AHA 2015 - An Indian Perspective

Directory of Open Access Journals (Sweden)

KV Sahasranam

2015-07-01

Full Text Available Acute Rheumatic Fever (ARF is still a major problem in some developing and low middle income countries though the incidence and prevalence has remarkably reduced in North America and Europe. Ever since T. Duckett Jones in 1944 proposed the Jones criteria, it was modified and later revised by the American Heart Association (AHA in 1992. This was reconfirmed in and AHA sponsored Work shop in 2002. No modification or change was suggested after the introduction of Doppler Echocardiography (DE for the diagnosis of clinical and "subclinical carditis". When a clinical diagnosis by the clinician fails to show evidence of carditis, DE may pick up cases of "subclinical carditis". Moreover, previous recommendations did not include the Classification of Recommendations (Class I, II a, II b, and III and Levels of Evidence (Levels A, B and C. Recently, however, a scientific statement from the American Heart Association (AHA has published an update to the Jones criteria including the use of DE in the diagnosis of ARF.

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

Staging Henry Fielding: The Author-Narrator in Tom Jones On Screen

Directory of Open Access Journals (Sweden)

Eli Løfaldli

2017-06-01

Full Text Available As recent adaptation theory has shown, classic-novel adaptation typically sets issues connected to authorship and literal and figurative ownership into play. This key feature of such adaptations is also central to the screen versions of Henry Fielding’s Tom Jones (1749. In much of Fielding’s fiction, the narrator, typically understood as an embodiment of Fielding himself, is a particularly prominent presence. The author-narrator in Tom Jones is no exception: not only is his presence strongly felt throughout the novel, but through a variety of means, ‘The History of Tom Jones, A Foundling’ is also distinctly marked as being under his control and ownership. The two adaptations of Fielding’s novel, a 1963 film and a 1997 television series, both retain the figure of the author-narrator, but differ greatly in their handling of this device and its consequent thematic ramifications. Although the 1963 film de-emphasises Henry Fielding’s status as proprietor of the story, the author-narrator as represented in the film’s voiceover commentary is a figure of authority and authorial control. In contrast, the 1997 adaptation emphasises Fielding’s ownership of the narrative and even includes the author-narrator as a character in the series, but this ownership is undermined by the irreverent treatment to which he is consistently subjected. The representations of Henry Fielding in the form of the author-narrator in both adaptations are not only indicative of shifting conceptions of authorship, but also of the important interplay between authorship, ownership and adaptation more generally.

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

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…

Technical considerations for surgical intervention of Jones fractures.

Science.gov (United States)

Mendicino, Robert W; Hentges, Matthew J; Mendicino, Michael R; Catanzariti, Alan R

2013-01-01

Jones fractures are a common injury treated by foot and ankle surgeons. Surgical intervention is recommended because of the high rate of delayed union, nonunion, and repeat fracture, when treated conservatively. Percutaneous intramedullary screw fixation is commonly used in the treatment of these fractures. We present techniques that can increase the surgical efficiency and decrease the complications associated with percutaneous delivery of internal fixation. Copyright © 2013 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

Collision kernels in the eikonal approximation for Lennard-Jones interaction potential

International Nuclear Information System (INIS)

Zielinska, S.

1985-03-01

The velocity changing collisions are conveniently described by collisional kernels. These kernels depend on an interaction potential and there is a necessity for evaluating them for realistic interatomic potentials. Using the collision kernels, we are able to investigate the redistribution of atomic population's caused by the laser light and velocity changing collisions. In this paper we present the method of evaluating the collision kernels in the eikonal approximation. We discuss the influence of the potential parameters Rsub(o)sup(i), epsilonsub(o)sup(i) on kernel width for a given atomic state. It turns out that unlike the collision kernel for the hard sphere model of scattering the Lennard-Jones kernel is not so sensitive to changes of Rsub(o)sup(i) as the previous one. Contrary to the general tendency of approximating collisional kernels by the Gaussian curve, kernels for the Lennard-Jones potential do not exhibit such a behaviour. (author)

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...... of double wells occur as the glass is warmed toward the fluid. This indicates that there might be a fundamental difference between the topologies of the constant-potential-energy hypersurfaces of crystalline and noncrystalline Lennard-Jones matter....

A density functional perturbative approach for simple fluids: the structure of a nonuniform Lennard-Jones fluid at interfaces

International Nuclear Information System (INIS)

Kim, Soon-Chul; Lee, Song Hi

2004-01-01

A density functional perturbation approximation (DFPT), which is based both on the fundamental-measure theory (FMT) to the hard-sphere repulsion and on the weighted-density approximations (WDAs) to the attractive contribution, has been proposed for studying the structural properties of model fluids with an attractive part of the potential. The advantage of the present theory is the simplicity of the calculation of the weight function due to the attractive contribution. It has been applied to predict the equilibrium particle density distributions and adsorption isotherms of Lennard-Jones fluids at interfaces. The theoretical results show that the present theory describes quite well the adsorption isotherms of a Lennard-Jones ethane in a graphite slit pore as well as the equilibrium particle density distributions of a Lennard-Jones fluid near a planar slit pore

Icosahedral binary clusters of glass-forming Lennard-Jones binary alloy

International Nuclear Information System (INIS)

Iwamatsu, Masao

2007-01-01

It is widely believed that the local icosahedral structure is related to the formation of bulk metallic glasses (BMGs). Specifically the existence of 13-atom icosahedral cluster in undercooled liquid is imagined to play a key role to initiate the glass formation as the seed of amorphous structure or to block the nucleation of regular crystal as the impurity. The existence of 13-atom icosahedral clusters in one-component liquids was predicted more than half a century ago by Frank from his total energy calculation for isolated clusters. In BMG alloys, however, the situation is less clear. In this report, we present the lowest-energy structures of 13-atom Lennard-Jones binary cluster calculated from the modified space-fixed genetic algorithm. We study, in particular, the artificial Lennard-Jones potential designed by Kob and Andersen [W. Kob, H.C. Andersen, Phys. Rev. E 51 (1995) 4626] that is known to form BMG. Curiously, the lowest-energy structures of 13-atom cluster are non-icosahedral for almost all compositions. Our result suggests that the existence of the icosahedral cluster is not a necessary condition but only a sufficient condition for glass formation

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.

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

This article deals with the images, metaphors and narratives in the media coverage of doping in the United States. It presents a case study with a focus on Marion Jones, the most celebrated track athlete of the turn of the millennium, and her husband, C.J. Hunter, a shot put world champion...... 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...

PHYTOREMEDIATION OF DREDGED SEDIMENTS: A CASE STUDY AT THE JONES ISLAND CDF

Science.gov (United States)

The Jones Island Confined Disposal Facility (CDF) is a 44 acre in-lake area that receives dredged material from Milwaukee Harbor and the surrounding waterways. Some of those materials are contaminated with industrial waste and urban run-off. The CDF is nearing the end of its desi...

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

International Nuclear Information System (INIS)

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

2016-01-01

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.

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

Energy Technology Data Exchange (ETDEWEB)

Goethe, Martin, E-mail: martingoethe@ub.edu; Rubi, J. Miguel [Departament de Física Fonamental, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona (Spain); Fita, Ignacio [Institut de Biologia Molecular de Barcelona, Baldiri Reixac 10, 08028 Barcelona (Spain)

2016-03-15

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.

An accurate expression for radial distribution function of the Lennard-Jones fluid

International Nuclear Information System (INIS)

Morsali, Ali; Goharshadi, Elaheh K.; Ali Mansoori, G.; Abbaspour, Mohsen

2005-01-01

A simple and accurate expression for radial distribution function (RDF) of the Lennard-Jones fluid is presented. The expression explicitly states the RDF as a continuous function of reduced interparticle distance, temperature, and density. It satisfies the limiting conditions of zero density and infinite distance imposed by statistical thermodynamics. The distance dependence of this expression is expressed by an equation which contains 11 adjustable parameters. These parameters are fitted to 353 RDF data, obtained by molecular dynamics calculations, and then expressed as functions of reduced distance, temperature and density. This expression, having a total of 65 constants, reproduces the RDF data with an average root-mean-squared deviation of 0.0152 for the range of state variables of 0.5= * = * = * =ρσ 3 are reduced temperature and density, respectively). The expression predicts the pressure and the internal energy of the Lennard-Jones fluid with an uncertainty that is comparable to that obtained directly from the molecular dynamics simulations

Fluctuations and thermodynamic response functions in a Lennard-Jones solid

International Nuclear Information System (INIS)

Li, M.; Johnson, W.L.

1992-01-01

Thermodynamic response functions of a nearest-neighbor Lennard-Jones solid--heat capacity, thermal-expansion coefficient, compressibility, and elastic constants--are calculated directly from fluctuations using molecular-dynamics simulations. The algorithm used is the earlier Parrinello-Rahman molecular dynamics modified to take into account symmetry and rotation invariance of the system under investigation. The convergence is very fast and results are in good agreement with existing Monte Carlo and molecular-dynamics results

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...

Flexible equation of state for a hard sphere and Lennard–Jones fluid ...

Indian Academy of Sciences (India)

Equation of state; Lennard–Jones potential; hard-sphere potential; liquid mixture; computer simulation. ... deviation than Barker–Henderson BH2 for LJ fluids, and results are much closer to molecular dynamics (MD) simulations than expectations and reproduce the existing simulation data and present EoS for LJ potential, ...

Mutability and Deformity: Models of the Body and the Art of Edward Burne-Jones

Directory of Open Access Journals (Sweden)

Caroline Arscott

2008-10-01

Full Text Available This essay discusses the alternatives that emerged in the Victorian period to a perfect and regular neoclassical conception of the heroic male body. It charts the evolving fascination with mutable forms, whether heroic or monstrous, imagined first of all in the 1850s in terms of a body conceived of as bolted together or modified by the fusion of organic and inorganic substances. The early work of Burne-Jones is discussed in relation to investigations of cell structure and mechanical inventions in the Great Exhibition of 1851 such as the 'Expanding Model of a Man' invented by Count Dunin. Arscott also discusses the cybernetic implications of Burne-Jones's gouache, 'The Merciful Knight' (1863. Later works of Burne-Jones, in particular 'Perseus and the Graiae' (1878 and the reworked composition 'Love Among the Ruins' (1894, are discussed in terms of a turn towards a sense of the spread and mutation of organic being through and beyond the self. Arscott considers this alongside contemporary investigations of the role of bacilli in disease, looking at leprosy and the heroisation of the Leper Priest of Molokai, Father Damien in the 1880s and 1890s. In the late-Victorian period, Arscott concludes, monstrous distortion was imagined as the unpredictable and unruly proliferation of the organic by the organism in both its vital and morbid states.

Phase Diagram of Kob-Andersen-Type Binary Lennard-Jones Mixtures

Science.gov (United States)

Pedersen, Ulf R.; Schrøder, Thomas B.; Dyre, Jeppe C.

2018-04-01

The binary Kob-Andersen (KA) Lennard-Jones mixture is the standard model for computational studies of viscous liquids and the glass transition. For very long simulations, the viscous KA system crystallizes, however, by phase separating into a pure A particle phase forming a fcc crystal. We present the thermodynamic phase diagram for KA-type mixtures consisting of up to 50% small (B ) particles showing, in particular, that the melting temperature of the standard KA system at liquid density 1.2 is 1.028(3) in A particle Lennard-Jones units. At large B particle concentrations, the system crystallizes into the CsCl crystal structure. The eutectic corresponding to the fcc and CsCl structures is cutoff in a narrow interval of B particle concentrations around 26% at which the bipyramidal orthorhombic PuBr3 structure is the thermodynamically stable phase. The melting temperature's variation with B particle concentration at two constant pressures, as well as at the constant density 1.2, is estimated from simulations at pressure 10.19 using isomorph theory. Our data demonstrate approximate identity between the melting temperature and the onset temperature below which viscous dynamics appears. Finally, the nature of the solid-liquid interface is briefly discussed.

Does the Watson-Jones or Modified Smith-Petersen Approach Provide Superior Exposure for Femoral Neck Fracture Fixation?

Science.gov (United States)

Lichstein, Paul M; Kleimeyer, John P; Githens, Michael; Vorhies, John S; Gardner, Michael J; Bellino, Michael; Bishop, Julius

2018-04-24

A well-reduced femoral neck fracture is more likely to heal than a poorly reduced one, and increasing the quality of the surgical exposure makes it easier to achieve anatomic fracture reduction. Two open approaches are in common use for femoral neck fractures, the modified Smith-Petersen and Watson-Jones; however, to our knowledge, the quality of exposure of the femoral neck exposure provided by each approach has not been investigated. (1) What is the respective area of exposed femoral neck afforded by the Watson-Jones and modified Smith-Petersen approaches? (2) Is there a difference in the ability to visualize and/or palpate important anatomic landmarks provided by the Watson-Jones and modified Smith-Petersen approaches? Ten fresh-frozen human pelvi underwent both modified Smith-Petersen (utilizing the caudal extent of the standard Smith-Petersen interval distal to the anterosuperior iliac spine and parallel to the palpable interval between the tensor fascia lata and the sartorius) and Watson-Jones approaches. Dissections were performed by three fellowship-trained orthopaedic traumatologists with extensive experience in both approaches. Exposure (in cm) was quantified with calibrated digital photographs and specialized software. Modified Smith-Petersen approaches were analyzed before and after rectus femoris tenotomy. The ability to visualize and palpate seven clinically relevant anatomic structures (the labrum, femoral head, subcapital femoral neck, basicervical femoral neck, greater trochanter, lesser trochanter, and medial femoral neck) was also recorded. The quantified area of the exposed proximal femur was utilized to compare which approach afforded the largest field of view of the femoral neck and articular surface for assessment of femoral neck fracture and associated femoral head injury. The ability to visualize and palpate surrounding structures was assessed so that we could better understand which approach afforded the ability to assess structures that

Measurement of the Jones matrix of liquid crystal displays using a common path interferometer

International Nuclear Information System (INIS)

Sarkadi, Tamás; Koppa, Pál

2011-01-01

We propose a robust interferometric method to measure the Jones matrix of polarization components, especially liquid crystal displays. Phase values are measured by a simple common path interferometer containing a birefringent crystal as beam splitter and a polarizer as beam combiner. This solution eliminates the sensitivity of traditional interferometric techniques to vibration, temperature variation or wavefront distortion. The proposed phase measurement method is applicable to the measurement of both spatially homogeneous and binary modulated states, thus the modulation transfer function and inter-pixel interference can also be studied. We demonstrate this technique by the measurement of a liquid crystal on silicon display. The resulting Jones matrix, as a function of displayed gray level, can be efficiently embedded in any numeric model of an optical system containing the analyzed spatial light modulator

Performance improvement of multi-class detection using greedy algorithm for Viola-Jones cascade selection

Science.gov (United States)

Tereshin, Alexander A.; Usilin, Sergey A.; Arlazarov, Vladimir V.

2018-04-01

This paper aims to study the problem of multi-class object detection in video stream with Viola-Jones cascades. An adaptive algorithm for selecting Viola-Jones cascade based on greedy choice strategy in solution of the N-armed bandit problem is proposed. The efficiency of the algorithm on the problem of detection and recognition of the bank card logos in the video stream is shown. The proposed algorithm can be effectively used in documents localization and identification, recognition of road scene elements, localization and tracking of the lengthy objects , and for solving other problems of rigid object detection in a heterogeneous data flows. The computational efficiency of the algorithm makes it possible to use it both on personal computers and on mobile devices based on processors with low power consumption.

Ab initio study of the atomic motion in liquid metal surfaces: comparison with Lennard-Jones systems

International Nuclear Information System (INIS)

Gonzalez, Luis E; Gonzalez, David J

2006-01-01

It is established that liquid metals exhibit surface layering at the liquid-vapour interface, while dielectric simple systems, like those interacting through Lennard-Jones potentials, show a monotonic decay from the liquid density to that of the vapour. First principles molecular dynamics simulations of the free liquid surface of several liquid metals (Li, Na, K, Rb, Cs, Mg, Ba, Al, Tl and Si), and the Na 3 K 7 alloy near their triple points have been performed in order to study the atomic motion at the interface, mainly at the outer layer. Comparison with the results of classical molecular dynamics simulations of a Lennard-Jones system shows interesting differences and similarities. The probability distribution function of the time of residence in a layer shows a peak at very short times and a long-lasting tail. The mean residence time in a layer increases when approaching the interfacial region, slightly in the Lennard-Jones system but strongly in the metallic systems. The motion within the layers, parallel to the interface, can be described as diffusion enhanced (strongly in the case of the outermost layer) with respect to the bulk, for both types of systems, despite its reduced dimensionality in metals

Solitary bone plasmacytoma: outcome and prognostic factors following radiotherapy

International Nuclear Information System (INIS)

Liebross, Robert H.; Ha, Chul S.; Cox, James D.; Weber, Donna; Delasalle, Kay; Alexanian, Raymond

1998-01-01

Purpose: To clarify the natural history of solitary plasmacytoma of bone (SBP) after radiation treatment. Methods and Materials: Between 1965-1996, we identified 57 previously untreated patients with a SBP. A serum myeloma protein was present in 33 patients (58%) and Bence Jones proteinuria was present in an additional eight patients (14%). The median radiotherapy dose was 50 Gy (range, 30-70 Gy). Overall survival, cause-specific survival, and freedom from progression to multiple myeloma were calculated actuarially. Results: Local control was achieved in 55 of 57 patients (96%). For those 29 patients (51%) who subsequently developed multiple myeloma, the median time to progression was 1.8 years. There was a direct correlation between persistence of abnormal protein following radiotherapy and the likelihood of developing multiple myeloma. Among 11 patients with disappearance of myeloma protein, only two developed multiple myeloma after 4 and 12 years, in contrast to progression in 57% of patients with a persistent protein peak and 63% of those with nonsecretory disease (p = 0.02). Among 23 patients with thoracolumbar spine disease, 7 of 8 patients staged with plain radiographs alone developed multiple myeloma in comparison with 1 of 7 patients who also had magnetic resonance imaging (MRI) (p = 0.08). For all patients, the median survival from radiotherapy was 11.0 years. The median cause-specific survival of patients with disappearance of myeloma protein was significantly longer than that of the remaining patients (p = 0.004). Conclusion: Results supported the importance of precise staging that includes MRI of the spine for optimum patient selection and the application of definitive radiotherapy. Those patients with myeloma protein that disappears following radiotherapy represent a category with a high likelihood of cure

Vere-Jones' self-similar branching model

International Nuclear Information System (INIS)

Saichev, A.; Sornette, D.

2005-01-01

Motivated by its potential application to earthquake statistics as well as for its intrinsic interest in the theory of branching processes, we study the exactly self-similar branching process introduced recently by Vere-Jones. This model extends the ETAS class of conditional self-excited branching point-processes of triggered seismicity by removing the problematic need for a minimum (as well as maximum) earthquake size. To make the theory convergent without the need for the usual ultraviolet and infrared cutoffs, the distribution of magnitudes m ' of daughters of first-generation of a mother of magnitude m has two branches m ' ' >m with exponent β+d, where β and d are two positive parameters. We investigate the condition and nature of the subcritical, critical, and supercritical regime in this and in an extended version interpolating smoothly between several models. We predict that the distribution of magnitudes of events triggered by a mother of magnitude m over all generations has also two branches m ' ' >m with exponent β+h, with h=d√(1-s), where s is the fraction of triggered events. This corresponds to a renormalization of the exponent d into h by the hierarchy of successive generations of triggered events. For a significant part of the parameter space, the distribution of magnitudes over a full catalog summed over an average steady flow of spontaneous sources (immigrants) reproduces the distribution of the spontaneous sources with a single branch and is blind to the exponents β,d of the distribution of triggered events. Since the distribution of earthquake magnitudes is usually obtained with catalogs including many sequences, we conclude that the two branches of the distribution of aftershocks are not directly observable and the model is compatible with real seismic catalogs. In summary, the exactly self-similar Vere-Jones model provides an attractive new approach to model triggered seismicity, which alleviates delicate questions on the role of

RASW : a Run-time Adaptive Sliding Window to Improve Viola-Jones object detection.

NARCIS (Netherlands)

Comaschi, F.; Stuijk, S.; Basten, T.; Corporaal, H.

2013-01-01

Abstract—In recent years accurate algorithms for detecting objects in images have been developed. Among these algorithms, the object detection scheme proposed by Viola and Jones gained great popularity, especially after the release of high-quality face classifiers by the OpenCV group. However, as

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

Radiation damage in an amorphous Lennard-Jones solid

International Nuclear Information System (INIS)

Chaki, T.K.; Li, J.C.M.

1985-01-01

A molecular-dynamics simulation of radiation damage in an amorphous Lennard-Jones solid has been undertaken. A three-dimensional structure of 685 atoms with periodic boundary conditions was used. An atom was injected inward from the middle of one surface, and as it lost its energy its velocity and position were recorded. The temperature profile around the injection direction was also calculated. The amorphous structure was examined before and after irradiation by calculating the volume distribution of the Voronoi polyhedra and its time evolution. The production of vacancies and interstitials was observed. The interstitials were found to disappear rapidly, and the vacancies slowly. (author)

Transport coefficients of dense fluids composed of globular molecules. Equilibrium molecular dynamics investigations using more-center Lennard-Jones potentials

Science.gov (United States)

Hoheisel, C.

1988-09-01

Equilibrium molecular dynamics calculations with constraints have been performed for model liquids SF6 and CF4. The computations were carried out with four- and six-center Lennard-Jones potentials and up to 2×105 integration steps. Shear, bulk viscosity and the thermal conductivity have been calculated with use of Green-Kubo relations in the formulation of ``molecule variables.'' Various thermodynamic states were investigated. For SF6, a detailed comparison with experimental data was possible. For CF4, the MD results could only be compared with experiment for one liquid state. For the latter liquid, a complementary comparison was performed using MD results obtained with a one-center Lennard-Jones potential. A limited test of the particle number dependence of the results is presented. Partial and total correlations functions are shown and discussed with respect to findings obtained for the one-center Lennard-Jones liquid.

Application of the RISM theory to Lennard-Jones interaction site molecular fluids

International Nuclear Information System (INIS)

Johnson, E.; Hazoume, R.P.

1979-01-01

It seems that reference interaction site model (RISM) theory atom--atom distribution functions have been obtained directly from the RISM equations only for fused hard sphere molecular fluids. RISM distribution functions for Lennard-Jones interaction site fluids are presented. Results presented suggest that these distribution functions are as accurate as RISM distribution functions for fused hard sphere molecular fluids

Vapour-liquid equilibrium properties for two- and three-dimensional Lennard-Jones fluids from equations of state

International Nuclear Information System (INIS)

Mulero, A.; Cuadros, F; Faundez, C.A.

1999-01-01

Vapour-liquid equilibrium properties for both three- and two-dimensional Lennard-Jones fluids were obtained using simple cubic-in-density equations of state proposed by the authors. Results were compared with those obtained by other workers from computer simulations and also with results given by other more complex semi-theoretical or semi-empirical equations of state. In the three-dimensional case good agreement is found for all properties and all temperatures. In the two-dimensional case only the coexistence densities were compared, producing good agreement for low temperatures only. The present work is the first to give numerical data for the vapour-liquid equilibrium properties of Lennard-Jones fluids calculated from equations of state. Copyright (1999) CSIRO Australia

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.

Machine News and Volatility: The Dow Jones Industrial Average and the TRNA Sentiment Series

NARCIS (Netherlands)

D.E. Allen (David); A.K. Singh (Abhay)

2014-01-01

markdownabstract__Abstract__ This paper features an analysis of the relationship between the volatility of the Dow Jones Industrial Average (DJIA) Index and a sentiment news series using daily data obtained from the Thomson Reuters News Analytics (TRNA) provided by SIRCA (The Securities Industry

Self-diffusion coefficients of the metastable Lennard-Jones vapor

International Nuclear Information System (INIS)

Nie Chu; Zhou Youhua; Marlow, W H; Hassan, Y A

2008-01-01

Self-diffusion coefficients of a metastable Lennard-Jones vapor were obtained using the memory function formalism and the frequency moments of the velocity autocorrelation function at reduced temperatures from 0.75 to 1.0. The radial density distribution functions used to evaluate the second, fourth and sixth frequency moments of the velocity autocorrelation function were obtained from the restricted canonical ensemble Monte Carlo simulation (Corti and Debenedetti 1994 Chem. Eng. Sci. 49 2717). The self-diffusion coefficients at reduced temperature 0.75 do not vary monotonically as the density increases, and for the other three temperatures the self-diffusion coefficients vary normally

Melting of 2D monatomic solids: Lennard-Jones system

International Nuclear Information System (INIS)

Yi, Y.M.; Guo, Z.C.

1987-09-01

The Lennard-Jones interaction has been introduced into the Collins mix lattice of 2D liquids. By means of rigorous calculation of the total potential and the free area, the Gibbs functions for 2D liquid and solid have been derived. The melting line obtained from the phase transition equation agrees quite well with the result of recent computer simulation experiments. The obtained reduced temperature of the triple point T* t =0.438 agrees with the data measured in experiments of some inert gas monolayers adsorbed on graphite as well as in computer simulation experiments. (author). 11 refs, 7 figs, 3 tabs

Self-diffusion coefficients of the metastable Lennard-Jones vapor

Energy Technology Data Exchange (ETDEWEB)

Nie Chu; Zhou Youhua [School of Physics and Information Engineering, Jianghan University, Wuhan 430056 (China); Marlow, W H; Hassan, Y A [Department of Nuclear Engineering, Texas A and M University, College Station, TX 77843 (United States)], E-mail: yhzhou@jhun.edu.cn

2008-10-15

Self-diffusion coefficients of a metastable Lennard-Jones vapor were obtained using the memory function formalism and the frequency moments of the velocity autocorrelation function at reduced temperatures from 0.75 to 1.0. The radial density distribution functions used to evaluate the second, fourth and sixth frequency moments of the velocity autocorrelation function were obtained from the restricted canonical ensemble Monte Carlo simulation (Corti and Debenedetti 1994 Chem. Eng. Sci. 49 2717). The self-diffusion coefficients at reduced temperature 0.75 do not vary monotonically as the density increases, and for the other three temperatures the self-diffusion coefficients vary normally.

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.

Numerical simulation of pool boiling of a Lennard-Jones liquid

KAUST Repository

Inaoka, Hajime; Ito, Nobuyasu

2013-01-01

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.

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.

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...

Threshold and Lennard-Jones resonances and elastic lifetimes in the scattering of atoms from crystalline surfaces

International Nuclear Information System (INIS)

Garcia, N.

1978-01-01

The GR method for solving the scattering equations of atoms from a hard corrugated surface is applied on accelerated particles above a hard corrugated surface and a hard corrugated surface with an attractive well. The solutions are given for the Rayleigh hypothesis that under the range of corrugation presented in this paper leads to the exact ones. Threshold resonances are studied observing that the appearance and disappearance of beams must be for a general theory with vertical tangent. The structure of the Lennard-Jones resonances given for the model mentioned above. For the first time it is stressed that Lennard-Jones resonances are not observed in metal surfaces in general, and, accordingly, they are unobserved in compact metallic surfaces. This is correlated with the fact that diffraction has not been observed. Both facts are due to the very weak corrugation of the gas-metal interaction potential. According to our results, the Lennard-Jones resonances in metals present greater difficulties to be observed experimentally. It is also noted that the absence of diffraction in compact metal surfaces is because they are almost plane and not because of the Debye-Waller effect. Finally, the lifetimes of the atoms at the crystal surfaces are calculated. These are larger, the smaller the incident energy and the larger the corrugation. But the lifetimes are particularly large at resonance conditions (10 -11 s). (Auth.)

Robin Huws Jones (United Kingdom, President 1976- 1980

Directory of Open Access Journals (Sweden)

2008-07-01

Full Text Available Robin Huws Jones, President of the International Association of Schools of Social Work from 1976 to 1980, lived a life of challenge and change. Born in Wales in 1909, he often remarked that learning to speak Welsh at age two was such a challenge that he didn’t bother to learn English until he was six. The death of his mother when he was three led to the first of many changes in a life that was not easy in the formative years. Robin remained in the care of his father while his sister became the ward of two aunts. With his father, a draper’sassistant, he left Wales to live in a crowded boarding house in Liverpool.

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

Serum protein changes in immune and nonimmune pigeons infected with various strains of Trichomonas gallinae

Science.gov (United States)

Kocan, R.M.; Herman, C.M.

1970-01-01

Serum protein changes were studied in immune and nonimmune pigeons infected with three different strains of Trichomonas gallinae. Strain I (nonvirulent) produced no change in the relative concentration of serum components. Strains II (oral canker) and III (Jones' Barn) produced decreases in albumin and alpha globulins, and increases in beta and gamma globulins between the 7th and 20th days post infection. Birds infected with strain II began to return to normal by the 20th day, while all those infected with strain III were dead between 10 and 14 days post infection. Two serum protein patterns resulted from infection of immune birds with the Jones' Barn strain. One showed no change in relative protein concentrations and no tissue invasion by the parasite while the other was similar to that seen in nonimmune birds infected with a strain producing oral canker. These also showed evidence of tissue invasion by the parasite. It was concluded that tissue invasion was necessary to evoke a quantitative change in serum protein concentrations.

Avaliação radiográfica dos efeitos do aparelho Jones Jig nas distalizações intra-bucais: um estudo piloto Radiographic evaluation of the effects of Jones Jig appliance in intrabuccal distalizations: a pilot study

Directory of Open Access Journals (Sweden)

Juliana Maria Monteiro de Oliveira

2004-10-01

Full Text Available Na Classe II dentária, aparelhos extra ou intra-bucais são utilizados na distalização dos molares superiores, sendo que o dispositivo extra-bucal, apesar de ser eficiente, apresenta uma série de inconvenientes, destacando-se entre eles, a necessidade de cooperação do paciente. Em virtude da total dependência da colaboração e aceitação do paciente, aparelhos alternativos intra-bucais foram sendo criados, promovendo assim, um maior controle do tratamento por parte do profissional. Dentre esses aparelhos, destaca-se o Jones Jig. Foram selecionados para a pesquisa seis pacientes, com idades compreendidas entre 12 a 18 anos, que apresentavam um padrão esquelético de Classe I ou Classe II suave, vertical normal e má oclusão de Classe II dentária. Esses pacientes utilizaram o Jones Jig numa primeira fase do tratamento ortodôntico. Radiografias laterais cefalométricas foram obtidas antes e após o tratamento com o Jones Jig e a partir delas, traçados cefalométricos foram feitos para obter medidas de tecidos moles, esqueléticas e dentárias. Os resultados encontrados foram determinados, comparando-se as medidas do pré e do pós-tratamento. A fim de avaliar a significância estatística desses resultados, utilizou-se o teste de Wilcoxon. A ocorrência de uma inclinação distal dos primeiros e segundos molares superiores foi a única alteração estatisticamente significante encontrada.In dental Class II relationship, extra or intrabuccal appliances are used during the upper molars distalization. The extrabuccal appliance, although to be efficient, present many inconveniences, such as the patient compliance. For these reasons, alternative intrabuccal appliances were created in order to get more control during the treatment of no compliances patients. One of these appliances is the Jones Jig. Six patients, as standard as possible, were selected for this research, with the age ranged from 12 to 18 years old. These patients shown a

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

2003-01-01

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...

Cell-model prediction of the melting of a Lennard-Jones solid

International Nuclear Information System (INIS)

Holian, B.L.

1980-01-01

The classical free energy of the Lennard-Jones 6-12 solid is computed from a single-particle anharmonic cell model with a correction to the entropy given by the classical correlational entropy of quasiharmonic lattice dynamics. The free energy of the fluid is obtained from the Hansen-Ree analytic fit to Monte Carlo equation-of-state calculations. The resulting predictions of the solid-fluid coexistence curves by this corrected cell model of the solid are in excellent agreement with the computer experiments

Molecular dynamics studies of the dynamics of supercooled Lennard-Jones liquids

International Nuclear Information System (INIS)

De Leeuw, S.W.; Brakkee, M.J.D.

1990-01-01

Results are presented of molecular dynamics experiments, in which the Lennard-Jones liquid is cooled isobarically into the metastable temperature region below the freezing temperature. The variation of the density-density and transverse current correlation functions with temperature is studied. We observed a power-law behaviour for the temperature dependence of dynamical properties (viscosity and coefficienty of self-diffusion) with an exponent in good agreement with prediction of mode coupling theories and recent experimental results. (author). 23 refs, 5 figs

Viscous Growth in Spinodal Decomposition of the Two-component Lennard-Jones Model in Two Dimensions

DEFF Research Database (Denmark)

Laradji, M.; Toxvaerd, S.; Mouritsen, Ole G.

1997-01-01

The dynamics of phase separation of a two-component Lennard-Jones model in three dimensions is investigated by means of large scale molecular dynamics simulation. A systematic study over a wide range of quench temperatures within the coexistence region shows that the binary system reaches...

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

OpenAIRE

P. Smetacek

2012-01-01

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 Sa...

Glass transitions in one-, two-, three-, and four-dimensional binary Lennard-Jones systems

Energy Technology Data Exchange (ETDEWEB)

Bruening, Ralf; St-Onge, Denis A; Patterson, Steve [Physics Department, Mount Allison University, Sackville, NB, E4L 1E6 (Canada); Kob, Walter [Laboratoire des Colloides, Verres et Nanomateriaux, UMR5587, Universite Montpellier II and CNRS, 34095 Montpellier Cedex (France)], E-mail: rbruening@mta.ca

2009-01-21

We investigate the calorimetric liquid-glass transition by performing simulations of a binary Lennard-Jones mixture in one through four dimensions. Starting at a high temperature, the systems are cooled to T = 0 and heated back to the ergodic liquid state at constant rates. Glass transitions are observed in two, three and four dimensions as a hysteresis between the cooling and heating curves. This hysteresis appears in the energy and pressure diagrams, and the scanning rate dependence of the area and height of the hysteresis can be described using power laws. The one-dimensional system does not experience a glass transition but its specific heat curve resembles the shape of the D{>=}2 results in the supercooled liquid regime above the glass transition. As D increases, the radial distribution functions reflect reduced geometric constraints. Nearest neighbor distances become smaller with increasing D due to interactions between nearest and next-nearest neighbors. Simulation data for the glasses are compared with crystal and melting data obtained with a Lennard-Jones system with only one type of particle and we find that with increasing D crystallization becomes increasingly more difficult.

Crystal phases of a glass-forming Lennard-Jones mixture

International Nuclear Information System (INIS)

Fernandez, Julian R.; Harrowell, Peter

2003-01-01

We compare the potential energy at zero temperature of a range of crystal structures for a glass-forming binary mixture of Lennard-Jones particles. The lowest-energy ordered state consists of coexisting phases of a single component face centered cubic structure and an equimolar cesium chloride structure. An infinite number of layered crystal structures are identified with energies close to this ground state. We demonstrate that the finite size increase of the energy of the coexisting crystal with incoherent interfaces is sufficient to destabilize this ordered phase in simulations of typical size. Two specific local coordination structures are identified as of possible structural significance in the amorphous state. We observe rapid crystal growth in the equimolar mixture

Lennard–Jones interactions between nano-rod like particles at an arbitrary orientation and an infinite flat solid surface

International Nuclear Information System (INIS)

Hamady, Saleem; Hijazi, Abbas; Atwi, Ali

2013-01-01

An analytical expression for the Lennard–Jones interaction between nano-rods and an infinite flat solid surface is presented. Starting from the elementary Lennard–Jones interaction between two particles, and taking the shape of the nano-rod to be a filled cylinder of radius r and length L, the obtained expression was valid for arbitrary orientation of the nano-rod at variable elevation from the surface. By differentiating the potential with respect to the orientation and elevation we were able to extract the torque and force, respectively, exerted on the nano-rods when approaching a flat surface. The derivation is subjected to the assumption of additivity and approximated for some limiting case

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…

Disordering scaling and generalized nearest-neighbor approach in the thermodynamics of Lennard-Jones systems

International Nuclear Information System (INIS)

Vorob'ev, V.S.

2003-01-01

We suggest a concept of multiple disordering scaling of the crystalline state. Such a scaling procedure applied to a crystal leads to the liquid and (in low density limit) gas states. This approach provides an explanation to a high value of configuration (common) entropy of liquefied noble gases, which can be deduced from experimental data. We use the generalized nearest-neighbor approach to calculate free energy and pressure of the Lennard-Jones systems after performing this scaling procedure. These thermodynamic functions depend on one parameter characterizing the disordering only. Condensed states of the system (liquid and solid) correspond to small values of this parameter. When this parameter tends to unity, we get an asymptotically exact equation of state for a gas involving the second virial coefficient. A reasonable choice of the values for the disordering parameter (ranging between zero and unity) allows us to find the lines of coexistence between different phase states in the Lennard-Jones systems, which are in a good agreement with the available experimental data

Melting in Two-Dimensional Lennard-Jones Systems: Observation of a Metastable Hexatic Phase

International Nuclear Information System (INIS)

Chen, K.; Kaplan, T.; Mostoller, M.

1995-01-01

Large scale molecular dynamics simulations of two-dimensional melting have been carried out using a recently revised Parrinello-Rahman scheme on massively parallel supercomputers. A metastable state is observed between the solid and liquid phases in Lennard-Jones systems of 36 864 and 102 400 atoms. This intermediate state shows the characteristics of the hexatic phase predicted by the theory of Kosterlitz, Thouless, Halperin, Nelson, and Young

Third-order WKBJ eigenvalues for Lennard-Jones and Varshni V potentials

International Nuclear Information System (INIS)

Kesarwani, R.N.; Varshni, Y.P.

1978-01-01

The WKBJ method is applied to the third order for obtaining the eigenvalues for the fifth potential of Varshni, and the relevant integrals are analytically evaluated. Numerical results are obtained for the Lennard-Jones Potential, which is a special case of the Varshni V potential, and are compared to the results of Harrison and Bernstein obtained by a numerical integration of the wave equation. Error estimates are made. It is shown that for diatomic potentials, the Langer correction is not needed if the WKBJ approximation is carried to second and higher orders. (author)

75 FR 43563 - Dow Jones & Company, Sharon Pennsylvania Print Plant a Subsidiary of News Corporation, West...

Science.gov (United States)

2010-07-26

..., Sharon Pennsylvania Print Plant a Subsidiary of News Corporation, West Middlesex, Pennsylvania; Notice of..., Sharon Pennsylvania Print Plant, a subsidiary of News Corporation, West Middlesex, Pennsylvania, was... between Dow Jones & Company, West Middlesex, Pennsylvania, and any Konica facility. The petitioner did not...

Glass of monatomic Lennard-Jones system at nanoscale

International Nuclear Information System (INIS)

Vo Van Hoang

2010-01-01

Structure and stability of glass of monatomic Lennard-Jones (LJ) system at nanoscale compared with those of the bulk counterparts have been studied using the classical molecular dynamics (MD) method. Models have been obtained by cooling from the melts. Structure of the systems was analyzed via radial distribution function (RDF), interatomic distances, the Honeycutt-Andersen analysis and coordination number distributions. Surface and core structures of LJ nanoparticles have been analyzed in details. Density dependence and cooling rate effects on structure of the systems have been found and discussed. In addition, size dependence of structure and properties of nanoparticles has been analyzed in detail. Indeed, we found glass formation in monatomic LJ systems; however, their stability is not high. Evolution of structure and thermodynamics of the systems upon cooling from the melts was found. We also discussed annealing-induced crystallization of LJ glass.

Lake Holocene Use of Wetland Habitats in Central California: A Reply to Jones

OpenAIRE

Hildebrandt, William R

1997-01-01

In this volume, Terry Jones (1997) provided a thorough critique of my summary (also in this volume [Hildebrandt 1977a]) of prehistoric hunter- gatherer adaptations in the southern Santa Clara Valley, California (also see Hildebrandt and Mikkelsen 1993). His review identified a variety of issues that warrant additional consideration, particularly those pertaining to settlement chronology, paleoenvironmental change, and Late Holocene subsistence intensification. I appreciate his comments, as my...

77 FR 59899 - Proposed Information Collection; Comment Request; Coastal Zone Management Act Walter B. Jones and...

Science.gov (United States)

2012-10-01

... Collection; Comment Request; Coastal Zone Management Act Walter B. Jones and NOAA Excellence Awards AGENCY... approved information collection. The 1990 reauthorization of the Coastal Zone Management Act (CZMA) authorized an awards program to ``implement a program to promote excellence in coastal zone management by...

Stability of relaxed Lennard-Jones models made of 500 to 6000 atoms

International Nuclear Information System (INIS)

Raoult, B.; Farges, J.; Feraudy, M.F. de; Torchet, G.

1989-01-01

We present a study of the stability of clusters models made of a number N of atoms in the range 500 to 6000 atoms, freely interacting through the Lennard-Jones potential. The potential energy per atom, calculated for relaxed models, shows that stable models belong to an icosahedral sequence when N<1600 and to a decahedral sequence beyond. A coexistence size range of both structures is discussed in connection with experimental results on argon clusters in free jet expansions. (orig.)

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.

A density functional theory study of magneto-electric Jones birefringence of noble gases, furan homologues, and mono-substituted benzenes

International Nuclear Information System (INIS)

Fahleson, Tobias; Norman, Patrick; Coriani, Sonia; Rizzo, Antonio; Rikken, Geert L. J. A.

2013-01-01

We report on the results of a systematic ab initio study of the Jones birefringence of noble gases, of furan homologues, and of monosubstituted benzenes, in the gas phase, with the aim of analyzing the behavior and the trends within a list of systems of varying size and complexity, and of identifying candidates for a combined experimental/theoretical study of the effect. We resort here to analytic linear and nonlinear response functions in the framework of time-dependent density functional theory. A correlation is made between the observable (the Jones constant) and the atomic radius for noble gases, or the permanent electric dipole and a structure/chemical reactivity descriptor as the para Hammett constant for substituted benzenes

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.

Surface Weather Observations Log Sheets from the USS John Paul Jones, April 12 - 23, 2004 (NODC Accession 0001512)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Meteorological data were collected using meteorological sensors from the USS JOHN PAUL JONES in the Northeast Pacific Ocean. Data were collected and recorded into...

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.

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

International Nuclear Information System (INIS)

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

2014-01-01

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

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.

Strategic Analysis and Associated Management Products Supporting the Reengineering of Bayne-Jones Army Community Hospital: Consultative Products and Findings

National Research Council Canada - National Science Library

Fulton, Larry

1998-01-01

.... ̂Product 2 - "Bayne-Jones Army Community Hospital Web Site," a strategic Internet web site for marketing health and wellness, the TRICARE medical network, the Joint Readiness Training Center Surgeon's...

Atomic size effect on the formation of ionized cluster beam epitaxy in Lennard-Jones systems

International Nuclear Information System (INIS)

Hsieh Horngming; Averback, R.S.

1991-01-01

Ionized cluster beam deposition is studied by molecular dynamics simulations in which the atomic size of incident cluster atoms is different from the size of substrate atoms. Lennard-Jones interatomic potentials are used for the two-component system. The results provide the morphologies of the overlayers for various atomic sizes and are compared to simulation results of molecular beam epitaxy. (orig.)

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

NARCIS (Netherlands)

D.E. Allen (David); M.J. McAleer (Michael); A.K. 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 potential energy landscape in the Lennard-Jones binary mixture model

International Nuclear Information System (INIS)

Sampoli, M; Benassi, P; Eramo, R; Angelani, L; Ruocco, G

2003-01-01

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

Phase behavior of the 38-atom Lennard-Jones cluster

International Nuclear Information System (INIS)

Sehgal, Ray M.; Maroudas, Dimitrios; Ford, David M.

2014-01-01

We have developed a coarse-grained description of the phase behavior of the isolated 38-atom Lennard-Jones cluster (LJ 38 ). The model captures both the solid-solid polymorphic transitions at low temperatures and the complex cluster breakup and melting transitions at higher temperatures. For this coarse model development, we employ the manifold learning technique of diffusion mapping. The outcome of the diffusion mapping analysis over a broad temperature range indicates that two order parameters are sufficient to describe the cluster's phase behavior; we have chosen two such appropriate order parameters that are metrics of condensation and overall crystallinity. In this well-justified coarse-variable space, we calculate the cluster's free energy landscape (FEL) as a function of temperature, employing Monte Carlo umbrella sampling. These FELs are used to quantify the phase behavior and onsets of phase transitions of the LJ 38 cluster

Solitons on H bonds in proteins

DEFF Research Database (Denmark)

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

2003-01-01

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....

Bacterial Biofilms in Jones Tubes.

Science.gov (United States)

Ahn, Eric S; Hauck, Matthew J; Kirk Harris, Jonathan; Robertson, Charles E; Dailey, Roger A

To investigate the presence and microbiology of bacterial biofilms on Jones tubes (JTs) by direct visualization with scanning electron microscopy and polymerase chain reaction (PCR) of representative JTs, and to correlate these findings with inflammation and/or infection related to the JT. In this study, prospective case series were performed. JTs were recovered from consecutive patients presenting to clinic for routine cleaning or recurrent irritation/infection. Four tubes were processed for scanning electron microscopy alone to visualize evidence of biofilms. Two tubes underwent PCR alone for bacterial quantification. One tube was divided in half and sent for scanning electron microscopy and PCR. Symptoms related to the JTs were recorded at the time of recovery. Seven tubes were obtained. Five underwent SEM, and 3 out of 5 showed evidence of biofilms (60%). Two of the 3 biofilms demonstrated cocci and the third revealed rods. Three tubes underwent PCR. The predominant bacteria identified were Pseudomonadales (39%), Pseudomonas (16%), and Staphylococcus (14%). Three of the 7 patients (43%) reported irritation and discharge at presentation. Two symptomatic patients, whose tubes were imaged only, revealed biofilms. The third symptomatic patient's tube underwent PCR only, showing predominantly Staphylococcus (56%) and Haemophilus (36%) species. Two of the 4 asymptomatic patients also showed biofilms. All symptomatic patients improved rapidly after tube exchange and steroid antibiotic drops. Bacterial biofilms were variably present on JTs, and did not always correlate with patients' symptoms. Nevertheless, routine JT cleaning is recommended to treat and possibly prevent inflammation caused by biofilms.

Evaporation of Lennard-Jones fluids.

Science.gov (United States)

Cheng, Shengfeng; Lechman, Jeremy B; Plimpton, Steven J; Grest, Gary S

2011-06-14

Evaporation and condensation at a liquid/vapor interface are ubiquitous interphase mass and energy transfer phenomena that are still not well understood. We have carried out large scale molecular dynamics simulations of Lennard-Jones (LJ) fluids composed of monomers, dimers, or trimers to investigate these processes with molecular detail. For LJ monomers in contact with a vacuum, the evaporation rate is found to be very high with significant evaporative cooling and an accompanying density gradient in the liquid domain near the liquid/vapor interface. Increasing the chain length to just dimers significantly reduces the evaporation rate. We confirm that mechanical equilibrium plays a key role in determining the evaporation rate and the density and temperature profiles across the liquid/vapor interface. The velocity distributions of evaporated molecules and the evaporation and condensation coefficients are measured and compared to the predictions of an existing model based on kinetic theory of gases. Our results indicate that for both monatomic and polyatomic molecules, the evaporation and condensation coefficients are equal when systems are not far from equilibrium and smaller than one, and decrease with increasing temperature. For the same reduced temperature T/T(c), where T(c) is the critical temperature, these two coefficients are higher for LJ dimers and trimers than for monomers, in contrast to the traditional viewpoint that they are close to unity for monatomic molecules and decrease for polyatomic molecules. Furthermore, data for the two coefficients collapse onto a master curve when plotted against a translational length ratio between the liquid and vapor phase.

Index der Titelbestandteile zu Dilwyn Jones: An Index of Ancient Egyptian Titles, Epithets and Phrases of the Old Kingdom

OpenAIRE

Schweitzer, Simon D.

2006-01-01

Vorliegender Index erschließt die nicht-ersten Titelbestandteile der in Dilwyn Jones: An index of ancient Egyptian titles, epithets and phrases of the Old Kingdom. Oxford : Archaeopress, 2000, verzettelten Titel und Epitheta des Alten Reiches.

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…

[Effectiveness of mini locking plate combined with Kirschner wire in treatment of comminuted Jones fracture].

Science.gov (United States)

Yan, Rongliang; Qu, Jiafu; Cao, Lihai; Liu, Hongda; Chen, Jianghua; Gao, Yan; Peng, Yi

2018-05-01

To summarize the effectiveness of mini locking plate combined with Kirschner wire in treatment of comminuted Jones fracture. Between January 2011 and October 2016, 25 cases with comminuted Jones fracture were treated with mini locking plate combined with Kirschner wire. There were 9 males and 16 females with an average age of 31.4 years (range, 16-66 years). The fractures located on the left side in 11 cases and on the right side in 14 cases. The causes of injury included spraining in 21 cases, falling down in 3 cases, and bruise in 1 case. The bone fragment of all cases was more than 3 pieces. The fracture line was mostly Y-shape or T-shape. Twelve of them were combined with other fractures. The time from injury to operation was 1-9 days (mean, 5 days). The mini locking plate and Kirschner wire were removed at 9-12 months postoperatively. At 12 months postoperatively, the pain was evaluated by the visual analogue scale (VAS) score, and the function by the American Orthopaedic Foot & Ankle Society (AOFAS) score. All incisions healed by first intention. All cases were followed up 12-36 months with an average of 21.7 months. Fracture union was observed in all patients without complications such as nonunion, delayed union, and malunion. The fracture union time was 8-12 weeks (mean, 9.4 weeks). At 12 months postoperatively, the VAS score was 1.15±0.87; the AOFAS score was 89.45±6.24, and the results were excellent in 14 cases, good in 9 cases, fair in 1 case, and poor in 1 case, with an excellent and good rate of 92%. The procedure of mini locking plate combined with Kirschner wire for comminuted Jones fracture has such advantages as convenient operation, more rigid fixation, high rate of fracture healing, and good functional recovery in foot.

Evidence of hexatic phase formation in two-dimensional Lennard-Jones binary arrays

International Nuclear Information System (INIS)

Li, M.; Johnson, W.L.; Goddard, W.A. III

1996-01-01

We report evidence of the hexatic phase formation in Lennard-Jones binary substitutional random arrays from isothermal-isobaric molecular-dynamics simulations. The hexatic phase is analogous to those predicted in Kosterlitz-Thouless theory of melting that is characterized by short-range translational order and quasi-long-range orientational order. At the crystal to hexatic phase transition, dislocation pairs are observed to unbind into isolated dislocations. Further disordering of the hexatic phase, however, does not lead to dissociation of dislocations into disclinations. Instead, the dislocations become clustered and form dislocation networks which results in formation of amorphous phases. copyright 1996 The American Physical Society

Crystallisation of a Lennard-Jones fluid by large scale molecular dynamics simulation

International Nuclear Information System (INIS)

Snook, I.

1998-01-01

Full text: The evolution of the structure of a large system of atoms interacting via a Lennard-Jones pair potential was simulated by the use of the Molecular Dynamics computer simulation technique. The system was initially equilibrated in the one phase region of the phase diagram at a temperature above critical then a temperature quench was performed which placed the system in a region were the single fluid phase was unstable. Quenches to below the triple point temperature gave rise to crystallisation The mechanism and final morphology is shown to depend strongly on the starting conditions e.g. the starting density

Density-scaling exponents and virial potential-energy correlation coefficients for the (2n, n) Lennard-Jones system

DEFF Research Database (Denmark)

Friisberg, Ida Marie; Costigliola, Lorenzo; Dyre, Jeppe C.

2017-01-01

This paper investigates the relation between the density-scaling exponent γ and the virial potentialenergy coefficient R at several thermodynamic state points in three dimensions for the generalized (2n, n) Lennard-Jones (LJ) system for n = 4, 9, 12, 18, as well as for the standard n = 6 LJ syste...

Finite-field evaluation of the Lennard-Jones atom-wall interaction constant C3 for alkali-metal atoms

International Nuclear Information System (INIS)

Johnson, W.R.; Dzuba, V.A.; Safronova, U.I.; Safronova, M.S.

2004-01-01

A finite-field scaling method is applied to evaluate the Lennard-Jones interaction constant C 3 for alkali-metal atoms. The calculations are based on the relativistic single-double approximation in which single and double excitations of Dirac-Hartree-Fock wave functions are included to all orders in perturbation theory

Hemibody irradiation in multiple myeloma

International Nuclear Information System (INIS)

Tobias, J.S.; Richards, J.D.M.; Blackman, G.M.; Joannides, T.; Trask, C.W.L.; Nathan, J.I.

1985-01-01

Eighteen patients with multiple myeloma were treated by hemibody irradiation using large single fractions, usually to a dose of 10 Gy (lower half) and 7.5 GY (upper half). All except one patient had previously been treated by multiple courses of conventional chemotherapy with melphalan and prednisone, and were considered to be resistant to further chemotherapy. In most cases, local field irradiation had also been given for symptomatic bone pain. Of the 13 patients who had symptoms at the start of hemibody irradiation, 11 improved sufficiently for their analgesia requirement to be reduced. In eight patients, there was a significant fall in circulating immunoglobulin but no patient with Bence-Jones proteinuria had complete resolution of this biochemical abnormality. Although thrombocytopenia and neutropenia were common, only two patients required platelet transfusion and the treatment was in general extremely well tolerated. Survival following hemibody irradiation was similar to the survival reported from the use of 'second-line' chemotherapy and we feel that hemibody irradiation is a more acceptable alternative for most patients. (orig.)

Twelve cases of multiple myeloma in Nagasaki (especially seven atomic bombing casualty cases). [In Japanese

Energy Technology Data Exchange (ETDEWEB)

Ichimaru, M; Yasuhi, S; Ouchuru, S

1963-12-01

Since 1958, there have been 12 cases of multiple myeloma in Nagasaki, and among them were 7 cases representing atomic bombing casualties, with 3 cases being with 2 km distance from the hypocenter. The age of onset was between 51 and 69 years, and the sex ratio was 8:4, it occurring mostly in males. Symptoms were predominantly low back pain and chest pain caused by the bone changes in 8 cases. Two cases complained of general malaise and palpitation which resulted from anemia. One developed persistent epistaris, and another complained of diplopia caused by the paralysis of the oculomotor nerve. Peripheral blood in all cases showed anemia, 9 with hyperchromic and 3 with normochromic or hypochromic anemia. Low platelet counts were seen in 3 cases. All showed leukopenia. All cases showed typical ..gamma..-globulin change with a myeloma peak, and in 4 cases showed an increase of ..beta..-globulin. Bence-Jones proteinuria was present in 5 cases. Average course was 1 year 4 months. Among complications, myeloma nephrosis, aplastic anemia, and pneumonia were the most important ones.

Pathogenesis of Renal Failure in Multiple Myeloma: Any Role of Contrast Media?

Science.gov (United States)

Mussap, Michele; Merlini, Giampaolo

2014-01-01

The spectrum of kidney disease-associated monoclonal immunoglobulin and plasma cell malignancies is remarkably broad and encompasses nearly all nephropathologic entities. Multiple myeloma with kidney impairment at presentation is a medical emergency since the recovery of kidney function is associated with survival benefits. In most cases, kidney impairment may be the first clinical manifestation of malignant plasma cell dyscrasias like multiple myeloma and light chain amyloidosis. Multiple myeloma per se cannot be considered a main risk factor for developing acute kidney injury following intravascular administration of iodinated contrast media. The risk is increased by comorbidities such as chronic kidney disease, diabetes, hypercalcemia, dehydration, and use of nephrotoxic drugs. Before the administration of contrast media, the current recommended laboratory tests for assessing kidney function are serum creatinine measurement and the estimation of glomerular filtration rate by using the CKD-EPI equation. The assessment of Bence Jones proteinuria is unnecessary for evaluating the risk of kidney failure in patients with multiple myeloma, since this test cannot be considered a surrogate biomarker of kidney function. PMID:24877060

Pathogenesis of Renal Failure in Multiple Myeloma: Any Role of Contrast Media?

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Michele Mussap

2014-01-01

Full Text Available The spectrum of kidney disease-associated monoclonal immunoglobulin and plasma cell malignancies is remarkably broad and encompasses nearly all nephropathologic entities. Multiple myeloma with kidney impairment at presentation is a medical emergency since the recovery of kidney function is associated with survival benefits. In most cases, kidney impairment may be the first clinical manifestation of malignant plasma cell dyscrasias like multiple myeloma and light chain amyloidosis. Multiple myeloma per se cannot be considered a main risk factor for developing acute kidney injury following intravascular administration of iodinated contrast media. The risk is increased by comorbidities such as chronic kidney disease, diabetes, hypercalcemia, dehydration, and use of nephrotoxic drugs. Before the administration of contrast media, the current recommended laboratory tests for assessing kidney function are serum creatinine measurement and the estimation of glomerular filtration rate by using the CKD-EPI equation. The assessment of Bence Jones proteinuria is unnecessary for evaluating the risk of kidney failure in patients with multiple myeloma, since this test cannot be considered a surrogate biomarker of kidney function.

77 FR 38051 - Jones Canyon Hydro, LLC; Notice of Application for Amendment of Preliminary Permit Accepted for...

Science.gov (United States)

2012-06-26

... proposed reservoirs from 6,225 feet to 7,330 feet; and (7) change the name of the project from ``Jones Canyon Pumped Storage Project'' to ``Oregon Winds Pumped Storage''. FERC Contact: Jennifer Harper, 202..., using the eComment system at http://www.ferc.gov/docs-filing/ecomment.asp . You must include your name...

Evaluation of linkages between equity indices : evidence from İstanbul Stock Exchange and Dow Jones

OpenAIRE

Ertan, Aytekin

2009-01-01

Ankara : The Department of Management, Bilkent Univiversity, 2009. Thesis (Master's) -- Bilkent University, 2009. Includes bibliographical references leaves 30-33. This study investigates the linkage between the major stock market indices of Turkey (ISE National 100) and USA (Dow Jones Industrial Average). Main purpose of this research is to measure the interdependence and cointegration between these indices and figure out the significance and the direction of short run r...

Nonlinear transport processes and fluid dynamics: Cylindrical Couette flow of Lennard-Jones fluids

International Nuclear Information System (INIS)

Khayat, R.E.; Eu, B.C.

1988-01-01

In this paper we report on calculations of flow profiles for cylindrical Couette flow of a Lennard-Jones fluid. The flow is subjected to a temperature gradient and thermoviscous effects are taken into consideration. We apply the generalized fluid dynamic equations which are provided by the modified moment method for the Boltzmann equation reported previously. The results of calculations are in good agreement with the Monte Carlo direct simulation method by K. Nanbu [Phys. Fluids 27, 2632 (1984)] for most of Knudsen numbers for which the simulation data are available

Percutaneous internal fixation of proximal fifth metatarsal jones fractures (Zones II and III) with Charlotte Carolina screw and bone marrow aspirate concentrate: an outcome study in athletes.

Science.gov (United States)

Murawski, Christopher D; Kennedy, John G

2011-06-01

Internal fixation is a popular first-line treatment method for proximal fifth metatarsal Jones fractures in athletes; however, nonunions and screw breakage can occur, in part because of nonspecific fixation hardware and poor blood supply. To report the results from 26 patients who underwent percutaneous internal fixation with a specialized screw system of a proximal fifth metatarsal Jones fracture (zones II and III) and bone marrow aspirate concentrate. Case series; Level of evidence, 4. Percutaneous internal fixation for a proximal fifth metatarsal Jones fracture (zones II and III) was performed on 26 athletic patients (mean age, 27.47 years; range, 18-47). All patients were competing at some level of sport and were assessed preoperatively and postoperatively using the Foot and Ankle Outcome Score and SF-12 outcome scores. The mean follow-up time was 20.62 months (range, 12-28). Of the 26 fractures, 17 were traditional zone II Jones fractures, and the remaining 9 were zone III proximal diaphyseal fractures. The mean Foot and Ankle Outcome Score significantly increased, from 51.15 points preoperatively (range, 14-69) to 90.91 at final follow-up (range, 71-100; P fracture healing on standard radiographs was 5 weeks after surgery (range, 4-24). Two patients did not return to their previous levels of sporting activity. One patient experienced a delayed union, and 1 healed but later refractured. Percutaneous internal fixation of proximal fifth metatarsal Jones fractures, with a Charlotte Carolina screw and bone marrow aspirate concentrate, provides more predictable results while permitting athletes a return to sport at their previous levels of competition, with few complications.

Curvature Dependence of Interfacial Properties for Associating Lennard—Jones Fluids: A Density Functional Study

International Nuclear Information System (INIS)

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 fluids on these properties are analyzed in detail. The results may provide helpful clues to understand the interfacial properties of other complex fluids. (condensed matter: structure, mechanical and thermal properties)

Dynamics of vacancies in two-dimensional Lennard-Jones crystals

Science.gov (United States)

Yao, Zhenwei; Olvera de La Cruz, Monica

2015-03-01

Vacancies represent an important class of crystallographic defects, and their behaviors can be strongly coupled with relevant material properties. We report the rich dynamics of vacancies in two-dimensional Lennard-Jones crystals in several thermodynamic states. Specifically, we numerically observe significantly faster diffusion of the 2-point vacancy with two missing particles in comparison with other types of vacancies; it opens the possibility of doping 2-point vacancies into atomic materials to enhance atomic migration. In addition, the resulting dislocations in the healing of a long vacancy suggest the intimate connection between vacancies and topological defects that may provide an extra dimension in the engineering of defects in extensive crystalline materials for desired properties. We thank the financial support from the U.S. Department of Commerce, National Institute of Standards and Technology, the Office of the Director of Defense Research and Engineering (DDR&E) and the Air Force Office of Scientific Research.

77 FR 17530 - Order Granting an Application of Edward Jones & Co. LLP Exemption From Exchange Act Section 11(d...

Science.gov (United States)

2012-03-26

...'') requested that the Securities and Exchange Commission (``Commission'') issue to Edward Jones an exemption... subject to the conditions contained in this order, is exempt from the new issue lending restriction of... SECURITIES AND EXCHANGE COMMISSION [Release No. 34-66624] Order Granting an Application of Edward...

Thermal conductivity of the Lennard-Jones fluid: An empirical correlation

International Nuclear Information System (INIS)

Bugel, Mathilde; Galliero, Guillaume

2008-01-01

In this work, is presented an empirical correlation on the thermal conductivity of the Lennard-Jones fluid based on extensive non-equilibrium molecular dynamics simulations results (103 points). Finite size and cutoff radius effects are investigated and taken into account to develop the correlation. This last, composed of low-density, residual and critical enhancement contributions, is built for a wide range of thermodynamics states, even at the vicinity of the critical point, and yields an average absolute deviation of 1.29% compared to our simulations. In addition, a careful analysis of the different contributions to the microscopic flux is carried out which sheds light on the underlying mechanism of the results. Finally, are discussed the limitations of the proposed model when applied to real simple fluids and mixtures using a standard corresponding states scheme and the van der Waals one-fluid approximation

Freezing and melting line invariants of the Lennard-Jones system

DEFF Research Database (Denmark)

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

2016-01-01

The invariance of several structural and dynamical properties of the Lennard-Jones (LJ) system along the freezing and melting lines is interpreted in terms of isomorph theory. First the freezing/melting lines of the LJ system are shown to be approximated by isomorphs. Then we show...... that the invariants observed along the freezing and melting isomorphs are also observed on other isomorphs in the liquid and crystalline phases. The structure is probed by the radial distribution function and the structure factor and dynamics are probed by the mean-square displacement, the intermediate scattering...... function, and the shear viscosity. Studying these properties with reference to isomorph theory explains why the known single-phase melting criteria hold, e.g., the Hansen–Verlet and the Lindemann criteria, and why the Andrade equation for the viscosity at freezing applies, e.g., for most liquid metals. Our...

Platform for Manipulating Polarization Modes Realized with Jones Vectors in MATHEMATICA

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Yong-Dae Choi

2015-06-01

Full Text Available The fundamental conception in physics of the propagation of the electromagnetic wave polarization in matter is newly understood as the cardinal keyword in free-space quantum communication technology and cosmology in astrophysics. Interactive visualization of the propagation mechanism of polarized electromagnetism in a medium with its helicity has accordingly received attention from scientists exploiting the protocol of quantum key distribution (QKD to guarantee unconditional security in cryptography communication. We have provided a dynamic polarization platform for presenting the polarization modes of a transverse electromagnetic wave, converting the state of polarization through the arrangement of optical elements, using Jones vectors calculations in Methematica. The platform graphically simulates the mechanism of production and propagation of the polarized waves in a medium while satisfying Maxwell's equations.

Analysis of a Lennard-Jones fcc structure melting to the corresponding frozen liquid: Differences between the bulk and the surface

International Nuclear Information System (INIS)

Olivi-Tran, N.; Faivre, A.

2009-01-01

We computed a Lennard-Jones frozen liquid with a free surface using classical molecular dynamics. The structure factor curves on the free surface of this sample were calculated for different depths knowing that we have periodic boundary conditions on the other parts of the sample. The resulting structure factor curves show an horizontal shift of their first peak depending on how deep in the sample the curves are computed. We analyze our resulting curves in the light of spatial correlation functions during melting. The conclusion is that the differences between bulk and surface are quite small during melting and that at the end of melting, only the very surface happens to be less dense than the bulk. This result is intrinsic to the shape of the Lennard-Jones potential and does not depend on any other parameter.

Importance of dispersion and electron correlation in ab initio protein folding.

Science.gov (United States)

He, Xiao; Fusti-Molnar, Laszlo; Cui, Guanglei; Merz, Kenneth M

2009-04-16

Dispersion is well-known to be important in biological systems, but the effect of electron correlation in such systems remains unclear. In order to assess the relationship between the structure of a protein and its electron correlation energy, we employed both full system Hartree-Fock (HF) and second-order Møller-Plesset perturbation (MP2) calculations in conjunction with the Polarizable Continuum Model (PCM) on the native structures of two proteins and their corresponding computer-generated decoy sets. Because of the expense of the MP2 calculation, we have utilized the fragment molecular orbital method (FMO) in this study. We show that the sum of the Hartree-Fock (HF) energy and force field (LJ6)-derived dispersion energy (HF + LJ6) is well correlated with the energies obtained using second-order Møller-Plesset perturbation (MP2) theory. In one of the two examples studied, the correlation energy as well as the empirical dispersive energy term was able to discriminate between native and decoy structures. On the other hand, for the second protein we studied, neither the correlation energy nor dispersion energy showed discrimination capabilities; however, the ab initio MP2 energy and the HF+LJ6 both ranked the native structure correctly. Furthermore, when we randomly scrambled the Lennard-Jones parameters, the correlation between the MP2 energy and the sum of the HF energy and dispersive energy (HF+LJ6) significantly drops, which indicates that the choice of Lennard-Jones parameters is important.

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

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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.

Plasmacytoma of the Breast: A Report of a Rare Disease.

Science.gov (United States)

Gabriel, Ugare; Joseph, Udosen; Bassey, Ima-Abasi; Joshua, Ayodele; Emmanuel, Djunda

2015-10-01

Extramedullary plasma cells tumours are rare. Much more rarer is their occurance in the breast tissue. Our aim is to report a single case of this very rare lesion (at least from an African perspective) that we incidentally diagnosed histopathologically as a primary extramedullary lesion in a 53 year old woman. Clinical records of a 53 year old postmenopausal woman was referred from a secondary health centre to our clinic with a three weeks' history of right breast lump were reviewed. There was no associated pain, nipple discharge, weight loss or systemic symptoms nor was there a previous history of trauma or surgery to the breast. On examination: two discrete lumps measuring 3x2 and 2 x 1.5cm in the upper medial quadrant of the right breast were identified. The lumps were firm, irregular in shape, not attached to the skin or underlying tissues. Tentative diagnosis of adenocarcinoma of the breast was made, with a differential as fat necrosis. A wide excision biopsy was done four days later for histology, after an inconclusive cytological examination of smear of which the result revealed plasmacytosis. The liver function test, Plasma proteins electrophoresis, electrolytes, urea, creatinine, bicarbonate and pelvic X-rays, and abdomino-pelvic ultrasonography were normal. Bence Jones proteins were negative in urine. Histology of bone marrow aspirate revealed scanty plasma cells. She received 20mg dexamethasone, 20mg adramycin, and 2mg vincristine intravenously and 200mg of alloperinol daily by mouth for three days before leaving by the 4th treatment day against medical advice for personal reasons. This rare lesion should sometimes be considered as a differential diagnosis of a breast lump, as it does not differ from the common lesions clinically, especially in older women.

Longitudinal and bulk viscosities of Lennard-Jones fluids

Science.gov (United States)

Tankeshwar, K.; Pathak, K. N.; Ranganathan, S.

1996-12-01

Expressions for the longitudinal and bulk viscosities have been derived using Green Kubo formulae involving the time integral of the longitudinal and bulk stress autocorrelation functions. The time evolution of stress autocorrelation functions are determined using the Mori formalism and a memory function which is obtained from the Mori equation of motion. The memory function is of hyperbolic secant form and involves two parameters which are related to the microscopic sum rules of the respective autocorrelation function. We have derived expressions for the zeroth-, second-and fourth- order sum rules of the longitudinal and bulk stress autocorrelation functions. These involve static correlation functions up to four particles. The final expressions for these have been put in a form suitable for numerical calculations using low- order decoupling approximations. The numerical results have been obtained for the sum rules of longitudinal and bulk stress autocorrelation functions. These have been used to calculate the longitudinal and bulk viscosities and time evolution of the longitudinal stress autocorrelation function of the Lennard-Jones fluids over wide ranges of densities and temperatures. We have compared our results with the available computer simulation data and found reasonable agreement.

The Monte Carlo dynamics of a binary Lennard-Jones glass-forming mixture

International Nuclear Information System (INIS)

Berthier, L; Kob, W

2007-01-01

We use a standard Monte Carlo algorithm to study the slow dynamics of a binary Lennard-Jones glass-forming mixture at low temperature. We find that the Monte Carlo approach is by far the most efficient way to simulate a stochastic dynamics since the relaxation is about 10 times faster than in Brownian dynamics and about 30 times faster than in stochastic dynamics. Moreover, the average dynamical behaviour of the system is in quantitative agreement with that obtained using Newtonian dynamics, apart from at very short times where thermal vibrations are suppressed. We show, however, that dynamic fluctuations quantified by four-point dynamic susceptibilities do retain a dependence on the microscopic dynamics, as recently predicted theoretically

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

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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.

A RARE CASE OF EXTRAMEDULLARY PLASMACYTOMA MASQUERADING AS JUVENILE NASOPHARYNGEAL ANGIOFIBROMA

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Harshita V. Sabhahit

2016-09-01

Full Text Available BACKGROUND Plasmacytomas are rare plasma cell tumours occurring consequent to monoclonal proliferation of plasma cells. They are divided into Solitary bone plasmacytoma, Extramedullary plasmacytoma (EMP and Multiple myeloma. EMPs are commonly housed in the head and neck region with a predilection to the mucosa associated lymphoid tissue in the aerodigestive tract. The nasal cavity, paranasal sinuses, and nasopharynx are the most common sites. OBJECTIVE We describe our experience with this tumour owing to its clinical rarity and a different way of presentation. METHODS After complete surgical excision of a nasal mass presenting in a young male with features masquerading that of Juvenile Nasopharyngeal Angiofibroma, a diagnosis of plasma cell tumour was made on histopathological analysis which was confirmed using immunohistochemistry. Serum electrophoresis, urine Bence Jones proteins, complete skeletal survey were done to rule out any progression into multiple myeloma. Radiation therapy was given with 45 Gy in 25 fractions at 1.8 Gy per day, 5 days a week. RESULTS Followup after 2 years showed no recurrence locally as well as in regional nodes. CONCLUSION Given to the rarity of the tumour, undefined manner of presentation and a predominant prevalence in the head and neck region, every otolaryngologist should keep EMP in mind while considering sinonasal masses. A multidisciplinary approach with a combination of surgery and radiotherapy is found to benefit the patient significantly. A long term watch out for progression to MM is mandatory to commence early treatment and thus prolonged disease-free survival from the same.

A molecular dynamics study of Lennard-Jones physisorption on W(100)

International Nuclear Information System (INIS)

Broughton, J.Q.

1980-01-01

The physisorption of Xe on W(100) was modeled by Lennard-Jones pair-wise interaction potentials and the dynamics of coverages ranging from one to four adlayers obtained by molecular dynamics simulation. At 115 K, the first two layers were well-ordered and each adsorbed with c(2 x 2) symmetry. Further adsorption produced a surface similar to that of a distorted Xe(100) face. In accord with the work of Broughton and Woodcock, the top layers of the three- and four-adlayer coverages were rough and had liquid-like diffusion coefficients. The potential energies of all layers other than the first were similar, thus corroborating one of the postulates of BET theory. Generally, the effect of adsorbing a layer was to reduce the entropy of all those beneath. (orig.)

Imaginando Palmares: a obra de Gayl Jones

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Stelamaris Coser

2005-01-01

Full Text Available http://dx.doi.org/10.1590/S0104-026X2005000300010 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.

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

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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

Vacancy behavior in a compressed fcc Lennard-Jones crystal

International Nuclear Information System (INIS)

Beeler, J.R. Jr.

1981-12-01

This computer experiment study concerns the determination of the stable vacancy configuration in a compressed fcc Lennard-Jones crystal and the migration of this defect in a compressed crystal. Isotropic and uniaxial compression stress conditions were studied. The isotropic and uniaxial compression magnitudes employed were 0.94 less than or equal to eta less than or equal to 1.5, and 1.0 less than or equal to eta less than or equal to 1.5, respectively. The site-centered vacancy (SCV) was the stable vacancy configuration whenever cubic symmetry was present. This includes all of the isotropic compression cases and the particular uniaxial compression case (eta = √2) that give a bcc structure. In addition, the SCV was the stable configuration for uniaxial compression eta 1.20, the SV-OP is an extended defect and, therefore, a saddle point for SV-OP migration could not be determined. The mechanism for the transformation from the SCV to the SV-OP as the stable form at eta = 1.29 appears to be an alternating sign [101] and/or [011] shear process

Shear viscosity of the Lennard-Jones fluid near the triple point: Green-Kubo results

International Nuclear Information System (INIS)

Erpenbeck, J.J.

1988-01-01

The long-standing disagreement over the shear viscosity coefficient of the Lennard-Jones fluid near the triple point is reexamined through a series of very extensive Monte Carlo molecular-dynamics calculations of this transport coefficient based on the Green-Kubo theory. The stress autocorrelation function is shown to exhibit a slow decay, principally in the kinetic-potential and the potential-potential terms, which is large compared with the kinetic-kinetic long-time tail predicted by simple mode-coupling theory. Nonetheless, the viscosity coefficient, exclusive of any correction for this tail for times greater than are accessible numerically, is found to agree with that of Schoen and Hoheisel (who discounted the existence of such a tail) as well as nonequilibrium molecular-dynamics calculations. The large value of the viscosity coefficient found by Levesque and co-workers for 864 particles is brought into statistical agreement with the present results by a modest, but not unrealistic, increase in its statistical uncertainty. The pressure is found to exhibit an anomalous dependence on the size of the system, but the viscosity as well as the self-diffusion constant appear to be linear in the inverse of the number of particles, within the precision of our calculations. The viscosity coefficient, including a long-time-tail contribution based on the extended mode-coupling theory is (3.796 +- 0.068)σepsilon-c/m)/sup 1/2/ for the Lennard-Jones potential, fitted to a cubic spline, and (3.345 +- 0.068)σepsilon-c/m)/sup 1/2/ for the potential truncated at 2.5σ

Liquid-vapour phase behaviour of a polydisperse Lennard-Jones fluid

International Nuclear Information System (INIS)

Wilding, Nigel B; Sollich, Peter

2005-01-01

We describe a simulation study of the liquid-vapour phase behaviour of a model polydisperse fluid. Particle interactions are given by a Lennard-Jones potential in which polydispersity features both in the particle sizes and the amplitude of their interactions. We address the computational problem of accurately locating the cloud curve for such a system using Monte Carlo simulations within the grand canonical ensemble. The strongly nonlinear variation of the fractional volumes of the phases across the coexistence region precludes naive extrapolation to determine the cloud point density. Instead we propose an improved estimator for the cloud point location and use scaling arguments to predicts its finite-size behaviour. Excellent agreement is found with the simulation results. Application of the method reveals that the measured cloud curve is highly sensitive to the presence of large particles, even when they are extremely rare. This finding is expected to have implications for the reproducibility of experimentally measured phase diagrams in colloids and polymers

Simulasi Sifat Fisis Model Molekuler Dinamik Gas Argon dengan Potensial Lennard-Jones

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Wira Bahari Nurdin

2014-01-01

Full Text Available DOWNLOAD PDFTelah  dilakukan  pembuatan  dan  pengujian  suatu  simulasi  tentang  sifat  fisis  gasargon  dengan  menggunakan  dinamika  molekuler  menggunakan  potensial Lennard-Jonesdalam sistem terisolasi (ensemble mikrokanonik. Jumlah molekul, energi total sistem danluas  kotak  simulasi  telah  divariasikan.  Untuk  menghitung  perubahan  posisi  digunakanalgoritma Verlet. Sifat fisis yang ditentukan dalam simulasi adalah temperatur dan energitotal  sistem  untuk  menentukan  adanya  fase  transisi.  Dari  hasil  simulasi,  terdapatkesesuaian antara simulasi dengan gas argon dan tidak diperoleh adanya fase transisi.Kata kunci: Simulasi dinamika molekul, argon, potensial Lennard-Jones, ensemblemikrokanonik, algoritma Verlet

Theoretical prediction of crystallization kinetics of a supercooled Lennard-Jones fluid

Science.gov (United States)

Gunawardana, K. G. S. H.; Song, Xueyu

2018-05-01

The first order curvature correction to the crystal-liquid interfacial free energy is calculated using a theoretical model based on the interfacial excess thermodynamic properties. The correction parameter (δ), which is analogous to the Tolman length at a liquid-vapor interface, is found to be 0.48 ± 0.05 for a Lennard-Jones (LJ) fluid. We show that this curvature correction is crucial in predicting the nucleation barrier when the size of the crystal nucleus is small. The thermodynamic driving force (Δμ) corresponding to available simulated nucleation conditions is also calculated by combining the simulated data with a classical density functional theory. In this paper, we show that the classical nucleation theory is capable of predicting the nucleation barrier with excellent agreement to the simulated results when the curvature correction to the interfacial free energy is accounted for.

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.

Jones index, secret sharing and total quantum dimension

Science.gov (United States)

Fiedler, Leander; Naaijkens, Pieter; Osborne, Tobias J.

2017-02-01

We study the total quantum dimension in the thermodynamic limit of topologically ordered systems. In particular, using the anyons (or superselection sectors) of such models, we define a secret sharing scheme, storing information invisible to a malicious party, and argue that the total quantum dimension quantifies how well we can perform this task. We then argue that this can be made mathematically rigorous using the index theory of subfactors, originally due to Jones and later extended by Kosaki and Longo. This theory provides us with a ‘relative entropy’ of two von Neumann algebras and a quantum channel, and we argue how these can be used to quantify how much classical information two parties can hide form an adversary. We also review the total quantum dimension in finite systems, in particular how it relates to topological entanglement entropy. It is known that the latter also has an interpretation in terms of secret sharing schemes, although this is shown by completely different methods from ours. Our work provides a different and independent take on this, which at the same time is completely mathematically rigorous. This complementary point of view might be beneficial, for example, when studying the stability of the total quantum dimension when the system is perturbed.

Simple approach to approximate predictions of the vapor–liquid equilibrium curve near the critical point and its application to Lennard-Jones fluids

International Nuclear Information System (INIS)

Staśkiewicz, B.; Okrasiński, W.

2012-01-01

We propose a simple analytical form of the vapor–liquid equilibrium curve near the critical point for Lennard-Jones fluids. Coexistence densities curves and vapor pressure have been determined using the Van der Waals and Dieterici equation of state. In described method the Bernoulli differential equations, critical exponent theory and some type of Maxwell's criterion have been used. Presented approach has not yet been used to determine analytical form of phase curves as done in this Letter. Lennard-Jones fluids have been considered for analysis. Comparison with experimental data is done. The accuracy of the method is described. -- Highlights: ► We propose a new analytical way to determine the VLE curve. ► Simple, mathematically straightforward form of phase curves is presented. ► Comparison with experimental data is discussed. ► The accuracy of the method has been confirmed.

The Value of Multivariate Model Sophistication: An Application to pricing Dow Jones Industrial Average options

DEFF Research Database (Denmark)

Rombouts, Jeroen V.K.; Stentoft, Lars; Violante, Francesco

innovation for a Laplace innovation assumption improves the pricing in a smaller way. Apart from investigating directly the value of model sophistication in terms of dollar losses, we also use the model condence set approach to statistically infer the set of models that delivers the best pricing performance.......We assess the predictive accuracy of a large number of multivariate volatility models in terms of pricing options on the Dow Jones Industrial Average. We measure the value of model sophistication in terms of dollar losses by considering a set 248 multivariate models that differer...

How accurate are pedotransfer functions for bulk density for Brazilian soils?

Directory of Open Access Journals (Sweden)

Raquel Stucchi Boschi

Full Text Available ABSTRACT: The aim of this study was to evaluate the performance of pedotransfer functions (PTFs available in the literature to estimate soil bulk density (ρb in different regions of Brazil, using different metrics. The predictive capacity of 25 PTFs was evaluated using the mean absolute error (MAE, mean error (ME, root mean squared error (RMSE, coefficient of determination (R2 and the regression error characteristic (REC curve. The models performed differently when comparing observed and estimated ρb values. In general, the PTFs showed a performance close to the mean value of the bulk density data, considered as the simplest possible estimation of an attribute and used as a parameter to compare the performance of existing models (null model. The models developed by Benites et al. (2007 (BEN-C and by Manrique and Jones (1991 (M&J-B presented the best results. The separation of data into two layers according to depth (0-10 cm and 10-30 cm demonstrated better performance in the 10-30 cm layer. The REC curve allowed for a simple and visual evaluation of the PTFs.

Effect of money supply on the Dow Jones Industrial Average stock index

Directory of Open Access Journals (Sweden)

Martin Širůček

2012-01-01

Full Text Available This focus of this paper are the effects and implications of a change in the money supply for share price indices in the USA during 1959–2011. The money supply will be measured by the M2 and MZM aggregates (money with zero maturity. The US stock market is represented by the Dow Jones Industrial Average index. The objective of this paper is to find, describe and evaluate the effects of changes to the money supply (M2 and MZM on the US stock market. A partial objective of this paper is to determine whether a change in the monetary aggregate shows in the stock index immediately or with a delay of several weeks. Another aim is to determine whether asset prices influence the money supply.

Dodecagonal order in a two-dimensional Lennard-Jones system

International Nuclear Information System (INIS)

Leung, P.W.; Henley, C.L.; Chester, G.V.

1989-01-01

We investigate a two-dimensional Lennard-Jones mixture with the interaction parameters chosen so as to favor configurations where the large atoms form squares and equilateral triangles. Many such configurations are possible which by our choice of interactions are nearly degenerate in energy. It is hypothesized that a thermal equilibrium state with 12-fold orientational order exists. Several Monte Carlo simulations were performed to cool the system to a temperature approaching zero. The ordering process was studied by following the evolution of the configurations with temperature. The onset of ordering seemed to be very diffuse in space rather than nucleated at a point. The resulting configurations consist of squares and triangles, except for a few dislocations, and thus have perfect orientational order. We also characterized the deviation from ideal quasiperiodicity in terms of the ''phason strain''; this was analyzed both by fitting a linear relation between the physical space coordinates of the atoms and the corresponding ''perpendicular space'' coordinates, and also by calculating the diffraction peaks. The latter are shifted and broadened, relative to an ideal 12-fold diffraction pattern, as in real quasicrystals

Entanglement entropy and the colored Jones polynomial

Science.gov (United States)

Balasubramanian, Vijay; DeCross, Matthew; Fliss, Jackson; Kar, Arjun; Leigh, Robert G.; Parrikar, Onkar

2018-05-01

We study the multi-party entanglement structure of states in Chern-Simons theory created by performing the path integral on 3-manifolds with linked torus boundaries, called link complements. For gauge group SU(2), the wavefunctions of these states (in a particular basis) are the colored Jones polynomials of the corresponding links. We first review the case of U(1) Chern-Simons theory where these are stabilizer states, a fact we use to re-derive an explicit formula for the entanglement entropy across a general link bipartition. We then present the following results for SU(2) Chern-Simons theory: (i) The entanglement entropy for a bipartition of a link gives a lower bound on the genus of surfaces in the ambient S 3 separating the two sublinks. (ii) All torus links (namely, links which can be drawn on the surface of a torus) have a GHZ-like entanglement structure — i.e., partial traces leave a separable state. By contrast, through explicit computation, we test in many examples that hyperbolic links (namely, links whose complements admit hyperbolic structures) have W-like entanglement — i.e., partial traces leave a non-separable state. (iii) Finally, we consider hyperbolic links in the complexified SL(2,C) Chern-Simons theory, which is closely related to 3d Einstein gravity with a negative cosmological constant. In the limit of small Newton constant, we discuss how the entanglement structure is controlled by the Neumann-Zagier potential on the moduli space of hyperbolic structures on the link complement.

Sophie's Defense Mechanism in Her Struggle to Break the Curse in Diana Wynne Jones' Howl's Moving Castle

OpenAIRE

Perwita, Ratnanggana Ausiyyah Mustika

2015-01-01

The experience that young people get has an effect to their personality and their problem solving. This is why older people tend to be more mature than the young people. In Diana Wynne Jones' Howl's Moving Castle, the main character has a development in her personality through experiences. Her experiences lead her to how she solves her problems while she unconsciously uses defense mechanism. In this case, in this study will be analyzed the characteristic of the main character, Sophie, when sh...

The effect of atom mismatch on the fragility of supercooled Lennard-Jones binary mixtures

International Nuclear Information System (INIS)

Sun Minhua; Sun Yongli; Wang Aiping; Ma Congxiao; Li Jiayun; Cheng Weidong; Liu Fang

2006-01-01

The shear viscosity of the well-known binary Lennard-Jones mixture is simulated under constant temperature and constant volume conditions (NVT) by a molecular-dynamics (MD) method. The effect of atomic size mismatch on the fragility parameter and glass-forming ability is studied. The fragility parameters calculated from shear viscosity data decrease with the increment of the atomic size mismatch. The value of the fragility changes from 168.963 to 22.976 when the mismatch changes from 0.023 to 0.25. It is shown that the fragility parameter is sensitive to the atomic size mismatch. The calculated pair distribution functions and mean square displacements indicate that the glass-forming ability increases with the atomic size mismatch

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

Science.gov (United States)

Onwah, A Lawretta; Adeyemo, Titilope A; Adediran, Adewumi; Ajibola, Sarah O; Akanmu, Alani S

2012-06-28

The prevalence of monoclonal gammopathy of undetermined significance (MGUS), a premalignant plasma-cell disorder has not been determined in our geographic area Nigeria. 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. 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. 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.

"No interest in human anatomy as such": Frederic Wood Jones dissects anatomical investigation in the United States in the 1920s.

Science.gov (United States)

Jones, Ross L

2014-03-01

In 1926, Frederic Wood Jones, professor of Anatomy at the University of Adelaide and a leading figure in the British anatomical world, took a Rockefeller Foundation funded trip to the United States in order to inspect anatomy programmes and medical museums and to meet leading figures in the anatomical and anthropological world. His later reflections paint a picture of a discipline in transition. Physical anthropology and gross anatomy were coming to a crisis point in the United States, increasingly displaced by research in histology, embryology and radiological anatomy. Meanwhile, in Britain and its colonial outposts, anatomists such as Wood Jones were attempting to re-invigorate the discipline in the field, studying biological specimens as functional and active agents in their particular milieus, but with human dissection at the core. Thus, an examination of this trip allows us to see how the interaction between two traditions in anatomy informed the process of the development of human biology in this critical period. Copyright © 2013 Elsevier Ltd. All rights reserved.

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.

Modified Kenneth Jones criteria for diagnosing tuberculous meningitis in children

International Nuclear Information System (INIS)

Anwar, M.; Ahmad, A.; Ahmad, F.; Mazhar, A.

2010-01-01

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)

Modeling Aggregation Processes of Lennard-Jones particles Via Stochastic Networks

Science.gov (United States)

Forman, Yakir; Cameron, Maria

2017-07-01

We model an isothermal aggregation process of particles/atoms interacting according to the Lennard-Jones pair potential by mapping the energy landscapes of each cluster size N onto stochastic networks, computing transition probabilities from the network for an N-particle cluster to the one for N+1, and connecting these networks into a single joint network. The attachment rate is a control parameter. The resulting network representing the aggregation of up to 14 particles contains 6427 vertices. It is not only time-irreversible but also reducible. To analyze its transient dynamics, we introduce the sequence of the expected initial and pre-attachment distributions and compute them for a wide range of attachment rates and three values of temperature. As a result, we find the configurations most likely to be observed in the process of aggregation for each cluster size. We examine the attachment process and conduct a structural analysis of the sets of local energy minima for every cluster size. We show that both processes taking place in the network, attachment and relaxation, lead to the dominance of icosahedral packing in small (up to 14 atom) clusters.

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.

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

KAUST Repository

Inaoka, Hajime; Yukawa, Satoshi; Ito, Nobuyasu

2010-01-01

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.

Dynamical properties and transport coefficients of one-dimensional Lennard-Jones fluids: A molecular dynamics study

Science.gov (United States)

Bazhenov, Alexiev M.; Heyes, David M.

1990-01-01

The thermodynamics, structure, and transport coefficients, as defined by the Green-Kubo integrals, of the one-dimensional Lennard-Jones fluid are evaluated for a wide range of state points by molecular dynamics computer simulation. These calculations are performed for the first time for thermal conductivity and the viscosity. We observe a transition from hard-rod behavior at low number density to harmonic-spring fluid behavior in the close-packed limit. The self-diffusion coefficient decays with increasing density to a finite limiting value. The thermal conductivity increases with density, tending to ∞ in the close-packed limit. The viscosity in contrast maximizes at intermediate density, tending to zero in the zero density and close-packed limits.

MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein-Protein Docking.

Science.gov (United States)

Klett, Javier; Núñez-Salgado, Alfonso; Dos Santos, Helena G; Cortés-Cabrera, Álvaro; Perona, Almudena; Gil-Redondo, Rubén; Abia, David; Gago, Federico; Morreale, Antonio

2012-09-11

An ultrafast and accurate scoring function for protein-protein docking is presented. It includes (1) a molecular mechanics (MM) part based on a 12-6 Lennard-Jones potential; (2) an electrostatic component based on an implicit solvent model (ISM) with individual desolvation penalties for each partner in the protein-protein complex plus a hydrogen bonding term; and (3) a surface area (SA) contribution to account for the loss of water contacts upon protein-protein complex formation. The accuracy and performance of the scoring function, termed MM-ISMSA, have been assessed by (1) comparing the total binding energies, the electrostatic term, and its components (charge-charge and individual desolvation energies), as well as the per residue contributions, to results obtained with well-established methods such as APBSA or MM-PB(GB)SA for a set of 1242 decoy protein-protein complexes and (2) testing its ability to recognize the docking solution closest to the experimental structure as that providing the most favorable total binding energy. For this purpose, a test set consisting of 15 protein-protein complexes with known 3D structure mixed with 10 decoys for each complex was used. The correlation between the values afforded by MM-ISMSA and those from the other methods is quite remarkable (r(2) ∼ 0.9), and only 0.2-5.0 s (depending on the number of residues) are spent on a single calculation including an all vs all pairwise energy decomposition. On the other hand, MM-ISMSA correctly identifies the best docking solution as that closest to the experimental structure in 80% of the cases. Finally, MM-ISMSA can process molecular dynamics trajectories and reports the results as averaged values with their standard deviations. MM-ISMSA has been implemented as a plugin to the widely used molecular graphics program PyMOL, although it can also be executed in command-line mode. MM-ISMSA is distributed free of charge to nonprofit organizations.

Perturbation and variational approach for the equation of state for hard-sphere and Lennard—Jones fluids

International Nuclear Information System (INIS)

Khasare, S.B.

2012-01-01

The present work uses the concept of a scaled particle along with the perturbation and variation approach, to develop an equation of state (EOS) for a mixture of hard sphere (HS), Lennard—Jones (LJ) fluids. A suitable flexible functional form for the radial distribution function G(R) is assumed for the mixture, with R as a variable. The function G(R) has an arbitrary parameter m and a different equation of state can be obtained with a suitable choice of m. For m = 0.75 and m = 0.83 results are close to molecular dynamics (MD) result for pure HS and LJ fluid respectively. (physics of gases, plasmas, and electric discharges)

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.

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.

Contact angle of sessile drops in Lennard-Jones systems.

Science.gov (United States)

Becker, Stefan; Urbassek, Herbert M; Horsch, Martin; Hasse, Hans

2014-11-18

Molecular dynamics simulations are used for studying the contact angle of nanoscale sessile drops on a planar solid wall in a system interacting via the truncated and shifted Lennard-Jones potential. The entire range between total wetting and dewetting is investigated by varying the solid-fluid dispersive interaction energy. The temperature is varied between the triple point and the critical temperature. A correlation is obtained for the contact angle in dependence of the temperature and the dispersive interaction energy. Size effects are studied by varying the number of fluid particles at otherwise constant conditions, using up to 150,000 particles. For particle numbers below 10,000, a decrease of the contact angle is found. This is attributed to a dependence of the solid-liquid surface tension on the droplet size. A convergence to a constant contact angle is observed for larger system sizes. The influence of the wall model is studied by varying the density of the wall. The effective solid-fluid dispersive interaction energy at a contact angle of θ = 90° is found to be independent of temperature and to decrease linearly with the solid density. A correlation is developed that describes the contact angle as a function of the dispersive interaction, the temperature, and the solid density. The density profile of the sessile drop and the surrounding vapor phase is described by a correlation combining a sigmoidal function and an oscillation term.

A perturbed Lennard-Jones chain equation of state for liquid metals

Energy Technology Data Exchange (ETDEWEB)

Mousazadeh, M H; Marageh, M Ghanadi [AEOI, JIH Research Laboratory, 11365/8486, Tehran (Iran, Islamic Republic of)

2006-05-24

The perturbed Lennard-Jones chain (PLJC) equation of state is formulated based on first-order variational perturbation theory. The model uses two parameters for a monatomic system, segment size, {sigma}, and segment energy, {epsilon}/k. In this work, we employed the PLJC equation to calculate the liquid density of 26 metals, including alkali and alkali earth metals, iron, cobalt, nickel, copper, silver, gold, zinc, cadmium, mercury, aluminium, gallium, indium, thallium, tin, lead, antimony, and bismuth, for which accurate experimental data exist in the literature. The calculations cover a broad range of temperatures ranging from the melting point to close to the critical point and pressures ranging from the vapour-pressure curve up to pressures as high as 2000 bar. The average absolute deviation in the liquid density predicted by the PLJC equation of state in the saturation line compared with experimental data is 1.26%. Also, using the normal melting temperature and liquid density at melting point (T{sub m}, {rho}{sub m}) as input data for the estimation of the equation of state parameters provides a good correlation of liquid density at saturated and compressed pressures.

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.

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

Energy Technology Data Exchange (ETDEWEB)

Zhukhovitskii, D. I., E-mail: dmr@ihed.ras.ru [Joint Institute of High Temperatures, Russian Academy of Sciences, Izhorskaya 13, Bd. 2, 125412 Moscow (Russian Federation)

2016-05-14

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.

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

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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.

John Paul Jones: An Overlooked Autopsy Finding that May Explain His Terminal Illness.

Science.gov (United States)

Hamrell, Burt B

2016-03-01

A finding in the autopsy of John Paul Jones, the American Revolutionary War naval hero, may explain his terminal illness. During his last 2 years, he had a persistent productive cough and dyspnea. Ten days before death, he developed rapidly progressive dependent edema and ascites. He died in France in 1792. His body, preserved in alcohol in a lead coffin, was, in 1905, removed to the United States. Glomerulonephritis was noted on an autopsy, performed in France, but there was no comment then or since about ventricular wall thickness being the same in both ventricles at 5-6 mm. Hypertrophy and dilatation with biventricular failure followed by tissue shrinkage during 113 years in alcohol could have resulted in these ventricular wall findings. Systemic hypertension and left ventricular failure are consistent with his respiratory symptoms complicated perhaps by pulmonary emboli, right ventricular failure with tricuspid regurgitation, peripheral congestion, and jaundice. © 2015 American Academy of Forensic Sciences.

Molecular dynamics calculation of half-lives for thermal decay of Lennard-Jones clusters

International Nuclear Information System (INIS)

Smith, R.W.

1991-01-01

Molecular dynamics has been used with a Lenard-Jones (6-12) potential in order to study the decay behavior of neutral Argon clusters containing between 12 and 14 atoms. The clusters were heated to temperatures well above their melting points and then tracked in time via molecular dynamics until evaporation of one or more atoms was observed. In each simulation, the mode of evaporation, energy released during evaporation, and cluster lifetime were recorded. Results from roughly 2000 simulation histories were combined in order to compute statistically significant values of cluster half-lives and decay energies. It was found that cluster half-life decreases with increasing energy and that for a given value of excess energy (defined as E=(E tot -E gnd )/n), the 13 atom cluster is more stable against decay than clusters containing either 12 or 14 atoms. The dominant decay mechanism for all clusters was determined to be single atom emission. (orig.)

An application of viola jones method for face recognition for absence process efficiency

Science.gov (United States)

Rizki Damanik, Rudolfo; Sitanggang, Delima; Pasaribu, Hendra; Siagian, Hendrik; Gulo, Frisman

2018-04-01

Absence was a list of documents that the company used to record the attendance time of each employee. The most common problem in a fingerprint machine is the identification of a slow sensor or a sensor not recognizing a finger. The employees late to work because they get difficulties at fingerprint system, they need about 3 – 5 minutes to absence when the condition of finger is wet or not fit. To overcome this problem, this research tried to utilize facial recognition for attendance process. The method used for facial recognition was Viola Jones. Through the processing phase of the RGB face image was converted into a histogram equalization face image for the next stage of recognition. The result of this research was the absence process could be done less than 1 second with a maximum slope of ± 700 and a distance of 20-200 cm. After implement facial recognition the process of absence is more efficient, just take less 1 minute to absence.

Method and system of Jones-matrix mapping of blood plasma films with "fuzzy" analysis in differentiation of breast pathology changes

Science.gov (United States)

Zabolotna, Natalia I.; Radchenko, Kostiantyn O.; Karas, Oleksandr V.

2018-01-01

A fibroadenoma diagnosing of breast using statistical analysis (determination and analysis of statistical moments of the 1st-4th order) of the obtained polarization images of Jones matrix imaginary elements of the optically thin (attenuation coefficient τ fibroadenoma" of breast was 82.7% by the method of linear discriminant analysis, and by the "fuzzy" logic method is 95.3%. The obtained results allow to confirm the potentially high level of reliability of the method of differentiation by "fuzzy" analysis.

Kinetic-contact-driven gigantic energy transfer in a two-dimensional Lennard-Jones fluid confined to a rotating pore

Science.gov (United States)

Karbowniczek, Paweł; Chrzanowska, Agnieszka

2017-11-01

A two-dimensional Lennard-Jones system in a circular and rotating container has been studied by means of molecular dynamics technique. A nonequilibrium transition to the rotating stage has been detected in a delayed time since an instant switching of the frame rotation. This transition is attributed to the increase of the density at the wall because of the centrifugal force. At the same time the phase transition occurs, the inner system changes its configuration of the solid-state type into the liquid type. Impact of angular frequency and molecular roughness on the transport properties of the nonrotating and rotating systems is analyzed.

An efficient and cost effective FPGA based implementation of the Viola-Jones face detection algorithm

Directory of Open Access Journals (Sweden)

Peter Irgens

2017-04-01

Full Text Available We present an field programmable gate arrays (FPGA based implementation of the popular Viola-Jones face detection algorithm, which is an essential building block in many applications such as video surveillance and tracking. Our implementation is a complete system level hardware design described in a hardware description language and validated on the affordable DE2-115 evaluation board. Our primary objective is to study the achievable performance with a low-end FPGA chip based implementation. In addition, we release to the public domain the entire project. We hope that this will enable other researchers to easily replicate and compare their results to ours and that it will encourage and facilitate further research and educational ideas in the areas of image processing, computer vision, and advanced digital design and FPGA prototyping.

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

Energy Technology Data Exchange (ETDEWEB)

Wynuveen, R.A.; Smith, W.H.; Sholeen, C.M.; Flynn, K.F.

1984-08-01

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.

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)

Wynuveen, R.A.; Smith, W.H.; Sholeen, C.M.; Flynn, K.F.

1984-08-01

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

A model-adaptivity method for the solution of Lennard-Jones based adhesive contact problems

Science.gov (United States)

Ben Dhia, Hachmi; Du, Shuimiao

2018-05-01

The surface micro-interaction model of Lennard-Jones (LJ) is used for adhesive contact problems (ACP). To address theoretical and numerical pitfalls of this model, a sequence of partitions of contact models is adaptively constructed to both extend and approximate the LJ model. It is formed by a combination of the LJ model with a sequence of shifted-Signorini (or, alternatively, -Linearized-LJ) models, indexed by a shift parameter field. For each model of this sequence, a weak formulation of the associated local ACP is developed. To track critical localized adhesive areas, a two-step strategy is developed: firstly, a macroscopic frictionless (as first approach) linear-elastic contact problem is solved once to detect contact separation zones. Secondly, at each shift-adaptive iteration, a micro-macro ACP is re-formulated and solved within the multiscale Arlequin framework, with significant reduction of computational costs. Comparison of our results with available analytical and numerical solutions shows the effectiveness of our global strategy.

Numerical computations of the Lennard-Jones resonances and ''relative displacements'' of the scattered atomic beams from the system He/LiF(001)

International Nuclear Information System (INIS)

Garcia, N.

1976-01-01

This paper considers the effect of the attractive part of the interaction potential on the scattering of He atoms from a LiF(001) surface. We calculate, in particular, the Lennard-Jones resonances on the intensities and the phases of the scattered amplitudes, using a square well in the front of a hard corrugated surface model. We show that the amplitudes for incident energies smaller than the depth of the well are dominated by the resonances

Kapitza thermal conductance at the interface between Lennard-Jones crystals using non-equilibrium molecular dynamics simulations

International Nuclear Information System (INIS)

Merabia, Samy; Termentzidis, Konstantinos

2012-01-01

We characterize the thermal Kapitza conductance between Lennard-Jones solids using non-equilibrium molecular dynamics simulations. We consider a series of perfect interfaces between mass-mismatched solids. We show that both the acoustic mismatch model (AMM) and the diffuse mismatch model (DMM) fail to predict the interfacial conductance even for large acoustic mismatched solids. This poor agreement may be explained by the use of equilibrium distributions of phonons in the expression of the conductance. On the other hand, we show that an extension of AMM taking into account the out-of-equilibrium phonon distribution on both sides of the interface leads to a good agreement with the simulation results, even for interfaces between almost similar materials. This opens the way to understand interfacial heat transport across real semi-conductors and dielectrics.

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

International Nuclear Information System (INIS)

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

2016-01-01

The recent theoretical prediction by Maimbourg and Kurchan [e-print http://arxiv.org/abs/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.

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

2016-04-01

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.

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

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

International Nuclear Information System (INIS)

Lin, T.; Bian, X.F.; Jiang, J.

2006-01-01

Two metallic bulk glasses, Cu 60 Zr 30 Ti 10 and Cu 47 Ti 33 Zr 11 Ni 8 Si 1 , 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 r 0 and the effective depth of pair potential V 0 . By assuming a Lennard-Jones potential, r 0 and V 0 were calculated to be 0.28 nm and 0.16 eV for Cu 60 Zr 30 Ti 10 and 0.27 nm and 0.13 eV for Cu 47 Ti 33 Zr 11 Ni 8 Si 1 , respectively. It was found that the glassy alloy Cu 60 Zr 30 Ti 10 was more stable than Cu 47 Ti 33 Zr 11 Ni 8 Si 1 against heating from both experiment and calculation

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

OpenAIRE

Vågslid, Gudfrid

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...

An efficient method for the determination of fourth virial coefficient with Lennard-Jones (12-6) potential and its application

Energy Technology Data Exchange (ETDEWEB)

Mamedov, Bahtiyar A. [Department of Physics, Gaziosmanpaşa University, 60250, Tokat (Turkey); Somuncu, Elif; Askerov, Iskender M. [Department of Physics, Giresun University, Giresun (Turkey)

2016-08-10

In this work, a new theoretical approach is proposed for calculating fourth virial coefficient with Lennard-Jones potential. The established algorithm can be used to evaluate the thermodynamics properties and the intermolecular interaction potentials of liquids and gases with an improved accuracy. Note that the evaluation of the high-order virial coefficients is very valuable for accurate calculation of thermodynamic parameters. By using the suggested method, the fourth virial coefficient of CH{sub 4}, Ar, C{sub 2}H{sub 6} and SF{sub 6} molecules are evaluated. The calculation results are useful for accurate interpretation of the experimental data and of the determination of related physical properties.

Genetic Analysis of Resistance to Benzimidazoles in Physarum: Differential Expression of β-Tubulin Genes

Science.gov (United States)

Burland, Timothy G.; Schedl, Tim; Gull, Keith; Dove, William F.

1984-01-01

Physarum displays two vegetative cell types, uninucleate myxamoebae and multinucleate plasmodia. Mutant myxamoebae of Physarum resistant to the antitubulin drug methylbenzimidazole-2-yl-carbamate (MBC) were isolated. All mutants tested were cross-resistant to other benzimidazoles but not to cycloheximide or emetine. Genetic analysis showed that mutation to MBC resistance can occur at any one of four unlinked loci, benA, benB, benC or benD. MBC resistance of benB and benD mutants was expressed in plasmodia, but benA and benC mutant plasmodia were MBC sensitive, suggesting that benA and benC encode myxamoeba-specific products. Myxamoebae carrying the recessive benD210 mutation express a β-tubulin with noval electrophoretic mobility, in addition to a β-tubulin with wild-type mobility. This and other evidence indicates that benD is a structural gene for β-tubulin, and that at least two β-tubulin genes are expressed in myxamoebae. Comparisons of the β-tubulins of wildtype and benD210 strains by gel electrophoresis revealed that, of the three (or more) β-tubulin genes expressed in Physarum, one, benD, is expressed in both myxamoebae and plasmodia, one is expressed specifically in myxamoebae and one is expressed specifically in plasmodia. However, mutation in only one gene, benD, is sufficient to confer MBC resistance on both myxamoebae and plasmodia. PMID:6479584

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

International Nuclear Information System (INIS)

Ely, J.F.

1986-01-01

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

Transport coefficients of liquid CF4 and SF6 computed by molecular dynamics using polycenter Lennard-Jones potentials

Science.gov (United States)

Hoheisel, C.

1989-01-01

For several liquid states of CF4 and SF4, the shear and the bulk viscosity as well as the thermal conductivity were determined by equilibrium molecular dynamics (MD) calculations. Lennard-Jones four- and six-center pair potentials were applied, and the method of constraints was chosen for the MD. The computed Green-Kubo integrands show a steep time decay, and no particular longtime behavior occurs. The molecule number dependence of the results is found to be small, and 3×105 integration steps allow an accuracy of about 10% for the shear viscosity and the thermal conductivity coefficient. Comparison with experimental data shows a fair agreement for CF4, while for SF6 the transport coefficients fall below the experimental ones by about 30%.

Transport coefficients of liquid CF4 and SF6 computed by molecular dynamics using polycenter Lennard-Jones potentials

International Nuclear Information System (INIS)

Hoheisel, C.

1989-01-01

For several liquid states of CF 4 and SF 6 , the shear and the bulk viscosity as well as the thermal conductivity were determined by equilibrium molecular dynamics (MD) calculations. Lennard-Jones four- and six-center pair potentials were applied, and the method of constraints were chosen for the MD. The computed Green-Kubo integrands show a steep time decay, and no particular longtime behavior occurs. The molecule number dependence of the results is found to be small, and 3 x 10 5 integration steps allow an accuracy of about 10% for the shear viscosity and the thermal conductivity coefficient. Comparison with experimental data shows a fair agreement for CF 4 , while for SF 6 the transport coefficients fall below the experimental ones by about 30%

The Analysis of the Possibility of Using Viola-Jones Algorithm to Recognise Hand Gestures in Human-Machine Interaction

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Golański Piotr

2017-08-01

Full Text Available The article concerns the issue of applying computer-aided systems of the maintenance of technical objects in difficult conditions. Difficult conditions shall be understood as these in which the maintenance takes place in a specific location making it hard or even preventing from using a computer. In these cases computers integrated with workwear should be used, the so-called wearable computers, with which the communication is possible by using hand gestures. The results of the analysis of the usefulness of one of methods of image recognition based on Viola-Jones algorithm were described. This algorithm enables to obtain the model of recognised image which might be used as a pattern in the application programme detecting a certain image.

Computational and theoretical studies of globular proteins

Science.gov (United States)

Pagan, Daniel L.

Protein crystallization is often achieved in experiment through a trial and error approach. To date, there exists a dearth of theoretical understanding of the initial conditions necessary to promote crystallization. While a better understanding of crystallization will help to create good crystals suitable for structure analysis, it will also allow us to prevent the onset of certain diseases. The core of this thesis is to model and, ultimately, understand the phase behavior of protein particles in solution. Toward this goal, we calculate the fluid-fluid coexistence curve in the vicinity of the metastable critical point of the modified Lennard-Jones potential, where it has been shown that nucleation is increased by many orders of magnitude. We use finite-size scaling techniques and grand canonical Monte Carlo simulation methods. This has allowed us to pinpoint the critical point and subcritical region with high accuracy in spite of the critical fluctuations that hinder sampling using other Monte Carlo techniques. We also attempt to model the phase behavior of the gamma-crystallins, mutations of which have been linked to genetic cataracts. The complete phase behavior of the square well potential at the ranges of attraction lambda = 1.15 and lambda = 1.25 is calculated and compared with that of the gammaII-crystallin. The role of solvent is also important in the crystallization process and affects the phase behavior of proteins in solution. We study a model that accounts for the contribution of the solvent free-energy to the free-energy of globular proteins. This model allows us to model phase behavior that includes solvent.

Effect of surface tension on the behavior of adhesive contact based on Lennard-Jones potential law

Science.gov (United States)

Zhu, Xinyao; Xu, Wei

2018-02-01

The present study explores the effect of surface tension on adhesive contact behavior where the adhesion is interpreted by long-range intermolecular forces. The adhesive contact is analyzed using the equivalent system of a rigid sphere and an elastic half space covered by a membrane with surface tension. The long-range intermolecular forces are modeled with the Lennard‒Jones (L‒J) potential law. The current adhesive contact issue can be represented by a nonlinear integral equation, which can be solved by Newton‒Raphson method. In contrast to previous studies which consider intermolecular forces as short-range, the present study reveals more details of the features of adhesive contact with surface tension, in terms of jump instabilities, pull-off forces, pressure distribution within the contact area, etc. The transition of the pull-off force is not only consistent with previous studies, but also presents some new interesting characteristics in the current situation.

Acute gouty arthritis and rapidly progressive renal failure as manifestation of multiple myeloma: clinical case description

Directory of Open Access Journals (Sweden)

O.V. Gudym

2017-08-01

Full Text Available The article describes a clinical case of multiple myeloma in 78-year-old man, its clinical onset was as an acute attack of gout. The patient was admitted to hospital due to the development of the first acute attack of gout. The attack was characterized by polyarthricular joint lesion of the upper and lower extremities, pronounced inflammatory reaction, insufficient response to the use of non-steroidal anti-inflammatory drugs, and a high level of hyperuricemia. The serum uric acid concentration ranged from 636 to 712 μmol/l. The study of the synovial fluid of the inflamed knee joint made it possible to reveal uric acid crystals and to confirm the diagnosis of acute gouty arthritis. Simultaneously, the patient had significant renal impairment: creatinine was 574 μmol/l, urea — 39.9 mmol/l, glomerular filtration rate according to CKD-EPI — 8 ml/min. The daily proteinuria was 1.8 g. A retrospective assessment of laboratory parameters allowed to reveal completely normal indicators of renal function 6 months ago. Considering the development of acute gouty arthritis, its polyarticular nature, persistent course, rapid involvement of new joints, high uric acid levels during an acute attack exceeding 600 μmol/l (10 mg/dL, rapid development of renal failure within 6 months until the terminal stage, it was suggested the secondary nature of gout on the background of kidney damage by another pathological process. Further clinical, laboratory and instrumental studies allowed verifying multiple myeloma with renal damage. Bence Jones protein in the urine was not detected, there was also no evidence of hyperproteinemia. However, pain in the spine, ribs and chest was the basis for carrying out an X-ray study of the bones of the skeleton. Changes in the skeleton typical for multiple myeloma have been identified. Myelogram showed a high content of plasma cells (21.1 %, electrophoresis of blood proteins showed a high M-gradient (30.42 %, and a cytochemical

NEWS: John Goronwy Jones (1920-1999)

Science.gov (United States)

Jennison, Brenda M.

2000-05-01

John Goronwy Jones Gron Jones, as he was known to all, was a champion of Physics Education and his death, shortly before his eightieth birthday, robbed physics teachers of a colleague who fought many battles on their behalf. He was not shy of taking issue with anyone in authority who might be putting forward policies which would harm his great love: Physics Education and Physics Teaching. His photograph shows a man with an impish grin, looking friend and foe alike straight in the eye, before delivering the death blow to an argument which was founded on less than common sense. At other times he would listen patiently to the woes of colleagues before offering them fatherly/grandfatherly advice so that whoever was on the receiving end would go away feeling better for the encounter. Gron was born in Swansea and educated at Lewis Boys Grammar School in Glamorgan before entering University College Cardiff first of all as a mathematician before graduating in Physics in 1941. After his war service in the RAF, working on signals and radar development, he returned to do an MSc in X-ray crystallography before completing a PGCE in Bristol. What then passed for teacher training in all institutions left him wary of returning to train teachers himself but after 14 years spent teaching physics in three schools he returned to Cardiff and began a 25 year career in teacher training. He and his two colleagues, Clifford Othen (chemistry) and Douglas Hillier (biology) built up the Cardiff Science Centre as a focus for initial and in-service science teacher training in South Wales. The triumvirate was well known and a power to be reckoned with. They created links between the University Science Departments and the Schools. Gron knew the local schools and their physics teachers intimately. Cardiff became a focus for science education both nationally and internationally. He was a frequent attender at both ICPE (International Commission for Physics Education) and GIREP (International Physics

Thermodynamic equivalence between the Lennard-Jones and hard-core attractive Yukawa systems

International Nuclear Information System (INIS)

Kadiri, Y.; Albaki, R.; Bretonnet, J.L.

2008-01-01

The investigation of the thermodynamic properties of the Lennard-Jones (LJ) fluid is made by means of a system of particles interacting with a potential of hard-core plus attractive Yukawa tail (HCY). Due to the similarity between the LJ potential and the HCY potential in its overall form, it is worthwhile seeking to approximate the LJ potential in much the same way that the hard-sphere reference potential has been so used. The study consists in describing the thermodynamics of the LJ fluid in terms of the equivalent HCY system, whose the properties are known accurately, by means of mapping the thermodynamic quantities for the HCY potential parameters. The method is feasible owing to a convenient analytical expression of the Helmholtz free energy from the mean-spherical approximation expanded in power of the inverse temperature. Two different procedures are used to determine the parameters of the HCY potential as a function of the thermodynamic states: one is based on the simultaneous fits of pressure and internal energy of the LJ system and the other uses the concept of collision frequency. The reasonable homogeneity of the results in both procedures of mapping makes that the HCY potential is a very good reference system, whose the proposed theoretical expressions can be used confidently to predict the thermodynamic properties of more realistic potentials

A multifractal detrended fluctuation analysis of financial market efficiency: Comparison using Dow Jones sector ETF indices

Science.gov (United States)

Tiwari, Aviral Kumar; Albulescu, Claudiu Tiberiu; Yoon, Seong-Min

2017-10-01

This study challenges the efficient market hypothesis, relying on the Dow Jones sector Exchange-Traded Fund (ETF) indices. For this purpose, we use the generalized Hurst exponent and multifractal detrended fluctuation analysis (MF-DFA) methods, using daily data over the timespan from 2000 to 2015. We compare the sector ETF indices in terms of market efficiency between short- and long-run horizons, small and large fluctuations, and before and after the global financial crisis (GFC). Our findings can be summarized as follows. First, there is clear evidence that the sector ETF markets are multifractal in nature. We also find a crossover in the multifractality of sector ETF market dynamics. Second, the utilities and consumer goods sector ETF markets are more efficient compared with the financial and telecommunications sector ETF markets, in terms of price prediction. Third, there are noteworthy discrepancies in terms of market efficiency, between the short- and long-term horizons. Fourth, the ETF market efficiency is considerably diminished after the global financial crisis.

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

International Nuclear Information System (INIS)

Adebayo, G.A.; Anusionwu, B.C.; Njah, A.N.; Adeniran, O.J.; Mathew, B.; Sunmonu, R.S.

2009-01-01

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)

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

KAUST Repository

Kadoura, Ahmad Salim

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.

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

International Nuclear Information System (INIS)

Mulero, A; Galan, C; Cuadros, F

2003-01-01

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

Kas loodus + foto = loodusfoto? / Indrek Rohtmets

Index Scriptorium Estoniae

Rohtmets, Indrek, 1953-

2006-01-01

Rahvusvaheline fotokonkursi näitus "Loodusfoto 2005" Kumus kuni 12. XI. Loodusfotograafiast, Shell Wildlife Photographer of the Year võistlusest. Peapreemia pälvis 2005. a. Manuel Presti, 2006. a. Göran Ehlme. Eric Hoskingi auhinna sai 2005. a. Bence Mate

IgD multiple myeloma: Clinical, biological features and prognostic value of the serum free light chain assay.

Science.gov (United States)

Djidjik, R; Lounici, Y; Chergeulaïne, K; Berkouk, Y; Mouhoub, S; Chaib, S; Belhani, M; Ghaffor, M

2015-09-01

IgD multiple myeloma (MM) is a rare subtype of myeloma, it affects less than 2% of patients with MM. To evaluate the clinical and prognostic attributes of serum free light chains (sFLCs) analysis, we examined 17 cases of IgD MM. From 1998 to 2012, we obtained 1250 monoclonal gammapathies including 590 multiple myeloma and 17 patients had IgD MM. With preponderance of men patients with a mean age at diagnosis of: 59±12years. Patients with IgD MM have a short survival (Median survival=9months). The presenting features included: bone pain (75%), lymphadenopathy (16%), hepatomegaly (25%), splenomegaly (8%), associated AL amyloidosis (6%), renal impairment function (82%), infections (47%), hypercalcemia (37%) and anemia (93%). Serum electrophoresis showed a subtle M-spike (Mean=13.22±10g/L) in all patients associated to a hypogammaglobulinemia. There was an over-representation of Lambda light chain (65%); high serum β2-microglobulin in 91% and Bence Jones proteinuria was identified in 71%. The median rate of sFLCs κ was 19.05mg/L and 296.75mg/L for sFLCs λ. sFLCR was abnormal in 93% of patients and it showed concordance between baseline sFLCR and the survival (P=0.034). The contribution of FLC assay is crucial for the prognosis of patients with IgD MM. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

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.

Inclusión social y educación integral a niños con discapacidad centro de educación Melvin Jones.

OpenAIRE

Granda Reyes, Raquel Eliana; Gavino González, Julia Dolores

2017-01-01

Este trabajo de investigación, sobre la inclusión social y educación integral a los niños y niñas y adolescentes, que sufren de algún tipo de discapacidad y que asisten al Centro de Educación Melvin Jones, se analizó el marco teórico, conceptual, las normas y leyes que respaldan esta investigación, como la Constitución de la República del Ecuador y la Ley Orgánica de Discapacidades. Se trataron temas como los derechos humanos la inclusión y exclusión social, la pobreza, desigualdad, y los gr...

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

Energy Technology Data Exchange (ETDEWEB)

Kadoura, Ahmad, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa; Sun, Shuyu, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa [Computational Transport Phenomena Laboratory, The Earth Sciences and Engineering Department, The Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900 (Saudi Arabia); Siripatana, Adil, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa; Hoteit, Ibrahim, E-mail: ibrahim.hoteit@kaust.edu.sa [Earth Fluid Modeling and Predicting Group, The Earth Sciences and Engineering Department, The Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900 (Saudi Arabia); Knio, Omar, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa [Uncertainty Quantification Center, The Applied Mathematics and Computational Science Department, The Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900 (Saudi Arabia)

2016-06-07

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 (CH{sub 4}, N{sub 2}, 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 CO{sub 2} and C{sub 2} H{sub 6}.

Reconciling the understanding of 'hydrophobicity' with physics-based models of proteins.

Science.gov (United States)

Harris, Robert C; Pettitt, B Montgomery

2016-03-02

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 (ΔGsolv) 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 (ΔGhyd) of ΔGsolv 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 (ΔG(LJ)) of ΔGhyd is that it is the free energy of turning on the Lennard-Jones (LJ) interactions between the solute and solvent. However, ΔG(LJ) decreases with A for alanine and glycine peptides. Here we argue that these apparent contradictions can be reconciled by defining ΔGhyd to be a near hard core insertion energy (ΔGrep), as in the partitioning proposed by Weeks, Chandler, and Andersen. However, recent results have shown that ΔGrep 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 ΔGhyd are therefore inadequate for proteins.

Imetabane väljapanek toob Kumu saali kogu maailma looduse kirevuse / Rein Maran

Index Scriptorium Estoniae

Maran, Rein, 1931-

2006-01-01

Rahvusvahelise fotokonkursi näitusest "Loodusfoto 2005" Kumu suures saalis. Briti Loodusloomuuseumi ja ajakirja BBC Wildlife Magazine korraldatud fotokonkursist. Lähemalt võidutöödest: Alexander Mustard (Suurbritannia) "Riffahvenate parv", Manuel Presti (Itaalia) "Taevane jaht", Bence Mate (Ungari) "Haigutav rebane", Thorsten Milse (Saksamaa) "Polaarretk"

Classification of facial-emotion expression in the application of psychotherapy using Viola-Jones and Edge-Histogram of Oriented Gradient.

Science.gov (United States)

Candra, Henry; Yuwono, Mitchell; Rifai Chai; Nguyen, Hung T; Su, Steven

2016-08-01

Psychotherapy requires appropriate recognition of patient's facial-emotion expression to provide proper treatment in psychotherapy session. To address the needs this paper proposed a facial emotion recognition system using Combination of Viola-Jones detector together with a feature descriptor we term Edge-Histogram of Oriented Gradients (E-HOG). The performance of the proposed method is compared with various feature sources including the face, the eyes, the mouth, as well as both the eyes and the mouth. Seven classes of basic emotions have been successfully identified with 96.4% accuracy using Multi-class Support Vector Machine (SVM). The proposed descriptor E-HOG is much leaner to compute compared to traditional HOG as shown by a significant improvement in processing time as high as 1833.33% (p-value = 2.43E-17) with a slight reduction in accuracy of only 1.17% (p-value = 0.0016).

Nematic-isotropic transition in some lattice models for rigid cores having semiflexible tails: segmental Lennard-Jones interactions

International Nuclear Information System (INIS)

Dowell, F.

1983-01-01

Two average-environment simple cubic lattice models: a refined model and a simple model, both having site-site (segmental) pair Lennard-Jones (LJ) interactions: for molecules composed of rigid cores having semiflexible tails are presented. The calculated values of the following properties at the nematic-isotropic transition for rigid rods of varying length are compared with relevant experimental data for PAA (p-azoxyanisole, or 4,4'-dimethoxyazoxybenzene): temperature, core orientational order parameter, nematic density and volume, relative density change, and relative entropy change. The temperature change as a function of volume change at constant order parameter is also discussed. In general, both LJ models give considerably better quantitative agreement with experiment, especially for the temperature and the relative density change, than do the earlier lattice models with hard repulsions, with or without constant segmental pair interaction energies. In most aspects, these LJ models give good quantitative agreement with experiment. These LJ models elucidate the importance of realistic intermolecular potentials, especially the role of soft repulsions, in describing an order-disorder transition between two condensed phases

Experimental studies on natural circulation in molten salt loops

International Nuclear Information System (INIS)

Srivastava, A.K.; Borgohain, A.; Maheshwari, N.K.; Vijayan, P.K.

2015-01-01

Molten salts are increasingly getting attention as a coolant and storage medium in solar thermal power plants and as a liquid fuel, blanket and coolant in Molten Salt Reactors (MSR’s). Two different test facilities named Molten Salt Natural Circulation Loop (MSNCL) and Molten Active Fluoride salt Loop (MAFL) have been setup for thermal hydraulics, instrument development and material related studies relevant to MSR and solar power plants. The working medium for MSNCL is a molten nitrate salt which is a mixture of NaNO 3 and KNO 3 in 60:40 ratio and proposed as one of the coolant option for molten salt based reactor and coolant as well as storage medium for solar thermal power application. On the other hand, the working medium for MAFL is a eutectic mixture of LiF and ThF 4 and proposed as a blanket salt for Indian Molten Salt Breeder Reactor (MSBR). Steady state natural circulation experiments at different power level have been performed in the MSNCL. Transient studies for startup of natural circulation, loss of heat sink, heater trip and step change in heater power have also been carried out in the same. A 1D code LeBENC, developed in-house to simulate the natural circulation characteristics in closed loops, has been validated with the experimental data obtained from MSNCL. Further, LeBENC has been used for Pretest analysis of MAFL. This paper deals with the description of both the loops and experimental studies carried out in MSNCL. Validation of LeBENC along with the pretest analysis of MAFL using the same are also reported in this paper. (author)

Determination of the friction coefficient via the force autocorrelation function. A molecular dynamics investigation for a dense Lennard-Jones fluid

International Nuclear Information System (INIS)

Vogelsang, R.; Hoheisel, C.

1987-01-01

For a large region of dense fluid states of a Lennard-Jones system, they have calculated the friction coefficient by the force autocorrelation function of a Brownian-type particle by molecular dynamics (MD). The time integral over the force autocorrelation function showed an interesting behavior and the expected plateau value when the mass of the Brownian particle was chosen to be about a factor of 100 larger than the mass of the fluid particle. Sufficient agreement was found for the friction coefficient calculated by this way and that obtained by calculations of the self-diffusion coefficient using the common relation between these coefficients. Furthermore, a modified friction coefficient was determined by integration of the force autocorrelation function up to the first maximum. This coefficient can successfully be used to derive a reasonable soft part of the friction coefficient necessary for the Rice-Allnatt approximation for the shear velocity and simple liquids

Influence of DC electric field on the Lennard-Jones potential and phonon vibrations of carbon nanotube on catalyst

International Nuclear Information System (INIS)

Saeidi, Mohammadreza; Vaezzadeh, Majid; Badakhshan, Farzaneh

2011-01-01

Influence of DC electric field on carbon nanotube (CNT) growth in chemical vapor deposition is studied. Investigation of electric field effect in van der Waals interaction shows that increase in DC electric field raises the magnitude of attractive term of the Lennard-Jones potential. By using a theoretical model based on phonon vibrations of CNT on catalyst, it is shown that there is an optimum field for growth. Also it is observed that CNT under optimum electric field is longer than CNT in the absence of field. Finally, the relation between optimum DC electric field and type of catalyst is investigated and for some intervals of electric field, the best catalyst is introduced, which is very useful for experimental researches. -- Research highlights: → Influence of DC electric field on CNT growth in CVD. → Effect of electric field on van der Waals interaction between CNT and its catalyst. → Applying DC electric field increases attractive term of Lennard-Jonespotential. → There is an optimum DC field for CNT growth. → For catalyst with stronger van der Waals interaction, optimum field is smaller.

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

Energy Technology Data Exchange (ETDEWEB)

Mulero, A [Departamento de Fisica, Universidad de Extremadura, 06071-Badajoz (Spain); Galan, C [Departamento de Fisica, Universidad de Extremadura, 06071-Badajoz (Spain); Cuadros, F [Departamento de Fisica, Universidad de Extremadura, 06071-Badajoz (Spain)

2003-04-16

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.

[Ungaris anti välja Jaan Krossi ja Jaan Kaplinski tõlkeraamatud] / Lauri Eesmaa

Index Scriptorium Estoniae

Eesmaa, Lauri

2003-01-01

Kross, Jaan. A hamutart̤ és más elbeszélések (Tuhatoos ja teisi jutte) / tõlkinud Béla Jávorszky; Kaplinski, Jaan. A jég és Titanic/A jég és a hanga (Jää ja Titanic/Jää ja kanarbik) / tõlkinud Bence Patat

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

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.

Inside the Literature: An Interview with Sally G. Hoskins, 2017 Recipient of the Elizabeth W. Jones Award for Excellence in Education.

Science.gov (United States)

Hoskins, Sally G

2017-12-01

The Genetics Society of America's Elizabeth W. Jones Award for Excellence in Education recognizes significant and sustained impact on genetics education. The 2017 recipient is Sally G. Hoskins, in recognition of her role in developing and promoting the transformative science education method CREATE (Consider, Read, Elucidate hypotheses, Analyze and interpret data, and Think of the next Experiment). This innovative approach uses primary literature to engage students, allowing them to experience for themselves the creativity and challenge of study design, analysis, interpretation, collaboration, and debate. Comprehensive evaluation of CREATE has consistently found that students improve in difficult-to-teach skills like critical thinking and experimental design, while showing improved attitudes and beliefs about science.This is an abridged version of the interview. The full interview is available on the Genes to Genomes blog, at genestogenomes.org/hoskins/. Copyright © 2017 by the Genetics Society of America.

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)

Flynn, K.F.; Smith, W.H.; Wynveen, R.A.

1984-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Flynn, K.F.; Smith, W.H.; Wynveen, R.A.

1984-01-01

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.

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

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

2016-08-19

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.

Comprehensive representation of the Lennard-Jones equation of state based on molecular dynamics simulation data

Science.gov (United States)

Pieprzyk, S.; Brańka, A. C.; Maćkowiak, Sz.; Heyes, D. M.

2018-03-01

The equation of state (EoS) of the Lennard-Jones fluid is calculated using a new set of molecular dynamics data which extends to higher temperature than in previous studies. The modified Benedict-Webb-Rubin (MBWR) equation, which goes up to ca. T ˜ 6, is reparametrized with new simulation data. A new analytic form for the EoS, which breaks the fluid range into two regions with different analytic forms and goes up to ca. T ≃ 35, is also proposed. The accuracy of the new formulas is at least as good as the MBWR fit and goes to much higher temperature allowing it to now encompass the Amagat line. The fitted formula extends into the high temperature range where the system can be well represented by inverse power potential scaling, which means that our specification of the equation of state covers the entire (ρ, T) plane. Accurate analytic fit formulas for the Boyle, Amagat, and inversion curves are presented. Parametrizations of the extrema loci of the isochoric, CV, and isobaric, CP, heat capacities are given. As found by others, a line maxima of CP terminates in the critical point region, and a line of minima of CP terminates on the freezing line. The line of maxima of CV terminates close to or at the critical point, and a line of minima of CV terminates to the right of the critical point. No evidence for a divergence in CV in the critical region is found.

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

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

International Nuclear Information System (INIS)

Martínez-Ruiz, F. J.; Blas, F. J.; Moreno-Ventas Bravo, A. I.

2015-01-01

We determine the interfacial properties of a symmetrical binary mixture of equal-sized spherical Lennard-Jones molecules, σ 11 = σ 22 , with the same dispersive energy between like species, ϵ 11 = ϵ 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 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 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 with a desorption of the

Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions.

Science.gov (United States)

Fischer, Nina M; van Maaren, Paul J; Ditz, Jonas C; Yildirim, Ahmet; van der Spoel, David

2015-07-14

In order to increase the accuracy of classical computer simulations, existing methodologies may need to be adapted. Hitherto, most force fields employ a truncated potential function to model van der Waals interactions, sometimes augmented with an analytical correction. Although such corrections are accurate for homogeneous systems with a long cutoff, they should not be used in inherently inhomogeneous systems such as biomolecular and interface systems. For such cases, a variant of the particle mesh Ewald algorithm (Lennard-Jones PME) was already proposed 20 years ago (Essmann et al. J. Chem. Phys. 1995, 103, 8577-8593), but it was implemented only recently (Wennberg et al. J. Chem. Theory Comput. 2013, 9, 3527-3537) in a major simulation code (GROMACS). The availability of this method allows surface tensions of liquids as well as bulk properties to be established, such as density and enthalpy of vaporization, without approximations due to truncation. Here, we report on simulations of ≈150 liquids (taken from a force field benchmark: Caleman et al. J. Chem. Theory Comput. 2012, 8, 61-74) using three different force fields and compare simulations with and without explicit long-range van der Waals interactions. We find that the density and enthalpy of vaporization increase for most liquids using the generalized Amber force field (GAFF, Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) and the Charmm generalized force field (CGenFF, Vanommeslaeghe et al. J. Comput. Chem. 2010, 31, 671-690) but less so for OPLS/AA (Jorgensen and Tirado-Rives, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670), which was parametrized with an analytical correction to the van der Waals potential. The surface tension increases by ≈10(-2) N/m for all force fields. These results suggest that van der Waals attractions in force fields are too strong, in particular for the GAFF and CGenFF. In addition to the simulation results, we introduce a new version of a web server, http

Plasma Renin Activity in Children with Protein Energy Malnutrition ...

African Journals Online (AJOL)

Date received: 11 October 1973. Reprint requests to Professor J. J. Jones. for analysis during each patient's last week in hospital. It was not possible ... oil, eggs, Multivite syrup, folic acid and potassium chlo- ride) and magnesium sulphate by intramuscular injection. No iron was given for the first 10 days. Intravenous trans-.

Kaplinski Ungaris

Index Scriptorium Estoniae

2003-01-01

11. juunil 2003 esitleti Budapestis Eesti Instituudi ruumes Jaan Kaplinski raamatut "A jég és a Titanic. A jég és a hanga", mis koondab "Jää ja Titanicu" ning "Jää ja kanarbiku" (tlk. Bence Petat, kirj. Korona Kiad̤). Vt. ka: Eesti Ekspress, 2003, 26. juuni, lk. B6 ; Looming, 2003, nr. 7, lk. 1111-1112

Identification of Insecticidal Constituents from the Essential Oil of Valeriana jatamansi Jones against Liposcelis bostrychophila Badonnel

Directory of Open Access Journals (Sweden)

Xin Chao Liu

2013-01-01

Full Text Available The aim of this research was to determine chemical composition and insecticidal activities of the essential oil of Valeriana jatamansi Jones roots against booklice, Liposcelis bostrychophila Badonnel, and to isolate insecticidal constituents from the oil. Essential oil of V. jatamansi was obtained by hydrodistillation and analyzed by GC-MS. A total of 27 components in the essential oil were identified. The major compounds were patchoulol (24.3%, α-bulnesene (13.8%, isovaleric acid (12.9%, α-guaiene (8.7%, and 3-methylvaleric acid (8.4%. Based on bioactivity-guided fractionation, isovaleric acid, 3-methylvaleric acid, and patchoulol were isolated and identified as the active constituents. The essential oil exhibited contact toxicity against L. bostrychophila with an LC50 value of 236.4 μg/cm2. Patchoulol (LC50 = 61.35 μg/cm2 exhibited stronger acute toxicity than 3-methylvaleric acid (LC50 = 210.69 μg/cm2 against the booklice. The essential oil also possessed fumigant toxicity against L. bostrychophila with an LC50 value of 6.0 mg/L, while 3-methylvaleric acid and isovaleric acid had LC50 values of 5.53 mg/L and 5.67 mg/L against the booklice, respectively. The results indicated that the essential oil and its constituent compounds have potential to develop into natural insecticides or fumigants for control of insects in stored grains.

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

International Nuclear Information System (INIS)

Farid, A.; Iqbal, S.M.J.; Hanif, A.

2013-01-01

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)

Radiographic study of the fifth metatarsal for optimal intramedullary screw fixation of Jones fracture.

Science.gov (United States)

Ochenjele, George; Ho, Bryant; Switaj, Paul J; Fuchs, Daniel; Goyal, Nitin; Kadakia, Anish R

2015-03-01

Jones fractures occur in the relatively avascular metadiaphyseal junction of the fifth metatarsal (MT), which predisposes these fractures to delayed union and nonunion. Operative treatment with intramedullary (IM) screw fixation is recommended in certain cases. Incorrect screw selection can lead to refractures, nonunion, and cortical blowout fractures. A better understanding of the anatomy of the fifth MT could aid in preoperative planning, guide screw size selection, and minimize complications. We retrospectively identified foot computed tomographic (CT) scans of 119 patients that met inclusion criteria. Using interactive 3-dimensional (3-D) models, the following measurements were calculated: MT length, "straight segment length" (distance from the base of the MT to the shaft curvature), and canal diameter. The diaphysis had a lateroplantar curvature where the medullary canal began to taper. The average straight segment length was 52 mm, and corresponded to 68% of the overall length of the MT from its proximal end. The medullary canal cross-section was elliptical rather than circular, with widest width in the sagittal plane and narrowest in coronal plane. The average coronal canal diameter at the isthmus was 5.0 mm. A coronal diameter greater than 4.5 mm at the isthmus was present in 81% of males and 74% of females. To our knowledge, this is the first anatomic description of the fifth metatarsal based on 3-D imaging. Excessive screw length could be avoided by keeping screw length less than 68% of the length of the fifth metatarsal. A greater than 4.5 mm diameter screw might be needed to provide adequate fixation for most study patients since the isthmus of the medullary canal for most were greater than 4.5 mm. Our results provide an improved understanding of the fifth metatarsal anatomy to guide screw diameter and length selection to maximize screw fixation and minimize complications. © The Author(s) 2014.

Winter distribution and abundance of Snowy Plovers in eastern North America and the West Indies

Science.gov (United States)

Elliott-Smith, Elise; Haig, Susan M.; Ferland, C.L.; Gorman, Leah

2004-01-01

Serum protein changes were studied in immune and nonimmune pigeons infected with three different strains of Trichomonas gallinae. Strain I (nonvirulent) produced no change in the relative concentration of serum components. Strains II (oral canker) and III (Jones' Barn) produced decreases in albumin and alpha globulins, and increases in beta and gamma globulins between the 7th and 20th days post infection. Birds infected with strain II began to return to normal by the 20th day, while all those infected with strain III were dead between 10 and 14 days post infection. Two serum protein patterns resulted from infection of immune birds with the Jones' Barn strain. One showed no change in relative protein concentrations and no tissue invasion by the parasite while the other was similar to that seen in nonimmune birds infected with a strain producing oral canker. These also showed evidence of tissue invasion by the parasite. It was concluded that tissue invasion was necessary to evoke a quantitative change in serum protein concentrations.

Maailma loodusfoto Kumus

Index Scriptorium Estoniae

2006-01-01

18.10-12.11 Kumu Kunstimuuseumis avatud 80 loodusfoto näitus, mille korraldajad olid Briti Loodusloomuuseum ja ajakiri BBC Wildlife Magazine. Illustratsioonidena "Loodusfoto 2005" üldvõitja Manuel Presti "Taevane jaht", loomaportreede kategooria võitja Alexander Mustard'i "Riffahvenate parv", imetajate käitumise kategooria II koht Thorsten Milse "Polaarretk" ja noortele fotograafidele mõeldud Eric Hoskingi kategooria võitja Bence Maté "Haigutav rebane"

KAJIAN METODE ANALISA DATA GOAL SEEK (MICROSOFT EXCEL UNTUK PENYELESAIAN PERSAMAAN SCHRÖDINGER DALAM MENENTUKAN KUANTISASI ENERGI DIBAWAH PENGARUH POTENSIAL LENNARD-JONES

Directory of Open Access Journals (Sweden)

W. Kurniawan

2016-11-01

Full Text Available Penyelesaian persamaan Schrödinger dengan berbagai model potensial sangat penting dilakukan untuk memberikan gambaran perilaku zarah di bawah pengaruh potensial tersebut. Solusinya berupa fungsi gelombang yang memuat informasi penting tentang perilaku gelombang yang ditunjukkan dengan energi terikatnya. Pada penelitian ini kasus yang ingin diteliti adalah model potensial Lennard-Jones dengan menggunakan metode analisa goal seek yang tersedia pada Microsoft excel. Persamaannya dijabarkan dengan metode Euler terlebih dahulu selanjutnya syarat batas ditentukan agar ketelitian hasil diperoleh. Agar perhitungan goal seek  dapat dilakukan maka harus diubah dari besaran fisis menjadi besaran yang tidak berdimensi dimana parameter v menunjukkan keklasikan suatu sistem dan nilai  ε   menunjukkan kuantisasi energi. Hasil yang diperoleh adalah bahwa dengan memasukkan parameter kontrol nilai v tertentu, telah diperoleh beberapa keadaan energi dengan batas zkiri dan zkanan tertentu. Ketika masukan parameter v yang diberikan semakin besar keadaan energinya pun lebih rapat (ditunjukkan energy state yang diperoleh semakin banyak dibandingkan bila masukan v-nya lebih kecil. Penelitian ini bermanfaat untuk menyederhanakan kasus potensial yang lebih rumit, dimana solusinya dapat diperoleh dengan mudah dan konsep kuantisasi energi akibat model potensial L-J dapat dipahami secara utuh. Solution of the Schrödinger equation in various  potential model is very important in order to provide an overview of  behaviour’s particle under influence of potential model. The solution is a wave function that contains important information are shown by energy state. In this research, the investigated is Lennard Jones potential by using Goal Seek analysis which are available in Microsoft Excel. The equation is described by the Euler method and then boundary condition is determined to perecision result which are obtained. It must be changed in terms dimensionless where

Friction between Two Brownian Particles in a Lennard-Jones Solvent: A Molecular Dynamics Simulation Study

International Nuclear Information System (INIS)

Lee, Song Hi

2010-01-01

We presented a molecular dynamics (MD) simulation study of friction behavior between two very massive Brownian particles (BPs) oriented along the z axis with BP centers at -R 12 /2 and R 12 /2 in a Lennard-Jones solvent as a function of the inter-particle separation, R 12 . In order to fix the BPs in space an MD simulation method with the mass of the BP as 10 90 g/mol was employed in which the total momentum of the system was conserved. The cross friction coefficients of x- and y-components are nearly insensitive to R 12 but that of z-component varies with R 12 in good accord with the simple hydrodynamic approximation. On the other hand, the self-friction coefficients are estimated as a very small difference from the single particle friction coefficients, ξ 0 , at all inter-particle separations which agrees with the simple hydrodynamic approximation. Consequently ξ (-) xx is nearly independent of R 12 and equal to its asymptotic value of twice the single particle friction coefficient, and the other relative friction, ξ (-) zz , is in good agreement with the simple hydrodynamic approximation. Molecular theory of Brownian motion of a single heavy particle in a fluid had received a considerable attention in earlier years. After molecular dynamics (MD) simulation technique was utilized, this subject has been widely studied by a variety of MD simulation methods. The common issues here were about the long time behavior of the force and velocity autocorrelation functions, the system size dependent friction coefficient of a massive Brownian particle, and test of the Stokes-Einstein law

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.

Equation of state and Helmholtz free energy for the atomic system of the repulsive Lennard-Jones particles.

Science.gov (United States)

Mirzaeinia, Ali; Feyzi, Farzaneh; Hashemianzadeh, Seyed Majid

2017-12-07

Simple and accurate expressions are presented for the equation of state (EOS) and absolute Helmholtz free energy of a system composed of simple atomic particles interacting through the repulsive Lennard-Jones potential model in the fluid and solid phases. The introduced EOS has 17 and 22 coefficients for fluid and solid phases, respectively, which are regressed to the Monte Carlo (MC) simulation data over the reduced temperature range of 0.6≤T * ≤6.0 and the packing fraction range of 0.1 ≤ η ≤ 0.72. The average absolute relative percent deviation in fitting the EOS parameters to the MC data is 0.06 and 0.14 for the fluid and solid phases, respectively. The thermodynamic integration method is used to calculate the free energy using the MC simulation results. The Helmholtz free energy of the ideal gas is employed as the reference state for the fluid phase. For the solid phase, the values of the free energy at the reduced density equivalent to the close-packed of a hard sphere are used as the reference state. To check the validity of the predicted values of the Helmholtz free energy, the Widom particle insertion method and the Einstein crystal technique of Frenkel and Ladd are employed. The results obtained from the MC simulation approaches are well agreed to the EOS results, which show that the proposed model can reliably be utilized in the framework of thermodynamic theories.

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

International Nuclear Information System (INIS)

Van Zon, Ramses; Ashwin, S S; Cohen, E G D

2008-01-01

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)

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

Target Glint Suppression Technology.

Science.gov (United States)

1980-09-01

Rayleigh for either horizontal or vertical polarization). 2.1.2 Spatial Characterization. Before the effects of diversity on target detection can be...ncs) dRCS T If the lower intergration limit is taken as zero for the Rayleigh targct model of interest, then this quantity is unbounded. In...port wing, inner section Trailing edge of starboard .:ing, inner section Leading edge of horizontal stabilizer, inner section, port side TLeal, -g

RESONANCIA MAGNÉTICA NUCLEAR DEL PRODUCTO GELIFICADO DE LA REACCIÓN DE CANNIZZARO

Directory of Open Access Journals (Sweden)

Lilia Fernández Sánchez

2015-01-01

Full Text Available Se presenta n los espectros de resonancia magnética nuclear ( RMN de protón 1 H, de carbón 13 C y bidimensionales , del produc to de una síntesis orgánica verde de óxido - reducción en la r eacción de Cannizzaro. El producto fue reportado como un gel triboquímico y elucidado por análisis de infrarrojo IR , ray os X y micrografía de barrido ( SEM . Los resultados en este artículo confirman su estructura a través de diversas técnicas de RMN y evalúan el contenido de benzoato de sodio y alcohol bencílico en la muestra e mpleada en la espectroscopia a través del examen de los valores de las integrales en la s señales de RMN de 1 H. El resultado del estudio indica que el alcohol bencílico se encuentra en un 33.44% mol (fase dispersa con respecto al cont enido de benzoato de sodio (fase continua . Estos resultado s confirma n la estruct ura de gel que con el tiempo pierde a la fase dispersa el alcohol produciendo un xerogel

Third-order nonlinearities and structural features in Langmuir-Blodgett films of 1-benzyl-9-hydrofullerene-60

International Nuclear Information System (INIS)

Shihong Ma; Liying Liu; Xingze Lu

1995-01-01

Third-order nonlinear susceptibilities χ xxxx (3) (-3ω; ω, ω, ω) have been deduced by measuring third-harmonic generation in Langmuir-Blodgett (LB) films of 1-benzyl-9-hydrofullerene-60 (C 60 -Be). The structural features of the condensed layer at the air-water interface and LB films of the C 60 -Be were investigated by small angle x-ray diffraction (SAXD) and optical measurements. The third-order nonlinear susceptibilities (χ (3) ) were obtained by measuring the THG intensities in LB films of C 60 -Be and comparing with that of CS 2 used as the reference. The value of χ xxxx (3) (2.1 x 10 -11 esu) was deduced at a 65 nm thick films. The χ (3) is attributed to a three-photon near resonance at the energy level of 29410 cm -1 . A new-type of two-chain amphiphilic molecule 1,10-bistearyl-4,6,13, 15-tetra-18-nitrogencrown-6 (NC) was used as insert material to construct mixed C 60 -Be/NC LB films. Our π-A, UV-visible absorption and SAXD measurements showed that the structural improvement in the mixed C 60 -Be/NC LB films was realized by insertion of the C 60 -Be molecules between the two hydrophobic chains of the NC molecules

Inequality or injustice in water use for food?

OpenAIRE

Carr, J. A.; Seekell, David A.; D'Odorico, P.

2015-01-01

The global distributions of water availability and population density are uneven and therefore inequality exists in human access to freshwater resources. Is this inequality unjust or only regrettable? To examine this question we formulated and evaluated elementary principles of water ethics relative to human rights for water, and the need for global trade to improve societal access to water by transferring 'virtual water' embedded in plant and animal commodities. We defined human welfare benc...

Abstracts from the Fourteenth Rambam Research Day, December 7, 2017

OpenAIRE

Shraga Blazer (Editor); Ehud Klein (Editor)

2018-01-01

This Supplement of Rambam Maimonides Medical Journal presents the abstracts from the Fourteenth Annual Rambam Research Day. These abstracts represent the newest basic and clinical research coming out of Rambam Health Care Campus—research that is the oxygen for education and development of tomorrow’s generation of physicians. Hence, the research presented on Rambam Research Day is the foundation for understanding patient needs and improving treatment modalities. Bringing research from the benc...

Computation and analysis of the transverse current autocorrelation function, Ct(k,t), for small wave vectors: A molecular-dynamics study for a Lennard-Jones fluid

Science.gov (United States)

Vogelsang, R.; Hoheisel, C.

1987-02-01

Molecular-dynamics (MD) calculations are reported for three thermodynamic states of a Lennard-Jones fluid. Systems of 2048 particles and 105 integration steps were used. The transverse current autocorrelation function, Ct(k,t), has been determined for wave vectors of the range 0.5viscosities which showed a systematic behavior as a function of k. Extrapolation to the hydrodynamic region at k=0 gave shear viscosity coefficients in good agreement with direct Green-Kubo results obtained in previous work. The two-exponential model fit for the memory function proposed by other authors does not provide a reasonable description of the MD results, as the fit parameters show no systematic wave-vector dependence, although the Ct(k,t) functions are somewhat better fitted. Similarly, the semiempirical interpolation formula for the decay time based on the viscoelastic concept proposed by Akcasu and Daniels fails to reproduce the correct k dependence for the wavelength range investigated herein.

Natural circulation studies in a LBE loop for a wide range of temperature

International Nuclear Information System (INIS)

Borgohain, A.; Srivastava, A.K.; Jana, S.S.; Maheshwari, N.K.; Kulkarni, R.D.; Vijayan, P.K.; Tewari, R.; Ram, A. Maruthi; Jha, S.K.

2016-01-01

Highlights: • A high temperature Lead Bismuth Eutectic loop named as Kilo Temperature Loop (KTL) has been made. • Natural circulation experimental studies were carried out and reported in the range of 200–780 °C. • The experiments at high temperature were carried in inert atmosphere to avoid oxidation of the loop material. • Theoretical studies are carried out to simulate the loop with natural circulation in primary as well as in the secondary side. • The predictions of the code LeBENC used to simulate the natural circulation in the loop are compared with the experimental results. - Abstract: Lead–Bismuth Eutectic (LBE) is increasingly getting more attention as a coolant for advanced reactor systems. It is also the primary coolant of the Compact High Temperature Reactor (CHTR) being designed at Bhabha Atomic Research Centre (BARC). A high temperature liquid metal loop named as Kilo Temperature Loop (KTL) has been installed at BARC for thermal hydraulics, instrument development and material related studies. Natural circulation experimental studies were carried out for the power range of 200–1200 W in the loop. The corresponding LBE flow rate is calculated to be in the range of 0.075–0.12 kg/s. Transient studies for start-up of natural circulation in the loop, loss of heat sink and step power change have also been carried out. The maximum temperature of the loop operated so far is 1100 °C. A computer code named LeBENC has been developed at BARC to simulate the natural circulation characteristics in closed loops. The salient features of the code include ability to handle non-uniform diameter components, axial thermal conduction in fluid and heat losses from the piping to the environment. The code has been modified to take into account of two natural circulation loops in series so that the natural cooling by argon gas in the secondary side of the loop can be simulated. This paper deals with the description of the loop and its operation. The various

Comparison of Green-Kubo and nonequilibrium calculations of the self-diffusion constant of a Lennard-Jones fluid

International Nuclear Information System (INIS)

Erpenbeck, J.J.

1987-01-01

We apply the so-called ''synthetic'' nonequilibrium molecular-dynamics method to the calculation of the self-diffusion constant of a Lennard-Jones fluid at a number density of 0.85/σ 3 and a temperature of 1.08 epsilon-c/k/sub B/ (where epsilon-c and σ are the energy and length parameters of the potential and k/sub B/ is the Boltzmann constant). By comparing with the Green-Kubo calculation for the same state of the system and for the same number of particles, N, we find the latter calculation to yield more precise values of the self-diffusion constant for a given number of molecular-dynamics time steps. Even at small values of the diffusion current, a nontrivial time is needed for the nonequilibrium calculation to reach the steady state. For larger values of the driving force, the steady-state flow appears to become unstable and evidence of a secondary flow pattern is presented. The presence of these instabilities acts as a limit to the range of the driving force for which the steady-state method can be applied. With increasing N the range of stable values of the diffusion current density decreases. For the Green-Kubo calculations, the N dependence of the self-diffusion constant is found to be anomalous for N = 108, with the 1/N dependence only exhibited for at least 500 particles. The nonequilibrium results, while approximately independent of N for 108 and 500 particles, are found to have a similar anomalous N dependence when we extend the calculations to 1372 particles, thereby bringing the Green-Kubo and nonequilibrium results into agreement in the large-system limit

Role of Protein Synthesis Initiation Factors in Dietary Soy Isoflavone-Mediated Effects on Breast Cancer Progression

Science.gov (United States)

2013-03-01

Collection,Manas- sas, VA)weremaintained in complete culturemedium:Dulbec- co’s modified Eagle’s medium (Invitrogen) supplemented with 10% fetal bovine ...Jankowska- Anyszka, M., Stepinski, J., Darzynkiewicz, E., Jones, D. N., and Davis, R. E. (2009) Structural insights into parasite eIF4E binding

Methods for measuring shrinkage

OpenAIRE

Chapman, Paul; Templar, Simon

2006-01-01

This paper presents findings from research amongst European grocery retailers into their methods for measuring shrinkage. The findings indicate that: there is no dominant method for valuing or stating shrinkage; shrinkage in the supply chain is frequently overlooked; data is essential in pinpointing where and when loss occurs and that many retailers collect data at the stock-keeping unit (SKU) level and do so every 6 months. These findings reveal that it is difficult to benc...

Self-consistent phonons revisited. I. The role of thermal versus quantum fluctuations on structural transitions in large Lennard-Jones clusters.

Science.gov (United States)

Georgescu, Ionuţ; Mandelshtam, Vladimir A

2012-10-14

The theory of self-consistent phonons (SCP) was originally developed to address the anharmonic effects in condensed matter systems. The method seeks a harmonic, temperature-dependent Hamiltonian that provides the "best fit" for the physical Hamiltonian, the "best fit" being defined as the one that optimizes the Helmholtz free energy at a fixed temperature. The present developments provide a scalable O(N) unified framework that accounts for anharmonic effects in a many-body system, when it is probed by either thermal (ℏ → 0) or quantum fluctuations (T → 0). In these important limits, the solution of the nonlinear SCP equations can be reached in a manner that requires only the multiplication of 3N × 3N matrices, with no need of diagonalization. For short range potentials, such as Lennard-Jones, the Hessian, and other related matrices are highly sparse, so that the scaling of the matrix multiplications can be reduced from O(N(3)) to ~O(N). We investigate the role of quantum effects by continuously varying the de-Boer quantum delocalization parameter Λ and report the N-Λ (T = 0), and also the classical N-T (Λ = 0) phase diagrams for sizes up to N ~ 10(4). Our results demonstrate that the harmonic approximation becomes inadequate already for such weakly quantum systems as neon clusters, or for classical systems much below the melting temperatures.

A New Therapeutic Strategy for Autosomal Dominant Polycystic Kidney Disease: Activation of AMP Kinase by Metformin. Addendum

Science.gov (United States)

2014-07-01

horseradish peroxidase-conjugated anti-rat, anti-rabbit, or anti-goat secondary antibodies (1:5,000–10:000; Jackson Labs ), and proteins were visualized...van Beest , M., van Es, J., Loureiro, J., Ypma, A., Hursh, D., Jones, T., Bejsovec, A., et al. (1997). Armadillo coactivates transcription driven by

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

Science.gov (United States)

2016-01-01

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

Response Surface Methodology: 1966-1986

Science.gov (United States)

1986-09-01

male broilers to examine quantitatively the protein levels in starter and Gnisher rations and the time of ration change to optimize body weight, carcass...1983). ’Akn Investigation of Protein Levels for Broiler Starter and Finisher Rations and the Time of Ration Change by Response Surface Methodology...when Responses Within a Litter are Correlated,’ Biometrics, 37, 153-156. Shek, E., Ghani, M. and Jones, R.E. (1980). "Simplex Search in Optimization

Microbial Physiology of the Conversion of Residual Oil to Methane: A Protein Prospective

Science.gov (United States)

Morris, Brandon E. L.; Bastida-Lopez, Felipe; von Bergen, Martin; Richnow, Hans-Hermann; Suflita, Joseph M.

2010-05-01

Traditional petroleum recovery techniques are unable to extract the majority of oil in most petroliferous deposits. The recovery of even a fraction of residual hydrocarbon in conventional reserves could represent a substantive energy supply. To this end, the microbial conversion of residual oil to methane has gained increasing relevance in recent years [1,2]. Worldwide demand for methane is expected to increase through 2030 [3], as it is a cleaner-burning alternative to traditional fuels [4]. To investigate the microbial physiology of hydrocarbon-decomposition and ultimate methanogenesis, we initiated a two-pronged approach. First, a model alkane-degrading sulfate-reducing bacterium, Desulfoglaeba alkanexedens, was used to interrogate the predominant metabolic pathway(s) differentially expressed during growth on either n-decane or butyrate. A total of 81 proteins were differentially expressed during bacterial growth on butyrate, while 100 proteins were unique to the alkane-grown condition. Proteins related to alkylsuccinate synthase, or the homologous 1-methyl alkylsuccinate synthase, were identified only in the presence of the hydrocarbon. Secondly, we used a newly developed stable isotope probing technique [5] targeted towards proteins to monitor the flux of carbon through a residual oil-degrading bacterial consortium enriched from a gas-condensate contaminated aquifer [1]. Combined carbon and hydrogen stable isotope fractionation identified acetoclastic methanogenesis as the dominant process in this system. Such findings agree with the previous clone library characterization of the consortium. Furthermore, hydrocarbon activation was determined to be the rate-limiting process during the net conversion of residual oil to methane. References 1. Gieg, L.M., K.E. Duncan, and J.M. Suflita, Bioenegy production via microbial conversion of residual oil to natural gas. Appl Environ Micro, 2008. 74(10): p. 3022-3029. 2. Jones, D.M., et al., Crude-oil biodegradation via

NCBI nr-aa BLAST: CBRC-TBEL-01-1221 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-TBEL-01-1221 ref|YP_635917.1| cell division protein [Helicosporidium sp. ex Simulium jones...ii] sp|Q2EEX7|FTSH_HELSJ Cell division protease ftsH homolog gb|ABD33966.1| ftsH protease [Helicosporidium sp. ex Simulium jonesii] YP_635917.1 3.4 24% ...

Esteroides de virola calophylloidea (markgraf)

OpenAIRE

Juan C. Martinez V.; Luis E. Cuca S

2009-01-01

Del extracto bencénico de la madera de Virola calophylloldea (Myristicaceae) se separaron seis sustancias tipo esteroidal, valiéndose de las técnicas de Cromatografía de gases (CG) y Cromatografía líquida de alta eficiencia (HPLC). Utilizando los tiempos de retención con relación al colesterol (t^j.) en CG y HPLC, junto con los pesos moleculares obtenidos por CG—MS se infiere la presencia de algunos esteroides.- " • ' ;

Esteroides de virola calophylloidea (markgraf

Directory of Open Access Journals (Sweden)

Juan C. Martinez V.

2009-07-01

Full Text Available Del extracto bencénico de la madera de Virola calophylloldea (Myristicaceae se separaron seis sustancias tipo esteroidal, valiéndose de las técnicas de Cromatografía de gases (CG y Cromatografía líquida de alta eficiencia (HPLC. Utilizando los tiempos de retención con relación al colesterol (t^j. en CG y HPLC, junto con los pesos moleculares obtenidos por CG—MS se infiere la presencia de algunos esteroides.- " • ' ;

Phenotypic and Genetic Characterization of Erwiniua carotovora spp. carotovora (JOnes Bergey et al. Isolates from Grafted Tomato in Sardinia, Italy

Directory of Open Access Journals (Sweden)

M. Fiori

2005-04-01

Full Text Available A disease symptomatically similar to that caused by Erwinia carotovora occurred on “Cuore di Bue” and “Cencara” tomato plants grafted on “Beaufort” and “He-Man”, or ungrafted, in greenhouses in Sardinia (Italy. Symptoms were: dark brown/black longitudinal stem lesions, soft stem rot, pith breakdown of the stems, hollow stems, vascular tissue discoloration, wilting and collapse of the plants. Numerous bacterial colonies from stem tissues were isolated on yeast extract salts (YS medium. Seven isolates (DPP As-1, DPP As-2, DPP As-3, DPP As-14, DPP Pu6, DPP Pu7 e DPP Pu8 were selected on the basis of their ability to cause rot on potato pieces and a hypersensitivity reaction in “White burley” tobacco leaves. Pathogenicity tests revealed that five of these isolates infected artichoke, basil, dwarf bean, fennel, marrow, melon, pepper, eggplant, grafted and ungrafted tomato, and white cabbage. Of the remaining two isolates, one (DPP As-1 did not infect white cabbage, and the other (DPP Pu8 did not infect basil, marrow or white cabbage. Phenotypic properties and ELISA, also performed on naturally infected tissues, revealed that all the isolates were E. c. ssp. carotovora (Jones Bergey et al. PCR-RFLP analysis placed two (DPP As-2 and DPP As-3 of the seven isolates in RFLP group 8. Five isolates belonged to a hitherto unknown RFLP group. Prevention and control measures for this disease are suggested.

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)

Schulke, Ch.

2009-01-01

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

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.

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

Directory of Open Access Journals (Sweden)

Li Karen

2008-12-01

Full Text Available Abstract Background Widely used substitution models for proteins, such as the Jones-Taylor-Thornton (JTT or Whelan and Goldman (WAG models, are based on empirical amino acid interchange matrices estimated from databases of protein alignments that incorporate the average amino acid frequencies of the data set under examination (e.g JTT + F. Variation in the evolutionary process between sites is typically modelled by a rates-across-sites distribution such as the gamma (Γ distribution. However, sites in proteins also vary in the kinds of amino acid interchanges that are favoured, a feature that is ignored by standard empirical substitution matrices. Here we examine the degree to which the pattern of evolution at sites differs from that expected based on empirical amino acid substitution models and evaluate the impact of these deviations on phylogenetic estimation. Results We analyzed 21 large protein alignments with two statistical tests designed to detect deviation of site-specific amino acid distributions from data simulated under the standard empirical substitution model: JTT+ F + Γ. We found that the number of states at a given site is, on average, smaller and the frequencies of these states are less uniform than expected based on a JTT + F + Γ substitution model. With a four-taxon example, we show that phylogenetic estimation under the JTT + F + Γ model is seriously biased by a long-branch attraction artefact if the data are simulated under a model utilizing the observed site-specific amino acid frequencies from an alignment. Principal components analyses indicate the existence of at least four major site-specific frequency classes in these 21 protein alignments. Using a mixture model with these four separate classes of site-specific state frequencies plus a fifth class of global frequencies (the JTT + cF + Γ model, significant improvements in model fit for real data sets can be achieved. This simple mixture model also reduces the long

Síntesis de nuevos monómeros para fotopolimerizaciones catiónicas

OpenAIRE

Acosta Ortiz, Ricardo; Crivello, James V.

2003-01-01

Se reportan los métodos de preparación de cinco nuevos monómeros susceptibles de ser fotopolimerizados catiónicamente. Estos incluyen compuestos del tipo epoxiciclohexano, vinil éter, propenil éter y oxetanos. La característica común de estos monómeros es que contienen en su estructura un grupo bencílico con sustituyentes donadores de electrones como los grupos metóxido o el grupo metilendioxolano. La síntesis de estos compuestos involucra reacciones de eterificación y oxidación. Se explica e...

Delovnopravni položaj gradbenih inšpektorjev v Sloveniji od 1918 do 2015

OpenAIRE

Rakuljič Zelov, Jasna

2016-01-01

Za delovnopravna razmerja gradbenih inšpektorjev veljajo določbe predpisov, ki veljajo za vse javne uslužbence (Zakon o javnih uslužbencih, Zakon o delovnih razmerjih in drugi), za vse inšpektorje na sploh (Zakon o inšpekcijskem nadzoru) in določbe 144. člena Zakona o graditvi objektov, kjer so določeni posebni pogoji glede izobrazbe, delovnih izkušenj in o strokovnih izpitih. V praksi se danes postavljajo vprašanja, ali je glede na pogoje, ki jih morajo izpolnjevati gradbeni inšpektorji, smi...

Renal toxicity after total body irradiation

International Nuclear Information System (INIS)

Borg, Martin; Hughes, Timothy; Horvath, Noemi; Rice, Michael; Thomas, Anthony C.

2002-01-01

Purpose: To evaluate the incidence of renal dysfunction after total body irradiation (TBI). Methods and Materials: Between 1990 and 1997, 64 patients (median age 50 years) received TBI as part of the conditioning regimen before bone marrow transplantation (BMT). Five patients with abnormal renal function at the beginning of treatment or with incomplete data were excluded. All patients received a total of 12 Gy (6 fractions twice daily for 3 consecutive days) prescribed to the peak lung dose (corrected for lung transmission) at a dose rate of 7.5 cGy/min. Renal shielding was not used. Renal dysfunction was assessed on the basis of the serum creatinine levels measured at the start and end of TBI and at 6, 12, 18, and 24 months after completion of BMT. Cox proportional hazard analysis was used to evaluate the various factors known to affect renal function. Results: Only 4 patients had elevated serum creatinine levels at 12 months and subsequently only 2 of the 33 surviving patients had persistent elevated renal serum creatinine levels 24 months after BMT. A fifth patient developed proteinuria and mildly elevated serum creatinine levels at 2.5 years. In 2 patients, the elevation coincided with disease relapse and normalized once remission was achieved. In the third patient, the elevation in serum creatinine levels coincided with relapse of multiple myeloma and the presence of Bence-Jones proteinuria. The fourth patient was the only patient who developed chronic renal failure secondary to radiation nephritis at 2 years. The etiology of the fifth patient's rise in creatinine was unknown, but may have been secondary to radiation nephritis. On univariate analysis, but not on multivariate analysis, a significant correlation was found between TBI-related renal dysfunction and hypertension before and after BMT. Conclusion: A dose of 12 Gy at 2 Gy/fraction resulted in only 1 case of radiation nephritis in the 59 patients studied 24 months after the completion of TBI and BMT

MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease.

Science.gov (United States)

Gunner, M R; Zhu, Xuyu; Klein, Max C

2011-12-01

The pK(a)s of 96 acids and bases introduced into buried sites in the staphylococcal nuclease protein (SNase) were calculated using the multiconformation continuum electrostatics (MCCE) program and the results compared with experimental values. The pK(a)s are obtained by Monte Carlo sampling of coupled side chain protonation and position as a function of pH. The dependence of the results on the protein dielectric constant (ε(prot)) in the continuum electrostatics analysis and on the Lennard-Jones non-electrostatics parameters was evaluated. The pK(a)s of the introduced residues have a clear dependence on ε(prot,) whereas native ionizable residues do not. The native residues have electrostatic interactions with other residues in the protein favoring ionization, which are larger than the desolvation penalty favoring the neutral state. Increasing ε(prot) scales both terms, which for these residues leads to small changes in pK(a). The introduced residues have a larger desolvation penalty and negligible interactions with residues in the protein. For these residues, changing ε(prot) has a large influence on the calculated pK(a). An ε(prot) of 8-10 and a Lennard-Jones scaling of 0.25 is best here. The X-ray crystal structures of the mutated proteins are found to provide somewhat better results than calculations carried out on mutations made in silico. Initial relaxation of the in silico mutations by Gromacs and extensive side chain rotamer sampling within MCCE can significantly improve the match with experiment. Copyright © 2011 Wiley-Liss, Inc.

The Air Force Fitness Test: Creating New Fitness Assessment Charts Using Waist to Height Ratios

Science.gov (United States)

2017-03-23

Cureton et al ., 1979; Jette et al ., 1990; Vogel and Friedl, Chapter 6; Jones, Bovee, and Knapick, 1992). Jones, Bovee, and Knapick found in a study...research report, No. 2654-74, Air Command and Staff College, Maxwell AFB AL , May 1974. Taylor, R. W., Jones, I. E., Williams, S. M., & Goulding , A...from AFFMS (Callendar, 2004; Knapik, Ang, Reynolds, and Jones, 1993; Knapik, Sharp, Canham-Chervak, Hauret, Patton, Jones, 2001; Mello and Murphy, 1988

Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

Science.gov (United States)

Gaines, J C; Acebes, S; Virrueta, A; Butler, M; Regan, L; O'Hern, C S

2018-05-01

We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins. © 2018 Wiley Periodicals, Inc.

76 FR 28483 - Self-Regulatory Organizations; NYSE Arca, Inc.; Notice of Filing of Proposed Rule Change To List...

Science.gov (United States)

2011-05-17

... performance of the benchmark index for each of the Funds (the ``Benchmark'' or ``Index''), the Dow Jones-UBS... Dow Jones & Company, Inc. (``Dow Jones'' or ``Index Provider'') and CME Group Inc. (``CME Group... index-related services to CME Indexes. Dow Jones also maintains a Code of Conduct applicable to all...

Experimental and theoretical studies in Molten Salt Natural Circulation Loop (MSNCL)

International Nuclear Information System (INIS)

Srivastava, A.K.; Borgohain, A.; Jana, S.S.; Bagul, R.K.; Singh, R.R.; Maheshwari, N.K.; Belokar, D.G.; Vijayan, P.K.

2014-12-01

High Temperature Reactors (HTR) and solar thermal power plants use molten salt as a coolant, as it has low melting point and high boiling point, enabling us to operate the system at low pressure. Molten fluoride salt and molten nitrate salt are proposed as a candidate coolant for High Temperature Reactors (HTR) and solar power plant respectively. BARC is developing a 600 MWth pebble bed high temperature reactor, cooled by natural circulation of fluoride salt and capable of supplying process heat at 1000°C to facilitate hydrogen production by splitting water. Beside this, BARC is also developing a 2MWe solar power tower system using molten nitrate salt. With these requirements, a Molten Salt Natural Circulation Loop (MSNCL) has been designed, fabricated, installed and commissioned in Hall-7, BARC for thermal hydraulic, instrumentation development and material compatibility related studies. Steady state natural circulation experiments with molten nitrate salt (mixture of NaNO 3 and KNO 3 in 60:40 ratio) have been carried out in the loop at different power level. Various transients viz. startup of natural circulation, step power change, loss of heat sink and heater trip has also been studied in the loop. A well known steady state correlation given by Vijayan et. al. has been compared with experimental data. In-house developed code LeBENC has also been validated against all steady state and transient experimental results. The detailed description of MSNCL, steady state and transient experimental results and validation of in-house developed code LeBENC have been described in this report. (author)

Holocene environmental and parasequence development of the St. Jones Estuary, Delaware (USA): Foraminiferal proxies of natural climatic and anthropogenic change

Science.gov (United States)

Leorri, E.; Martin, R.; McLaughlin, P.

2006-01-01

The benthic foraminiferal record of marshes located along western Delaware Bay (St. Jones Estuary, USA) reflects the response of estuaries to sea-level and paleoclimate change during the Holocene. System tracts are recognized and within them parasequences based on sedimentological and foraminiferal assemblages identification. The parasequences defined by foraminiferal assemblages appear correlative with rapid Holocene climate changes that are of worldwide significance: 6000-5000, 4200-3800, 3500-2500, 1200-1000, and 600??cal years BP. Following postglacial sea-level rise, modern subestuaries and marshes in the region began to develop between 6000 and 4000??years BP, depending on their proximity to the mouth of Delaware Bay and coastal geomorphology. Initial sediments were fluvial in origin, with freshwater marshes established around 4000??years BP. The subsequent sea-level transgression occurred sufficiently slowly that freshwater marshes alternated with salt marshes at the same sites to around 3000??years BP. Locally another two transgressions are identified at 1800 and 1000??years BP respectively. Marine influence increased in the estuaries until 600??years BP (Little Ice Age), when regression occurred. Sea-level began to rise again during the mid-19th Century at the end of the Little Ice Age, when marshes became established. The presence of a sand lens in the upper and middle estuary and the reduction in the number of tests in the top samples in cores from the same area also suggest an anthropogenic influence. The estuary infill resulted in a sharp transgressive sequence, represented by salt marsh foraminiferal assemblages in the upper part of the cores. The increase in marsh foraminifera in both areas suggests an increase in marine influence that might be due to the transgression beginning at the end of the Little Ice Age about 150-180??years ago coupled with anthropogenic straightening of the channel in 1913. ?? 2006 Elsevier B.V. All rights reserved.

Delayed Union of a Jones Fracture in a Patient With Rothmund-Thomson Syndrome: A Case Report and Review of the Literature.

Science.gov (United States)

Barisonek, Kirsten L; Protzman, Nicole M; Wobst, Garrett M; Brigido, Stephen A

2016-01-01

Rothmund-Thomson syndrome is a rare autosomal recessive genodermatosis, characterized by poikiloderma, small stature, juvenile cataracts, sparse hair, skeletal abnormalities, and a predisposition to osteogenic sarcomas and skin cancers. Although numerous skeletal abnormalities have been described in patients with Rothmund-Thomson syndrome, to our knowledge, only 1 study has shown evidence of delayed fracture healing in a patient with Rothmund-Thomson syndrome. We present the case of a 13-year-old female diagnosed with Rothmund-Thomson syndrome who demonstrated delayed union of her fifth metatarsal after a Jones fracture. She was treated conservatively for 6 weeks with non-weightbearing cast immobilization and was then transitioned to a controlled ankle motion walker for an additional 4 weeks. Two months later, however, she continued to experience pain, and, on radiographic examination, the fracture remained unchanged. Therefore, with her guardian's consent, the patient elected to undergo open reduction and internal fixation of the fifth metatarsal fracture. At 8 weeks postoperatively, the patient reported a subsidence of symptoms and had returned to normal activity. With our report, we hope to increase practitioner awareness that delayed bone healing could be a possibility in patients with Rothmund-Thomson syndrome and encourage consideration of routine imaging and supplementation with calcium and vitamin D. Additionally, the present findings suggest that patients with Rothmund-Thomson syndrome could benefit from early surgical intervention, given their poor bone healing capacity and high likelihood of nonunion. Although the association between impaired bone healing and Rothmund-Thomson syndrome is rational, additional studies are needed to determine the prevalence of chronic nonunion in this patient population. Copyright © 2016 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

Protein docking prediction using predicted protein-protein interface

Directory of Open Access Journals (Sweden)

Li Bin

2012-01-01

Full Text Available Abstract Background Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. Results We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm, is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. Conclusion We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

Protein docking prediction using predicted protein-protein interface.

Science.gov (United States)

Li, Bin; Kihara, Daisuke

2012-01-10

Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm), is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

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

Directory of Open Access Journals (Sweden)

Peng Liu

2015-01-01

Full Text Available 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 network. Based on different complex sets detected by various algorithms, we can obtain different prediction sets of protein-protein interactions. The reliability of the predicted interaction sets is proved by using estimations with statistical tests and direct confirmation of the biological data. In comparison with the approaches which predict the interactions based on the cliques, the overlap of the predictions is small. Similarly, the overlaps among the predicted sets of interactions derived from various complex sets are also small. Thus, every predicted set of interactions may complement and improve the quality of the original network data. Meanwhile, the predictions from the proposed method replenish protein-protein interactions associated with protein complexes using only the network topology.

Derivados del Nylon 3 con grupos laterales alcoxicarbonilos ramificados y cíclicos

OpenAIRE

García Álvarez, Montserrat

1997-01-01

El presente trabajo se ha centrado en la síntesis, caracterización y estudio estructural de poli(alfa-alquil-beta-L-aspartato)s con grupos laterales ramificados y cíclicos. Se han sintetizado los monómero: (S)-4-alcoxicarbonil-2-azetidinonas cuya síntesis se basa en la transesterificación de la beta-lactama del éster bencílico del ácido L-aspártico con el correspondiente alcohol. Se han establecido las condiciones óptimas de la polimerización aniónica por apertura del anillo de lactama, hacie...

Indiana protiv KGB / Anna Fedina, Pjotr Obraztsov

Index Scriptorium Estoniae

Fedina, Anna

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

Superkangelase neljas tulemine / Signe Sillasoo

Index Scriptorium Estoniae

Sillasoo, Signe

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

Sangari naasmine / 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

Vana ja tuttav, aga liiga turvaline / Alar Niineväli

Index Scriptorium Estoniae

Niineväli, Alar

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

Nad avantjuristom godõ ne vlastnõ / Boris Tuch

Index Scriptorium Estoniae

Tuch, Boris, 1946-

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

X-Files kohtub Indy'ga / Rivo Sarapik

Index Scriptorium Estoniae

Sarapik, Rivo, 1981-

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

Mis te Indyga teete?

Index Scriptorium Estoniae

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

"Salatoimikud" Indiana Jonesi moodi / Inna-Katrin Hein

Index Scriptorium Estoniae

Hein, Inna-Katrin

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

Väike psühhoanalüüs Indiana Jonesile / Aarne Ruben

Index Scriptorium Estoniae

Ruben, Aarne, 1971-

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

Culicoides variipennis (Diptera: Ceratopogonidae) complex in California.

Science.gov (United States)

Holbrook, F R; Tabachnick, W J

1995-07-01

Genetic relationships were examined among 24 collections, representing 23 populations of Culicoides variipennis (Coquillett) using isozyme electrophoresis of 11 protein encoding loci. The populations were collected from alkaline or fresh water larval habitats in California. Distance analysis demonstrated that C. v. occidentalis Wirth and Jones and C. v. sonorensis Wirth and Jones are genetically distinct. All C. v. occidentalis were geographically isolated from each other in highly alkaline or saline larval habitats, whereas C. v. sonorensis populations were collected from artificial freshwater habitats that were polluted with organic wastes. Higher levels of gene flow were found between C. v. sonorensis populations than from C. v. sonorensis populations to nearby C. v. occidentalis populations, indicative of genetic isolation between subspecies. Northern California C. v. sonorensis were genetically distinguishable from southern California C. v. sonorensis. The relationship between this variation and bluetongue disease epidemiology in California is discussed.

Kolm tundi päevas jõusaalis ja dieet : nii voolis Harrison Ford end taas Indiana Jonesiks / Triin Tael

Index Scriptorium Estoniae

Tael, Triin

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. Indiana Jonesi tähestik

Phase separation of a Lennard-Jones fluid interacting with a long, condensed polymer chain: implications for the nuclear body formation near chromosomes.

Science.gov (United States)

Oh, Inrok; Choi, Saehyun; Jung, YounJoon; Kim, Jun Soo

2015-08-28

Phase separation in a biological cell nucleus occurs in a heterogeneous environment filled with a high density of chromatins and thus it is inevitably influenced by interactions with chromatins. As a model system of nuclear body formation in a cell nucleus filled with chromatins, we simulate the phase separation of a low-density Lennard-Jones (LJ) fluid interacting with a long, condensed polymer chain. The influence of the density variation of LJ particles above and below the phase boundary and the role of attractive interactions between LJ particles and polymer segments are investigated at a fixed value of strong self-interaction between LJ particles. For a density of LJ particles above the phase boundary, phase separation occurs and a dense domain of LJ particles forms irrespective of interactions with the condensed polymer chain whereas its localization relative to the polymer chain is determined by the LJ-polymer attraction strength. Especially, in the case of moderately weak attractions, the domain forms separately from the polymer chain and subsequently associates with the polymer chain. When the density is below the phase boundary, however, the formation of a dense domain is possible only when the LJ-polymer attraction is strong enough, for which the domain grows in direct contact with the interacting polymer chain. In this work, different growth behaviors of LJ particles result from the differences in the density of LJ particles and in the LJ-polymer interaction, and this work suggests that the distinct formation of activity-dependent and activity-independent nuclear bodies (NBs) in a cell nucleus may originate from the differences in the concentrations of body-specific NB components and in their interaction with chromatins.

Oligomeric protein structure networks: insights into protein-protein interactions

Directory of Open Access Journals (Sweden)

Brinda KV

2005-12-01

Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

Nostalgiline nagu soe tekk / Lauri Kaare

Index Scriptorium Estoniae

Kaare, Lauri

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")

Tippvormis Harrison Ford / Harrison Ford ; toim. Robert Aps

Index Scriptorium Estoniae

Ford, Harrison

2008-01-01

Näitleja järjekordse Indiana Jones'i filmi "Indiana Jones ja kristallpealuu kuningriik" ("Indiana Jones and the Kingdom of the Crystal Skull") väljatuleku eel. Sama ka Teleleht nr. 23, lk. 47 : ill

Indiana Dzhons vozvrashtshajetsja / Melor Sturua

Index Scriptorium Estoniae

Sturua, Melor

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")

Protein nanoparticles for therapeutic protein delivery.

Science.gov (United States)

Herrera Estrada, L P; Champion, J A

2015-06-01

Therapeutic proteins can face substantial challenges to their activity, requiring protein modification or use of a delivery vehicle. Nanoparticles can significantly enhance delivery of encapsulated cargo, but traditional small molecule carriers have some limitations in their use for protein delivery. Nanoparticles made from protein have been proposed as alternative carriers and have benefits specific to therapeutic protein delivery. This review describes protein nanoparticles made by self-assembly, including protein cages, protein polymers, and charged or amphipathic peptides, and by desolvation. It presents particle fabrication and delivery characterization for a variety of therapeutic and model proteins, as well as comparison of the features of different protein nanoparticles.

Harrison Ford : opjat skripit potertoje sedlo... / Harrison Ford ; interv. Barbara Hanson

Index Scriptorium Estoniae

Ford, Harrison

2008-01-01

Näitleja järjekordse (arvult neljanda, 19-aastase vaheaja järel!) Indiana Jones'i filmi "Indiana Jones ja kristallpealuu kuningriik" ("Indiana Jones and the Kingdom of the Crystal Skull") väljatuleku eel. Väljaandest Famous

Protein-protein interactions: an application of Tus-Ter mediated protein microarray system.

Science.gov (United States)

Sitaraman, Kalavathy; Chatterjee, Deb K

2011-01-01

In this chapter, we present a novel, cost-effective microarray strategy that utilizes expression-ready plasmid DNAs to generate protein arrays on-demand and its use to validate protein-protein interactions. These expression plasmids were constructed in such a way so as to serve a dual purpose of synthesizing the protein of interest as well as capturing the synthesized protein. The microarray system is based on the high affinity binding of Escherichia coli "Tus" protein to "Ter," a 20 bp DNA sequence involved in the regulation of DNA replication. The protein expression is carried out in a cell-free protein synthesis system, with rabbit reticulocyte lysates, and the target proteins are detected either by labeled incorporated tag specific or by gene-specific antibodies. This microarray system has been successfully used for the detection of protein-protein interaction because both the target protein and the query protein can be transcribed and translated simultaneously in the microarray slides. The utility of this system for detecting protein-protein interaction is demonstrated by a few well-known examples: Jun/Fos, FRB/FKBP12, p53/MDM2, and CDK4/p16. In all these cases, the presence of protein complexes resulted in the localization of fluorophores at the specific sites of the immobilized target plasmids. Interestingly, during our interactions studies we also detected a previously unknown interaction between CDK2 and p16. Thus, this Tus-Ter based system of protein microarray can be used for the validation of known protein interactions as well as for identifying new protein-protein interactions. In addition, it can be used to examine and identify targets of nucleic acid-protein, ligand-receptor, enzyme-substrate, and drug-protein interactions.

Truly Absorbed Microbial Protein Synthesis, Rumen Bypass Protein, Endogenous Protein, and Total Metabolizable Protein from Starchy and Protein-Rich Raw Materials

NARCIS (Netherlands)

Parand, Ehsan; Vakili, Alireza; Mesgaran, Mohsen Danesh; Duinkerken, Van Gert; Yu, Peiqiang

2015-01-01

This study was carried out to measure truly absorbed microbial protein synthesis, rumen bypass protein, and endogenous protein loss, as well as total metabolizable protein, from starchy and protein-rich raw feed materials with model comparisons. Predictions by the DVE2010 system as a more

Towers of algebras in rational conformal field theories

International Nuclear Information System (INIS)

Gomez, C.; Sierra, G.

1991-01-01

This paper reports on Jones fundamental construction applied to rational conformal field theories. The Jones algebra which emerges in this application is realized in terms of duality operations. The generators of the algebra are an open version of Verlinde's operators. The polynomial equations appear in this context as sufficient conditions for the existence of Jones algebra. The ADE classification of modular invariant partition functions is put in correspondence with Jones classification of subfactors

Auction dynamics: A volume constrained MBO scheme

Science.gov (United States)

Jacobs, Matt; Merkurjev, Ekaterina; Esedoǧlu, Selim

2018-02-01

We show how auction algorithms, originally developed for the assignment problem, can be utilized in Merriman, Bence, and Osher's threshold dynamics scheme to simulate multi-phase motion by mean curvature in the presence of equality and inequality volume constraints on the individual phases. The resulting algorithms are highly efficient and robust, and can be used in simulations ranging from minimal partition problems in Euclidean space to semi-supervised machine learning via clustering on graphs. In the case of the latter application, numerous experimental results on benchmark machine learning datasets show that our approach exceeds the performance of current state-of-the-art methods, while requiring a fraction of the computation time.

Area selection using magnetotellurics examples from Southern Africa.

CSIR Research Space (South Africa)

Jones, AG

2008-09-01

Full Text Available The electrical conductivity of the continental upper mantle is highly sensitive to ambient temperature (e.g., Jones et al., 2008; Ledo and Jones, 2005), to iron content (Mg) (Jones et al., 2008), to the presence of an interconnected conducting phase...

Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces.

Directory of Open Access Journals (Sweden)

Ruzianisra Mohamed

Full Text Available Protein-protein interactions (PPIs play a major role in many biological processes and they represent an important class of targets for therapeutic intervention. However, targeting PPIs is challenging because often no convenient natural substrates are available as starting point for small-molecule design. Here, we explored the characteristics of protein interfaces in five non-redundant datasets of 174 protein-protein (PP complexes, and 161 protein-ligand (PL complexes from the ABC database, 436 PP complexes, and 196 PL complexes from the PIBASE database and a dataset of 89 PL complexes from the Timbal database. In all cases, the small molecule ligands must bind at the respective PP interface. We observed similar amino acid frequencies in all three datasets. Remarkably, also the characteristics of PP contacts and overlapping PL contacts are highly similar.

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.

75 FR 41896 - Colville Indian Precision Pine, Colville Tribal Enterprise Corporation, Wood Products Division...

Science.gov (United States)

2010-07-19

... Logging, Lone Rock Contracting, Mawdsley Logging, McCuen Jones, San Poil Logging, Scott Thorndike, Silver..., Laramie Logging, Lone Rock Contracting, Mawdsley Logging, McCuen Jones, San Poil Logging, Scott Thorndike... Contracting, Mawdsley Logging, McCuen Jones, San Poil Logging, Scott Thorndike, Silver Nichol Trucking and...

Identification of Protein-Protein Interactions with Glutathione-S-Transferase (GST) Fusion Proteins.

Science.gov (United States)

Einarson, Margret B; Pugacheva, Elena N; Orlinick, Jason R

2007-08-01

INTRODUCTIONGlutathione-S-transferase (GST) fusion proteins have had a wide range of applications since their introduction as tools for synthesis of recombinant proteins in bacteria. GST was originally selected as a fusion moiety because of several desirable properties. First and foremost, when expressed in bacteria alone, or as a fusion, GST is not sequestered in inclusion bodies (in contrast to previous fusion protein systems). Second, GST can be affinity-purified without denaturation because it binds to immobilized glutathione, which provides the basis for simple purification. Consequently, GST fusion proteins are routinely used for antibody generation and purification, protein-protein interaction studies, and biochemical analysis. This article describes the use of GST fusion proteins as probes for the identification of protein-protein interactions.

Protein-protein interaction network-based detection of functionally similar proteins within species.

Science.gov (United States)

Song, Baoxing; Wang, Fen; Guo, Yang; Sang, Qing; Liu, Min; Li, Dengyun; Fang, Wei; Zhang, Deli

2012-07-01

Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting protein-protein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven protein-protein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent. Copyright © 2012 Wiley Periodicals, Inc.

Jürjens vs. Lucas / Gert Kiiler

Index Scriptorium Estoniae

Kiiler, Gert

2009-01-01

Neljandast Indiana Jones'i filmist "Indiana Jones ja kristallpealuu kuningriik" ("Indiana Jones and the Kingdom of the Crystal Skull"), režissöör Georg Lucas. Viljandist pärit Hollywoodis filme tegeva Priit Jürjensi (Brad Jurjensi) märulifilmist "Palgamõrtsukas" ("Hired Gun")

Protein-Protein Docking in Drug Design and Discovery.

Science.gov (United States)

Kaczor, Agnieszka A; Bartuzi, Damian; Stępniewski, Tomasz Maciej; Matosiuk, Dariusz; Selent, Jana

2018-01-01

Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available. In this context in silico approaches, in particular protein-protein docking, are a valuable complement to experimental methods for elucidating 3D structure of protein complexes. Protein-protein docking is easy to use and does not require significant computer resources and time (in contrast to molecular dynamics) and it results in 3D structure of a protein complex (in contrast to sequence-based methods of predicting binding interfaces). However, protein-protein docking cannot address all the aspects of protein dynamics, in particular the global conformational changes during protein complex formation. In spite of this fact, protein-protein docking is widely used to model complexes of water-soluble proteins and less commonly to predict structures of transmembrane protein assemblies, including dimers and oligomers of G protein-coupled receptors (GPCRs). In this chapter we review the principles of protein-protein docking, available algorithms and software and discuss the recent examples, benefits, and drawbacks of protein-protein docking application to water-soluble proteins, membrane anchoring and transmembrane proteins, including GPCRs.

Evolution of protein-protein interactions

Indian Academy of Sciences (India)

Evolution of protein-protein interactions · Our interests in protein-protein interactions · Slide 3 · Slide 4 · Slide 5 · Slide 6 · Slide 7 · Slide 8 · Slide 9 · Slide 10 · Slide 11 · Slide 12 · Slide 13 · Slide 14 · Slide 15 · Slide 16 · Slide 17 · Slide 18 · Slide 19 · Slide 20.

Protein function prediction using neighbor relativity in protein-protein interaction network.

Science.gov (United States)

Moosavi, Sobhan; Rahgozar, Masoud; Rahimi, Amir

2013-04-01

There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interaction information to predict function for un-annotated proteins. In this paper, we propose a novel approach called "Neighbor Relativity Coefficient" (NRC) based on interaction network topology which estimates the functional similarity between two proteins. NRC is calculated for each pair of proteins based on their graph-based features including distance, common neighbors and the number of paths between them. In order to ascribe function to an un-annotated protein, NRC estimates a weight for each neighbor to transfer its annotation to the unknown protein. Finally, the unknown protein will be annotated by the top score transferred functions. We also investigate the effect of using different coefficients for various types of functions. The proposed method has been evaluated on Saccharomyces cerevisiae and Homo sapiens interaction networks. The performance analysis demonstrates that NRC yields better results in comparison with previous protein function prediction approaches that utilize interaction network. Copyright © 2012 Elsevier Ltd. All rights reserved.

Specificity and affinity quantification of protein-protein interactions.

Science.gov (United States)

Yan, Zhiqiang; Guo, Liyong; Hu, Liang; Wang, Jin

2013-05-01

Most biological processes are mediated by the protein-protein interactions. Determination of the protein-protein structures and insight into their interactions are vital to understand the mechanisms of protein functions. Currently, compared with the isolated protein structures, only a small fraction of protein-protein structures are experimentally solved. Therefore, the computational docking methods play an increasing role in predicting the structures and interactions of protein-protein complexes. The scoring function of protein-protein interactions is the key responsible for the accuracy of the computational docking. Previous scoring functions were mostly developed by optimizing the binding affinity which determines the stability of the protein-protein complex, but they are often lack of the consideration of specificity which determines the discrimination of native protein-protein complex against competitive ones. We developed a scoring function (named as SPA-PP, specificity and affinity of the protein-protein interactions) by incorporating both the specificity and affinity into the optimization strategy. The testing results and comparisons with other scoring functions show that SPA-PP performs remarkably on both predictions of binding pose and binding affinity. Thus, SPA-PP is a promising quantification of protein-protein interactions, which can be implemented into the protein docking tools and applied for the predictions of protein-protein structure and affinity. The algorithm is implemented in C language, and the code can be downloaded from http://dl.dropbox.com/u/1865642/Optimization.cpp.

A planar calculus for infinite index subfactors

OpenAIRE

Penneys, David

2011-01-01

We develop an analog of Jones' planar calculus for II_1-factor bimodules with arbitrary left and right von Neumann dimension. We generalize to bimodules Burns' results on rotations and extremality for infinite index subfactors. These results are obtained without Jones' basic construction and the resulting Jones projections.

A Planar Calculus for Infinite Index Subfactors

Science.gov (United States)

Penneys, David

2013-05-01

We develop an analog of Jones' planar calculus for II 1-factor bimodules with arbitrary left and right von Neumann dimension. We generalize to bimodules Burns' results on rotations and extremality for infinite index subfactors. These results are obtained without Jones' basic construction and the resulting Jones projections.

Bio-Physicochemical Interactions of Engineered Nanomaterials in in Vitro Cell Culture Model

Science.gov (United States)

2014-10-11

properties of these manufactured materials (Edwards-Jones, 2009). The principal reason for producing and exploiting NMs is that their behaviour is...butanol layer was collected and read at 532 nm. The MDA level of the sample was calculated using an extinction coefficient of 1.56x105 M-1cm-1. The...glutathione content in the cell samples was expressed as µmoles GSH/mg protein and calculated using extinction coefficient of 13600 M-1cm-1. 2.12

Detection of protein complex from protein-protein interaction network using Markov clustering

International Nuclear Information System (INIS)

Ochieng, P J; Kusuma, W A; Haryanto, T

2017-01-01

Detection of complexes, or groups of functionally related proteins, is an important challenge while analysing biological networks. However, existing algorithms to identify protein complexes are insufficient when applied to dense networks of experimentally derived interaction data. Therefore, we introduced a graph clustering method based on Markov clustering algorithm to identify protein complex within highly interconnected protein-protein interaction networks. Protein-protein interaction network was first constructed to develop geometrical network, the network was then partitioned using Markov clustering to detect protein complexes. The interest of the proposed method was illustrated by its application to Human Proteins associated to type II diabetes mellitus. Flow simulation of MCL algorithm was initially performed and topological properties of the resultant network were analysed for detection of the protein complex. The results indicated the proposed method successfully detect an overall of 34 complexes with 11 complexes consisting of overlapping modules and 20 non-overlapping modules. The major complex consisted of 102 proteins and 521 interactions with cluster modularity and density of 0.745 and 0.101 respectively. The comparison analysis revealed MCL out perform AP, MCODE and SCPS algorithms with high clustering coefficient (0.751) network density and modularity index (0.630). This demonstrated MCL was the most reliable and efficient graph clustering algorithm for detection of protein complexes from PPI networks. (paper)

Injuries from Participation in Sports, Exercise, and Recreational Activities Among Active Duty Service Members - Analysis of the April 2008 Status of Forces Survey of Active Duty Members

Science.gov (United States)

2011-09-13

ankle brace. (Prepared by Knapik JJ, Spiess A, Darakjy S, Grier T, Manning F, Swedler D, Amoroso P, and Jones BH.) 29. USAPHC. 2011. USAPHC... Spiess A, Grier TL, Lester ME, Sharp MA, Tobler SK, Swedler DI, and Jones BH). 42. Bullock SH, Jones BH, Gilchrist J, and Marshall SW. 2010

Coarse-grain modelling of protein-protein interactions

NARCIS (Netherlands)

Baaden, Marc; Marrink, Siewert J.

2013-01-01

Here, we review recent advances towards the modelling of protein-protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely used to understand protein affinity, aggregation and self-assembly behaviour. PPI models of soluble proteins and membrane proteins are

Detection of protein-protein interactions by ribosome display and protein in situ immobilisation.

Science.gov (United States)

He, Mingyue; Liu, Hong; Turner, Martin; Taussig, Michael J

2009-12-31

We describe a method for identification of protein-protein interactions by combining two cell-free protein technologies, namely ribosome display and protein in situ immobilisation. The method requires only PCR fragments as the starting material, the target proteins being made through cell-free protein synthesis, either associated with their encoding mRNA as ribosome complexes or immobilised on a solid surface. The use of ribosome complexes allows identification of interacting protein partners from their attached coding mRNA. To demonstrate the procedures, we have employed the lymphocyte signalling proteins Vav1 and Grb2 and confirmed the interaction between Grb2 and the N-terminal SH3 domain of Vav1. The method has promise for library screening of pairwise protein interactions, down to the analytical level of individual domain or motif mapping.

Coevolution study of mitochondria respiratory chain proteins: toward the understanding of protein--protein interaction.

Science.gov (United States)

Yang, Ming; Ge, Yan; Wu, Jiayan; Xiao, Jingfa; Yu, Jun

2011-05-20

Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein--protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein--protein interaction in intra-complex and the binary protein--protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 × 10(-6)). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein--protein interaction. Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study. Copyright © 2011. Published by Elsevier Ltd.

A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction

Directory of Open Access Journals (Sweden)

Meijing Li

2015-01-01

Full Text Available Many researchers focus on developing protein-named entity recognition (Protein-NER or PPI extraction systems. However, the studies about these two topics cannot be merged well; then existing PPI extraction systems’ Protein-NER still needs to improve. In this paper, we developed the protein-protein interaction extraction system named PPIMiner based on Support Vector Machine (SVM and parsing tree. PPIMiner consists of three main models: natural language processing (NLP model, Protein-NER model, and PPI discovery model. The Protein-NER model, which is named ProNER, identifies the protein names based on two methods: dictionary-based method and machine learning-based method. ProNER is capable of identifying more proteins than dictionary-based Protein-NER model in other existing systems. The final discovered PPIs extracted via PPI discovery model are represented in detail because we showed the protein interaction types and the occurrence frequency through two different methods. In the experiments, the result shows that the performances achieved by our ProNER and PPI discovery model are better than other existing tools. PPIMiner applied this protein-named entity recognition approach and parsing tree based PPI extraction method to improve the performance of PPI extraction. We also provide an easy-to-use interface to access PPIs database and an online system for PPIs extraction and Protein-NER.

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...

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...

Protein complex prediction in large ontology attributed protein-protein interaction networks.

Science.gov (United States)

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng; Xu, Bo

2013-01-01

Protein complexes are important for unraveling the secrets of cellular organization and function. Many computational approaches have been developed to predict protein complexes in protein-protein interaction (PPI) networks. However, most existing approaches focus mainly on the topological structure of PPI networks, and largely ignore the gene ontology (GO) annotation information. In this paper, we constructed ontology attributed PPI networks with PPI data and GO resource. After constructing ontology attributed networks, we proposed a novel approach called CSO (clustering based on network structure and ontology attribute similarity). Structural information and GO attribute information are complementary in ontology attributed networks. CSO can effectively take advantage of the correlation between frequent GO annotation sets and the dense subgraph for protein complex prediction. Our proposed CSO approach was applied to four different yeast PPI data sets and predicted many well-known protein complexes. The experimental results showed that CSO was valuable in predicting protein complexes and achieved state-of-the-art performance.

Protein surface shielding agents in protein crystallization

International Nuclear Information System (INIS)

Hašek, J.

2011-01-01

The crystallization process can be controlled by protein surface shielding agents blocking undesirable competitive adhesion modes during non-equilibrium processes of deposition of protein molecules on the surface of growing crystalline blocks. The hypothesis is based on a number of experimental proofs from diffraction experiments and also retrieved from the Protein Data Bank. The molecules adhering temporarily on the surface of protein molecules change the propensity of protein molecules to deposit on the crystal surface in a definite position and orientation. The concepts of competitive adhesion modes and protein surface shielding agents acting on the surface of molecules in a non-equilibrium process of protein crystallization provide a useful platform for the control of crystallization. The desirable goal, i.e. a transient preference of a single dominating adhesion mode between protein molecules during crystallization, leads to uniform deposition of proteins in a crystal. This condition is the most important factor for diffraction quality and thus also for the accuracy of protein structure determination. The presented hypothesis is a generalization of the experimentally well proven behaviour of hydrophilic polymers on the surface of protein molecules of other compounds

The Development of Protein Microarrays and Their Applications in DNA-Protein and Protein-Protein Interaction Analyses of Arabidopsis Transcription Factors

Science.gov (United States)

Gong, Wei; He, Kun; Covington, Mike; Dinesh-Kumar, S. P.; Snyder, Michael; Harmer, Stacey L.; Zhu, Yu-Xian; Deng, Xing Wang

2009-01-01

We used our collection of Arabidopsis transcription factor (TF) ORFeome clones to construct protein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both protein-DNA and protein-protein interaction analyses. For protein-DNA interaction studies, we examined AP2/ERF family TFs and their cognate cis-elements. By careful comparison of the DNA-binding specificity of 13 TFs on the protein microarray with previous non-microarray data, we showed that protein microarrays provide an efficient and high throughput tool for genome-wide analysis of TF-DNA interactions. This microarray protein-DNA interaction analysis allowed us to derive a comprehensive view of DNA-binding profiles of AP2/ERF family proteins in Arabidopsis. It also revealed four TFs that bound the EE (evening element) and had the expected phased gene expression under clock-regulation, thus providing a basis for further functional analysis of their roles in clock regulation of gene expression. We also developed procedures for detecting protein interactions using this TF protein microarray and discovered four novel partners that interact with HY5, which can be validated by yeast two-hybrid assays. Thus, plant TF protein microarrays offer an attractive high-throughput alternative to traditional techniques for TF functional characterization on a global scale. PMID:19802365

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.

Piits, kaabu ja kulunud nahkjakk / Laurence Lumiere, Jaanus Noormets

Index Scriptorium Estoniae

Lumiere, Laurence

2008-01-01

Cannes'i festivalil esilinastus Steven Spielbergi järjekordne (arvult neljas) Indiana Jones'i film Harrison Fordiga nimiosas "Indiana Jones ja kristallpealuu kuningriik" ("Indiana Jones and the Kingdom of the Crystal Skull"). Viimase filmi sünnist, varasemate filmide lühikokkuvõtted, näitlejad, kes on seda rolli mänginud eri elujärkudes ja seriaalides

On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking

DEFF Research Database (Denmark)

Feliu, Elisenda; Aloy, Patrick; Oliva, Baldo

2011-01-01

Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions for s...... and with independence of the partner. This information is encoded at the residue level and could be easily incorporated in the initial grid scoring for Fast Fourier Transform rigid-body docking methods.......Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions...... for selecting rigid-body docking poses. These potentials include the energetic component that provides the residues with a particular secondary structure and surface accessibility. These scoring functions have been tested on a state-of-art benchmark dataset and on a decoy dataset of permanent interactions. Our...

Proteins interacting with cloning scars: a source of false positive protein-protein interactions.

Science.gov (United States)

Banks, Charles A S; Boanca, Gina; Lee, Zachary T; Florens, Laurence; Washburn, Michael P

2015-02-23

A common approach for exploring the interactome, the network of protein-protein interactions in cells, uses a commercially available ORF library to express affinity tagged bait proteins; these can be expressed in cells and endogenous cellular proteins that copurify with the bait can be identified as putative interacting proteins using mass spectrometry. Control experiments can be used to limit false-positive results, but in many cases, there are still a surprising number of prey proteins that appear to copurify specifically with the bait. Here, we have identified one source of false-positive interactions in such studies. We have found that a combination of: 1) the variable sequence of the C-terminus of the bait with 2) a C-terminal valine "cloning scar" present in a commercially available ORF library, can in some cases create a peptide motif that results in the aberrant co-purification of endogenous cellular proteins. Control experiments may not identify false positives resulting from such artificial motifs, as aberrant binding depends on sequences that vary from one bait to another. It is possible that such cryptic protein binding might occur in other systems using affinity tagged proteins; this study highlights the importance of conducting careful follow-up studies where novel protein-protein interactions are suspected.

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

Fluorogen-activating proteins: beyond classical fluorescent proteins

Directory of Open Access Journals (Sweden)

Shengnan Xu

2018-05-01

Full Text Available Fluorescence imaging is a powerful technique for the real-time noninvasive monitoring of protein dynamics. Recently, fluorogen activating proteins (FAPs/fluorogen probes for protein imaging were developed. Unlike the traditional fluorescent proteins (FPs, FAPs do not fluoresce unless bound to their specific small-molecule fluorogens. When using FAPs/fluorogen probes, a washing step is not required for the removal of free probes from the cells, thus allowing rapid and specific detection of proteins in living cells with high signal-to-noise ratio. Furthermore, with different fluorogens, living cell multi-color proteins labeling system was developed. In this review, we describe about the discovery of FAPs, the design strategy of FAP fluorogens, the application of the FAP technology and the advances of FAP technology in protein labeling systems. KEY WORDS: Fluorogen activating proteins, Fluorogens, Genetically encoded sensors, Fluorescence imaging, Molecular imaging

The phonological loop unmasked? A comment on the evidence for a "perceptual-gestural" alternative.

Science.gov (United States)

Baddeley, Alan D; Larsen, Janet D

2007-04-01

Jones et al. (Jones, Hughes, & Macken, 2006; Jones, Macken, & Nicholls, 2004) identify the interaction between phonological similarity, articulatory suppression, and stimulus presentation mode in verbal short-term memory as potentially providing important support for the phonological loop hypothesis. They find such an interaction but attribute it to "perceptual organization masquerading as phonological storage". We present data using shorter letter sequences and find clear evidence of the interaction predicted by the phonological loop hypothesis, which, unlike the evidence of Jones et al., is not limited to recency, and which provides continued support for the phonological loop hypothesis.

Blood-Based Biomarkers for Lung Cancer Early Detection and Evaluation of CT-Based Lesions

Science.gov (United States)

2013-12-01

conserved protein in eukaryotic nuclei, binds to NuMA. J Biol Chem 2000;275: 31979–85. 45. Debernardi S, Bassini A, Jones LK, Chaplin T, Linder B, de Bruijn...level and two-hit gene dosage and/or DNA methylation alterations and (ii) undergoing concomitant alterations at the mRNA level would be indicative of...methylated in our cohort ( indicated in Supplementary Table S2). Of these, we focused on the putative TSG EYA4, based on the high frequency of

Protein immobilization strategies for protein biochips

NARCIS (Netherlands)

Rusmini, F.; Rusmini, Federica; Zhong, Zhiyuan; Feijen, Jan

2007-01-01

In the past few years, protein biochips have emerged as promising proteomic and diagnostic tools for obtaining information about protein functions and interactions. Important technological innovations have been made. However, considerable development is still required, especially regarding protein

Development of a tuned interfacial force field parameter set for the simulation of protein adsorption to silica glass.

Science.gov (United States)

Snyder, James A; Abramyan, Tigran; Yancey, Jeremy A; Thyparambil, Aby A; Wei, Yang; Stuart, Steven J; Latour, Robert A

2012-12-01

Adsorption free energies for eight host-guest peptides (TGTG-X-GTGT, with X = N, D, G, K, F, T, W, and V) on two different silica surfaces [quartz (100) and silica glass] were calculated using umbrella sampling and replica exchange molecular dynamics and compared with experimental values determined by atomic force microscopy. Using the CHARMM force field, adsorption free energies were found to be overestimated (i.e., too strongly adsorbing) by about 5-9 kcal/mol compared to the experimental data for both types of silica surfaces. Peptide adsorption behavior for the silica glass surface was then adjusted using a modified version of the CHARMM program, which we call dual force-field CHARMM, which allows separate sets of nonbonded parameters (i.e., partial charge and Lennard-Jones parameters) to be used to represent intra-phase and inter-phase interactions within a given molecular system. Using this program, interfacial force field (IFF) parameters for the peptide-silica glass systems were corrected to obtain adsorption free energies within about 0.5 kcal/mol of their respective experimental values, while IFF tuning for the quartz (100) surface remains for future work. The tuned IFF parameter set for silica glass will subsequently be used for simulations of protein adsorption behavior on silica glass with greater confidence in the balance between relative adsorption affinities of amino acid residues and the aqueous solution for the silica glass surface.

Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

International Nuclear Information System (INIS)

Yu, P.

2007-01-01

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.

Information assessment on predicting protein-protein interactions

Directory of Open Access Journals (Sweden)

Gerstein Mark

2004-10-01

Full Text Available Abstract Background Identifying protein-protein interactions is fundamental for understanding the molecular machinery of the cell. Proteome-wide studies of protein-protein interactions are of significant value, but the high-throughput experimental technologies suffer from high rates of both false positive and false negative predictions. In addition to high-throughput experimental data, many diverse types of genomic data can help predict protein-protein interactions, such as mRNA expression, localization, essentiality, and functional annotation. Evaluations of the information contributions from different evidences help to establish more parsimonious models with comparable or better prediction accuracy, and to obtain biological insights of the relationships between protein-protein interactions and other genomic information. Results Our assessment is based on the genomic features used in a Bayesian network approach to predict protein-protein interactions genome-wide in yeast. In the special case, when one does not have any missing information about any of the features, our analysis shows that there is a larger information contribution from the functional-classification than from expression correlations or essentiality. We also show that in this case alternative models, such as logistic regression and random forest, may be more effective than Bayesian networks for predicting interactions. Conclusions In the restricted problem posed by the complete-information subset, we identified that the MIPS and Gene Ontology (GO functional similarity datasets as the dominating information contributors for predicting the protein-protein interactions under the framework proposed by Jansen et al. Random forests based on the MIPS and GO information alone can give highly accurate classifications. In this particular subset of complete information, adding other genomic data does little for improving predictions. We also found that the data discretizations used in the

Mapping Protein-Protein Interactions by Quantitative Proteomics

DEFF Research Database (Denmark)

Dengjel, Joern; Kratchmarova, Irina; Blagoev, Blagoy

2010-01-01

spectrometry (MS)-based proteomics in combination with affinity purification protocols has become the method of choice to map and track the dynamic changes in protein-protein interactions, including the ones occurring during cellular signaling events. Different quantitative MS strategies have been used...... to characterize protein interaction networks. In this chapter we describe in detail the use of stable isotope labeling by amino acids in cell culture (SILAC) for the quantitative analysis of stimulus-dependent dynamic protein interactions.......Proteins exert their function inside a cell generally in multiprotein complexes. These complexes are highly dynamic structures changing their composition over time and cell state. The same protein may thereby fulfill different functions depending on its binding partners. Quantitative mass...

ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval.

Science.gov (United States)

Wang, Jingyan; Gao, Xin; Wang, Quanquan; Li, Yongping

2012-05-08

The need to retrieve or classify protein molecules using structure or sequence-based similarity measures underlies a wide range of biomedical applications. Traditional protein search methods rely on a pairwise dissimilarity/similarity measure for comparing a pair of proteins. This kind of pairwise measures suffer from the limitation of neglecting the distribution of other proteins and thus cannot satisfy the need for high accuracy of the retrieval systems. Recent work in the machine learning community has shown that exploiting the global structure of the database and learning the contextual dissimilarity/similarity measures can improve the retrieval performance significantly. However, most existing contextual dissimilarity/similarity learning algorithms work in an unsupervised manner, which does not utilize the information of the known class labels of proteins in the database. In this paper, we propose a novel protein-protein dissimilarity learning algorithm, ProDis-ContSHC. ProDis-ContSHC regularizes an existing dissimilarity measure dij by considering the contextual information of the proteins. The context of a protein is defined by its neighboring proteins. The basic idea is, for a pair of proteins (i, j), if their context N(i) and N(j) is similar to each other, the two proteins should also have a high similarity. We implement this idea by regularizing dij by a factor learned from the context N(i) and N(j).Moreover, we divide the context to hierarchial sub-context and get the contextual dissimilarity vector for each protein pair. Using the class label information of the proteins, we select the relevant (a pair of proteins that has the same class labels) and irrelevant (with different labels) protein pairs, and train an SVM model to distinguish between their contextual dissimilarity vectors. The SVM model is further used to learn a supervised regularizing factor. Finally, with the new Supervised learned Dissimilarity measure, we update the Protein Hierarchial

Flora and Field Guide References Supporting All U.S. Army Corps of Engineers Wetland Regional Supplements

Science.gov (United States)

2011-11-01

Guide. Bloomington, IN: Indiana University Press. Jones, A. 1992. Aster and Brachyactis (Asteraceae) in Oklahoma. Sida Bot. Miscellany No. 8. Fort...author. Jones, A. 1992. Aster and Brachyactis (Asteraceae) in Oklahoma. Sida Bot. Miscellany No. 8. Fort Worth, TX: Research Institute of Texas...Agricultural Experiment Station. Jones, A. 1992. Aster and Brachyactis (Asteraceae) in Oklahoma. Sida Bot. Miscellany No. 8. Fort Worth, TX: Research

Design of Experiment Approach to Hydrogen Re-embrittlement Evaluation WP-2152

Science.gov (United States)

2015-04-01

2152 by Scott M Grendahl, Hoang Nguyen, Franklin Kellogg , Shuying Zhu, and Stephen Jones Approved for public release...and Materials Research Directorate, ARL Hoang Nguyen and Franklin Kellogg Bowhead Science and Technology, LLC Shuying Zhu and Stephen Jones The...ELEMENT NUMBER 6. AUTHOR(S) Scott M Grendahl, Hoang Nguyen, Franklin Kellogg , Shuying Zhu, and Stephen Jones 5d. PROJECT NUMBER W74RDV20769717 5e

Biophysics of protein evolution and evolutionary protein biophysics

Science.gov (United States)

Sikosek, Tobias; Chan, Hue Sun

2014-01-01

The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599

High quality protein microarray using in situ protein purification

Directory of Open Access Journals (Sweden)

Fleischmann Robert D

2009-08-01

Full Text Available Abstract Background In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC. This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. Results Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents

Can infrared spectroscopy provide information on protein-protein interactions?

Science.gov (United States)

Haris, Parvez I

2010-08-01

For most biophysical techniques, characterization of protein-protein interactions is challenging; this is especially true with methods that rely on a physical phenomenon that is common to both of the interacting proteins. Thus, for example, in IR spectroscopy, the carbonyl vibration (1600-1700 cm(-1)) associated with the amide bonds from both of the interacting proteins will overlap extensively, making the interpretation of spectral changes very complicated. Isotope-edited infrared spectroscopy, where one of the interacting proteins is uniformly labelled with (13)C or (13)C,(15)N has been introduced as a solution to this problem, enabling the study of protein-protein interactions using IR spectroscopy. The large shift of the amide I band (approx. 45 cm(-1) towards lower frequency) upon (13)C labelling of one of the proteins reveals the amide I band of the unlabelled protein, enabling it to be used as a probe for monitoring conformational changes. With site-specific isotopic labelling, structural resolution at the level of individual amino acid residues can be achieved. Furthermore, the ability to record IR spectra of proteins in diverse environments means that isotope-edited IR spectroscopy can be used to structurally characterize difficult systems such as protein-protein complexes bound to membranes or large insoluble peptide/protein aggregates. In the present article, examples of application of isotope-edited IR spectroscopy for studying protein-protein interactions are provided.

Protein and protein hydrolysates in sports nutrition.

Science.gov (United States)

van Loon, Luc J C; Kies, Arie K; Saris, Wim H M

2007-08-01

With the increasing knowledge about the role of nutrition in increasing exercise performance, it has become clear over the last 2 decades that amino acids, protein, and protein hydrolysates can play an important role. Most of the attention has been focused on their effects at a muscular level. As these nutrients are ingested, however, it also means that gastrointestinal digestibility and absorption can modulate their efficacy significantly. Therefore, discussing the role of amino acids, protein, and protein hydrolysates in sports nutrition entails holding a discussion on all levels of the metabolic route. On May 28-29, 2007, a small group of researchers active in the field of exercise science and protein metabolism presented an overview of the different aspects of the application of protein and protein hydrolysates in sports nutrition. In addition, they were asked to share their opinions on the future progress in their fields of research. In this overview, an introduction to the workshop and a short summary of its outcome is provided.

ProDis-ContSHC: Learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval

KAUST Repository

Wang, Jim Jing-Yan

2012-05-08

Background: The need to retrieve or classify protein molecules using structure or sequence-based similarity measures underlies a wide range of biomedical applications. Traditional protein search methods rely on a pairwise dissimilarity/similarity measure for comparing a pair of proteins. This kind of pairwise measures suffer from the limitation of neglecting the distribution of other proteins and thus cannot satisfy the need for high accuracy of the retrieval systems. Recent work in the machine learning community has shown that exploiting the global structure of the database and learning the contextual dissimilarity/similarity measures can improve the retrieval performance significantly. However, most existing contextual dissimilarity/similarity learning algorithms work in an unsupervised manner, which does not utilize the information of the known class labels of proteins in the database.Results: In this paper, we propose a novel protein-protein dissimilarity learning algorithm, ProDis-ContSHC. ProDis-ContSHC regularizes an existing dissimilarity measure dij by considering the contextual information of the proteins. The context of a protein is defined by its neighboring proteins. The basic idea is, for a pair of proteins (i, j), if their context N (i) and N (j) is similar to each other, the two proteins should also have a high similarity. We implement this idea by regularizing dij by a factor learned from the context N (i) and N (j). Moreover, we divide the context to hierarchial sub-context and get the contextual dissimilarity vector for each protein pair. Using the class label information of the proteins, we select the relevant (a pair of proteins that has the same class labels) and irrelevant (with different labels) protein pairs, and train an SVM model to distinguish between their contextual dissimilarity vectors. The SVM model is further used to learn a supervised regularizing factor. Finally, with the new Supervised learned Dissimilarity measure, we update

Targeting protein-protein interaction between MLL1 and reciprocal proteins for leukemia therapy.

Science.gov (United States)

Wang, Zhi-Hui; Li, Dong-Dong; Chen, Wei-Lin; You, Qi-Dong; Guo, Xiao-Ke

2018-01-15

The mixed lineage leukemia protein-1 (MLL1), as a lysine methyltransferase, predominantly regulates the methylation of histone H3 lysine 4 (H3K4) and functions in hematopoietic stem cell (HSC) self-renewal. MLL1 gene fuses with partner genes that results in the generation of MLL1 fusion proteins (MLL1-FPs), which are frequently detected in acute leukemia. In the progress of leukemogenesis, a great deal of proteins cooperate with MLL1 to form multiprotein complexes serving for the dysregulation of H3K4 methylation, the overexpression of homeobox (HOX) cluster genes, and the consequent generation of leukemia. Hence, disrupting the interactions between MLL1 and the reciprocal proteins has been considered to be a new treatment strategy for leukemia. Here, we reviewed potential protein-protein interactions (PPIs) between MLL1 and its reciprocal proteins, and summarized the inhibitors to target MLL1 PPIs. The druggability of MLL1 PPIs for leukemia were also discussed. Copyright © 2017. Published by Elsevier Ltd.

Protein kinase substrate identification on functional protein arrays

Directory of Open Access Journals (Sweden)

Zhou Fang

2008-02-01

Full Text Available Abstract Background Over the last decade, kinases have emerged as attractive therapeutic targets for a number of different diseases, and numerous high throughput screening efforts in the pharmaceutical community are directed towards discovery of compounds that regulate kinase function. The emerging utility of systems biology approaches has necessitated the development of multiplex tools suitable for proteomic-scale experiments to replace lower throughput technologies such as mass spectroscopy for the study of protein phosphorylation. Recently, a new approach for identifying substrates of protein kinases has applied the miniaturized format of functional protein arrays to characterize phosphorylation for thousands of candidate protein substrates in a single experiment. This method involves the addition of protein kinases in solution to arrays of immobilized proteins to identify substrates using highly sensitive radioactive detection and hit identification algorithms. Results To date, the factors required for optimal performance of protein array-based kinase substrate identification have not been described. In the current study, we have carried out a detailed characterization of the protein array-based method for kinase substrate identification, including an examination of the effects of time, buffer compositions, and protein concentration on the results. The protein array approach was compared to standard solution-based assays for assessing substrate phosphorylation, and a correlation of greater than 80% was observed. The results presented here demonstrate how novel substrates for protein kinases can be quickly identified from arrays containing thousands of human proteins to provide new clues to protein kinase function. In addition, a pooling-deconvolution strategy was developed and applied that enhances characterization of specific kinase-substrate relationships and decreases reagent consumption. Conclusion Functional protein microarrays are an

Formerly utilized MED/AEC sites remedial action program. Radiological survey of The George Herbert Jones Chemical Laboratory, The University of Chicago, Chicago, Illinois, June 13-17, 1977

International Nuclear Information System (INIS)

Wynveen, R.A.; Smith, W.H.; Mayes, C.B.; Justus, A.L.

1982-05-01

A comprehensive radiological survey was conducted at George Herbert Jones Chemical Laboratory at the University of Chicago, Chicago, Illinois. Radiochemistry for the MED/AEC project was performed in this building in the 1940s. The building is now used as laboratories, offices, and classrooms. The survey was undertaken to determine the location and quantities of any radioactive materials remaining from the MED/AEC operations. Forty-three spots of contamination possibly resulting from MED/AEC occupancy in 17 rooms exceeded the allowable limits as given in the ANSI Standard N13.12. Under current use conditions, the potential for radiation exposure to occupants of this building from these sources of contamination is remote. Concentrations of radon daughters in the air of the building, as measured with grab-sampling techniques, were below the limit of 0.01 WL above background as given in the Surgeon General's Guidelines. No long-lived radionuclides were detected in any air sample. Concentrations of radionuclides in soil samples from near the laboratory generally indicated background levels. In order to reduce the potential for radiation exposure, remedial measures such as stabilization of the contamination in place would be applicable as a short-term measure. In order to reduce the risk in the event that building modifications take place in the future, health physics procedures and coverage are recommended. The long-term solution would involve decontamination by removal of the radioactive residues from the 17 rooms or areas where contamination possibly resulting from MED/AEC activities was detected

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.

HKC: An Algorithm to Predict Protein Complexes in Protein-Protein Interaction Networks

Directory of Open Access Journals (Sweden)

Xiaomin Wang

2011-01-01

Full Text Available With the availability of more and more genome-scale protein-protein interaction (PPI networks, research interests gradually shift to Systematic Analysis on these large data sets. A key topic is to predict protein complexes in PPI networks by identifying clusters that are densely connected within themselves but sparsely connected with the rest of the network. In this paper, we present a new topology-based algorithm, HKC, to detect protein complexes in genome-scale PPI networks. HKC mainly uses the concepts of highest k-core and cohesion to predict protein complexes by identifying overlapping clusters. The experiments on two data sets and two benchmarks show that our algorithm has relatively high F-measure and exhibits better performance compared with some other methods.

Molecular tweezers modulate 14-3-3 protein-protein interactions

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Bier, David; Rose, Rolf; Bravo-Rodriguez, Kenny; Bartel, Maria; Ramirez-Anguita, Juan Manuel; Dutt, Som; Wilch, Constanze; Klärner, Frank-Gerrit; Sanchez-Garcia, Elsa; Schrader, Thomas; Ottmann, Christian

2013-03-01

Supramolecular chemistry has recently emerged as a promising way to modulate protein functions, but devising molecules that will interact with a protein in the desired manner is difficult as many competing interactions exist in a biological environment (with solvents, salts or different sites for the target biomolecule). We now show that lysine-specific molecular tweezers bind to a 14-3-3 adapter protein and modulate its interaction with partner proteins. The tweezers inhibit binding between the 14-3-3 protein and two partner proteins—a phosphorylated (C-Raf) protein and an unphosphorylated one (ExoS)—in a concentration-dependent manner. Protein crystallography shows that this effect arises from the binding of the tweezers to a single surface-exposed lysine (Lys214) of the 14-3-3 protein in the proximity of its central channel, which normally binds the partner proteins. A combination of structural analysis and computer simulations provides rules for the tweezers' binding preferences, thus allowing us to predict their influence on this type of protein-protein interactions.

On a novel matrix method for three-dimensional photoelasticity

International Nuclear Information System (INIS)

Theocaris, P.S.; Gdoutos, E.E.

1978-01-01

A non-destructive method for the photoelastic determination of three-dimensional stress distributions, based on the Mueller and Jones calculi, is developed. The differential equations satisfied by the Stokes and Jones vectors, when a polarized light beam passes through a photoelastic model, presenting rotation of the secondary principal stress directions, are established in matrix form. The Peano-Baker method is used for the solution of these differential equations in a matrix series form, establishing the elements of the Mueller and Jones matrices of the photoelastic model. These matrices are experimentally determined by using different wavelengths in conjunction with Jones' 'equivalence theorem'. The Neumann equations are immediately deduced from the above-mentioned differential equations. (orig.) [de

Changes in protein composition and protein phosphorylation during ...

African Journals Online (AJOL)

Changes in protein profiles and protein phosphorylation were studied in various stages of germinating somatic and zygotic embryos. Many proteins, which were expressed in cotyledonary stage somatic embryos, were also present in the zygotic embryos obtained from mature dry seed. The intensity of 22 kDa protein was ...

An ontology-based search engine for protein-protein interactions.

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Park, Byungkyu; Han, Kyungsook

2010-01-18

Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology.

Water-Protein Interactions: The Secret of Protein Dynamics

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Silvia Martini

2013-01-01

Full Text Available Water-protein interactions help to maintain flexible conformation conditions which are required for multifunctional protein recognition processes. The intimate relationship between the protein surface and hydration water can be analyzed by studying experimental water properties measured in protein systems in solution. In particular, proteins in solution modify the structure and the dynamics of the bulk water at the solute-solvent interface. The ordering effects of proteins on hydration water are extended for several angstroms. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on the analysis of the effects of protein-solvent interactions on water protons NMR relaxation parameters. NMR relaxation parameters, especially the nonselective (R1NS and selective (R1SE spin-lattice relaxation rates of water protons, are useful for investigating the solvent dynamics at the macromolecule-solvent interfaces as well as the perturbation effects caused by the water-macromolecule interactions on the solvent dynamical properties. In this paper we demonstrate that Nuclear Magnetic Resonance Spectroscopy can be used to determine the dynamical contributions of proteins to the water molecules belonging to their hydration shells.

Two Chimeric Regulators of G-protein Signaling (RGS) Proteins Differentially Modulate Soybean Heterotrimeric G-protein Cycle*

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Roy Choudhury, Swarup; Westfall, Corey S.; Laborde, John P.; Bisht, Naveen C.; Jez, Joseph M.; Pandey, Sona

2012-01-01

Heterotrimeric G-proteins and the regulator of G-protein signaling (RGS) proteins, which accelerate the inherent GTPase activity of Gα proteins, are common in animals and encoded by large gene families; however, in plants G-protein signaling is thought to be more limited in scope. For example, Arabidopsis thaliana contains one Gα, one Gβ, three Gγ, and one RGS protein. Recent examination of the Glycine max (soybean) genome reveals a larger set of G-protein-related genes and raises the possibility of more intricate G-protein networks than previously observed in plants. Stopped-flow analysis of GTP-binding and GDP/GTP exchange for the four soybean Gα proteins (GmGα1–4) reveals differences in their kinetic properties. The soybean genome encodes two chimeric RGS proteins with an N-terminal seven transmembrane domain and a C-terminal RGS box. Both GmRGS interact with each of the four GmGα and regulate their GTPase activity. The GTPase-accelerating activities of GmRGS1 and -2 differ for each GmGα, suggesting more than one possible rate of the G-protein cycle initiated by each of the Gα proteins. The differential effects of GmRGS1 and GmRGS2 on GmGα1–4 result from a single valine versus alanine difference. The emerging picture suggests complex regulation of the G-protein cycle in soybean and in other plants with expanded G-protein networks. PMID:22474294

Alignment of non-covalent interactions at protein-protein interfaces.

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Hongbo Zhu

Full Text Available BACKGROUND: The study and comparison of protein-protein interfaces is essential for the understanding of the mechanisms of interaction between proteins. While there are many methods for comparing protein structures and protein binding sites, so far no methods have been reported for comparing the geometry of non-covalent interactions occurring at protein-protein interfaces. METHODOLOGY/PRINCIPAL FINDINGS: Here we present a method for aligning non-covalent interactions between different protein-protein interfaces. The method aligns the vector representations of van der Waals interactions and hydrogen bonds based on their geometry. The method has been applied to a dataset which comprises a variety of protein-protein interfaces. The alignments are consistent to a large extent with the results obtained using two other complementary approaches. In addition, we apply the method to three examples of protein mimicry. The method successfully aligns respective interfaces and allows for recognizing conserved interface regions. CONCLUSIONS/SIGNIFICANCE: The Galinter method has been validated in the comparison of interfaces in which homologous subunits are involved, including cases of mimicry. The method is also applicable to comparing interfaces involving non-peptidic compounds. Galinter assists users in identifying local interface regions with similar patterns of non-covalent interactions. This is particularly relevant to the investigation of the molecular basis of interaction mimicry.

The Ser/Thr Protein Kinase Protein-Protein Interaction Map of M. tuberculosis.

Science.gov (United States)

Wu, Fan-Lin; Liu, Yin; Jiang, He-Wei; Luan, Yi-Zhao; Zhang, Hai-Nan; He, Xiang; Xu, Zhao-Wei; Hou, Jing-Li; Ji, Li-Yun; Xie, Zhi; Czajkowsky, Daniel M; Yan, Wei; Deng, Jiao-Yu; Bi, Li-Jun; Zhang, Xian-En; Tao, Sheng-Ce

2017-08-01

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, the leading cause of death among all infectious diseases. There are 11 eukaryotic-like serine/threonine protein kinases (STPKs) in Mtb, which are thought to play pivotal roles in cell growth, signal transduction and pathogenesis. However, their underlying mechanisms of action remain largely uncharacterized. In this study, using a Mtb proteome microarray, we have globally identified the binding proteins in Mtb for all of the STPKs, and constructed the first STPK protein interaction (KPI) map that includes 492 binding proteins and 1,027 interactions. Bioinformatics analysis showed that the interacting proteins reflect diverse functions, including roles in two-component system, transcription, protein degradation, and cell wall integrity. Functional investigations confirmed that PknG regulates cell wall integrity through key components of peptidoglycan (PG) biosynthesis, e.g. MurC. The global STPK-KPIs network constructed here is expected to serve as a rich resource for understanding the key signaling pathways in Mtb, thus facilitating drug development and effective control of Mtb. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces.

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Ching-Tai Chen

Full Text Available Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins and were tested on an independent dataset (consisting of 142 proteins. The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted

Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces

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Chen, Ching-Tai; Peng, Hung-Pin; Jian, Jhih-Wei; Tsai, Keng-Chang; Chang, Jeng-Yih; Yang, Ei-Wen; Chen, Jun-Bo; Ho, Shinn-Ying; Hsu, Wen-Lian; Yang, An-Suei

2012-01-01

Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with

Bioinformatic Prediction of WSSV-Host Protein-Protein Interaction

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Zheng Sun

2014-01-01

Full Text Available WSSV is one of the most dangerous pathogens in shrimp aquaculture. However, the molecular mechanism of how WSSV interacts with shrimp is still not very clear. In the present study, bioinformatic approaches were used to predict interactions between proteins from WSSV and shrimp. The genome data of WSSV (NC_003225.1 and the constructed transcriptome data of F. chinensis were used to screen potentially interacting proteins by searching in protein interaction databases, including STRING, Reactome, and DIP. Forty-four pairs of proteins were suggested to have interactions between WSSV and the shrimp. Gene ontology analysis revealed that 6 pairs of these interacting proteins were classified into “extracellular region” or “receptor complex” GO-terms. KEGG pathway analysis showed that they were involved in the “ECM-receptor interaction pathway.” In the 6 pairs of interacting proteins, an envelope protein called “collagen-like protein” (WSSV-CLP encoded by an early virus gene “wsv001” in WSSV interacted with 6 deduced proteins from the shrimp, including three integrin alpha (ITGA, two integrin beta (ITGB, and one syndecan (SDC. Sequence analysis on WSSV-CLP, ITGA, ITGB, and SDC revealed that they possessed the sequence features for protein-protein interactions. This study might provide new insights into the interaction mechanisms between WSSV and shrimp.

Protein subcellular localization assays using split fluorescent proteins

Science.gov (United States)

Waldo, Geoffrey S [Santa Fe, NM; Cabantous, Stephanie [Los Alamos, NM

2009-09-08

The invention provides protein subcellular localization assays using split fluorescent protein systems. The assays are conducted in living cells, do not require fixation and washing steps inherent in existing immunostaining and related techniques, and permit rapid, non-invasive, direct visualization of protein localization in living cells. The split fluorescent protein systems used in the practice of the invention generally comprise two or more self-complementing fragments of a fluorescent protein, such as GFP, wherein one or more of the fragments correspond to one or more beta-strand microdomains and are used to "tag" proteins of interest, and a complementary "assay" fragment of the fluorescent protein. Either or both of the fragments may be functionalized with a subcellular targeting sequence enabling it to be expressed in or directed to a particular subcellular compartment (i.e., the nucleus).

Human cancer protein-protein interaction network: a structural perspective.

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Gozde Kar

2009-12-01

Full Text Available Protein-protein interaction networks provide a global picture of cellular function and biological processes. Some proteins act as hub proteins, highly connected to others, whereas some others have few interactions. The dysfunction of some interactions causes many diseases, including cancer. Proteins interact through their interfaces. Therefore, studying the interface properties of cancer-related proteins will help explain their role in the interaction networks. Similar or overlapping binding sites should be used repeatedly in single interface hub proteins, making them promiscuous. Alternatively, multi-interface hub proteins make use of several distinct binding sites to bind to different partners. We propose a methodology to integrate protein interfaces into cancer interaction networks (ciSPIN, cancer structural protein interface network. The interactions in the human protein interaction network are replaced by interfaces, coming from either known or predicted complexes. We provide a detailed analysis of cancer related human protein-protein interfaces and the topological properties of the cancer network. The results reveal that cancer-related proteins have smaller, more planar, more charged and less hydrophobic binding sites than non-cancer proteins, which may indicate low affinity and high specificity of the cancer-related interactions. We also classified the genes in ciSPIN according to phenotypes. Within phenotypes, for breast cancer, colorectal cancer and leukemia, interface properties were found to be discriminating from non-cancer interfaces with an accuracy of 71%, 67%, 61%, respectively. In addition, cancer-related proteins tend to interact with their partners through distinct interfaces, corresponding mostly to multi-interface hubs, which comprise 56% of cancer-related proteins, and constituting the nodes with higher essentiality in the network (76%. We illustrate the interface related affinity properties of two cancer-related hub

Hot-spot analysis for drug discovery targeting protein-protein interactions.

Science.gov (United States)

Rosell, Mireia; Fernández-Recio, Juan

2018-04-01

Protein-protein interactions are important for biological processes and pathological situations, and are attractive targets for drug discovery. However, rational drug design targeting protein-protein interactions is still highly challenging. Hot-spot residues are seen as the best option to target such interactions, but their identification requires detailed structural and energetic characterization, which is only available for a tiny fraction of protein interactions. Areas covered: In this review, the authors cover a variety of computational methods that have been reported for the energetic analysis of protein-protein interfaces in search of hot-spots, and the structural modeling of protein-protein complexes by docking. This can help to rationalize the discovery of small-molecule inhibitors of protein-protein interfaces of therapeutic interest. Computational analysis and docking can help to locate the interface, molecular dynamics can be used to find suitable cavities, and hot-spot predictions can focus the search for inhibitors of protein-protein interactions. Expert opinion: A major difficulty for applying rational drug design methods to protein-protein interactions is that in the majority of cases the complex structure is not available. Fortunately, computational docking can complement experimental data. An interesting aspect to explore in the future is the integration of these strategies for targeting PPIs with large-scale mutational analysis.

Interaction between plate make and protein in protein crystallisation screening.

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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.

Protein Charge and Mass Contribute to the Spatio-temporal Dynamics of Protein-Protein Interactions in a Minimal Proteome

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Xu, Yu; Wang, Hong; Nussinov, Ruth; Ma, Buyong

2013-01-01

We constructed and simulated a ‘minimal proteome’ model using Langevin dynamics. It contains 206 essential protein types which were compiled from the literature. For comparison, we generated six proteomes with randomized concentrations. We found that the net charges and molecular weights of the proteins in the minimal genome are not random. The net charge of a protein decreases linearly with molecular weight, with small proteins being mostly positively charged and large proteins negatively charged. The protein copy numbers in the minimal genome have the tendency to maximize the number of protein-protein interactions in the network. Negatively charged proteins which tend to have larger sizes can provide large collision cross-section allowing them to interact with other proteins; on the other hand, the smaller positively charged proteins could have higher diffusion speed and are more likely to collide with other proteins. Proteomes with random charge/mass populations form less stable clusters than those with experimental protein copy numbers. Our study suggests that ‘proper’ populations of negatively and positively charged proteins are important for maintaining a protein-protein interaction network in a proteome. It is interesting to note that the minimal genome model based on the charge and mass of E. Coli may have a larger protein-protein interaction network than that based on the lower organism M. pneumoniae. PMID:23420643

Prediction of heterodimeric protein complexes from weighted protein-protein interaction networks using novel features and kernel functions.

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Peiying Ruan

Full Text Available Since many proteins express their functional activity by interacting with other proteins and forming protein complexes, it is very useful to identify sets of proteins that form complexes. For that purpose, many prediction methods for protein complexes from protein-protein interactions have been developed such as MCL, MCODE, RNSC, PCP, RRW, and NWE. These methods have dealt with only complexes with size of more than three because the methods often are based on some density of subgraphs. However, heterodimeric protein complexes that consist of two distinct proteins occupy a large part according to several comprehensive databases of known complexes. In this paper, we propose several feature space mappings from protein-protein interaction data, in which each interaction is weighted based on reliability. Furthermore, we make use of prior knowledge on protein domains to develop feature space mappings, domain composition kernel and its combination kernel with our proposed features. We perform ten-fold cross-validation computational experiments. These results suggest that our proposed kernel considerably outperforms the naive Bayes-based method, which is the best existing method for predicting heterodimeric protein complexes.

Estudio químico de piper steerni1

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Rafael Posso O.

2010-07-01

Full Text Available Del extracto clorofórmico de las hojas de Piper steerni se aislaron por métodos cromatográficos 5,7-dihidroxyflavanona, 5-hidroxi-7-metoxinavona y P-sitosterol; cl extracto en acetato de etilo del tallo del mismo vegetal presentó iguales constituyentes que las hojas junto con bases nitrogenadas de las cuales se identificó N-(4-hidroxifcniletilen cinamamida como un nuevo compuesto en la familia Piperaceae. Los metabolitos secundarios mayoritarios del aceite esencial de las hojas de P. steerni fueron caracterizados como benzaldehido, alcohol bencílico y benzoato de etilo. Las estructuras de los compuestos fueron establecidas por métodos quimicos y espectroscópicos y por correlaciones con substancias conocidas.

NMR Studies of Protein Hydration and Protein-Ligand Interactions

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Chong, Yuan

Water on the surface of a protein is called hydration water. Hydration water is known to play a crucial role in a variety of biological processes including protein folding, enzymatic activation, and drug binding. Although the significance of hydration water has been recognized, the underlying mechanism remains far from being understood. This dissertation employs a unique in-situ nuclear magnetic resonance (NMR) technique to study the mechanism of protein hydration and the role of hydration in alcohol-protein interactions. Water isotherms in proteins are measured at different temperatures via the in-situ NMR technique. Water is found to interact differently with hydrophilic and hydrophobic groups on the protein. Water adsorption on hydrophilic groups is hardly affected by the temperature, while water adsorption on hydrophobic groups strongly depends on the temperature around 10 C, below which the adsorption is substantially reduced. This effect is induced by the dramatic decrease in the protein flexibility below 10 C. Furthermore, nanosecond to microsecond protein dynamics and the free energy, enthalpy, and entropy of protein hydration are studied as a function of hydration level and temperature. A crossover at 10 C in protein dynamics and thermodynamics is revealed. The effect of water at hydrophilic groups on protein dynamics and thermodynamics shows little temperature dependence, whereas water at hydrophobic groups has stronger effect above 10 C. In addition, I investigate the role of water in alcohol binding to the protein using the in-situ NMR detection. The isotherms of alcohols are first measured on dry proteins, then on proteins with a series of controlled hydration levels. The free energy, enthalpy, and entropy of alcohol binding are also determined. Two distinct types of alcohol binding are identified. On the one hand, alcohols can directly bind to a few specific sites on the protein. This type of binding is independent of temperature and can be

Mapping monomeric threading to protein-protein structure prediction.

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Guerler, Aysam; Govindarajoo, Brandon; Zhang, Yang

2013-03-25

The key step of template-based protein-protein structure prediction is the recognition of complexes from experimental structure libraries that have similar quaternary fold. Maintaining two monomer and dimer structure libraries is however laborious, and inappropriate library construction can degrade template recognition coverage. We propose a novel strategy SPRING to identify complexes by mapping monomeric threading alignments to protein-protein interactions based on the original oligomer entries in the PDB, which does not rely on library construction and increases the efficiency and quality of complex template recognitions. SPRING is tested on 1838 nonhomologous protein complexes which can recognize correct quaternary template structures with a TM score >0.5 in 1115 cases after excluding homologous proteins. The average TM score of the first model is 60% and 17% higher than that by HHsearch and COTH, respectively, while the number of targets with an interface RMSD benchmark proteins. Although the relative performance of SPRING and ZDOCK depends on the level of homology filters, a combination of the two methods can result in a significantly higher model quality than ZDOCK at all homology thresholds. These data demonstrate a new efficient approach to quaternary structure recognition that is ready to use for genome-scale modeling of protein-protein interactions due to the high speed and accuracy.

DiffSLC: A graph centrality method to detect essential proteins of a protein-protein interaction network.

Science.gov (United States)

Mistry, Divya; Wise, Roger P; Dickerson, Julie A

2017-01-01

Identification of central genes and proteins in biomolecular networks provides credible candidates for pathway analysis, functional analysis, and essentiality prediction. The DiffSLC centrality measure predicts central and essential genes and proteins using a protein-protein interaction network. Network centrality measures prioritize nodes and edges based on their importance to the network topology. These measures helped identify critical genes and proteins in biomolecular networks. The proposed centrality measure, DiffSLC, combines the number of interactions of a protein and the gene coexpression values of genes from which those proteins were translated, as a weighting factor to bias the identification of essential proteins in a protein interaction network. Potentially essential proteins with low node degree are promoted through eigenvector centrality. Thus, the gene coexpression values are used in conjunction with the eigenvector of the network's adjacency matrix and edge clustering coefficient to improve essentiality prediction. The outcome of this prediction is shown using three variations: (1) inclusion or exclusion of gene co-expression data, (2) impact of different coexpression measures, and (3) impact of different gene expression data sets. For a total of seven networks, DiffSLC is compared to other centrality measures using Saccharomyces cerevisiae protein interaction networks and gene expression data. Comparisons are also performed for the top ranked proteins against the known essential genes from the Saccharomyces Gene Deletion Project, which show that DiffSLC detects more essential proteins and has a higher area under the ROC curve than other compared methods. This makes DiffSLC a stronger alternative to other centrality methods for detecting essential genes using a protein-protein interaction network that obeys centrality-lethality principle. DiffSLC is implemented using the igraph package in R, and networkx package in Python. The python package can be

A credit-card library approach for disrupting protein-protein interactions.

Science.gov (United States)

Xu, Yang; Shi, Jin; Yamamoto, Noboru; Moss, Jason A; Vogt, Peter K; Janda, Kim D

2006-04-15

Protein-protein interfaces are prominent in many therapeutically important targets. Using small organic molecules to disrupt protein-protein interactions is a current challenge in chemical biology. An important example of protein-protein interactions is provided by the Myc protein, which is frequently deregulated in human cancers. Myc belongs to the family of basic helix-loop-helix leucine zipper (bHLH-ZIP) transcription factors. It is biologically active only as heterodimer with the bHLH-ZIP protein Max. Herein, we report a new strategy for the disruption of protein-protein interactions that has been corroborated through the design and synthesis of a small parallel library composed of 'credit-card' compounds. These compounds are derived from a planar, aromatic scaffold and functionalized with four points of diversity. From a 285 membered library, several hits were obtained that disrupted the c-Myc-Max interaction and cellular functions of c-Myc. The IC50 values determined for this small focused library for the disruption of Myc-Max dimerization are quite potent, especially since small molecule antagonists of protein-protein interactions are notoriously difficult to find. Furthermore, several of the compounds were active at the cellular level as shown by their biological effects on Myc action in chicken embryo fibroblast assays. In light of our findings, this approach is considered a valuable addition to the armamentarium of new molecules being developed to interact with protein-protein interfaces. Finally, this strategy for disrupting protein-protein interactions should prove applicable to other families of proteins.

76 FR 35474 - Colville Indian Plywood and Veneer, Colville Tribal Enterprise Corporation Wood Products Division...

Science.gov (United States)

2011-06-17

... Logging, Mccuen Jones, San Poil Logging, Scott Thorndike, Silver Nichol Trucking and Stensgar Logging..., Mawdsley Logging, McCuen Jones, San Poil Logging, Scott Thorndike, Silver Nichol Trucking and Stensgar...

Protein Correlation Profiles Identify Lipid Droplet Proteins with High Confidence*

Science.gov (United States)

Krahmer, Natalie; Hilger, Maximiliane; Kory, Nora; Wilfling, Florian; Stoehr, Gabriele; Mann, Matthias; Farese, Robert V.; Walther, Tobias C.

2013-01-01

Lipid droplets (LDs) are important organelles in energy metabolism and lipid storage. Their cores are composed of neutral lipids that form a hydrophobic phase and are surrounded by a phospholipid monolayer that harbors specific proteins. Most well-established LD proteins perform important functions, particularly in cellular lipid metabolism. Morphological studies show LDs in close proximity to and interacting with membrane-bound cellular organelles, including the endoplasmic reticulum, mitochondria, peroxisomes, and endosomes. Because of these close associations, it is difficult to purify LDs to homogeneity. Consequently, the confident identification of bona fide LD proteins via proteomics has been challenging. Here, we report a methodology for LD protein identification based on mass spectrometry and protein correlation profiles. Using LD purification and quantitative, high-resolution mass spectrometry, we identified LD proteins by correlating their purification profiles to those of known LD proteins. Application of the protein correlation profile strategy to LDs isolated from Drosophila S2 cells led to the identification of 111 LD proteins in a cellular LD fraction in which 1481 proteins were detected. LD localization was confirmed in a subset of identified proteins via microscopy of the expressed proteins, thereby validating the approach. Among the identified LD proteins were both well-characterized LD proteins and proteins not previously known to be localized to LDs. Our method provides a high-confidence LD proteome of Drosophila cells and a novel approach that can be applied to identify LD proteins of other cell types and tissues. PMID:23319140

ProteinShop: A tool for interactive protein manipulation and steering

Energy Technology Data Exchange (ETDEWEB)

Crivelli, Silvia; Kreylos, Oliver; Max, Nelson; Hamann, Bernd; Bethel, Wes

2004-05-25

We describe ProteinShop, a new visualization tool that streamlines and simplifies the process of determining optimal protein folds. ProteinShop may be used at different stages of a protein structure prediction process. First, it can create protein configurations containing secondary structures specified by the user. Second, it can interactively manipulate protein fragments to achieve desired folds by adjusting the dihedral angles of selected coil regions using an Inverse Kinematics method. Last, it serves as a visual framework to monitor and steer a protein structure prediction process that may be running on a remote machine. ProteinShop was used to create initial configurations for a protein structure prediction method developed by a team that competed in CASP5. ProteinShop's use accelerated the process of generating initial configurations, reducing the time required from days to hours. This paper describes the structure of ProteinShop and discusses its main features.

Identification and Characterization of Ovarian Carcinoma Peptide Epitopes Recognized by Cylotoxic T Lymphocytes

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2008-11-01

50. Sigalotti L, Altomonte M , Colizzi F, Degan M , Rupolo M , Zago - nel V, Pinto A, Gattei V, Maio M , Lubbert M , Wijermans PW, Jones PA, Hellstrom...cell lines. Cancer Immunol. Immunother. 57:31-42. 2. Adair, S.J., Carr, T.M., Fink, M . J., Slingluff, C. L., and Hogan, K. T. (2008) The TAG family...Source Protein HLA-A1 HLA-A2 HLA-A3 HLA-B7 HLA-B8 Binding Motifsb --E-----Y D - M ------V L L I - M ------Y L K -PR-----L

Prioritizing disease candidate proteins in cardiomyopathy-specific protein-protein interaction networks based on "guilt by association" analysis.

Directory of Open Access Journals (Sweden)

Wan Li

Full Text Available The cardiomyopathies are a group of heart muscle diseases which can be inherited (familial. Identifying potential disease-related proteins is important to understand mechanisms of cardiomyopathies. Experimental identification of cardiomyophthies is costly and labour-intensive. In contrast, bioinformatics approach has a competitive advantage over experimental method. Based on "guilt by association" analysis, we prioritized candidate proteins involving in human cardiomyopathies. We first built weighted human cardiomyopathy-specific protein-protein interaction networks for three subtypes of cardiomyopathies using the known disease proteins from Online Mendelian Inheritance in Man as seeds. We then developed a method in prioritizing disease candidate proteins to rank candidate proteins in the network based on "guilt by association" analysis. It was found that most candidate proteins with high scores shared disease-related pathways with disease seed proteins. These top ranked candidate proteins were related with the corresponding disease subtypes, and were potential disease-related proteins. Cross-validation and comparison with other methods indicated that our approach could be used for the identification of potentially novel disease proteins, which may provide insights into cardiomyopathy-related mechanisms in a more comprehensive and integrated way.

Modular protein switches derived from antibody mimetic proteins.

Science.gov (United States)

Nicholes, N; Date, A; Beaujean, P; Hauk, P; Kanwar, M; Ostermeier, M

2016-02-01

Protein switches have potential applications as biosensors and selective protein therapeutics. Protein switches built by fusion of proteins with the prerequisite input and output functions are currently developed using an ad hoc process. A modular switch platform in which existing switches could be readily adapted to respond to any ligand would be advantageous. We investigated the feasibility of a modular protein switch platform based on fusions of the enzyme TEM-1 β-lactamase (BLA) with two different antibody mimetic proteins: designed ankyrin repeat proteins (DARPins) and monobodies. We created libraries of random insertions of the gene encoding BLA into genes encoding a DARPin or a monobody designed to bind maltose-binding protein (MBP). From these libraries, we used a genetic selection system for β-lactamase activity to identify genes that conferred MBP-dependent ampicillin resistance to Escherichia coli. Some of these selected genes encoded switch proteins whose enzymatic activity increased up to 14-fold in the presence of MBP. We next introduced mutations into the antibody mimetic domain of these switches that were known to cause binding to different ligands. To different degrees, introduction of the mutations resulted in switches with the desired specificity, illustrating the potential modularity of these platforms. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Protein-protein interactions and cancer: targeting the central dogma.

Science.gov (United States)

Garner, Amanda L; Janda, Kim D

2011-01-01

Between 40,000 and 200,000 protein-protein interactions have been predicted to exist within the human interactome. As these interactions are of a critical nature in many important cellular functions and their dysregulation is causal of disease, the modulation of these binding events has emerged as a leading, yet difficult therapeutic arena. In particular, the targeting of protein-protein interactions relevant to cancer is of fundamental importance as the tumor-promoting function of several aberrantly expressed proteins in the cancerous state is directly resultant of its ability to interact with a protein-binding partner. Of significance, these protein complexes play a crucial role in each of the steps of the central dogma of molecular biology, the fundamental processes of genetic transmission. With the many important discoveries being made regarding the mechanisms of these genetic process, the identification of new chemical probes are needed to better understand and validate the druggability of protein-protein interactions related to the central dogma. In this review, we provide an overview of current small molecule-based protein-protein interaction inhibitors for each stage of the central dogma: transcription, mRNA splicing and translation. Importantly, through our analysis we have uncovered a lack of necessary probes targeting mRNA splicing and translation, thus, opening up the possibility for expansion of these fields.

Targeting protein-protein interactions for parasite control.

Directory of Open Access Journals (Sweden)

Christina M Taylor

2011-04-01

Full Text Available Finding new drug targets for pathogenic infections would be of great utility for humanity, as there is a large need to develop new drugs to fight infections due to the developing resistance and side effects of current treatments. Current drug targets for pathogen infections involve only a single protein. However, proteins rarely act in isolation, and the majority of biological processes occur via interactions with other proteins, so protein-protein interactions (PPIs offer a realm of unexplored potential drug targets and are thought to be the next-generation of drug targets. Parasitic worms were chosen for this study because they have deleterious effects on human health, livestock, and plants, costing society billions of dollars annually and many sequenced genomes are available. In this study, we present a computational approach that utilizes whole genomes of 6 parasitic and 1 free-living worm species and 2 hosts. The species were placed in orthologous groups, then binned in species-specific orthologous groups. Proteins that are essential and conserved among species that span a phyla are of greatest value, as they provide foundations for developing broad-control strategies. Two PPI databases were used to find PPIs within the species specific bins. PPIs with unique helminth proteins and helminth proteins with unique features relative to the host, such as indels, were prioritized as drug targets. The PPIs were scored based on RNAi phenotype and homology to the PDB (Protein DataBank. EST data for the various life stages, GO annotation, and druggability were also taken into consideration. Several PPIs emerged from this study as potential drug targets. A few interactions were supported by co-localization of expression in M. incognita (plant parasite and B. malayi (H. sapiens parasite, which have extremely different modes of parasitism. As more genomes of pathogens are sequenced and PPI databases expanded, this methodology will become increasingly

ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.

Directory of Open Access Journals (Sweden)

John A Capra

Full Text Available The evolutionary history of a protein reflects the functional history of its ancestors. Recent phylogenetic studies identified distinct evolutionary signatures that characterize proteins involved in cancer, Mendelian disease, and different ontogenic stages. Despite the potential to yield insight into the cellular functions and interactions of proteins, such comparative phylogenetic analyses are rarely performed, because they require custom algorithms. We developed ProteinHistorian to make tools for performing analyses of protein origins widely available. Given a list of proteins of interest, ProteinHistorian estimates the phylogenetic age of each protein, quantifies enrichment for proteins of specific ages, and compares variation in protein age with other protein attributes. ProteinHistorian allows flexibility in the definition of protein age by including several algorithms for estimating ages from different databases of evolutionary relationships. We illustrate the use of ProteinHistorian with three example analyses. First, we demonstrate that proteins with high expression in human, compared to chimpanzee and rhesus macaque, are significantly younger than those with human-specific low expression. Next, we show that human proteins with annotated regulatory functions are significantly younger than proteins with catalytic functions. Finally, we compare protein length and age in many eukaryotic species and, as expected from previous studies, find a positive, though often weak, correlation between protein age and length. ProteinHistorian is available through a web server with an intuitive interface and as a set of command line tools; this allows biologists and bioinformaticians alike to integrate these approaches into their analysis pipelines. ProteinHistorian's modular, extensible design facilitates the integration of new datasets and algorithms. The ProteinHistorian web server, source code, and pre-computed ages for 32 eukaryotic genomes are

Mitochondrial nucleoid interacting proteins support mitochondrial protein synthesis.

Science.gov (United States)

He, J; Cooper, H M; Reyes, A; Di Re, M; Sembongi, H; Litwin, T R; Gao, J; Neuman, K C; Fearnley, I M; Spinazzola, A; Walker, J E; Holt, I J

2012-07-01

Mitochondrial ribosomes and translation factors co-purify with mitochondrial nucleoids of human cells, based on affinity protein purification of tagged mitochondrial DNA binding proteins. Among the most frequently identified proteins were ATAD3 and prohibitin, which have been identified previously as nucleoid components, using a variety of methods. Both proteins are demonstrated to be required for mitochondrial protein synthesis in human cultured cells, and the major binding partner of ATAD3 is the mitochondrial ribosome. Altered ATAD3 expression also perturbs mtDNA maintenance and replication. These findings suggest an intimate association between nucleoids and the machinery of protein synthesis in mitochondria. ATAD3 and prohibitin are tightly associated with the mitochondrial membranes and so we propose that they support nucleic acid complexes at the inner membrane of the mitochondrion.

Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure.

Science.gov (United States)

Li, Tao; Li, Qian-Zhong

2012-11-07

RNA-protein interactions play important roles in various biological processes. The precise detection of RNA-protein interaction sites is very important for understanding essential biological processes and annotating the function of the proteins. In this study, based on various features from amino acid sequence and structure, including evolutionary information, solvent accessible surface area and torsion angles (φ, ψ) in the backbone structure of the polypeptide chain, a computational method for predicting RNA-binding sites in proteins is proposed. When the method is applied to predict RNA-binding sites in three datasets: RBP86 containing 86 protein chains, RBP107 containing 107 proteins chains and RBP109 containing 109 proteins chains, better sensitivities and specificities are obtained compared to previously published methods in five-fold cross-validation tests. In order to make further examination for the efficiency of our method, the RBP107 dataset is used as training set, RBP86 and RBP109 datasets are used as the independent test sets. In addition, as examples of our prediction, RNA-binding sites in a few proteins are presented. The annotated results are consistent with the PDB annotation. These results show that our method is useful for annotating RNA binding sites of novel proteins.

Evolutionary diversification of protein-protein interactions by interface add-ons.

Science.gov (United States)

Plach, Maximilian G; Semmelmann, Florian; Busch, Florian; Busch, Markus; Heizinger, Leonhard; Wysocki, Vicki H; Merkl, Rainer; Sterner, Reinhard

2017-10-03

Cells contain a multitude of protein complexes whose subunits interact with high specificity. However, the number of different protein folds and interface geometries found in nature is limited. This raises the question of how protein-protein interaction specificity is achieved on the structural level and how the formation of nonphysiological complexes is avoided. Here, we describe structural elements called interface add-ons that fulfill this function and elucidate their role for the diversification of protein-protein interactions during evolution. We identified interface add-ons in 10% of a representative set of bacterial, heteromeric protein complexes. The importance of interface add-ons for protein-protein interaction specificity is demonstrated by an exemplary experimental characterization of over 30 cognate and hybrid glutamine amidotransferase complexes in combination with comprehensive genetic profiling and protein design. Moreover, growth experiments showed that the lack of interface add-ons can lead to physiologically harmful cross-talk between essential biosynthetic pathways. In sum, our complementary in silico, in vitro, and in vivo analysis argues that interface add-ons are a practical and widespread evolutionary strategy to prevent the formation of nonphysiological complexes by specializing protein-protein interactions.

The interface of protein structure, protein biophysics, and molecular evolution

Science.gov (United States)

Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

2012-01-01

Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

Racemic & quasi-racemic protein crystallography enabled by chemical protein synthesis.

Science.gov (United States)

Kent, Stephen Bh

2018-04-04

A racemic protein mixture can be used to form centrosymmetric crystals for structure determination by X-ray diffraction. Both the unnatural d-protein and the corresponding natural l-protein are made by total chemical synthesis based on native chemical ligation-chemoselective condensation of unprotected synthetic peptide segments. Racemic protein crystallography is important for structure determination of the many natural protein molecules that are refractory to crystallization. Racemic mixtures facilitate the crystallization of recalcitrant proteins, and give diffraction-quality crystals. Quasi-racemic crystallization, using a single d-protein molecule, can facilitate the determination of the structures of a series of l-protein analog molecules. Copyright © 2018 Elsevier Ltd. All rights reserved.

General protein-protein cross-linking.

Science.gov (United States)

Alegria-Schaffer, Alice

2014-01-01

This protocol describes a general protein-to-protein cross-linking procedure using the water-soluble amine-reactive homobifunctional BS(3) (bis[sulfosuccinimidyl] suberate); however, the protocol can be easily adapted using other cross-linkers of similar properties. BS(3) is composed of two sulfo-NHS ester groups and an 11.4 Å linker. Sulfo-NHS ester groups react with primary amines in slightly alkaline conditions (pH 7.2-8.5) and yield stable amide bonds. The reaction releases N-hydroxysuccinimide (see an application of NHS esters on Labeling a protein with fluorophores using NHS ester derivitization). © 2014 Elsevier Inc. All rights reserved.

Quality control methodology for high-throughput protein-protein interaction screening.

Science.gov (United States)

Vazquez, Alexei; Rual, Jean-François; Venkatesan, Kavitha

2011-01-01

Protein-protein interactions are key to many aspects of the cell, including its cytoskeletal structure, the signaling processes in which it is involved, or its metabolism. Failure to form protein complexes or signaling cascades may sometimes translate into pathologic conditions such as cancer or neurodegenerative diseases. The set of all protein interactions between the proteins encoded by an organism constitutes its protein interaction network, representing a scaffold for biological function. Knowing the protein interaction network of an organism, combined with other sources of biological information, can unravel fundamental biological circuits and may help better understand the molecular basics of human diseases. The protein interaction network of an organism can be mapped by combining data obtained from both low-throughput screens, i.e., "one gene at a time" experiments and high-throughput screens, i.e., screens designed to interrogate large sets of proteins at once. In either case, quality controls are required to deal with the inherent imperfect nature of experimental assays. In this chapter, we discuss experimental and statistical methodologies to quantify error rates in high-throughput protein-protein interactions screens.

Quantifying the molecular origins of opposite solvent effects on protein-protein interactions.

Directory of Open Access Journals (Sweden)

Vincent Vagenende

Full Text Available Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments.

Our interests in protein-protein interactions

Indian Academy of Sciences (India)

protein interactions. Evolution of P-P partnerships. Evolution of P-P structures. Evolutionary dynamics of P-P interactions. Dynamics of P-P interaction network. Host-pathogen interactions. CryoEM mapping of gigantic protein assemblies.

A Library of Plasmodium vivax Recombinant Merozoite Proteins Reveals New Vaccine Candidates and Protein-Protein Interactions

Science.gov (United States)

Hostetler, Jessica B.; Sharma, Sumana; Bartholdson, S. Josefin; Wright, Gavin J.; Fairhurst, Rick M.; Rayner, Julian C.

2015-01-01

Background A vaccine targeting Plasmodium vivax will be an essential component of any comprehensive malaria elimination program, but major gaps in our understanding of P. vivax biology, including the protein-protein interactions that mediate merozoite invasion of reticulocytes, hinder the search for candidate antigens. Only one ligand-receptor interaction has been identified, that between P. vivax Duffy Binding Protein (PvDBP) and the erythrocyte Duffy Antigen Receptor for Chemokines (DARC), and strain-specific immune responses to PvDBP make it a complex vaccine target. To broaden the repertoire of potential P. vivax merozoite-stage vaccine targets, we exploited a recent breakthrough in expressing full-length ectodomains of Plasmodium proteins in a functionally-active form in mammalian cells and initiated a large-scale study of P. vivax merozoite proteins that are potentially involved in reticulocyte binding and invasion. Methodology/Principal Findings We selected 39 P. vivax proteins that are predicted to localize to the merozoite surface or invasive secretory organelles, some of which show homology to P. falciparum vaccine candidates. Of these, we were able to express 37 full-length protein ectodomains in a mammalian expression system, which has been previously used to express P. falciparum invasion ligands such as PfRH5. To establish whether the expressed proteins were correctly folded, we assessed whether they were recognized by antibodies from Cambodian patients with acute vivax malaria. IgG from these samples showed at least a two-fold change in reactivity over naïve controls in 27 of 34 antigens tested, and the majority showed heat-labile IgG immunoreactivity, suggesting the presence of conformation-sensitive epitopes and native tertiary protein structures. Using a method specifically designed to detect low-affinity, extracellular protein-protein interactions, we confirmed a predicted interaction between P. vivax 6-cysteine proteins P12 and P41, further

[Detection of protein-protein interactions by FRET and BRET methods].

Science.gov (United States)

Matoulková, E; Vojtěšek, B

2014-01-01

Nowadays, in vivo protein-protein interaction studies have become preferable detecting meth-ods that enable to show or specify (already known) protein interactions and discover their inhibitors. They also facilitate detection of protein conformational changes and discovery or specification of signaling pathways in living cells. One group of in vivo methods enabling these findings is based on fluorescent resonance energy transfer (FRET) and its bio-luminescent modification (BRET). They are based on visualization of protein-protein interactions via light or enzymatic excitation of fluorescent or bio-luminescent proteins. These methods allow not only protein localization within the cell or its organelles (or small animals) but they also allow us to quantify fluorescent signals and to discover weak or strong interaction partners. In this review, we explain the principles of FRET and BRET, their applications in the characterization of protein-protein interactions and we describe several findings using these two methods that clarify molecular and cellular mechanisms and signals related to cancer biology.

Protein degradation and protein synthesis in long-term memory formation

Directory of Open Access Journals (Sweden)

Timothy J Jarome

2014-06-01

Full Text Available Long-term memory (LTM formation requires transient changes in the activity of intracellular signaling cascades that are thought to regulate new gene transcription and de novo protein synthesis in the brain. Consistent with this, protein synthesis inhibitors impair LTM for a variety of behavioral tasks when infused into the brain around the time of training or following memory retrieval, suggesting that protein synthesis is a critical step in LTM storage in the brain. However, evidence suggests that protein degradation mediated by the ubiquitin-proteasome system may also be a critical regulator of LTM formation and stability following retrieval. This requirement for increased protein degradation has been shown in the same brain regions in which protein synthesis is required for LTM storage. Additionally, increases in the phosphorylation of proteins involved in translational control parallel increases in protein polyubiquitination and the increased demand for protein degradation is regulated by intracellular signaling molecules thought to regulate protein synthesis during LTM formation. In some cases inhibiting proteasome activity can rescue memory impairments that result from pharmacological blockade of protein synthesis, suggesting that protein degradation may control the requirement for protein synthesis during the memory storage process. Results such as these suggest that protein degradation and synthesis are both critical for LTM formation and may interact to properly consolidate and store memories in the brain. Here, we review the evidence implicating protein synthesis and degradation in LTM storage and highlight the areas of overlap between these two opposing processes. We also discuss evidence suggesting these two processes may interact to properly form and store memories. LTM storage likely requires a coordinated regulation between protein degradation and synthesis at multiple sites in the mammalian brain.

Evolutionary reprograming of protein-protein interaction specificity.

Science.gov (United States)

Akiva, Eyal; Babbitt, Patricia C

2015-10-22

Using mutation libraries and deep sequencing, Aakre et al. study the evolution of protein-protein interactions using a toxin-antitoxin model. The results indicate probable trajectories via "intermediate" proteins that are promiscuous, thus avoiding transitions via non-interactions. These results extend observations about other biological interactions and enzyme evolution, suggesting broadly general principles. Copyright © 2015 Elsevier Inc. All rights reserved.

Analysis of Faraday Mirror in Auto-Compensating Quantum Key Distribution

International Nuclear Information System (INIS)

Wei Ke-Jin; Ma Hai-Qiang; Li Rui-Xue; Zhu Wu; Liu Hong-Wei; Zhang Yong; Jiao Rong-Zhen

2015-01-01

The ‘plug and play’ quantum key distribution system is the most stable and the earliest commercial system in the quantum communication field. Jones matrix and Jones calculus are widely used in the analysis of this system and the improved version, which is called the auto-compensating quantum key distribution system. Unfortunately, existing analysis has two drawbacks: only the auto-compensating process is analyzed and existing systems do not fully consider laser phase affected by a Faraday mirror (FM). In this work, we present a detailed analysis of the output of light pulse transmitting in a plug and play quantum key distribution system that contains only an FM, by Jones calculus. A similar analysis is made to a home-made auto-compensating system which contains two FMs to compensate for environmental effects. More importantly, we show that theoretical and experimental results are different in the plug and play interferometric setup due to the fact that a conventional Jones matrix of FM neglected an additional phase π on alternative polarization direction. To resolve the above problem, we give a new Jones matrix of an FM according to the coordinate rotation. This new Jones matrix not only resolves the above contradiction in the plug and play interferometric setup, but also is suitable for the previous analyses about auto-compensating quantum key distribution. (paper)

Investigations of electronic structure of Bi and Sb by the method of the angular correlation of annihilation quanta

International Nuclear Information System (INIS)

Szuszkiewicz, M.

1977-01-01

The work is devoted to the investigations of electronic structure of solid bismuth and antymony using the method of the angular correlation of annihilation quanta, originated from the two-photons annihilation of positrons with the electrons of a sample. The measurements of the angular correlation were performed for monocrystallic samples of Bi and Sb for three crystallographic directions: /011/,/011/, /111/. The analysis of the obtained results is based upon the Brillouin zones theory extended by Jones for the crystalline structure of those semimetals. For Bi for the direction /111/, a distinct discrepancy has been found between the experimental and expected distribution, calculated on the base of the completely occupied Jones zone. This diveragence is assumed to be due to the conductivity electrons occupying the electronic states outside the Jones zone. The angular distributions for all directions of Sb turned out to be inconsistent with the model of Jones zone, containing 10 quasi-free electrons per unit cell. It is possible to give a satisfactory interpretation of the experimental data for Sb under the assumption that the first Brillouin zone in Jones zone is occupied by the electrons, behaving as being strongly localized, (about 2 electrons per unit cell) and the remaining part of Jones zone is occupied by quasi-free electrons, similarly to Bi. (author)

PORTNUS Project

Energy Technology Data Exchange (ETDEWEB)

Loyal, Rebecca E. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2015-07-14

The objective of the Portunus Project is to create large, automated offshore ports that will the pace and scale of international trade. Additionally, these ports would increase the number of U.S. domestic trade vessels needed, as the imported goods would need to be transported from these offshore platforms to land-based ports such as Boston, Los Angeles, and Newark. Currently, domestic trade in the United States can only be conducted by vessels that abide by the Merchant Marine Act of 1920 – also referred to as the Jones Act. The Jones Act stipulates that vessels involved in domestic trade must be U.S. owned, U.S. built, and manned by a crew made up of U.S. citizens. The Portunus Project would increase the number of Jones Act vessels needed, which raises an interesting economic concern. Are Jones Act ships more expensive to operate than foreign vessels? Would it be more economically efficient to modify the Jones Act and allow vessels manned by foreign crews to engage in U.S. domestic trade? While opposition to altering the Jones Act is strong, it is important to consider the possibility that ship-owners who employ foreign crews will lobby for the chance to enter a growing domestic trade market. Their success would mean potential job loss for thousands of Americans currently employed in maritime trade.

Protein Annotation from Protein Interaction Networks and Gene Ontology

OpenAIRE

Nguyen, Cao D.; Gardiner, Katheleen J.; Cios, Krzysztof J.

2011-01-01

We introduce a novel method for annotating protein function that combines Naïve Bayes and association rules, and takes advantage of the underlying topology in protein interaction networks and the structure of graphs in the Gene Ontology. We apply our method to proteins from the Human Protein Reference Database (HPRD) and show that, in comparison with other approaches, it predicts protein functions with significantly higher recall with no loss of precision. Specifically, it achieves 51% precis...

Protein supplementation with sports protein bars in renal patients.

Science.gov (United States)

Meade, Anthony

2007-05-01

Malnutrition prevalence in patients on dialysis is well established. The protein requirements for both hemodialysis and peritoneal dialysis have been documented elsewhere, including the Kidney Disease Outcomes Quality Initiative Clinical Practice Guidelines for Nutrition in Chronic Renal Failure. The clinical challenge is to assist patients in meeting these targets, especially in those with anorexia. Traditional supplements have included fluid, which is an issue for patients who are fluid restricted. The study objectives were to (1) investigate the range of sports protein supplements that may be suitable for patients on hemodialysis to use and (2) trial nonfluid protein supplements in patients on hemodialysis. Known manufacturers of sports protein bars and other sports supplements available in Australia were contacted for the nutrient breakdown of high-protein products, specifically potassium, protein, and phosphorus contents. As a result, selected high-protein sports bars (Protein FX, Aussie Bodies, Port Melbourne, Victoria, Australia) were used as an alternative to the more commonly used renal-specific fluid supplements (Nepro, Abbott Laboratories, Abbott Park, IL; Novasource Renal, Novartis Nutrition Corporation, Fremont, MI; and Renilon, Nutricia, Wiltshire, UK) in patients with poor nutritional status requiring supplementation. Patient satisfaction and clinical nutrition markers were investigated. The study took place at inpatient, in-center, and satellite hemodialysis settings in Adelaide, South Australia. A total of 32 patients (16 females and 16 males) with an average age of 62.9 years (range 32-86 years) undergoing hemodialysis (acute and maintenance) were included. Subjects were selected by the author as part of routine clinical nutrition care. Patients trialed sports protein bars as a protein supplement alone or in conjunction with other supplementary products. All patients were in favor of the trial, with 22 of 32 patients continuing with the protein

SYNTHESIS, CHARACTERIZATION, AND CRYSTAL STRUCTURE ...

African Journals Online (AJOL)

a

KEY WORDS: Barium, Crystal structure, 2,6-Pyridinedicarboxylic acid .... The rational design of novel metal-organic frameworks has attracted great ..... Bond, A.D.; Jones, W. Supramolecular Organization and Materials Design, Jones, W.; Rao,.

CrossTalk: The Journal of Defense Software Engineering. Volume 20, Number 12

National Research Council Canada - National Science Library

Jones, Capers; Huff, Lloyd; Novak, George; Lau, Yun-Tung; Torri, Stephen; Sanders, Derek; Hamilton, Drew; Evans, Gordon; Frost, Alison A; Campo, Michael J

2007-01-01

CONTENTS: 1) Geriatric Issues of Aging Software by Capers Jones: Capers Jones discusses the need of every company to evaluate and consider best practices for maintenance and to avoid common worst practices. 2...

Protein enriched pasta: structure and digestibility of its protein network.

Science.gov (United States)

Laleg, Karima; Barron, Cécile; Santé-Lhoutellier, Véronique; Walrand, Stéphane; Micard, Valérie

2016-02-01

Wheat (W) pasta was enriched in 6% gluten (G), 35% faba (F) or 5% egg (E) to increase its protein content (13% to 17%). The impact of the enrichment on the multiscale structure of the pasta and on in vitro protein digestibility was studied. Increasing the protein content (W- vs. G-pasta) strengthened pasta structure at molecular and macroscopic scales but reduced its protein digestibility by 3% by forming a higher covalently linked protein network. Greater changes in the macroscopic and molecular structure of the pasta were obtained by varying the nature of protein used for enrichment. Proteins in G- and E-pasta were highly covalently linked (28-32%) resulting in a strong pasta structure. Conversely, F-protein (98% SDS-soluble) altered the pasta structure by diluting gluten and formed a weak protein network (18% covalent link). As a result, protein digestibility in F-pasta was significantly higher (46%) than in E- (44%) and G-pasta (39%). The effect of low (55 °C, LT) vs. very high temperature (90 °C, VHT) drying on the protein network structure and digestibility was shown to cause greater molecular changes than pasta formulation. Whatever the pasta, a general strengthening of its structure, a 33% to 47% increase in covalently linked proteins and a higher β-sheet structure were observed. However, these structural differences were evened out after the pasta was cooked, resulting in identical protein digestibility in LT and VHT pasta. Even after VHT drying, F-pasta had the best amino acid profile with the highest protein digestibility, proof of its nutritional interest.

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.

Different protein-protein interface patterns predicted by different machine learning methods.

Science.gov (United States)

Wang, Wei; Yang, Yongxiao; Yin, Jianxin; Gong, Xinqi

2017-11-22

Different types of protein-protein interactions make different protein-protein interface patterns. Different machine learning methods are suitable to deal with different types of data. Then, is it the same situation that different interface patterns are preferred for prediction by different machine learning methods? Here, four different machine learning methods were employed to predict protein-protein interface residue pairs on different interface patterns. The performances of the methods for different types of proteins are different, which suggest that different machine learning methods tend to predict different protein-protein interface patterns. We made use of ANOVA and variable selection to prove our result. Our proposed methods taking advantages of different single methods also got a good prediction result compared to single methods. In addition to the prediction of protein-protein interactions, this idea can be extended to other research areas such as protein structure prediction and design.

Molecular simulations of lipid-mediated protein-protein interactions

NARCIS (Netherlands)

de Meyer, F.J.M.; Venturoli, M.; Smit, B.

2008-01-01

Recent experimental results revealed that lipid-mediated interactions due to hydrophobic forces may be important in determining the protein topology after insertion in the membrane, in regulating the protein activity, in protein aggregation and in signal transduction. To gain insight into the

Detecting protein-protein interactions in living cells

DEFF Research Database (Denmark)

Gottschalk, Marie; Bach, Anders; Hansen, Jakob Lerche

2009-01-01

to the endogenous C-terminal peptide of the NMDA receptor, as evaluated by a cell-free protein-protein interaction assay. However, it is important to address both membrane permeability and effect in living cells. Therefore a bioluminescence resonance energy transfer (BRET) assay was established, where the C......-terminal of the NMDA receptor and PDZ2 of PSD-95 were fused to green fluorescent protein (GFP) and Renilla luciferase (Rluc) and expressed in COS7 cells. A robust and specific BRET signal was obtained by expression of the appropriate partner proteins and subsequently, the assay was used to evaluate a Tat......The PDZ domain mediated interaction between the NMDA receptor and its intracellular scaffolding protein, PSD-95, is a potential target for treatment of ischemic brain diseases. We have recently developed a number of peptide analogues with improved affinity for the PDZ domains of PSD-95 compared...

Personalizing Protein Nourishment

Science.gov (United States)

DALLAS, DAVID C.; SANCTUARY, MEGAN R.; QU, YUNYAO; KHAJAVI, SHABNAM HAGHIGHAT; VAN ZANDT, ALEXANDRIA E.; DYANDRA, MELISSA; FRESE, STEVEN A.; BARILE, DANIELA; GERMAN, J. BRUCE

2016-01-01

Proteins are not equally digestible—their proteolytic susceptibility varies by their source and processing method. Incomplete digestion increases colonic microbial protein fermentation (putrefaction), which produces toxic metabolites that can induce inflammation in vitro and have been associated with inflammation in vivo. Individual humans differ in protein digestive capacity based on phenotypes, particularly disease states. To avoid putrefaction-induced intestinal inflammation, protein sources and processing methods must be tailored to the consumer’s digestive capacity. This review explores how food processing techniques alter protein digestibility and examines how physiological conditions alter digestive capacity. Possible solutions to improving digestive function or matching low digestive capacity with more digestible protein sources are explored. Beyond the ileal digestibility measurements of protein digestibility, less invasive, quicker and cheaper techniques for monitoring the extent of protein digestion and fermentation are needed to personalize protein nourishment. Biomarkers of protein digestive capacity and efficiency can be identified with the toolsets of peptidomics, metabolomics, microbial sequencing and multiplexed protein analysis of fecal and urine samples. By monitoring individual protein digestive function, the protein component of diets can be tailored via protein source and processing selection to match individual needs to minimize colonic putrefaction and, thus, optimize gut health. PMID:26713355

Reactions of Ions with Ionic Liquid Vapors by Selected-Ion Flow Tube Mass Spectrometry

Science.gov (United States)

2011-03-29

Emel’yanenko, V. N.; Verevkin, S. P.; Heintz, A.; Corfield, J.-A.; Deyko, A.; Lovelock , K. R. J.; Licence, P.; Jones, R. G. Pyrrolidinium- Based Ionic...112, 11734–11742. (2) Lovelock , K. R. J.; Deyko, A.; Licence, P.; Jones, R. G. Vaporisa- tion of an Ionic Liquid Near Room Temperature. Phys. Chem...Relevance of pKa from Aqueous Solutions. J. Am. Chem. Soc. 2003, 125, 15411–15419. (15) Armstrong, J. P.; Hurst, C.; Jones, R. G.; Licence, P.; Lovelock , K

A scored human protein-protein interaction network to catalyze genomic interpretation

DEFF Research Database (Denmark)

Li, Taibo; Wernersson, Rasmus; Hansen, Rasmus B

2017-01-01

Genome-scale human protein-protein interaction networks are critical to understanding cell biology and interpreting genomic data, but challenging to produce experimentally. Through data integration and quality control, we provide a scored human protein-protein interaction network (InWeb_InBioMap,......Genome-scale human protein-protein interaction networks are critical to understanding cell biology and interpreting genomic data, but challenging to produce experimentally. Through data integration and quality control, we provide a scored human protein-protein interaction network (In...

Acrodysostosis

Science.gov (United States)

... hands and feet Short bones Shortening of the forearm bones near the wrist Two genes have been ... Arkless-Graham; Acrodysplasia; Maroteaux-Malamut Images Anterior skeletal anatomy References Jones KL, Jones MC, Del Campo M. ...

Transduction proteins of olfactory receptor cells: identification of guanine nucleotide binding proteins and protein kinase C

International Nuclear Information System (INIS)

Anholt, R.R.H.; Mumby, S.M.; Stoffers, D.A.; Girard, P.R.; Kuo, J.F.; Snyder, S.H.

1987-01-01

The authors have analyzed guanine nucleotide binding proteins (G-proteins) in the olfactory epithelium of Rana catesbeiana using subunit-specific antisera. The olfactory epithelium contained the α subunits of three G-proteins, migrating on polyacrylamide gels in SDS with apparent molecular weights of 45,000, 42,000, and 40,000, corresponding to G/sub s/, G/sub i/, and G/sub o/, respectively. A single β subunit with an apparent molecular weight of 36,000 was detected. An antiserum against the α subunit of retinal transducin failed to detect immunoreactive proteins in olfactory cilia detached from the epithelium. The olfactory cilia appeared to be enriched in immunoreactive G/sub sα/ relative to G/sub ichemical bond/ and G/sub ochemical bond/ when compared to membranes prepared from the olfactory epithelium after detachment of the cilia. Bound antibody was detected by autoradiography after incubation with [ 125 I]protein. Immunohistochemical studies using an antiserum against the β subunit of G-proteins revealed intense staining of the ciliary surface of the olfactory epithelium and of the axon bundles in the lamina propria. In contrast, an antiserum against a common sequence of the α subunits preferentially stained the cell membranes of the olfactory receptor cells and the acinar cells of Bowman's glands and the deep submucosal glands. In addition to G-proteins, they have identified protein kinase C in olfactory cilia via a protein kinase C specific antiserum and via phorbol ester binding. However, in contrast to the G-proteins, protein kinase C occurred also in cilia isolated from respiratory epithelium

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

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)

Martínez-Ruiz, F. J.; Blas, F. J.; Mendiboure, B.; Moreno-Ventas Bravo, A. I.

2014-01-01

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 c = 2.5, 3, 4, and 5σ. In addition, we have also considered cutoff distances r 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 thickness

Diffusion of Integral Membrane Proteins in Protein-Rich Membranes

DEFF Research Database (Denmark)

Javanainen, Matti; Martinez-Seara, Hector; Metzler, Ralf

2017-01-01

of being protein-poor, native cell membranes are extremely crowded with proteins. On the basis of extensive molecular simulations, we here demonstrate that protein crowding of the membrane at physiological levels leads to deviations from the SD relation and to the emergence of a stronger Stokes......-like dependence D ∝ 1/R. We propose that this 1/R law mainly arises due to geometrical factors: smaller proteins are able to avoid confinement effects much better than their larger counterparts. The results highlight that the lateral dynamics in the crowded setting found in native membranes is radically different......The lateral diffusion of embedded proteins along lipid membranes in protein-poor conditions has been successfully described in terms of the Saffman-Delbrück (SD) model, which predicts that the protein diffusion coefficient D is weakly dependent on its radius R as D ∝ ln(1/R). However, instead...