Thermal unfolding of a Ca- and Lanthanide-binding protein

Energy Technology Data Exchange (ETDEWEB)

Fahmy, Karim [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Biophysics; Goettfert, M. [Technische Univ. Dresden (Germany); Knoeppel, J.

2017-06-01

The MIIA (metal ion-induced autocleavage)-domain of the protein Vic001052 from the pathogen Vibrio coralliilyticus, comprises 173 amino acids and exhibits Ca-dependent autoproteolytic activity. It shows homology to nodulation proteins which are secreted by Rhizobiacea into plant host cells where they exert Ca-dependent functions. We have studied the structural and energetic aspects of metal protein interactions of the MIIA domain which appear attractive for engineering metal-binding synthetic peptides. Using a non-cleavable MIIA domain construct, we detected very similar structural changes upon binding to Ca{sup 2+} and Eu{sup 3+}. The thermal denaturation of the Ca-bound state was studied by circular dichroism spectroscopy. The metal-bound folded state unfolds reversibly into an unstructured metal-free state similar to the metal-free state at room temperature.

Verification of unfold error estimates in the unfold operator code

International Nuclear Information System (INIS)

Fehl, D.L.; Biggs, F.

1997-01-01

Spectral unfolding is an inverse mathematical operation that attempts to obtain spectral source information from a set of response functions and data measurements. Several unfold algorithms have appeared over the past 30 years; among them is the unfold operator (UFO) code written at Sandia National Laboratories. In addition to an unfolded spectrum, the UFO code also estimates the unfold uncertainty (error) induced by estimated random uncertainties in the data. In UFO the unfold uncertainty is obtained from the error matrix. This built-in estimate has now been compared to error estimates obtained by running the code in a Monte Carlo fashion with prescribed data distributions (Gaussian deviates). In the test problem studied, data were simulated from an arbitrarily chosen blackbody spectrum (10 keV) and a set of overlapping response functions. The data were assumed to have an imprecision of 5% (standard deviation). One hundred random data sets were generated. The built-in estimate of unfold uncertainty agreed with the Monte Carlo estimate to within the statistical resolution of this relatively small sample size (95% confidence level). A possible 10% bias between the two methods was unresolved. The Monte Carlo technique is also useful in underdetermined problems, for which the error matrix method does not apply. UFO has been applied to the diagnosis of low energy x rays emitted by Z-pinch and ion-beam driven hohlraums. copyright 1997 American Institute of Physics

Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model.

Science.gov (United States)

Zeng, Xiaojun; Zhang, Liyun; Xiao, Xiuchan; Jiang, Yuanyuan; Guo, Yanzhi; Yu, Xinyan; Pu, Xuemei; Li, Menglong

2016-04-05

Thrombin-binding aptamer (TBA) with the sequence 5'GGTTGGTGTGGTTGG3' could fold into G-quadruplex, which correlates with functionally important genomic regionsis. However, unfolding mechanism involved in the structural stability of G-quadruplex has not been satisfactorily elucidated on experiments so far. Herein, we studied the unfolding pathway of TBA by a combination of molecular dynamics simulation (MD) and Markov State Model (MSM). Our results revealed that the unfolding of TBA is not a simple two-state process but proceeds along multiple pathways with multistate intermediates. One high flux confirms some observations from NMR experiment. Another high flux exhibits a different and simpler unfolding pathway with less intermediates. Two important intermediate states were identified. One is similar to the G-triplex reported in the folding of G-quadruplex, but lack of H-bonding between guanines in the upper plane. More importantly, another intermediate state acting as a connector to link the folding region and the unfolding one, was the first time identified, which exhibits higher population and stability than the G-triplex-like intermediate. These results will provide valuable information for extending our understanding the folding landscape of G-quadruplex formation.

Experience with using unfolding procedures in ATLAS

CERN Document Server

Biondi, Silvia; The ATLAS collaboration

2016-01-01

In ATLAS, several unfolding methods are used to correct experimental measurements for detector effects, like acceptance and resolution. These methods use as input the raw experimental distributions, as well as Monte Carlo simulation for the description of the detector effects. The systematic uncertainties associated to the various unfolding methods are evaluated. The statistical and systematic uncertainties affecting the raw measurements and/or the simulation are propagated through the unfolding procedure. The resulting corrected measurements with their uncertainties can be directly compared with the corresponding theoretical predictions.

Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water.

Science.gov (United States)

Paschek, Dietmar; Nymeyer, Hugh; García, Angel E

2007-03-01

We simulate the folding/unfolding equilibrium of the 20-residue miniprotein Trp-cage. We use replica exchange molecular dynamics simulations of the AMBER94 atomic detail model of the protein explicitly solvated by water, starting from a completely unfolded configuration. We employ a total of 40 replicas, covering the temperature range between 280 and 538 K. Individual simulation lengths of 100 ns sum up to a total simulation time of about 4 micros. Without any bias, we observe the folding of the protein into the native state with an unfolding-transition temperature of about 440 K. The native state is characterized by a distribution of root mean square distances (RMSD) from the NMR data that peaks at 1.8A, and is as low as 0.4A. We show that equilibration times of about 40 ns are required to yield convergence. A folded configuration in the entire extended ensemble is found to have a lifetime of about 31 ns. In a clamp-like motion, the Trp-cage opens up during thermal denaturation. In line with fluorescence quenching experiments, the Trp-residue sidechain gets hydrated when the protein opens up, roughly doubling the number of water molecules in the first solvation shell. We find the helical propensity of the helical domain of Trp-cage rather well preserved even at very high temperatures. In the folded state, we can identify states with one and two buried internal water molecules interconnecting parts of the Trp-cage molecule by hydrogen bonds. The loss of hydrogen bonds of these buried water molecules in the folded state with increasing temperature is likely to destabilize the folded state at elevated temperatures.

Experience with using unfolding procedures in ATLAS

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00407321; The ATLAS collaboration

2016-01-01

In the ATLAS experiment, several unfolding methods are used to correct experimental measurements for detector effects, like acceptance and resolution. These methods use as input the raw experimental distributions, as well as Monte Carlo simulation for the description of the detector effects. The systematic uncertainties associated to the various unfolding methods are evaluated. The statistical and systematic uncertainties affecting the raw measurements and/or the simulation are propagated through the unfolding procedure. The resulting corrected measurements with their uncertainties can be directly compared with the corresponding theoretical predictions.

Unfolding neutron spectra from simulated response of thermoluminescence dosimeters inside a polyethylene sphere using GRNN neural network

Science.gov (United States)

Lotfalizadeh, F.; Faghihi, R.; Bahadorzadeh, B.; Sina, S.

2017-07-01

Neutron spectrometry using a single-sphere containing dosimeters has been developed recently, as an effective replacement for Bonner sphere spectrometry. The aim of this study is unfolding the neutron energy spectra using GRNN artificial neural network, from the response of thermoluminescence dosimeters, TLDs, located inside a polyethylene sphere. The spectrometer was simulated using MCNP5. TLD-600 and TLD-700 dosimeters were simulated at different positions in all directions. Then the GRNN was used for neutron spectra prediction, using the TLDs' readings. Comparison of spectra predicted by the network with the real spectra, show that the single-sphere dosimeter is an effective instrument in unfolding neutron spectra.

Conformational fluctuation dynamics of domain I of human serum albumin in the course of chemically and thermally induced unfolding using fluorescence correlation spectroscopy.

Science.gov (United States)

Yadav, Rajeev; Sengupta, Bhaswati; Sen, Pratik

2014-05-22

The present study elucidates the involvement of conformational fluctuation dynamics during chemically and thermally induced unfolding of human serum albumin (HSA) by fluorescence correlation spectroscopic (FCS) study, time-resolved fluorescence measurements, and circular dichroism (CD) spectroscopic methods. Two fluorescent probes, tetramethylrhodamine-5-maleimide (TMR) and N-(7-dimethylamino-4-methylcoumarin-3-yl) iodoacetamide (DACIA) were used to selectively label the domain I of HSA through the reaction with cys-34 for these studies. The guanidine hydrochloride (GnHCl) induced global structural change of HSA is monitored through its hydrodynamic radius (r(H)) and CD response, which is found to be two step in nature. In FCS experiment, along with the diffusion time component we have observed an exponential relaxation time component (τ(R)) that has been ascribed to the concerted chain dynamics of HSA. Unlike in the global structural change, we found that the τ(R) value changes in a different manner in the course of the unfolding. The dependence of τ(R) on the concentration of GnHCl was best fitted with a four state model, indicating the involvement of two intermediate states during the unfolding process, which were not observed through the CD response and r(H) data. The fluorescence lifetime measurement also supports our observation of intermediate states during the unfolding of HSA. However, no such intermediate states were observed during thermally induced unfolding of HSA.

Simulation study on unfolding methods for diagnostic X-rays and mixed gamma rays

International Nuclear Information System (INIS)

Hashimoto, Makoto; Ohtaka, Masahiko; Ara, Kuniaki; Kanno, Ikuo; Imamura, Ryo; Mikami, Kenta; Nomiya, Seiichiro; Onabe, Hideaki

2009-01-01

A photon detector operating in current mode that can sense X-ray energy distribution has been reported. This detector consists of a row of several segment detectors. The energy distribution is derived using an unfolding technique. In this paper, comparisons of the unfolding techniques among error reduction, spectrum surveillance, and neural network methods are discussed through simulation studies on the detection of diagnostic X-rays and gamma rays emitted by a mixture of 137 Cs and 60 Co. For diagnostic X-ray measurement, the spectrum surveillance and neural network methods appeared promising, while the error reduction method yielded poor results. However, in the case of measuring mixtures of gamma rays, the error reduction method was both sufficient and effective. (author)

A statistical approach to the estimation of mechanical unfolding parameters from the unfolding patterns of protein heteropolymers

International Nuclear Information System (INIS)

Beddard, G S; Brockwell, D J

2010-01-01

A statistical calculation is described with which the saw-tooth-like unfolding patterns of concatenated heteropolymeric proteins can be used to estimate the forced unfolding parameters of a previously uncharacterized protein. The chance of observing the various sequences of unfolding events, such as ABAABBB or BBAAABB etc, for two proteins of types A and B is calculated using proteins with various ratios of A and B and at different values of effective unfolding rate constants. If the experimental rate constant for forced unfolding, k 0 , and distance to the transition state x u are known for one protein, then the calculation allows an estimation of values for the other. The predictions are compared with Monte Carlo simulations and experimental data. (communication)

High-Temperature unfolding of a trp-Cage mini-protein: a molecular dynamics simulation study

Directory of Open Access Journals (Sweden)

Seshasayee Aswin Sai Narain

2005-03-01

Full Text Available Abstract Background Trp cage is a recently-constructed fast-folding miniprotein. It consists of a short helix, a 3,10 helix and a C-terminal poly-proline that packs against a Trp in the alpha helix. It is known to fold within 4 ns. Results High-temperature unfolding molecular dynamics simulations of the Trp cage miniprotein have been carried out in explicit water using the OPLS-AA force-field incorporated in the program GROMACS. The radius of gyration (Rg and Root Mean Square Deviation (RMSD have been used as order parameters to follow the unfolding process. Distributions of Rg were used to identify ensembles. Conclusion Three ensembles could be identified. While the native-state ensemble shows an Rg distribution that is slightly skewed, the second ensemble, which is presumably the Transition State Ensemble (TSE, shows an excellent fit. The denatured ensemble shows large fluctuations, but a Gaussian curve could be fitted. This means that the unfolding process is two-state. Representative structures from each of these ensembles are presented here.

Mechanics of collective unfolding

Science.gov (United States)

Caruel, M.; Allain, J.-M.; Truskinovsky, L.

2015-03-01

Mechanically induced unfolding of passive crosslinkers is a fundamental biological phenomenon encountered across the scales from individual macro-molecules to cytoskeletal actin networks. In this paper we study a conceptual model of athermal load-induced unfolding and use a minimalistic setting allowing one to emphasize the role of long-range interactions while maintaining full analytical transparency. Our model can be viewed as a description of a parallel bundle of N bistable units confined between two shared rigid backbones that are loaded through a series spring. We show that the ground states in this model correspond to synchronized, single phase configurations where all individual units are either folded or unfolded. We then study the fine structure of the wiggly energy landscape along the reaction coordinate linking the two coherent states and describing the optimal mechanism of cooperative unfolding. Quite remarkably, our study shows the fundamental difference in the size and the structure of the folding-unfolding energy barriers in the hard (fixed displacements) and soft (fixed forces) loading devices which persists in the continuum limit. We argue that both, the synchronization and the non-equivalence of the mechanical responses in hard and soft devices, have their origin in the dominance of long-range interactions. We then apply our minimal model to skeletal muscles where the power-stroke in acto-myosin crossbridges can be interpreted as passive folding. A quantitative analysis of the muscle model shows that the relative rigidity of myosin backbone provides the long-range interaction mechanism allowing the system to effectively synchronize the power-stroke in individual crossbridges even in the presence of thermal fluctuations. In view of the prototypical nature of the proposed model, our general conclusions pertain to a variety of other biological systems where elastic interactions are mediated by effective backbones.

Folding and unfolding pathway of chaperonin GroEL monomer and elucidation of thermodynamic parameters.

Science.gov (United States)

Puri, Sarita; Chaudhuri, Tapan K

2017-03-01

The conformation and thermodynamic stability of monomeric GroEL were studied by CD and fluorescence spectroscopy. GroEL denaturation with urea and dilution in buffer leads to formation of a folded GroEL monomer. The monomeric nature of this protein was verified by size-exclusion chromatography and native PAGE. It has a well-defined secondary and tertiary structure, folding activity (prevention of aggregation) for substrate protein and is resistant to proteolysis. Being a properly folded and reversibly refoldable, monomeric GroEL is amenable for the study of thermodynamic stability by unfolding transition methods. We present the equilibrium unfolding of monomeric GroEL as studied by urea and heat mediated unfolding processes. The urea mediated unfolding shows two transitions and a single transition in the heat mediated unfolding process. In the case of thermal unfolding, some residual structure unfolds at a higher temperature (70-75°C). The process of folding/unfolding is reversible in both cases. Analysis of folding/unfolding data provides a measure of ΔG NU H 2 O , T m , ΔH van and ΔS van of monomeric GroEL. The thermodynamic stability parameter ΔG NU H 2 O is similar with both CD and intrinsic fluorescence i.e. 7.10±1.0kcal/mol. The calculated T m , ΔH van and ΔS van from the thermal unfolding transition is 46±0.5°C, 43.3±0.1kcal/mol and 143.9±0.1cal/mol/k respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

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

Science.gov (United States)

Tischer, Alexander; Auton, Matthew

2013-01-01

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

Casting thermal simulation

International Nuclear Information System (INIS)

Shamsuddin bin Sulaiman

1994-01-01

The whole of this study is concerned with process simulation in casting processes. This study describes the application of the finite element method as an aid to simulating the thermal design of a high pressure die casting die by analysing the cooling transients in the casting cycle. Two types of investigation were carried out to model the linear and non-linear cooling behavior with consideration of a thermal interface effect. The simulated cooling for different stages were presented in temperature contour form. These illustrate the successful application of the Finite Element Method to model the process and they illustrate the significance of the thermal interface at low pressure

Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin.

Directory of Open Access Journals (Sweden)

Vasyl V Mykuliak

2018-04-01

Full Text Available Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins.

BUMS--Bonner sphere Unfolding Made Simple an HTML based multisphere neutron spectrometer unfolding package

CERN Document Server

Sweezy, J; Veinot, K

2002-01-01

A new multisphere neutron spectrometer unfolding package, Bonner sphere Unfolding Made Simple (BUMS) has been developed that uses an HTML interface to simplify data input and code execution for the novice and the advanced user. This new unfolding package combines the unfolding algorithms contained in other popular unfolding codes under one easy to use interface. The interface makes use of web browsing software to provide a graphical user interface to the unfolding algorithms. BUMS integrates the SPUNIT, BON, MAXIET, and SAND-II unfolding algorithms into a single package. This package also includes a library of 14 response matrices, 58 starting spectra, and 24 dose and detector responses. BUMS has several improvements beyond the addition of unfolding algorithms. It has the ability to search for the most appropriate starting spectra. Also, plots of the unfolded neutron spectra are automatically generated. The BUMS package runs via a web server and may be accessed by any computer with access to the Internet at h...

BUMS--Bonner sphere Unfolding Made Simple: an HTML based multisphere neutron spectrometer unfolding package

International Nuclear Information System (INIS)

Sweezy, Jeremy; Hertel, Nolan; Veinot, Ken

2002-01-01

A new multisphere neutron spectrometer unfolding package, Bonner sphere Unfolding Made Simple (BUMS) has been developed that uses an HTML interface to simplify data input and code execution for the novice and the advanced user. This new unfolding package combines the unfolding algorithms contained in other popular unfolding codes under one easy to use interface. The interface makes use of web browsing software to provide a graphical user interface to the unfolding algorithms. BUMS integrates the SPUNIT, BON, MAXIET, and SAND-II unfolding algorithms into a single package. This package also includes a library of 14 response matrices, 58 starting spectra, and 24 dose and detector responses. BUMS has several improvements beyond the addition of unfolding algorithms. It has the ability to search for the most appropriate starting spectra. Also, plots of the unfolded neutron spectra are automatically generated. The BUMS package runs via a web server and may be accessed by any computer with access to the Internet at http://nukeisit.gatech.edu/bums

Highly Perturbed pKa Values in the Unfolded State of Hen Egg White Lysozyme

OpenAIRE

Bradley, John; O'Meara, Fergal; Farrell, Damien; Nielsen, Jens Erik

2012-01-01

The majority of pKa values in protein unfolded states are close to the amino acid model pKa values, thus reflecting the weak intramolecular interactions present in the unfolded ensemble of most proteins. We have carried out thermal denaturation measurements on the WT and eight mutants of HEWL from pH 1.5 to pH 11.0 to examine the unfolded state pKa values and the pH dependence of protein stability for this enzyme. The availability of accurate pKa values for the folded state of HEWL and separa...

Detection and characterization of partially unfolded oligomers of the SH3 domain of α-Spectrin

NARCIS (Netherlands)

Casares, S.; Sadqi, M.; López-Mayorga, O.; Conejero-Lara, F.; van Nuland, N.A.J.

2004-01-01

For the purpose of equilibrium and kinetic folding-unfolding studies, the SH3 domain of α-spectrin (spc-SH3) has long been considered a classic two-state folding protein. In this work we have indeed observed that the thermal unfolding curves of spc-SH3 measured at pH 3.0 by differential scanning

A genetic algorithm based method for neutron spectrum unfolding

International Nuclear Information System (INIS)

Suman, Vitisha; Sarkar, P.K.

2013-03-01

An approach to neutron spectrum unfolding based on a stochastic evolutionary search mechanism - Genetic Algorithm (GA) is presented. It is tested to unfold a set of simulated spectra, the unfolded spectra is compared to the output of a standard code FERDOR. The method was then applied to a set of measured pulse height spectrum of neutrons from the AmBe source as well as of emitted neutrons from Li(p,n) and Ag(C,n) nuclear reactions carried out in the accelerator environment. The unfolded spectra compared to the output of FERDOR show good agreement in the case of AmBe spectra and Li(p,n) spectra. In the case of Ag(C,n) spectra GA method results in some fluctuations. Necessity of carrying out smoothening of the obtained solution is also studied, which leads to approximation of the solution yielding an appropriate solution finally. Few smoothing techniques like second difference smoothing, Monte Carlo averaging, combination of both and gaussian based smoothing methods are also studied. Unfolded results obtained after inclusion of the smoothening criteria are in close agreement with the output obtained from the FERDOR code. The present method is also tested on a set of underdetermined problems, the outputs of which is compared to the unfolded spectra obtained from the FERDOR applied to a completely determined problem, shows a good match. The distribution of the unfolded spectra is also studied. Uncertainty propagation in the unfolded spectra due to the errors present in the measurement as well as the response function is also carried out. The method appears to be promising for unfolding the completely determined as well as underdetermined problems. It also has provisions to carry out the uncertainty analysis. (author)

Unfolding and smoothing applied to the quality enhancement of neutron tomographic images

International Nuclear Information System (INIS)

Almeida, Gevaldo L. de; Silvani, Maria I.; Lopes, Ricardo T.

2008-01-01

Resolution and contrast are the major parameters defining the quality of a computer-aided tomographic image. These parameters depend upon several features of the image acquisition system, such as detector resolution, geometrical arrangement of the source-object-detector, beam divergence, source strength, detector efficiency and counting time. Roughly, the detector finite resolution is the main source of systematic errors affecting the separation power of the image acquisition system, while the electronic noise and statistical fluctuation are responsible for the data dispersion, which spoils the contrast. An algorithm has been developed in this work aiming at the improvement of the image quality through the minimization of both types of errors. The systematic ones are reduced by a mathematical unfolding of the position spectra - used as projections to reconstruct the 2D-images - using the Line Spread Function - LSF of the neutron tomographic system. The principle behind this technique is that every single channel contains information about all channels of the spectrum, but it is concealed due to the automatic integration carried out by the detector. Therefore, knowing the shape of this curve, it is possible to retrieve the original spectra. These spectra are unfortunately corrupted by the unavoidable statistical fluctuation, and by oscillations arising from the unfolding process, which strongly affects the quality of the final unfolded image. In order to reduce this impact, the spectra have been filtered by a Fourier transform technique or smoothed with a least square fitting procedure. The algorithm has been applied to spectra of some test-bodies generated by an earlier developed tomographic simulator, which reproduces the spectra furnished by a thermal neutron tomographic system employing a position sensitive detector. The obtained results have shown that the unfolded spectra produce final images capable to resolve features otherwise not achievable with the

Unfolding Participation

DEFF Research Database (Denmark)

Saad-Sulonen, Joanna; Halskov, Kim; Eriksson, Eva

2015-01-01

The aim of the Unfolding Participation workshop is to outline an agenda for the next 10 years of participatory design (PD) and participatory human computer interaction (HCI) research. We will do that through a double strategy: 1) by critically interrogating the concept of participation (unfolding...... the concept itself), while at the same time, 2) reflecting on the way that participation unfolds across different participatory configurations. We invite researchers and practitioners from PD and HCI and fields in which information technology mediated participation is embedded (e.g. in political studies......, urban planning, participatory arts, business, science and technology studies) to bring a plurality of perspectives and expertise related to participation....

Many channel spectrum unfolding

International Nuclear Information System (INIS)

Najzer, M.; Glumac, B.; Pauko, M.

1980-01-01

The principle of the ITER unfolding code as used for the many channel spectrum unfolding is described. Its unfolding ability is tested on seven typical neutron spectra. The effect of the initial spectrum approximation upon the solution is discussed

[Unfolding item response model using best-worst scaling].

Science.gov (United States)

Ikehara, Kazuya

2015-02-01

In attitude measurement and sensory tests, the unfolding model is typically used. In this model, response probability is formulated by the distance between the person and the stimulus. In this study, we proposed an unfolding item response model using best-worst scaling (BWU model), in which a person chooses the best and worst stimulus among repeatedly presented subsets of stimuli. We also formulated an unfolding model using best scaling (BU model), and compared the accuracy of estimates between the BU and BWU models. A simulation experiment showed that the BWU modell performed much better than the BU model in terms of bias and root mean square errors of estimates. With reference to Usami (2011), the proposed models were apllied to actual data to measure attitudes toward tardiness. Results indicated high similarity between stimuli estimates generated with the proposed models and those of Usami (2011).

Geometrical analysis of cytochrome c unfolding

Science.gov (United States)

Urie, Kristopher G.; Pletneva, Ekaterina; Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

2011-01-01

A geometrical model has been developed to study the unfolding of iso-1 cytochrome c. The model draws on the crystallographic data reported for this protein. These data were used to calculate the distance between specific residues in the folded state, and in a sequence of extended states defined by n = 3, 5, 7, 9, 11, 13, and 15 residue units. Exact calculations carried out for each of the 103 residues in the polypeptide chain demonstrate that different regions of the chain have different unfolding histories. Regions where there is a persistence of compact structures can be identified, and this geometrical characterization is fully consistent with analyses of time-resolved fluorescence energy-transfer (TrFET) data using dansyl-derivatized cysteine side-chain probes at positions 39, 50, 66, 85, and 99. The calculations were carried out assuming that different regions of the polypeptide chain unfold synchronously. To test this assumption, lattice Monte Carlo simulations were performed to study systematically the possible importance of asynchronicity. Calculations show that small departures from synchronous dynamics can arise if displacements of residues in the main body of the chain are much more sluggish than near-terminal residues.

Reversible Unfolding of Rhomboid Intramembrane Proteases.

Science.gov (United States)

Panigrahi, Rashmi; Arutyunova, Elena; Panwar, Pankaj; Gimpl, Katharina; Keller, Sandro; Lemieux, M Joanne

2016-03-29

Denaturant-induced unfolding of helical membrane proteins provides insights into their mechanism of folding and domain organization, which take place in the chemically heterogeneous, anisotropic environment of a lipid membrane. Rhomboid proteases are intramembrane proteases that play key roles in various diseases. Crystal structures have revealed a compact helical bundle with a buried active site, which requires conformational changes for the cleavage of transmembrane substrates. A dimeric form of the rhomboid protease has been shown to be important for activity. In this study, we examine the mechanism of refolding for two distinct rhomboids to gain insight into their secondary structure-activity relationships. Although helicity is largely abolished in the unfolded states of both proteins, unfolding is completely reversible for HiGlpG but only partially reversible for PsAarA. Refolding of both proteins results in reassociation of the dimer, with a 90% regain of catalytic activity for HiGlpG but only a 70% regain for PsAarA. For both proteins, a broad, gradual transition from the native, folded state to the denatured, partly unfolded state was revealed with the aid of circular dichroism spectroscopy as a function of denaturant concentration, thus arguing against a classical two-state model as found for many globular soluble proteins. Thermal denaturation has irreversible destabilizing effects on both proteins, yet reveals important functional details regarding substrate accessibility to the buried active site. This concerted biophysical and functional analysis demonstrates that HiGlpG, with a simple six-transmembrane-segment organization, is more robust than PsAarA, which has seven predicted transmembrane segments, thus rendering HiGlpG amenable to in vitro studies of membrane-protein folding. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The interrelationship between ligand binding and thermal unfolding of the folate binding protein. The role of self-association and pH

DEFF Research Database (Denmark)

Holm, Jan; Babol, Linnea N.; Markova, Natalia

2014-01-01

The present study utilized a combination of DLS (dynamic light scattering) and DSC (differential scanning calorimetry) to address thermostability of high-affinity folate binding protein (FBP), a transport protein and cellular receptor for the vitamin folate. At pH7.4 (pI=7-8) ligand binding......, intermolecular forces involved in concentration-dependent multimerization thus contribute to the thermostability of holo-FBP. Hence, thermal unfolding and dissociation of holo-FBP multimers occur simultaneously consistent with a gradual decrease from octameric to monomeric holo-FBP (10μM) in DLS after a step-wise...

Influence of the initial guess spectrum in the unfolding of Bss data obtained inside a bunker of a PET cyclotron

Energy Technology Data Exchange (ETDEWEB)

Benavente C, J. A.; Lacerda, M. A. S.; Guimaraes, A. M.; Da Silva, T. A. [Universidade Federal de Minas Gerais, Departamento de Engenharia Nuclear, Programa de Pos-graduacao em Ciencias e Tecnicas Nucleares, Pte. Antonio Carlos 6627, Belo Horizonte 31270-901, Minas Gerais (Brazil); Vega C, H. R. [Universidad Autonoma de Zacatecas, Unidad Academica de Estudios Nucleares, Cipres No. 10, Fracc. La Penuela, 98060 Zacatecas, Zac. (Mexico)

2015-10-15

In a cyclotron facility is strongly advised the use of spectrometry techniques to support workplace neutron dosimetry. Bonner sphere spectrometer (Bss) is the most used for radiation protection applications. Bss data must be unfolded to determine the spectral particle fluence. Some computer codes have been utilized for this purpose. These codes allow unfolding the spectrum from the Bss count rates through different algorithms. Some iterative routines need an initial guess spectrum to start the unfolding. The adequate choice of this initial spectrum is a critical part of the process and can affect the final solution. In this work, we evaluate the influence of the initial guess spectrum in the unfolding of Bss data obtained in four points inside the bunker of a PET cyclotron. The measurements were done utilizing a modified Bss system with thermoluminescent detectors (TLDs). Codes BUNKIUT and NSDUAZ were utilized to unfold the Bss data. For the NSDUAZ the starting spectrum is automatically obtained from a library initial guess spectra. For the BUNKIUT code were utilized two different initial guess spectra: (a) a Maxwellian spectrum with temperature of 1.4 MeV and shape factor of 0.1, created with the MAXIET algorithm and; (b) the spectra obtained through simulation with the MCNPX code version 2.7. Spectra obtained with both unfold codes and with the different initial guess spectra presented epithermal and thermal neutrons due to room-return effects. However, the contribution of the fast neutron to the total fluence were quite different for the different cases studied. These differences highlight the importance of an appropriate choice of an initial guess spectra for the quality of the results. (Author)

Influence of the initial guess spectrum in the unfolding of Bss data obtained inside a bunker of a PET cyclotron

International Nuclear Information System (INIS)

Benavente C, J. A.; Lacerda, M. A. S.; Guimaraes, A. M.; Da Silva, T. A.; Vega C, H. R.

2015-10-01

In a cyclotron facility is strongly advised the use of spectrometry techniques to support workplace neutron dosimetry. Bonner sphere spectrometer (Bss) is the most used for radiation protection applications. Bss data must be unfolded to determine the spectral particle fluence. Some computer codes have been utilized for this purpose. These codes allow unfolding the spectrum from the Bss count rates through different algorithms. Some iterative routines need an initial guess spectrum to start the unfolding. The adequate choice of this initial spectrum is a critical part of the process and can affect the final solution. In this work, we evaluate the influence of the initial guess spectrum in the unfolding of Bss data obtained in four points inside the bunker of a PET cyclotron. The measurements were done utilizing a modified Bss system with thermoluminescent detectors (TLDs). Codes BUNKIUT and NSDUAZ were utilized to unfold the Bss data. For the NSDUAZ the starting spectrum is automatically obtained from a library initial guess spectra. For the BUNKIUT code were utilized two different initial guess spectra: (a) a Maxwellian spectrum with temperature of 1.4 MeV and shape factor of 0.1, created with the MAXIET algorithm and; (b) the spectra obtained through simulation with the MCNPX code version 2.7. Spectra obtained with both unfold codes and with the different initial guess spectra presented epithermal and thermal neutrons due to room-return effects. However, the contribution of the fast neutron to the total fluence were quite different for the different cases studied. These differences highlight the importance of an appropriate choice of an initial guess spectra for the quality of the results. (Author)

Identification of an Unfolding Intermediate for a DNA Lesion Bypass Polymerase

Science.gov (United States)

Sherrer, Shanen M.; Maxwell, Brian A.; Pack, Lindsey R.; Fiala, Kevin A.; Fowler, Jason D.; Zhang, Jun; Suo, Zucai

2012-01-01

Sulfolobus solfataricusDNA Polymerase IV (Dpo4), a prototype Y-family DNA polymerase, has been well characterized biochemically and biophysically at 37 °C or lower temperatures. However, the physiological temperature of the hyperthermophile S. solfataricus is approximately 80 °C. With such a large discrepancy in temperature, the in vivo relevance of these in vitro studies of Dpo4 has been questioned. Here, we employed circular dichroism spectroscopy and fluorescence-based thermal scanning to investigate the secondary structural changes of Dpo4 over a temperature range from 26 to 119 °C. Dpo4 was shown to display a high melting temperature characteristic of hyperthermophiles. Unexpectedly, the Little Finger domain of Dpo4, which is only found in the Y-family DNA polymerases, was shown to be more thermostable than the polymerase core. More interestingly, Dpo4 exhibited a three-state cooperative unfolding profile with an unfolding intermediate. The linker region between the Little Finger and Thumb domains of Dpo4 was found to be a source of structural instability. Through site-directed mutagenesis, the interactions between the residues in the linker region and the Palm domain were identified to play a critical role in the formation of the unfolding intermediate. Notably, the secondary structure of Dpo4 was not altered when the temperature was increased from 26 to 87.5 °C. Thus, in addition to providing structural insights into the thermal stability and an unfolding intermediate of Dpo4, our work also validated the relevance of the in vitro studies of Dpo4 performed at temperatures significantly lower than 80 °C. PMID:22667759

Genetic algorithms - A new technique for solving the neutron spectrum unfolding problem

International Nuclear Information System (INIS)

Freeman, David W.; Edwards, D. Ray; Bolon, Albert E.

1999-01-01

A new technique utilizing genetic algorithms has been applied to the Bonner sphere neutron spectrum unfolding problem. Genetic algorithms are part of a relatively new field of 'evolutionary' solution techniques that mimic living systems with computer-simulated 'chromosome' solutions. Solutions mate and mutate to create better solutions. Several benchmark problems, considered representative of radiation protection environments, have been evaluated using the newly developed UMRGA code which implements the genetic algorithm unfolding technique. The results are compared with results from other well-established unfolding codes. The genetic algorithm technique works remarkably well and produces solutions with relatively high spectral qualities. UMRGA appears to be a superior technique in the absence of a priori data - it does not rely on 'lucky' guesses of input spectra. Calculated personnel doses associated with the unfolded spectra match benchmark values within a few percent

Amyloid protein unfolding and insertion kinetics on neuronal membrane mimics

Science.gov (United States)

Qiu, Liming; Buie, Creighton; Vaughn, Mark; Cheng, Kwan

2010-03-01

Atomistic details of beta-amyloid (Aβ ) protein unfolding and lipid interaction kinetics mediated by the neuronal membrane surface are important for developing new therapeutic strategies to prevent and cure Alzheimer's disease. Using all-atom MD simulations, we explored the early unfolding and insertion kinetics of 40 and 42 residue long Aβ in binary lipid mixtures with and without cholesterol that mimic the cholesterol-depleted and cholesterol-enriched lipid nanodomains of neurons. The protein conformational transition kinetics was evaluated from the secondary structure profile versus simulation time plot. The extent of membrane disruption was examined by the calculated order parameters of lipid acyl chains and cholesterol fused rings as well as the density profiles of water and lipid headgroups at defined regions across the lipid bilayer from our simulations. Our results revealed that both the cholesterol content and the length of the protein affect the protein-insertion and membrane stability in our model lipid bilayer systems.

Unfolding intermediates of the mutant His-107-Tyr of human ...

Indian Academy of Sciences (India)

Srabani Taraphder

We present in this article a detailed analysis of representative structures and proton transfer activity of .... cal molecular dynamics simulations to identify potential unfolding ... clustering parameters to carry out K-means cluster- ing of different ...

The fluorescence intensities ratio is not a reliable parameter for evaluation of protein unfolding transitions.

Science.gov (United States)

Žoldák, Gabriel; Jancura, Daniel; Sedlák, Erik

2017-06-01

Monitoring the fluorescence of proteins, particularly the fluorescence of intrinsic tryptophan residues, is a popular method often used in the analysis of unfolding transitions (induced by temperature, chemical denaturant, and pH) in proteins. The tryptophan fluorescence provides several suitable parameters, such as steady-state fluorescence intensity, apparent quantum yield, mean fluorescence lifetime, position of emission maximum that are often utilized for the observation of the conformational/unfolding transitions of proteins. In addition, the fluorescence intensities ratio at different wavelengths (usually at 330 nm and 350 nm) is becoming an increasingly popular parameter for the evaluation of thermal transitions. We show that, under certain conditions, the use of this parameter for the analysis of unfolding transitions leads to the incorrect determination of thermodynamic parameters characterizing unfolding transitions in proteins (e.g., melting temperature) and, hence, can compromise the hit identification during high-throughput drug screening campaigns. © 2017 The Protein Society.

Time-dependent, x-ray spectral unfolds and brightness temperatures for intense Li+ ion beam-driven hohlraums

International Nuclear Information System (INIS)

Fehl, D.L.; Chandler, G.A.; Biggs, F.; Dukart, R.J.; Moats, A.R.; Leeper, R.J.

1996-01-01

X-ray-producing hohlraums are being studied as indirect drives for Inertial Confinement Fusion targets. In a 1994 target series on the PBFAII accelerator, cylindrical hohlraum targets were heated by an intense Li + ion beam and viewed by an array of 13 time-resolved, filtered x-ray detectors (XRDs). The UFO unfold code and its suite of auxiliary functions were used extensively in obtaining time- resolved x-ray spectra and radiation temperatures from this diagnostic. UFO was also used to obtain fitted response functions from calibration data, to simulate data from blackbody x-ray spectra of interest, to determine the suitability of various unfolding parameters (e.g., energy domain, energy partition, smoothing conditions, and basis functions), to interpolate the XRD signal traces, and to unfold experimental data. The simulation capabilities of the code were useful in understanding an anomalous feature in the unfolded spectra at low photon energies (≤ 100 eV). Uncertainties in the differential and energy-integrated unfolded spectra were estimated from uncertainties in the data. The time-history of the radiation temperature agreed well with independent calculations of the wall temperature in the hohlraum

Time-dependent, x-ray spectral unfolds and brightness temperatures for intense Li+ ion beam-driven hohlraums

International Nuclear Information System (INIS)

Fehl, D.L.; Chandler, G.A.; Biggs, F.; Dukart, R.J.; Moats, A.R.; Leeper, R.J.

1997-01-01

X-ray-producing hohlraums are being studied as indirect drives for inertial confinement fusion targets. In a 1994 target series on the PBFAII accelerator, cylindrical hohlraum targets were heated by an intense Li + ion beam and viewed by an array of 13 time-resolved, filtered x-ray detectors (XRDs). The unfold operator (UFO) code and its suite of auxiliary functions were used extensively in obtaining time-resolved x-ray spectra and radiation temperatures from this diagnostic. The UFO was also used to obtain fitted response functions from calibration data, to simulate data from blackbody x-ray spectra of interest, to determine the suitability of various unfolding parameters (e.g., energy domain, energy partition, smoothing conditions, and basis functions), to interpolate the XRD signal traces, and to unfold experimental data. The simulation capabilities of the code were useful in understanding an anomalous feature in the unfolded spectra at low photon energies (≤100 eV). Uncertainties in the differential and energy-integrated unfolded spectra were estimated from uncertainties in the data. The time endash history of the radiation temperature agreed well with independent calculations of the wall temperature in the hohlraum. copyright 1997 American Institute of Physics

Enthalpy-entropy compensation in protein unfolding

Institute of Scientific and Technical Information of China (English)

无

2000-01-01

Enthalpy-entropy compensation was found to be a universal law in protein unfolding based on over 3 000 experimental data. Water molecular reorganization accompanying the protein unfolding was suggested as the origin of the enthalpy-entropy compensation in protein unfolding. It is indicated that the enthalpy-entropy compensation constitutes the physical foundation that satisfies the biological need of the small free energy changes in protein unfolding, without the sacrifice of the bio-diversity of proteins. The enthalpy-entropy compensation theory proposed herein also provides valuable insights into the Privalov's puzzle of enthalpy and entropy convergence in protein unfolding.

β-sheet-like formation during the mechanical unfolding of prion protein

Science.gov (United States)

Tao, Weiwei; Yoon, Gwonchan; Cao, Penghui; Eom, Kilho; Park, Harold S.

2015-09-01

Single molecule experiments and simulations have been widely used to characterize the unfolding and folding pathways of different proteins. However, with few exceptions, these tools have not been applied to study prion protein, PrPC, whose misfolded form PrPSc can induce a group of fatal neurodegenerative diseases. Here, we apply novel atomistic modeling based on potential energy surface exploration to study the constant force unfolding of human PrP at time scales inaccessible with standard molecular dynamics. We demonstrate for forces around 100 pN, prion forms a stable, three-stranded β-sheet-like intermediate configuration containing residues 155-214 with a lifetime exceeding hundreds of nanoseconds. A mutant without the disulfide bridge shows lower stability during the unfolding process but still forms the three-stranded structure. The simulations thus not only show the atomistic details of the mechanically induced structural conversion from the native α-helical structure to the β-rich-like form but also lend support to the structural theory that there is a core of the recombinant PrP amyloid, a misfolded form reported to induce transmissible disease, mapping to C-terminal residues ≈160-220.

β-sheet-like formation during the mechanical unfolding of prion protein

Energy Technology Data Exchange (ETDEWEB)

Tao, Weiwei; Cao, Penghui; Park, Harold S., E-mail: parkhs@bu.edu [Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215 (United States); Yoon, Gwonchan [Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215 (United States); Department of Mechanical Engineering, Korea University, Seoul 136-701 (Korea, Republic of); Eom, Kilho [Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University, Suwon 16419 (Korea, Republic of)

2015-09-28

Single molecule experiments and simulations have been widely used to characterize the unfolding and folding pathways of different proteins. However, with few exceptions, these tools have not been applied to study prion protein, PrP{sup C}, whose misfolded form PrP{sup Sc} can induce a group of fatal neurodegenerative diseases. Here, we apply novel atomistic modeling based on potential energy surface exploration to study the constant force unfolding of human PrP at time scales inaccessible with standard molecular dynamics. We demonstrate for forces around 100 pN, prion forms a stable, three-stranded β-sheet-like intermediate configuration containing residues 155-214 with a lifetime exceeding hundreds of nanoseconds. A mutant without the disulfide bridge shows lower stability during the unfolding process but still forms the three-stranded structure. The simulations thus not only show the atomistic details of the mechanically induced structural conversion from the native α-helical structure to the β-rich-like form but also lend support to the structural theory that there is a core of the recombinant PrP amyloid, a misfolded form reported to induce transmissible disease, mapping to C-terminal residues ≈160-220.

β-sheet-like formation during the mechanical unfolding of prion protein

International Nuclear Information System (INIS)

Tao, Weiwei; Cao, Penghui; Park, Harold S.; Yoon, Gwonchan; Eom, Kilho

2015-01-01

Single molecule experiments and simulations have been widely used to characterize the unfolding and folding pathways of different proteins. However, with few exceptions, these tools have not been applied to study prion protein, PrP C , whose misfolded form PrP Sc can induce a group of fatal neurodegenerative diseases. Here, we apply novel atomistic modeling based on potential energy surface exploration to study the constant force unfolding of human PrP at time scales inaccessible with standard molecular dynamics. We demonstrate for forces around 100 pN, prion forms a stable, three-stranded β-sheet-like intermediate configuration containing residues 155-214 with a lifetime exceeding hundreds of nanoseconds. A mutant without the disulfide bridge shows lower stability during the unfolding process but still forms the three-stranded structure. The simulations thus not only show the atomistic details of the mechanically induced structural conversion from the native α-helical structure to the β-rich-like form but also lend support to the structural theory that there is a core of the recombinant PrP amyloid, a misfolded form reported to induce transmissible disease, mapping to C-terminal residues ≈160-220

Thermal simulation and validation of 8W LED lamp

NARCIS (Netherlands)

Jakovenko, J.; Werkhoven, R.J.; Formánek, J.; Kunen, J.M.G.; Bolt, P.J.; Kulha, P.

2011-01-01

This work deals with thermal simulation and characterization of solid state lightening (SSL) LED Lamp in order to get precise 3D thermal models for further lamp thermal optimization. Simulations are performed with ANSYS-CFX and CoventorWare software tools. The simulated thermal distribution has been

Design and Test of Advanced Thermal Simulators for an Alkali Metal-Cooled Reactor Simulator

Science.gov (United States)

Garber, Anne E.; Dickens, Ricky E.

2011-01-01

The Early Flight Fission Test Facility (EFF-TF) at NASA Marshall Space Flight Center (MSFC) has as one of its primary missions the development and testing of fission reactor simulators for space applications. A key component in these simulated reactors is the thermal simulator, designed to closely mimic the form and function of a nuclear fuel pin using electric heating. Continuing effort has been made to design simple, robust, inexpensive thermal simulators that closely match the steady-state and transient performance of a nuclear fuel pin. A series of these simulators have been designed, developed, fabricated and tested individually and in a number of simulated reactor systems at the EFF-TF. The purpose of the thermal simulators developed under the Fission Surface Power (FSP) task is to ensure that non-nuclear testing can be performed at sufficiently high fidelity to allow a cost-effective qualification and acceptance strategy to be used. Prototype thermal simulator design is founded on the baseline Fission Surface Power reactor design. Recent efforts have been focused on the design, fabrication and test of a prototype thermal simulator appropriate for use in the Technology Demonstration Unit (TDU). While designing the thermal simulators described in this paper, effort were made to improve the axial power profile matching of the thermal simulators. Simultaneously, a search was conducted for graphite materials with higher resistivities than had been employed in the past. The combination of these two efforts resulted in the creation of thermal simulators with power capacities of 2300-3300 W per unit. Six of these elements were installed in a simulated core and tested in the alkali metal-cooled Fission Surface Power Primary Test Circuit (FSP-PTC) at a variety of liquid metal flow rates and temperatures. This paper documents the design of the thermal simulators, test program, and test results.

A neutron spectrum unfolding computer code based on artificial neural networks

Science.gov (United States)

Ortiz-Rodríguez, J. M.; Reyes Alfaro, A.; Reyes Haro, A.; Cervantes Viramontes, J. M.; Vega-Carrillo, H. R.

2014-02-01

The Bonner Spheres Spectrometer consists of a thermal neutron sensor placed at the center of a number of moderating polyethylene spheres of different diameters. From the measured readings, information can be derived about the spectrum of the neutron field where measurements were made. Disadvantages of the Bonner system are the weight associated with each sphere and the need to sequentially irradiate the spheres, requiring long exposure periods. Provided a well-established response matrix and adequate irradiation conditions, the most delicate part of neutron spectrometry, is the unfolding process. The derivation of the spectral information is not simple because the unknown is not given directly as a result of the measurements. The drawbacks associated with traditional unfolding procedures have motivated the need of complementary approaches. Novel methods based on Artificial Intelligence, mainly Artificial Neural Networks, have been widely investigated. In this work, a neutron spectrum unfolding code based on neural nets technology is presented. This code is called Neutron Spectrometry and Dosimetry with Artificial Neural networks unfolding code that was designed in a graphical interface. The core of the code is an embedded neural network architecture previously optimized using the robust design of artificial neural networks methodology. The main features of the code are: easy to use, friendly and intuitive to the user. This code was designed for a Bonner Sphere System based on a 6LiI(Eu) neutron detector and a response matrix expressed in 60 energy bins taken from an International Atomic Energy Agency compilation. The main feature of the code is that as entrance data, for unfolding the neutron spectrum, only seven rate counts measured with seven Bonner spheres are required; simultaneously the code calculates 15 dosimetric quantities as well as the total flux for radiation protection purposes. This code generates a full report with all information of the unfolding in

A neutron spectrum unfolding computer code based on artificial neural networks

International Nuclear Information System (INIS)

Ortiz-Rodríguez, J.M.; Reyes Alfaro, A.; Reyes Haro, A.; Cervantes Viramontes, J.M.; Vega-Carrillo, H.R.

2014-01-01

The Bonner Spheres Spectrometer consists of a thermal neutron sensor placed at the center of a number of moderating polyethylene spheres of different diameters. From the measured readings, information can be derived about the spectrum of the neutron field where measurements were made. Disadvantages of the Bonner system are the weight associated with each sphere and the need to sequentially irradiate the spheres, requiring long exposure periods. Provided a well-established response matrix and adequate irradiation conditions, the most delicate part of neutron spectrometry, is the unfolding process. The derivation of the spectral information is not simple because the unknown is not given directly as a result of the measurements. The drawbacks associated with traditional unfolding procedures have motivated the need of complementary approaches. Novel methods based on Artificial Intelligence, mainly Artificial Neural Networks, have been widely investigated. In this work, a neutron spectrum unfolding code based on neural nets technology is presented. This code is called Neutron Spectrometry and Dosimetry with Artificial Neural networks unfolding code that was designed in a graphical interface. The core of the code is an embedded neural network architecture previously optimized using the robust design of artificial neural networks methodology. The main features of the code are: easy to use, friendly and intuitive to the user. This code was designed for a Bonner Sphere System based on a 6 LiI(Eu) neutron detector and a response matrix expressed in 60 energy bins taken from an International Atomic Energy Agency compilation. The main feature of the code is that as entrance data, for unfolding the neutron spectrum, only seven rate counts measured with seven Bonner spheres are required; simultaneously the code calculates 15 dosimetric quantities as well as the total flux for radiation protection purposes. This code generates a full report with all information of the unfolding

Declining global warming effects on the phenology of spring leaf unfolding.

Science.gov (United States)

Fu, Yongshuo H; Zhao, Hongfang; Piao, Shilong; Peaucelle, Marc; Peng, Shushi; Zhou, Guiyun; Ciais, Philippe; Huang, Mengtian; Menzel, Annette; Peñuelas, Josep; Song, Yang; Vitasse, Yann; Zeng, Zhenzhong; Janssens, Ivan A

2015-10-01

Earlier spring leaf unfolding is a frequently observed response of plants to climate warming. Many deciduous tree species require chilling for dormancy release, and warming-related reductions in chilling may counteract the advance of leaf unfolding in response to warming. Empirical evidence for this, however, is limited to saplings or twigs in climate-controlled chambers. Using long-term in situ observations of leaf unfolding for seven dominant European tree species at 1,245 sites, here we show that the apparent response of leaf unfolding to climate warming (ST, expressed in days advance of leaf unfolding per °C warming) has significantly decreased from 1980 to 2013 in all monitored tree species. Averaged across all species and sites, ST decreased by 40% from 4.0 ± 1.8 days °C(-1) during 1980-1994 to 2.3 ± 1.6 days °C(-1) during 1999-2013. The declining ST was also simulated by chilling-based phenology models, albeit with a weaker decline (24-30%) than observed in situ. The reduction in ST is likely to be partly attributable to reduced chilling. Nonetheless, other mechanisms may also have a role, such as 'photoperiod limitation' mechanisms that may become ultimately limiting when leaf unfolding dates occur too early in the season. Our results provide empirical evidence for a declining ST, but also suggest that the predicted strong winter warming in the future may further reduce ST and therefore result in a slowdown in the advance of tree spring phenology.

Multistage unfolding of an SH3 domain: an initial urea-filled dry molten globule precedes a wet molten globule with non-native structure.

Science.gov (United States)

Dasgupta, Amrita; Udgaonkar, Jayant B; Das, Payel

2014-06-19

The unfolding of the SH3 domain of the PI3 kinase in aqueous urea has been studied using a synergistic experiment-simulation approach. The experimental observation of a transient wet molten globule intermediate, IU, with an unusual non-native burial of the sole Trp residue, W53, provides the benchmark for the unfolding simulations performed (eight in total, each at least 0.5 μs long). The simulations reveal that the partially unfolded IU ensemble is preceded by an early native-like molten globule intermediate ensemble I*. In the very initial stage of unfolding, dry globule conformations with the protein core filled with urea instead of water are transiently observed within the I* ensemble. Water penetration into the urea-filled core of dry globule conformations is frequently accompanied by very transient burial of W53. Later during gradual unfolding, W53 is seen to again become transiently buried in the IU ensemble for a much longer time. In the structurally heterogeneous IU ensemble, conformational flexibility of the C-terminal β-strands enables W53 burial by the formation of non-native, tertiary contacts with hydrophobic residues, which could serve to protect the protein from aggregation during unfolding.

Protein unfolding with a steric trap.

Science.gov (United States)

Blois, Tracy M; Hong, Heedeok; Kim, Tae H; Bowie, James U

2009-10-07

The study of protein folding requires a method to drive unfolding, which is typically accomplished by altering solution conditions to favor the denatured state. This has the undesirable consequence that the molecular forces responsible for configuring the polypeptide chain are also changed. It would therefore be useful to develop methods that can drive unfolding without the need for destabilizing solvent conditions. Here we introduce a new method to accomplish this goal, which we call steric trapping. In the steric trap method, the target protein is labeled with two biotin tags placed close in space so that both biotin tags can only be bound by streptavidin when the protein unfolds. Thus, binding of the second streptavidin is energetically coupled to unfolding of the target protein. Testing the method on a model protein, dihydrofolate reductase (DHFR), we find that streptavidin binding can drive unfolding and that the apparent binding affinity reports on changes in DHFR stability. Finally, by employing the slow off-rate of wild-type streptavidin, we find that DHFR can be locked in the unfolded state. The steric trap method provides a simple method for studying aspects of protein folding and stability in native solvent conditions, could be used to specifically unfold selected domains, and could be applicable to membrane proteins.

Microscopic dynamics of water around unfolded structures of barstar at room temperature

Energy Technology Data Exchange (ETDEWEB)

Pal, Somedatta; Chakraborty, Kaushik; Khatua, Prabir; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302 (India)

2015-02-07

The breaking of the native structure of a protein and its influences on the dynamic response of the surrounding solvent is an important issue in protein folding. In this work, we have carried out atomistic molecular dynamics simulations to unfold the protein barstar at two different temperatures (400 K and 450 K). The two unfolded forms obtained at such high temperatures are further studied at room temperature to explore the effects of nonuniform unfolding of the protein secondary structures along two different pathways on the microscopic dynamical properties of the surface water molecules. It is demonstrated that though the structural transition of the protein in general results in less restricted water motions around its segments, but there are evidences of formation of new conformational motifs upon unfolding with increasingly confined environment around them, thereby resulting in further restricted water mobility in their hydration layers. Moreover, it is noticed that the effects of nonuniform unfolding of the protein segments on the relaxation times of the protein–water (PW) and the water–water (WW) hydrogen bonds are correlated with hindered hydration water motions. However, the kinetics of breaking and reformation of such hydrogen bonds are found to be influenced differently at the interface. It is observed that while the effects of unfolding on the PW hydrogen bond kinetics seem to be minimum, but the kinetics involving the WW hydrogen bonds around the protein segments exhibit noticeably heterogeneous characteristics. We believe that this is an important observation, which can provide valuable insights on the origin of heterogeneous influence of unfolding of a protein on the microscopic properties of its hydration water.

Molecular dynamics simulation reveals insights into the mechanism of unfolding by the A130T/V mutations within the MID1 zinc-binding Bbox1 domain.

Directory of Open Access Journals (Sweden)

Yunjie Zhao

Full Text Available The zinc-binding Bbox1 domain in protein MID1, a member of the TRIM family of proteins, facilitates the ubiquitination of the catalytic subunit of protein phosphatase 2A and alpha4, a protein regulator of PP2A. The natural mutation of residue A130 to a valine or threonine disrupts substrate recognition and catalysis. While NMR data revealed the A130T mutant Bbox1 domain failed to coordinate both structurally essential zinc ions and resulted in an unfolded structure, the unfolding mechanism is unknown. Principle component analysis revealed that residue A130 served as a hinge point between the structured β-strand-turn-β-strand (β-turn-β and the lasso-like loop sub-structures that constitute loop1 of the ββα-RING fold that the Bbox1 domain adopts. Backbone RMSD data indicate significant flexibility and departure from the native structure within the first 5 ns of the molecular dynamics (MD simulation for the A130V mutant (>6 Å and after 30 ns for A130T mutant (>6 Å. Overall RMSF values were higher for the mutant structures and showed increased flexibility around residues 125 and 155, regions with zinc-coordinating residues. Simulated pKa values of the sulfhydryl group of C142 located near A130 suggested an increased in value to ~9.0, paralleling the increase in the apparent dielectric constants for the small cavity near residue A130. Protonation of the sulfhydryl group would disrupt zinc-coordination, directly contributing to unfolding of the Bbox1. Together, the increased motion of residues of loop 1, which contains four of the six zinc-binding cysteine residues, and the increased pKa of C142 could destabilize the structure of the zinc-coordinating residues and contribute to the unfolding.

RADYN Simulations of Non-thermal and Thermal Models of Ellerman Bombs

Energy Technology Data Exchange (ETDEWEB)

Hong, Jie; Ding, M. D. [School of Astronomy and Space Science, Nanjing University, Nanjing 210023 (China); Carlsson, Mats, E-mail: dmd@nju.edu.cn [Institute of Theoretical Astrophysics, University of Oslo, P.O. Box 1029 Blindern, NO-0315 Oslo (Norway)

2017-08-20

Ellerman bombs (EBs) are brightenings in the H α line wings that are believed to be caused by magnetic reconnection in the lower atmosphere. To study the response and evolution of the chromospheric line profiles, we perform radiative hydrodynamic simulations of EBs using both non-thermal and thermal models. Overall, these models can generate line profiles that are similar to observations. However, in non-thermal models we find dimming in the H α line wings and continuum when the heating begins, while for the thermal models dimming occurs only in the H α line core, and with a longer lifetime. This difference in line profiles can be used to determine whether an EB is dominated by non-thermal heating or thermal heating. In our simulations, if a higher heating rate is applied, then the H α line will be unrealistically strong and there are still no clear UV burst signatures.

RADYN Simulations of Non-thermal and Thermal Models of Ellerman Bombs

Science.gov (United States)

Hong, Jie; Carlsson, Mats; Ding, M. D.

2017-08-01

Ellerman bombs (EBs) are brightenings in the Hα line wings that are believed to be caused by magnetic reconnection in the lower atmosphere. To study the response and evolution of the chromospheric line profiles, we perform radiative hydrodynamic simulations of EBs using both non-thermal and thermal models. Overall, these models can generate line profiles that are similar to observations. However, in non-thermal models we find dimming in the Hα line wings and continuum when the heating begins, while for the thermal models dimming occurs only in the Hα line core, and with a longer lifetime. This difference in line profiles can be used to determine whether an EB is dominated by non-thermal heating or thermal heating. In our simulations, if a higher heating rate is applied, then the Hα line will be unrealistically strong and there are still no clear UV burst signatures.

Simulation-based optimization of thermal systems

International Nuclear Information System (INIS)

Jaluria, Yogesh

2009-01-01

This paper considers the design and optimization of thermal systems on the basis of the mathematical and numerical modeling of the system. Many complexities are often encountered in practical thermal processes and systems, making the modeling challenging and involved. These include property variations, complicated regions, combined transport mechanisms, chemical reactions, and intricate boundary conditions. The paper briefly presents approaches that may be used to accurately simulate these systems. Validation of the numerical model is a particularly critical aspect and is discussed. It is important to couple the modeling with the system performance, design, control and optimization. This aspect, which has often been ignored in the literature, is considered in this paper. Design of thermal systems based on concurrent simulation and experimentation is also discussed in terms of dynamic data-driven optimization methods. Optimization of the system and of the operating conditions is needed to minimize costs and improve product quality and system performance. Different optimization strategies that are currently used for thermal systems are outlined, focusing on new and emerging strategies. Of particular interest is multi-objective optimization, since most thermal systems involve several important objective functions, such as heat transfer rate and pressure in electronic cooling systems. A few practical thermal systems are considered in greater detail to illustrate these approaches and to present typical simulation, design and optimization results

A highly compliant protein native state with a spontaneous-like mechanical unfolding pathway

DEFF Research Database (Denmark)

Heiðarsson, Pétur Orri; Valpapuram, Immanuel; Camilloni, Carlo

2012-01-01

The mechanical properties of proteins and their force-induced structural changes play key roles in many biological processes. Previous studies have shown that natively folded proteins are brittle under tension, unfolding after small mechanical deformations, while partially folded intermediate...... states, such as molten globules, are compliant and can deform elastically a great amount before crossing the transition state barrier. Moreover, under tension proteins appear to unfold through a different sequence of events than during spontaneous unfolding. Here, we describe the response to force...... of the four-α-helix acyl-CoA binding protein (ACBP) in the low-force regime using optical tweezers and ratcheted molecular dynamics simulations. The results of our studies reveal an unprecedented mechanical behavior of a natively folded protein. ACBP displays an atypical compliance along two nearly orthogonal...

Energy spectra unfolding of fast neutron sources using the group method of data handling and decision tree algorithms

Energy Technology Data Exchange (ETDEWEB)

Hosseini, Seyed Abolfazl, E-mail: sahosseini@sharif.edu [Department of Energy Engineering, Sharif University of Technology, Tehran 8639-11365 (Iran, Islamic Republic of); Afrakoti, Iman Esmaili Paeen [Faculty of Engineering & Technology, University of Mazandaran, Pasdaran Street, P.O. Box: 416, Babolsar 47415 (Iran, Islamic Republic of)

2017-04-11

Accurate unfolding of the energy spectrum of a neutron source gives important information about unknown neutron sources. The obtained information is useful in many areas like nuclear safeguards, nuclear nonproliferation, and homeland security. In the present study, the energy spectrum of a poly-energetic fast neutron source is reconstructed using the developed computational codes based on the Group Method of Data Handling (GMDH) and Decision Tree (DT) algorithms. The neutron pulse height distribution (neutron response function) in the considered NE-213 liquid organic scintillator has been simulated using the developed MCNPX-ESUT computational code (MCNPX-Energy engineering of Sharif University of Technology). The developed computational codes based on the GMDH and DT algorithms use some data for training, testing and validation steps. In order to prepare the required data, 4000 randomly generated energy spectra distributed over 52 bins are used. The randomly generated energy spectra and the simulated neutron pulse height distributions by MCNPX-ESUT for each energy spectrum are used as the output and input data. Since there is no need to solve the inverse problem with an ill-conditioned response matrix, the unfolded energy spectrum has the highest accuracy. The {sup 241}Am-{sup 9}Be and {sup 252}Cf neutron sources are used in the validation step of the calculation. The unfolded energy spectra for the used fast neutron sources have an excellent agreement with the reference ones. Also, the accuracy of the unfolded energy spectra obtained using the GMDH is slightly better than those obtained from the DT. The results obtained in the present study have good accuracy in comparison with the previously published paper based on the logsig and tansig transfer functions. - Highlights: • The neutron pulse height distribution was simulated using MCNPX-ESUT. • The energy spectrum of the neutron source was unfolded using GMDH. • The energy spectrum of the neutron source was

Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach

KAUST Repository

Guardiani, Carlo; Marino, Daniele Di; Tramontano, Anna; Chinappi, Mauro; Cecconi, Fabio

2014-01-01

© 2014 American Chemical Society. Recent single-molecule force spectroscopy experiments on the Maltose Binding Proteins (MBPs) identified four stable structural units, termed unfoldons, that resist mechanical stress and determine the intermediates of the unfolding pathway. In this work, we analyze the topological origin and the dynamical role of the unfoldons using an integrated approach which combines a graph-theoretical analysis of the interaction network of the MBP native-state with steered molecular dynamics simulations. The topological analysis of the native state, while revealing the structural nature of the unfoldons, provides a framework to interpret the MBP mechanical unfolding pathway. Indeed, the experimental pathway can be effectively predicted by means of molecular dynamics simulations with a simple topology-based and low-resolution model of the MBP. The results obtained from the coarse-grained approach are confirmed and further refined by all-atom molecular dynamics.

Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach

KAUST Repository

Guardiani, Carlo

2014-09-09

© 2014 American Chemical Society. Recent single-molecule force spectroscopy experiments on the Maltose Binding Proteins (MBPs) identified four stable structural units, termed unfoldons, that resist mechanical stress and determine the intermediates of the unfolding pathway. In this work, we analyze the topological origin and the dynamical role of the unfoldons using an integrated approach which combines a graph-theoretical analysis of the interaction network of the MBP native-state with steered molecular dynamics simulations. The topological analysis of the native state, while revealing the structural nature of the unfoldons, provides a framework to interpret the MBP mechanical unfolding pathway. Indeed, the experimental pathway can be effectively predicted by means of molecular dynamics simulations with a simple topology-based and low-resolution model of the MBP. The results obtained from the coarse-grained approach are confirmed and further refined by all-atom molecular dynamics.

Haptization of molecular dynamics simulation with thermal display

International Nuclear Information System (INIS)

Tamura, Yuichi; Fujiwara, Susumu; Nakamura, Hiroaki

2010-01-01

Thermal display, which is a type of haptic display, is effective in providing intuitive information of temperature. However, in many studies, the user has assumed a sitting position during the use of these devices. In contrast, the user generally watches 3D objects while standing and walking around in large-scale virtual reality system, In addition, in scientific visualization, the response time is very important for observing physical phenomena, especially for dynamic numerical simulation. One solution is to provide two types of thermal information: information about the rate of thermal change and information about the actual temperature. We propose a thermal display with two Peltier elements which can show above two pairs of information and the result (for example energy and temperature, as thermal information) of numerical simulation. Finally, we represent an example of visualizing and haptizing the result of molecular dynamics simulation. (author)

Common features in the unfolding and misfolding of PDZ domains and beyond: the modulatory effect of domain swapping and extra-elements.

Science.gov (United States)

Murciano-Calles, Javier; Güell-Bosch, Jofre; Villegas, Sandra; Martinez, Jose C

2016-01-12

PDZ domains are protein-protein interaction modules sharing the same structural arrangement. To discern whether they display common features in their unfolding/misfolding behaviour we have analyzed in this work the unfolding thermodynamics, together with the misfolding kinetics, of the PDZ fold using three archetypical examples: the second and third PDZ domains of the PSD95 protein and the Erbin PDZ domain. Results showed that all domains passed through a common intermediate, which populated upon unfolding, and that this in turn drove the misfolding towards worm-like fibrillar structures. Thus, the unfolding/misfolding behaviour appears to be shared within these domains. We have also analyzed how this landscape can be modified upon the inclusion of extra-elements, as it is in the nNOS PDZ domain, or the organization of swapped species, as happens in the second PDZ domain of the ZO2 protein. Although the intermediates still formed upon thermal unfolding, the misfolding was prevented to varying degrees.

Recent developments in numerical simulation techniques of thermal recovery processes

Energy Technology Data Exchange (ETDEWEB)

Tamim, M. [Bangladesh University of Engineering and Technology, Bangladesh (Bangladesh); Abou-Kassem, J.H. [Chemical and Petroleum Engineering Department, UAE University, Al-Ain 17555 (United Arab Emirates); Farouq Ali, S.M. [University of Alberta, Alberta (Canada)

2000-05-01

Numerical simulation of thermal processes (steam flooding, steam stimulation, SAGD, in-situ combustion, electrical heating, etc.) is an integral part of a thermal project design. The general tendency in the last 10 years has been to use commercial simulators. During the last decade, only a few new models have been reported in the literature. More work has been done to modify and refine solutions to existing problems to improve the efficiency of simulators. The paper discusses some of the recent developments in simulation techniques of thermal processes such as grid refinement, grid orientation, effect of temperature on relative permeability, mathematical models, and solution methods. The various aspects of simulation discussed here promote better understanding of the problems encountered in the simulation of thermal processes and will be of value to both simulator users and developers.

Investigating the structural origin of trpzip2 temperature dependent unfolding fluorescence line shape based on a Markov state model simulation.

Science.gov (United States)

Song, Jian; Gao, Fang; Cui, Raymond Z; Shuang, Feng; Liang, Wanzhen; Huang, Xuhui; Zhuang, Wei

2012-10-25

Vibrationally resolved fluorescence spectra of the β-hairpin trpzip2 peptide at two temperatures as well as during a T-jump unfolding process are simulated on the basis of a combination of Markov state models and quantum chemistry schemes. The broad asymmetric spectral line shape feature is reproduced by considering the exciton-phonon couplings. The temperature dependent red shift observed in the experiment has been attributed to the state population changes of specific chromophores. Through further theoretical study, it is found that both the environment's electric field and the chromophores' geometry distortions are responsible for tryptophan fluorescence shift.

Thermal expansion of UO2 and simulated DUPIC fuel

International Nuclear Information System (INIS)

Ho Kang, Kweon; Jin Ryu, Ho; Chan Song, Kee; Seung Yang, Myung

2002-01-01

The lattice parameters of simulated DUPIC fuel and UO 2 were measured from room temperature to 1273 K using neutron diffraction to investigate the thermal expansion and density variation with temperature. The lattice parameter of simulated DUPIC fuel is lower than that of UO 2 , and the linear thermal expansion of simulated DUPIC fuel is higher than that of UO 2 . For the temperature range from 298 to 1273 K, the average linear thermal expansion coefficients for UO 2 and simulated DUPIC fuel are 10.471x10 -6 and 10.751x10 -6 K -1 , respectively

Thermal Fluctuations in Smooth Dissipative Particle Dynamics simulation of mesoscopic thermal systems

Science.gov (United States)

Gatsonis, Nikolaos; Yang, Jun

2013-11-01

The SDPD-DV is implemented in our work for arbitrary 3D wall bounded geometries. The particle position and momentum equations are integrated with a velocity-Verlet algorithm and the entropy equation is integrated with a Runge-Kutta algorithm. Simulations of nitrogen gas are performed to evaluate the effects of timestep and particle scale on temperature, self-diffusion coefficient and shear viscosity. The hydrodynamic fluctuations in temperature, density, pressure and velocity from the SDPD-DV simulations are evaluated and compared with theoretical predictions. Steady planar thermal Couette flows are simulated and compared with analytical solutions. Simulations cover the hydrodynamic and mesocopic regime and show thermal fluctuations and their dependence on particle size.

Electro-Thermal-Mechanical Simulation Capability Final Report

International Nuclear Information System (INIS)

White, D

2008-01-01

This is the Final Report for LDRD 04-ERD-086, 'Electro-Thermal-Mechanical Simulation Capability'. The accomplishments are well documented in five peer-reviewed publications and six conference presentations and hence will not be detailed here. The purpose of this LDRD was to research and develop numerical algorithms for three-dimensional (3D) Electro-Thermal-Mechanical simulations. LLNL has long been a world leader in the area of computational mechanics, and recently several mechanics codes have become 'multiphysics' codes with the addition of fluid dynamics, heat transfer, and chemistry. However, these multiphysics codes do not incorporate the electromagnetics that is required for a coupled Electro-Thermal-Mechanical (ETM) simulation. There are numerous applications for an ETM simulation capability, such as explosively-driven magnetic flux compressors, electromagnetic launchers, inductive heating and mixing of metals, and MEMS. A robust ETM simulation capability will enable LLNL physicists and engineers to better support current DOE programs, and will prepare LLNL for some very exciting long-term DoD opportunities. We define a coupled Electro-Thermal-Mechanical (ETM) simulation as a simulation that solves, in a self-consistent manner, the equations of electromagnetics (primarily statics and diffusion), heat transfer (primarily conduction), and non-linear mechanics (elastic-plastic deformation, and contact with friction). There is no existing parallel 3D code for simulating ETM systems at LLNL or elsewhere. While there are numerous magnetohydrodynamic codes, these codes are designed for astrophysics, magnetic fusion energy, laser-plasma interaction, etc. and do not attempt to accurately model electromagnetically driven solid mechanics. This project responds to the Engineering R and D Focus Areas of Simulation and Energy Manipulation, and addresses the specific problem of Electro-Thermal-Mechanical simulation for design and analysis of energy manipulation systems

Unfolding neutron spectra with BS-TLD system using genetic algorithms

Energy Technology Data Exchange (ETDEWEB)

Santos, Joelan A.L., E-mail: jasantos@cnen.gov.br [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de Energia Nuclear; Centro Regional de Ciencias Nucleares do Nordeste (CRCN-NE/CNEN-PE), Recife, PE (Brazil); Silva, Everton R. [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Centro de Informatica; Ferreira, Tiago A.E. [Universidade Federal Rural de Pernambuco (UFRPE), Recife, PE (Brazil). Dept. de Estatistica e Informatica; Fonseca, Evaldo S. [Instituto de Radioprotecao e Dosimetria (IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil); Vilela, Eudice C., E-mail: ecvilela@cnen.gov.br [Centro Regional de Ciencias Nucleares do Nordeste (CRCN-NE/CNEN-PE), Recife, PE (Brazil)

2011-07-01

Due to the variability of neutron spectrum within the same environment, it is essential that the spectral distribution as function of energy to be characterized. To perform this task, the neutron spectrometer has a primary role in determining the neutron flux ({Phi}{sub E}(E)). Precise information allows radiological quantities establishment related to that spectrum but it is necessary, however, a series of steps with a spectrometric system that can cover a large interval of energy and whose answer is isotropic. The most widely used for accomplishing this task is the spectrometric Bonner spheres system. One of the biggest problems related to neutron spectrometry is the process of data analysis, known as unfolding. Most of the work undertaken to implement new techniques of this process, using data obtained with the scintillator {sup 6}LiI(I). However, characteristics related to the dead time make it not be so effective when used in high flow neutron fields. An alternative to this problem is the use of thermoluminescent detectors (TLD), but the codes used do not provide a more specific response matrix to unfolding the information obtained through these materials, which makes the development of a specific response matrix important to adequately characterize the response obtained by them. This paper proposes using a technique of artificial intelligence called genetic algorithm, which uses bio-inspired mathematical models and through the implementation of a specific matrix to unfolding data obtained from a combination of TLDs embedded in a system of Bonner spheres, such as thermal neutron detectors, to characterize the neutron spectrum as a function of energy. The results obtained with this method were in accordance with reference spectra, thus enables of this technique to unfolding neutrons spectra with BS-TLD system. (author)

Unfolding neutron spectra with BS-TLD system using genetic algorithms

International Nuclear Information System (INIS)

Santos, Joelan A.L.; Silva, Everton R.; Vilela, Eudice C.

2011-01-01

Due to the variability of neutron spectrum within the same environment, it is essential that the spectral distribution as function of energy to be characterized. To perform this task, the neutron spectrometer has a primary role in determining the neutron flux (Φ E (E)). Precise information allows radiological quantities establishment related to that spectrum but it is necessary, however, a series of steps with a spectrometric system that can cover a large interval of energy and whose answer is isotropic. The most widely used for accomplishing this task is the spectrometric Bonner spheres system. One of the biggest problems related to neutron spectrometry is the process of data analysis, known as unfolding. Most of the work undertaken to implement new techniques of this process, using data obtained with the scintillator 6 LiI(I). However, characteristics related to the dead time make it not be so effective when used in high flow neutron fields. An alternative to this problem is the use of thermoluminescent detectors (TLD), but the codes used do not provide a more specific response matrix to unfolding the information obtained through these materials, which makes the development of a specific response matrix important to adequately characterize the response obtained by them. This paper proposes using a technique of artificial intelligence called genetic algorithm, which uses bio-inspired mathematical models and through the implementation of a specific matrix to unfolding data obtained from a combination of TLDs embedded in a system of Bonner spheres, such as thermal neutron detectors, to characterize the neutron spectrum as a function of energy. The results obtained with this method were in accordance with reference spectra, thus enables of this technique to unfolding neutrons spectra with BS-TLD system. (author)

The Role of E27-K31 and E56-K10 Salt-Bridge Pairs in the Unfolding Mechanism of the B1 Domain of Protein G

Directory of Open Access Journals (Sweden)

Tony Ibnu Sumaryada

2018-02-01

Full Text Available Molecular dynamics simulations of the B1 fragment of protein G (56 residues have been performed at 325, 350, 375, 400, 450 and 500 K for 10 ns. An analysis of its structural and energetic parameters has indicated that the unfolding process of the GB1 protein begins at 900 ps of a 500-K simulation. The unfolding process is initiated when hydrogen bonds in the hydrophobic core region are broken; it continues with the α-helix transformation into coils and turns and ends with the destruction of the β-hairpins. These unfolding events are consistent with the hybrid model of the protein folding/unfolding mechanism, which is a compromise between the hydrophobic core collapse model and the zipper model. Salt-bridge pairs were found to play an important role in the unfolding process by maintaining the integrity of the tertiary structure of the protein. The breaking (or disappearance of the salt-bridge pairs E27–K31 (in the α-helix and E56–K10 (connecting β4 and β1 has resulted in the destruction of secondary structures and indicates the beginning of the unfolding process. Our results also suggest that the unfolding process in this simulation was not a complete denaturation of the protein because some β-hairpins remained

Defining a methodology for benchmarking spectrum unfolding codes

International Nuclear Information System (INIS)

Meyer, W.; Kirmser, P.G.; Miller, W.H.; Hu, K.K.

1976-01-01

It has long been recognized that different neutron spectrum unfolding codes will produce significantly different results when unfolding the same measured data. In reviewing the results of such analyses it has been difficult to determine which result if any is the best representation of what was measured by the spectrometer detector. A proposal to develop a benchmarking procedure for spectrum unfolding codes is presented. The objective of the procedure will be to begin to develop a methodology and a set of data with a well established and documented result that could be used to benchmark and standardize the various unfolding methods and codes. It is further recognized that development of such a benchmark must involve a consensus of the technical community interested in neutron spectrum unfolding

Thermal simulation of the magnesium thermal of metallic uranium reduction

International Nuclear Information System (INIS)

Borges, W.A.; Saliba-Silva, A.M.

2008-01-01

Metallic uranium production is vital to fabricate fuel elements for nuclear research reactors and to produce radioisotopes and radiopharmaceuticals. Metallic uranium is got via magnesiothermal reduction of UF 4 . This reaction is carried out inside a closed graphite crucible inserted in a metallic reactor adequately sealed without any outside contact. The assembled set is gradually heated up inside a pit furnace up to reach the reaction ignition temperature (between 600-650 deg C). The optimization of the reactive system depends on the mathematical modeling using simulation by finite elements and computational calculation with specialized programs. In this way, the reactants' thermal behavior is forecast until they reach the ignition temperature. The optimization of the uranium production reaction is based on minimization of thermal losses using better the exo thermal reaction heat. As lower the thermal losses, as higher would be the heat amount to raise the temperature of reaction products. This promotes the adequate melting of uranium and slag, so allowing better metal/slag separation with higher metallic yield. This work shows how the mathematical simulation is made and supplies some preliminary results. (author)

Electrical power system integrated thermal/electrical system simulation

International Nuclear Information System (INIS)

Freeman, W.E.

1992-01-01

This paper adds thermal properties to previously developed electrical Saber templates and incorporates these templates into a functional Electrical Power Subsystem (EPS) simulation. These combined electrical and thermal templates enable the complete and realistic simulation of a vehicle EPS on-orbit. Applications include on-orbit energy balance determinations for system load changes, initial array and battery EPS sizing for new EPS development, and array and battery technology trade studies. This effort proves the versatility of the Saber simulation program in handling varied and complex simulations accurately and in a reasonable amount of computer time. 9 refs

Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases

Science.gov (United States)

Vriend, Gert; Eijsink, Vincent

1993-08-01

Bacillus neutral proteases (NPs) form a group of well-characterized homologous enzymes, that exhibit large differences in thermostability. The three-dimensional (3D) structures of several of these enzymes have been modelled on the basis of the crystal structures of the NPs of B. thermoproteolyticus (thermolysin) and B. cercus. Several new techniques have been developed to improve the model-building procedures. Also a model-building by mutagenesis' strategy was used, in which mutants were designed just to shed light on parts of the structures that were particularly hard to model. The NP models have been used for the prediction of site-directed mutations aimed at improving the thermostability of the enzymes. Predictions were made using several novel computational techniques, such as position-specific rotamer searching, packing quality analysis and property-profile database searches. Many stabilizing mutations were predicted and produced: improvement of hydrogen bonding, exclusion of buried water molecules, capping helices, improvement of hydrophobic interactions and entropic stabilization have been applied successfully. At elevated temperatures NPs are irreversibly inactivated as a result of autolysis. It has been shown that this denaturation process is independent of the protease activity and concentration and that the inactivation follows first-order kinetics. From this it has been conjectured that local unfolding of (surface) loops, which renders the protein susceptible to autolysis, is the rate-limiting step. Despite the particular nature of the thermal denaturation process, normal rules for protein stability can be applied to NPs. However, rather than stabilizing the whole protein against global unfolding, only a small region has to be protected against local unfolding. In contrast to proteins in general, mutational effects in proteases are not additive and their magnitude is strongly dependent on the location of the mutation. Mutations that alter the stability

Desorption of Lipases Immobilized on Octyl-Agarose Beads and Coated with Ionic Polymers after Thermal Inactivation. Stronger Adsorption of Polymers/Unfolded Protein Composites

Directory of Open Access Journals (Sweden)

Jose J. Virgen-Ortíz

2017-01-01

Full Text Available Lipases from Candida antarctica (isoform B and Rhizomucor miehei (CALB and RML have been immobilized on octyl-agarose (OC and further coated with polyethylenimine (PEI and dextran sulfate (DS. The enzymes just immobilized on OC supports could be easily released from the support using 2% SDS at pH 7, both intact or after thermal inactivation (in fact, after inactivation most enzyme molecules were already desorbed. The coating with PEI and DS greatly reduced the enzyme release during thermal inactivation and improved enzyme stability. However, using OC-CALB/RML-PEI-DS, the full release of the immobilized enzyme to reuse the support required more drastic conditions: a pH value of 3, a buffer concentration over 2 M, and temperatures above 45 °C. However, even these conditions were not able to fully release the thermally inactivated enzyme molecules from the support, being necessary to increase the buffer concentration to 4 M sodium phosphate and decrease the pH to 2.5. The formation of unfolded protein/polymers composites seems to be responsible for this strong interaction between the octyl and some anionic groups of OC supports. The support could be reused five cycles using these conditions with similar loading capacity of the support and stability of the immobilized enzyme.

Uncertainty analysis of dosimetry spectrum unfolding

International Nuclear Information System (INIS)

Perey, F.G.

1977-01-01

The propagation of uncertainties in the input data is analyzed for the usual dosimetry unfolding solution. A new formulation of the dosimetry unfolding problem is proposed in which the most likely value of the spectrum is obtained. The relationship of this solution to the usual one is discussed

Unfolding four-helix bundles

Science.gov (United States)

Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

2011-03-01

A geometrical model has been developed to describe the early stages of unfolding of cytochromes c‧ and c-b562 . Calculations are based on a step-wise extension of the polypeptide chain subject to the constraint that the spatial relationship among the residues of each triplet is fixed by the native-state crystallographic data. The response of each protein to these structural perturbations allows the evolution of each of the four helices in these two proteins to be differentiated. It is found that the two external helices in c‧ unfold before its two internal helices, whereas exactly the opposite behaviour is demonstrated by c-b562 . Each of these cytochromes has an extended, internal, non-helical ('turning') region that initially lags behind the most labile helix but then, at a certain stage (identified for each cytochrome), unravels before any of the four helices present in the native structure. It is believed that these predictions will be useful in guiding future experimental studies on the unfolding of these two cytochromes.

UNFOLDED REGULAR AND SEMI-REGULAR POLYHEDRA

Directory of Open Access Journals (Sweden)

IONIŢĂ Elena

2015-06-01

Full Text Available This paper proposes a presentation unfolding regular and semi-regular polyhedra. Regular polyhedra are convex polyhedra whose faces are regular and equal polygons, with the same number of sides, and whose polyhedral angles are also regular and equal. Semi-regular polyhedra are convex polyhedra with regular polygon faces, several types and equal solid angles of the same type. A net of a polyhedron is a collection of edges in the plane which are the unfolded edges of the solid. Modeling and unfolding Platonic and Arhimediene polyhedra will be using 3dsMAX program. This paper is intended as an example of descriptive geometry applications.

Neutron spectrum unfolding using computer code SAIPS

International Nuclear Information System (INIS)

Karim, S.

1999-01-01

The main objective of this project was to study the neutron energy spectrum at rabbit station-1 in Pakistan Research Reactor (PARR-I). To do so, multiple foils activation method was used to get the saturated activities. The computer code SAIPS was used to unfold the neutron spectra from the measured reaction rates. Of the three built in codes in SAIPS, only SANDI and WINDOWS were used. Contribution of thermal part of the spectra was observed to be higher than the fast one. It was found that the WINDOWS gave smooth spectra while SANDII spectra have violet oscillations in the resonance region. The uncertainties in the WINDOWS results are higher than those of SANDII. The results show reasonable agreement with the published results. (author)

A study on the thermal expansion characteristics of simulated spent fuel and simulated DUPIC fuel

International Nuclear Information System (INIS)

Kang, Kweon Ho; Ryu, H. J.; Kim, H. S.; Song, K. C.; Yang, M. S.

2001-10-01

Thermal expansions of simulated spent PWR fuel and simulated DUPIC fuel were studied using a dilatometer in the temperature range from 298 to 1900 K. The densities of simulated spent PWR fuel and simulated DUPIC fuel used in the measurement were 10.28 g/cm3 (95.35 % of TD) and 10.26 g/cm3 (95.14 % of TD), respectively. Their linear thermal expansions of simulated fuels are higher than that of UO2, and the difference between these fuels and UO2 increases progressively as temperature increases. However, the difference between simulated spent PWR fuel and simulated DUPIC fuel can hardly be observed. For the temperature range from 298 to 1900 K, the values of the average linear thermal expansion coefficients for simulated spent PWR fuel and simulated DUPIC fuel are 1.391 10-5 and 1.393 10-5 K-1, respectively. As temperature increases to 1900 K, the relative densities of simulated spent PWR fuel and simulated DUPIC fuel decrease to 93.81 and 93.76 % of initial densities at 298 K, respectively

Unfolding study of a trimeric membrane protein AcrB.

Science.gov (United States)

Ye, Cui; Wang, Zhaoshuai; Lu, Wei; Wei, Yinan

2014-07-01

The folding of a multi-domain trimeric α-helical membrane protein, Escherichia coli inner membrane protein AcrB, was investigated. AcrB contains both a transmembrane domain and a large periplasmic domain. Protein unfolding in sodium dodecyl sulfate (SDS) and urea was monitored using the intrinsic fluorescence and circular dichroism spectroscopy. The SDS denaturation curve displayed a sigmoidal profile, which could be fitted with a two-state unfolding model. To investigate the unfolding of separate domains, a triple mutant was created, in which all three Trp residues in the transmembrane domain were replaced with Phe. The SDS unfolding profile of the mutant was comparable to that of the wild type AcrB, suggesting that the observed signal change was largely originated from the unfolding of the soluble domain. Strengthening of trimer association through the introduction of an inter-subunit disulfide bond had little effect on the unfolding profile, suggesting that trimer dissociation was not the rate-limiting step in unfolding monitored by fluorescence emission. Under our experimental condition, AcrB unfolding was not reversible. Furthermore, we experimented with the refolding of a monomeric mutant, AcrBΔloop , from the SDS unfolded state. The CD spectrum of the refolded AcrBΔloop superimposed well onto the spectra of the original folded protein, while the fluorescence spectrum was not fully recovered. In summary, our results suggested that the unfolding of the trimeric AcrB started with a local structural rearrangement. While the refolding of secondary structure in individual monomers could be achieved, the re-association of the trimer might be the limiting factor to obtain folded wild-type AcrB. © 2014 The Protein Society.

Adaptive implicit method for thermal compositional reservoir simulation

Energy Technology Data Exchange (ETDEWEB)

Agarwal, A.; Tchelepi, H.A. [Society of Petroleum Engineers, Richardson, TX (United States)]|[Stanford Univ., Palo Alto (United States)

2008-10-15

As the global demand for oil increases, thermal enhanced oil recovery techniques are becoming increasingly important. Numerical reservoir simulation of thermal methods such as steam assisted gravity drainage (SAGD) is complex and requires a solution of nonlinear mass and energy conservation equations on a fine reservoir grid. The most currently used technique for solving these equations is the fully IMplicit (FIM) method which is unconditionally stable, allowing for large timesteps in simulation. However, it is computationally expensive. On the other hand, the method known as IMplicit pressure explicit saturations, temperature and compositions (IMPEST) is computationally inexpensive, but it is only conditionally stable and restricts the timestep size. To improve the balance between the timestep size and computational cost, the thermal adaptive IMplicit (TAIM) method uses stability criteria and a switching algorithm, where some simulation variables such as pressure, saturations, temperature, compositions are treated implicitly while others are treated with explicit schemes. This presentation described ongoing research on TAIM with particular reference to thermal displacement processes such as the stability criteria that dictate the maximum allowed timestep size for simulation based on the von Neumann linear stability analysis method; the switching algorithm that adapts labeling of reservoir variables as implicit or explicit as a function of space and time; and, complex physical behaviors such as heat and fluid convection, thermal conduction and compressibility. Key numerical results obtained by enhancing Stanford's General Purpose Research Simulator (GPRS) were also presented along with a list of research challenges. 14 refs., 2 tabs., 11 figs., 1 appendix.

Computer simulation of thermal plant operations

CERN Document Server

O'Kelly, Peter

2012-01-01

This book describes thermal plant simulation, that is, dynamic simulation of plants which produce, exchange and otherwise utilize heat as their working medium. Directed at chemical, mechanical and control engineers involved with operations, control and optimization and operator training, the book gives the mathematical formulation and use of simulation models of the equipment and systems typically found in these industries. The author has adopted a fundamental approach to the subject. The initial chapters provide an overview of simulation concepts and describe a suitable computer environment.

Characterization and error analysis of an N×N unfolding procedure applied to filtered, photoelectric x-ray detector arrays. I. Formulation and testing

Directory of Open Access Journals (Sweden)

D. L. Fehl

2010-12-01

Full Text Available An algorithm for spectral reconstructions (unfolds and spectrally integrated flux estimates from data obtained by a five-channel, filtered x-ray-detector array (XRD is described in detail and characterized. This diagnostic is a broad-channel spectrometer, used primarily to measure time-dependent soft x-ray flux emitted by z-pinch plasmas at the Z pulsed-power accelerator (Sandia National Laboratories, Albuquerque, New Mexico, USA, and serves as both a plasma probe and a gauge of accelerator performance. The unfold method, suitable for online analysis, arises naturally from general assumptions about the x-ray source and spectral properties of the channel responses; a priori constraints control the ill-posed nature of the inversion. The unfolded spectrum is not assumed to be Planckian. This study is divided into two consecutive papers. This paper considers three major issues: (a Formulation of the unfold method.—The mathematical background, assumptions, and procedures leading to the algorithm are described: the spectral reconstruction S_{unfold}(E,t—five histogram x-ray bins j over the x-ray interval, 137≤E≤2300  eV at each time step t—depends on the shape and overlap of the calibrated channel responses and on the maximum electrical power delivered to the plasma. The x-ray flux F_{unfold} is estimated as ∫S_{unfold}(E,tdE. (b Validation with simulations.—Tests of the unfold algorithm with known static and time-varying spectra are described. These spectra included—but were not limited to—Planckian spectra S_{bb}(E,T (25≤T≤250  eV, from which noise-free channel data were simulated and unfolded. For Planckian simulations with 125≤T≤250  eV and typical responses, the binwise unfold values S_{j} and the corresponding binwise averages ⟨S_{bb}⟩_{j} agreed to ∼20%, except where S_{bb}≪max⁡{S_{bb}}. Occasionally, unfold values S_{j}≲0 (artifacts were encountered. The algorithm recovered ≳90% of the x

Thermal expansion study of simulated DUPIC fuel using neutron diffraction

International Nuclear Information System (INIS)

Kang, Kweon Ho; Ryu, H. J.; Bae, J. H.; Kim, H. S.; Song, K. C.; Yang, M. S.; Choi, Y. N.; Han, Y. S.; Oh, H. S.

2001-07-01

The lattice parameters of simulated DUPIC fuel and UO2 were measured from room temperature to 1273 K using neutron diffraction to investigate the thermal expansion and density variation with temperature. The lattice parameter of simulated DUPIC fuel is lower than that of UO2 and the linear thermal expansion of simulated DUPIC fuel is higher than that of UO2. For the temperature range from 298 to 1273 K, the average linear thermal expansion coefficients for UO2 and simulated DUPIC fuel are 10.471 ''10-6 and 10.751 ''10-6 K-1, respectively

Salt bridge as a gatekeeper against partial unfolding.

Science.gov (United States)

Hinzman, Mark W; Essex, Morgan E; Park, Chiwook

2016-05-01

Salt bridges are frequently observed in protein structures. Because the energetic contribution of salt bridges is strongly dependent on the environmental context, salt bridges are believed to contribute to the structural specificity rather than the stability. To test the role of salt bridges in enhancing structural specificity, we investigated the contribution of a salt bridge to the energetics of native-state partial unfolding in a cysteine-free version of Escherichia coli ribonuclease H (RNase H*). Thermolysin cleaves a protruding loop of RNase H(*) through transient partial unfolding under native conditions. Lys86 and Asp108 in RNase H(*) form a partially buried salt bridge that tethers the protruding loop. Investigation of the global stability of K86Q/D108N RNase H(*) showed that the salt bridge does not significantly contribute to the global stability. However, K86Q/D108N RNase H(*) is greatly more susceptible to proteolysis by thermolysin than wild-type RNase H(*) is. The free energy for partial unfolding determined by native-state proteolysis indicates that the salt bridge significantly increases the energy for partial unfolding by destabilizing the partially unfolded form. Double mutant cycles with single and double mutations of the salt bridge suggest that the partially unfolded form is destabilized due to a significant decrease in the interaction energy between Lys86 and Asp108 upon partial unfolding. This study demonstrates that, even in the case that a salt bridge does not contribute to the global stability, the salt bridge may function as a gatekeeper against partial unfolding that disturbs the optimal geometry of the salt bridge. © 2016 The Protein Society.

Molecular dynamics simulation of thermal conductivities of superlattice nanowires

Institute of Scientific and Technical Information of China (English)

YANG; Juekuan(杨决宽); CHEN; Yunfei(陈云飞); YAN; Jingping(颜景平)

2003-01-01

Nonequilibrium molecular dynamics simulations were carried out to investigate heat transfer in superlattice nanowires. Results show that for fixed period length superlattice nanowires, the ratio of the total interfacial thermal resistance to the total thermal resistance and the effective thermal conductivities are invariant with the changes in interface numbers. Increasing the period length leads to an increase in the average interfacial thermal resistance, which indicates that the interfacial thermal resistance depends not only on the materials that constitute the alternating segments of superlattice nanowires, but also on the lattice strain throughout the segments. The modification of the lattice structure due to the lattice mismatch should be taken into account in the acoustic mismatch model. Simulation results also demonstrated the size confinement effect on the thermal conductivities for low dimensional structures, i.e. the thermal conductivities and the interfacial thermal resistance increase as the nanowire cross-sectional area increases.

Applied multidimensional scaling and unfolding

CERN Document Server

Borg, Ingwer; Mair, Patrick

2018-01-01

This book introduces multidimensional scaling (MDS) and unfolding as data analysis techniques for applied researchers. MDS is used for the analysis of proximity data on a set of objects, representing the data as distances between points in a geometric space (usually of two dimensions). Unfolding is a related method that maps preference data (typically evaluative ratings of different persons on a set of objects) as distances between two sets of points (representing the persons and the objects, resp.). This second edition has been completely revised to reflect new developments and the coverage of unfolding has also been substantially expanded. Intended for applied researchers whose main interests are in using these methods as tools for building substantive theories, it discusses numerous applications (classical and recent), highlights practical issues (such as evaluating model fit), presents ways to enforce theoretical expectations for the scaling solutions, and addresses the typical mistakes that MDS/unfoldin...

Tutorial: Determination of thermal boundary resistance by molecular dynamics simulations

Science.gov (United States)

Liang, Zhi; Hu, Ming

2018-05-01

Due to the high surface-to-volume ratio of nanostructured components in microelectronics and other advanced devices, the thermal resistance at material interfaces can strongly affect the overall thermal behavior in these devices. Therefore, the thermal boundary resistance, R, must be taken into account in the thermal analysis of nanoscale structures and devices. This article is a tutorial on the determination of R and the analysis of interfacial thermal transport via molecular dynamics (MD) simulations. In addition to reviewing the commonly used equilibrium and non-equilibrium MD models for the determination of R, we also discuss several MD simulation methods which can be used to understand interfacial thermal transport behavior. To illustrate how these MD models work for various interfaces, we will show several examples of MD simulation results on thermal transport across solid-solid, solid-liquid, and solid-gas interfaces. The advantages and drawbacks of a few other MD models such as approach-to-equilibrium MD and first-principles MD are also discussed.

Understanding how biodiversity unfolds through time under neutral theory.

Science.gov (United States)

Missa, Olivier; Dytham, Calvin; Morlon, Hélène

2016-04-05

Theoretical predictions for biodiversity patterns are typically derived under the assumption that ecological systems have reached a dynamic equilibrium. Yet, there is increasing evidence that various aspects of ecological systems, including (but not limited to) species richness, are not at equilibrium. Here, we use simulations to analyse how biodiversity patterns unfold through time. In particular, we focus on the relative time required for various biodiversity patterns (macroecological or phylogenetic) to reach equilibrium. We simulate spatially explicit metacommunities according to the Neutral Theory of Biodiversity (NTB) under three modes of speciation, which differ in how evenly a parent species is split between its two daughter species. We find that species richness stabilizes first, followed by species area relationships (SAR) and finally species abundance distributions (SAD). The difference in timing of equilibrium between these different macroecological patterns is the largest when the split of individuals between sibling species at speciation is the most uneven. Phylogenetic patterns of biodiversity take even longer to stabilize (tens to hundreds of times longer than species richness) so that equilibrium predictions from neutral theory for these patterns are unlikely to be relevant. Our results suggest that it may be unwise to assume that biodiversity patterns are at equilibrium and provide a first step in studying how these patterns unfold through time. © 2016 The Author(s).

Osmolyte Effects on the Unfolding Pathway of β-Lactoglobulin

International Nuclear Information System (INIS)

Meng Wei; Pan Hai; Qin Meng; Cao Yi; Wang Wei

2013-01-01

There are large amounts of osmolytes inside cells, which impact many physiological processes by complicated mechanisms. The osmolyte effects on the stability and folding of proteins have been studied in detail using simple two-state folding proteins. However, many important functional proteins fold in complex pathways involving various intermediates. Little is known about the osmolyte effects on the folding and unfolding of these proteins. It is noted that β-lactoglobulin (BLG) is an example of such proteins, whose unfolding involves an obvious intermediate state. Using equilibrium chemical denaturation and stopped-flow kinetics, we investigate the unfolding of BLG in the presence of different osmolytes, e.g., glycerol, ethylene glycol (EG) and poly(ethylene glycol)400 (PEG400). It is found that all these osmolytes can stabilize the unfolding intermediate by modulating the relative unfolding kinetics of the native and the intermediate states. The stabilization effects are similar for EG and PEG400 but distinct for glycerol. Since the unfolding intermediates of many proteins are directly related to protein misfolding diseases, evaluation of the osmolyte effects for the unfolding of these proteins in vitro should be beneficial for the understanding of the occurrence of the related diseases in vivo

Main factors of thermal fatigue failure induced by thermal striping and total simulation of thermal hydraulic and structural behaviors (research report)

International Nuclear Information System (INIS)

Kasahara, Naoto; Muramatsu, Toshiharu

1999-01-01

At incomplete mixing area of high temperature and low temperature fluids near the surface of structures, temperature fluctuation of fluid gives thermal fatigue damage to wall structures. This phenomenon is called thermal striping, which becomes sometimes a critical problem in LMFR plants. Since thermal striping phenomenon is characterized by the complex thermohydraulic and thermomechanical coupled problem, conventional evaluation procedures require mock-up experiments. In order to replace them by simulation-base methods, the authors have developed numerical simulation codes and applied them to analyze a tee junction of the PHENIX secondary circuit due to thermal striping phenomenon, in the framework of the IAEA coordinated research program (CRP). Through this analysis, thermohydraulic and thermomechanical mechanism of thermal striping phenomenon was clarified, and main factors on structural integrity was extracted in each stage of thermal striping phenomenon. Furthermore, simulation base evaluation methods were proposed taking above factors of structural integrity into account. Finally, R and D problems were investigated for future development of design evaluation methods. (author)

Thermal simulation of storage in TSS-Galleries

International Nuclear Information System (INIS)

Lain Huerta, R.; Martinez Santiago, T.; Ramirez Oyangueren, P.

1993-01-01

This report describes the experiment ''thermal simulation of storage in TSS-galleries'' what is been developed in salt mine of Asse, Germany. The report has 3 part: 1) Analysis of objectives and general description of boundary layers. 2) Geomechanics parameters of salt mine. 3) Thermal modelization, thermomechanics modelization and data acquisition

Neutron spectrum unfolding: Pt. 2

International Nuclear Information System (INIS)

Matiullah; Wiyaja, D.S.; Berzonis, M.A.; Bondars, H.; Lapenas, A.A.; Kudo, K.; Majeed, A.; Durrani, S.A.

1991-01-01

In Part I of this paper, we described the use of the computer code SAIPS in neutron spectrum unfolding. Here in Part II, we present our experimental work carried out to study the shape of the neutron spectrum in different experimental channels of a 5 MW light-water cooled and moderated research reactor. The spectral neutron flux was determined using various fission foils (placed in close contact with mica track detectors) and activation detectors. From the measured activities, the neutron spectrum was unfolded by SAIPS. (author)

Studying pressure denaturation of a protein by molecular dynamics simulations.

Science.gov (United States)

Sarupria, Sapna; Ghosh, Tuhin; García, Angel E; Garde, Shekhar

2010-05-15

Many globular proteins unfold when subjected to several kilobars of hydrostatic pressure. This "unfolding-up-on-squeezing" is counter-intuitive in that one expects mechanical compression of proteins with increasing pressure. Molecular simulations have the potential to provide fundamental understanding of pressure effects on proteins. However, the slow kinetics of unfolding, especially at high pressures, eliminates the possibility of its direct observation by molecular dynamics (MD) simulations. Motivated by experimental results-that pressure denatured states are water-swollen, and theoretical results-that water transfer into hydrophobic contacts becomes favorable with increasing pressure, we employ a water insertion method to generate unfolded states of the protein Staphylococcal Nuclease (Snase). Structural characteristics of these unfolded states-their water-swollen nature, retention of secondary structure, and overall compactness-mimic those observed in experiments. Using conformations of folded and unfolded states, we calculate their partial molar volumes in MD simulations and estimate the pressure-dependent free energy of unfolding. The volume of unfolding of Snase is negative (approximately -60 mL/mol at 1 bar) and is relatively insensitive to pressure, leading to its unfolding in the pressure range of 1500-2000 bars. Interestingly, once the protein is sufficiently water swollen, the partial molar volume of the protein appears to be insensitive to further conformational expansion or unfolding. Specifically, water-swollen structures with relatively low radii of gyration have partial molar volume that are similar to that of significantly more unfolded states. We find that the compressibility change on unfolding is negligible, consistent with experiments. We also analyze hydration shell fluctuations to comment on the hydration contributions to protein compressibility. Our study demonstrates the utility of molecular simulations in estimating volumetric properties

Characterization and error analysis of an N×N unfolding procedure applied to filtered, photoelectric x-ray detector arrays. II. Error analysis and generalization

Directory of Open Access Journals (Sweden)

D. L. Fehl

2010-12-01

Full Text Available A five-channel, filtered-x-ray-detector (XRD array has been used to measure time-dependent, soft-x-ray flux emitted by z-pinch plasmas at the Z pulsed-power accelerator (Sandia National Laboratories, Albuquerque, New Mexico, USA. The preceding, companion paper [D. L. Fehl et al., Phys. Rev. ST Accel. Beams 13, 120402 (2010PRABFM1098-4402] describes an algorithm for spectral reconstructions (unfolds and spectrally integrated flux estimates from data obtained by this instrument. The unfolded spectrum S_{unfold}(E,t is based on (N=5 first-order B-splines (histograms in contiguous unfold bins j=1,…,N; the recovered x-ray flux F_{unfold}(t is estimated as ∫S_{unfold}(E,tdE, where E is x-ray energy and t is time. This paper adds two major improvements to the preceding unfold analysis: (a Error analysis.—Both data noise and response-function uncertainties are propagated into S_{unfold}(E,t and F_{unfold}(t. Noise factors ν are derived from simulations to quantify algorithm-induced changes in the noise-to-signal ratio (NSR for S_{unfold} in each unfold bin j and for F_{unfold} (ν≡NSR_{output}/NSR_{input}: for S_{unfold}, 1≲ν_{j}≲30, an outcome that is strongly spectrally dependent; for F_{unfold}, 0.6≲ν_{F}≲1, a result that is less spectrally sensitive and corroborated independently. For nominal z-pinch experiments, the combined uncertainty (noise and calibrations in F_{unfold}(t at peak is estimated to be ∼15%. (b Generalization of the unfold method.—Spectral sensitivities (called here passband functions are constructed for S_{unfold} and F_{unfold}. Predicting how the unfold algorithm reconstructs arbitrary spectra is thereby reduced to quadratures. These tools allow one to understand and quantitatively predict algorithmic distortions (including negative artifacts, to identify potentially troublesome spectra, and to design more useful response functions.

Iterative nonlinear unfolding code: TWOGO

International Nuclear Information System (INIS)

Hajnal, F.

1981-03-01

a new iterative unfolding code, TWOGO, was developed to analyze Bonner sphere neutron measurements. The code includes two different unfolding schemes which alternate on successive iterations. The iterative process can be terminated either when the ratio of the coefficient of variations in terms of the measured and calculated responses is unity, or when the percentage difference between the measured and evaluated sphere responses is less than the average measurement error. The code was extensively tested with various known spectra and real multisphere neutron measurements which were performed inside the containments of pressurized water reactors

Branches of Triangulated Origami Near the Unfolded State

Directory of Open Access Journals (Sweden)

Bryan Gin-ge Chen

2018-02-01

Full Text Available Origami structures are characterized by a network of folds and vertices joining unbendable plates. For applications to mechanical design and self-folding structures, it is essential to understand the interplay between the set of folds in the unfolded origami and the possible 3D folded configurations. When deforming a structure that has been folded, one can often linearize the geometric constraints, but the degeneracy of the unfolded state makes a linear approach impossible there. We derive a theory for the second-order infinitesimal rigidity of an initially unfolded triangulated origami structure and use it to study the set of nearly unfolded configurations of origami with four boundary vertices. We find that locally, this set consists of a number of distinct “branches” which intersect at the unfolded state, and that the number of these branches is exponential in the number of vertices. We find numerical and analytical evidence that suggests that the branches are characterized by choosing each internal vertex to either “pop up” or “pop down.” The large number of pathways along which one can fold an initially unfolded origami structure strongly indicates that a generic structure is likely to become trapped in a “misfolded” state. Thus, new techniques for creating self-folding origami are likely necessary; controlling the popping state of the vertices may be one possibility.

Branches of Triangulated Origami Near the Unfolded State

Science.gov (United States)

Chen, Bryan Gin-ge; Santangelo, Christian D.

2018-01-01

Origami structures are characterized by a network of folds and vertices joining unbendable plates. For applications to mechanical design and self-folding structures, it is essential to understand the interplay between the set of folds in the unfolded origami and the possible 3D folded configurations. When deforming a structure that has been folded, one can often linearize the geometric constraints, but the degeneracy of the unfolded state makes a linear approach impossible there. We derive a theory for the second-order infinitesimal rigidity of an initially unfolded triangulated origami structure and use it to study the set of nearly unfolded configurations of origami with four boundary vertices. We find that locally, this set consists of a number of distinct "branches" which intersect at the unfolded state, and that the number of these branches is exponential in the number of vertices. We find numerical and analytical evidence that suggests that the branches are characterized by choosing each internal vertex to either "pop up" or "pop down." The large number of pathways along which one can fold an initially unfolded origami structure strongly indicates that a generic structure is likely to become trapped in a "misfolded" state. Thus, new techniques for creating self-folding origami are likely necessary; controlling the popping state of the vertices may be one possibility.

Evolution and thermodynamics of the slow unfolding of hyperstable monomeric proteins

Directory of Open Access Journals (Sweden)

Koga Yuichi

2010-07-01

Full Text Available Abstract Background The unfolding speed of some hyperthermophilic proteins is dramatically lower than that of their mesostable homologs. Ribonuclease HII from the hyperthermophilic archaeon Thermococcus kodakaraensis (Tk-RNase HII is stabilized by its remarkably slow unfolding rate, whereas RNase HI from the thermophilic bacterium Thermus thermophilus (Tt-RNase HI unfolds rapidly, comparable with to that of RNase HI from Escherichia coli (Ec-RNase HI. Results To clarify whether the difference in the unfolding rate is due to differences in the types of RNase H or differences in proteins from archaea and bacteria, we examined the equilibrium stability and unfolding reaction of RNases HII from the hyperthermophilic bacteria Thermotoga maritima (Tm-RNase HII and Aquifex aeolicus (Aa-RNase HII and RNase HI from the hyperthermophilic archaeon Sulfolobus tokodaii (Sto-RNase HI. These proteins from hyperthermophiles are more stable than Ec-RNase HI over all the temperature ranges examined. The observed unfolding speeds of all hyperstable proteins at the different denaturant concentrations studied are much lower than those of Ec-RNase HI, which is in accordance with the familiar slow unfolding of hyperstable proteins. However, the unfolding rate constants of these RNases H in water are dispersed, and the unfolding rate constant of thermophilic archaeal proteins is lower than that of thermophilic bacterial proteins. Conclusions These results suggest that the nature of slow unfolding of thermophilic proteins is determined by the evolutionary history of the organisms involved. The unfolding rate constants in water are related to the amount of buried hydrophobic residues in the tertiary structure.

Peripheral Protein Unfolding Drives Membrane Bending.

Science.gov (United States)

Siaw, Hew Ming Helen; Raghunath, Gokul; Dyer, R Brian

2018-06-20

Dynamic modulation of lipid membrane curvature can be achieved by a number of peripheral protein binding mechanisms such as hy-drophobic insertion of amphipathic helices and membrane scaffolding. Recently, an alternative mechanism was proposed in which crowding of peripherally bound proteins induces membrane curvature through steric pressure generated by lateral collisions. This effect was enhanced using intrinsically disordered proteins that possess high hydrodynamic radii, prompting us to explore whether membrane bending can be triggered by the folding-unfolding transition of surface-bound proteins. We utilized histidine-tagged human serum albumin bound to Ni-NTA-DGS containing liposomes as our model system to test this hypothesis. We found that reduction of the disulfide bonds in the protein resulted in unfolding of HSA, which subsequently led to membrane tubule formation. The frequency of tubule formation was found to be significantly higher when the proteins were unfolded while being localized to a phase-separated domain as opposed to randomly distributed in fluid phase liposomes, indicating that the steric pressure generated from protein unfolding is directly responsible for membrane deformation. Our results are critical for the design of peripheral membrane protein-immobilization strategies and open new avenues for exploring mechanisms of membrane bending driven by conformational changes of peripheral membrane proteins.

Kinetically controlled thermal response of beta2-microglobulin amyloid fibrils.

Science.gov (United States)

Sasahara, Kenji; Naiki, Hironobu; Goto, Yuji

2005-09-23

Calorimetric measurements were carried out using a differential scanning calorimeter in the temperature range from 10 to 120 degrees C for characterizing the thermal response of beta2-microglobulin amyloid fibrils. The thermograms of amyloid fibril solution showed a remarkably large decrease in heat capacity that was essentially released upon the thermal unfolding of the fibrils, in which the magnitude of negative heat capacity change was not explicable in terms of the current accessible surface area model of protein structural thermodynamics. The heat capacity-temperature curve of amyloid fibrils prior to the fibril unfolding exhibited an unusual dependence on the fibril concentration and the heating rate. Particularly, the heat needed to induce the thermal response was found to be linearly dependent on the heating rate, indicating that its thermal response is under a kinetic control and precluding the interpretation in terms of equilibrium thermodynamics. Furthermore, amyloid fibrils of amyloid beta peptides also exhibited a heating rate-dependent exothermic process before the fibril unfolding, indicating that the kinetically controlled thermal response may be a common phenomenon to amyloid fibrils. We suggest that the heating rate-dependent negative change in heat capacity is coupled to the association of amyloid fibrils with characteristic hydration pattern.

The unfolding effects of transfer functions and processing of the pulse height distributions

Directory of Open Access Journals (Sweden)

Avdić Senada

2010-01-01

Full Text Available This paper deals with the improvements of the linear artificial neural network unfolding approach aimed at accurately determining the incident neutron spectrum. The effects of the transfer functions and pre-processing of the simulated pulse height distributions from liquid scintillation detectors on the artificial neural networks performance have been studied. A better energy resolution and higher reliability of the linear artificial neural network technique have been achieved after implementation of the results of this study. The optimized structure of the network was used to unfold both monoenergetic and continuous neutron energy spectra, such as the spectra of 252Cf and 241Am-Be sources, traditionally used in the nuclear safeguards experiments. We have demonstrated that the artificial neural network energy resolution of 0.1 MeV is comparable with the one obtained by the reference maximum likelihood expectation-maximization method which was implemented by using the one step late algorithm. Although the maximum likelihood algorithm provides the unfolded results of higher accuracy, especially for continuous neutron sources, the artificial neural network approach with the improved performances is more suitable for fast and robust determination of the neutron spectra with sufficient accuracy.

Solar panel thermal cycling testing by solar simulation and infrared radiation methods

Science.gov (United States)

Nuss, H. E.

1980-01-01

For the solar panels of the European Space Agency (ESA) satellites OTS/MAROTS and ECS/MARECS the thermal cycling tests were performed by using solar simulation methods. The performance data of two different solar simulators used and the thermal test results are described. The solar simulation thermal cycling tests for the ECS/MARECS solar panels were carried out with the aid of a rotatable multipanel test rig by which simultaneous testing of three solar panels was possible. As an alternative thermal test method, the capability of an infrared radiation method was studied and infrared simulation tests for the ultralight panel and the INTELSAT 5 solar panels were performed. The setup and the characteristics of the infrared radiation unit using a quartz lamp array of approx. 15 sq and LN2-cooled shutter and the thermal test results are presented. The irradiation uniformity, the solar panel temperature distribution, temperature changing rates for both test methods are compared. Results indicate the infrared simulation is an effective solar panel thermal testing method.

Unfolding of Ubiquitin Studied by Picosecond Time-Resolved Fluorescence of the Tyrosine Residue

OpenAIRE

Noronha, Melinda; Lima, João C.; Bastos, Margarida; Santos, Helena; Maçanita, António L.

2004-01-01

The photophysics of the single tyrosine in bovine ubiquitin (UBQ) was studied by picosecond time-resolved fluorescence spectroscopy, as a function of pH and along thermal and chemical unfolding, with the following results: First, at room temperature (25°C) and below pH 1.5, native UBQ shows single-exponential decays. From pH 2 to 7, triple-exponential decays were observed and the three decay times were attributed to the presence of tyrosine, a tyrosine-carboxylate hydrogen-bonded complex, and...

Solar thermal power plants simulation using the TRNSYS software

Energy Technology Data Exchange (ETDEWEB)

Popel, O.S.; Frid, S.E.; Shpilrain, E.E. [Institute for High Temperatures, Russian Academy of Sciences (IVTAN), Moscow (Russian Federation)

1999-03-01

The paper describes activity directed on the TRNSYS software application for mathematical simulation of solar thermal power plants. First stage of developments has been devoted to simulation and thermodynamic analysis of the Hybrid Solar-Fuel Thermal Power Plants (HSFTPP) with gas turbine installations. Three schemes of HSFTPP, namely: Gas Turbine Regenerative Cycle, Brayton Cycle with Steam Injection and Combined Brayton-Rankine Cycle,- have been assembled and tested under the TRNSYS. For this purpose 18 new models of the schemes components (gas and steam turbines, compressor, heat-exchangers, steam generator, solar receiver, condenser, controllers, etc) have been elaborated and incorporated into the TRNSYS library of 'standard' components. The authors do expect that this initiative and received results will stimulate experts involved in the mathematical simulation of solar thermal power plants to join the described activity to contribute to acceleration of development and expansion of 'Solar Thermal Power Plants' branch of the TRNSYS. The proposed approach could provide an appropriate basis for standardization of analysis, models and assumptions for well-founded comparison of different schemes of advanced solar power plants. (authors)

NEUPAC, Experimental Neutron Spectra Unfolding with Sensitivities

International Nuclear Information System (INIS)

Sasaki, Makoto; Nakazawa, Masaharu

1986-01-01

1 - Description of problem or function: The code is able to determine the integral quantities and their sensitivities, together with an estimate of the unfolded spectrum and integral quantities. The code also performs a chi-square test of the input/output data, and contains many options for the calculational routines. 2 - Method of solution: The code is based on the J1-type unfolding method, and the estimated neutron flux spectrum is obtained as its solution. 3 - Restrictions on the complexity of the problem: The maximum number of energy groups used for unfolding is 620. The maximum number of reaction rates and the window functions given as input is 20. The total storage requirement depends on the amount of input data

History, rare, and multiple events of mechanical unfolding of repeat proteins

Science.gov (United States)

Sumbul, Fidan; Marchesi, Arin; Rico, Felix

2018-03-01

Mechanical unfolding of proteins consisting of repeat domains is an excellent tool to obtain large statistics. Force spectroscopy experiments using atomic force microscopy on proteins presenting multiple domains have revealed that unfolding forces depend on the number of folded domains (history) and have reported intermediate states and rare events. However, the common use of unspecific attachment approaches to pull the protein of interest holds important limitations to study unfolding history and may lead to discarding rare and multiple probing events due to the presence of unspecific adhesion and uncertainty on the pulling site. Site-specific methods that have recently emerged minimize this uncertainty and would be excellent tools to probe unfolding history and rare events. However, detailed characterization of these approaches is required to identify their advantages and limitations. Here, we characterize a site-specific binding approach based on the ultrastable complex dockerin/cohesin III revealing its advantages and limitations to assess the unfolding history and to investigate rare and multiple events during the unfolding of repeated domains. We show that this approach is more robust, reproducible, and provides larger statistics than conventional unspecific methods. We show that the method is optimal to reveal the history of unfolding from the very first domain and to detect rare events, while being more limited to assess intermediate states. Finally, we quantify the forces required to unfold two molecules pulled in parallel, difficult when using unspecific approaches. The proposed method represents a step forward toward more reproducible measurements to probe protein unfolding history and opens the door to systematic probing of rare and multiple molecule unfolding mechanisms.

Unfolding methods in high-energy physics experiments

International Nuclear Information System (INIS)

Blobel, V.

1985-01-01

Distributions measured in high-energy physics experiments are often distorted or transformed by limited acceptance and finite resolution of the detectors. The unfolding of measured distributions is an important, but due to inherent instabilities a very difficult problem. Methods for unfolding, applicable for the analysis of high-energy physics experiments, and their properties are discussed. An introduction is given to the method of regularization. (orig.)

Unfolding methods in high-energy physics experiments

International Nuclear Information System (INIS)

Blobel, V.

1984-12-01

Distributions measured in high-energy physics experiments are often distorted or transformed by limited acceptance and finite resolution of the detectors. The unfolding of measured distributions is an important, but due to inherent instabilities a very difficult problem. Methods for unfolding, applicable for the analysis of high-energy physics experiments, and their properties are discussed. An introduction is given to the method of regularization. (orig.)

Unfolding energetics and stability of banana lectin.

Science.gov (United States)

Gupta, Garima; Sinha, Sharmistha; Surolia, Avadhesha

2008-08-01

The unfolding pathway of banana lectin from Musa paradisiaca was determined by isothermal denaturation induced by the chaotrope GdnCl. The unfolding was found to be a reversible process. The data obtained by isothermal denaturation provided information on conformational stability of banana lectin. The high values of DeltaG of unfolding at various temperatures indicated the strength of intersubunit interactions. It was found that banana lectin is a very stable and denatures at high chaotrope concentrations only. The basis of the stability may be attributed to strong hydrogen bonds of the order 2.5-3.1 A at the dimeric interface along with the presence of water bridges. This is perhaps very unique example in proteins where subunit association is not a consequence of the predominance of hydrophobic interactions. (c) 2008 Wiley-Liss, Inc.

D19S Mutation of the Cationic, Cysteine-Rich Protein PAF: Novel Insights into Its Structural Dynamics, Thermal Unfolding and Antifungal Function.

Directory of Open Access Journals (Sweden)

Christoph Sonderegger

Full Text Available The cysteine-rich, cationic, antifungal protein PAF is abundantly secreted into the culture supernatant of the filamentous Ascomycete Penicillium chrysogenum. The five β-strands of PAF form a compact β-barrel that is stabilized by three disulphide bonds. The folding of PAF allows the formation of four surface-exposed loops and distinct charged motifs on the protein surface that might regulate the interaction of PAF with the sensitive target fungus. The growth inhibitory activity of this highly stable protein against opportunistic fungal pathogens provides great potential in antifungal drug research. To understand its mode of action, we started to investigate the surface-exposed loops of PAF and replaced one aspartic acid at position 19 in loop 2 that is potentially involved in PAF active or binding site, with a serine (Asp19 to Ser19. We analysed the overall effects, such as unfolding, electrostatic changes, sporadic conformers and antifungal activity when substituting this specific amino acid to the fairly indifferent amino acid serine. Structural analyses revealed that the overall 3D solution structure is virtually identical with that of PAF. However, PAFD19S showed slightly increased dynamics and significant differences in the surface charge distribution. Thermal unfolding identified PAFD19S to be rather a two-state folder in contrast to the three-state folder PAF. Functional comparison of PAFD19S and PAF revealed that the exchange at residue 19 caused a dramatic loss of antifungal activity: the binding and internalization of PAFD19S by target cells was reduced and the protein failed to trigger an intracellular Ca2+ response, all of which are closely linked to the antifungal toxicity of PAF. We conclude that the negatively charged residue Asp19 in loop 2 is essential for full function of the cationic protein PAF.

Characterization and error analysis of an N×N unfolding procedure applied to filtered, photoelectric x-ray detector arrays. I. Formulation and testing

Science.gov (United States)

Fehl, D. L.; Chandler, G. A.; Stygar, W. A.; Olson, R. E.; Ruiz, C. L.; Hohlfelder, J. J.; Mix, L. P.; Biggs, F.; Berninger, M.; Frederickson, P. O.; Frederickson, R.

2010-12-01

An algorithm for spectral reconstructions (unfolds) and spectrally integrated flux estimates from data obtained by a five-channel, filtered x-ray-detector array (XRD) is described in detail and characterized. This diagnostic is a broad-channel spectrometer, used primarily to measure time-dependent soft x-ray flux emitted by z-pinch plasmas at the Z pulsed-power accelerator (Sandia National Laboratories, Albuquerque, New Mexico, USA), and serves as both a plasma probe and a gauge of accelerator performance. The unfold method, suitable for online analysis, arises naturally from general assumptions about the x-ray source and spectral properties of the channel responses; a priori constraints control the ill-posed nature of the inversion. The unfolded spectrum is not assumed to be Planckian. This study is divided into two consecutive papers. This paper considers three major issues: (a) Formulation of the unfold method.—The mathematical background, assumptions, and procedures leading to the algorithm are described: the spectral reconstruction Sunfold(E,t)—five histogram x-ray bins j over the x-ray interval, 137≤E≤2300eV at each time step t—depends on the shape and overlap of the calibrated channel responses and on the maximum electrical power delivered to the plasma. The x-ray flux Funfold is estimated as ∫Sunfold(E,t)dE. (b) Validation with simulations.—Tests of the unfold algorithm with known static and time-varying spectra are described. These spectra included—but were not limited to—Planckian spectra Sbb(E,T) (25≤T≤250eV), from which noise-free channel data were simulated and unfolded. For Planckian simulations with 125≤T≤250eV and typical responses, the binwise unfold values Sj and the corresponding binwise averages ⟨Sbb⟩j agreed to ˜20%, except where Sbb≪max⁡{Sbb}. Occasionally, unfold values Sj≲0 (artifacts) were encountered. The algorithm recovered ≳90% of the x-ray flux over the wider range, 75≤T≤250eV. For lower T, the

NMR of unfolded proteins

Indian Academy of Sciences (India)

Unknown

2005-01-03

Jan 3, 2005 ... covering all the systems, so far discovered.5,7,8,12. With the increasing ... Structural investigations on proteins by NMR are, currently ... rapid analysis of unfolded proteins. ...... and hence help in design of drugs against them.

GOTHIC code simulation of thermal stratification in POOLEX facility

International Nuclear Information System (INIS)

Li, H.; Kudinov, P.

2009-07-01

Pressure suppression pool is an important element of BWR containment. It serves as a heat sink and steam condenser to prevent containment pressure buildup during loss of coolant accident or safety relief valve opening during normal operations of a BWR. Insufficient mixing in the pool, in case of low mass flow rate of steam, can cause development of thermal stratification and reduction of pressure suppression pool capacity. For reliable prediction of mixing and stratification phenomena validation of simulation tools has to be performed. Data produced in POOLEX/PPOOLEX facility at Lappeenranta University of Technology about development of thermal stratification in a large scale model of a pressure suppression pool is used for GOTHIC lumped and distributed parameter validation. Sensitivity of GOTHIC solution to different boundary conditions and grid convergence study for 2D simulations of POOLEX STB-20 experiment are performed in the present study. CFD simulation was carried out with FLUENT code in order to get additional insights into physics of stratification phenomena. In order to support development of experimental procedures for new tests in the PPOOLEX facility lumped parameter pre-test GOTHIC simulations were performed. Simulations show that drywell and wetwell pressures can be kept within safety margins during a long transient necessary for development of thermal stratification. (au)

GOTHIC code simulation of thermal stratification in POOLEX facility

Energy Technology Data Exchange (ETDEWEB)

Li, H.; Kudinov, P. (Royal Institute of Technology (KTH) (Sweden))

2009-07-15

Pressure suppression pool is an important element of BWR containment. It serves as a heat sink and steam condenser to prevent containment pressure buildup during loss of coolant accident or safety relief valve opening during normal operations of a BWR. Insufficient mixing in the pool, in case of low mass flow rate of steam, can cause development of thermal stratification and reduction of pressure suppression pool capacity. For reliable prediction of mixing and stratification phenomena validation of simulation tools has to be performed. Data produced in POOLEX/PPOOLEX facility at Lappeenranta University of Technology about development of thermal stratification in a large scale model of a pressure suppression pool is used for GOTHIC lumped and distributed parameter validation. Sensitivity of GOTHIC solution to different boundary conditions and grid convergence study for 2D simulations of POOLEX STB-20 experiment are performed in the present study. CFD simulation was carried out with FLUENT code in order to get additional insights into physics of stratification phenomena. In order to support development of experimental procedures for new tests in the PPOOLEX facility lumped parameter pre-test GOTHIC simulations were performed. Simulations show that drywell and wetwell pressures can be kept within safety margins during a long transient necessary for development of thermal stratification. (au)

Catalogue to select the initial guess spectrum during unfolding

CERN Document Server

Vega-Carrillo, H R

2002-01-01

A new method to select the initial guess spectrum is presented. Neutron spectra unfolded from Bonner sphere data are dependent on the initial guess spectrum used in the unfolding code. The method is based on a catalogue of detector count rates calculated from a set of reported neutron spectra. The spectra of three isotopic neutron sources sup 2 sup 5 sup 2 Cf, sup 2 sup 3 sup 9 PuBe and sup 2 sup 5 sup 2 Cf/D sub 2 O, were measured to test the method. The unfolding was carried out using the three initial guess options included in the BUNKIUT code. Neutron spectra were also calculated using MCNP code. Unfolded spectra were compared with those calculated; in all the cases our method gives the best results.

Note: Local thermal conductivities from boundary driven non-equilibrium molecular dynamics simulations

International Nuclear Information System (INIS)

Bresme, F.; Armstrong, J.

2014-01-01

We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation

TRSM-a thermal-hydraulic real-time simulation model for PWR

International Nuclear Information System (INIS)

Zhou Weichang

1997-01-01

TRSM (a Thermal-hydraulic Real-time Simulation Model) has been developed for PWR real-time simulation and best-estimate prediction of normal operating and abnormal accident conditions. It is a non-equilibrium two phase flow thermal-hydraulic model based on five basic conservation equations. A drift flux model is used to account for the unequal velocities of liquid and gaseous mixture, with or without the presence of the noncondensibles. Critical flow models are applied for break flow and valve flow calculations. A 5-regime two phase heat convection model is applied for clad-to-coolant as well as fluid-to-tubing heat transfer. A rigorous reactor coolant pump model is used to calculate the pressure drop and rise for the suction and discharge ends with complete pump characteristics curves included. The TRSM model has been adapted in the full-scale training simulator of Qinshan Nuclear Power Plant 300 MW unit to simulate the thermal-hydraulic performance of the NSSS. The simulation results of a cold leg LOCA and a steam generator tube rupture (SGTR) accident are presented

OPERATOR NORM INEQUALITIES BETWEEN TENSOR UNFOLDINGS ON THE PARTITION LATTICE.

Science.gov (United States)

Wang, Miaoyan; Duc, Khanh Dao; Fischer, Jonathan; Song, Yun S

2017-05-01

Interest in higher-order tensors has recently surged in data-intensive fields, with a wide range of applications including image processing, blind source separation, community detection, and feature extraction. A common paradigm in tensor-related algorithms advocates unfolding (or flattening) the tensor into a matrix and applying classical methods developed for matrices. Despite the popularity of such techniques, how the functional properties of a tensor changes upon unfolding is currently not well understood. In contrast to the body of existing work which has focused almost exclusively on matricizations, we here consider all possible unfoldings of an order- k tensor, which are in one-to-one correspondence with the set of partitions of {1, …, k }. We derive general inequalities between the l p -norms of arbitrary unfoldings defined on the partition lattice. In particular, we demonstrate how the spectral norm ( p = 2) of a tensor is bounded by that of its unfoldings, and obtain an improved upper bound on the ratio of the Frobenius norm to the spectral norm of an arbitrary tensor. For specially-structured tensors satisfying a generalized definition of orthogonal decomposability, we prove that the spectral norm remains invariant under specific subsets of unfolding operations.

Review of unfolding methods for neutron flux dosimetry

International Nuclear Information System (INIS)

Stallmann, F.W.; Kam, F.B.K.

1975-01-01

The primary method in reactor dosimetry is the foil activation technique. To translate the activation measurements into neutron fluxes, a special data processing technique called unfolding is needed. Some general observations about the problems and the reliability of this approach to reactor dosimetry are presented. Current unfolding methods are reviewed. 12 references. (auth)

Deep Unfolding for Topic Models.

Science.gov (United States)

Chien, Jen-Tzung; Lee, Chao-Hsi

2018-02-01

Deep unfolding provides an approach to integrate the probabilistic generative models and the deterministic neural networks. Such an approach is benefited by deep representation, easy interpretation, flexible learning and stochastic modeling. This study develops the unsupervised and supervised learning of deep unfolded topic models for document representation and classification. Conventionally, the unsupervised and supervised topic models are inferred via the variational inference algorithm where the model parameters are estimated by maximizing the lower bound of logarithm of marginal likelihood using input documents without and with class labels, respectively. The representation capability or classification accuracy is constrained by the variational lower bound and the tied model parameters across inference procedure. This paper aims to relax these constraints by directly maximizing the end performance criterion and continuously untying the parameters in learning process via deep unfolding inference (DUI). The inference procedure is treated as the layer-wise learning in a deep neural network. The end performance is iteratively improved by using the estimated topic parameters according to the exponentiated updates. Deep learning of topic models is therefore implemented through a back-propagation procedure. Experimental results show the merits of DUI with increasing number of layers compared with variational inference in unsupervised as well as supervised topic models.

Contact Thermal Analysis and Wear Simulation of a Brake Block

Directory of Open Access Journals (Sweden)

Nándor Békési

2013-01-01

Full Text Available The present paper describes an experimental test and a coupled contact-thermal-wear analysis of a railway wheel/brake block system through the braking process. During the test, the friction, the generated heat, and the wear were evaluated. It was found that the contact between the brake block and the wheel occurs in relatively small and slowly moving hot spots, caused by the wear and the thermal effects. A coupled simulation method was developed including numerical frictional contact, transient thermal and incremental wear calculations. In the 3D simulation, the effects of the friction, the thermal expansion, the wear, and the temperature-dependent material properties were also considered. A good agreement was found between the results of the test and the calculations, both for the thermal and wear results. The proposed method is suitable for modelling the slowly oscillating wear caused by the thermal expansions in the contact area.

A broadband gamma-ray spectrometry using novel unfolding algorithms for characterization of laser wakefield-generated betatron radiation

Energy Technology Data Exchange (ETDEWEB)

Jeon, Jong Ho, E-mail: jhjeon07@ibs.re.kr; Nakajima, Kazuhisa, E-mail: naka115@dia-net.ne.jp; Pathak, Vishwa Bandhu; Cho, Myung Hoon; Yoo, Byung Ju; Shin, Kang Woo [Center for Relativistic Laser Science, Institute for Basic Science (IBS), Gwangju 500-712 (Korea, Republic of); Kim, Hyung Taek; Sung, Jae Hee; Lee, Seung Ku; Choi, Il Woo [Center for Relativistic Laser Science, Institute for Basic Science (IBS), Gwangju 500-712 (Korea, Republic of); Advanced Photonics Research Institute, GIST, Gwangju 500-712 (Korea, Republic of); Rhee, Yong Joo [Nuclear Data Center, Korea Atomic Energy Research Institute, Daejeon 305-353 (Korea, Republic of); Shin, Jung Hun; Jo, Sung Ha [Advanced Photonics Research Institute, GIST, Gwangju 500-712 (Korea, Republic of); Hojbota, Calin; Cho, Byeoung Ick; Nam, Chang Hee [Center for Relativistic Laser Science, Institute for Basic Science (IBS), Gwangju 500-712 (Korea, Republic of); Department of Physics and Photon Science, GIST, Gwangju 500-712 (Korea, Republic of)

2015-12-15

We present a high-flux, broadband gamma-ray spectrometry capable of characterizing the betatron radiation spectrum over the photon energy range from 10 keV to 20 MeV with respect to the peak photon energy, spectral bandwidth, and unique discrimination from background radiations, using a differential filtering spectrometer and the unfolding procedure based on the Monte Carlo code GEANT4. These properties are experimentally verified by measuring betatron radiation from a cm-scale laser wakefield accelerator (LWFA) driven by a 1-PW laser, using a differential filtering spectrometer consisting of a 15-filter and image plate stack. The gamma-ray spectra were derived by unfolding the photostimulated luminescence (PSL) values recorded on the image plates, using the spectrometer response matrix modeled with the Monte Carlo code GEANT4. The accuracy of unfolded betatron radiation spectra was assessed by unfolding the test PSL data simulated with GEANT4, showing an ambiguity of less than 20% and clear discrimination from the background radiation with less than 10%. The spectral analysis of betatron radiation from laser wakefield-accelerated electron beams with energies up to 3 GeV revealed radiation spectra characterized by synchrotron radiation with the critical photon energy up to 7 MeV. The gamma-ray spectrometer and unfolding method presented here facilitate an in-depth understanding of betatron radiation from LWFA process and a novel radiation source of high-quality photon beams in the MeV regime.

Advances in Integrated Vehicle Thermal Management and Numerical Simulation

Directory of Open Access Journals (Sweden)

Yan Wang

2017-10-01

Full Text Available With the increasing demands for vehicle dynamic performance, economy, safety and comfort, and with ever stricter laws concerning energy conservation and emissions, vehicle power systems are becoming much more complex. To pursue high efficiency and light weight in automobile design, the power system and its vehicle integrated thermal management (VITM system have attracted widespread attention as the major components of modern vehicle technology. Regarding the internal combustion engine vehicle (ICEV, its integrated thermal management (ITM mainly contains internal combustion engine (ICE cooling, turbo-charged cooling, exhaust gas recirculation (EGR cooling, lubrication cooling and air conditioning (AC or heat pump (HP. As for electric vehicles (EVs, the ITM mainly includes battery cooling/preheating, electric machines (EM cooling and AC or HP. With the rational effective and comprehensive control over the mentioned dynamic devices and thermal components, the modern VITM can realize collaborative optimization of multiple thermodynamic processes from the aspect of system integration. Furthermore, the computer-aided calculation and numerical simulation have been the significant design methods, especially for complex VITM. The 1D programming can correlate multi-thermal components and the 3D simulating can develop structuralized and modularized design. Additionally, co-simulations can virtualize simulation of various thermo-hydraulic behaviors under the vehicle transient operational conditions. This article reviews relevant researching work and current advances in the ever broadening field of modern vehicle thermal management (VTM. Based on the systematic summaries of the design methods and applications of ITM, future tasks and proposals are presented. This article aims to promote innovation of ITM, strengthen the precise control and the performance predictable ability, furthermore, to enhance the level of research and development (R&D.

The simulation of transients in thermal plant. Part II: Applications

International Nuclear Information System (INIS)

Morini, G.L.; Piva, S.

2008-01-01

This paper deals with the simulation of the transients of thermal plant with control systems. In the companion paper forming part I of this article [G.L. Morini, S. Piva, The simulation of transients in thermal plant. Part I: Mathematical model, Applied Thermal Engineering 27 (2007) 2138-2144] it has been described how a 'thermal-library' of customised blocks can be built and used, in an intuitive way, to study the transients of any kind of thermal plant. Each component of plant such as valves, boilers, and pumps, is represented by a single block. In this paper, the 'thermal-library' approach is demonstrated by the analysis of the dynamic behaviour of a central heating plant of a typical apartment house during a sinusoidal variation of the external temperature. A comparison of the behaviour of such a plant with three way valve working either in flow rate or in temperature control, is presented and discussed. Finally, the results show the delaying effect of the thermal capacity of the building on the performance of the control system

Influence of cross-section structure on unfolded neutron spectra

International Nuclear Information System (INIS)

Ertek, C.; Vlasov, M.F.; Cross, B.; Smith, P.M.

1979-01-01

The influence of cross-section structure on neutron spectra unfolded by multiple foil activation technique, SAND-II case, has been studied. For three reactions with evident structure in neutron cross-section above threshold: 27Al(n,α)24Na, 31P(n,p)31Si and 32S(n,p)32P, two remarkably different sets of evaluated data were selected from the available evaluations; one set of data was ''smooth'', the structure having been averaged over by a smooth curve; the other set was ''sharp'' with structure given in detail. These data were used in unfolding procedure together with other reactions, the same in both cases (as well as input spectra and measured reaction rates). It was found that during unfolding calculations less iteration steps were needed to unfold the neutron flux spectrum with the set of ''sharp'' data. In case of ''smooth'' data it was difficult to obtain an agreement between measured and calculated activity values even by increasing the number of iteration steps. Contrary to expectations, considerable deformation of unfolded neutron flux spectrum has been observed in the case of the ''smooth'' data set. (author)

Combined simulation of energy and thermal management for an electric vehicle

Energy Technology Data Exchange (ETDEWEB)

Mohrmann, Bjoern; Jeck, Peter [Institut fuer Kraftfahrzeuge Aachen (Germany); Simon, Carsten [fortiss GmbH, Muenchen (Germany); Ungermann, Jochen [Audi AG, Ingolstadt (Germany)

2012-11-01

The project eperformance, which is funded by the BMBF, is conducted by project partners from RWTH Aachen, Audi, Bosch Engineering and fortiss GmbH, in order to demonstrate the concept of an electric vehicle on the basis of a holistic development approach. To support this, several simulation platforms come into use, i.e. CFD Simulation for cooling concepts, electromagnetic simulations for electric machine design, physical simulation of cooling circuits as well as vehicle mechanics and controller design. To develop an energy efficient vehicle management, some of these simulation domains have to be combined, to simulate interdependencies between for example usage of high-voltage batteries, their thermal response and the impact for controller strategies. Within the project it was decided to use the Tool TISC (TLK Inter Software Connector) to combine as well a physical model, based on Modelica/Dymola to simulate thermal behaviours of components with a longitudinal vehicle model and a controller model, both based in MATLAB/Simulink. Advantages of such a coupled simulation are the re-usability of existing models in both tools with their tool-specific benefits as well as the possibility to cluster the models on different computers. The article will explain how the combined simulation is set up and parameterized, and will show two use cases: the thermal management of the two independent battery systems of the demonstrator vehicle and the torque distribution on the three electric machines in the vehicle, depending on the drive situation and the thermal state of the machines. (orig)

A Temperature-Dependent Thermal Model of IGBT Modules Suitable for Circuit-Level Simulations

DEFF Research Database (Denmark)

Wu, Rui; Wang, Huai; Pedersen, Kristian Bonderup

2016-01-01

A basic challenge in the IGBT transient simulation study is to obtain the realistic junction temperature, which demands not only accurate electrical simulations but also precise thermal impedance. This paper proposed a transient thermal model for IGBT junction temperature simulations during short...

Protein unfolding versus β-sheet separation in spider silk nanocrystals

International Nuclear Information System (INIS)

Alam, Parvez

2014-01-01

In this communication a mechanism for spider silk strain hardening is proposed. Shear failure of β-sheet nanocrystals is the first failure mode that gives rise to the creation of smaller nanocrystals, which are of higher strength and stiffness. β-sheet unfolding requires more energy than nanocrystal separation in a shear mode of failure. As a result, unfolding occurs after the nanocrystals separate in shear. β-sheet unfolding yields a secondary strain hardening effect once the β-sheet conformation is geometrically stable and acts like a unidirectional fibre in a fibre reinforced composite. The mechanism suggested herein is based on molecular dynamics calculations of residual inter-β-sheet separation strengths against residual intra-β-sheet unfolding strengths. (paper)

Thermal properties of graphene from path-integral simulations

Science.gov (United States)

Herrero, Carlos P.; Ramírez, Rafael

2018-03-01

Thermal properties of graphene monolayers are studied by path-integral molecular dynamics simulations, which take into account the quantization of vibrational modes in the crystalline membrane and allow one to consider anharmonic effects in these properties. This system was studied at temperatures in the range from 12 to 2000 K and zero external stress, by describing the interatomic interactions through the LCBOPII effective potential. We analyze the internal energy and specific heat and compare the results derived from the simulations with those yielded by a harmonic approximation for the vibrational modes. This approximation turns out to be rather precise up to temperatures of about 400 K. At higher temperatures, we observe an influence of the elastic energy due to the thermal expansion of the graphene sheet. Zero-point and thermal effects on the in-plane and "real" surface of graphene are discussed. The thermal expansion coefficient α of the real area is found to be positive at all temperatures, in contrast to the expansion coefficient αp of the in-plane area, which is negative at low temperatures and becomes positive for T ≳ 1000 K.

Thermal shale fracturing simulation using the Cohesive Zone Method (CZM)

KAUST Repository

Enayatpour, Saeid; van Oort, Eric; Patzek, Tadeusz

2018-01-01

Extensive research has been conducted over the past two decades to improve hydraulic fracturing methods used for hydrocarbon recovery from tight reservoir rocks such as shales. Our focus in this paper is on thermal fracturing of such tight rocks to enhance hydraulic fracturing efficiency. Thermal fracturing is effective in generating small fractures in the near-wellbore zone - or in the vicinity of natural or induced fractures - that may act as initiation points for larger fractures. Previous analytical and numerical results indicate that thermal fracturing in tight rock significantly enhances rock permeability, thereby enhancing hydrocarbon recovery. Here, we present a more powerful way of simulating the initiation and propagation of thermally induced fractures in tight formations using the Cohesive Zone Method (CZM). The advantages of CZM are: 1) CZM simulation is fast compared to similar models which are based on the spring-mass particle method or Discrete Element Method (DEM); 2) unlike DEM, rock material complexities such as scale-dependent failure behavior can be incorporated in a CZM simulation; 3) CZM is capable of predicting the extent of fracture propagation in rock, which is more difficult to determine in a classic finite element approach. We demonstrate that CZM delivers results for the challenging fracture propagation problem of similar accuracy to the eXtended Finite Element Method (XFEM) while reducing complexity and computational effort. Simulation results for thermal fracturing in the near-wellbore zone show the effect of stress anisotropy in fracture propagation in the direction of the maximum horizontal stress. It is shown that CZM can be used to readily obtain the extent and the pattern of induced thermal fractures.

Thermal shale fracturing simulation using the Cohesive Zone Method (CZM)

KAUST Repository

Enayatpour, Saeid

2018-05-17

Extensive research has been conducted over the past two decades to improve hydraulic fracturing methods used for hydrocarbon recovery from tight reservoir rocks such as shales. Our focus in this paper is on thermal fracturing of such tight rocks to enhance hydraulic fracturing efficiency. Thermal fracturing is effective in generating small fractures in the near-wellbore zone - or in the vicinity of natural or induced fractures - that may act as initiation points for larger fractures. Previous analytical and numerical results indicate that thermal fracturing in tight rock significantly enhances rock permeability, thereby enhancing hydrocarbon recovery. Here, we present a more powerful way of simulating the initiation and propagation of thermally induced fractures in tight formations using the Cohesive Zone Method (CZM). The advantages of CZM are: 1) CZM simulation is fast compared to similar models which are based on the spring-mass particle method or Discrete Element Method (DEM); 2) unlike DEM, rock material complexities such as scale-dependent failure behavior can be incorporated in a CZM simulation; 3) CZM is capable of predicting the extent of fracture propagation in rock, which is more difficult to determine in a classic finite element approach. We demonstrate that CZM delivers results for the challenging fracture propagation problem of similar accuracy to the eXtended Finite Element Method (XFEM) while reducing complexity and computational effort. Simulation results for thermal fracturing in the near-wellbore zone show the effect of stress anisotropy in fracture propagation in the direction of the maximum horizontal stress. It is shown that CZM can be used to readily obtain the extent and the pattern of induced thermal fractures.

The Effect of Ethylene Glycol, Glycine Betaine, and Urea on Lysozyme Thermal Stability

Science.gov (United States)

Schwinefus, Jeffrey J.; Leslie, Elizabeth J.; Nordstrom, Anna R.

2010-01-01

The four-week student project described in this article is an extension of protein thermal denaturation experiments to include effects of added cosolutes ethylene glycol, glycine betaine, and urea on the unfolding of lysozyme. The transition temperatures and van't Hoff enthalpies for unfolding are evaluated for six concentrations of each cosolute,…

The l z ( p ) * Person-Fit Statistic in an Unfolding Model Context.

Science.gov (United States)

Tendeiro, Jorge N

2017-01-01

Although person-fit analysis has a long-standing tradition within item response theory, it has been applied in combination with dominance response models almost exclusively. In this article, a popular log likelihood-based parametric person-fit statistic under the framework of the generalized graded unfolding model is used. Results from a simulation study indicate that the person-fit statistic performed relatively well in detecting midpoint response style patterns and not so well in detecting extreme response style patterns.

Energy improvement of a conventional dwelling in Argentina through thermal simulation

Energy Technology Data Exchange (ETDEWEB)

Filippin, C. [CONICET-CC302, Santa Rosa 6300, La Pampa (Argentina); Flores Larsen, S. [INENCO-Instituto de Investigaciones en Energias No Convencionales, Universidad Nacional de Salta, CONICET, Avda. Bolivia 5150, CP 4400 Salta Capital (Argentina); Lopez Gay, E.

2008-10-15

This paper analyses the design, technology, thermal behaviour, and energy consumption of both a conventional and a refurbished dwelling located in a region with a temperate-cold climate in central Argentina. The thermal behaviour and the energy consumption of the conventional building were monitored during winter. The experimental data were analysed and included in a simulation of the transient thermal behaviour of the house. Measurements and simulation were in agreement, showing a mean deviation below 0.5{sup o}C. To reduce the heating and cooling loads, the dwelling was refurbished and its thermal behaviour was studied through a computer simulation, for the critical seasons (winter and summer) and for two occupancy schedules (with and without inhabitants). The refurbishment included passive solar heating, shading, and an insulated envelope. These successful changes allowed energy savings of 66% and 52% for winter and summer, respectively. (author)

Equipping simulators with an advanced thermal hydraulics model EDF's experience

International Nuclear Information System (INIS)

Soldermann, R.; Poizat, F.; Sekri, A.; Faydide, B.; Dumas, J.M.

1997-01-01

The development of an accelerated version of the advanced CATHARe-1 thermal hydraulics code designed for EDF training simulators (CATHARE-SIMU) was successfully completed as early as 1991. Its successful integration as the principal model of the SIPA Post-Accident Simulator meant that its use could be extended to full-scale simulators as part of the renovation of the stock of existing simulators. In order to further extend the field of application to accidents occurring in shutdown states requiring action and to catch up with developments in respect of the CATHARE code, EDF initiated the SCAR Project designed to adapt CATHARE-2 to simulator requirements (acceleration, parallelization of the computation and extension of the simulation range). In other respects, the installation of SIPA on workstations means that the authors can envisage the application of this remarkable training facility to the understanding of thermal hydraulics accident phenomena

Evidence of β-sheet structure induced kinetic stability of papain upon thermal and sodium dodecyl sulphate denaturation

Directory of Open Access Journals (Sweden)

Rašković Brankica

2015-01-01

Full Text Available Papain is a protease that consists of α-helical and β-sheet domains which unfold almost independently. Both, papain considerable thermal stability and sodium dodecyl sulphate (SDS resistance have been shown. However, the ability of each domain to unfold upon thermal and SDS denaturation has never been studied. This work shows that fruit papain has slightly higher thermal inactivation resistance when it is compared to stem papain with rather high activation energy (Ea of 223 ± 16 kJmol-1 and Tm50 value of 79 ± 2 °C. SDS resistance of fruit papain was estimated by SDS-PAGE analysis and activity staining. It has been noted that, in the presence of SDS, unless heat energy was applied in order to unfold papain, the protein remained active. Furthermore, it has been proven via Fourier transform infrared spectroscopy (FT-IR that α-helical domain of fruit papain is more prone to unfolding at elevated temperatures and in the presence of SDS then β-sheet rich domain. Thermal denaturation of papain without detergent present led to accelerated formation of aggregation specific intermolecular β-sheets as compared to native protein. Presented results are both, of fundamental and application importance. [Projekat Ministarstva nauke Republike Srbije, br. 172049

Unfolding of cytochrome c immobilized on self-assembled monolayers. An electrochemical study

International Nuclear Information System (INIS)

Monari, Stefano; Ranieri, Antonio; Bortolotti, Carlo Augusto; Peressini, Silvia; Tavagnacco, Claudio; Borsari, Marco

2011-01-01

Highlights: → Denaturation involves intermediate and partially unfolded forms. → An unfolded species displaying the haem with Fe coordinated by two His is observed. → Under unfolding conditions the nature of the SAM influences conformation of protein. → Concentration of the unfolding agent affects redox properties of immobilized protein. - Abstract: The electron transfer (ET) process of progressively unfolded bovine cytochrome c immobilized on different self-assembled monolayers (SAMs) was investigated. Insight is gained on the role of the SAM surface on the functionality of the partially unfolded and non-native forms of the adsorbed protein. Direct electrochemical measurements were performed on cytochrome c adsorbed on mercaptopyridine (MP) and mixed 11-mercapto-1-undecanoic acid/11-mercapto-1-undecanol (MUA/MU) at varying temperature, in the presence of urea as unfolding agent. Under strongly unfolding conditions, a non-native form of cytochrome c, in which the methionine ligand is replaced by a histidine, was observed on both MP and MUA/MU SAMs. The E o ' of the native form, in which the haem is axially coordinated by methionine and histidine, slightly shifts to negative values upon increasing urea concentration. However, the non-native bis-histidinate species shows a much lower E o ' value (by approximately 0.4 V) which is by far enthalpic in origin and largely determined by axial ligand swapping. Analysis of the reduction enthalpies and entropies and of the ET rate constants indicate that the nature of the SAM (hydrophilic or anionic) results in changes in the conformational rearrangement of the cytochrome c under unfolding conditions.

Unfolding of cytochrome c immobilized on self-assembled monolayers. An electrochemical study

Energy Technology Data Exchange (ETDEWEB)

Monari, Stefano; Ranieri, Antonio; Bortolotti, Carlo Augusto; Peressini, Silvia [Department of Chemistry, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena (Italy); Tavagnacco, Claudio [Department of Chemistry, University of Trieste, via Giorgieri 1, 34127 Trieste (Italy); Borsari, Marco, E-mail: marco.borsari@unimore.it [Department of Chemistry, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena (Italy)

2011-08-01

Highlights: > Denaturation involves intermediate and partially unfolded forms. > An unfolded species displaying the haem with Fe coordinated by two His is observed. > Under unfolding conditions the nature of the SAM influences conformation of protein. > Concentration of the unfolding agent affects redox properties of immobilized protein. - Abstract: The electron transfer (ET) process of progressively unfolded bovine cytochrome c immobilized on different self-assembled monolayers (SAMs) was investigated. Insight is gained on the role of the SAM surface on the functionality of the partially unfolded and non-native forms of the adsorbed protein. Direct electrochemical measurements were performed on cytochrome c adsorbed on mercaptopyridine (MP) and mixed 11-mercapto-1-undecanoic acid/11-mercapto-1-undecanol (MUA/MU) at varying temperature, in the presence of urea as unfolding agent. Under strongly unfolding conditions, a non-native form of cytochrome c, in which the methionine ligand is replaced by a histidine, was observed on both MP and MUA/MU SAMs. The E{sup o}' of the native form, in which the haem is axially coordinated by methionine and histidine, slightly shifts to negative values upon increasing urea concentration. However, the non-native bis-histidinate species shows a much lower E{sup o}' value (by approximately 0.4 V) which is by far enthalpic in origin and largely determined by axial ligand swapping. Analysis of the reduction enthalpies and entropies and of the ET rate constants indicate that the nature of the SAM (hydrophilic or anionic) results in changes in the conformational rearrangement of the cytochrome c under unfolding conditions.

Finite-difference time-domain simulation of thermal noise in open cavities

International Nuclear Information System (INIS)

Andreasen, Jonathan; Cao Hui; Taflove, Allen; Kumar, Prem; Cao Changqi

2008-01-01

A numerical model based on the finite-difference time-domain (FDTD) method is developed to simulate thermal noise in open cavities owing to output coupling. The absorbing boundary of the FDTD grid is treated as a blackbody, whose thermal radiation penetrates the cavity in the grid. The calculated amount of thermal noise in a one-dimensional dielectric cavity recovers the standard result of the quantum Langevin equation in the Markovian regime. Our FDTD simulation also demonstrates that in the non-Markovian regime the buildup of the intracavity noise field depends on the ratio of the cavity photon lifetime to the coherence time of thermal radiation. The advantage of our numerical method is that the thermal noise is introduced in the time domain without prior knowledge of cavity modes

Coupled large-eddy simulation of thermal mixing in a T-junction

International Nuclear Information System (INIS)

Kloeren, D.; Laurien, E.

2011-01-01

Analyzing thermal fatigue due to thermal mixing in T-junctions is part of the safety assessment of nuclear power plants. Results of two large-eddy simulations of mixing flow in a T-junction with coupled and adiabatic boundary condition are presented and compared. The temperature difference is set to 100 K, which leads to strong stratification of the flow. The main and the branch pipe intersect horizontally in this simulation. The flow is characterized by steady wavy pattern of stratification and temperature distribution. The coupled solution approach shows highly reduced temperature fluctuations in the near wall region due to thermal inertia of the wall. A conjugate heat transfer approach is necessary in order to simulate unsteady heat transfer accurately for large inlet temperature differences. (author)

Evaluation of uranium dioxide thermal conductivity using molecular dynamics simulations

International Nuclear Information System (INIS)

Kim, Woongkee; Kaviany, Massoud; Shim, J. H.

2014-01-01

It can be extended to larger space, time scale and even real reactor situation with fission product as multi-scale formalism. Uranium dioxide is a fluorite structure with Fm3m space group. Since it is insulator, dominant heat carrier is phonon, rather than electrons. So, using equilibrium molecular dynamics (MD) simulation, we present the appropriate calculation parameters in MD simulation by calculating thermal conductivity and application of it to the thermal conductivity of polycrystal. In this work, we investigate thermal conductivity of uranium dioxide and optimize the parameters related to its process. In this process, called Green Kubo formula, there are two parameters i.e correlation length and sampling interval, which effect on ensemble integration in order to obtain thermal conductivity. Through several comparisons, long correlation length and short sampling interval give better results. Using this strategy, thermal conductivity of poly crystal is obtained and comparison with that of pure crystal is made. Thermal conductivity of poly crystal show lower value that that of pure crystal. In further study, we broaden the study to transport coefficient of radiation damaged structures using molecular dynamics. Although molecular dynamics is tools for treating microscopic scale, most macroscopic issues related to nuclear materials such as voids in fuel materials and weakened mechanical properties by radiation are based on microscopic basis. Thus, research on microscopic scale would be expanded in this field and many hidden mechanism in atomic scales will be revealed via both atomic scale simulations and experiments

The effect of thermal velocities on structure formation in N-body simulations of warm dark matter

Science.gov (United States)

Leo, Matteo; Baugh, Carlton M.; Li, Baojiu; Pascoli, Silvia

2017-11-01

We investigate the impact of thermal velocities in N-body simulations of structure formation in warm dark matter models. Adopting the commonly used approach of adding thermal velocities, randomly selected from a Fermi-Dirac distribution, to the gravitationally-induced velocities of the simulation particles, we compare the matter and velocity power spectra measured from CDM and WDM simulations, in the latter case with and without thermal velocities. This prescription for adding thermal velocities introduces numerical noise into the initial conditions, which influences structure formation. At early times, the noise affects dramatically the power spectra measured from simulations with thermal velocities, with deviations of the order of ~ Script O(10) (in the matter power spectra) and of the order of ~ Script O(102) (in the velocity power spectra) compared to those extracted from simulations without thermal velocities. At late times, these effects are less pronounced with deviations of less than a few percent. Increasing the resolution of the N-body simulation shifts these discrepancies to higher wavenumbers. We also find that spurious haloes start to appear in simulations which include thermal velocities at a mass that is ~3 times larger than in simulations without thermal velocities.

Standard Practice for Solar Simulation for Thermal Balance Testing of Spacecraft

CERN Document Server

American Society for Testing and Materials. Philadelphia

1973-01-01

1.1 Purpose: 1.1.1 The primary purpose of this practice is to provide guidance for making adequate thermal balance tests of spacecraft and components where solar simulation has been determined to be the applicable method. Careful adherence to this practice should ensure the adequate simulation of the radiation environment of space for thermal tests of space vehicles. 1.1.2 A corollary purpose is to provide the proper test environment for systems-integration tests of space vehicles. An accurate space-simulation test for thermal balance generally will provide a good environment for operating all electrical and mechanical systems in their various mission modes to determine interferences within the complete system. Although adherence to this practice will provide the correct thermal environment for this type of test, there is no discussion of the extensive electronic equipment and procedures required to support systems-integration testing. 1.2 Nonapplicability—This practice does not apply to or provide inco...

Simulation of Thermal-hydraulic Process in Reactor of HTR-PM

International Nuclear Information System (INIS)

Zhou Kefeng; Zhou Yangping; Sui Zhe; Ma Yuanle

2014-01-01

This paper provides the physical process in the reactor of High Temperature Gas-cooled Reactor Pebble-bed Module (HTR-PM) and introduces the standard operation conditions. The FORTRAN code developed for the thermal hydraulic module of Full-Scale Simulator (FSS) of HTR-PM is used to simulate two typical operation transients including cold startup process and cold shutdown process. And the results were compared to the safety analysis code, namely TINTE. The good agreement indicates that the code is applicable for simulating the thermal-hydraulic process in reactor of HTR-PM. And for long time transient process, the code shows good stability and convergence. (author)

Spontaneous Unfolding-Refolding of Fibronectin Type III Domains Assayed by Thiol Exchange: THERMODYNAMIC STABILITY CORRELATES WITH RATES OF UNFOLDING RATHER THAN FOLDING.

Science.gov (United States)

Shah, Riddhi; Ohashi, Tomoo; Erickson, Harold P; Oas, Terrence G

2017-01-20

Globular proteins are not permanently folded but spontaneously unfold and refold on time scales that can span orders of magnitude for different proteins. A longstanding debate in the protein-folding field is whether unfolding rates or folding rates correlate to the stability of a protein. In the present study, we have determined the unfolding and folding kinetics of 10 FNIII domains. FNIII domains are one of the most common protein folds and are present in 2% of animal proteins. FNIII domains are ideal for this study because they have an identical seven-strand β-sandwich structure, but they vary widely in sequence and thermodynamic stability. We assayed thermodynamic stability of each domain by equilibrium denaturation in urea. We then assayed the kinetics of domain opening and closing by a technique known as thiol exchange. For this we introduced a buried Cys at the identical location in each FNIII domain and measured the kinetics of labeling with DTNB over a range of urea concentrations. A global fit of the kinetics data gave the kinetics of spontaneous unfolding and refolding in zero urea. We found that the folding rates were relatively similar, ∼0.1-1 s -1 , for the different domains. The unfolding rates varied widely and correlated with thermodynamic stability. Our study is the first to address this question using a set of domains that are structurally homologous but evolved with widely varying sequence identity and thermodynamic stability. These data add new evidence that thermodynamic stability correlates primarily with unfolding rate rather than folding rate. The study also has implications for the question of whether opening of FNIII domains contributes to the stretching of fibronectin matrix fibrils. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Spectroscopic and MD simulation studies on unfolding processes of mitochondrial carbonic anhydrase VA induced by urea.

Science.gov (United States)

Idrees, Danish; Prakash, Amresh; Haque, Md Anzarul; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

2016-09-01

Carbonic anhydrase VA (CAVA) is primarily expressed in the mitochondria and involved in numerous physiological processes including lipogenesis, insulin secretion from pancreatic cells, ureagenesis, gluconeogenesis and neuronal transmission. To understand the biophysical properties of CAVA, we carried out a reversible urea-induced isothermal denaturation at pH 7.0 and 25°C. Spectroscopic probes, [θ]222 (mean residue ellipticity at 222 nm), F344 (Trp-fluorescence emission intensity at 344 nm) and Δε280 (difference absorption at 280 nm) were used to monitor the effect of urea on the structure and stability of CAVA. The urea-induced reversible denaturation curves were used to estimate [Formula: see text], Gibbs free energy in the absence of urea; Cm, the mid-point of the denaturation curve, i.e. molar urea concentration ([urea]) at which ΔGD = 0; and m, the slope (=∂ΔGD/∂[urea]). Coincidence of normalized transition curves of all optical properties suggests that unfolding/refolding of CAVA is a two-state process. We further performed 40 ns molecular dynamics simulation of CAVA to see the dynamics at different urea concentrations. An excellent agreement was observed between in silico and in vitro studies.

Solving inverse problems with the unfolding program TRUEE: Examples in astroparticle physics

International Nuclear Information System (INIS)

Milke, N.; Doert, M.; Klepser, S.; Mazin, D.; Blobel, V.; Rhode, W.

2013-01-01

The unfolding program TRUEE is a software package for the numerical solution of inverse problems. The algorithm was first applied in the FORTRAN 77 program RUN. RUN is an event-based unfolding algorithm which makes use of the Tikhonov regularization. It has been tested and compared to different unfolding applications and stood out with notably stable results and reliable error estimation. TRUEE is a conversion of RUN to C++, which works within the powerful ROOT framework. The program has been extended for more user-friendliness and delivers unfolding results which are identical to RUN. Beside the simplicity of the installation of the software and the generation of graphics, there are new functions, which facilitate the choice of unfolding parameters and observables for the user. In this paper, we introduce the new unfolding program and present its performance by applying it to two exemplary data sets from astroparticle physics, taken with the MAGIC telescopes and the IceCube neutrino detector, respectively.

Design and simulation of a low concentrating photovoltaic/thermal system

International Nuclear Information System (INIS)

Rosell, J.I.; Vallverdu, X.; Lechon, M.A.; Ibanez, M.

2005-01-01

The advantages of photovoltaic/thermal (PV/T) collectors and low solar concentration technologies are combined into a photovoltaic/thermal system to increase the solar energy conversion efficiency. This paper presents a prototype 11X concentration rate and two axis tracking system. The main novelty is the coupling of a linear Fresnel concentrator with a channel photovoltaic/thermal collector. An analytical model to simulate the thermal behaviour of the prototype is proposed and validated. Measured thermal performance of the solar system gives values above 60%. Theoretical analysis confirms that thermal conduction between the PV cells and the absorber plate is a critical parameter

A Fast Electro-Thermal Co-Simulation Modeling Approach for SiC Power MOSFETs

DEFF Research Database (Denmark)

Ceccarelli, Lorenzo; Bahman, Amir Sajjad; Iannuzzo, Francesco

2017-01-01

The purpose of this work is to propose a novel electro-thermal co-simulation approach for the new generation of SiC MOSFETs, by development of a PSpice-based compact and physical SiC MOSFET model including temperature dependency of several parameters and a Simulink-based thermal network. The PSpice...... the FEM simulation of the DUT’s structure, performed in ANSYS Icepack. A MATLAB script is used to process the simulation data and feed the needed settings and parameters back into the simulation. The parameters for a CREE 1.2 kV/30 A SiC MOSFET have been identified and the electro-thermal model has been...

Nuclear Thermal Rocket Element Environmental Simulator (NTREES) Phase II Upgrade Activities

Science.gov (United States)

Emrich, William J.; Moran, Robert P.; Pearson, J. Bose

2013-01-01

To support the on-going nuclear thermal propulsion effort, a state-of-the-art non nuclear experimental test setup has been constructed to evaluate the performance characteristics of candidate fuel element materials and geometries in representative environments. The facility to perform this testing is referred to as the Nuclear Thermal Rocket Element Environment Simulator (NTREES). This device can simulate the environmental conditions (minus the radiation) to which nuclear rocket fuel components will be subjected during reactor operation. Test articles mounted in the simulator are inductively heated in such a manner so as to accurately reproduce the temperatures and heat fluxes which would normally occur as a result of nuclear fission and would be exposed to flowing hydrogen. Initial testing of a somewhat prototypical fuel element has been successfully performed in NTREES and the facility has now been shutdown to allow for an extensive reconfiguration of the facility which will result in a significant upgrade in its capabilities. Keywords: Nuclear Thermal Propulsion, Simulator

Network Unfolding Map by Vertex-Edge Dynamics Modeling.

Science.gov (United States)

Verri, Filipe Alves Neto; Urio, Paulo Roberto; Zhao, Liang

2018-02-01

The emergence of collective dynamics in neural networks is a mechanism of the animal and human brain for information processing. In this paper, we develop a computational technique using distributed processing elements in a complex network, which are called particles, to solve semisupervised learning problems. Three actions govern the particles' dynamics: generation, walking, and absorption. Labeled vertices generate new particles that compete against rival particles for edge domination. Active particles randomly walk in the network until they are absorbed by either a rival vertex or an edge currently dominated by rival particles. The result from the model evolution consists of sets of edges arranged by the label dominance. Each set tends to form a connected subnetwork to represent a data class. Although the intrinsic dynamics of the model is a stochastic one, we prove that there exists a deterministic version with largely reduced computational complexity; specifically, with linear growth. Furthermore, the edge domination process corresponds to an unfolding map in such way that edges "stretch" and "shrink" according to the vertex-edge dynamics. Consequently, the unfolding effect summarizes the relevant relationships between vertices and the uncovered data classes. The proposed model captures important details of connectivity patterns over the vertex-edge dynamics evolution, in contrast to the previous approaches, which focused on only vertex or only edge dynamics. Computer simulations reveal that the new model can identify nonlinear features in both real and artificial data, including boundaries between distinct classes and overlapping structures of data.

Quantification of Uncertainty in Thermal Building Simulation

DEFF Research Database (Denmark)

Brohus, Henrik; Haghighat, F.; Frier, Christian

In order to quantify uncertainty in thermal building simulation stochastic modelling is applied on a building model. An application of stochastic differential equations is presented in Part 1 comprising a general heat balance for an arbitrary number of loads and zones in a building to determine...

Monte Carlo simulation of a coded-aperture thermal neutron camera

International Nuclear Information System (INIS)

Dioszegi, I.; Salwen, C.; Forman, L.

2011-01-01

We employed the MCNPX Monte Carlo code to simulate image formation in a coded-aperture thermal-neutron camera. The camera, developed at Brookhaven National Laboratory (BNL), consists of a 20 x 17 cm"2 active area "3He-filled position-sensitive wire chamber in a cadmium enclosure box. The front of the box is a coded-aperture cadmium mask (at present with three different resolutions). We tested the detector experimentally with various arrangements of moderated point-neutron sources. The purpose of using the Monte Carlo modeling was to develop an easily modifiable model of the device to predict the detector's behavior using different mask patterns, and also to generate images of extended-area sources or large numbers (up to ten) of them, that is important for nonproliferation and arms-control verification, but difficult to achieve experimentally. In the model, we utilized the advanced geometry capabilities of the MCNPX code to simulate the coded aperture mask. Furthermore, the code simulated the production of thermal neutrons from fission sources surrounded by a thermalizer. With this code we also determined the thermal-neutron shadow cast by the cadmium mask; the calculations encompassed fast- and epithermal-neutrons penetrating into the detector through the mask. Since the process of signal production in "3He-filled position-sensitive wire chambers is well known, we omitted this part from our modeling. Simplified efficiency values were used for the three (thermal, epithermal, and fast) neutron-energy regions. Electronic noise and the room's background were included as a uniform irradiation component. We processed the experimental- and simulated-images using identical LabVIEW virtual instruments. (author)

Simulation of adiabatic thermal beams in a periodic solenoidal magnetic focusing field

Directory of Open Access Journals (Sweden)

T. J. Barton

2012-12-01

Full Text Available Self-consistent particle-in-cell simulations are performed to verify earlier theoretical predictions of adiabatic thermal beams in a periodic solenoidal magnetic focusing field [K. R. Samokhvalova, J. Zhou, and C. Chen, Phys. Plasmas 14, 103102 (2007PHPAEN1070-664X10.1063/1.2779281; J. Zhou, K. R. Samokhvalova, and C. Chen, Phys. Plasmas 15, 023102 (2008PHPAEN1070-664X10.1063/1.2837891]. In particular, results are obtained for adiabatic thermal beams that do not rotate in the Larmor frame. For such beams, the theoretical predictions of the rms beam envelope, the conservations of the rms thermal emittances, the adiabatic equation of state, and the Debye length are verified in the simulations. Furthermore, the adiabatic thermal beam is found be stable in the parameter regime where the simulations are performed.

TO THE QUESTION ABOUT THE SIMULATION OF TURBULENT THERMAL FLOWS

Directory of Open Access Journals (Sweden)

2016-01-01

Full Text Available The main purpose of this work was the simulation of turbulent thermal flows, which is aimed at improving the visualization and the modeling of the flow fields of wind flows, which are necessary for aviation. The physical-mathematical model of gas flow in thermal is proposed on the basis of thermodynamic model and dynamic model under the assumption that the condensation energy, when the movement of the thermal is upward, becomes the turbulent fluctuations. A thermal is an air mass, which goes up and is capable to intermix with ambient air. In the work the thermodynamic model of thermal is presented, the equations and the system of equations are derived, that describe the main characteristics of wind flow, which are required for the modeling of airflows. The generation of vertical turbulent gust with von Karman spectrum is shown. The basic assumption in the construction of the dynamic model of generation was that the energy, which is stood out in the thermal due to the condensation of steam, is converted into the energy of turbulent pulsations. Some examples of numerical simulation are given in the article. The visualizations of the generation of the vertical velocity of random wind gust are given depending on the size of the considered space and depending on the pitch of cell partition. The analysis and comparison of the obtained results of the calculation are presented. The conducted studies are aimed at the simulation of the atmospheric background and atmospheric processes and, in the final result, at the increasing of flight safety.

The Development of Dispatcher Training Simulator in a Thermal Energy Generation System

Science.gov (United States)

Hakim, D. L.; Abdullah, A. G.; Mulyadi, Y.; Hasan, B.

2018-01-01

A dispatcher training simulator (DTS) is a real-time Human Machine Interface (HMI)-based control tool that is able to visualize industrial control system processes. The present study was aimed at developing a simulator tool for boilers in a thermal power station. The DTS prototype was designed using technical data of thermal power station boilers in Indonesia. It was then designed and implemented in Wonderware Intouch 10. The resulting simulator came with component drawing, animation, control display, alarm system, real-time trend, historical trend. This application used 26 tagnames and was equipped with a security system. The test showed that the principles of real-time control worked well. It is expected that this research could significantly contribute to the development of thermal power station, particularly in terms of its application as a training simulator for beginning dispatchers.

Micromagnetic simulation of thermally activated switching in fine particles

International Nuclear Information System (INIS)

Scholz, Werner; Schrefl, Thomas; Fidler, J.

2001-01-01

Effects of thermal activation are included in micromagnetic simulations by adding a random thermal field to the effective magnetic field. As a result, the Landau-Lifshitz equation is converted into a stochastic differential equation of Langevin type with multiplicative noise. The Stratonovich interpretation of the stochastic Landau-Lifshitz equation leads to the correct thermal equilibrium properties. The proper generalization of Taylor expansions to stochastic calculus gives suitable time integration schemes. For a single rigid magnetic moment the thermal equilibrium properties are investigated. It is found, that the Heun scheme is a good compromise between numerical stability and computational complexity. Small cubic and spherical ferromagnetic particles are studied

Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding.

Science.gov (United States)

Nagpal, Suhani; Tiwari, Satyam; Mapa, Koyeli; Thukral, Lipi

2015-01-01

Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central "hubs". Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates.

Dry molten globule intermediates and the mechanism of protein unfolding.

Science.gov (United States)

Baldwin, Robert L; Frieden, Carl; Rose, George D

2010-10-01

New experimental results show that either gain or loss of close packing can be observed as a discrete step in protein folding or unfolding reactions. This finding poses a significant challenge to the conventional two-state model of protein folding. Results of interest involve dry molten globule (DMG) intermediates, an expanded form of the protein that lacks appreciable solvent. When an unfolding protein expands to the DMG state, side chains unlock and gain conformational entropy, while liquid-like van der Waals interactions persist. Four unrelated proteins are now known to form DMGs as the first step of unfolding, suggesting that such an intermediate may well be commonplace in both folding and unfolding. Data from the literature show that peptide amide protons are protected in the DMG, indicating that backbone structure is intact despite loss of side-chain close packing. Other complementary evidence shows that secondary structure formation provides a major source of compaction during folding. In our model, the major free-energy barrier separating unfolded from native states usually occurs during the transition between the unfolded state and the DMG. The absence of close packing at this barrier provides an explanation for why phi-values, derived from a Brønsted-Leffler plot, depend primarily on structure at the mutational site and not on specific side-chain interactions. The conventional two-state folding model breaks down when there are DMG intermediates, a realization that has major implications for future experimental work on the mechanism of protein folding. 2010 Wiley-Liss, Inc.

CalFitter: a web server for analysis of protein thermal denaturation data.

Science.gov (United States)

Mazurenko, Stanislav; Stourac, Jan; Kunka, Antonin; Nedeljkovic, Sava; Bednar, David; Prokop, Zbynek; Damborsky, Jiri

2018-05-14

Despite significant advances in the understanding of protein structure-function relationships, revealing protein folding pathways still poses a challenge due to a limited number of relevant experimental tools. Widely-used experimental techniques, such as calorimetry or spectroscopy, critically depend on a proper data analysis. Currently, there are only separate data analysis tools available for each type of experiment with a limited model selection. To address this problem, we have developed the CalFitter web server to be a unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. The server allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways. The server provides an interactive and easy-to-use interface that allows users to directly analyse input datasets and simulate modelled output based on the model parameters. CalFitter web server is available free at https://loschmidt.chemi.muni.cz/calfitter/.

Experiments and numerical simulations of fluctuating thermal stratification in a branch pipe

Energy Technology Data Exchange (ETDEWEB)

Nakamura, Akira; Murase, Michio; Sasaki, Toru [Inst. of Nuclear Safety System Inc., Mihama, Fukui (Japan); Takenaka, Nobuyuki; Hamatani, Daisuke [Kobe Univ. (Japan)

2002-09-01

Many pipes branch off from the main pipe in plants. When the main flow in the main pipe is hotter than a branch pipe that branches off downward, the hot water penetrates into the branch pipe with the cavity flow that is induced by the main flow and causes thermal stratification. If the interface of the stratification fluctuates in an occluded branch pipe, thermal fatigue may occur in pipe wall. Some experiments and numerical simulations were conducted to elucidate the mechanism of this fluctuating thermal stratification. The vortex structures were observed in the experiments of straight or bent branch pipes. When the main flow was heated and the thermal stratification interface was at the elbow, a ''burst'' phenomenon occurred in the interface in connection with large heat fluctuation. The effects of pipe shape on the length of penetration were investigated in order to modify simulation conditions. The vortex structures and the fluctuating thermal stratification at elbow in the numerical simulation showed good agreement with experiments. (author)

Distribution, transition and thermodynamic stability of protein conformations in the denaturant-induced unfolding of proteins.

Science.gov (United States)

Bian, Liujiao; Ji, Xu

2014-01-01

Extensive and intensive studies on the unfolding of proteins require appropriate theoretical model and parameter to clearly illustrate the feature and characteristic of the unfolding system. Over the past several decades, four approaches have been proposed to describe the interaction between proteins and denaturants, but some ambiguity and deviations usually occur in the explanation of the experimental data. In this work, a theoretical model was presented to show the dependency of the residual activity ratio of the proteins on the molar denaturant concentration. Through the characteristic unfolding parameters ki and Δmi in this model, the distribution, transition and thermodynamic stability of protein conformations during the unfolding process can be quantitatively described. This model was tested with the two-state unfolding of bovine heart cytochrome c and the three-state unfolding of hen egg white lysozyme induced by both guanidine hydrochloride and urea, the four-state unfolding of bovine carbonic anhydrase b induced by guanidine hydrochloride and the unfolding of some other proteins induced by denaturants. The results illustrated that this model could be used accurately to reveal the distribution and transition of protein conformations in the presence of different concentrations of denaturants and to evaluate the unfolding tendency and thermodynamic stability of different conformations. In most denaturant-induced unfolding of proteins, the unfolding became increasingly hard in next transition step and the proteins became more unstable as they attained next successive stable conformation. This work presents a useful method for people to study the unfolding of proteins and may be used to describe the unfolding and refolding of other biopolymers induced by denaturants, inducers, etc.

Thermal boundary resistance at Si/Ge interfaces by molecular dynamics simulation

Directory of Open Access Journals (Sweden)

Tianzhuo Zhan

2015-04-01

Full Text Available In this study, we investigated the temperature dependence and size effect of the thermal boundary resistance at Si/Ge interfaces by non-equilibrium molecular dynamics (MD simulations using the direct method with the Stillinger-Weber potential. The simulations were performed at four temperatures for two simulation cells of different sizes. The resulting thermal boundary resistance decreased with increasing temperature. The thermal boundary resistance was smaller for the large cell than for the small cell. Furthermore, the MD-predicted values were lower than the diffusion mismatch model (DMM-predicted values. The phonon density of states (DOS was calculated for all the cases to examine the underlying nature of the temperature dependence and size effect of thermal boundary resistance. We found that the phonon DOS was modified in the interface regions. The phonon DOS better matched between Si and Ge in the interface region than in the bulk region. Furthermore, in interface Si, the population of low-frequency phonons was found to increase with increasing temperature and cell size. We suggest that the increasing population of low-frequency phonons increased the phonon transmission coefficient at the interface, leading to the temperature dependence and size effect on thermal boundary resistance.

Thermal-hydraulic simulation and analysis of Research Reactor Cooling Systems

International Nuclear Information System (INIS)

EL Khatib, H.H.A.

2013-01-01

The objective of the present study is to formulate a model to simulate the thermal hydraulic behavior of integrated cooling system in a typical material testing reactor (MTR) under loss of ultimate heat sink, the model involves three interactively coupled sub-models for reactor core, heat exchanger and cooling tower. The developed model predicts the temperature profiles in addition it predicts inlet and outlet temperatures of the hot and cold stream as well as the heat exchangers and cooling tower. The model is validated against PARET code for steady-state operation and also verified by the reactor operational records, and then the model is used to simulate the thermal-hydraulic behavior of the reactor under a loss of ultimate heat sink. The simulation is performed for two operational regimes named regime I of (11 MW) thermal power and three operated cooling tower cells and regime II of (22 MW) thermal power and six operated cooling tower cells. In regime I, the simulation is performed for 1, 2 and 3 cooling tower failed cells while in regime II, it is performed for 1, 2, 3, 4, 5 and 6 cooling tower failed cells. The safety action is conducted by the reactor protection system (RPS) named power reduction safety action, it is triggered to decrease the reactor power by amount of 20% of the present power when the water inlet temperature to the core reaches 43 degree C and a scram (emergency shutdown) is triggered in case of the inlet temperature reaches 44 degree C. The model results are analyzed and discussed. The temperature profiles of fuel, clad and coolant are predicted during transient where its maximum values are far from thermal hydraulic limits.

Application of long-range order to predict unfolding rates of two-state proteins.

Science.gov (United States)

Harihar, B; Selvaraj, S

2011-03-01

Predicting the experimental unfolding rates of two-state proteins and models describing the unfolding rates of these proteins is quite limited because of the complexity present in the unfolding mechanism and the lack of experimental unfolding data compared with folding data. In this work, 25 two-state proteins characterized by Maxwell et al. (Protein Sci 2005;14:602–616) using a consensus set of experimental conditions were taken, and the parameter long-range order (LRO) derived from their three-dimensional structures were related with their experimental unfolding rates ln(k(u)). From the total data set of 30 proteins used by Maxwell et al. (Protein Sci 2005;14:602–616), five slow-unfolding proteins with very low unfolding rates were considered to be outliers and were not included in our data set. Except all beta structural class, LRO of both the all-alpha and mixed-class proteins showed a strong inverse correlation of r = -0.99 and -0.88, respectively, with experimental ln(k(u)). LRO shows a correlation of -0.62 with experimental ln(k(u)) for all-beta proteins. For predicting the unfolding rates, a simple statistical method has been used and linear regression equations were developed for individual structural classes of proteins using LRO, and the results obtained showed a better agreement with experimental results. Copyright © 2010 Wiley-Liss, Inc.

Regularization and error assignment to unfolded distributions

CERN Document Server

Zech, Gunter

2011-01-01

The commonly used approach to present unfolded data only in graphical formwith the diagonal error depending on the regularization strength is unsatisfac-tory. It does not permit the adjustment of parameters of theories, the exclusionof theories that are admitted by the observed data and does not allow the com-bination of data from different experiments. We propose fixing the regulariza-tion strength by a p-value criterion, indicating the experimental uncertaintiesindependent of the regularization and publishing the unfolded data in additionwithout regularization. These considerations are illustrated with three differentunfolding and smoothing approaches applied to a toy example.

Engineering-Based Thermal CFD Simulations on Massive Parallel Systems

KAUST Repository

Frisch, Jérôme

2015-05-22

The development of parallel Computational Fluid Dynamics (CFD) codes is a challenging task that entails efficient parallelization concepts and strategies in order to achieve good scalability values when running those codes on modern supercomputers with several thousands to millions of cores. In this paper, we present a hierarchical data structure for massive parallel computations that supports the coupling of a Navier–Stokes-based fluid flow code with the Boussinesq approximation in order to address complex thermal scenarios for energy-related assessments. The newly designed data structure is specifically designed with the idea of interactive data exploration and visualization during runtime of the simulation code; a major shortcoming of traditional high-performance computing (HPC) simulation codes. We further show and discuss speed-up values obtained on one of Germany’s top-ranked supercomputers with up to 140,000 processes and present simulation results for different engineering-based thermal problems.

Power cables thermal protection by interval simulation of imprecise dynamical systems

Energy Technology Data Exchange (ETDEWEB)

Bontempi, G. [Universite Libre de Brussels (Belgium). Dept. d' Informatique; Vaccaro, A.; Villacci, D. [Universita del Sannio Benevento (Italy). Dept. of Engineering

2004-11-01

The embedding of advanced simulation techniques in power cables enables improved thermal protection because of higher accuracy, adaptiveness and. flexibility. In particular, they make possible (i) the accurate solution of differential equations describing the cables thermal dynamics and (ii) the adoption of the resulting solution in the accomplishment of dedicated protective functions. However, the use of model-based protective systems is exposed to the uncertainty affecting some model components (e.g. weather along the line route, thermophysical properties of the soil, cable parameters). When uncertainty can be described in terms of probability distribution, well-known techniques, such as Monte Carlo, are used to simulate the system behaviour. On the other hand, when the description of uncertainty in probabilistic terms is unfeasible or problematic, nonprobabilistic alternatives should be taken into consideration. This paper will discuss and compare three interval-based techniques as alternatives to probabilistic methods in the simulation of power cable dynamics. The experimental session will assess the interval-based approaches by simulating the thermal behaviour of medium voltage power cables.(author)

Simulation of Thermal Hydraulic at Supercritical Pressures with APROS

Energy Technology Data Exchange (ETDEWEB)

Kurki, Joona [VTT Technical Research Centre of Finland, P.O. Box 1000, FI02044 VTT (Finland)

2008-07-01

The proposed concepts for the fourth generation of nuclear reactors include a reactor operating with water at thermodynamically supercritical state, the Supercritical Water Reactor (SCWR). For the design and safety demonstrations of such a reactor, the possibility to accurately simulate the thermal hydraulics of the supercritical coolant is an absolute prerequisite. For this purpose, the one-dimensional two-phase thermal hydraulics solution of APROS process simulation software was developed to function at the supercritical pressure region. Software modifications included the redefinition of some parameters that have physical significance only at the subcritical pressures, improvement of the steam tables, and addition of heat transfer and friction correlations suitable for the supercritical pressure region. (author)

The effects of crowding agents Dextran-70k and PEG-8k on actin structure and unfolding reaction

Science.gov (United States)

Gagarskaia, Iuliia A.; Povarova, Olga I.; Uversky, Vladimir N.; Kuznetsova, Irina M.; Turoverov, Konstantin K.

2017-07-01

Recently, an increasing number of studies on proteins' structure, stability and folding are trying to bring the experimental conditions closer to those existing in a living cell, namely to the conditions of macromolecular crowding. In vitro such conditions are typically imitated by the ;inert; highly water-soluble polymers with different hydrodynamic dimensions. In this work, the effects of crowded milieu on the structure and conformational stability of actin, which is a key component of the muscle contraction system, was examined. The crowded milieu was simulated by high concentrations of PEG-8k or Dextran-70k. It was revealed that both crowding agents decelerated but not inhibited actin unfolding and made a compact state of inactivated actin thermodynamically more favorable in comparison with the unfolded state. At the same time, the high viscosity of the solution of crowding agents slowed down all processes and especially inactivated actin formation, since it involves the interaction of 14-16 partially unfolded actin molecules. The effects of crowding agent were larger when its hydrodynamic dimensions were closer to the size of globular actin.

Thermal Expansion of Ni3Al Intermetallic Compound: Experiment and Simulation

International Nuclear Information System (INIS)

Wang Hai-Peng; Lü Peng; Zhou Kai; Wei Bing-Bo

2016-01-01

The thermal expansion of Ni 3 Al intermetallic compound is determined by a thermal dilatometer and simulated by the molecular dynamics method. The results of the linear thermal expansion coefficients are presented from 200 K up to the maximum temperature of 1600 K. The single phase of Ni 3 Al intermetallic compound is confirmed by x-ray diffraction together with DSC melting and solidification peaks, from which the solidus and the liquidus temperatures are obtained to be 1660 and 1695 K, respectively. The measured linear thermal expansion coefficient increases from 1.5 × 10 −5 to 2.7 × 10 −5 K −1 in the experimental temperature range, in good agreement with the data obtained by the molecular dynamics simulation, just a slight difference from the temperature dependence coefficient. Furthermore, the atomic structure and position are presented to reveal the atom distribution change during thermal expansion of Ni 3 Al compound. (paper)

Becoming a Peroxidase: Cardiolipin-Induced Unfolding of Cytochrome c

Science.gov (United States)

Muenzner, Julia; Toffey, Jason R.; Hong, Yuning; Pletneva, Ekaterina V.

2014-01-01

Interactions of cytochrome c (cyt c) with a unique mitochondrial glycerophospholipid cardiolipin (CL) are relevant for the protein’s function in oxidative phosphorylation and apoptosis. Binding to CL-containing membranes promotes cyt c unfolding and dramatically enhances the protein’s peroxidase activity, which is critical in early stages of apoptosis. We have employed a collection of seven dansyl variants of horse heart cyt c to probe the sequence of steps in this functional transformation. Kinetic measurements have unraveled four distinct processes during CL-induced cyt c unfolding: rapid protein binding to CL liposomes; rearrangements of protein substructures with small unfolding energies; partial insertion of the protein into the lipid bilayer; and extensive protein restructuring leading to “open” extended structures. While early rearrangements depend on a hierarchy of foldons in the native structure, the later process of large-scale unfolding is influenced by protein interactions with the membrane surface. The opening of the cyt c structure exposes the heme group, which enhances the protein’s peroxidase activity and also frees the C-terminal helix to aid in the translocation of the protein through CL membranes. PMID:23713573

Cysteine residue is not essential for CPM protein thermal-stability assay.

Science.gov (United States)

Wang, Zhaoshuai; Ye, Cui; Zhang, Xinyi; Wei, Yinan

2015-05-01

A popular thermal-stability assay developed especially for the study of membrane proteins uses a thiol-specific probe, 7-diethylamino-3-(4-maleimidophenyl)-4-methylcoumarin (CPM). The fluorescence emission of CPM surges when it forms a covalent bond with the side chain of a free Cys, which becomes more readily accessible upon protein thermal denaturation. Interestingly, the melting temperatures of membrane proteins determined using the CPM assay in literature are closely clustered in the temperature range 45-55 °C. A thorough understanding of the mechanism behind the observed signal change is critical for the accurate interpretation of the protein unfolding. Here we used two α-helical membrane proteins, AqpZ and AcrB, as model systems to investigate the nature of the fluorescence surge in the CPM assay. We found that the transition temperatures measured using circular-dichroism (CD) spectroscopy and the CPM assay were significantly different. To eliminate potential artifact that might arise from the presence of detergent, we monitored the unfolding of two soluble proteins. We found that, contrary to current understanding, the presence of a sulfhydryl group was not a prerequisite for the CPM thermal-stability assay. The observed fluorescence increase is probably caused by binding of the fluorophore to hydrophobic patches exposed upon protein unfolding.

Numerical simulation of thermal fracture in functionally graded

Indian Academy of Sciences (India)

Numerical simulation of thermal fracture in functionally graded materials using element-free ... Initially, the temperature distribution over the domain is obtained by solving the heat transfer problem. ... Department of Mechanical Engineering, National Institute of Technology, Hamirpur 177005, India ... Contact | Site index.

Communication: Minimum in the thermal conductivity of supercooled water: A computer simulation study

Energy Technology Data Exchange (ETDEWEB)

Bresme, F., E-mail: f.bresme@imperial.ac.uk [Chemical Physics Section, Department of Chemistry, Imperial College, London SW7 2AZ, United Kingdom and Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491 (Norway); Biddle, J. W.; Sengers, J. V.; Anisimov, M. A. [Institute for Physical Science and Technology, and Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742 (United States)

2014-04-28

We report the results of a computer simulation study of the thermodynamic properties and the thermal conductivity of supercooled water as a function of pressure and temperature using the TIP4P-2005 water model. The thermodynamic properties can be represented by a two-structure equation of state consistent with the presence of a liquid-liquid critical point in the supercooled region. Our simulations confirm the presence of a minimum in the thermal conductivity, not only at atmospheric pressure, as previously found for the TIP5P water model, but also at elevated pressures. This anomalous behavior of the thermal conductivity of supercooled water appears to be related to the maximum of the isothermal compressibility or the minimum of the speed of sound. However, the magnitudes of the simulated thermal conductivities are sensitive to the water model adopted and appear to be significantly larger than the experimental thermal conductivities of real water at low temperatures.

Communication: Minimum in the thermal conductivity of supercooled water: A computer simulation study

International Nuclear Information System (INIS)

Bresme, F.; Biddle, J. W.; Sengers, J. V.; Anisimov, M. A.

2014-01-01

We report the results of a computer simulation study of the thermodynamic properties and the thermal conductivity of supercooled water as a function of pressure and temperature using the TIP4P-2005 water model. The thermodynamic properties can be represented by a two-structure equation of state consistent with the presence of a liquid-liquid critical point in the supercooled region. Our simulations confirm the presence of a minimum in the thermal conductivity, not only at atmospheric pressure, as previously found for the TIP5P water model, but also at elevated pressures. This anomalous behavior of the thermal conductivity of supercooled water appears to be related to the maximum of the isothermal compressibility or the minimum of the speed of sound. However, the magnitudes of the simulated thermal conductivities are sensitive to the water model adopted and appear to be significantly larger than the experimental thermal conductivities of real water at low temperatures

Molecular origin of urea driven hydrophobic polymer collapse and unfolding depending on side chain chemistry.

Science.gov (United States)

Nayar, Divya; Folberth, Angelina; van der Vegt, Nico F A

2017-07-19

Osmolytes affect hydrophobic collapse and protein folding equilibria. The underlying mechanisms are, however, not well understood. We report large-scale conformational sampling of two hydrophobic polymers with secondary and tertiary amide side chains using extensive molecular dynamics simulations. The calculated free energy of unfolding increases with urea for the secondary amide, yet decreases for the tertiary amide, in agreement with experiment. The underlying mechanism is rooted in opposing entropic driving forces: while urea screens the hydrophobic macromolecular interface and drives unfolding of the tertiary amide, urea's concomitant loss in configurational entropy drives collapse of the secondary amide. Only at sufficiently high urea concentrations bivalent urea hydrogen bonding interactions with the secondary amide lead to further stabilisation of its collapsed state. The observations provide a new angle on the interplay between side chain chemistry, urea hydrogen bonding, and the role of urea in attenuating or strengthening the hydrophobic effect.

Thermal Simulation of the Component Rework Profile Temperature

OpenAIRE

Nurminen, Janne

2015-01-01

The aim of this study was to clarify the possibilities and feasibility of the ther-mal simulation for the modeling of the rework process. The rework process modeling could enable an easy and fast access to the component and PWB level thermally critical effects like over and under heating of the component during the rework process. The modeling could also be used as a help of the real rework profile definition at an early phase of the electrical device development. The work includes a...

The unfolding effects on the protein hydration shell and partial molar volume: a computational study.

Science.gov (United States)

Del Galdo, Sara; Amadei, Andrea

2016-10-12

In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes. Moreover, by using both the native and unfolded protein partial molar volumes, we obtain the corresponding variations (unfolding partial molar volumes) to be compared with the available experimental estimates. We also reconstruct the temperature and pressure dependence of the unfolding partial molar volume of Myoglobin dissecting the structural and hydration effects involved in the process.

Nuclear Thermal Rocket Element Environmental Simulator (NTREES) Upgrade Activities

Science.gov (United States)

Emrich, William J. Jr.; Moran, Robert P.; Pearson, J. Boise

2012-01-01

To support the on-going nuclear thermal propulsion effort, a state-of-the-art non nuclear experimental test setup has been constructed to evaluate the performance characteristics of candidate fuel element materials and geometries in representative environments. The facility to perform this testing is referred to as the Nuclear Thermal Rocket Element Environment Simulator (NTREES). This device can simulate the environmental conditions (minus the radiation) to which nuclear rocket fuel components will be subjected during reactor operation. Test articles mounted in the simulator are inductively heated in such a manner so as to accurately reproduce the temperatures and heat fluxes which would normally occur as a result of nuclear fission and would be exposed to flowing hydrogen. Initial testing of a somewhat prototypical fuel element has been successfully performed in NTREES and the facility has now been shutdown to allow for an extensive reconfiguration of the facility which will result in a significant upgrade in its capabilities

Conformational dynamics of a protein in the folded and the unfolded state

Energy Technology Data Exchange (ETDEWEB)

Fitter, Joerg

2003-08-01

In a quasielastic neutron scattering experiment, the picosecond dynamics of {alpha}-amylase was investigated for the folded and the unfolded state of the protein. In order to ensure a reasonable interpretation of the internal protein dynamics, the protein was measured in D{sub 2}O-buffer solution. The much higher structural flexibility of the pH induced unfolded state as compared to the native folded state was quantified using a simple analytical model, describing a local diffusion inside a sphere. In terms of this model the conformational volume, which is explored mainly by confined protein side-chain movements, is parameterized by the radius of a sphere (folded state, r=1.2 A; unfolded state, 1.8 A). Differences in conformational dynamics between the folded and the unfolded state of a protein are of fundamental interest in the field of protein science, because they are assumed to play an important role for the thermodynamics of folding/unfolding transition and for protein stability.

Unfolding code for neutron spectrometry based on neural nets technology

International Nuclear Information System (INIS)

Ortiz R, J. M.; Vega C, H. R.

2012-10-01

The most delicate part of neutron spectrometry, is the unfolding process. The derivation of the spectral information is not simple because the unknown is not given directly as a result of the measurements. The drawbacks associated with traditional unfolding procedures have motivated the need of complementary approaches. Novel methods based on Artificial Neural Networks have been widely investigated. In this work, a neutron spectrum unfolding code based on neural nets technology is presented. This unfolding code called Neutron Spectrometry and Dosimetry by means of Artificial Neural Networks was designed in a graphical interface under LabVIEW programming environment. The core of the code is an embedded neural network architecture, previously optimized by the R obust Design of Artificial Neural Networks Methodology . The main features of the code are: is easy to use, friendly and intuitive to the user. This code was designed for a Bonner Sphere System based on a 6 Lil(Eu) neutron detector and a response matrix expressed in 60 energy bins taken from an International Atomic Energy Agency compilation. The main feature of the code is that as entrance data, only seven rate counts measurement with a Bonner spheres spectrometer are required for simultaneously unfold the 60 energy bins of the neutron spectrum and to calculate 15 dosimetric quantities, for radiation protection porpoises. This code generates a full report in html format with all relevant information. (Author)

Unfolding neutron spectra obtained from BS–TLD system using genetic algorithm

International Nuclear Information System (INIS)

Santos, J.A.L.; Silva, E.R.; Ferreira, T.A.E; Vilela, E.C.

2012-01-01

Due to the variability of neutron spectrum within the same environment, it is essential that the spectral distribution as a function of energy should be characterized. The precise information allows radiological quantities establishment related to that spectrum, but it is necessary that a spectrometric system covers a large interval of energy and an unfolding process is appropriate. This paper proposes use of a technique of Artificial Intelligence (AI) called genetic algorithm (GA), which uses bio-inspired mathematical models with the implementation of a specific matrix to unfolding data obtained from a combination of TLDs embedded in a BS system to characterize the neutron spectrum as a function of energy. The results obtained with this method were in accordance with reference spectra, thus enabling this technique to unfold neutron spectra with the BS–TLD system. - Highlights: ► The unfolding code used the artificial intelligence technique called genetic algorithms. ► A response matrix specific to the unfolding data obtained with the BS–TLD system is used by the AGLN. ► The observed results demonstrate the potential use of genetic algorithms in solving complex nuclear problems.

Thermal simulation of quenching uranium-0.75% titanium alloy in water

International Nuclear Information System (INIS)

Siman-Tov, M.; Llewellyn, G.H.; Childs, K.W.; Ludtka, G.M.; Aramayo, G.A.

1985-01-01

A computer model, The Quench Simulator, has been developed to simulate and predict in detail the behavior of U-0.75 Ti alloy when quenched at high temperature (about 850 0 C) in cold water. The code allows one to determine the time- and space-dependent distributions of temperature, residual stress, distortion, and microstructure that evolve during the quenching process. The nonlinear temperature- and microstructure-dependent properties, as well as the cooling rate-dependent heats of transformation, are incorporated into the model. The complex boiling heat transfer with its various regimes and other thermal boundary conditions are simulated. Experiments have been performed and incorporated into the model. Both sudden submersion and gradual controlled immersion can be applied. A parametric and sensitivity study has been performed demonstrating the importance of the thermal boundary conditions applied for achieving certain product characteristics. The thermal aspects of the model and its applications are discussed and demonstrated

Neutron spectra unfolding with maximum entropy and maximum likelihood

International Nuclear Information System (INIS)

Itoh, Shikoh; Tsunoda, Toshiharu

1989-01-01

A new unfolding theory has been established on the basis of the maximum entropy principle and the maximum likelihood method. This theory correctly embodies the Poisson statistics of neutron detection, and always brings a positive solution over the whole energy range. Moreover, the theory unifies both problems of overdetermined and of underdetermined. For the latter, the ambiguity in assigning a prior probability, i.e. the initial guess in the Bayesian sense, has become extinct by virtue of the principle. An approximate expression of the covariance matrix for the resultant spectra is also presented. An efficient algorithm to solve the nonlinear system, which appears in the present study, has been established. Results of computer simulation showed the effectiveness of the present theory. (author)

Unfolding in particle physics: A window on solving inverse problems

International Nuclear Information System (INIS)

Spano, F.

2013-01-01

Unfolding is the ensemble of techniques aimed at resolving inverse, ill-posed problems. A pedagogical introduction to the origin and main problems related to unfolding is presented and used as the the stepping stone towards the illustration of some of the most common techniques that are currently used in particle physics experiments. (authors)

Large Eddy Simulation of a thermal mixing tee in order to assess the thermal fatigue

International Nuclear Information System (INIS)

Galpin, J.; Simoneau, J.P.

2011-01-01

Highlights: → In this study, we perform a Large Eddy Simulation of a mixing tee, for which experimental thermal statistics are available. → A special methodology has been set up for comparing properly the fluctuations with the experiment. → A comparison between the Smagorinsky and the structure-function sub-grid scale model is achieved out. → Slight better predictions are obtained with the structure-function model. → The possibility to reduce the computational domain by prescribing synthetic turbulence at the inlet is tested. First results are encouraging and underline the advantage of considering this technique instead of a standard noise at the entrance of the domain. - Abstract: The present paper deals with thermal fatigue phenomenon, and more particularly with the numerical simulation using Large Eddy Simulation technique of a mixing tee, for which experimental thermal statistics are available. The sensitivity to the sub-grid scale closure is first evaluated by comparing the experimental statistics with the numerical results obtained via both the Smagorinsky and the structure-function models. Because of a difference of temporal resolution between the experiment and the simulation, the direct comparison of the fluctuations is not possible. Therefore, a methodology based on filtering the numerical results is proposed in order to achieve a proper comparison. The comparison of the numerical results with the experiment suggests that slight better predictions are obtained with the structure-function model even if the dependency of the results to the sub-grid scale model is low. Then, the possibility to reduce the fluid computational domain by prescribing synthetic turbulence at the inlet is tested. First results are encouraging and underline the advantage of considering this technique instead of a standard noise at the entrance of the domain. All the simulations are conducted with the commercial CFD code STAR-CD.

Minerve: thermal-hydraulic phenomena simulation and virtual reality

International Nuclear Information System (INIS)

Laffont, A.; Pentori, B.

2003-01-01

MINERVE is a 3D interactive application representing the thermal-hydraulic phenomena happening in a nuclear plant. Therefore, the 3D geometric model of the French 900 MW PWR installations has been built. The users can interact in real time with this model to see at each step of the simulation what happens in the pipes. The thermal-hydraulic simulation is made by CATHARE-2, which calculates at every time step data on about one thousand meshes (the whole primary circuit, a part of the second circuit, and the Residual Heat Removal System). The simulation covers incidental and accidental cases on these systems. There are two main innovations in MINERVE: In the domain of nuclear plant's visualization, it is to introduce interactive 3D software mechanisms to visualize results of a physical simulation. In the domain of real-time 3D, it is to visualize fluids in a pipe, while they can have several configurations, like bubbles or single liquid phase. These mechanisms enable better comprehension and better visual representation of the possible phenomena. This paper describes the functionalities of MINERVE, and the difficulties to represent fluids with several characteristics like speed, configuration,..., in 3D. On the end, we talk about the future of MINERVE, and more widely of the possible futures of such an application in scientific visualization. (authors)

Minerve: thermal-hydraulic phenomena simulation and virtual reality

Energy Technology Data Exchange (ETDEWEB)

Laffont, A.; Pentori, B. [EDF R and D, EDF SEPTEN Electricity of France - Research and Development, Department SINETICS, 92 - Clamart (France)

2003-07-01

MINERVE is a 3D interactive application representing the thermal-hydraulic phenomena happening in a nuclear plant. Therefore, the 3D geometric model of the French 900 MW PWR installations has been built. The users can interact in real time with this model to see at each step of the simulation what happens in the pipes. The thermal-hydraulic simulation is made by CATHARE-2, which calculates at every time step data on about one thousand meshes (the whole primary circuit, a part of the second circuit, and the Residual Heat Removal System). The simulation covers incidental and accidental cases on these systems. There are two main innovations in MINERVE: In the domain of nuclear plant's visualization, it is to introduce interactive 3D software mechanisms to visualize results of a physical simulation. In the domain of real-time 3D, it is to visualize fluids in a pipe, while they can have several configurations, like bubbles or single liquid phase. These mechanisms enable better comprehension and better visual representation of the possible phenomena. This paper describes the functionalities of MINERVE, and the difficulties to represent fluids with several characteristics like speed, configuration,..., in 3D. On the end, we talk about the future of MINERVE, and more widely of the possible futures of such an application in scientific visualization. (authors)

Numerical simulation of thermal loading produced by shaped high power laser onto engine parts

International Nuclear Information System (INIS)

Song Hongwei; Li Shaoxia; Zhang Ling; Yu Gang; Zhou Liang; Tan Jiansong

2010-01-01

Recently a new method for simulating the thermal loading on pistons of diesel engines was reported. The spatially shaped high power laser is employed as the heat source, and some preliminary experimental and numerical work was carried out. In this paper, a further effort was made to extend this simulation method to some other important engine parts such as cylinder heads. The incident Gaussian beam was transformed into concentric multi-circular patterns of specific intensity distributions, with the aid of diffractive optical elements (DOEs). By incorporating the appropriate repetitive laser pulses, the designed transient temperature fields and thermal loadings in the engine parts could be simulated. Thermal-structural numerical models for pistons and cylinder heads were built to predict the transient temperature and thermal stress. The models were also employed to find the optimal intensity distributions of the transformed laser beam that could produce the target transient temperature fields. Comparison of experimental and numerical results demonstrated that this systematic approach is effective in simulating the thermal loading on the engine parts.

Particle-in-cell simulations on spontaneous thermal magnetic field fluctuations

Energy Technology Data Exchange (ETDEWEB)

Simões, F. J. R. Jr.; Pavan, J. [Instituto de Física e Matemática, UFPel, Pelotas, RS (Brazil); Gaelzer, R.; Ziebell, L. F. [Instituto de Física, UFRGS, Porto Alegre, RS (Brazil); Yoon, P. H. [Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742 (United States)

2013-10-15

In this paper an electromagnetic particle code is used to investigate the spontaneous thermal emission. Specifically we perform particle-in-cell simulations employing a non-relativistic isotropic Maxwellian particle distribution to show that thermal fluctuations are related to the origin of spontaneous magnetic field fluctuation. These thermal fluctuations can become seed for further amplification mechanisms and thus be considered at the origin of the cosmological magnetic field, at microgauss levels. Our numerical results are in accordance with theoretical results presented in the literature.

Test results of the new NSSS thermal-hydraulics program of the KNPEC-2 simulator

International Nuclear Information System (INIS)

Jeong, J. Z.; Kim, K. D.; Lee, M. S.; Hong, J. H.; Lee, Y. K.; Seo, J. S.; Kweon, K. J.; Lee, S. W.

2001-01-01

As a part of the KNPEC-2 Simulator Upgrade Project, KEPRI and KAERI have developed a new NSSS thermal-hydraulics program, which is based on the best-estimate system code, RETRAN. The RETRAN code was originally developed for realistic simulation of thermal-hydraulic transient in power plant systems. The capability of 'real-time simulation' and robustness' should be first developed before being implemented in full-scope simulators. For this purpose, we have modified the RETRAN code by (i) eliminating the correlations' discontinuities between flow regime maps, (ii) simplifying physical correlations, (iii) correcting errors in the original program, and (iv) others. This paper briefly presents the test results fo the new NSSS thermal-hydraulics program

Optical and thermal simulation chain for LED package

NARCIS (Netherlands)

Tapaninen, O.; Myohanen, P.; Majanen, M.; Sitomaniemi, A.; Olkkonen, J.; Hildenbrand, V.; Gielen, A.W.J.; Mackenzie, F.V.; Barink, M.; Smilauer, V.; Patzak, B.

2016-01-01

This paper presents a test case for coupling two physical aspects of an LED, optical and thermal, using specific simulation models coupled through an open source platform for distributed multi-physics modelling. The glue code for coupling is written with Python programming language including

Numerical simulation of thermal stratification in cold legs by using openFOAM

International Nuclear Information System (INIS)

Cai, Jiejin; Watanabe, Tadashi

2010-01-01

During a small-break loss-of-coolant accident in pressurized water reactors (PWRs), emergency core cooling system (ECCS) is actuated and cold water is injected into cold legs. Insufficient mixing of injected cold water and hot primary coolant results in thermal stratification, which is a matter of concern for evaluation of pressurized thermal shock (PTS) in view of aging and life extension of nuclear power plants. In this study, an open source CFD software, OpenFOAM, is used to simulate mixing and thermal stratification in the cold leg of ROSA/LSTF, which is the largest thermal-hydraulic integral test facility simulating PWR. One of the cold-leg is numerically simulated from the outlet of primary coolant pump to the inlet of downcomer. ECCS water is injected from injection nozzle connected at the top of the cold leg into the steady-state natural circulation flow under high-pressure and high-temperature conditions. The temperature distribution in the cold leg is compared with experimental and FLUENT's results. Effects of turbulent flow models and secondary flow due to the elbow section of the cold leg are discussed for the case with the single-phase natural circulation. Injection into a two-phase stratified flow is also simulated and predictive and numerical capabilities of OpenFOAM are discussed. (author)

Simulation of Thermal Transients using CSMP

International Nuclear Information System (INIS)

Konuk, A.A.

1981-01-01

A mathematical model has been developed to simulate thermal transientes for the Hellum Loop of the 'Instituto de Pesquisas Energeticas e Nuleares', Sao Paulo. The model is based on the energy equation applied to the various components of the loop. The non-linear system of first order ordinary differential equation and algebraic equations has been solved using IBM'S 'System/360-Continuous System Modeling Program-CSMP'. The model has been tested satisfactory with experimental results. (Author) [pt

Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding

Science.gov (United States)

Nagpal, Suhani; Tiwari, Satyam; Mapa, Koyeli; Thukral, Lipi

2015-01-01

Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central “hubs”. Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates. PMID:26394388

Experimental Study of Turbine Fuel Thermal Stability in an Aircraft Fuel System Simulator

Science.gov (United States)

Vranos, A.; Marteney, P. J.

1980-01-01

The thermal stability of aircraft gas turbines fuels was investigated. The objectives were: (1) to design and build an aircraft fuel system simulator; (2) to establish criteria for quantitative assessment of fuel thermal degradation; and (3) to measure the thermal degradation of Jet A and an alternative fuel. Accordingly, an aircraft fuel system simulator was built and the coking tendencies of Jet A and a model alternative fuel (No. 2 heating oil) were measured over a range of temperatures, pressures, flows, and fuel inlet conditions.

Unfolding code for neutron spectrometry based on neural nets technology

Energy Technology Data Exchange (ETDEWEB)

Ortiz R, J. M.; Vega C, H. R., E-mail: morvymm@yahoo.com.mx [Universidad Autonoma de Zacatecas, Unidad Academica de Ingenieria Electrica, Apdo. Postal 336, 98000 Zacatecas (Mexico)

2012-10-15

The most delicate part of neutron spectrometry, is the unfolding process. The derivation of the spectral information is not simple because the unknown is not given directly as a result of the measurements. The drawbacks associated with traditional unfolding procedures have motivated the need of complementary approaches. Novel methods based on Artificial Neural Networks have been widely investigated. In this work, a neutron spectrum unfolding code based on neural nets technology is presented. This unfolding code called Neutron Spectrometry and Dosimetry by means of Artificial Neural Networks was designed in a graphical interface under LabVIEW programming environment. The core of the code is an embedded neural network architecture, previously optimized by the {sup R}obust Design of Artificial Neural Networks Methodology{sup .} The main features of the code are: is easy to use, friendly and intuitive to the user. This code was designed for a Bonner Sphere System based on a {sup 6}Lil(Eu) neutron detector and a response matrix expressed in 60 energy bins taken from an International Atomic Energy Agency compilation. The main feature of the code is that as entrance data, only seven rate counts measurement with a Bonner spheres spectrometer are required for simultaneously unfold the 60 energy bins of the neutron spectrum and to calculate 15 dosimetric quantities, for radiation protection porpoises. This code generates a full report in html format with all relevant information. (Author)

UMG 3.3, Analysis of data measured with spectrometers using unfolding techniques

International Nuclear Information System (INIS)

Reginatto, Marcel; Wiegel, Burkhard; Zimbal, Andreas; Langner, Frank

2004-01-01

1 - Description of program or function: UMG (Unfolding with MAXED and GRAVEL) is a package of seven programs written for the analysis of data measured with spectrometers that require the use of unfolding techniques. The program MAXED applies the maximum entropy principle to the unfolding problem, and the program GRAVEL uses a modified SAND-II algorithm to do the unfolding. There are two versions of each: MXD F C33 and GRV F C33 for 'few-channel' unfolding (e.g., Bonner sphere spectrometers) and MXD M C33 and GRV M C33 for 'multi-channel' unfolding (e.g., NE-213). The program IQU can be used to calculate integral quantities for both MAXED and GRAVEL solution spectra and, in the case of MAXED solutions, it can also be used to calculate the uncertainty in these values as well as the uncertainty in the solution spectrum. The uncertainty calculation is handled in the following way: given a solution spectrum generated by MAXED, the program IQU considers variations in the measured data and in the default spectrum and uses standard Methods to do sensitivity analysis and uncertainty propagation. There are two versions: IQU F C33 for 'few-channel' unfolding and IQU M C33 for 'multi-channel' unfolding. The program UMGPlot can be used to display the results from the unfolding programs MAXED and GRAVEL in graphical form in a quick and easy way. 2 - Methods: MAXED is based on the maximum entropy principle. The solution to the unfolding problem is obtained by maximisation of the relative entropy (used here in the form due to Skilling, which is a generalisation of the usual expression to distributions that are not necessarily normalized) subject to constraints imposed by the measurements. This approach permits the inclusion of prior information in a well-defined and mathematically consistent way, and it leads to a solution spectrum that is a non-negative function which can be written in closed form. This last feature permits the use of standard Methods for sensitivity analysis and

Insights into the folding and unfolding processes of wild-type and mutated SH3 domain by molecular dynamics and replica exchange molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Wen-Ting Chu

Full Text Available Src-homology regions 3 (SH3 domain is essential for the down-regulation of tyrosine kinase activity. Mutation A39V/N53P/V55L of SH3 is found to be relative to the urgent misfolding diseases. To gain insight, the human and gallus SH3 domains (PDB ID: 1NYG and 2LP5, including 58 amino acids in each protein, were selected for MD simulations (Amber11, ff99SB force field and cluster analysis to investigate the influence of mutations on the spatial structure of the SH3 domain. It is found that the large conformational change of mutations mainly exists in three areas in the vicinity of protein core: RT loop, N-src loop, distal β-hairpin to 310 helix. The C-terminus of the mutated gallus SH3 is disordered after simulation, which represents the intermediate state of aggregation. The disappeared strong Hbond net in the mutated human and gallus systems will make these mutated proteins looser than the wild-type proteins. Additionally, by performing the REMD simulations on the gallus SH3 domain, the mutated domain is found to have an obvious effect on the unfolding process. These studies will be helpful for further aggregation mechanisms investigations on SH3 family.

Simulation of thermal-hydraulic process in reactor of HTR-PM based on flow and heat transfer network

International Nuclear Information System (INIS)

Zhou Kefeng; Zhou Yangping; Sui Zhe; Ma Yuanle

2012-01-01

The development of HTR-PM full scale simulator (FSS) is an important part in the project. The simulation of thermal-hydraulic process in reactor is one of the key technologies in the development of FSS. The simulation of thermal-hydraulic process in reactor was studied. According to the geometry structures and the characteristics of thermal-hydraulic process in reactor, the model was setup in components construction way. Based on the established simulation method of flow and heat transfer network, a Fortran code was developed and the simulation of thermal-hydraulic process was achieved. The simulation results of 50% FP steady state, 100% FP steady state and control rod mistakenly ascension accidents were given. The verification of simulation results was carried out by comparing with the design and analysis code THERMIX. The results show that the method and model based on flow and heat transfer network can meet the requirements of FSS and reflect the features of thermal-hydraulic process in HTR-PM. (authors)

A simplified tool for building layout design based on thermal comfort simulations

Directory of Open Access Journals (Sweden)

Prashant Anand

2017-06-01

Full Text Available Thermal comfort aspects of indoor spaces are crucial during the design stages of building layout planning. This study presents a simplified tool based on thermal comfort using predicted mean vote (PMV index. Thermal comfort simulations were performed for 14 different possible room layouts based on window configurations. ECOTECT 12 was used to determine the PMV of these rooms for one full year, leading to 17,808 simulations. Simulations were performed for three different climatic zones in India and were validated using in-situ measurements from one of these climatic zones. For moderate climates, rooms with window openings on the south façade exhibited the best thermal comfort conditions for nights, with comfort conditions prevailing for approximately 79.25% of the time annually. For operation during the day, windows on the north façade are favored, with thermal comfort conditions prevailing for approximately 77.74% of the time annually. Similar results for day and night time operation for other two climatic zones are presented. Such an output is essential in deciding the layout of buildings on the basis of functionality of the different rooms (living room, bedroom, kitchen corresponding to different operation times of the day.

Unfolded equations for massive higher spin supermultiplets in AdS{sub 3}

Energy Technology Data Exchange (ETDEWEB)

Buchbinder, I.L. [Department of Theoretical Physics, Tomsk State Pedagogical University,60 Kievskaya Str., Tomsk, 634061 (Russian Federation); National Research Tomsk State University,36 Lenina Ave., Tomsk, 634050 (Russian Federation); Snegirev, T.V. [Department of Theoretical Physics, Tomsk State Pedagogical University,60 Kievskaya Str., Tomsk, 634061 (Russian Federation); Department of Higher Mathematics and Mathematical Physics,National Research Tomsk Polytechnic University, 30 Lenina Ave., Tomsk, 634050 (Russian Federation); Zinoviev, Yu.M. [Department of Theoretical Physics,Institute for High Energy Physics of National Research Center “Kurchatov Institute”, 1 Pobedy Str., Protvino, Moscow Region, 142280 (Russian Federation)

2016-08-10

In this paper we give an explicit construction of unfolded equations for massive higher spin supermultiplets of the minimal (1,0) supersymmetry in AdS{sub 3} space. For that purpose we use an unfolded formulation for massive bosonic and fermionic higher spins and find supertransformations leaving appropriate set of unfolded equations invariant. We provide two general supermultiplets (s,s+1/2) and (s,s−1/2) with arbitrary integer s, as well as a number of lower spin examples.

Thermal comfort in residential buildings: Comfort values and scales for building energy simulation

NARCIS (Netherlands)

Peeters, L.F.R.; Dear, de R.; Hensen, J.L.M.; D'Haeseleer, W.

2009-01-01

Building Energy Simulation (BES) programmes often use conventional thermal comfort theories to make decisions, whilst recent research in the field of thermal comfort clearly shows that important effects are not incorporated. The conventional theories of thermal comfort were set up based on steady

On unfolding counting-rate spectra of recoil-proton neutron detectors

International Nuclear Information System (INIS)

Yeivin, Yehuda

1983-01-01

This note proposes a possible scheme for unfolding recoil-proton neutron detector data, in which at first the undistorted proton source spectrum is derived. The main argument in favour of this scheme is that, compared with the conventional scheme, it necessitates somewhat weaker assumptions with respect to the unknown spectrum above the detector's upper energy cutoff, and would therefore be more reliable. We also demonstrate a simple, elementary proof of the wall effect correction for spherical detectors, and, in order to gain insight of the potential merits of the proposed unfolding scheme, illustrate our main argument by considering a hypothetic linear range-energy relation, in which case complete unfolding becomes possible with no assumptions at all on the proton spectrum above the cutoff energy. (author)

A Thermal Runaway Simulation on a Lithium Titanate Battery and the Battery Module

Directory of Open Access Journals (Sweden)

Man Chen

2015-01-01

Full Text Available Based on the electrochemical and thermal model, a coupled electro-thermal runaway model was developed and implemented using finite element methods. The thermal decomposition reactions when the battery temperature exceeds the material decomposition temperature were embedded into the model. The temperature variations of a lithium titanate battery during a series of charge-discharge cycles under different current rates were simulated. The results of temperature and heat generation rate demonstrate that the greater the current, the faster the battery temperature is rising. Furthermore, the thermal influence of the overheated cell on surrounding batteries in the module was simulated, and the variation of temperature and heat generation during thermal runaway was obtained. It was found that the overheated cell can induce thermal runaway in other adjacent cells within 3 mm distance in the battery module if the accumulated heat is not dissipated rapidly.

Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model

Energy Technology Data Exchange (ETDEWEB)

Li, Chunhua [College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124 (China); Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 45108 (United States); Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin [College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124 (China); Su, Jiguo, E-mail: jiguosu@ysu.edu.cn, E-mail: zhng@umich.edu [College of Science, Yanshan University, Qinhuangdao 066004 (China); Zhang, Yang, E-mail: jiguosu@ysu.edu.cn, E-mail: zhng@umich.edu [Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 45108 (United States)

2016-07-07

Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.

Thermal Simulation of Switching Pulses in an Insulated Gate Bipolar Transistor (IGBT) Power Module

Science.gov (United States)

2015-02-01

executed with SolidWorks Flow Simulation , a computational fluid-dynamics code. The graph in Fig. 2 shows the timing and amplitudes of power pulses...defined a convective flow of air perpendicular to the bottom surface of the mounting plate, with a velocity of 10 ft/s. The thermal simulations were...Thermal Simulation of Switching Pulses in an Insulated Gate Bipolar Transistor (IGBT) Power Module by Gregory K Ovrebo ARL-TR-7210

A non-equilibrium simulation of thermal constriction in a cascaded arc hydrogen plasma

International Nuclear Information System (INIS)

Peerenboom, K S C; Goedheer, W J; Van Dijk, J; Kroesen, G M W

2014-01-01

The cascaded arc hydrogen plasma of Pilot-PSI is studied in a non-LTE model. We demonstrate that the effect of vibrationally excited molecules on the heavy-particle-assisted dissociation is crucial for obtaining thermal constriction. To the best of our knowledge, thermal constriction has not been obtained before in a non-LTE simulation. Probably, realistic numerical studies of this type of plasma were hindered by numerical problems, preventing the non-LTE simulations to show characteristic physical mechanisms such as thermal constriction. In this paper we show that with the help of appropriate numerical strategies thermal constriction can be obtained in a non-LTE simulation. To this end, a new source term linearization technique is developed, which ensures physical solutions even near chemical equilibrium where the composition is dominated by chemical source terms. Results of the model are compared with experiments on Pilot-PSI and show good agreement with pressure and voltage measurements in the source. (paper)

The construction of periodic unfolding operators on some compact Riemannian manifolds

DEFF Research Database (Denmark)

Dobberschütz, Sören; Böhm, Michael

2014-01-01

The notion of periodic unfolding has become a standard tool in the theory of periodic homogenization. However, all the results obtained so far are only applicable to the "flat" Euclidean space R n. In this paper, we present a generalization of the method of periodic unfolding applicable to struct...

Multiscale development of a fission gas thermal conductivity model: Coupling atomic, meso and continuum level simulations

International Nuclear Information System (INIS)

Tonks, Michael R.; Millett, Paul C.; Nerikar, Pankaj; Du, Shiyu; Andersson, David; Stanek, Christopher R.; Gaston, Derek; Andrs, David; Williamson, Richard

2013-01-01

Fission gas production and evolution significantly impact the fuel performance, causing swelling, a reduction in the thermal conductivity and fission gas release. However, typical empirical models of fuel properties treat each of these effects separately and uncoupled. Here, we couple a fission gas release model to a model of the impact of fission gas on the fuel thermal conductivity. To quantify the specific impact of grain boundary (GB) bubbles on the thermal conductivity, we use atomistic and mesoscale simulations. Atomistic molecular dynamic simulations were employed to determine the GB thermal resistance. These values were then used in mesoscale heat conduction simulations to develop a mechanistic expression for the effective GB thermal resistance of a GB containing gas bubbles, as a function of the percentage of the GB covered by fission gas. The coupled fission gas release and thermal conductivity model was implemented in Idaho National Laboratory’s BISON fuel performance code to model the behavior of a 10-pellet LWR fuel rodlet, showing how the fission gas impacts the UO 2 thermal conductivity. Furthermore, additional BISON simulations were conducted to demonstrate the impact of average grain size on both the fuel thermal conductivity and the fission gas release

RPA-mediated unfolding of systematically varying G-quadruplex structures.

Science.gov (United States)

Ray, Sujay; Qureshi, Mohammad H; Malcolm, Dominic W; Budhathoki, Jagat B; Celik, Uğur; Balci, Hamza

2013-05-21

G-quadruplex (GQ) is a noncanonical nucleic acid structure that is formed by guanine rich sequences. Unless it is destabilized by proteins such as replication protein A (RPA), GQ could interfere with DNA metabolic functions, such as replication or repair. We studied RPA-mediated GQ unfolding using single-molecule FRET on two groups of GQ structures that have different loop lengths and different numbers of G-tetrad layers. We observed a linear increase in the steady-state stability of the GQ against RPA-mediated unfolding with increasing number of layers or decreasing loop length. The stability demonstrated by different GQ structures varied by at least three orders of magnitude. Those with shorter loops (less than three nucleotides long) or a greater number of layers (more than three layers) maintained a significant folded population even at physiological RPA concentration (≈1 μM), raising the possibility of physiological viability of such GQ structures. Finally, we measured the transition time between the start and end of the RPA-mediated GQ unfolding process to be 0.35 ± 0.10 s for all GQ constructs we studied, despite significant differences in their steady-state stabilities. We propose a two-step RPA-mediated GQ unfolding mechanism that is consistent with our observations. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Thermal large Eddy simulations and experiments in the framework of non-isothermal blowing

International Nuclear Information System (INIS)

Brillant, G.

2004-06-01

The aim of this work is to study thermal large-eddy simulations and to determine the nonisothermal blowing impact on a turbulent boundary layer. An experimental study is also carried out in order to complete and validate simulation results. In a first time, we developed a turbulent inlet condition for the velocity and the temperature, which is necessary for the blowing simulations.We studied the asymptotic behavior of the velocity, the temperature and the thermal turbulent fluxes in a large-eddy simulation point of view. We then considered dynamics models for the eddy-diffusivity and we simulated a turbulent channel flow with imposed temperature, imposed flux and adiabatic walls. The numerical and experimental study of blowing permitted to obtain to the modifications of a thermal turbulent boundary layer with the blowing rate. We observed the consequences of the blowing on mean and rms profiles of velocity and temperature but also on velocity-velocity and velocity-temperature correlations. Moreover, we noticed an increase of the turbulent structures in the boundary layer with blowing. (author)

Numerical simulation of thermal stratification in cold legs by using OpenFOAM

International Nuclear Information System (INIS)

Cai, Jiejin; Watanabe, Tadashi

2011-01-01

During a small-break loss-of-coolant accident in pressurized water reactors (PWRs), emergency core cooling system (ECCS) is actuated and cold water is injected into cold legs. Insufficient mixing of injected cold water and hot primary coolant results in thermal stratification, which is a matter of concern for evaluation of pressurized thermal shock (PTS) in view of aging and life extension of nuclear power plants. In this study, an open source CFD software, OpenFOAM, is used to simulate mixing and thermal stratification in the cold leg of ROSA/LSTF, which is the largest thermal-hydraulic integral test facility simulating PWR. One of the cold-leg is numerically simulated from the outlet of primary coolant pump to the inlet of downcomer. ECCS water is injected from injection nozzle connected at the top of the cold leg into the steady-state natural circulation flow under high-pressure and high-temperature conditions. The temperature distribution in the cold leg is compared with experimental and FLUENT's results. Effects of turbulent flow models and secondary flow due to the elbow section of the cold leg are discussed for the case with the single-phase natural circulation. Injection into a two-phase stratified flow is also simulated and predictive and numerical capabilities of OpenFOAM are discussed. (author)

NSDUAZ unfolding package for neutron spectrometry and dosimetry with Bonner spheres

Energy Technology Data Exchange (ETDEWEB)

Vega C, H. R.; Martinez B, M. R. [Universidad Autonoma de Zacatecas, Unidad Academica de Estudios Nucleares, Calle Cipres No. 10, Fracc. La Penuela, 98068 Zacatecas (Mexico); Ortiz R, J. M., E-mail: fermineutron@yahoo.com [Universidad Autonoma de Zacatecas, Unidad Academica de Ingenieria Electrica, Av. Ramon Lopez Velarde 801, Col. Centro, 98000 Zacatecas (Mexico)

2011-10-15

NSDUAZ (Neutron Spectrometry and Dosimetry for the Universidad Autonoma de Zacatecas) is a user friendly neutron unfolding package for Bonner sphere spectrometer with {sup 6}Lil(Eu) developed under Lab View environment. Unfolding is carried out using a recursive iterative procedure with the SPUNIT algorithm, where the starting spectrum is obtained from a library initial guess spectrum to start the iterations, the package include a statistical procedure based on the count rates relative to the count rate in the 8 inches-diameter sphere to select the initial spectrum. Neutron spectrum is unfolded in 32 energy groups ranging from 10{sup -8} up to 231.2 MeV. (Author)

User's manual for computer code SOLTES-1 (simulator of large thermal energy systems)

International Nuclear Information System (INIS)

Fewell, M.E.; Grandjean, N.R.; Dunn, J.C.; Edenburn, M.W.

1978-09-01

SOLTES simulates the steady-state response of thermal energy systems to time-varying data such as weather and loads. Thermal energy system models of both simple and complex systems can easily be modularly constructed from a library of routines. These routines mathematically model solar collectors, pumps, switches, thermal energy storage, thermal boilers, auxiliary boilers, heat exchangers, extraction turbines, extraction turbine/generators, condensers, regenerative heaters, air conditioners, heating and cooling of buildings, process vapor, etc.; SOLTES also allows user-supplied routines. The analyst need only specify fluid names to obtain readout of property data for heat-transfer fluids and constants that characterize power-cycle working fluids from a fluid property data bank. A load management capability allows SOLTES to simulate total energy systems that simultaneously follow heat and power loads and demands. Generalized energy accounting is available, and values for system performance parameters may be automatically determined by SOLTES. Because of its modularity and flexibility, SOLTES can be used to simulate a wide variety of thermal energy systems such as solar power/total energy, fossil fuel power plants/total energy, nuclear power plants/total energy, solar energy heating and cooling, geothermal energy, and solar hot water heaters

Spectrum unfolding in X-ray spectrometry using the maximum entropy method

International Nuclear Information System (INIS)

Fernandez, Jorge E.; Scot, Viviana; Di Giulio, Eugenio

2014-01-01

The solution of the unfolding problem is an ever-present issue in X-ray spectrometry. The maximum entropy technique solves this problem by taking advantage of some known a priori physical information and by ensuring an outcome with only positive values. This method is implemented in MAXED (MAXimum Entropy Deconvolution), a software code contained in the package UMG (Unfolding with MAXED and GRAVEL) developed at PTB and distributed by NEA Data Bank. This package contains also the code GRAVEL (used to estimate the precision of the solution). This article introduces the new code UMESTRAT (Unfolding Maximum Entropy STRATegy) which applies a semi-automatic strategy to solve the unfolding problem by using a suitable combination of MAXED and GRAVEL for applications in X-ray spectrometry. Some examples of the use of UMESTRAT are shown, demonstrating its capability to remove detector artifacts from the measured spectrum consistently with the model used for the detector response function (DRF). - Highlights: ► A new strategy to solve the unfolding problem in X-ray spectrometry is presented. ► The presented strategy uses a suitable combination of the codes MAXED and GRAVEL. ► The applied strategy provides additional information on the Detector Response Function. ► The code UMESTRAT is developed to apply this new strategy in a semi-automatic mode

Immobilized unfolded cytochrome c acts as a catalyst for dioxygen reduction.

Science.gov (United States)

Tavagnacco, Claudio; Monari, Stefano; Ranieri, Antonio; Bortolotti, Carlo Augusto; Peressini, Silvia; Borsari, Marco

2011-10-21

Unfolding turns immobilized cytochrome c into a His-His ligated form endowed with catalytic activity towards O(2), which is absent in the native protein. Dioxygen could be used by naturally occurring unfolded cytochrome c as a substrate for the production of partially reduced oxygen species (PROS) contributing to the cell oxidative stress.

Testing thermal gradient driving force for grain boundary migration using molecular dynamics simulations

International Nuclear Information System (INIS)

Bai, Xian-Ming; Zhang, Yongfeng; Tonks, Michael R.

2015-01-01

Strong thermal gradients in low-thermal-conductivity ceramics may drive extended defects, such as grain boundaries and voids, to migrate in preferential directions. In this work, molecular dynamics simulations are conducted to study thermal gradient driven grain boundary migration and to verify a previously proposed thermal gradient driving force equation, using uranium dioxide as a model system. It is found that a thermal gradient drives grain boundaries to migrate up the gradient and the migration velocity increases under a constant gradient owing to the increase in mobility with temperature. Different grain boundaries migrate at very different rates due to their different intrinsic mobilities. The extracted mobilities from the thermal gradient driven simulations are compared with those calculated from two other well-established methods and good agreement between the three different methods is found, demonstrating that the theoretical equation of the thermal gradient driving force is valid, although a correction of one input parameter should be made. The discrepancy in the grain boundary mobilities between modeling and experiments is also discussed.

A Multi-Wavelength Thermal Infrared and Reflectance Scene Simulation Model

Science.gov (United States)

Ballard, J. R., Jr.; Smith, J. A.; Smith, David E. (Technical Monitor)

2002-01-01

Several theoretical calculations are presented and our approach discussed for simulating overall composite scene thermal infrared exitance and canopy bidirectional reflectance of a forest canopy. Calculations are performed for selected wavelength bands of the DOE Multispectral Thermal Imagery and comparisons with atmospherically corrected MTI imagery are underway. NASA EO-1 Hyperion observations also are available and the favorable comparison of our reflective model results with these data are reported elsewhere.

Thermal unit availability modeling in a regional simulation model

International Nuclear Information System (INIS)

Yamayee, Z.A.; Port, J.; Robinett, W.

1983-01-01

The System Analysis Model (SAM) developed under the umbrella of PNUCC's System Analysis Committee is capable of simulating the operation of a given load/resource scenario. This model employs a Monte-Carlo simulation to incorporate uncertainties. Among uncertainties modeled is thermal unit availability both for energy simulation (seasonal) and capacity simulations (hourly). This paper presents the availability modeling in the capacity and energy models. The use of regional and national data in deriving the two availability models, the interaction between the two and modifications made to the capacity model in order to reflect regional practices is presented. A sample problem is presented to show the modification process. Results for modeling a nuclear unit using NERC-GADS is presented

Nuclear Thermal Rocket Element Environmental Simulator (NTREES)

International Nuclear Information System (INIS)

Emrich, William J. Jr.

2008-01-01

To support a potential future development of a nuclear thermal rocket engine, a state-of-the-art non nuclear experimental test setup has been constructed to evaluate the performance characteristics of candidate fuel element materials and geometries in representative environments. The test device simulates the environmental conditions (minus the radiation) to which nuclear rocket fuel components could be subjected during reactor operation. Test articles mounted in the simulator are inductively heated in such a manner as to accurately reproduce the temperatures and heat fluxes normally expected to occur as a result of nuclear fission while at the same time being exposed to flowing hydrogen. This project is referred to as the Nuclear Thermal Rocket Element Environment Simulator or NTREES. The NTREES device is located at the Marshall Space flight Center in a laboratory which has been modified to accommodate the high powers required to heat the test articles to the required temperatures and to handle the gaseous hydrogen flow required for the tests. Other modifications to the laboratory include the installation of a nitrogen gas supply system and a cooling water supply system. During the design and construction of the facility, every effort was made to comply with all pertinent regulations to provide assurance that the facility could be operated in a safe and efficient manner. The NTREES system can currently supply up to 50 kW of inductive heating to the fuel test articles, although the facility has been sized to eventually allow test article heating levels of up to several megawatts

Empirical Validation of Heat Transfer Performance Simulation of Graphite/PCM Concrete Materials for Thermally Activated Building System

Directory of Open Access Journals (Sweden)

Jin-Hee Song

2017-01-01

Full Text Available To increase the heat capacity in lightweight construction materials, a phase change material (PCM can be introduced to building elements. A thermally activated building system (TABS with graphite/PCM concrete hollow core slab is suggested as an energy-efficient technology to shift and reduce the peak thermal load in buildings. An evaluation of heat storage and dissipation characteristics of TABS in graphite/PCM concrete has been conducted using dynamic simulations, but empirical validation is necessary to acceptably predict the thermal behavior of graphite/PCM concrete. This study aimed to validate the thermal behavior of graphite/PCM concrete through a three-dimensional transient heat transfer simulation. The simulation results were compared to experimental results from previous studies of concrete and graphite/PCM concrete. The overall thermal behavior for both materials was found to be similar to experiment results. Limitations in the simulation modeling, which included determination of the indoor heat transfer coefficient, assumption of constant thermal conductivity with temperature, and assumption of specimen homogeneity, led to slight differences between the measured and simulated results.

Thermal dynamic simulation of wall for building energy efficiency under varied climate environment

Science.gov (United States)

Wang, Xuejin; Zhang, Yujin; Hong, Jing

2017-08-01

Aiming at different kind of walls in five cities of different zoning for thermal design, using thermal instantaneous response factors method, the author develops software to calculation air conditioning cooling load temperature, thermal response factors, and periodic response factors. On the basis of the data, the author gives the net work analysis about the influence of dynamic thermal of wall on air-conditioning load and thermal environment in building of different zoning for thermal design regional, and put forward the strategy how to design thermal insulation and heat preservation wall base on dynamic thermal characteristic of wall under different zoning for thermal design regional. And then provide the theory basis and the technical references for the further study on the heat preservation with the insulation are in the service of energy saving wall design. All-year thermal dynamic load simulating and energy consumption analysis for new energy-saving building is very important in building environment. This software will provide the referable scientific foundation for all-year new thermal dynamic load simulation, energy consumption analysis, building environment systems control, carrying through farther research on thermal particularity and general particularity evaluation for new energy -saving walls building. Based on which, we will not only expediently design system of building energy, but also analyze building energy consumption and carry through scientific energy management. The study will provide the referable scientific foundation for carrying through farther research on thermal particularity and general particularity evaluation for new energy saving walls building.

ELECTROMAGNETIC AND THERMAL SIMULATIONS FOR THE SWITCH REGION OF A COMPACT PROTON ACCELERATOR

International Nuclear Information System (INIS)

Wang, L; Caporaso, G J; Sullivan, J S

2007-01-01

A compact proton accelerator for medical applications is being developed at Lawrence Livermore National Laboratory. The accelerator architecture is based on the dielectric wall accelerator (DWA) concept. One critical area to consider is the switch region. Electric field simulations and thermal calculations of the switch area were performed to help determine the operating limits of rmed SiC switches. Different geometries were considered for the field simulation including the shape of the thin Indium solder meniscus between the electrodes and SiC. Electric field simulations were also utilized to demonstrate how the field stress could be reduced. Both transient and steady steady-state thermal simulations were analyzed to find the average power capability of the switches

A 3-D wellbore simulator (WELLTHER-SIM) to determine the thermal diffusivity of rock-formations

Science.gov (United States)

Wong-Loya, J. A.; Santoyo, E.; Andaverde, J.

2017-06-01

Acquiring thermophysical properties of rock-formations in geothermal systems is an essential task required for the well drilling and completion. Wellbore thermal simulators require such properties for predicting the thermal behavior of a wellbore and the formation under drilling and shut-in conditions. The estimation of static formation temperatures also needs the use of these properties for the wellbore and formation materials (drilling fluids and pipes, cements, casings, and rocks). A numerical simulator (WELLTHER-SIM) has been developed for modeling the drilling fluid circulation and shut-in processes of geothermal wellbores, and for the in-situ determination of thermal diffusivities of rocks. Bottomhole temperatures logged under shut-in conditions (BHTm), and thermophysical and transport properties of drilling fluids were used as main input data. To model the thermal disturbance and recovery processes in the wellbore and rock-formation, initial drilling fluid and static formation temperatures were used as initial and boundary conditions. WELLTHER-SIM uses these temperatures together with an initial thermal diffusivity for the rock-formation to solve the governing equations of the heat transfer model. WELLTHER-SIM was programmed using the finite volume technique to solve the heat conduction equations under 3-D and transient conditions. Thermal diffusivities of rock-formations were inversely computed by using an iterative and efficient numerical simulation, where simulated thermal recovery data sets (BHTs) were statistically compared with those temperature measurements (BHTm) logged in some geothermal wellbores. The simulator was validated using a well-documented case reported in the literature, where the thermophysical properties of the rock-formation are known with accuracy. The new numerical simulator has been successfully applied to two wellbores drilled in geothermal fields of Japan and Mexico. Details of the physical conceptual model, the numerical

Numerical Simulation of Non-Thermal Food Preservation

Science.gov (United States)

Rauh, C.; Krauss, J.; Ertunc, Ö.; Delgado, a.

2010-09-01

Food preservation is an important process step in food technology regarding product safety and product quality. Novel preservation techniques are currently developed, that aim at improved sensory and nutritional value but comparable safety than in conventional thermal preservation techniques. These novel non-thermal food preservation techniques are based for example on high pressures up to one GPa or pulsed electric fields. in literature studies the high potential of high pressures (HP) and of pulsed electric fields (PEF) is shown due to their high retention of valuable food components as vitamins and flavour and selective inactivation of spoiling enzymes and microorganisms. for the design of preservation processes based on the non-thermal techniques it is crucial to predict the effect of high pressure and pulsed electric fields on the food components and on the spoiling enzymes and microorganisms locally and time-dependent in the treated product. Homogenous process conditions (especially of temperature fields in HP and PEF processing and of electric fields in PEF) are aimed at to avoid the need of over-processing and the connected quality loss and to minimize safety risks due to under-processing. the present contribution presents numerical simulations of thermofluiddynamical phenomena inside of high pressure autoclaves and pulsed electric field treatment chambers. in PEF processing additionally the electric fields are considered. Implementing kinetics of occurring (bio-) chemical reactions in the numerical simulations of the temperature, flow and electric fields enables the evaluation of the process homogeneity and efficiency connected to different process parameters of the preservation techniques. Suggestions to achieve safe and high quality products are concluded out of the numerical results.

Counting Unfolding Events in Stretched Helices with Induced Oscillation by Optical Tweezers

Science.gov (United States)

Bacabac, Rommel Gaud; Otadoy, Roland

Correlation measures based on embedded probe fluctuations, single or paired, are now widely used for characterizing the viscoelastic properties of biological samples. However, more robust applications using this technique are still lacking. Considering that the study of living matter routinely demonstrates new and complex phenomena, mathematical and experimental tools for analysis have to catch up in order to arrive at newer insights. Therefore, we derive ways of probing non-equilibrium events in helical biopolymers provided by stretching beyond thermal forces. We generalize, for the first time, calculations for winding turn probabilities to account for unfolding events in single fibrous biopolymers and globular proteins under tensile stretching using twin optical traps. The approach is based on approximating the ensuing probe fluctuations as originating from a damped harmonic oscillator under oscillatory forcing.

Proving the correctness of unfold/fold program transformations using bisimulation

DEFF Research Database (Denmark)

Hamilton, Geoff W.; Jones, Neil

2011-01-01

by a labelled transition system whose bisimilarity relation is a congruence that coincides with contextual equivalence. Labelled transition systems are well-suited to represent global program behaviour. On the other hand, unfold/fold program transformations use generalization and folding, and neither is easy......This paper shows that a bisimulation approach can be used to prove the correctness of unfold/fold program transformation algorithms. As an illustration, we show how our approach can be use to prove the correctness of positive supercompilation (due to Sørensen et al). Traditional program equivalence...... to describe contextually, due to use of non-local information. We show that weak bisimulation on labelled transition systems gives an elegant framework to prove contextual equivalence of original and transformed programs. One reason is that folds can be seen in the context of corresponding unfolds....

Simulation of electron thermal transport in H-mode discharges

International Nuclear Information System (INIS)

Rafiq, T.; Pankin, A. Y.; Bateman, G.; Kritz, A. H.; Halpern, F. D.

2009-01-01

Electron thermal transport in DIII-D H-mode tokamak plasmas [J. L. Luxon, Nucl. Fusion 42, 614 (2002)] is investigated by comparing predictive simulation results for the evolution of electron temperature profiles with experimental data. The comparison includes the entire profile from the magnetic axis to the bottom of the pedestal. In the simulations, carried out using the automated system for transport analysis (ASTRA) integrated modeling code, different combinations of electron thermal transport models are considered. The combinations include models for electron temperature gradient (ETG) anomalous transport and trapped electron mode (TEM) anomalous transport, as well as a model for paleoclassical transport [J. D. Callen, Nucl. Fusion 45, 1120 (2005)]. It is found that the electromagnetic limit of the Horton ETG model [W. Horton et al., Phys. Fluids 31, 2971 (1988)] provides an important contribution near the magnetic axis, which is a region where the ETG mode in the GLF23 model [R. E. Waltz et al., Phys. Plasmas 4, 2482 (1997)] is below threshold. In simulations of DIII-D discharges, the observed shape of the H-mode edge pedestal is produced when transport associated with the TEM component of the GLF23 model is suppressed and transport given by the paleoclassical model is included. In a study involving 15 DIII-D H-mode discharges, it is found that with a particular combination of electron thermal transport models, the average rms deviation of the predicted electron temperature profile from the experimental profile is reduced to 9% and the offset to -4%.

The unfolded protein response has a protective role in yeast models of classic galactosemia

Directory of Open Access Journals (Sweden)

Evandro A. De-Souza

2014-01-01

Full Text Available Classic galactosemia is a human autosomal recessive disorder caused by mutations in the GALT gene (GAL7 in yeast, which encodes the enzyme galactose-1-phosphate uridyltransferase. Here we show that the unfolded protein response pathway is triggered by galactose in two yeast models of galactosemia: lithium-treated cells and the gal7Δ mutant. The synthesis of galactose-1-phosphate is essential to trigger the unfolded protein response under these conditions because the deletion of the galactokinase-encoding gene GAL1 completely abolishes unfolded protein response activation and galactose toxicity. Impairment of the unfolded protein response in both yeast models makes cells even more sensitive to galactose, unmasking its cytotoxic effect. These results indicate that endoplasmic reticulum stress is induced under galactosemic conditions and underscores the importance of the unfolded protein response pathway to cellular adaptation in these models of classic galactosemia.

Thermal transport in semicrystalline polyethylene by molecular dynamics simulation

Science.gov (United States)

Lu, Tingyu; Kim, Kyunghoon; Li, Xiaobo; Zhou, Jun; Chen, Gang; Liu, Jun

2018-01-01

Recent research has highlighted the potential to achieve high-thermal-conductivity polymers by aligning their molecular chains. Combined with other merits, such as low-cost, corrosion resistance, and light weight, such polymers are attractive for heat transfer applications. Due to their quasi-one-dimensional structural nature, the understanding on the thermal transport in those ultra-drawn semicrystalline polymer fibers or films is still lacking. In this paper, we built the ideal repeating units of semicrystalline polyethylene and studied their dependence of thermal conductivity on different crystallinity and interlamellar topology using the molecular dynamics simulations. We found that the conventional models, such as the Choy-Young's model, the series model, and Takayanagi's model, cannot accurately predict the thermal conductivity of the quasi-one-dimensional semicrystalline polyethylene. A modified Takayanagi's model was proposed to explain the dependence of thermal conductivity on the bridge number at intermediate and high crystallinity. We also analyzed the heat transfer pathways and demonstrated the substantial role of interlamellar bridges in the thermal transport in the semicrystalline polyethylene. Our work could contribute to the understanding of the structure-property relationship in semicrystalline polymers and shed some light on the development of plastic heat sinks and thermal management in flexible electronics.

Simulation of the diffusion of implanted impurities in silicon structures at the rapid thermal annealing

International Nuclear Information System (INIS)

Komarov, F.F.; Komarov, A.F.; Mironov, A.M.; Makarevich, Yu.V.; Miskevich, S.A.; Zayats, G.M.

2011-01-01

Physical and mathematical models and numerical simulation of the diffusion of implanted impurities during rapid thermal treatment of silicon structures are discussed. The calculation results correspond to the experimental results with a sufficient accuracy. A simulation software system has been developed that is integrated into ATHENA simulation system developed by Silvaco Inc. This program can simulate processes of the low-energy implantation of B, BF 2 , P, As, Sb, C ions into the silicon structures and subsequent rapid thermal annealing. (authors)

Effects of Anisotropic Thermal Conductivity in Magnetohydrodynamics Simulations of a Reversed-Field Pinch

International Nuclear Information System (INIS)

Onofri, M.; Malara, F.; Veltri, P.

2010-01-01

A compressible magnetohydrodynamics simulation of the reversed-field pinch is performed including anisotropic thermal conductivity. When the thermal conductivity is much larger in the direction parallel to the magnetic field than in the perpendicular direction, magnetic field lines become isothermal. As a consequence, as long as magnetic surfaces exist, a temperature distribution is observed displaying a hotter confined region, while an almost uniform temperature is produced when the magnetic field lines become chaotic. To include this effect in the numerical simulation, we use a multiple-time-scale analysis, which allows us to reproduce the effect of a large parallel thermal conductivity. The resulting temperature distribution is related to the existence of closed magnetic surfaces, as observed in experiments. The magnetic field is also affected by the presence of an anisotropic thermal conductivity.

CFD simulation for thermal mixing of a SMART flow mixing header assembly

International Nuclear Information System (INIS)

Kim, Young In; Bae, Youngmin; Chung, Young Jong; Kim, Keung Koo

2015-01-01

Highlights: • Thermal mixing performance of a FMHA installed in SMART is investigated numerically. • Effects of operating condition and discharge hole configuration are examined. • FMHA performance satisfies the design requirements under various abnormal conditions. - Abstract: A flow mixing header assembly (FMHA) is installed in a system-integrated modular advanced reactor (SMART) to enhance the thermal mixing capability and create a uniform core flow distribution under both normal operation and accident conditions. In this study, the thermal mixing characteristics of the FMHA are investigated for various steam generator conditions using a commercial CFD code. Simulations include investigations for the effects of FMHA discharge flow rate differences, turbulence models, and steam generator conditions. The results of the analysis show that the FMHA works effectively for thermal mixing in various conditions and makes the temperature difference at the core inlet decrease noticeably. We verified that the mixing capability of the FMHA is excellent and satisfies the design requirement in all simulation cases tested here

Weldability prediction of high strength steel S960QL after weld thermal cycle simulation

Directory of Open Access Journals (Sweden)

M. Dunđer

2014-10-01

Full Text Available This paper presents weld thermal cycle simulation of high strength steel S960QL, and describes influence of cooling time t8/5 on hardness and impact toughness of weld thermal cycle simulated specimens. Furthermore, it presents analysis of characteristic fractions done by electron scanning microscope which can contribute to determination of welding parameters for S960QL steel.

Non-leftmost Unfolding in Partial Evaluation of Logic Programs with Impure Predicates

DEFF Research Database (Denmark)

Albert, Elvira; Puebla, German; Gallagher, John Patrick

2006-01-01

-leftmost unfolding steps can result in incorrect results since the independence of the computation rule no longer holds in the presence of impure predicates. Existing proposals allow non-leftmost unfolding steps, but at the cost of accuracy: bindings and failure are not propagated backwards to predicates which...

Probing force-induced unfolding intermediates of a single staphylococcal nuclease molecule and the effect of ligand binding

International Nuclear Information System (INIS)

Ishii, Takaaki; Murayama, Yoshihiro; Katano, Atsuto; Maki, Kosuke; Kuwajima, Kunihiro; Sano, Masaki

2008-01-01

Single-molecule manipulation techniques have given experimental access to unfolding intermediates of proteins that are inaccessible in conventional experiments. A detailed characterization of the intermediates is a challenging problem that provides new possibilities for directly probing the energy landscape of proteins. We investigated single-molecule mechanical unfolding of a small globular protein, staphylococcal nuclease (SNase), using atomic force microscopy. The unfolding trajectories of the protein displayed sub-molecular and stochastic behavior with typical lengths corresponding to the size of the unfolded substructures. Our results support the view that the single protein unfolds along multiple pathways as suggested in recent theoretical studies. Moreover, we found the drastic change, caused by the ligand and inhibitor bindings, in the mechanical unfolding dynamics

Individual globular domains and domain unfolding visualized in overstretched titin molecules with atomic force microscopy.

Directory of Open Access Journals (Sweden)

Zsolt Mártonfalvi

Full Text Available Titin is a giant elastomeric protein responsible for the generation of passive muscle force. Mechanical force unfolds titin's globular domains, but the exact structure of the overstretched titin molecule is not known. Here we analyzed, by using high-resolution atomic force microscopy, the structure of titin molecules overstretched with receding meniscus. The axial contour of the molecules was interrupted by topographical gaps with a mean width of 27.7 nm that corresponds well to the length of an unfolded globular (immunoglobulin and fibronectin domain. The wide gap-width distribution suggests, however, that additional mechanisms such as partial domain unfolding and the unfolding of neighboring domain multimers may also be present. In the folded regions we resolved globules with an average spacing of 5.9 nm, which is consistent with a titin chain composed globular domains with extended interdomain linker regions. Topographical analysis allowed us to allocate the most distal unfolded titin region to the kinase domain, suggesting that this domain systematically unfolds when the molecule is exposed to overstretching forces. The observations support the prediction that upon the action of stretching forces the N-terminal ß-sheet of the titin kinase unfolds, thus exposing the enzyme's ATP-binding site and hence contributing to the molecule's mechanosensory function.

Simulation of attenuation of thermal fluctuations near a plate impinged by jets

International Nuclear Information System (INIS)

Simoneau, J.P.

2001-01-01

In nuclear reactors, and especially in liquid sodium cooled ones, the combination of temperature differences inside cooling fluid, turbulent flows and high heat transfer coefficients is a potential source of the thermal striping process. Such a phenomenon has been studied for several years by using Large Eddy Simulation models. The present paper focuses on the attenuation of the thermal fluctuations in the boundary layer. The knowledge of this amplitude reduction is of prime importance for subsequent mechanical analyses. A Large Eddy Simulation model is implemented in the Star-cd code, including discretization of the viscous sublayer. The numerical simulation of two parallel jets impinging a flat plate in water is then performed and positively compared to corresponding experimental results. (author)

MHD simulations of coronal dark downflows considering thermal conduction

Science.gov (United States)

Zurbriggen, E.; Costa, A.; Esquivel, A.; Schneiter, M.; Cécere, M.

2017-10-01

While several scenarios have been proposed to explain supra-arcade downflows (SADs) observed descending through turbulent hot regions, none of them have systematically addressed the consideration of thermal conduction. The SADs are known to be voided cavities. Our model assumes that SADs are triggered by bursty localized reconnection events that produce non-linear waves generating the voided cavity. These subdense cavities are sustained in time because they are hotter than their surrounding medium. Due to the low density and large temperature values of the plasma we expect the thermal conduction to be an important process. Our main aim here is to study if it is possible to generate SADs in the framework of our model considering thermal conduction. We carry on 2D MHD simulations including anisotropic thermal conduction, and find that if the magnetic lines envelope the cavities, they can be isolated from the hot environment and be identified as SADs.

Complete all-atom hydrodynamics of protein unfolding in uniform flow

International Nuclear Information System (INIS)

Wang, Guan M; Sandberg, William C

2010-01-01

The unfolding dynamics of a protein, ubiquitin, pinned in several uniform flows, was studied at low and high flow rates in an all-atom style through a non-equilibrium molecular dynamics approach with explicit water molecules included. Atomic hydrodynamic force components on individual amino acids, as a function of time, due to the collisional interactions with the flowing water molecules were calculated explicitly. The protein conformational change in response to those time-varying forces was computed completely at the high flow rate up to nanosecond until the fully stretched state was reached. The end-to-end length of the single ubiquitin protein molecule at high flow rate is smoothly increasing. The step-like jumps between metastable states that describe the μm ms -1 scale force pulling experiments conducted on polyubiquitins at low flow rates, are not seen at the high flow speeds necessary to computationally probe the ns nm -1 scale regime. No unfolding was observed in the low flow rate atomic computations at nanosecond scale while partial and complete unfolding was observed in the coarse-grained low flow rate computations at microsecond scale. Examination of the all-atom computation of the time variation of the hydrodynamic forces on, and the velocity components of, the protein molecule unveiled to some extent the details of the complexity of the hydrodynamic friction variation in the nm ns -1 regime of high rate flow-driven protein unfolding. This demonstrates quantitatively that all-atom computations are more suitable than the Langevin equation or Brownian dynamics methods for probing the interaction dynamics and resulting conformational dynamics of protein unfolding in strong flows on nm ns -1 time/length scales while the reverse is true for investigation of slow, diffusively driven systems.

A novel neutron energy spectrum unfolding code using particle swarm optimization

International Nuclear Information System (INIS)

Shahabinejad, H.; Sohrabpour, M.

2017-01-01

A novel neutron Spectrum Deconvolution using Particle Swarm Optimization (SDPSO) code has been developed to unfold the neutron spectrum from a pulse height distribution and a response matrix. The Particle Swarm Optimization (PSO) imitates the bird flocks social behavior to solve complex optimization problems. The results of the SDPSO code have been compared with those of the standard spectra and recently published Two-steps Genetic Algorithm Spectrum Unfolding (TGASU) code. The TGASU code have been previously compared with the other codes such as MAXED, GRAVEL, FERDOR and GAMCD and shown to be more accurate than the previous codes. The results of the SDPSO code have been demonstrated to match well with those of the TGASU code for both under determined and over-determined problems. In addition the SDPSO has been shown to be nearly two times faster than the TGASU code. - Highlights: • Introducing a novel method for neutron spectrum unfolding. • Implementation of a particle swarm optimization code for neutron unfolding. • Comparing results of the PSO code with those of recently published TGASU code. • Match results of the PSO code with those of TGASU code. • Greater convergence rate of implemented PSO code than TGASU code.

Unfolding Semantics of the Untyped λ-Calculus with lectrec-Calculus with letrec

NARCIS (Netherlands)

Rochel, J.

2016-01-01

We investigate the relationship between finite terms in lambda-letrec, the lambda calculus with letrec, and the infinite lambda terms they express. We say that a lambda-letrec term expresses a lambda term if the latter can be obtained as an infinite unfolding of the former. Unfolding is the process

Mapping of unfolding states of integral helical membrane proteins by GPS-NMR and scattering techniques

DEFF Research Database (Denmark)

Calcutta, Antonello; Jessen, Christian M; Behrens, Manja Annette

2012-01-01

induced by unfolding of an integral membrane protein, namely TFE-induced unfolding of KcsA solubilized by the n-dodecyl ß-d-maltoside (DDM) surfactant is investigated by the recently introduced GPS-NMR (Global Protein folding State mapping by multivariate NMR) (Malmendal et al., PlosONE 5, e10262 (2010......)) along with dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS). GPS-NMR is used as a tool for fast analysis of the protein unfolding processes upon external perturbation, and DLS and SAXS are used for further structural characterization of the unfolding states. The combination allows...

Bosonic Fradkin-Tseytlin equations unfolded

Energy Technology Data Exchange (ETDEWEB)

Shaynkman, O.V. [I.E.Tamm Theory Department, Lebedev Physical Institute,Leninski prospect 53, 119991, Moscow (Russian Federation)

2016-12-22

We test infinite-dimensional extension of algebra su(k,k) proposed by Fradkin and Linetsky as the candidate for conformal higher spin algebra. Adjoint and twisted-adjoint representations of su(k,k) on the space of this algebra are carefully explored. For k=2 corresponding unfolded system is analyzed and it is shown to encode Fradkin-Tseytlin equations for the set of all integer spins 1,2,… with infinite multiplicity.

Development of the NSSS thermal-hydraulic program for YGN unit 1 simulator

Energy Technology Data Exchange (ETDEWEB)

Kim, Kyung Doo; Jeong, Jae Jun; Lee, Won Jae; Chung, Bub Dong; Ha, Kwi Seok; Kang, Kyung Ho

2000-09-01

The NSSS thermal-hydraulic programs installed in the domestic full-scope power plant simulators were provided in early 1980s by foreign vendors. Because of limited computational capability at that time, they usually adopt very simplified physical models for a real-time simulation of NSSS thermal-hydraulic phenomena, which entails inaccurate results and the possibility of so-called 'negative training', especially for complicated two-phase flows in the reactor coolant system. To resolve the problem, we developed a realistic NSSS T/H program (named 'ARTS' code) for use in YongGwang Nuclear Unit 1 full-scope simulator. The best-estimate code RETRAN03, developed by EPRI and approved by USNRC, was selected as a reference code of ARTS. For the development of ARTS, the followings have been performed: -Improvement of the robustness of RETRAN - Improvement of the real-time simulation capability of RETRAN - Optimum input data generation for the NSSS simulation - New model development that cannot be efficiently modeled by RETRAN - Assessment of the ARTS code. The systematic assessment of ARTS has been conducted in both personal computers (Windows 98, Visual fortran) and the simulator development environment (Windows NT, GSE simulator development tool). The results were resonable in terms of accuracy, real-time simulation and robustness.

Development of the NSSS thermal-hydraulic program for YGN unit 1 simulator

International Nuclear Information System (INIS)

Kim, Kyung Doo; Jeong, Jae Jun; Lee, Won Jae; Chung, Bub Dong; Ha, Kwi Seok; Kang, Kyung Ho

2000-09-01

The NSSS thermal-hydraulic programs installed in the domestic full-scope power plant simulators were provided in early 1980s by foreign vendors. Because of limited computational capability at that time, they usually adopt very simplified physical models for a real-time simulation of NSSS thermal-hydraulic phenomena, which entails inaccurate results and the possibility of so-called 'negative training', especially for complicated two-phase flows in the reactor coolant system. To resolve the problem, we developed a realistic NSSS T/H program (named 'ARTS' code) for use in YongGwang Nuclear Unit 1 full-scope simulator. The best-estimate code RETRAN03, developed by EPRI and approved by USNRC, was selected as a reference code of ARTS. For the development of ARTS, the followings have been performed: -Improvement of the robustness of RETRAN - Improvement of the real-time simulation capability of RETRAN - Optimum input data generation for the NSSS simulation - New model development that cannot be efficiently modeled by RETRAN - Assessment of the ARTS code. The systematic assessment of ARTS has been conducted in both personal computers (Windows 98, Visual fortran) and the simulator development environment (Windows NT, GSE simulator development tool). The results were resonable in terms of accuracy, real-time simulation and robustness

Comparison of intra-organellar chaperone capacity for dealing with stress-induced protein unfolding

NARCIS (Netherlands)

Hageman, Jurre; Vos, Michel J.; van Waarde, Maria A. W. H.; Kampinga, Harm H.

2007-01-01

Molecular chaperones are essential for cells to prevent that partially unfolded proteins form non-functional, toxic aggregates. This requirement is increased when cells experience protein unfolding stresses and such could affect all compartments in the eukaryotic cell. Whether all organelles are

Comparison of neutron spectrum unfolding codes

International Nuclear Information System (INIS)

Zijp, W.

1979-02-01

This final report contains a set of four ECN-reports. The first is dealing with the comparison of the neutron spectrum unfolding codes CRYSTAL BALL, RFSP-JUL, SAND II and STAY'SL. The other three present the results of calculations about the influence of statistical weights in CRYSTAL BALL, SAND II and RFSP-JUL

ATWS thermal-hydraulic analysis for Krsko Full Scope Simulator validation

International Nuclear Information System (INIS)

Parzer, I.; Kljenak, I.

2005-01-01

The purpose of this analysis was to simulate Anticipated Transient without Scram transient for Krsko NPP. The results of these calculations were used for annual ANSI/ANS validation of reactor coolant system thermal-hydraulic response predicted by Krsko Full Scope Simulator. For the thermal-hydraulic analyses the RELAP5/MOD3.3 code and the input model for NPP Krsko, delivered by NPP Krsko, was used. In the presented paper the most severe ATWS scenario has been analyzed, starting with the loss of Main Feedwater at both steam generators. Thus, gradual loss of secondary heat sink occurred. On top of that, control rods were not supposed to scram, leaving the chain reaction to be controlled only by inherent physical properties of the fuel and moderator and eventual actions of the BOP system. The primary system response has been studied assuming AMSAC availability. (author)

HELIOSEISMIC HOLOGRAPHY OF SIMULATED SUNSPOTS: MAGNETIC AND THERMAL CONTRIBUTIONS TO TRAVEL TIMES

Energy Technology Data Exchange (ETDEWEB)

Felipe, T. [Departamento de Astrofísica, Universidad de La Laguna, E-38205 La Laguna, Tenerife (Spain); Braun, D. C.; Crouch, A. D. [NorthWest Research Associates, Colorado Research Associates, Boulder, CO 80301 (United States); Birch, A. C., E-mail: tobias@iac.es [Max-Planck-Institut für Sonnensystemforschung, Justus-von-Liebig-Weg 3, D-37077 Göttingen (Germany)

2016-10-01

Wave propagation through sunspots involves conversion between waves of acoustic and magnetic character. In addition, the thermal structure of sunspots is very different than that of the quiet Sun. As a consequence, the interpretation of local helioseismic measurements of sunspots has long been a challenge. With the aim of understanding these measurements, we carry out numerical simulations of wave propagation through sunspots. Helioseismic holography measurements made from the resulting simulated wavefields show qualitative agreement with observations of real sunspots. We use additional numerical experiments to determine, separately, the influence of the thermal structure of the sunspot and the direct effect of the sunspot magnetic field. We use the ray approximation to show that the travel-time shifts in the thermal (non-magnetic) sunspot model are primarily produced by changes in the wave path due to the Wilson depression rather than variations in the wave speed. This shows that inversions for the subsurface structure of sunspots must account for local changes in the density. In some ranges of horizontal phase speed and frequency there is agreement (within the noise level in the simulations) between the travel times measured in the full magnetic sunspot model and the thermal model. If this conclusion proves to be robust for a wide range of models, it would suggest a path toward inversions for sunspot structure.

HELIOSEISMIC HOLOGRAPHY OF SIMULATED SUNSPOTS: MAGNETIC AND THERMAL CONTRIBUTIONS TO TRAVEL TIMES

International Nuclear Information System (INIS)

Felipe, T.; Braun, D. C.; Crouch, A. D.; Birch, A. C.

2016-01-01

Wave propagation through sunspots involves conversion between waves of acoustic and magnetic character. In addition, the thermal structure of sunspots is very different than that of the quiet Sun. As a consequence, the interpretation of local helioseismic measurements of sunspots has long been a challenge. With the aim of understanding these measurements, we carry out numerical simulations of wave propagation through sunspots. Helioseismic holography measurements made from the resulting simulated wavefields show qualitative agreement with observations of real sunspots. We use additional numerical experiments to determine, separately, the influence of the thermal structure of the sunspot and the direct effect of the sunspot magnetic field. We use the ray approximation to show that the travel-time shifts in the thermal (non-magnetic) sunspot model are primarily produced by changes in the wave path due to the Wilson depression rather than variations in the wave speed. This shows that inversions for the subsurface structure of sunspots must account for local changes in the density. In some ranges of horizontal phase speed and frequency there is agreement (within the noise level in the simulations) between the travel times measured in the full magnetic sunspot model and the thermal model. If this conclusion proves to be robust for a wide range of models, it would suggest a path toward inversions for sunspot structure.

Moessbauer spectroscopic evidence on the heme binding to the proximal histidine in unfolded carbonmonoxy myoglobin by guanidine hydrochloride

Energy Technology Data Exchange (ETDEWEB)

Harami, Taikan, E-mail: harami.taikan@jaea.go.jp [Japan Atomic Energy Agency (Japan); Kitao, Shinji; Kobayashi, Yasuhiro [Kyoto University, Research Reactor Institute (Japan); Mitsui, Takaya [Japan Atomic Energy Agency (Japan)

2008-01-15

The unfolded heme structure in myoglobin is controversial because of no chance of direct X-ray structure analyses. The unfolding of carbonmonoxy myoglobin (MbCO) by guanidine hydrochloride (GdnHCl) was studied by the Moessbauer spectroscopy. The spectra show the presence of a sort of spectrum in the unfolded MbCO, independent on the concentration of GdnHCl from 1 to 6 M and the increase of the fraction of unfolded MbCO, depending on the GdnHCl concentration. The isomer shift of the iron of heme in the unfolded MbCO was identified to be different from that of the native MbCO as the globin structure in Mb collapses under the unfolded conditions. This result and the existing related Moessbauer data proved that the heme in the unfolded MbCO may remain coordinated to the proximal histidine.

thermal characteristics of a simulated non-radioactive agricultural waste

International Nuclear Information System (INIS)

Ahmed, A.Z.; Soliman, H.M.; Abdelmoniem, M.

2004-01-01

characterization of thermal degradation of a mixture of a simulated non radioactive contaminated almond shell and cotton straw is important to check possibility of its safe treatment by pyrolysis. thermal analysis of the mixture was carried out using thermal gravimetric analysis (TGA) under inert atmosphere. thermal degradation of almond shell and cotton straw mixture takes place in two stages namely, volatilization stage and decarbonization stage. kinetics of the thermal degradation was studied to determine the reaction rate, activation energy, entropy change, enthalpy change and free energy for both stages. during pyrolysis, 5.8% water Vapor, 46.4% condensed gases, 29.2% condensed gases, and 18.6% pyrolysis coke residue by weight were obtained . analysis of pyrolysis condensed gases showed that it contained 24.2% N 2 ,7.1% CO, 14% H 2 and 17.3 CO 2 by weight. in addition, results revealed that the heavy elements are concentrated in the coke residue. it was found that the rate constant of the reacion increases by the increase in the temperature for both sages. more above, results revealed that the activation energy for volatilization stage is higher than decarbonization stage

Comparison of intra-organellar chaperone capacity for dealing with stress-induced protein unfolding.

Science.gov (United States)

Hageman, Jurre; Vos, Michel J; van Waarde, Maria A W H; Kampinga, Harm H

2007-11-23

Molecular chaperones are essential for cells to prevent that partially unfolded proteins form non-functional, toxic aggregates. This requirement is increased when cells experience protein unfolding stresses and such could affect all compartments in the eukaryotic cell. Whether all organelles are equipped with comparable chaperone capacities is largely unknown, mainly due to the lack of suitable reporters that allow such a comparison. Here we describe the development of fluorescent luciferase reporters that are sorted to various cellular locations (nucleus, cytoplasm, endoplasmic reticulum, and peroxisomes) and that differ minimally in their intrinsic thermal stability properties. When heating living cells, the rate of inactivation was most rapid for the nuclear-targeted luciferase, indicating that the nucleus is the most sensitive organelle toward heat-induced denaturing stress. Post-heat re-activation, however, occurred at equal kinetics irrespective of luciferase localization. Also, induction of thermotolerance by a priming heat treatment, that coordinately up-regulates all heat-inducible chaperones, resulted in a transient heat resistance of the luciferase in all organelles in a comparable manner. Overexpression of the main heat-inducible Hsp70 family member, HspA1A, protected only the cytosolic and nuclear, but not the other luciferases. Together, our data suggest that in each compartment investigated, including the peroxisome in which so far no chaperones could be detected, chaperone machines are present and can be induced with activities similar to those present in the cytosolic/nuclear compartment.

The thermal pressure distribution of a simulated cold neutral medium

Energy Technology Data Exchange (ETDEWEB)

Gazol, Adriana, E-mail: a.gazol@crya.unam.mx [Centro de Radioastronomía y Astrofísica, UNAM, A. P. 3-72, c.p. 58089 Morelia, Michoacán (Mexico)

2014-07-01

We numerically study the thermal pressure distribution in a gas with thermal properties similar to those of the cold neutral interstellar gas by analyzing three-dimensional hydrodynamic models in boxes with sides of 100 pc with turbulent compressible forcing at 50 pc and different Mach numbers. We find that at high pressures and for large Mach numbers, both the volume-weighted and the density-weighted distributions can be appropriately described by a log-normal distribution, whereas for small Mach numbers they are better described by a power law. Thermal pressure distributions resulting from similar simulations but with self-gravity differ only for low Mach numbers; in this case, they develop a high pressure tail.

Thermal inertia and energy efficiency – Parametric simulation assessment on a calibrated case study

International Nuclear Information System (INIS)

Aste, Niccolò; Leonforte, Fabrizio; Manfren, Massimiliano; Mazzon, Manlio

2015-01-01

Highlights: • We perform a parametric simulation study on a calibrated building energy model. • We introduce adaptive shadings and night free cooling in simulations. • We analyze the effect of thermal capacity on the parametric simulations results. • We recognize that cooling demand and savings scales linearly with thermal capacity. • We assess the advantage of medium-heavy over medium and light configurations. - Abstract: The reduction of energy consumption for heating and cooling services in the existing building stock is a key challenge for global sustainability today and buildings’ envelopes retrofit is one the main issues. Most of the existing buildings’ envelopes have low levels of insulation, high thermal losses due to thermal bridges and cracks, absence of appropriate solar control, etc. Further, in building refurbishment, the importance of a system level approach is often undervalued in favour of simplistic “off the shelf” efficient solutions, focused on the reduction of thermal transmittance and on the enhancement of solar control capabilities. In many cases, the importance of the dynamic thermal properties is often neglected or underestimated and the effective thermal capacity is not properly considered as one of the design parameters. The research presented aims to critically assess the influence of the dynamic thermal properties of the building fabric (roof, walls and floors) on sensible heating and cooling energy demand for a case study. The case study chosen is an existing office building which has been retrofitted in recent years and whose energy model has been calibrated according to the data collected in the monitoring process. The research illustrates the variations of the sensible thermal energy demand of the building in different retrofit scenarios, and relates them to the variations of the dynamic thermal properties of the construction components. A parametric simulation study has been performed, encompassing the use of

BONDI-97 A novel neutron energy spectrum unfolding tool using a genetic algorithm

CERN Document Server

Mukherjee, B

1999-01-01

The neutron spectrum unfolding procedure using the count rate data obtained from a set of Bonner sphere neutron detectors requires the solution of the Fredholm integral equation of the first kind by using complex mathematical methods. This paper reports a new approach for the unfolding of neutron spectra using the Genetic Algorithm tool BONDI-97 (BOnner sphere Neutron DIfferentiation). The BONDI-97 was used as the input for Genetic Algorithm engine EVOLVER to search for a globally optimised solution vector from a population of randomly generated solutions. This solution vector corresponds to the unfolded neutron energy spectrum. The Genetic Algorithm engine emulates the Darwinian 'Survival of the Fittest' strategy, the key ingredient of the 'Theory of Evolution'. The spectra of sup 2 sup 4 sup 1 Am/Be (alpha,n) and sup 2 sup 3 sup 9 Pu/Be (alpha,n) neutron sources were unfolded using the BONDI-97 tool. (author)

Practical considerations in developing numerical simulators for thermal recovery

Energy Technology Data Exchange (ETDEWEB)

Abou-Kassem, J.H. [Chemical and Petroleum Engineering Department, UAE University, Al-Ain (United Arab Emirates)

1996-08-15

Numerical simulation of steam injection and in-situ combustion-based oil recovery processes is of great importance in project design. Development of such numerical simulators is an on-going process, with improvements made as the process description becomes more complete, and also as better methods are devised to resolve certain numerical difficulties. This paper addresses some of the latter, and based on the author`s experience gives useful guidelines for developing more efficient numerical simulators of steam injection and in-situ combustion. The paper takes up a series of questions related to simulating thermal processes. Included are: the elimination of constraint equations at the matrix level, phase change, steam injection rate, alternative treatments of heat loss, relative permeabilities and importance of hysteresis effects, improved solutions to the grid orientation problem and other simulation problems such as potential inversion, grid block size, time-step size control and induced fractures. The points discussed in the paper should be of use to both simulator developers and users alike, and will lead to a better understanding of simulation results

The criteria for selecting a method for unfolding neutron spectra based on the information entropy theory

International Nuclear Information System (INIS)

Zhu, Qingjun; Song, Fengquan; Ren, Jie; Chen, Xueyong; Zhou, Bin

2014-01-01

To further expand the application of an artificial neural network in the field of neutron spectrometry, the criteria for choosing between an artificial neural network and the maximum entropy method for the purpose of unfolding neutron spectra was presented. The counts of the Bonner spheres for IAEA neutron spectra were used as a database, and the artificial neural network and the maximum entropy method were used to unfold neutron spectra; the mean squares of the spectra were defined as the differences between the desired and unfolded spectra. After the information entropy of each spectrum was calculated using information entropy theory, the relationship between the mean squares of the spectra and the information entropy was acquired. Useful information from the information entropy guided the selection of unfolding methods. Due to the importance of the information entropy, the method for predicting the information entropy using the Bonner spheres' counts was established. The criteria based on the information entropy theory can be used to choose between the artificial neural network and the maximum entropy method unfolding methods. The application of an artificial neural network to unfold neutron spectra was expanded. - Highlights: • Two neutron spectra unfolding methods, ANN and MEM, were compared. • The spectrum's entropy offers useful information for selecting unfolding methods. • For the spectrum with low entropy, the ANN was generally better than MEM. • The spectrum's entropy was predicted based on the Bonner spheres' counts

The Modeling and Simulation of Thermal Analysis at Hydro Generator Stator Winding Insulation

Directory of Open Access Journals (Sweden)

Mihaela Raduca

2006-10-01

Full Text Available This paper presents the modelling and simulation of thermal analysis at hydro generator stator winding. The winding stator is supplied at high voltage of 11 kV for high power hydro generator. To present the thermal analysis for stator winding is presented at supply of coil by 11 kV, when coil is heat and thermal transfer in insulation at ambient temperature.

FERD and FERDOR type unfolding codes

International Nuclear Information System (INIS)

Burrus, W.R.

1976-01-01

FERD and FERDO are unfolding codes which were developed at the Neutron Physics Division of Oak Ridge National Laboratory in 1965 and 1966. FERDO variants such as FERDOR and FORIST have been widely used, and many useful supplementary procedures have been developed for neutron and gamma-ray spectroscopy and other diverse applications. Algorithms for the codes are discussed

Development of the unfolding procedures in fast neutron scintillation spectrometry; Razvoj unfolding procedura u scintilacionoj spektrometriji brzih neutrona

Energy Technology Data Exchange (ETDEWEB)

Marinkovic, P [Elektrotehnicki fakultet, Belgrade (Yugoslavia)

1988-07-01

Two unfolding procedures have been developed for obtaining fast neutron spectrum from proton-recoil spectrum assigned for spectrometry with organic scintillators. First is the method of differentiation of proton-recoil spectrum, and the second is the method based on solution of integral equation of Fredholm of first kind. (author)

Sequential Events in the Irreversible Thermal Denaturation of Human Brain-Type Creatine Kinase by Spectroscopic Methods

Directory of Open Access Journals (Sweden)

Yan-Song Gao

2010-06-01

Full Text Available The non-cooperative or sequential events which occur during protein thermal denaturation are closely correlated with protein folding, stability, and physiological functions. In this research, the sequential events of human brain-type creatine kinase (hBBCK thermal denaturation were studied by differential scanning calorimetry (DSC, CD, and intrinsic fluorescence spectroscopy. DSC experiments revealed that the thermal denaturation of hBBCK was calorimetrically irreversible. The existence of several endothermic peaks suggested that the denaturation involved stepwise conformational changes, which were further verified by the discrepancy in the transition curves obtained from various spectroscopic probes. During heating, the disruption of the active site structure occurred prior to the secondary and tertiary structural changes. The thermal unfolding and aggregation of hBBCK was found to occur through sequential events. This is quite different from that of muscle-type CK (MMCK. The results herein suggest that BBCK and MMCK undergo quite dissimilar thermal unfolding pathways, although they are highly conserved in the primary and tertiary structures. A minor difference in structure might endow the isoenzymes dissimilar local stabilities in structure, which further contribute to isoenzyme-specific thermal stabilities.

MATLAB Simulation of Photovoltaic and Photovoltaic/Thermal Systems Performance

Science.gov (United States)

Nasir, Farah H. M.; Husaini, Yusnira

2018-03-01

The efficiency of the photovoltaic reduces when the photovoltaic cell temperature increased due to solar irradiance. One solution is come up with the cooling system photovoltaic system. This combination is forming the photovoltaic-thermal (PV/T) system. Not only will it generate electricity also heat at the same time. The aim of this research is to focus on the modeling and simulation of photovoltaic (PV) and photovoltaic-thermal (PV/T) electrical performance by using single-diode equivalent circuit model. Both PV and PV/T models are developed in Matlab/Simulink. By providing the cooling system in PV/T, the efficiency of the system can be increased by decreasing the PV cell temperature. The maximum thermal, electrical and total efficiency values of PV/T in the present research are 35.18%, 15.56% and 50.74% at solar irradiance of 400 W/m2, mass flow rate of 0.05kgs-1 and inlet temperature of 25 °C respectively has been obtained. The photovoltaic-thermal shows that the higher efficiency performance compared to the photovoltaic system.

Thermal Field Analysis and Simulation of an Infrared Belt Furnace Used for Solar Cells

Directory of Open Access Journals (Sweden)

Bai Lu

2014-01-01

Full Text Available During solar cell firing, volatile organic compounds (VOC and a small number of metal particles were removed using the gas flow. When the gas flow was disturbed by the thermal field of infrared belt furnace and structure, the metal particles in the discharging gas flow randomly adhered to the surface of solar cell, possibly causing contamination. Meanwhile, the gas flow also affected the thermal uniformity of the solar cell. In this paper, the heating mechanism of the solar cell caused by radiation, convection, and conduction during firing was analyzed. Afterward, four 2-dimensional (2D models of the furnace were proposed. The transient thermal fields with different gas inlets, outlets, and internal structures were simulated. The thermal fields and the temperature of the solar cell could remain stable and uniform when the gas outlets were installed at the ends and in the middle of the furnace, with the gas inlets being distributed evenly. To verify the results, we produced four types of furnaces according to the four simulated results. The experimental results indicated that the thermal distribution of the furnace and the characteristics of the solar cells were consistent with the simulation. These experiments improved the efficiency of the solar cells while optimizing the solar cell manufacturing equipment.

Thermal lattice Boltzmann simulation for multispecies fluid equilibration

International Nuclear Information System (INIS)

Vahala, Linda; Wah, Darren; Vahala, George; Carter, Jonathan; Pavlo, Pavol

2000-01-01

The equilibration rate for multispecies fluids is examined using thermal lattice Boltzmann simulations. Two-dimensional free-decay simulations are performed for effects of velocity shear layer turbulence on sharp temperature profiles. In particular, parameters are so chosen that the lighter species is turbulent while the heavier species is laminar--and so its vorticity layers would simply decay and diffuse in time. With species coupling, however, there is velocity equilibration followed by the final relaxation to one large co- and one large counter-rotating vortex. The temperature equilibration proceeds on a slower time scale and is in good agreement with the theoretical order of magnitude estimate of Morse [Phys. Fluids 6, 1420 (1963)]. (c) 2000 The American Physical Society

Thermal lattice Boltzmann simulation for multispecies fluid equilibration

Energy Technology Data Exchange (ETDEWEB)

Vahala, Linda [Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, Virginia 23529 (United States); Wah, Darren [Department of Physics, William and Mary College, Williamsburg, Virginia 23187 (United States); Vahala, George [Department of Physics, William and Mary College, Williamsburg, Virginia 23187 (United States); Carter, Jonathan [NERSC, Lawrence Berkeley Laboratory, Berkeley, California 97320 (United States); Pavlo, Pavol [Institute of Plasma Physics, Czech Academy of Science, Praha 8, (Czech Republic)

2000-07-01

The equilibration rate for multispecies fluids is examined using thermal lattice Boltzmann simulations. Two-dimensional free-decay simulations are performed for effects of velocity shear layer turbulence on sharp temperature profiles. In particular, parameters are so chosen that the lighter species is turbulent while the heavier species is laminar--and so its vorticity layers would simply decay and diffuse in time. With species coupling, however, there is velocity equilibration followed by the final relaxation to one large co- and one large counter-rotating vortex. The temperature equilibration proceeds on a slower time scale and is in good agreement with the theoretical order of magnitude estimate of Morse [Phys. Fluids 6, 1420 (1963)]. (c) 2000 The American Physical Society.

Modeling and simulation of thermally actuated bilayer plates

Science.gov (United States)

Bartels, Sören; Bonito, Andrea; Muliana, Anastasia H.; Nochetto, Ricardo H.

2018-02-01

We present a mathematical model of polymer bilayers that undergo large bending deformations when actuated by non-mechanical stimuli such as thermal effects. The simple model captures a large class of nonlinear bending effects and can be discretized with standard plate elements. We devise a fully practical iterative scheme and apply it to the simulation of folding of several practically useful compliant structures comprising of thin elastic layers.

Calorimetric studies of the thermal denaturation of cytochrome c peroxidase

International Nuclear Information System (INIS)

Kresheck, G.C.; Erman, J.E.

1988-01-01

Two endotherms are observed by differential scanning calorimetry during the thermal denaturation of cytochrome c peroxidase at pH 7.0. The transition midpoint temperatures (t/sub m/) were 43.9 +- 1.4 and 63.3 +- 1.6 0 C, independent of concentration. The two endotherms were observed at all pH values between 4 and 8, with the transition temperatures varying with pH. Precipitation was observed between pH 4 and 6, and only qualitative data are presented for this region. The thermal unfolding of cytochrome c peroxidase was sensitive to the presence and ligation state of the heme. Only a single endotherm was observed for the unfolding of the apoprotein, and this transition was similar to the high-temperature transition in the holoenzyme. Addition of KCN to the holoenzyme increases the midpoint of the high-temperature transition whereas the low-temperature transition was increased upon addition of KF. Binding of the natural substrate ferricytochrome c to the enzyme increases the low-temperature transition by 4.8 +- 1.3 0 C but has no effect on the high-temperature transition at pH 7. The presence of cytochrome c peroxidase decreases the stability of cytochrome c, and both proteins appear to unfold simultaneously. The results are discussed in terms of the two domains evident in the X-ray crystallographic structure of cytochrome c peroxidase

3D COMSOL Simulations for Thermal Deflection of HFIR Fuel Plate in the "Cheverton-Kelley" Experiments

Energy Technology Data Exchange (ETDEWEB)

Jain, Prashant K [ORNL; Freels, James D [ORNL; Cook, David Howard [ORNL

2012-08-01

Three dimensional simulation capabilities are currently being developed at Oak Ridge National Laboratory using COMSOL Multiphysics, a finite element modeling software, to investigate thermal expansion of High Flux Isotope Reactor (HFIR) s low enriched uranium fuel plates. To validate simulations, 3D models have also been developed for the experimental setup used by Cheverton and Kelley in 1968 to investigate the buckling and thermal deflections of HFIR s highly enriched uranium fuel plates. Results for several simulations are presented in this report, and comparisons with the experimental data are provided when data are available. A close agreement between the simulation results and experimental findings demonstrates that the COMSOL simulations are able to capture the thermal expansion physics accurately and that COMSOL could be deployed as a predictive tool for more advanced computations at realistic HFIR conditions to study temperature-induced fuel plate deflection behavior.

Detailed Balance of Thermalization Dynamics in Rydberg-Atom Quantum Simulators.

Science.gov (United States)

Kim, Hyosub; Park, YeJe; Kim, Kyungtae; Sim, H-S; Ahn, Jaewook

2018-05-04

Dynamics of large complex systems, such as relaxation towards equilibrium in classical statistical mechanics, often obeys a master equation that captures essential information from the complexities. Here, we find that thermalization of an isolated many-body quantum state can be described by a master equation. We observe sudden quench dynamics of quantum Ising-like models implemented in our quantum simulator, defect-free single-atom tweezers in conjunction with Rydberg-atom interaction. Saturation of their local observables, a thermalization signature, obeys a master equation experimentally constructed by monitoring the occupation probabilities of prequench states and imposing the principle of the detailed balance. Our experiment agrees with theories and demonstrates the detailed balance in a thermalization dynamics that does not require coupling to baths or postulated randomness.

Detailed Balance of Thermalization Dynamics in Rydberg-Atom Quantum Simulators

Science.gov (United States)

Kim, Hyosub; Park, YeJe; Kim, Kyungtae; Sim, H.-S.; Ahn, Jaewook

2018-05-01

Dynamics of large complex systems, such as relaxation towards equilibrium in classical statistical mechanics, often obeys a master equation that captures essential information from the complexities. Here, we find that thermalization of an isolated many-body quantum state can be described by a master equation. We observe sudden quench dynamics of quantum Ising-like models implemented in our quantum simulator, defect-free single-atom tweezers in conjunction with Rydberg-atom interaction. Saturation of their local observables, a thermalization signature, obeys a master equation experimentally constructed by monitoring the occupation probabilities of prequench states and imposing the principle of the detailed balance. Our experiment agrees with theories and demonstrates the detailed balance in a thermalization dynamics that does not require coupling to baths or postulated randomness.

Thermal Simulations, Open Boundary Conditions and Switches

Science.gov (United States)

Burnier, Yannis; Florio, Adrien; Kaczmarek, Olaf; Mazur, Lukas

2018-03-01

SU(N) gauge theories on compact spaces have a non-trivial vacuum structure characterized by a countable set of topological sectors and their topological charge. In lattice simulations, every topological sector needs to be explored a number of times which reflects its weight in the path integral. Current lattice simulations are impeded by the so-called freezing of the topological charge problem. As the continuum is approached, energy barriers between topological sectors become well defined and the simulations get trapped in a given sector. A possible way out was introduced by Lüscher and Schaefer using open boundary condition in the time extent. However, this solution cannot be used for thermal simulations, where the time direction is required to be periodic. In this proceedings, we present results obtained using open boundary conditions in space, at non-zero temperature. With these conditions, the topological charge is not quantized and the topological barriers are lifted. A downside of this method are the strong finite-size effects introduced by the boundary conditions. We also present some exploratory results which show how these conditions could be used on an algorithmic level to reshuffle the system and generate periodic configurations with non-zero topological charge.

Thermal Simulations, Open Boundary Conditions and Switches

Directory of Open Access Journals (Sweden)

Burnier Yannis

2018-01-01

Full Text Available SU(N gauge theories on compact spaces have a non-trivial vacuum structure characterized by a countable set of topological sectors and their topological charge. In lattice simulations, every topological sector needs to be explored a number of times which reflects its weight in the path integral. Current lattice simulations are impeded by the so-called freezing of the topological charge problem. As the continuum is approached, energy barriers between topological sectors become well defined and the simulations get trapped in a given sector. A possible way out was introduced by Lüscher and Schaefer using open boundary condition in the time extent. However, this solution cannot be used for thermal simulations, where the time direction is required to be periodic. In this proceedings, we present results obtained using open boundary conditions in space, at non-zero temperature. With these conditions, the topological charge is not quantized and the topological barriers are lifted. A downside of this method are the strong finite-size effects introduced by the boundary conditions. We also present some exploratory results which show how these conditions could be used on an algorithmic level to reshuffle the system and generate periodic configurations with non-zero topological charge.

Unfolding the phenomenon of inter-rater agreement

DEFF Research Database (Denmark)

Slaug, Bjørn; Schilling, Oliver; Helle, Tina

2011-01-01

Objective: The overall objective was to unfold the phenomenon of inter-rater agreement: to identify potential sources of variation in agreement data and to explore how they can be statistically accounted for. The ultimate aim was to propose recommendations for in-depth examination of agreement, i...

Thermal Simulation of the Fresh Food Compartment in a Domestic Refrigerator

Directory of Open Access Journals (Sweden)

Juan M. Belman-Flores

2017-01-01

Full Text Available In the field of domestic refrigeration, it is important to look for methods that can be used to simulate, and, thus, improve the thermal behavior of the fresh food compartment. In this sense, this study proposes some methods to model the thermal behavior of this compartment when the shelves’ positions are changed. Temperature measurements at specific locations in this compartment were obtained. Several shelf position combinations were performed to use three 2D interpolation methods in order to simulate the temperature mean and the temperature variance. The methods used were: Lagrange’s interpolation, cubic spline interpolation and bilinear interpolation. Two validation points were chosen to verify the proposed methods. By comparing the experimental results with the computer simulations, it was possible to conclude that the method of Lagrange’s interpolation provided values that were not close to the real measured values. On the other hand, it was observed that the method of bilinear interpolation offered the best results, estimating values which were very close to the actual experimental measurements. These interpolation methods were used to build color thermal graphs that can be used to find some of the most appropriate shelf position combinations in this type of refrigerator. By inspection of these thermal graphs, it can be seen that the lowest average temperature was obtained when one shelf was located at 24.5 cm while the second shelf was located at 29.5 cm measured from the top of the compartment. In the same way, it can be seen that the minimum temperature variance was obtained when only one shelf was inside the compartment and this shelf was located at 29.5 cm.

Sequence-dependent unfolding kinetics of DNA hairpins studied by nanopore force spectroscopy

International Nuclear Information System (INIS)

Renner, Stephan; Bessonov, Andrey; Simmel, Friedrich C; Gerland, Ulrich

2010-01-01

Nanopore force spectroscopy is used to study the unzipping kinetics of two DNA hairpin molecules with a 12 base pair long stem containing two contiguous stretches of six GC and six AT base pairs in interchanged order. Even though the thermodynamic stabilities of the two structures are nearly the same, they differ greatly in their unzipping kinetics. When the GC segment has to be broken before the AT segment, the unfolding rate is orders of magnitude smaller than in the opposite case. We also investigated hairpins with stem regions consisting only of AT or GC base pairs. The pure AT hairpins translocate much faster than the other hairpins, whereas the pure GC hairpins translocate on similar timescales to the hairpins with only an initial GC segment. For each hairpin, nanopore force spectroscopy is performed for different loading rates and the resulting unzipping distributions are mathematically transformed to a master curve that yields the unfolding rate as a function of applied voltage. This is compared with a stochastic model of the unfolding process for the two sequences for different voltages. The results can be rationalized in terms of the different natures of the free energy landscapes for the unfolding process.

Neutron spectra unfolding in Bonner spheres spectrometry using neural networks

International Nuclear Information System (INIS)

Kardan, M.R.; Setayeshi, S.; Koohi-Fayegh, R.; Ghiassi-Nejad, M.

2003-01-01

The neural network method has been used for the unfolding of neutron spectra in neutron spectrometry by Bonner spheres. A back propagation algorithm was used for training of neural networks 4mm x 4 mm bare LiI(Eu) and in a polyethylene sphere set: 2, 3, 4, 5, 6, 7, 8, 10, 12, 18 inch diameter have been used for unfolding of neutron spectra. Neural networks were trained by 199 sets of neutron spectra, which were subdivided into 6, 8, 10, 12, 15 and 20 energy bins and for each of them an appropriate neural network was designed and trained. The validation was performed by the 21 sets of neutron spectra. A neural network with 10 energy bins which had a mean value of error of 6% for dose equivalent estimation of spectra in the validation set showed the best results. The obtained results show that neural networks can be applied as an effective method for unfolding neutron spectra especially when the main target is neutron dosimetry. (author)

Thermal simulation of a cooling system of hybrid commercial vehicles; Thermalsimulation eine Hybrid-LKW-Kuehlsystems

Energy Technology Data Exchange (ETDEWEB)

Stroh, Christoph; Schnoerch, Stefan; Rathberger, Christian [Magna Powertrain Engineering Center Steyr GmbH und Co. KG, St. Valentin (Austria)

2012-11-01

In the past few years hybrid vehicles have been in the center of automotive engineering efforts, in particular in the field of passenger cars. But hybrid powertrains will also be important for commercial trucks. This focus on hybrid vehicles leads to high demands on thermal management since the additional components in a hybrid vehicle need appropriate cooling or even heating. In the given paper the simulation of a complete cooling system of a hybrid commercial vehicle will be explained. For this virtual examination the commercial 1D thermal management software KULI will be used, a co-simulation with several programs will not be done deliberately. Yet all aspects which are relevant for a global assessment of the thermal management are considered. The main focus is put on the investigation of appropriate concepts for the fluid circuits, including low and high temperature circuits, electric water pumps, etc. Moreover, also a refrigerant circuit with a chiller for active battery cooling will be used, the appropriate control strategy is implemented as well. For simulating transient profiles a simple driving simulation model is included, using road profile, ambient conditions, and various vehicle parameters as input. In addition an engine model is included which enables the investigation of fuel consumption potentials. This simulation model shows how the thermal management of a hybrid vehicle can be investigated with a single program and with reasonable effort. (orig.)

Measurement and simulation of thermal neutron flux distribution in the RTP core

Science.gov (United States)

Rabir, Mohamad Hairie B.; Jalal Bayar, Abi Muttaqin B.; Hamzah, Na'im Syauqi B.; Mustafa, Muhammad Khairul Ariff B.; Karim, Julia Bt. Abdul; Zin, Muhammad Rawi B. Mohamed; Ismail, Yahya B.; Hussain, Mohd Huzair B.; Mat Husin, Mat Zin B.; Dan, Roslan B. Md; Ismail, Ahmad Razali B.; Husain, Nurfazila Bt.; Jalil Khan, Zareen Khan B. Abdul; Yakin, Shaiful Rizaide B. Mohd; Saad, Mohamad Fauzi B.; Masood, Zarina Bt.

2018-01-01

The in-core thermal neutron flux distribution was determined using measurement and simulation methods for the Malaysian’s PUSPATI TRIGA Reactor (RTP). In this work, online thermal neutron flux measurement using Self Powered Neutron Detector (SPND) has been performed to verify and validate the computational methods for neutron flux calculation in RTP calculations. The experimental results were used as a validation to the calculations performed with Monte Carlo code MCNP. The detail in-core neutron flux distributions were estimated using MCNP mesh tally method. The neutron flux mapping obtained revealed the heterogeneous configuration of the core. Based on the measurement and simulation, the thermal flux profile peaked at the centre of the core and gradually decreased towards the outer side of the core. The results show a good agreement (relatively) between calculation and measurement where both show the same radial thermal flux profile inside the core: MCNP model over estimation with maximum discrepancy around 20% higher compared to SPND measurement. As our model also predicts well the neutron flux distribution in the core it can be used for the characterization of the full core, that is neutron flux and spectra calculation, dose rate calculations, reaction rate calculations, etc.

3D thermal simulations and modeling of multi-finger InP DHBTs for millimeter-wave power amplifiers

DEFF Research Database (Denmark)

Midili, Virginio; Nodjiadjim, V.; Johansen, Tom Keinicke

2017-01-01

This paper presents the comparison between the simulated and measured thermal resistance of InP Double Heterojunction Bipolar Transistors (DHBT). 3D thermal simulations were carried out in order to compute the temperature distribution across the full structure due to a constant power excitation...

Simulation and test of the thermal behavior of pressure switch

Science.gov (United States)

Liu, Yifang; Chen, Daner; Zhang, Yao; Dai, Tingting

2018-04-01

Little, lightweight, low-power microelectromechanical system (MEMS) pressure switches offer a good development prospect for small, ultra-long, simple atmosphere environments. In order to realize MEMS pressure switch, it is necessary to solve one of the key technologies such as thermal robust optimization. The finite element simulation software is used to analyze the thermal behavior of the pressure switch and the deformation law of the pressure switch film under different temperature. The thermal stress releasing schemes are studied by changing the structure of fixed form and changing the thickness of the substrate, respectively. Finally, the design of the glass substrate thickness of 2.5 mm is used to ensure that the maximum equivalent stress is reduced to a quarter of the original value, only 154 MPa when the structure is in extreme temperature (80∘C). The test results show that after the pressure switch is thermally optimized, the upper and lower electrodes can be reliably contacted to accommodate different operating temperature environments.

Thermal Comfort in Simulated Office Environment with Four Convective and Radiant Cooling Systems

DEFF Research Database (Denmark)

Bolashikov, Zhecho Dimitrov; Mustakallio, Panu; Kolencíková, Sona

2013-01-01

with overhead mixing ventilation (MVRC). Whole body thermal sensation (TS) and whole body TS acceptability under the four systems in a simulated office room for one hour exposure were collected. The simulated two-man office (4.12 x 4.20 x 2.89 m, L x W x H) was kept at 26 oC room air temperature. Moderate heat...... to “neutral” compared to male, whose votes were closer to the “slightly warm” thermal sensation. The whole body TS acceptability was rated close to ''clearly acceptable'' (EN 15251-2007) and was independent of subject's gender for all tested systems....

Motional properties of unfolded ubiquitin: a model for a random coil protein

Energy Technology Data Exchange (ETDEWEB)

Wirmer, Julia [Johann Wolfgang GoeUniversityFrankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (Germany); Peti, Wolfgang [Brown University, Department of Molecular Pharmacology, Physiology and Biotechnology (United States); Schwalbe, Harald [Johann Wolfgang GoeUniversityFrankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (Germany)], E-mail: schwalbe@nmr.uni-frankfurt.de

2006-07-15

The characterization of unfolded states of proteins has recently attracted considerable interest, as the residual structure present in these states may play a crucial role in determining their folding and misfolding behavior. Here, we investigated the dynamics in the denatured state of ubiquitin in 8 M urea at pH2. Under these conditions, ubiquitin does not have any detectable local residual structure, and uniform {sup 15}N relaxation rates along the sequence indicate the absence of motional restrictions caused by residual secondary structure and/or long-range interactions. A comparison of different models to predict relaxation data in unfolded proteins suggests that the subnanosecond dynamics in unfolded states depend on segmental motions only and do not show a dependence on the residue type but for proline and glycine residues.

Comparison of fabric skins for the simulation of sweating on thermal manikins

Science.gov (United States)

Koelblen, Barbara; Psikuta, Agnes; Bogdan, Anna; Annaheim, Simon; Rossi, René M.

2017-09-01

Sweating is an important thermoregulatory process helping to dissipate heat and, thus, to prevent overheating of the human body. Simulations of human thermo-physiological responses in hot conditions or during exercising are helpful for assessing heat stress; however, realistic sweating simulation and evaporative cooling is needed. To this end, thermal manikins dressed with a tight fabric skin can be used, and the properties of this skin should help human-like sweat evaporation simulation. Four fabrics, i.e., cotton with elastane, polyester, polyamide with elastane, and a skin provided by a manikin manufacturer (Thermetrics) were compared in this study. The moisture management properties of the fabrics have been investigated in basic tests with regard to all phases of sweating relevant for simulating human thermo-physiological responses, namely, onset of sweating, fully developed sweating, and drying. The suitability of the fabrics for standard tests, such as clothing evaporative resistance measurements, was evaluated based on tests corresponding to the middle phase of sweating. Simulations with a head manikin coupled to a thermo-physiological model were performed to evaluate the overall performance of the skins. The results of the study showed that three out of four evaluated fabrics have adequate moisture management properties with regard to the simulation of sweating, which was confirmed in the coupled simulation with the head manikin. The presented tests are helpful for comparing the efficiency of different fabrics to simulate sweat-induced evaporative cooling on thermal manikins.

Evaluation of a new neutron energy spectrum unfolding code based on an Adaptive Neuro-Fuzzy Inference System (ANFIS).

Science.gov (United States)

Hosseini, Seyed Abolfazl; Esmaili Paeen Afrakoti, Iman

2018-01-17

The purpose of the present study was to reconstruct the energy spectrum of a poly-energetic neutron source using an algorithm developed based on an Adaptive Neuro-Fuzzy Inference System (ANFIS). ANFIS is a kind of artificial neural network based on the Takagi-Sugeno fuzzy inference system. The ANFIS algorithm uses the advantages of both fuzzy inference systems and artificial neural networks to improve the effectiveness of algorithms in various applications such as modeling, control and classification. The neutron pulse height distributions used as input data in the training procedure for the ANFIS algorithm were obtained from the simulations performed by MCNPX-ESUT computational code (MCNPX-Energy engineering of Sharif University of Technology). Taking into account the normalization condition of each energy spectrum, 4300 neutron energy spectra were generated randomly. (The value in each bin was generated randomly, and finally a normalization of each generated energy spectrum was performed). The randomly generated neutron energy spectra were considered as output data of the developed ANFIS computational code in the training step. To calculate the neutron energy spectrum using conventional methods, an inverse problem with an approximately singular response matrix (with the determinant of the matrix close to zero) should be solved. The solution of the inverse problem using the conventional methods unfold neutron energy spectrum with low accuracy. Application of the iterative algorithms in the solution of such a problem, or utilizing the intelligent algorithms (in which there is no need to solve the problem), is usually preferred for unfolding of the energy spectrum. Therefore, the main reason for development of intelligent algorithms like ANFIS for unfolding of neutron energy spectra is to avoid solving the inverse problem. In the present study, the unfolded neutron energy spectra of 252Cf and 241Am-9Be neutron sources using the developed computational code were

An unfolding method for high energy physics experiments

International Nuclear Information System (INIS)

Blobel, V.

2002-06-01

Finite detector resolution and limited acceptance require one to apply unfolding methods in high energy physics experiments. Information on the detector resolution is usually given by a set of Monte Carlo events. Based on the experience with a widely used unfolding program (RUN) a modified method has been developed. The first step of the method is a maximum likelihood fit of the Monte Carlo distributions to the measured distribution in one, two or three dimensions; the finite statistics of the Monte Carlo events is taken into account by the use of Barlow's method with a new method of solution. A clustering method is used before combining bins in sparsely populated areas. In the second step a regularization is applied to the solution, which introduces only a small bias. The regularization parameter is determined from the data after a diagonalization and rotation procedure. (orig.)

FERDO/FERD, Unfolding of Pulse-Height Spectrometer Spectra

International Nuclear Information System (INIS)

Rust, B.W.; Ingersoll, D.T.; Burrus, W.R.

1985-01-01

1 - Description of problem or function: FERDO and FERD are unfolding codes which can be used to correct observed pulse-height distributions for the non-ideal response of a pulse-height spectrometer or to solve poorly conditioned linear equations. 2 - Method of solution: It is assumed that the response of the spectrometer is given by Ax = b, where A is the spectrometer response function matrix, x is the unknown spectrum, and b is the pulse-height distribution. FERDO does not resolve directly for x but instead solves for p = Wx, where W is a 'window function matrix'. Typically, W is the resolution function of an ideal spectrometer which has a single Gaussian response. The effective resolution of the unfolding solution may be varied by the choice of W. Confidence intervals are found for each element of the solution p

Unfolding, aggregation, and seeded amyloid formation of lysine-58-cleaved beta(2)-microglobulin

DEFF Research Database (Denmark)

Heegaard, N.H.H.; Jørgensen, T.J.D.; Rozlosnik, N.

2005-01-01

. Using amide hydrogen/deuterium exchange monitored by mass spectrometry, we show that Delta K58-beta(2)m has increased unfolding rates compared to wt-beta(2)m and that unfolding is highly temperature dependent. The unfolding rate is I order of magnitude faster in Delta K58-beta(2)M than in wt-beta(2)m...... in the circulation of dialysis patients. This beta(2)M variant, Delta K58-beta(2)m, is a disulfide-linked two-chain molecule consisting of amino acid residues 1-57 and 59-99 of intact beta(2)m, and we here demonstrate and characterize its decreased conformational stability as compared to wild-type (wt) beta(2)M...

THE SURFACE-MEDIATED UNFOLDING KINETICS OF GLOBULAR PROTEINS IS DEPENDENT ON MOLECULAR WEIGHT AND TEMPERATURE

Energy Technology Data Exchange (ETDEWEB)

Patananan, A.N.; Goheen, S.C.

2008-01-01

The adsorption and unfolding pathways of proteins on rigid surfaces are essential in numerous complex processes associated with biomedical engineering, nanotechnology, and chromatography. It is now well accepted that the kinetics of unfolding are characterized by chemical and physical interactions dependent on protein deformability and structure, as well as environmental pH, temperature, and surface chemistry. Although this fundamental process has broad implications in medicine and industry, little is known about the mechanism because of the atomic lengths and rapid time scales involved. Therefore, the unfolding kinetics of myoglobin, β-glucosidase, and ovalbumin were investigated by adsorbing the globular proteins to non-porous cationic polymer beads. The protein fractions were adsorbed at different residence times (0, 9, 10, 20, and 30 min) at near-physiological conditions using a gradient elution system similar to that in high-performance liquid chromatography. The elution profi les and retention times were obtained by ultraviolet/visible spectrophotometry. A decrease in recovery was observed with time for almost all proteins and was attributed to irreversible protein unfolding on the non-porous surfaces. These data, and those of previous studies, fi t a positively increasing linear trend between percent unfolding after a fi xed (9 min) residence time (71.8%, 31.1%, and 32.1% of myoglobin, β-glucosidase, and ovalbumin, respectively) and molecular weight. Of all the proteins examined so far, only myoglobin deviated from this trend with higher than predicted unfolding rates. Myoglobin also exhibited an increase in retention time over a wide temperature range (0°C and 55°C, 4.39 min and 5.74 min, respectively) whereas ovalbumin and β-glucosidase did not. Further studies using a larger set of proteins are required to better understand the physiological and physiochemical implications of protein unfolding kinetics. This study confi rms that surface

Analytical tools for thermal infrared engineerig: a thermal sensor simulation package

Science.gov (United States)

Jaggi, Sandeep

1992-09-01

The Advanced Sensor Development Laboratory (ASDL) at the Stennis Space Center develops, maintains and calibrates remote sensing instruments for the National Aeronautics & Space Administration. To perform system design trade-offs, analysis, and establish system parameters, ASDL has developed a software package for analytical simulation of sensor systems. This package called 'Analytical Tools for Thermal InfraRed Engineering'--ATTIRE, simulates the various components of a sensor system. The software allows each subsystem of the sensor to be analyzed independently for its performance. These performance parameters are then integrated to obtain system level information such as SNR, NER, NETD etc. This paper describes the uses of the package and the physics that were used to derive the performance parameters. In addition, ATTIRE can be used as a tutorial for understanding the distribution of thermal flux or solar irradiance over selected bandwidths of the spectrum. This spectrally distributed incident flux can then be analyzed as it propagates through the subsystems that constitute the entire sensor. ATTIRE provides a variety of functions ranging from plotting black-body curves for varying bandwidths and computing the integral flux, to performing transfer function analysis of the sensor system. The package runs from a menu- driven interface in a PC-DOS environment. Each sub-system of the sensor is represented by windows and icons. A user-friendly mouse-controlled point-and-click interface allows the user to simulate various aspects of a sensor. The package can simulate a theoretical sensor system. Trade-off studies can be easily done by changing the appropriate parameters and monitoring the effect of the system performance. The package can provide plots of system performance versus any system parameter. A parameter (such as the entrance aperture of the optics) could be varied and its effect on another parameter (e.g., NETD) can be plotted. A third parameter (e.g., the

Unfolding Green Defense

DEFF Research Database (Denmark)

Larsen, Kristian Knus

2015-01-01

In recent years, many states have developed and implemented green solutions for defense. Building on these initiatives NATO formulated the NATO Green Defence Framework in 2014. The framework provides a broad basis for cooperation within the Alliance on green solutions for defense. This report aims...... to inform and support the further development of green solutions by unfolding how green technologies and green strategies have been developed and used to handle current security challenges. The report, initially, focuses on the security challenges that are being linked to green defense, namely fuel...... consumption in military operations, defense expenditure, energy security, and global climate change. The report then proceeds to introduce the NATO Green Defence Framework before exploring specific current uses of green technologies and green strategies for defense. The report concludes that a number...

An approach to unfold the response of a multi-element system using an artificial neural network

International Nuclear Information System (INIS)

Cordes, E.; Fehrenbacher, G.; Schuetz, R.; Sprunck, M.; Hahn, K.; Hofmann, R.; Wahl, W.

1998-01-01

An unfolding procedure is proposed which aims at obtaining spectral information of a neutron radiation field by the analysis of the response of a multi-element system consisting of converter type semiconductors. For the unfolding procedure an artificial neural network (feed forward network), trained by the back-propagation method, was used. The response functions of the single elements to neutron radiation were calculated by application of a computational model for an energy range from 10 -2 eV to 10 MeV. The training of the artificial neural network was based on the computation of responses of a six-element system for a set of 300 neutron spectra and the application of the back-propagation method. The validation was performed by the unfolding of 100 computed responses. Two unfolding examples were pointed out for the determination of the neutron spectra. The spectra resulting from the unfolding procedure agree well with the original spectra used for the response computation

Thermal plume above a simulated sitting person with different complexity of body geometry

DEFF Research Database (Denmark)

Zukowska, Daria; Melikov, Arsen Krikor; Popiolek, Zbigniew J.

2007-01-01

Occupants are one of the main heat sources in rooms. They generate thermal plumes with characteristics, which depend on geometry, surface temperature and area of the human body in contact with the surrounding air as well as temperature, velocity and turbulence intensity distribution in the room....... The characteristics of the thermal plume generated by a sitting person were studied using four human body simulators with different complexity of geometry but equal surface area: a vertical cylinder, a rectangular box, a dummy, and a thermal manikin. The results show that the dummy and the thermal manikin generate...

Design of 6 Mev linear accelerator based pulsed thermal neutron source: FLUKA simulation and experiment

Energy Technology Data Exchange (ETDEWEB)

Patil, B.J., E-mail: bjp@physics.unipune.ac.in [Department of Physics, University of Pune, Pune 411 007 (India); Chavan, S.T.; Pethe, S.N.; Krishnan, R. [SAMEER, IIT Powai Campus, Mumbai 400 076 (India); Bhoraskar, V.N. [Department of Physics, University of Pune, Pune 411 007 (India); Dhole, S.D., E-mail: sanjay@physics.unipune.ac.in [Department of Physics, University of Pune, Pune 411 007 (India)

2012-01-15

The 6 MeV LINAC based pulsed thermal neutron source has been designed for bulk materials analysis. The design was optimized by varying different parameters of the target and materials for each region using FLUKA code. The optimized design of thermal neutron source gives flux of 3 Multiplication-Sign 10{sup 6}ncm{sup -2}s{sup -1} with more than 80% of thermal neutrons and neutron to gamma ratio was 1 Multiplication-Sign 10{sup 4}ncm{sup -2}mR{sup -1}. The results of prototype experiment and simulation are found to be in good agreement with each other. - Highlights: Black-Right-Pointing-Pointer The optimized 6 eV linear accelerator based thermal neutron source using FLUKA simulation. Black-Right-Pointing-Pointer Beryllium as a photonuclear target and reflector, polyethylene as a filter and shield, graphite as a moderator. Black-Right-Pointing-Pointer Optimized pulsed thermal neutron source gives neutron flux of 3 Multiplication-Sign 10{sup 6} n cm{sup -2} s{sup -1}. Black-Right-Pointing-Pointer Results of the prototype experiment were compared with simulations and are found to be in good agreement. Black-Right-Pointing-Pointer This source can effectively be used for the study of bulk material analysis and activation products.

Numerical simulation of thermal behaviors of a clothed human body with evaluation of indoor solar radiation

International Nuclear Information System (INIS)

Mao, Aihua; Luo, Jie; Li, Yi

2017-01-01

Highlights: • Solar radiation evaluation is integrated with the thermal transfer in clothed humans. • Thermal models are developed for clothed humans exposed in indoor solar radiation. • The effect of indoor solar radiation on humans can be predicted in different situations in living. • The green solar energy can be efficiently utilized in the building development. - Abstract: Solar radiation is a valuable green energy, which is important in achieving a successful building design for thermal comfort in indoor environment. This paper considers solar radiation indoors into the transient thermal transfer models of a clothed human body and offers a new numerical method to analyze the dynamic thermal status of a clothed human body under different solar radiation incidences. The evaluation model of solar radiation indoors and a group of coupled thermal models of the clothed human body are developed and integrated. The simulation capacities of these integrated models are validated through a comparison between the predicted results and the experimental data in reference. After that, simulation cases are also conducted to show the influence of solar radiation on the thermal status of individual clothed body segments when the human body is staying indoors in different seasons. This numerical simulation method provides a useful tool to analyze the thermal status of clothed human body under different solar radiation incidences indoors and thus enables the architect to efficiently utilize the green solar energy in building development.

Considerably Unfolded Transthyretin Monomers Preceed and Exchange with Dynamically Structured Amyloid Protofibrils

DEFF Research Database (Denmark)

Groenning, Minna; Campos, Raul I; Hirschberg, Daniel

2015-01-01

describe an unexpectedly dynamic TTR protofibril structure which exchanges protomers with highly unfolded monomers in solution. The protofibrils only grow to an approximate final size of 2,900 kDa and a length of 70 nm and a comparative HXMS analysis of native and aggregated samples revealed a much higher...... average solvent exposure of TTR upon fibrillation. With SAXS, we reveal the continuous presence of a considerably unfolded TTR monomer throughout the fibrillation process, and show that a considerable fraction of the fibrillating protein remains in solution even at a late maturation state. Together......, these data reveal that the fibrillar state interchanges with the solution state. Accordingly, we suggest that TTR fibrillation proceeds via addition of considerably unfolded monomers, and the continuous presence of amyloidogenic structures near the protofibril surface offers a plausible explanation...

An integrated algorithm for hypersonic fluid-thermal-structural numerical simulation

Science.gov (United States)

Li, Jia-Wei; Wang, Jiang-Feng

2018-05-01

In this paper, a fluid-structural-thermal integrated method is presented based on finite volume method. A unified integral equations system is developed as the control equations for physical process of aero-heating and structural heat transfer. The whole physical field is discretized by using an up-wind finite volume method. To demonstrate its capability, the numerical simulation of Mach 6.47 flow over stainless steel cylinder shows a good agreement with measured values, and this method dynamically simulates the objective physical processes. Thus, the integrated algorithm proves to be efficient and reliable.

2-D CFD time-dependent thermal-hydraulic simulations of CANDU-6 moderator flows

Energy Technology Data Exchange (ETDEWEB)

Mehdi Zadeh, Foad [Department of Engineering Physics/Polytechnique Montréal, Montréal, QC (Canada); Étienne, Stéphane [Department of Mechanical Engineering/Polytechnique Montréal, Montréal, QC (Canada); Teyssedou, Alberto, E-mail: alberto.teyssedou@polymtl.ca [Department of Engineering Physics/Polytechnique Montréal, Montréal, QC (Canada)

2016-12-01

Highlights: • 2-D time-dependent CFD simulations of CANDU-6 moderator flows are presented. • A thermal-hydraulic code using thermal physical fluid properties is used. • The numerical approach and convergence is validated against available data. • Flow configurations are correlated using Richardson’s number. • Frequency components indicate moderator flow oscillations vs. Richardson numbers. - Abstract: The distribution of the fluid temperature and mass density of the moderator flow in CANDU-6 nuclear power reactors may affect the reactivity coefficient. For this reason, any possible moderator flow configuration and consequently the corresponding temperature distributions must be studied. In particular, the variations of the reactivity may result in major safety issues. For instance, excessive temperature excursions in the vicinity of the calandria tubes nearby local flow stagnation zones, may bring about partial boiling. Moreover, steady-state simulations have shown that for operating condition, intense buoyancy forces may be dominant, which can trigger a thermal stratification. Therefore, the numerical study of the time-dependent flow transition to such a condition, is of fundamental safety concern. Within this framework, this paper presents detailed time-dependent numerical simulations of CANDU-6 moderator flow for a wide range of flow conditions. To get a better insight of the thermal-hydraulic phenomena, the simulations were performed by covering long physical-time periods using an open-source code (Code-Saturne V3) developed by Électricité de France. The results show not only a region where the flow is characterized by coherent structures of flow fluctuations but also the existence of two limit cases where fluid oscillations disappear almost completely.

Joint mapping of genes and conditions via multidimensional unfolding analysis

Directory of Open Access Journals (Sweden)

Engelen Kristof

2007-06-01

Full Text Available Abstract Background Microarray compendia profile the expression of genes in a number of experimental conditions. Such data compendia are useful not only to group genes and conditions based on their similarity in overall expression over profiles but also to gain information on more subtle relations between genes and conditions. Getting a clear visual overview of all these patterns in a single easy-to-grasp representation is a useful preliminary analysis step: We propose to use for this purpose an advanced exploratory method, called multidimensional unfolding. Results We present a novel algorithm for multidimensional unfolding that overcomes both general problems and problems that are specific for the analysis of gene expression data sets. Applying the algorithm to two publicly available microarray compendia illustrates its power as a tool for exploratory data analysis: The unfolding analysis of a first data set resulted in a two-dimensional representation which clearly reveals temporal regulation patterns for the genes and a meaningful structure for the time points, while the analysis of a second data set showed the algorithm's ability to go beyond a mere identification of those genes that discriminate between different patient or tissue types. Conclusion Multidimensional unfolding offers a useful tool for preliminary explorations of microarray data: By relying on an easy-to-grasp low-dimensional geometric framework, relations among genes, among conditions and between genes and conditions are simultaneously represented in an accessible way which may reveal interesting patterns in the data. An additional advantage of the method is that it can be applied to the raw data without necessitating the choice of suitable genewise transformations of the data.

Importance of thermal nonequilibrium considerations for the simulation of nuclear reactor LOCA transients

International Nuclear Information System (INIS)

Fischer, S.R.; Nelson, R.A.; Sullivan, L.H.

1980-01-01

The purpose of this paper is to show the importance of considering thermal nonequilibrium effects in computer simulations of the refill and reflood portions of pressurized water reactor (PWR) loss-of-coolnat accident (LOCA) transients. Although RELAP4 assumes thermodynamic equilibrium between phases, models that account for the nonequilibrium phenomena associated with the mixing of subcooled emergency cooling water with steam and the superheating of vapor in the presence of liquid droplets have recently been incorporated into the code. Code calculated results, both with and without these new models, have been compared with experimental test data to assess the importance of including thermal nonequilibrium phenomena in computer code simulations

JPL Thermal Design Modeling Philosophy and NASA-STD-7009 Standard for Models and Simulations - A Case Study

Science.gov (United States)

Avila, Arturo

2011-01-01

The Standard JPL thermal engineering practice prescribes worst-case methodologies for design. In this process, environmental and key uncertain thermal parameters (e.g., thermal blanket performance, interface conductance, optical properties) are stacked in a worst case fashion to yield the most hot- or cold-biased temperature. Thus, these simulations would represent the upper and lower bounds. This, effectively, represents JPL thermal design margin philosophy. Uncertainty in the margins and the absolute temperatures is usually estimated by sensitivity analyses and/or by comparing the worst-case results with "expected" results. Applicability of the analytical model for specific design purposes along with any temperature requirement violations are documented in peer and project design review material. In 2008, NASA released NASA-STD-7009, Standard for Models and Simulations. The scope of this standard covers the development and maintenance of models, the operation of simulations, the analysis of the results, training, recommended practices, the assessment of the Modeling and Simulation (M&S) credibility, and the reporting of the M&S results. The Mars Exploration Rover (MER) project thermal control system M&S activity was chosen as a case study determining whether JPL practice is in line with the standard and to identify areas of non-compliance. This paper summarizes the results and makes recommendations regarding the application of this standard to JPL thermal M&S practices.

Characterization of the residual structure in the unfolded state of the Delta 131 Delta fragment of staphylococcal nuclease

DEFF Research Database (Denmark)

Francis, C. J.; Lindorff-Larsen, Kresten; Best, R. B.

2006-01-01

dynamics simulations to characterise the residual structure of the 131 fragment of staphylococcal nuclease under physiological conditions. Our findings indicate that 131 under these conditions shows a tendency to form transiently hydrophobic clusters similar to those present in the native state of wild......The determination of the conformational preferences in unfolded states of proteins constitutes an important challenge in structural biology. We use inter-residue distances estimated from site-directed spin-labeling NMR experimental measurements as ensemble-averaged restraints in all-atom molecular...

Experimental Preparation and Numerical Simulation of High Thermal Conductive Cu/CNTs Nanocomposites

Directory of Open Access Journals (Sweden)

Muhsan Ali Samer

2014-07-01

Full Text Available Due to the rapid growth of high performance electronics devices accompanied by overheating problem, heat dissipater nanocomposites material having ultra-high thermal conductivity and low coefficient of thermal expansion was proposed. In this work, a nanocomposite material made of copper (Cu reinforced by multi-walled carbon nanotubes (CNTs up to 10 vol. % was prepared and their thermal behaviour was measured experimentally and evaluated using numerical simulation. In order to numerically predict the thermal behaviour of Cu/CNTs composites, three different prediction methods were performed. The results showed that rules of mixture method records the highest thermal conductivity for all predicted composites. In contrast, the prediction model which takes into account the influence of the interface thermal resistance between CNTs and copper particles, has shown the lowest thermal conductivity which considered as the closest results to the experimental measurement. The experimentally measured thermal conductivities showed remarkable increase after adding 5 vol.% CNTs and higher than the thermal conductivities predicted via Nan models, indicating that the improved fabrication technique of powder injection molding that has been used to produced Cu/CNTs nanocomposites has overcome the challenges assumed in the mathematical models.

Thermal conductivity of nanofluids and size distribution of nanoparticles by Monte Carlo simulations

International Nuclear Information System (INIS)

Feng Yongjin; Yu Boming; Feng Kaiming; Xu Peng; Zou Mingqing

2008-01-01

Nanofluids, a class of solid-liquid suspensions, have received an increasing attention and studied intensively because of their anomalously high thermal conductivites at low nanoparticle concentration. Based on the fractal character of nanoparticles in nanofluids, the probability model for nanoparticle's sizes and the effective thermal conductivity model are derived, in which the effect of the microconvection due to the Brownian motion of nanoparticles in the fluids is taken into account. The proposed model is expressed as a function of the thermal conductivities of the base fluid and the nanoparticles, the volume fraction, fractal dimension for particles, the size of nanoparticles, and the temperature, as well as random number. This model has the characters of both analytical and numerical solutions. The Monte Carlo simulations combined with the fractal geometry theory are performed. The predictions by the present Monte Carlo simulations are shown in good accord with the existing experimental data.

Experiment-based thermal micromagnetic simulations of the magnetization reversal for ns-range clocked nanomagnetic logic

Science.gov (United States)

Ziemys, Grazvydas; Breitkreutz-v. Gamm, Stephan; Csaba, Gyorgy; Schmitt-Landsiedel, Doris; Becherer, Markus

2017-05-01

Extensive thermal micromagnetic simulations, based on experimental data and parameters, were performed to investigate the magnetization reversal in Co/Pt nanomagnets with locally reduced perpendicular anisotropy on the nanosecond range. The simulations were supported by experimental data gained on manufactured Co/Pt nanomagnets, as used in nanomagnetic logic. It is known that magnetization reversal is governed by two mechanisms. At pulse lengths longer than 100 ns, thermal activation dominates the magnetization reversal processes and follows the common accepted Arrhenius law. For pulse lengths shorter than 100 ns, the dynamic reversal dominates. With the help of thermal micro-magnetic simulations we found out that the point where the both mechanisms meet is determined by the damping constant α of the multilayer film stack. The optimization of ferromagnetic multilayer film stacks enables higher clocking rates with lower power consumption and, therefore, further improve the performance of pNML.

Measurement of the unfolded protein response (UPR) in monocytes.

LENUS (Irish Health Repository)

Carroll, Tomás P

2011-01-01

In mammalian cells, the primary function of the endoplasmic reticulum (ER) is to synthesize and assemble membrane and secreted proteins. As the main site of protein folding and posttranslational modification in the cell, the ER operates a highly conserved quality control system to ensure only correctly assembled proteins exit the ER and misfolded and unfolded proteins are retained for disposal. Any disruption in the equilibrium of the ER engages a multifaceted intracellular signaling pathway termed the unfolded protein response (UPR) to restore normal conditions in the cell. A variety of pathological conditions can induce activation of the UPR, including neurodegenerative disorders such as Parkinson\\'s disease, metabolic disorders such as atherosclerosis, and conformational disorders such as cystic fibrosis. Conformational disorders are characterized by mutations that modify the final structure of a protein and any cells that express abnormal protein risk functional impairment. The monocyte is an important and long-lived immune cell and acts as a key immunological orchestrator, dictating the intensity and duration of the host immune response. Monocytes expressing misfolded or unfolded protein may exhibit UPR activation and this can compromise the host immune system. Here, we describe in detail methods and protocols for the examination of UPR activation in peripheral blood monocytes. This guide should provide new investigators to the field with a broad understanding of the tools required to investigate the UPR in the monocyte.

Measurement of the unfolded protein response (UPR) in monocytes.

LENUS (Irish Health Repository)

Carroll, Tomas P

2012-02-01

In mammalian cells, the primary function of the endoplasmic reticulum (ER) is to synthesize and assemble membrane and secreted proteins. As the main site of protein folding and posttranslational modification in the cell, the ER operates a highly conserved quality control system to ensure only correctly assembled proteins exit the ER and misfolded and unfolded proteins are retained for disposal. Any disruption in the equilibrium of the ER engages a multifaceted intracellular signaling pathway termed the unfolded protein response (UPR) to restore normal conditions in the cell. A variety of pathological conditions can induce activation of the UPR, including neurodegenerative disorders such as Parkinson\\'s disease, metabolic disorders such as atherosclerosis, and conformational disorders such as cystic fibrosis. Conformational disorders are characterized by mutations that modify the final structure of a protein and any cells that express abnormal protein risk functional impairment. The monocyte is an important and long-lived immune cell and acts as a key immunological orchestrator, dictating the intensity and duration of the host immune response. Monocytes expressing misfolded or unfolded protein may exhibit UPR activation and this can compromise the host immune system. Here, we describe in detail methods and protocols for the examination of UPR activation in peripheral blood monocytes. This guide should provide new investigators to the field with a broad understanding of the tools required to investigate the UPR in the monocyte.

Optimal control of building storage systems using both ice storage and thermal mass – Part I: Simulation environment

International Nuclear Information System (INIS)

Hajiah, Ali; Krarti, Moncef

2012-01-01

Highlights: ► A simulation environment is described to account for both passive and active thermal energy storage (TES) systems. ► Laboratory testing results have been used to validate the predictions from the simulation environment. ► Optimal control strategies for TES systems have been developed as part of the simulation environment. - Abstract: This paper presents a simulation environment that can evaluate the benefits of using simultaneously building thermal capacitance and ice storage system to reduce total operating costs including energy and demand charges while maintaining adequate occupant comfort conditions within commercial buildings. The building thermal storage is controlled through pre-cooling strategies by setting space indoor air temperatures. The ice storage system is controlled by charging the ice tank and operating the chiller during low electrical charge periods and melting the ice during on-peak periods. Optimal controls for both building thermal storage and ice storage are developed to minimize energy charges, demand charges, or combined energy and demand charges. The results obtained from the simulation environment are validated using laboratory testing for an optimal controller.

Dante-unfolding code for energy spectra evaluation

International Nuclear Information System (INIS)

Petilli, M.

1979-01-01

The code DANTE, using the last square method in unfolding for dosimetry purpose, solves the neutron spectra evaluation problem starting by activity measurements. The code DANTE introduced for the first time the correlation between available data by mean of flux and activity variance-covariance matrices and the error propagation. In the present report the solution method is detailed described

Thermal System Upgrade of the Space Environment Simulation Test Chamber

Science.gov (United States)

Desai, Ashok B.

1997-01-01

The paper deals with the refurbishing and upgrade of the thermal system for the existing thermal vacuum test facility, the Space Environment Simulator, at NASA's Goddard Space Flight Center. The chamber is the largest such facility at the center. This upgrade is the third phase of the long range upgrade of the chamber that has been underway for last few years. The first phase dealt with its vacuum system, the second phase involved the GHe subsystem. The paper describes the considerations of design philosophy options for the thermal system; approaches taken and methodology applied, in the evaluation of the remaining "life" in the chamber shrouds and related equipment by conducting special tests and studies; feasibility and extent of automation, using computer interfaces and Programmable Logic Controllers in the control system and finally, matching the old components to the new ones into an integrated, highly reliable and cost effective thermal system for the facility. This is a multi-year project just started and the paper deals mainly with the plans and approaches to implement the project successfully within schedule and costs.

Nuclear power plant accident simulations of gasket materials under simultaneous radiation plus thermal plus mechanical stress conditions

International Nuclear Information System (INIS)

Gillen, K.T.; Malone, G.M.

1997-07-01

In order to probe the response of silicone door gasket materials to a postulated severe accident in an Italian nuclear power plant, compression stress relaxation (CSR) and compression set (CS) measurements were conducted under combined radiation (approximately 6 kGy/h) and temperature (up to 230 degrees C) conditions. By making some reasonable initial assumptions, simplified constant temperature and dose rates were derived that should do a reasonable job of simulating the complex environments for worst-case severe events that combine overall aging plus accidents. Further simplification coupled with thermal-only experiments allowed us to derive thermal-only conditions that can be used to achieve CSR and CS responses similar to those expected from the combined environments that are more difficult to simulate. Although the thermal-only simulations should lead to sealing forces similar to those expected during a severe accident, modulus and density results indicate that significant differences in underlying chemistry are expected for the thermal-only and the combined environment simulations. 15 refs., 31 figs., 15 tabs

Simulation of thermal environment in a three-layer vinyl greenhouse by natural ventilation control

Science.gov (United States)

Jin, Tea-Hwan; Shin, Ki-Yeol; Yoon, Si-Won; Im, Yong-Hoon; Chang, Ki-Chang

2017-11-01

A high energy, efficient, harmonious, ecological greenhouse has been highlighted by advanced future agricultural technology recently. This greenhouse is essential for expanding the production cycle toward growth conditions through combined thermal environmental control. However, it has a negative effect on farming income via huge energy supply expenses. Because not only production income, but operating costs related to thermal load for thermal environment control is important in farming income, it needs studies such as a harmonious ecological greenhouse using natural ventilation control. This study is simulated for energy consumption and thermal environmental conditions in a three-layered greenhouse by natural ventilation using window opening. A virtual 3D model of a three-layered greenhouse was designed based on the real one in the Gangneung area. This 3D model was used to calculate a thermal environment state such as indoor temperature, relative humidity, and thermal load in the case of a window opening rate from 0 to 100%. There was also a heat exchange operated for heating or cooling controlled by various setting temperatures. The results show that the cooling load can be reduced by natural ventilation control in the summer season, and the heat exchange capacity for heating can also be simulated for growth conditions in the winter season.

Simulation of thermal environment in a three-layer vinyl greenhouse by natural ventilation control

Directory of Open Access Journals (Sweden)

Jin Tea-Hwan

2017-01-01

Full Text Available A high energy, efficient, harmonious, ecological greenhouse has been highlighted by advanced future agricultural technology recently. This greenhouse is essential for expanding the production cycle toward growth conditions through combined thermal environmental control. However, it has a negative effect on farming income via huge energy supply expenses. Because not only production income, but operating costs related to thermal load for thermal environment control is important in farming income, it needs studies such as a harmonious ecological greenhouse using natural ventilation control. This study is simulated for energy consumption and thermal environmental conditions in a three-layered greenhouse by natural ventilation using window opening. A virtual 3D model of a three-layered greenhouse was designed based on the real one in the Gangneung area. This 3D model was used to calculate a thermal environment state such as indoor temperature, relative humidity, and thermal load in the case of a window opening rate from 0 to 100%. There was also a heat exchange operated for heating or cooling controlled by various setting temperatures. The results show that the cooling load can be reduced by natural ventilation control in the summer season, and the heat exchange capacity for heating can also be simulated for growth conditions in the winter season.

Atomistic simulation of the thermal conductivity in amorphous SiO2 matrix/Ge nanocrystal composites

Science.gov (United States)

Kuryliuk, Vasyl V.; Korotchenkov, Oleg A.

2017-04-01

We use nonequilibrium molecular dynamics computer simulations with the Tersoff potential aiming to provide a comprehensive picture of the thermal conductivity of amorphous SiO2 (a-SiO2) matrix with embedded Ge nanocrystals (nc-Ge). The modelling predicts the a-SiO2 matrix thermal conductivity in a temperature range of 50 fair agreement with experiment at around room temperature. It is worth noticing that the predicted room-temperature thermal conductivity in a-SiO2 is in very good agreement with the experimental result, which is in marked contrast with the thermal conductivity calculated employing the widely used van Beest-Kramer-van Santen (BKS) potential. We show that the thermal conductivity of composite nc-Ge/a-SiO2 systems decreases steadily with increasing the volume fraction of Ge inclusions, indicative of enhanced interface scattering of phonons imposed by embedded Ge nanocrystals. We also observe that increasing the volume fractions above a certain threshold value results in a progressively increased thermal conductivity of the nanocomposite, which can be explained by increasing volume fraction of a better thermally conducting Ge. Finally, non-equilibrium molecular dynamics simulations with the Tersoff potential are promising for computing the thermal conductivity of nanocomposites based on amorphous SiO2 and can be readily scaled to more complex composite structures with embedded nanoparticles, which thus help design nanocomposites with desired thermal properties.

Numerical simulation of a passive scalar transport from thermal power plants

Science.gov (United States)

Issakhov, Alibek; Baitureyeva, Aiymzhan

2017-06-01

The active development of the industry leads to an increase in the number of factories, plants, thermal power plants, nuclear power plants, thereby increasing the amount of emissions into the atmosphere. Harmful chemicals are deposited on the soil surface, remain in the atmosphere, which leads to a variety of environmental problems which are harmful for human health and the environment, flora and fauna. Considering the above problems, it is very important to control the emissions to keep them at an acceptable level for the environment. In order to do that it is necessary to investigate the spread of harmful emissions. The best way to assess it is the creating numerical simulation of gaseous substances' motion. In the present work the numerical simulation of the spreading of emissions from the thermal power plant chimney is considered. The model takes into account the physical properties of the emitted substances and allows to calculate the distribution of the mass fractions, depending on the wind velocity and composition of emissions. The numerical results were performed using the ANSYS Fluent software package. As a result, the results of numerical simulations and the graphs are given.

A high-resolution neutron spectra unfolding method using the Genetic Algorithm technique

CERN Document Server

Mukherjee, B

2002-01-01

The Bonner sphere spectrometers (BSS) are commonly used to determine the neutron spectra within various nuclear facilities. Sophisticated mathematical tools are used to unfold the neutron energy distribution from the output data of the BSS. This paper highlights a novel high-resolution neutron spectra-unfolding method using the Genetic Algorithm (GA) technique. The GA imitates the biological evolution process prevailing in the nature to solve complex optimisation problems. The GA method was utilised to evaluate the neutron energy distribution, average energy, fluence and equivalent dose rates at important work places of a DIDO class research reactor and a high-energy superconducting heavy ion cyclotron. The spectrometer was calibrated with a sup 2 sup 4 sup 1 Am/Be (alpha,n) neutron standard source. The results of the GA method agreed satisfactorily with the results obtained by using the well-known BUNKI neutron spectra unfolding code.

CFD simulation of a cabin thermal environment with and without human body - thermal comfort evaluation

Science.gov (United States)

Danca, Paul; Bode, Florin; Nastase, Ilinca; Meslem, Amina

2018-02-01

Nowadays, thermal comfort became one of the criteria in choosing a vehicle. In last decades time spent by people in vehicles had risen substantially. During each trip, thermal comfort must to be ensured for a good psychological and physical state of the passengers. Also, a comfortable environment leads to a higher power concentration of the driver thereby to a safe trip for vehicle occupants and for all traffic participants. The present study numerically investigated the effect of human body sited in the driver's place, over the air velocity distribution and over the thermal comfort in a passenger compartment. CFD simulations were made with different angles of the left inlet grill, in both cases, with and without driver presence. In majority of the actual vehicles environment studies, are made without consideration of human body geometry, in this case, the results precision can be affected. The results show that the presence of human body, lead to global changing of the whole flow pattern inside the vehicular cabin. Also, the locations of the maximum velocities are changing with the angle of the guiding vanes. The thermal comfort PMV/PPD indexes were calculated for each case. The presence of human body leads to a more comfortable environment.

Simulation of thermal stress and buckling instability in Si/Ge and Ge/Si core/shell nanowires.

Science.gov (United States)

Das, Suvankar; Moitra, Amitava; Bhattacharya, Mishreyee; Dutta, Amlan

2015-01-01

The present study employs the method of atomistic simulation to estimate the thermal stress experienced by Si/Ge and Ge/Si, ultrathin, core/shell nanowires with fixed ends. The underlying technique involves the computation of Young's modulus and the linear coefficient of thermal expansion through separate simulations. These two material parameters are combined to obtain the thermal stress on the nanowires. In addition, the thermally induced stress is perceived in the context of buckling instability. The analysis provides a trade-off between the geometrical and operational parameters of the nanostructures. The proposed methodology can be extended to other materials and structures and helps with the prediction of the conditions under which a nanowire-based device might possibly fail due to elastic instability.

Effects of deformability and thermal motion of lipid membrane on electroporation: By molecular dynamics simulations

KAUST Repository

Sun, Sheng; Yin, Guangyao; Lee, Yi-Kuen; Wong, Joseph T.Y.; Zhang, Tong-Yi

2011-01-01

Effects of mechanical properties and thermal motion of POPE lipid membrane on electroporation were studied by molecular dynamics simulations. Among simulations in which specific atoms of lipids were artificially constrained at their equilibrium

In-flight thermal experiments for LISA Pathfinder: Simulating temperature noise at the Inertial Sensors

International Nuclear Information System (INIS)

Armano, M; Audley, H; Born, M; Danzmann, K; Diepholz, I; Auger, G; Binetruy, P; Baird, J; Bortoluzzi, D; Brandt, N; Fitzsimons, E; Bursi, A; Caleno, M; Cavalleri, A; Cesarini, A; Dolesi, R; Ferroni, V; Cruise, M; Dunbar, N; Ferraioli, L

2015-01-01

Thermal Diagnostics experiments to be carried out on board LISA Pathfinder (LPF) will yield a detailed characterisation of how temperature fluctuations affect the LTP (LISA Technology Package) instrument performance, a crucial information for future space based gravitational wave detectors as the proposed eLISA. Amongst them, the study of temperature gradient fluctuations around the test masses of the Inertial Sensors will provide as well information regarding the contribution of the Brownian noise, which is expected to limit the LTP sensitivity at frequencies close to 1 mHz during some LTP experiments. In this paper we report on how these kind of Thermal Diagnostics experiments were simulated in the last LPF Simulation Campaign (November, 2013) involving all the LPF Data Analysis team and using an end-to-end simulator of the whole spacecraft. Such simulation campaign was conducted under the framework of the preparation for LPF operations. (paper)

Thermal radiators with embedded pulsating heat pipes: Infra-red thermography and simulations

International Nuclear Information System (INIS)

Hemadri, Vadiraj A.; Gupta, Ashish; Khandekar, Sameer

2011-01-01

With the aim of exploring potential applications of Pulsating Heat Pipes (PHP), for space/terrestrial sectors, experimental study of embedded PHP thermal radiators, having two different effective Biot numbers respectively, and subjected to conjugate heat transfer conditions on their surface, i.e., natural convection and radiation, has been carried out under different thermo-mechanical boundary conditions. High resolution infrared camera is used to obtain spatial temperature profiles of the radiators. To complement the experimental study, detailed 3D computational heat transfer simulation has also been undertaken. By embedding PHP structures, it was possible to make the net thermal resistance of the mild steel radiator plate equivalent to the aluminum radiator plate, in spite of the large difference in their respective thermal conductivities (k Al ∼ 4k MS ). The study reveals that embedded PHP structures can be beneficial only under certain boundary conditions. The degree of isothermalization achieved in these structures strongly depends on its effective Biot number. The relative advantage of embedded PHP is appreciably higher if the thermal conductivity of the radiator plate material itself is low. The study indicates that the effective thermal conductivity of embedded PHP structure is of the order of 400 W/mK to 2300 W/mK, depending on the operating conditions. - Research highlights: → Study of radiator plates with embedded Pulsating Heat Pipe by infrared thermography. → Radiator is subjected to natural convection and radiation boundary conditions. → Experimental study is supported by 3D simulation. → Effective thermal conductivity of PHPs of the order of 2000 W/mK is obtained. → Efficacy of embedded PHPs depends on the effective Biot number of the system.

Randomized quasi-Monte Carlo simulation of fast-ion thermalization

Science.gov (United States)

Höök, L. J.; Johnson, T.; Hellsten, T.

2012-01-01

This work investigates the applicability of the randomized quasi-Monte Carlo method for simulation of fast-ion thermalization processes in fusion plasmas, e.g. for simulation of neutral beam injection and radio frequency heating. In contrast to the standard Monte Carlo method, the quasi-Monte Carlo method uses deterministic numbers instead of pseudo-random numbers and has a statistical weak convergence close to {O}(N^{-1}) , where N is the number of markers. We have compared different quasi-Monte Carlo methods for a neutral beam injection scenario, which is solved by many realizations of the associated stochastic differential equation, discretized with the Euler-Maruyama scheme. The statistical convergence of the methods is measured for time steps up to 214.

Measurements of Regolith Simulant Thermal Conductivity Under Asteroid and Mars Surface Conditions

Science.gov (United States)

Ryan, A. J.; Christensen, P. R.

2017-12-01

Laboratory measurements have been necessary to interpret thermal data of planetary surfaces for decades. We present a novel radiometric laboratory method to determine temperature-dependent thermal conductivity of complex regolith simulants under rough to high vacuum and across a wide range of temperatures. This method relies on radiometric temperature measurements instead of contact measurements, eliminating the need to disturb the sample with thermal probes. We intend to determine the conductivity of grains that are up to 2 cm in diameter and to parameterize the effects of angularity, sorting, layering, composition, and eventually cementation. We present the experimental data and model results for a suite of samples that were selected to isolate and address regolith physical parameters that affect bulk conductivity. Spherical glass beads of various sizes were used to measure the effect of size frequency distribution. Spherical beads of polypropylene and well-rounded quartz sand have respectively lower and higher solid phase thermal conductivities than the glass beads and thus provide the opportunity to test the sensitivity of bulk conductivity to differences in solid phase conductivity. Gas pressure in our asteroid experimental chambers is held at 10^-6 torr, which is sufficient to negate gas thermal conduction in even our coarsest of samples. On Mars, the atmospheric pressure is such that the mean free path of the gas molecules is comparable to the pore size for many regolith particulates. Thus, subtle variations in pore size and/or atmospheric pressure can produce large changes in bulk regolith conductivity. For each sample measured in our martian environmental chamber, we repeat thermal measurement runs at multiple pressures to observe this behavior. Finally, we present conductivity measurements of angular basaltic simulant that is physically analogous to sand and gravel that may be present on Bennu. This simulant was used for OSIRIS-REx TAGSAM Sample Return

Thermography During Thermal Test of the Gaia Deployable Sunshield Assembly Qualification Model in the ESTEC Large Space Simulator

Science.gov (United States)

Simpson, R.; Broussely, M.; Edwards, G.; Robinson, D.; Cozzani, A.; Casarosa, G.

2012-07-01

The National Physical Laboratory (NPL) and The European Space Research and Technology Centre (ESTEC) have performed for the first time successful surface temperature measurements using infrared thermal imaging in the ESTEC Large Space Simulator (LSS) under vacuum and with the Sun Simulator (SUSI) switched on during thermal qualification tests of the GAIA Deployable Sunshield Assembly (DSA). The thermal imager temperature measurements, with radiosity model corrections, show good agreement with thermocouple readings on well characterised regions of the spacecraft. In addition, the thermal imaging measurements identified potentially misleading thermocouple temperature readings and provided qualitative real-time observations of the thermal and spatial evolution of surface structure changes and heat dissipation during hot test loadings, which may yield additional thermal and physical measurement information through further research.

Monte Carlo simulations to advance characterisation of landmines by pulsed fast/thermal neutron analysis

NARCIS (Netherlands)

Maucec, M.; Rigollet, C.

The performance of a detection system based on the pulsed fast/thermal neutron analysis technique was assessed using Monte Carlo simulations. The aim was to develop and implement simulation methods, to support and advance the data analysis techniques of the characteristic gamma-ray spectra,

Dynamic simulation of a biomass domestic boiler under thermally thick considerations

NARCIS (Netherlands)

Gómez, M. A.; Porteiro, J.; De la Cuesta de Cal, Daniel; Patiño, D.; Míguez, J. L.

2017-01-01

A biomass combustion model with a thermally thick approach is presented and applied to the simulation of a commercial biomass domestic boiler. A subgrid scale model is used to divide the particles into several grid points, each representing one of the different combustion stages. These grid points

UNFOLDINGS OF THE CYLINDRICA L SURFACES USED IN THE INDUSTRIAL INSTALLATIONS

Directory of Open Access Journals (Sweden)

VASILE GHEORGHITA

2013-02-01

Full Text Available The connections in the construction of the various industrial installations: pipes, boilers, joints elements and fittings have a cylindrical configuration, or similar cylindrical shape. The execution and their installation require knowledge of the unfolding and intersection curves, which compose them. The graphical solving of the problems of tech nical representation has enabled the formation of abstract geometric of the pieces forms and the ability to see into space. The paper proposes to establish the unfolding of a connection, used in the industrial equipments, by the classical method of the des criptive geometry and mathematics, using appropriate software

Thermal conductivity predictions of herringbone graphite nanofibers using molecular dynamics simulations.

Science.gov (United States)

Khadem, Masoud H; Wemhoff, Aaron P

2013-02-28

Non-equilibrium molecular dynamics (NEMD) simulations are used to investigate the thermal conductivity of herringbone graphite nanofibers (GNFs) at room temperature by breaking down the axial and transverse conductivity values into intralayer and interlayer components. The optimized Tersoff potential is used to account for intralayer carbon-carbon interactions while the Lennard-Jones potential is used to model the interlayer carbon-carbon interactions. The intralayer thermal conductivity of the graphene layers near room temperature is calculated for different crease angles and number of layers using NEMD with a constant applied heat flux. The edge effect on a layer's thermal conductivity is investigated by computing the thermal conductivity values in both zigzag and armchair directions of the heat flow. The interlayer thermal conductivity is also predicted by imposing hot and cold Nosé-Hoover thermostats on two layers. The limiting case of a 90° crease angle is used to compare the results with those of single-layer graphene and few-layer graphene. The axial and transverse thermal conductivities are then calculated using standard trigonometric conversions of the calculated intralayer and interlayer thermal conductivities, along with calculations of few-layer graphene without a crease. The results show a large influence of the crease angle on the intralayer thermal conductivity, and the saturation of thermal conductivity occurs when number of layers is more than three. The axial thermal conductivity, transverse thermal conductivity in the crease direction, and transverse thermal conductivity normal to the crease for the case of a five-layer herringbone GNF with a 45° crease angle are calculated to be 27 W∕m K, 263 W∕m K, and 1500 W∕m K, respectively, where the axial thermal conductivity is in good agreement with experimental measurements.

The relevance of thermal hydraulics pipeline simulation as a regulatory support tool

Energy Technology Data Exchange (ETDEWEB)

Silva, Patricia Mannarino; Santos, Almir Beserra dos [Agencia Nacional do Petroleo, Gas Natural e Biocombustiveis (ANP), Rio de Janeiro, RJ (Brazil)

2009-07-01

The capacity definition of a pipeline, along with its allocation, is very relevant to assure market transparency, nondiscriminatory access, security of supply, and also to give consistent signs for expansion needs. Nevertheless, the capacity definition is a controversial issue, and may widely vary depending on the technical and commercial assumptions made. To calculate a pipeline's nominal capacity, there are a variety of simulation tools, which include steady state, transient and on-line computer programs. It is desirable that the simulation tool is robust enough to predict the pipeline's capacity under different conditions. There are many variables that impact the flow through a pipeline, like gas characteristics, pipe and environmental variables. Designing a thermal model is a time-consuming task that requests understanding the level of detail need, in order to achieve success in its application. This article discusses the capacity definition, its role and calculation guidelines, describes ANP's experience with capacity calculation and further challenges according to the new regulation, and debates the role of thermal hydraulic simulation as a regulatory tool. (author)

Thermal conductivity of nanocrystalline SiGe alloys using molecular dynamics simulations

Science.gov (United States)

Abs da Cruz, Carolina; Katcho, Nebil A.; Mingo, Natalio; Veiga, Roberto G. A.

2013-10-01

We have studied the effect of nanocrystalline microstructure on the thermal conductivity of SiGe alloys using molecular dynamics simulations. Nanograins are modeled using both the coincidence site lattice and the Voronoi tessellation methods, and the thermal conductivity is computed using the Green-Kubo formalism. We analyze the dependence of the thermal conductivity with temperature, grain size L, and misorientation angle. We find a power dependence of L1/4 of the thermal conductivity with the grain size, instead of the linear dependence shown by non-alloyed nanograined systems. This dependence can be derived analytically underlines the important role that disorder scattering plays even when the grains are of the order of a few nm. This is in contrast to non-alloyed systems, where phonon transport is governed mainly by the boundary scattering. The temperature dependence is weak, in agreement with experimental measurements. The effect of angle misorientation is also small, which stresses the main role played by the disorder scattering.

The simulation of transients in thermal plant. Part I: Mathematical model

International Nuclear Information System (INIS)

Morini, G.L.; Piva, S.

2007-01-01

This paper deals with the simulation of the transient behaviour of thermal plant with control systems. It is always more difficult for a designer to predict the effects on the plant of the control processes because of the increasing complexity of plants and control systems. The easiest way to obtain information about the dynamic behaviour of a thermal plant at the design-stage involves assessing the suitability of specific computer codes. To this end, the present work demonstrates that nowadays it is possible, by using the opportunities offered by some general purpose calculation systems, to obtain such significant information. It is described how a 'thermal-library' of customized blocks (one for each component of a thermal plant such as valves, boilers, and pumps) can be built and used, in an intuitive way, to study any kind of plant. As an example, the dynamic behaviour of a residential heating system will be shown in a companion paper, forming part II of the present article

Numerical Simulations of Pillar Structured Solid State Thermal Neutron Detector Efficiency and Gamma Discrimination

Energy Technology Data Exchange (ETDEWEB)

Conway, A; Wang, T; Deo, N; Cheung, C; Nikolic, R

2008-06-24

This work reports numerical simulations of a novel three-dimensionally integrated, {sup 10}boron ({sup 10}B) and silicon p+, intrinsic, n+ (PIN) diode micropillar array for thermal neutron detection. The inter-digitated device structure has a high probability of interaction between the Si PIN pillars and the charged particles (alpha and {sup 7}Li) created from the neutron - {sup 10}B reaction. In this work, the effect of both the 3-D geometry (including pillar diameter, separation and height) and energy loss mechanisms are investigated via simulations to predict the neutron detection efficiency and gamma discrimination of this structure. The simulation results are demonstrated to compare well with the measurement results. This indicates that upon scaling the pillar height, a high efficiency thermal neutron detector is possible.

Stable intermediates determine proteins' primary unfolding sites in the presence of surfactants

DEFF Research Database (Denmark)

Petersen, Steen Vang; Andersen, Kell kleiner; Enghild, Jan J.

2009-01-01

Despite detailed knowledge of the overall structural changes and stoichiometries of surfactant binding, little is known about which protein regions constitute the preferred sites of attack for initial unfolding. Here we have exposed three proteins to limited proteolysis at anionic (SDS) and catio......Despite detailed knowledge of the overall structural changes and stoichiometries of surfactant binding, little is known about which protein regions constitute the preferred sites of attack for initial unfolding. Here we have exposed three proteins to limited proteolysis at anionic (SDS......) and cationic (DTAC) surfactant concentrations corresponding to specific conformational transitions, using the surfactant-robust broad-specificity proteases Savinase and Alcalase. Cleavage sites are identified by SDS-PAGE and N-terminal sequencing. We observe well-defined cleavage fragments, which suggest......, cleavage sites can be rationalized from the structure of the protein's folding transition state and the position of loops in the native state. Nevertheless, they are more sensitive to choice of surfactant and protease, probably reflecting a heterogeneous and fluctuating ensemble of partially unfolded...

Design process for applying the nonlocal thermal transport iSNB model to a Polar-Drive ICF simulation

Science.gov (United States)

Cao, Duc; Moses, Gregory; Delettrez, Jacques; Collins, Timothy

2014-10-01

A design process is presented for the nonlocal thermal transport iSNB (implicit Schurtz, Nicolai, and Busquet) model to provide reliable nonlocal thermal transport in polar-drive ICF simulations. Results from the iSNB model are known to be sensitive to changes in the SNB ``mean free path'' formula, and the latter's original form required modification to obtain realistic preheat levels. In the presented design process, SNB mean free paths are first modified until the model can match temperatures from Goncharov's thermal transport model in 1D temperature relaxation simulations. Afterwards the same mean free paths are tested in a 1D polar-drive surrogate simulation to match adiabats from Goncharov's model. After passing the two previous steps, the model can then be run in a full 2D polar-drive simulation. This research is supported by the University of Rochester Laboratory for Laser Energetics.

Simulator with integrated HW and SW for prediction of thermal comfort to provide feedback to the climate control system

Science.gov (United States)

Pokorný, Jan; Kopečková, Barbora; Fišer, Jan; JÍcha, Miroslav

2018-06-01

The aim of the paper is to assemble a simulator for evaluation of thermal comfort in car cabins in order to give a feedback to the HVAC (heating, ventilation and air conditioning) system. The HW (hardware) part of simulator is formed by thermal manikin Newton and RH (relative humidity), velocity and temperature probes. The SW (software) part consists of the Thermal Comfort Analyser (using ISO 14505-2) and Virtual Testing Stand of Car Cabin defining the heat loads of car cabin. Simulator can provide recommendation for the climate control how to improve thermal comfort in cabin by distribution and directing of air flow, and also by amount of ventilation power to keep optimal temperature inside a cabin. The methods of evaluation of thermal comfort were verified by tests with 10 test subjects for summer (summer clothing, ambient air temperature 30 °C, HVAC setup: +24 °C auto) and winter conditions (winter clothing, ambient air temperature -5 °C, HVAC setup: +18 °C auto). The tests confirmed the validity of the thermal comfort evaluation using the thermal manikin and ISO 14505-2.

Stochastic simulation of PWR vessel integrity for pressurized thermal shock conditions

International Nuclear Information System (INIS)

Jackson, P.S.; Moelling, D.S.

1984-01-01

A stochastic simulation methodology is presented for performing probabilistic analyses of Pressurized Water Reactor vessel integrity. Application of the methodology to vessel-specific integrity analyses is described in the context of Pressurized Thermal Shock (PTS) conditions. A Bayesian method is described for developing vessel-specific models of the density of undetected volumetric flaws from ultrasonic inservice inspection results. Uncertainty limits on the probabilistic results due to sampling errors are determined from the results of the stochastic simulation. An example is provided to illustrate the methodology

Molecular dynamics simulations for the motion of evaporative droplets driven by thermal gradients along nanochannels

KAUST Repository

Wu, Congmin

2013-04-04

For a one-component fluid on a solid substrate, a thermal singularity may occur at the contact line where the liquid-vapor interface intersects the solid surface. Physically, the liquid-vapor interface is almost isothermal at the liquid-vapor coexistence temperature in one-component fluids while the solid surface is almost isothermal for solids of high thermal conductivity. Therefore, a temperature discontinuity is formed if the two isothermal interfaces are of different temperatures and intersect at the contact line. This leads to the so-called thermal singularity. The localized hydrodynamics involving evaporation/condensation near the contact line leads to a contact angle depending on the underlying substrate temperature. This dependence has been shown to lead to the motion of liquid droplets on solid substrates with thermal gradients (Xu and Qian 2012 Phys. Rev. E 85 061603). In the present work, we carry out molecular dynamics (MD) simulations as numerical experiments to further confirm the predictions made from our previous continuum hydrodynamic modeling and simulations, which are actually semi-quantitatively accurate down to the small length scales in the problem. Using MD simulations, we investigate the motion of evaporative droplets in one-component Lennard-Jones fluids confined in nanochannels with thermal gradients. The droplet is found to migrate in the direction of decreasing temperature of solid walls, with a migration velocity linearly proportional to the temperature gradient. This agrees with the prediction of our continuum model. We then measure the effect of droplet size on the droplet motion. It is found that the droplet mobility is inversely proportional to a dimensionless coefficient associated with the total rate of dissipation due to droplet movement. Our results show that this coefficient is of order unity and increases with the droplet size for the small droplets (∼10 nm) simulated in the present work. These findings are in semi

Evaluation of the litcit software for thermal simulation of superficial lasers such as hair removal lasers

Directory of Open Access Journals (Sweden)

Shirkavand A

2007-01-01

Full Text Available Background and Objectives : In this study, we evaluate LITCIT software for its application as a thermal simulation software for superficial hair removal laser systems. Materials and Methods: Two articles were used as our references. Complete information regarding the tissues, such as optical/thermal properties and geometrical modeling and also the laser systems such as wavelength, spot size, pulse duration and fluence were extracted from these texts. Then, this information regarding the tissues and systems was entered into the LITCIT simulation software. Further, we ran the program and saved the results. Finally, we compared our results with the results in references and evaluated the. Results : Output results of the LITCIT show that they are consistent with the results of references that were calculated with a different thermal modeling. Such a small average error shows the accuracy of the software for simulation and calculating the temperature. Conclusions : This simulating software has a good ability to be used as a treatment planning software for superficial lasers. Thus, it can be used for the optimization of treatment parameters and protocols.

Weldability investigation steel P 91 by weld thermal cycle simulation

Directory of Open Access Journals (Sweden)

M. Dunđer

2015-07-01

Full Text Available This paper elaborates results of hardness and impact energy of thermal cycle simulated specimens of high-alloy steel P 91 and their dependence on cooling time from 800 to 500 °C. Results were obtained by measuring hardness HV 1 and by experimental testing of Charpy notched specimens. Metallographic analysis of samples was performed on scanning electronic microscope.

3D thermal modeling of TRISO fuel coupled with neutronic simulation

Energy Technology Data Exchange (ETDEWEB)

Hu, Jianwei [Los Alamos National Laboratory; Uddin, Rizwan [UNIV OF ILLINIOS

2010-01-01

The Very High Temperature Gas Reactor (VHTR) is widely considered as one of the top candidates identified in the Next Generation Nuclear Power-plant (NGNP) Technology Roadmap under the U.S . Depanment of Energy's Generation IV program. TRlSO particle is a common element among different VHTR designs and its performance is critical to the safety and reliability of the whole reactor. A TRISO particle experiences complex thermo-mechanical changes during reactor operation in high temperature and high burnup conditions. TRISO fuel performance analysis requires evaluation of these changes on micro scale. Since most of these changes are temperature dependent, 3D thermal modeling of TRISO fuel is a crucial step of the whole analysis package. In this paper, a 3D numerical thermal model was developed to calculate temperature distribution inside TRISO and pebble under different scenarios. 3D simulation is required because pebbles or TRISOs are always subjected to asymmetric thermal conditions since they are randomly packed together. The numerical model was developed using finite difference method and it was benchmarked against ID analytical results and also results reported from literature. Monte-Carlo models were set up to calculate radial power density profile. Complex convective boundary condition was applied on the pebble outer surface. Three reactors were simulated using this model to calculate temperature distribution under different power levels. Two asymmetric boundary conditions were applied to the pebble to test the 3D capabilities. A gas bubble was hypothesized inside the TRISO kernel and 3D simulation was also carried out under this scenario. Intuition-coherent results were obtained and reported in this paper.

Randomized quasi-Monte Carlo simulation of fast-ion thermalization

International Nuclear Information System (INIS)

Höök, L J; Johnson, T; Hellsten, T

2012-01-01

This work investigates the applicability of the randomized quasi-Monte Carlo method for simulation of fast-ion thermalization processes in fusion plasmas, e.g. for simulation of neutral beam injection and radio frequency heating. In contrast to the standard Monte Carlo method, the quasi-Monte Carlo method uses deterministic numbers instead of pseudo-random numbers and has a statistical weak convergence close to O(N -1 ), where N is the number of markers. We have compared different quasi-Monte Carlo methods for a neutral beam injection scenario, which is solved by many realizations of the associated stochastic differential equation, discretized with the Euler-Maruyama scheme. The statistical convergence of the methods is measured for time steps up to 2 14 . (paper)

PPARγ Ligand-Induced Unfolded Protein Responses in Monocytes

African Journals Online (AJOL)

High levels of oxLDL lead to cell dysfunction and apoptosis, a phenomenon known as lipotoxicity. Disturbing endoplasmic reticulum (ER) function results in ER stress and unfolded protein response (UPR), which tends to restore ER homeostasis but switches to apoptosis when ER stress is prolonged. In the present study the ...

PPARγ Ligand-Induced Unfolded Protein Responses in Monocytes ...

African Journals Online (AJOL)

acer

Disturbing endoplasmic reticulum (ER) function results in ER stress and unfolded protein response. (UPR), which tends to ... in mnocyte/macrophage cell lines as evident of the activation/up-regulation of ER stress/UPR genes. Cholesterol does not seem to exert ... inflammation (Tiwari et al., 2008). One prominent feature of ...

Simulation, optimization and control of a thermal cracking furnace

International Nuclear Information System (INIS)

Masoumi, M.E.; Sadrameli, S.M.; Towfighi, J.; Niaei, A.

2006-01-01

The ethylene production process is one of the most important aspect of a petrochemical plant and the cracking furnace is the heart of the process. Since, ethylene is one of the raw materials in the chemical industry and the market situation of not only the feed and the product, but also the utility is rapidly changing, the optimal operation and control of the plant is important. A mathematical model, which describes the static and dynamic operations of a pilot plant furnace, was developed. The static simulation was used to predict the steady-state profiles of temperature, pressure and products yield. The dynamic simulation of the process was used to predict the transient behavior of thermal cracking reactor. Using a dynamic programming technique, an optimal temperature profile was developed along the reactor. Performances of temperature control loop were tested for different controller parameters and disturbances. The results of the simulation were tested experimentally in a computer control pilot plant

Simulation of Missing Pellet Surface thermal behavior with 3D dynamic gap element

International Nuclear Information System (INIS)

Kim, Hyo Chan; Yang, Yong Sik; Koo, Yang Hyun; Kang, Chang Hak; Lee Sung Uk; Yang, Dong Yol

2014-01-01

Most of the fuel performance codes that are able to simulate a multidimensional analysis are used to calculate the radial temperature distribution and perform a multidimensional mechanical analysis based on a one-dimensional (1D) temperature result. The FRAPCON-FRAPTRAN code system incorporates a 1D thermal module and two-dimensional (2D) mechanical module when FEM option is activated. In this method, the multidimensional gap conductance model is not required because one-dimensional thermal analysis is carried out. On the other hand, a gap conductance model for a multi-dimension should be developed in the code to perform a multidimensional thermal analysis. ALCYONE developed by CEA introduces an equivalent heat convection coefficient that represents the multidimensional gap conductance. However, the code does not employ dynamic gap conductance which is a function of gap thickness and gap characteristics in direct. The BISON code, which has been developed by INL (Idaho National Laboratory), employed a thermo-mechanical contact method that is specifically designed for tightly-coupled implicit solutions that employ Jacobian-free solution methods. Owing to tightly-coupled implicit solutions, the BISON code solves gap conductance and gap thickness simultaneously with given boundary conditions. In this paper, 3D dynamic gap element has been proposed to resolve convergence issue and nonlinear characteristic of multidimensional gap conductance. To evaluate 3D dynamic gap element module, 3D thermomechanical module using FORTRAN77 has been implemented incorporating 3D dynamic gap element. To demonstrate effect of 3D dynamic gap element, thermal behavior of missing pellet surface (MPS) has been simulated by the developed module. LWR fuel performance codes should incorporate thermo-mechanical loop to solve gap conductance problem, iteratively. However, gap conductance in multidimensional model is difficult issue owing to its nonlinearity and convergence characteristics. In

A numerical simulation package for analysis of neutronics and thermal fluids of space nuclear power and propulsion systems

International Nuclear Information System (INIS)

Anghaie, S.; Feller, G.J.; Peery, S.D.; Parsley, R.C.

1993-01-01

A system of computer codes for engineering simulation and in-depth analysis of nuclear and thermal fluid design of nuclear thermal rockets is developed. The computational system includes a neutronic solver package, a thermal fluid solver package and a propellant and materials property package. The Rocket Engine Transient Simulation (ROCETS) system code is incorporated with computational modules specific to nuclear powered engines. ROCETS features a component based performance architecture that interfaces component modules into the user designed configuration, interprets user commands, creates an executable FORTRAN computer program, and executes the program to provide output to the user. Basic design features of the Pratt ampersand Whitney XNR2000 nuclear rocket concept and its operational performance are analyzed and simulated

Development of unfolding method to obtain pin-wise source strength distribution from PWR spent fuel assembly measurement

International Nuclear Information System (INIS)

Sitompul, Yos Panagaman; Shin, Hee-Sung; Park, Se-Hwan; Oh, Jong Myeong; Seo, Hee; Kim, Ho Dong

2013-01-01

An unfolding method has been developed to obtain a pin-wise source strength distribution of a 14 × 14 pressurized water reactor (PWR) spent fuel assembly. Sixteen measured gamma dose rates at 16 control rod guide tubes of an assembly are unfolded to 179 pin-wise source strengths of the assembly. The method calculates and optimizes five coefficients of the quadratic fitting function for X-Y source strength distribution, iteratively. The pin-wise source strengths are obtained at the sixth iteration, with a maximum difference between two sequential iterations of about 0.2%. The relative distribution of pin-wise source strength from the unfolding is checked using a comparison with the design code (Westinghouse APA code). The result shows that the relative distribution from the unfolding and design code is consistent within a 5% difference. The absolute value of the pin-wise source strength is also checked by reproducing the dose rates at the measurement points. The result shows that the pin-wise source strengths from the unfolding reproduce the dose rates within a 2% difference. (author)

Neutron response matrix for unfolding NE-213 measurements to 21 MeV

International Nuclear Information System (INIS)

Ingersoll, D.T.; Wehring, B.W.; Johnson, R.H.

1976-01-01

A neutron response matrix from measured neutron responses of NE-213 in the energy range of 0.2 to 22 MeV is presented. An interpolation scheme was used to construct an 81-column matrix from the data of Verbinski, Burrus, Love, Zobel, and Hill. As a test of the new response matrix, the Cf-252 neutron spectrum was measured and unfolded using the new response matrix and the FORIST unfolding code. The spectrum agrees well with previous measurements at lower energies, while providing new information above 8 MeV

Thermal transport in UO₂ with defects and fission products by molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Liu, Xiang-Yang [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Cooper, Michael William Donald [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Mcclellan, Kenneth James [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Lashley, Jason Charles [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Byler, Darrin David [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Stanek, Christopher Richard [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Andersson, Anders David Ragnar [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2015-10-14

The importance of the thermal transport in nuclear fuel has motivated a wide range of experimental and modelling studies. In this report, the reduction of thermal transport in UO₂ due to defects and fission products has been investigated using non-equilibrium MD simulations, with two sets of empirical potentials for studying the degregation of UO₂ thermal conductivity including a Buckingham type interatomic potential and a recently developed EAM type interatomic potential. Additional parameters for U⁵⁺ and Zr⁴⁺ in UO₂ have been developed for the EAM potential. The thermal conductivity results from MD simulations are then corrected for the spin-phonon scattering through Callaway model formulations. To validate the modelling results, comparison was made with experimental measurements on single crystal hyper-stoichiometric UO_2+x samples.

Using lattice tools and unfolding methods for hpge detector efficiency simulation with the Monte Carlo code MCNP5

International Nuclear Information System (INIS)

Querol, A.; Gallardo, S.; Ródenas, J.; Verdú, G.

2015-01-01

In environmental radioactivity measurements, High Purity Germanium (HPGe) detectors are commonly used due to their excellent resolution. Efficiency calibration of detectors is essential to determine activity of radionuclides. The Monte Carlo method has been proved to be a powerful tool to complement efficiency calculations. In aged detectors, efficiency is partially deteriorated due to the dead layer increasing and consequently, the active volume decreasing. The characterization of the radiation transport in the dead layer is essential for a realistic HPGe simulation. In this work, the MCNP5 code is used to calculate the detector efficiency. The F4MESH tally is used to determine the photon and electron fluence in the dead layer and the active volume. The energy deposited in the Ge has been analyzed using the ⁎F8 tally. The F8 tally is used to obtain spectra and to calculate the detector efficiency. When the photon fluence and the energy deposition in the crystal are known, some unfolding methods can be used to estimate the activity of a given source. In this way, the efficiency is obtained and serves to verify the value obtained by other methods. - Highlights: • The MCNP5 code is used to estimate the dead layer thickness of an HPGe detector. • The F4MESH tally is applied to verify where interactions occur into the Ge crystal. • PHD and the energy deposited are obtained with F8 and ⁎F8 tallies, respectively. • An average dead layer between 70 and 80 µm is obtained for the HPGe studied. • The efficiency is calculated applying the TSVD method to the response matrix.

Communication: Role of explicit water models in the helix folding/unfolding processes

Science.gov (United States)

Palazzesi, Ferruccio; Salvalaglio, Matteo; Barducci, Alessandro; Parrinello, Michele

2016-09-01

In the last years, it has become evident that computer simulations can assume a relevant role in modelling protein dynamical motions for their ability to provide a full atomistic image of the processes under investigation. The ability of the current protein force-fields in reproducing the correct thermodynamics and kinetics systems behaviour is thus an essential ingredient to improve our understanding of many relevant biological functionalities. In this work, employing the last developments of the metadynamics framework, we compare the ability of state-of-the-art all-atom empirical functions and water models to consistently reproduce the folding and unfolding of a helix turn motif in a model peptide. This theoretical study puts in evidence that the choice of the water models can influence the thermodynamic and the kinetics of the system under investigation, and for this reason cannot be considered trivial.

Simulator with integrated HW and SW for prediction of thermal comfort to provide feedback to the climate control system

Directory of Open Access Journals (Sweden)

Pokorný Jan

2018-01-01

Full Text Available The aim of the paper is to assemble a simulator for evaluation of thermal comfort in car cabins in order to give a feedback to the HVAC (heating, ventilation and air conditioning system. The HW (hardware part of simulator is formed by thermal manikin Newton and RH (relative humidity, velocity and temperature probes. The SW (software part consists of the Thermal Comfort Analyser (using ISO 14505-2 and Virtual Testing Stand of Car Cabin defining the heat loads of car cabin. Simulator can provide recommendation for the climate control how to improve thermal comfort in cabin by distribution and directing of air flow, and also by amount of ventilation power to keep optimal temperature inside a cabin. The methods of evaluation of thermal comfort were verified by tests with 10 test subjects for summer (summer clothing, ambient air temperature 30 °C, HVAC setup: +24 °C auto and winter conditions (winter clothing, ambient air temperature -5 °C, HVAC setup: +18 °C auto. The tests confirmed the validity of the thermal comfort evaluation using the thermal manikin and ISO 14505-2.

Effects of deformability and thermal motion of lipid membrane on electroporation: By molecular dynamics simulations

International Nuclear Information System (INIS)

Sun, Sheng; Yin, Guangyao; Lee, Yi-Kuen; Wong, Joseph T.Y.; Zhang, Tong-Yi

2011-01-01

Research highlights: → MD simulations show that deformability and thermal motion of membrane affect electroporation. → Stiffer membrane inhibits electroporation and makes water penetrate from both sides. → Higher temperature accelerates electroporation. -- Abstract: Effects of mechanical properties and thermal motion of POPE lipid membrane on electroporation were studied by molecular dynamics simulations. Among simulations in which specific atoms of lipids were artificially constrained at their equilibrium positions using a spring with force constant of 2.0 kcal/(mol A 2 ) in the external electric field of 1.4 kcal/(mol A e), only constraint on lateral motions of lipid tails prohibited electroporation while non-tail parts had little effects. When force constant decreased to 0.2 kcal/(mol A 2 ) in the position constraints on lipid tails in the external electric field of 2.0 kcal/(mol A e), water molecules began to enter the membrane. Position constraints of lipid tails allow water to penetrate from both sides of membrane. Thermal motion of lipids can induce initial defects in the hydrophobic core of membrane, which are favorable nucleation sites for electroporation. Simulations at different temperatures revealed that as the temperature increases, the time taken to the initial pore formation will decrease.

Plant transducers of the endoplasmic reticulum unfolded protein response

KAUST Repository

Iwata, Yuji; Koizumi, Nozomu

2012-01-01

The unfolded protein response (UPR) activates a set of genes to overcome accumulation of unfolded proteins in the endoplasmic reticulum (ER), a condition termed ER stress, and constitutes an essential part of ER protein quality control that ensures efficient maturation of secretory and membrane proteins in eukaryotes. Recent studies on Arabidopsis and rice identified the signaling pathway in which the ER membrane-localized ribonuclease IRE1 (inositol-requiring enzyme 1) catalyzes unconventional cytoplasmic splicing of mRNA, thereby producing the active transcription factor Arabidopsis bZIP60 (basic leucine zipper 60) and its ortholog in rice. Here we review recent findings identifying the molecular components of the plant UPR, including IRE1/bZIP60 and the membrane-bound transcription factors bZIP17 and bZIP28, and implicating its importance in several physiological phenomena such as pathogen response. © 2012 Elsevier Ltd.

Plant transducers of the endoplasmic reticulum unfolded protein response

KAUST Repository

Iwata, Yuji

2012-12-01

The unfolded protein response (UPR) activates a set of genes to overcome accumulation of unfolded proteins in the endoplasmic reticulum (ER), a condition termed ER stress, and constitutes an essential part of ER protein quality control that ensures efficient maturation of secretory and membrane proteins in eukaryotes. Recent studies on Arabidopsis and rice identified the signaling pathway in which the ER membrane-localized ribonuclease IRE1 (inositol-requiring enzyme 1) catalyzes unconventional cytoplasmic splicing of mRNA, thereby producing the active transcription factor Arabidopsis bZIP60 (basic leucine zipper 60) and its ortholog in rice. Here we review recent findings identifying the molecular components of the plant UPR, including IRE1/bZIP60 and the membrane-bound transcription factors bZIP17 and bZIP28, and implicating its importance in several physiological phenomena such as pathogen response. © 2012 Elsevier Ltd.

Molecular Origin of Gerstmann-Str ussler-Scheinker Syndrome: Insight from Computer Simulation of an Amyloidogenic Prion Peptide

Energy Technology Data Exchange (ETDEWEB)

Diadone, Isabella [University of L' Aquila, L' Aquila, Italy; DiNola, Alfredo [University of Rome; Smith, Jeremy C [ORNL

2011-01-01

Prion proteins become pathogenic through misfolding. Here, we characterize the folding of a peptide consisting of residues 109 122 of the Syrian hamster prion protein (the H1 peptide) and of a more amyloidogenic A117V point mutant that leads in humans to an inheritable form of the Gerstmann-Straeussler-Scheinker syndrome. Atomistic molecular dynamics simulations are performed for 2.5 s. Both peptides lose their -helical starting conformations and assume a -hairpin that is structurally similar in both systems. In each simulation several unfolding/refolding events occur, leading to convergence of the thermodynamics of the conformational states to within 1 kJ/mol. The similar stability of the -hairpin relative to the unfolded state is observed in the two peptides. However, substantial differences are found between the two unfolded states. A local minimum is found within the free energy unfolded basin of the A117V mutant populated by misfolded collapsed conformations of comparable stability to the -hairpin state, consistent with increased amyloidogenicity. This population, in which V117 stabilizes a hydrophobic core, is absent in the wild-type peptide. These results are supported by simulations of oligomers showing a slightly higher stability of the associated structures and a lower barrier to association for the mutated peptide. Hence, a single point mutation carrying only two additional methyl groups is here shown to be responsible for rather dramatic differences of structuring within the unfolded (misfolded) state.

Laser treatment of female stress urinary incontinence: optical, thermal, and tissue damage simulations

Science.gov (United States)

Hardy, Luke A.; Chang, Chun-Hung; Myers, Erinn M.; Kennelly, Michael J.; Fried, Nathaniel M.

2016-02-01

Treatment of female stress urinary incontinence (SUI) by laser thermal remodeling of subsurface tissues is studied. Light transport, heat transfer, and thermal damage simulations were performed for transvaginal and transurethral methods. Monte Carlo (MC) provided absorbed photon distributions in tissue layers (vaginal wall, endopelvic fascia, urethral wall). Optical properties (n,μa,μs,g) were assigned to each tissue at λ=1064 nm. A 5-mm-diameter laser beam and power of 5 W for 15 s was used, based on previous experiments. MC output was converted into absorbed energy, serving as input for ANSYS finite element heat transfer simulations of tissue temperatures over time. Convective heat transfer was simulated with contact cooling probe set at 0 °C. Thermal properties (κ,c,ρ) were assigned to each tissue layer. MATLAB code was used for Arrhenius integral thermal damage calculations. A temperature matrix was constructed from ANSYS output, and finite sum was incorporated to approximate Arrhenius integral calculations. Tissue damage properties (Ea,A) were used to compute Arrhenius sums. For the transvaginal approach, 37% of energy was absorbed in endopelvic fascia layer with 0.8% deposited beyond it. Peak temperature was 71°C, treatment zone was 0.8-mm-diameter, and almost all of 2.7-mm-thick vaginal wall was preserved. For transurethral approach, 18% energy was absorbed in endopelvic fascia with 0.3% deposited beyond it. Peak temperature was 80°C, treatment zone was 2.0-mm-diameter, and only 0.6 mm of 2.4-mm-thick urethral wall was preserved. A transvaginal approach is more feasible than transurethral approach for laser treatment of SUI.

Simulating the Thermal History of the Unsaturated Zone at Yucca Mountain, Nevada

International Nuclear Information System (INIS)

B.D. Marshal; J.F. Whelan

2001-01-01

Heat transfer within Earth's upper crust is primarily by conduction, and conductive thermal models adequately explain the cooling history of deep, batholith-scale intrusions and surrounding wall rocks, as confirmed by numerous thermochronometric studies. However, caldera magmatic systems require consideration of the small and localized component of hydrothermal convection and numerical models to simulate additional boundary conditions, irregular magma chamber shapes, and complex intrusive histories. At Yucca Mountain, Nevada, the site of a potential high-level nuclear waste repository, simulating the detailed thermal history at any location in the unsaturated zone requires knowledge of the shape of the magma chamber and its proximity to Yucca Mountain (the southern margin of the Timber Mountain caldera complex is approximately 8 km north of the potential repository site), the temporal and spatial extent of hydrothermal convection, the erosional history of the area, and past levels of the water table

Model based rib-cage unfolding for trauma CT

Science.gov (United States)

von Berg, Jens; Klinder, Tobias; Lorenz, Cristian

2018-03-01

A CT rib-cage unfolding method is proposed that does not require to determine rib centerlines but determines the visceral cavity surface by model base segmentation. Image intensities are sampled across this surface that is flattened using a model based 3D thin-plate-spline registration. An average rib centerline model projected onto this surface serves as a reference system for registration. The flattening registration is designed so that ribs similar to the centerline model are mapped onto parallel lines preserving their relative length. Ribs deviating from this model appear deviating from straight parallel ribs in the unfolded view, accordingly. As the mapping is continuous also the details in intercostal space and those adjacent to the ribs are rendered well. The most beneficial application area is Trauma CT where a fast detection of rib fractures is a crucial task. Specifically in trauma, automatic rib centerline detection may not be guaranteed due to fractures and dislocations. The application by visual assessment on the large public LIDC data base of lung CT proved general feasibility of this early work.

Development of a hot water tank simulation program with improved prediction of thermal stratification in the tank

DEFF Research Database (Denmark)

Fan, Jianhua; Furbo, Simon; Yue, Hongqiang

2015-01-01

A simulation program SpiralSol was developed in previous investigations to calculate thermal performance of a solar domestic hot water (SDHW) system with a hot water tank with a built-in heat exchanger spiral [1]. The simulation program is improved in the paper in term of prediction of thermal...... stratification in the tank. The transient fluid flow and heat transfer in the hot water tank during cooling caused by standby heat loss are investigated by validated computational fluid dynamics (CFD) calculations. Detailed CFD investigations are carried out to determine the influence of thickness and material...... property of the tank wall on thermal stratification in the tank. It is elucidated how thermal stratification in the tank is influenced by the natural convection and how the heat loss from the tank sides will be distributed at different levels of the tank at different thermal conditions. The existing...

The Unfolded Protein Response in Homeostasis and Modulation of Mammalian Immune Cells.

Science.gov (United States)

Martins, Ana Sofia; Alves, Inês; Helguero, Luisa; Domingues, Maria Rosário; Neves, Bruno Miguel

2016-11-01

The endoplasmic reticulum (ER) plays important roles in eukaryotic protein folding and lipid biosynthesis. Several exogenous and endogenous cellular sources of stress can perturb ER homeostasis leading to the accumulation of unfolded proteins in the lumen. Unfolded protein accumulation triggers a signal-transduction cascade known as the unfolded protein response (UPR), an adaptive mechanism which aims to protect cells from protein aggregates and to restore ER functions. Further to this protective mechanism, in immune cells, UPR molecular effectors have been shown to participate in a wide range of biological processes such as cell differentiation, survival and immunoglobulin and cytokine production. Recent findings also highlight the involvement of the UPR machinery in the maturational program and antigen presentation capacities of dendritic cells. UPR is therefore a key element in immune system homeostasis with direct implications on both adaptive and innate immune responses. The present review summarizes the knowledge on the emerging roles of UPR signaling cascades in mammalian immune cells as well as the consequences of their dysregulation in relation to the pathogenesis of several diseases.

Two-dimensional simulation of the thermal stress effect on static and dynamic VDMOS characteristics

International Nuclear Information System (INIS)

Alwan, M.; Beydoun, B.; Ketata, K.; Zoaeter, M.

2005-01-01

Using a two-dimensional simulator, the effect of the thermal stress on static and dynamic vertical double-diffusion metal oxide semiconductor (VDMOS) characteristics have been investigated. The use of the device under certain thermal stress conditions can produce modifications of its physical and electrical properties. Based on physics and 2D simulations, this paper proposes an analysis of this stress effect observed on the electrical characteristics of the device. Parameters responsible of these modifications are determined. Approximate expressions of the ionization coefficients and breakdown voltage in terms of temperature are proposed. Non-punch-through junction theory is used to express the breakdown voltage and the space charge extension with respect to the impurity concentration and the temperature. The capacitances of the device have been also studied. The effect of the stress on C-V characteristics is observed and analyzed. We notice that the drain-gate, drain-source and gate-source capacitances are shifted due to the degradation of device physical properties versus thermal stress

Simulation and Experimental Study on Thermal Conductivity of [EMIM][DEP] + H_2 O + SWCNTs Nanofluids as a New Working Pairs

Science.gov (United States)

Li, Chang; Zhao, Zongchang; Zhang, Xiaodong; Li, Tianyu

2018-03-01

In this paper, the single-wall carbon nanotubes (SWCNTs) were dispersed into ionic liquid, 1-ethyl-3-methylimidazolium diethylphosphate ([EMIM][DEP]), and its aqueous solution [EMIM][DEP](1) + H2O(2) to enhance the thermal conductivity of base liquids, which will be the promising working pairs for absorption heat pumps and refrigerators. The enhancement effects on thermal conductivity were studied by experiment and molecular dynamic simulation (MD) methods. The thermal conductivities of [EMIM][DEP] + SWCNTs (INF) and [EMIM][DEP](1) + H2O(2) + SWCNT(SNF) both with SWCNT mass fraction of 0.5, 1, and 2 (wt%) were measured by transient hot-wire method. The results indicate that the enhancement ratio of thermal conductivity of INF, and SNF can approach 1.30 when SWCNT is 2 (wt%). Moreover, SWCNTs has a higher enhancement ratio than multi-wall carbon nanotubes (MWCNTs). Density and thermal conductivity of [EMIM][DEP], [EMIM][DEP](1) + H2O(2), INF and SNF systems, together with self-diffusion coefficients of [EMIM]+, [DEP]-, [EMIM][DEP] and water in solution [EMIM][DEP](1) + H2O(2), were investigated by MD simulations. The results indicate that the maximum relative error between the simulated and experimental densities is about 2 %, and the simulated self-diffusion coefficient of [EMIM][DEP] is in the order of magnitude of 10^{-11} m2\\cdot s^{-1}. The average relative deviation for the simulated thermal conductivity of [EMIM][DEP](1) + H2O(2), INF and SNF from experimental ones are 23.57 %, 5 %, and 5 %, respectively. In addition, the contributions of kinetic energy, potential energy, and virial and partial enthalpy terms to thermal conductivity were also calculated. The results indicate that virial term's contribution to thermal conductivity is the maximum, which accounts for 75 % to 80 % of total thermal conductivity.

Computational Simulation of Thermal and Spattering Phenomena and Microstructure in Selective Laser Melting of Inconel 625

Science.gov (United States)

Özel, Tuğrul; Arısoy, Yiğit M.; Criales, Luis E.

Computational modelling of Laser Powder Bed Fusion (L-PBF) processes such as Selective laser Melting (SLM) can reveal information that is hard to obtain or unobtainable by in-situ experimental measurements. A 3D thermal field that is not visible by the thermal camera can be obtained by solving the 3D heat transfer problem. Furthermore, microstructural modelling can be used to predict the quality and mechanical properties of the product. In this paper, a nonlinear 3D Finite Element Method based computational code is developed to simulate the SLM process with different process parameters such as laser power and scan velocity. The code is further improved by utilizing an in-situ thermal camera recording to predict spattering which is in turn included as a stochastic heat loss. Then, thermal gradients extracted from the simulations applied to predict growth directions in the resulting microstructure.

Evaluating the performance of coupled snow-soil models in SURFEXv8 to simulate the permafrost thermal regime at a high Arctic site

Science.gov (United States)

Barrere, Mathieu; Domine, Florent; Decharme, Bertrand; Morin, Samuel; Vionnet, Vincent; Lafaysse, Matthieu

2017-09-01

Climate change projections still suffer from a limited representation of the permafrost-carbon feedback. Predicting the response of permafrost temperature to climate change requires accurate simulations of Arctic snow and soil properties. This study assesses the capacity of the coupled land surface and snow models ISBA-Crocus and ISBA-ES to simulate snow and soil properties at Bylot Island, a high Arctic site. Field measurements complemented with ERA-Interim reanalyses were used to drive the models and to evaluate simulation outputs. Snow height, density, temperature, thermal conductivity and thermal insulance are examined to determine the critical variables involved in the soil and snow thermal regime. Simulated soil properties are compared to measurements of thermal conductivity, temperature and water content. The simulated snow density profiles are unrealistic, which is most likely caused by the lack of representation in snow models of the upward water vapor fluxes generated by the strong temperature gradients within the snowpack. The resulting vertical profiles of thermal conductivity are inverted compared to observations, with high simulated values at the bottom of the snowpack. Still, ISBA-Crocus manages to successfully simulate the soil temperature in winter. Results are satisfactory in summer, but the temperature of the top soil could be better reproduced by adequately representing surface organic layers, i.e., mosses and litter, and in particular their water retention capacity. Transition periods (soil freezing and thawing) are the least well reproduced because the high basal snow thermal conductivity induces an excessively rapid heat transfer between the soil and the snow in simulations. Hence, global climate models should carefully consider Arctic snow thermal properties, and especially the thermal conductivity of the basal snow layer, to perform accurate predictions of the permafrost evolution under climate change.

Monte Carlo simulations of the pulsed thermal neutron flux in two-region hydrogenous systems (using standard MCNP data libraries)

International Nuclear Information System (INIS)

Wiacek, U.; Krynicka, E.

2005-02-01

Monte Carlo simulations of the pulsed neutron experiment in two- region systems (two concentric spheres and two coaxial finite cylinders) are presented. The MCNP code is used. Aqueous solutions of H 3 BO 3 or KCl are used in the inner region. The outer region is the moderator of Plexiglas. Standard data libraries of the thermal neutron scattering cross-sections of hydrogen in hydrogenous substances are used. The time-dependent thermal neutron transport is simulated when the inner region has a constant size and the external size of the surrounding outer region is variable. The time decay constant of the thermal neutron flux in the system is found in each simulation. The results of the simulations are compared with results of real pulsed neutron experiments on the corresponding systems. (author)

Multiscale simulation of thermal disruption in resistance switching process in amorphous carbon

International Nuclear Information System (INIS)

Popov, A M; Nikishin, N G; Shumkin, G N

2015-01-01

The switching of material atomic structure and electric conductivity is used in novel technologies of making memory on the base of phase change. The possibility of making memory on the base of amorphous carbon is shown in experiment [1]. Present work is directed to simulation of experimentally observed effects. Ab initio quantum calculations were used for simulation of atomic structure changes in amorphous carbon [2]. These simulations showed that the resistance change is connected with thermally induced effects. The temperature was supposed to be the function of time. In present paper we propose a new multiscale, self-consistent model which combines three levels of simulation scales and takes into account the space and time dependencies of the temperature. On the first level of quantum molecular dynamic we provide the calculations of phase change in atomic structure with space and time dependence of the temperature. Nose-Hover thermostats are used for MD simulations to reproduce space dependency of the temperature. It is shown that atomic structure is localized near graphitic layers in conducting dot. Structure parameter is used then on the next levels of the modeling. Modified Ehrenfest Molecular Dynamics is used on the second level. Switching evolution of electronic subsystem is obtained. In macroscopic scale level the heat conductivity equation for continuous media is used for calculation space-time dependence of the temperature. Joule heat source depends on structure parameter and electric conductivity profiles obtained on previous levels of modeling. Iterative procedure is self-consistently repeated combining three levels of simulation. Space localization of Joule heat source leads to the thermal disruption. Obtained results allow us to explain S-form of the Volt-Ampere characteristic observed in experiment. Simulations were performed on IBM Blue Gene/P supercomputer at Moscow State University. (paper)

Advances in thermal hydraulic and neutronic simulation for reactor analysis and safety

International Nuclear Information System (INIS)

Tentner, A.M.; Blomquist, R.N.; Canfield, T.R.; Ewing, T.F.; Garner, P.L.; Gelbard, E.M.; Gross, K.C.; Minkoff, M.; Valentin, R.A.

1993-01-01

This paper describes several large-scale computational models developed at Argonne National Laboratory for the simulation and analysis of thermal-hydraulic and neutronic events in nuclear reactors and nuclear power plants. The impact of advanced parallel computing technologies on these computational models is emphasized

Clinical evaluation of coronary territory map by using unfolded map of Tl-201 myocardial SPECT

International Nuclear Information System (INIS)

Uehara, Toshiisa; Nishimura, Tsunehiko; Katafuchi, Tetsuro; Yamagami, Hidetoshi; Kumita, Shinichirou; Hayashida, Kohei; Hayashi, Makoto

1990-01-01

Coronary territory map was developed on unfolded map of exercise Tl-201 myocardial SPECT. Each coronary territory was determined by summing the each unfolded map of 54 cases of single vessel disease respectively, and standardizing with normal pattern obtained from normal patients. The diagnostic accuracy of coronary territory map to identify the diseased coronary artery was analyzed in 104 clinical cases and was compared with that of planar and SPECT visual diagnosis, simple unfolded map (raw map) and extent and severity map. The results were as follows. (1) Territory map showed excellent diagnostic accuracy in single or double vessel disease, especially in diagnosis of left circumflex coronary artery lesion. (2) In triple vessel disease, the diagnostic accuracy of territory map or other unfolded maps was 30% at best, and was inferior to planar or SPECT visual analysis. The cause of this inferiority seemed that the quantitatively analyzed map had no information about the degree of Tl-uptake into lung or myocardium, which give useful information in visual diagnosis. (3) The diagnostic agreement ratio in two observers was the highest in territory map diagnosis, so that the territory map diagnosis seemed to be the most objective one. (4) The unfolded map diagnosis with apical display obtained from long-axis tomogram was useful to diagnose left anteior descending coronary (LAD) lesion, which improve not only the sensitivity of LAD but also specificity of right coronary artery single vessel disease. (author)

Calculation of inter-plane thermal resistance of few-layer graphene from equilibrium molecular dynamics simulations

International Nuclear Information System (INIS)

Ni, Y; Chalopin, Y; Volz, S

2012-01-01

Inter-plane thermal resistance in 5-layer graphene is calculated from equilibrium molecular dynamics (EMD) by calculating the autocorrelation function of temperature difference. Our simulated inter-plane resistance for 5-layer graphene is 4.83 × 10 −9 m 2 K/W. This data is in the same order of magnitude with the reported values from NEMD simulations and Debye model calculations, and the possible reasons for the slight differences are discussed in details. The inter-plane resistance is not dependent on temperature, according to the results of the EMD simulation. Phonon density of states (DOSs) were plotted to better understand the mechanism behind the obtained values. These results provide a better insight in the heat transfer across a few layer graphene and yield useful information on the design of graphene based thermal materials.

Thermal transport characterization of hexagonal boron nitride nanoribbons using molecular dynamics simulation

Directory of Open Access Journals (Sweden)

Asir Intisar Khan

2017-10-01

Full Text Available Due to similar atomic bonding and electronic structure to graphene, hexagonal boron nitride (h-BN has broad application prospects such as the design of next generation energy efficient nano-electronic devices. Practical design and efficient performance of these devices based on h-BN nanostructures would require proper thermal characterization of h-BN nanostructures. Hence, in this study we have performed equilibrium molecular dynamics (EMD simulation using an optimized Tersoff-type interatomic potential to model the thermal transport of nanometer sized zigzag hexagonal boron nitride nanoribbons (h-BNNRs. We have investigated the thermal conductivity of h-BNNRs as a function of temperature, length and width. Thermal conductivity of h-BNNRs shows strong temperature dependence. With increasing width, thermal conductivity increases while an opposite pattern is observed with the increase in length. Our study on h-BNNRs shows considerably lower thermal conductivity compared to GNRs. To elucidate these aspects, we have calculated phonon density of states for both h-BNNRs and GNRs. Moreover, using EMD we have explored the impact of different vacancies, namely, point vacancy, edge vacancy and bi-vacancy on the thermal conductivity of h-BNNRs. With varying percentages of vacancies, significant reduction in thermal conductivity is observed and it is found that, edge and point vacancies are comparatively more destructive than bi-vacancies. Such study would contribute further into the growing interest for accurate thermal transport characterization of low dimensional nanostructures.

Inter-regulation of the unfolded protein response and auxin signaling

Czech Academy of Sciences Publication Activity Database

Chen, Y.N.; Aung, K.; Rolčík, Jakub; Walicki, K.; Friml, J.; Brandizzi, F.

2014-01-01

Roč. 77, č. 1 (2014), s. 97-107 ISSN 0960-7412 Institutional support: RVO:61389030 Keywords : endoplasmic reticulum stress * unfolded protein response * auxin response Subject RIV: ED - Physiology Impact factor: 5.972, year: 2014

Performance of artificial neural networks and genetical evolved artificial neural networks unfolding techniques

International Nuclear Information System (INIS)

Ortiz R, J. M.; Martinez B, M. R.; Vega C, H. R.; Gallego D, E.; Lorente F, A.; Mendez V, R.; Los Arcos M, J. M.; Guerrero A, J. E.

2011-01-01

With the Bonner spheres spectrometer neutron spectrum is obtained through an unfolding procedure. Monte Carlo methods, Regularization, Parametrization, Least-squares, and Maximum Entropy are some of the techniques utilized for unfolding. In the last decade methods based on Artificial Intelligence Technology have been used. Approaches based on Genetic Algorithms and Artificial Neural Networks (Ann) have been developed in order to overcome the drawbacks of previous techniques. Nevertheless the advantages of Ann still it has some drawbacks mainly in the design process of the network, vg the optimum selection of the architectural and learning Ann parameters. In recent years the use of hybrid technologies, combining Ann and genetic algorithms, has been utilized to. In this work, several Ann topologies were trained and tested using Ann and Genetically Evolved Artificial Neural Networks in the aim to unfold neutron spectra using the count rates of a Bonner sphere spectrometer. Here, a comparative study of both procedures has been carried out. (Author)

Contribution of long-range interactions to the secondary structure of an unfolded globin.

Science.gov (United States)

Fedyukina, Daria V; Rajagopalan, Senapathy; Sekhar, Ashok; Fulmer, Eric C; Eun, Ye-Jin; Cavagnero, Silvia

2010-09-08

This work explores the effect of long-range tertiary contacts on the distribution of residual secondary structure in the unfolded state of an alpha-helical protein. N-terminal fragments of increasing length, in conjunction with multidimensional nuclear magnetic resonance, were employed. A protein representative of the ubiquitous globin fold was chosen as the model system. We found that, while most of the detectable alpha-helical population in the unfolded ensemble does not depend on the presence of the C-terminal region (corresponding to the native G and H helices), specific N-to-C long-range contacts between the H and A-B-C regions enhance the helical secondary structure content of the N terminus (A-B-C regions). The simple approach introduced here, based on the evaluation of N-terminal polypeptide fragments of increasing length, is of general applicability to identify the influence of long-range interactions in unfolded proteins. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Characteristics of SiC neutron sensor spectrum unfolding process based on Bayesian inference

Energy Technology Data Exchange (ETDEWEB)

Cetnar, Jerzy; Krolikowski, Igor [Faculty of Energy and Fuels AGH - University of Science and Technology, Al. Mickiewicza 30, 30-059 Krakow (Poland); Ottaviani, L. [IM2NP, UMR CNRS 7334, Aix-Marseille University, Case 231 -13397 Marseille Cedex 20 (France); Lyoussi, A. [CEA, DEN, DER, Instrumentation Sensors and Dosimetry Laboratory, Cadarache, F-13108 St-Paul-Lez-Durance (France)

2015-07-01

This paper deals with SiC detector signal interpretation in neutron radiation measurements in mixed neutron gamma radiation fields, which is called the detector inverse problem or the spectrum unfolding, and it aims in finding a representation of the primary radiation, based on the measured detector signals. In our novel methodology we resort to Bayesian inference approach. In the developed procedure the resultant spectra is unfolded form detector channels reading, where the estimated neutron fluence in a group structure is obtained with its statistical characteristic comprising of standard deviation and correlation matrix. In the paper we present results of unfolding process for case of D-T neutron source in neutron moderating environment. Discussions of statistical properties of obtained results are presented as well as of the physical meaning of obtained correlation matrix of estimated group fluence. The presented works has been carried out within the I-SMART project, which is part of the KIC InnoEnergy R and D program. (authors)

Decay of the pulsed thermal neutron flux in two-zone hydrogenous systems - Monte Carlo simulations using MCNP standard data libraries

International Nuclear Information System (INIS)

Wiacek, Urszula; Krynicka, Ewa

2006-01-01

Pulsed neutron experiments in two-zone spherical and cylindrical geometry has been simulated using the MCNP code. The systems are built of hydrogenous materials. The inner zone is filled with aqueous solutions of absorbers (H 3 BO 3 or KCl). It is surrounded by the outer zone built of Plexiglas. The system is irradiated with the pulsed thermal neutron flux and the thermal neutron decay in time is observed. Standard data libraries of the thermal neutron scattering cross-sections of hydrogen in hydrogenous substances have been used to simulate the neutron transport. The time decay constant of the fundamental mode of the thermal neutron flux determined in each simulation has been compared with the corresponding result of the real pulsed neutron experiment

Validating subject-specific RF and thermal simulations in the calf muscle using MR-based temperature measurements

NARCIS (Netherlands)

Simonis, Ffj; Raaijmakers, Aje; Lagendijk, Jjw; van den Berg, Cat

2017-01-01

Purpose: Ongoing discussions occur to translate the safety restrictions on MR scanners from specific absorption rate (SAR) to thermal dose. Therefore, this research focuses on the accuracy of thermal simulations in human subjects during an MR exam, which is fundamental information in that debate.

Thermal large Eddy simulations and experiments in the framework of non-isothermal blowing; Simulations des grandes echelles thermiques et experiences dans le cadre d'effusion anisotherme

Energy Technology Data Exchange (ETDEWEB)

Brillant, G

2004-06-15

The aim of this work is to study thermal large-eddy simulations and to determine the nonisothermal blowing impact on a turbulent boundary layer. An experimental study is also carried out in order to complete and validate simulation results. In a first time, we developed a turbulent inlet condition for the velocity and the temperature, which is necessary for the blowing simulations.We studied the asymptotic behavior of the velocity, the temperature and the thermal turbulent fluxes in a large-eddy simulation point of view. We then considered dynamics models for the eddy-diffusivity and we simulated a turbulent channel flow with imposed temperature, imposed flux and adiabatic walls. The numerical and experimental study of blowing permitted to obtain to the modifications of a thermal turbulent boundary layer with the blowing rate. We observed the consequences of the blowing on mean and rms profiles of velocity and temperature but also on velocity-velocity and velocity-temperature correlations. Moreover, we noticed an increase of the turbulent structures in the boundary layer with blowing. (author)

Effect of point defects on the thermal conductivity of UO2: molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Liu, Xiang-Yang [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Stanek, Christopher Richard [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Andersson, Anders David Ragnar [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2015-07-21

The thermal conductivity of uranium dioxide (UO₂) fuel is an important materials property that affects fuel performance since it is a key parameter determining the temperature distribution in the fuel, thus governing, e.g., dimensional changes due to thermal expansion, fission gas release rates, etc. [1] The thermal conductivity of UO₂ nuclear fuel is also affected by fission gas, fission products, defects, and microstructural features such as grain boundaries. Here, molecular dynamics (MD) simulations are carried out to determine quantitatively, the effect of irradiation induced point defects on the thermal conductivity of UO₂, as a function of defect concentrations, for a range of temperatures, 300 – 1500 K. The results will be used to develop enhanced continuum thermal conductivity models for MARMOT and BISON by INL. These models express the thermal conductivity as a function of microstructure state-variables, thus enabling thermal conductivity models with closer connection to the physical state of the fuel [2].

RDANN a new methodology to solve the neutron spectra unfolding problem

Energy Technology Data Exchange (ETDEWEB)

Ortiz R, J.M.; Martinez B, M.R.; Vega C, H.R. [UAZ, Av. Ramon Lopez Velarde No. 801, 98000 Zacatecas (Mexico)

2006-07-01

The optimization processes known as Taguchi method and DOE methodology are applied to the design, training and testing of Artificial Neural Networks in the neutron spectrometry field, which offer potential benefits in the evaluation of the behavior of the net as well as the ability to examine the interaction of the weights and neurons inside the same one. In this work, the Robust Design of Artificial Neural Networks methodology is used to solve the neutron spectra unfolding problem, designing, training and testing an ANN using a set of 187 neutron spectra compiled by the International Atomic Energy Agency, to obtain the better neutron spectra unfolded from the Bonner spheres spectrometer's count rates. (Author)

RDANN a new methodology to solve the neutron spectra unfolding problem

International Nuclear Information System (INIS)

Ortiz R, J.M.; Martinez B, M.R.; Vega C, H.R.

2006-01-01

The optimization processes known as Taguchi method and DOE methodology are applied to the design, training and testing of Artificial Neural Networks in the neutron spectrometry field, which offer potential benefits in the evaluation of the behavior of the net as well as the ability to examine the interaction of the weights and neurons inside the same one. In this work, the Robust Design of Artificial Neural Networks methodology is used to solve the neutron spectra unfolding problem, designing, training and testing an ANN using a set of 187 neutron spectra compiled by the International Atomic Energy Agency, to obtain the better neutron spectra unfolded from the Bonner spheres spectrometer's count rates. (Author)

Effective electrochemical method for investigation of hemoglobin unfolding based on the redox property of heme groups at glassy carbon electrodes.

Science.gov (United States)

Li, Xianchan; Zheng, Wei; Zhang, Limin; Yu, Ping; Lin, Yuqing; Su, Lei; Mao, Lanqun

2009-10-15

This study demonstrates a facile and effective electrochemical method for investigation of hemoglobin (Hb) unfolding based on the electrochemical redox property of heme groups in Hb at bare glassy carbon (GC) electrodes. In the native state, the heme groups are deeply buried in the hydrophobic pockets of Hb with a five-coordinate high-spin complex and thus show a poor electrochemical property at bare GC electrodes. Upon the unfolding of Hb induced by the denaturant of guanidine hydrochloride (GdnHCl), the fifth coordinative bond between the heme groups and the residue of the polypeptides (His-F8) is broken, and as a result, the heme groups initially buried deeply in the hydrophobic pockets dissociate from the polypeptide chains and are reduced electrochemically at GC electrodes, which can be used to probe the unfolding of Hb. The results on the GdnHCl-induced Hb unfolding obtained with the electrochemical method described here well coincide with those studied with other methods, such as UV-vis spectroscopy, fluorescence, and circular dichroism. The application of the as-established electrochemical method is illustrated to study the kinetics of GdnHCl-induced Hb unfolding, the GdnHCl-induced unfolding of another kind of hemoprotein, catalase, and the pH-induced Hb unfolding/refolding.

CFD SIMULATION FOR DEMILITARIZATION OF RDX IN A ROTARY KILN BY THERMAL DECOMPOSITION

Directory of Open Access Journals (Sweden)

SI H. LEE

2017-06-01

Full Text Available Demilitarization requires the recovery and disposal of obsolete ammunition and explosives. Since open burning/detonation of hazardous waste has caused serious environmental and safety problems, thermal decomposition has emerged as one of the most feasible methods. RDX is widely used as a military explosive due to its high melting temperature and detonation power. In this work, the feasible conditions under which explosives can be safely incinerated have been investigated via a rotary kiln simulation. To solve this problem, phase change along with the reactions of RDX has been incisively analyzed. A global reaction mechanism consisting of condensed phase and gas phase reactions are used in Computational Fluid Dynamics simulation. User Defined Functions in FLUENT is utilized in this study to inculcate the reactions and phase change into the simulation. The results divulge the effect of temperature and the varying amounts of gas produced in the rotary kiln during the thermal decomposition of RDX. The result leads to the prospect of demilitarizing waste explosives to avoid the possibility of detonation.

Simulated transient thermal infrared emissions of forest canopies during rainfall events

Science.gov (United States)

Ballard, Jerrell R.; Hawkins, William R.; Howington, Stacy E.; Kala, Raju V.

2017-05-01

We describe the development of a centimeter-scale resolution simulation framework for a theoretical tree canopy that includes rainfall deposition, evaporation, and thermal infrared emittance. Rainfall is simulated as discrete raindrops with specified rate. The individual droplets will either fall through the canopy and intersect the ground; adhere to a leaf; bounce or shatter on impact with a leaf resulting in smaller droplets that are propagated through the canopy. Surface physical temperatures are individually determined by surface water evaporation, spatially varying within canopy wind velocities, solar radiation, and water vapor pressure. Results are validated by theoretical canopy gap and gross rainfall interception models.

Direct numerical simulation of stable and unstable turbulent thermal boundary layers

International Nuclear Information System (INIS)

Hattori, Hirofumi; Houra, Tomoya; Nagano, Yasutaka

2007-01-01

This paper presents direct numerical simulations (DNS) of stable and unstable turbulent thermal boundary layers. Since a buoyancy-affected boundary layer is often encountered in an urban environmental space where stable and unstable stratifications exist, exploring a buoyancy-affected boundary layer is very important to know the transport phenomena of the flow in an urban space. Although actual observation may qualitatively provide the characteristics of these flows, the relevant quantitative turbulent quantities are very difficult to measure. Thus, in order to quantitatively investigate a buoyancy-affected boundary layer in detail, we have here carried out for the first time time- and space-developing DNS of slightly stable and unstable turbulent thermal boundary layers. The DNS results show the quantitative turbulent statistics and structures of stable and unstable thermal boundary layers, in which the characteristic transport phenomena of thermally stratified boundary layers are demonstrated by indicating the budgets of turbulent shear stress and turbulent heat flux. Even though the input of buoyant force is not large, the influence of buoyancy is clearly revealed in both stable and unstable turbulent boundary layers. In particular, it is found that both stable and unstable thermal stratifications caused by the weak buoyant force remarkably alter the structure of near-wall turbulence

Semiquantum molecular dynamics simulation of thermal properties and heat transport in low-dimensional nanostructures

Science.gov (United States)

Savin, Alexander V.; Kosevich, Yuriy A.; Cantarero, Andres

2012-08-01

We present a detailed description of semiquantum molecular dynamics simulation of stochastic dynamics of a system of interacting particles. Within this approach, the dynamics of the system is described with the use of classical Newtonian equations of motion in which the effects of phonon quantum statistics are introduced through random Langevin-like forces with a specific power spectral density (the color noise). The color noise describes the interaction of the molecular system with the thermostat. We apply this technique to the simulation of thermal properties and heat transport in different low-dimensional nanostructures. We describe the determination of temperature in quantum lattice systems, to which the equipartition limit is not applied. We show that one can determine the temperature of such a system from the measured power spectrum and temperature- and relaxation-rate-independent density of vibrational (phonon) states. We simulate the specific heat and heat transport in carbon nanotubes, as well as the heat transport in molecular nanoribbons with perfect (atomically smooth) and rough (porous) edges, and in nanoribbons with strongly anharmonic periodic interatomic potentials. We show that the effects of quantum statistics of phonons are essential for the carbon nanotube in the whole temperature range T<500K, in which the values of the specific heat and thermal conductivity of the nanotube are considerably less than that obtained within the description based on classical statistics of phonons. This conclusion is also applicable to other carbon-based materials and systems with high Debye temperature like graphene, graphene nanoribbons, fullerene, diamond, diamond nanowires, etc. We show that the existence of rough edges and quantum statistics of phonons change drastically the low-temperature thermal conductivity of the nanoribbon in comparison with that of the nanoribbon with perfect edges and classical phonon dynamics and statistics. The semiquantum molecular

Model of natural ventilation by using a coupled thermal-airflow simulation program

DEFF Research Database (Denmark)

Oropeza-Perez, Ivan; Østergaard, Poul Alberg; Remmen, Arne

2012-01-01

This article presents a model of natural ventilation of buildings at the stage of design and a consequence of the behaviour of the occupants. An evaluation is made by coupling multizone air modelling and thermal building simulation using a deterministic set of input factors comprising among others...

Na,K-ATPase reconstituted in ternary liposome: the presence of cholesterol affects protein activity and thermal stability.

Science.gov (United States)

Yoneda, Juliana Sakamoto; Rigos, Carolina Fortes; de Lourenço, Thaís Fernanda Aranda; Sebinelli, Heitor Gobbi; Ciancaglini, Pietro

2014-12-15

Differential scanning calorimetry (DSC) was applied to investigate the effect of cholesterol on the thermotropic properties of the lipid membrane (DPPC and DPPE). The thermostability and unfolding of solubilized and reconstituted Na,K-ATPase in DPPC:DPPE:cholesterol-liposomes was also studied to gain insight into the role of cholesterol in the Na,K-ATPase modulation of enzyme function and activity. The tertiary system (DPPC:DPPE:cholesterol) (molar ratio DPPC:DPPE equal 1:1) when cholesterol content was increased from 0% up to 40% results in a slight decrease in the temperature of transition and enthalpy, and an increase in width. We observed that, without heating treatment, at 37°C, the activity was higher for 20mol% cholesterol. However, thermal inactivation experiments showed that the enzyme activity loss time depends on the cholesterol membrane content. The unfolding of the enzyme incorporated to liposomes of DPPC:DPPE (1:1mol) with different cholesterol contents, ranging from 0% to 40% mol was also studied by DSC. Some differences between the thermograms indicate that the presence of lipids promotes a conformational change in protein structure and this change is enough to change the way Na,K-ATPase thermally unfolds. Copyright © 2014 Elsevier Inc. All rights reserved.

Thermal simulation for 35 kW powered prototype radio frequency quadrapole

International Nuclear Information System (INIS)

Kothari, Ashok; Ahuja, Rajeev; Safvan, C.P.; Kumar, Sugam

2011-01-01

As part of the accelerator augmentation program at IUAC, a high current injector (HCI) is being developed to inject highly charged ions into the superconducting LINAC. The HCI consists of a superconducting (High T c ) ECR source operated on a high voltage deck, producing the high currents of highly charged ions. The ion beams produced by the ECR (PKDELIS) source will be injected into a Radio Frequency Quadrupole accelerator (RFQ) and be accelerated to 180 keV/u. RF power of about 100 kW at 48.5 MHz will be fed to the RFQ during it's actual working. Most of the power fed is dissipated in the system as heat. So a continuous removal of this heat is necessary to maintain tuning parameters and normal running of the RFQ. The IUAC RFQ is a four rod cavity structure consisting of individual, demountable vanes on vane posts. All the components are made of copper except the high vacuum chamber. High vacuum chamber is made of stainless steel and electroplated with 100 microns copper on the inner surface. To take out the heat from the system cooling holes for water circulation are provided in the design of the vanes and vane posts, which together form cooling circuits. There are fourteen vanes in three different lengths and these are mounted on five vane posts. Water enters and exits from the vane posts base. From each post it enters into two or three circuits in parallel and exits into the next vane post and the flow combines again. In effect five cooling circuits are further divided into fourteen circuits. Thermal design of the system is analyzed and optimized using a computational fluid dynamics (CFD) software. The CFD software simultaneously solves the equations of mass, momentum and energy with the given structure, material, fluid and applied boundary conditions. An actual 3-dimensional model of the assembly was made using Solidworks modelling software. To save on simulation time, small holes and minor components were suppressed during analysis. The software used for

A method for unfolding high-energy scintillation gamma-ray spectra up to 8 MeV

International Nuclear Information System (INIS)

Dymke, N.; Hofmann, B.

1982-01-01

In unfolding a high-energy scintillation gamma-ray spectrum up to 8 MeV with the help of a response matrix, the means of linear algebra fail if the matrix is ill conditioned. In such cases, unfolding could be accomplished by means of a mathematical method based on a priori knowledge of the photon spectrum to be expected. The method which belongs to the class of regularization techniques was tested on in-situ gamma-ray spectra of 16 N recorded in a nuclear power plant near the primary circuit, using an 1.5 x 1.5 in. NaI(Tl) scintillation detector. For one regularized unfolding the results were presented in the form of an energy and a dose-rate spectrum. (author)

The simulation methods based on 1D/3D collaborative computing for the vehicle integrated thermal management

International Nuclear Information System (INIS)

Lu, Pengyu; Gao, Qing; Wang, Yan

2016-01-01

Highlights: • A 1D/3D collaborative computing simulation method for vehicle thermal management. • Analyzing the influence of the thermodynamic systems and the engine compartment geometry on the vehicle performance. • Providing the basis for the matching energy consumptions of thermodynamic systems in the underhood. - Abstract: The vehicle integrated thermal management containing the engine cooling circuit, the air conditioning circuit, the turbocharged inter-cooled circuit, the engine lubrication circuit etc. is the important means of enhancing power performance, promoting economy, saving energy and reducing emission. In this study, a 1D/3D collaborative simulation method is proposed with the engine cooling circuit and air conditioning circuit being the research object. The mathematical characterizations of the multiple thermodynamic systems are achieved by 1D calculation and the underhood structure is described by 3D simulation. Through analyzing the engine compartment integrated heat transfer process, the model of the integrated thermal management system is formed after coupling the cooling circuit and air conditioning circuit. This collaborative simulation method establishes structured correlation of engine-cooling and air conditioning thermal dissipation in the engine compartment, comprehensively analyzing the engine working process and air condition operational process in order to research the interaction effect of them. In the calculation examples, to achieve the integrated optimization of multiple thermal systems design and performance prediction, by describing the influence of system thermomechanical parameters and operating duty to underhood heat transfer process, performance evaluation of the engine cooling circuit and the air conditioning circuit are realized.

Numerical simulation of CTE mismatch and thermal-structural stresses in the design of interconnects

Science.gov (United States)

Peter, Geoffrey John M.

With the ever-increasing chip complexity, interconnects have to be designed to meet the new challenges. Advances in optical lithography have made chip feature sizes available today at 70 nm dimensions. With advances in Extreme Ultraviolet Lithography, X-ray Lithography, and Ion Projection Lithography it is expected that the line width will further decrease to 20 nm or less. With the decrease in feature size, the number of active devices on the chip increases. With higher levels of circuit integration, the challenge is to dissipate the increased heat flux from the chip surface area. Thermal management considerations include coefficient of thermal expansion (CTE) matching to prevent failure between the chip and the board. This in turn calls for improved system performance and reliability of the electronic structural systems. Experience has shown that in most electronic systems, failures are mostly due to CTE mismatch between the chip, board, and the solder joint (solder interconnect). The resulting high thermal-structural stress and strain due to CTE mismatch produces cracks in the solder joints with eventual failure of the electronic component. In order to reduce the thermal stress between the chip, board, and the solder joint, this dissertation examines the effect of inserting wire bundle (wire interconnect) between the chip and the board. The flexibility of the wires or fibers would reduce the stress at the rigid joints. Numerical simulations of two, and three-dimensional models of the solder and wire interconnects are examined. The numerical simulation is linear in nature and is based on linear isotropic material properties. The effect of different wire material properties is examined. The effect of varying the wire diameter is studied by changing the wire diameter. A major cause of electronic equipment failure is due to fatigue failure caused by thermal cycling, and vibrations. A two-dimensional modal and harmonic analysis was simulated for the wire interconnect

Thermal comfort in residential buildings: Comfort values and scales for building energy simulation

Energy Technology Data Exchange (ETDEWEB)

Peeters, Leen; D' haeseleer, William [Division of Applied Mechanics and Energy Conversion, University of Leuven (K.U.Leuven), Celestijnenlaan 300 A, B-3001 Leuven (Belgium); Dear, Richard de [Division of Environmental and Life Sciences, Macquarie University, Sydney (Australia); Hensen, Jan [Faculty of Architecture, Building and Planning, Technische Universiteit Eindhoven, Vertigo 6.18, P.O. Box 513, 5600 MB Eindhoven (Netherlands)

2009-05-15

Building Energy Simulation (BES) programmes often use conventional thermal comfort theories to make decisions, whilst recent research in the field of thermal comfort clearly shows that important effects are not incorporated. The conventional theories of thermal comfort were set up based on steady state laboratory experiments. This, however, is not representing the real situation in buildings, especially not when focusing on residential buildings. Therefore, in present analysis, recent reviews and adaptations are considered to extract acceptable temperature ranges and comfort scales. They will be defined in an algorithm, easily implementable in any BES code. The focus is on comfortable temperature levels in the room, more than on the detailed temperature distribution within that room. (author)

Heat, Acid and Chemically Induced Unfolding Pathways, Conformational Stability and Structure-Function Relationship in Wheat α-Amylase.

Directory of Open Access Journals (Sweden)

Kritika Singh

Full Text Available Wheat α-amylase, a multi-domain protein with immense industrial applications, belongs to α+β class of proteins with native molecular mass of 32 kDa. In the present study, the pathways leading to denaturation and the relevant unfolded states of this multi-domain, robust enzyme from wheat were discerned under the influence of temperature, pH and chemical denaturants. The structural and functional aspects along with thermodynamic parameters for α-amylase unfolding were probed and analyzed using fluorescence, circular dichroism and enzyme assay methods. The enzyme exhibited remarkable stability up to 70°C with tendency to aggregate at higher temperature. Acid induced unfolding was also incomplete with respect to the structural content of the enzyme. Strong ANS binding at pH 2.0 suggested the existence of a partially unfolded intermediate state. The enzyme was structurally and functionally stable in the pH range 4.0-9.0 with 88% recovery of hydrolytic activity. Careful examination of biophysical properties of intermediate states populated in urea and GdHCl induced denaturation suggests that α-amylase unfolding undergoes irreversible and non-coincidental cooperative transitions, as opposed to previous reports of two-state unfolding. Our investigation highlights several structural features of the enzyme in relation to its catalytic activity. Since, α-amylase has been comprehensively exploited for use in a range of starch-based industries, in addition to its physiological significance in plants and animals, knowledge regarding its stability and folding aspects will promote its biotechnological applications.

Accuracy of unfolded map method for determining the left ventricular border. Evaluation of the cut-off value from autopsy finding

International Nuclear Information System (INIS)

Sugibayashi, Keiichi; Abe, Yoshiteru; Suga, Yutaka

1996-01-01

To improve the quantification of the left ventricular surface area (LVSA) by unfolded map method, we evaluated the cut-off value for determining the left ventricular border. The LVSA measured by unfolded map was compared with those measured using myocardial phantom and autopsy findings. The relative error (RE) was calculated as difference between LVSA in phantom and area of unfolded map. In phantom study, the cut-off value was calculated as 73.3±0.5% when the RE was zero. In autopsy study, the cut-off value was 74.0±7.2%. The area of unfolded map had good correlation with LVSA at autopsy when the cut-off value was 74% (r=0.83, p<0.003). The diameter of left ventricle at autopsy was compared with that of beating heart obtained by two-dimensional echocardiography, because the area of unfolded map was greater than LVSA at autopsy. The ratio of LVSA at autopsy to beating heart was calculated as 1.37. The suitable cut-off value was evaluated as 55.6% when the unfolded map area obtained by autopsy was increased 1.37 magnifications. There was a good correlation between LVSA of unfolded map (cut-off=56%) and the LVSA at autopsy (r=0.90, p<0.001). These results suggest that the cut-off value for determining the left ventricular border in vivo is 56%. (author)

Effects of spermine NONOate and ATP on the thermal stability of hemoglobin

Directory of Open Access Journals (Sweden)

Bassam Rasha

2012-08-01

Full Text Available Abstract Background Minor changes in protein structure induced by small organic and inorganic molecules can result in significant metabolic effects. The effects can be even more profound if the molecular players are chemically active and present in the cell in considerable amounts. The aim of our study was to investigate effects of a nitric oxide donor (spermine NONOate, ATP and sodium/potassium environment on the dynamics of thermal unfolding of human hemoglobin (Hb. The effect of these molecules was examined by means of circular dichroism spectrometry (CD in the temperature range between 25°C and 70°C. The alpha-helical content of buffered hemoglobin samples (0.1 mg/ml was estimated via ellipticity change measurements at a heating rate of 1°C/min. Results Major results were: 1 spermine NONOate persistently decreased the hemoglobin unfolding temperature Tuirrespectively of the Na + /K + environment, 2 ATP instead increased the unfolding temperature by 3°C in both sodium-based and potassium-based buffers and 3 mutual effects of ATP and NO were strongly influenced by particular buffer ionic compositions. Moreover, the presence of potassium facilitated a partial unfolding of alpha-helical structures even at room temperature. Conclusion The obtained data might shed more light on molecular mechanisms and biophysics involved in the regulation of protein activity by small solutes in the cell.

Collaborative Classroom Simulation (CCS): An Innovative Pedagogy Using Simulation in Nursing Education.

Science.gov (United States)

Berndt, Jodi; Dinndorf-Hogenson, Georgia; Herheim, Rena; Hoover, Carrie; Lanc, Nicole; Neuwirth, Janet; Tollefson, Bethany

2015-01-01

Collaborative Classroom Simulation (CCS) is a pedagogy designed to provide a simulation learning experience for a classroom of students simultaneously through the use of unfolding case scenarios. The purpose of this descriptive study was to explore the effectiveness of CCS based on student perceptions. Baccalaureate nursing students (n = 98) participated in the study by completing a survey after participation in the CCS experience. Opportunities for collaboration, clinical judgment, and participation as both observer and active participant were seen as strengths of the experience. Developed as a method to overcome barriers to simulation, CCS was shown to be an effective active learning technique that may prove to be sustainable.

A model selection support system for numerical simulations of nuclear thermal-hydraulics

International Nuclear Information System (INIS)

Gofuku, Akio; Shimizu, Kenji; Sugano, Keiji; Yoshikawa, Hidekazu; Wakabayashi, Jiro

1990-01-01

In order to execute efficiently a dynamic simulation of a large-scaled engineering system such as a nuclear power plant, it is necessary to develop intelligent simulation support system for all phases of the simulation. This study is concerned with the intelligent support for the program development phase and is engaged in the adequate model selection support method by applying AI (Artificial Intelligence) techniques to execute a simulation consistent with its purpose and conditions. A proto-type expert system to support the model selection for numerical simulations of nuclear thermal-hydraulics in the case of cold leg small break loss-of-coolant accident of PWR plant is now under development on a personal computer. The steps to support the selection of both fluid model and constitutive equations for the drift flux model have been developed. Several cases of model selection were carried out and reasonable model selection results were obtained. (author)

The thermodynamics of protein folding: a critique of widely used quasi-thermodynamic interpretations and a restatement based on the Gibbs-Duhem relation and consistent with the Phase Rule.

Science.gov (United States)

Pethica, Brian A

2010-07-21

Interpretations of data in the extensive literature on the unfolding of proteins in aqueous solution follow a variety of methods involving assumptions leading to estimates of thermodynamic quantities associated with the unfolding transition. Inconsistencies and thermodynamic errors in these methods are identified. Estimates of standard molar free energies and enthalpies of unfolding using incompletely defined equilibrium constants and the van't Hoff relation are unsound, and typically contradict model-free interpretation of the data. A widely used routine for estimating the change in heat capacity associated with unfolding based on changes in the unfolding temperature and enthalpy co-induced by addition of denaturant or protective additives is thermodynamically incorrect by neglect of the Phase Rule. Many models and simulations predicting thermodynamic measures of unfolding are presently making comparisons with insecure quantities derived by incorrect thermodynamic analyses of experimental data. Analysis of unfolding via the Gibbs-Duhem equation with the correct Phase Rule constraints avoids the assumptions associated with incomplete equilibrium constants and misuse of the van't Hoff relation, and applies equally to positive, negative, sitewise or diffuse solute binding to the protein. The method gives the necessary relations between the thermodynamic parameters for thermal and isothermal unfolding and is developed for the case of two-state unfolding. The differences in binding of denaturants or stabilizers to the folded and unfolded forms of the protein are identified as major determinants of the unfolding process. The Phase Rule requires the temperature and enthalpy of unfolding to depend generally on the protein concentration. The available evidence bears out this expectation for thermal unfolding, indicating that protein-protein interactions influence folding. A parallel dependence of the denaturant concentrations for isothermal unfolding on the protein

The effects of nuclear data library processing on Geant4 and MCNP simulations of the thermal neutron scattering law

Science.gov (United States)

Hartling, K.; Ciungu, B.; Li, G.; Bentoumi, G.; Sur, B.

2018-05-01

Monte Carlo codes such as MCNP and Geant4 rely on a combination of physics models and evaluated nuclear data files (ENDF) to simulate the transport of neutrons through various materials and geometries. The grid representation used to represent the final-state scattering energies and angles associated with neutron scattering interactions can significantly affect the predictions of these codes. In particular, the default thermal scattering libraries used by MCNP6.1 and Geant4.10.3 do not accurately reproduce the ENDF/B-VII.1 model in simulations of the double-differential cross section for thermal neutrons interacting with hydrogen nuclei in a thin layer of water. However, agreement between model and simulation can be achieved within the statistical error by re-processing ENDF/B-VII.I thermal scattering libraries with the NJOY code. The structure of the thermal scattering libraries and sampling algorithms in MCNP and Geant4 are also reviewed.

Directional Unfolded Source Term (DUST) for Compton Cameras.

Energy Technology Data Exchange (ETDEWEB)

Mitchell, Dean J.; Mitchell, Dean J.; Horne, Steven M.; O' Brien, Sean; Thoreson, Gregory G

2018-03-01

A Directional Unfolded Source Term (DUST) algorithm was developed to enable improved spectral analysis capabilities using data collected by Compton cameras. Achieving this objective required modification of the detector response function in the Gamma Detector Response and Analysis Software (GADRAS). Experimental data that were collected in support of this work include measurements of calibration sources at a range of separation distances and cylindrical depleted uranium castings.

Geometrically engineering the standard model: Locally unfolding three families out of E8

International Nuclear Information System (INIS)

Bourjaily, Jacob L.

2007-01-01

This paper extends and builds upon the results of [J. L. Bourjaily, arXiv:0704.0444.], in which we described how to use the tools of geometrical engineering to deform geometrically engineered grand unified models into ones with lower symmetry. This top-down unfolding has the advantage that the relative positions of singularities giving rise to the many 'low-energy' matter fields are related by only a few parameters which deform the geometry of the unified model. And because the relative positions of singularities are necessary to compute the superpotential, for example, this is a framework in which the arbitrariness of geometrically engineered models can be greatly reduced. In [J. L. Bourjaily, arXiv:0704.0444.], this picture was made concrete for the case of deforming the representations of an SU 5 model into their standard model content. In this paper we continue that discussion to show how a geometrically engineered 16 of SO 10 can be unfolded into the standard model, and how the three families of the standard model uniquely emerge from the unfolding of a single, isolated E 8 singularity

Structural changes during the unfolding of Bovine serum albumin

Indian Academy of Sciences (India)

The native form of serum albumin is the most important soluble protein in the body plasma. In order to investigate the structural changes of Bovine serum albumin (BSA) during its unfolding in the presence of urea, a small-angle neutron scattering (SANS) study was performed. The scattering curves of dilute solutions of BSA ...

Kinetics and thermodynamics of the thermal inactivation and chaperone assisted folding of zebrafish dihydrofolate reductase.

Science.gov (United States)

Thapliyal, Charu; Jain, Neha; Rashid, Naira; Chaudhuri Chattopadhyay, Pratima

2018-01-01

The maintenance of thermal stability is a major issue in protein engineering as many proteins tend to form inactive aggregates at higher temperatures. Zebrafish DHFR, an essential protein for the survival of cells, shows irreversible thermal unfolding transition. The protein exhibits complete unfolding and loss of activity at 50 °C as monitored by UV-Visible, fluorescence and far UV-CD spectroscopy. The heat induced inactivation of zDHFR follows first-order kinetics and Arrhenius law. The variation in the value of inactivation rate constant, k with increasing temperatures depicts faster inactivation at elevated temperatures. We have attempted to study the chaperoning ability of a shorter variant of GroEL (minichaperone) and compared it with that of conventional GroEL-GroES chaperone system. Both the chaperone system prevented the aggregation and assisted in refolding of zDHFR. The rate of thermal inactivation was significantly retarded in the presence of chaperones which indicate that it enhances the thermal stability of the enzyme. As minichaperone is less complex, and does not require high energy co-factors like ATP, for its function as compared to conventional GroEL-GroES system, it can act as a very good in vitro as well as in vivo chaperone model for monitoring assisted protein folding phenomenon. Copyright © 2017 Elsevier Inc. All rights reserved.

Simulation studies on structural and thermal properties of alkane thiol capped gold nanoparticles.

Science.gov (United States)

Devi, J Meena

2017-06-01

The structural and thermal properties of the passivated gold nanoparticles were explored employing molecular dynamics simulation for the different surface coverage densities of the self-assembled monolayer (SAM) of alkane thiol. The structural properties of the monolayer protected gold nanoparticles such us overall shape, organization and conformation of the capping alkane thiol chains were found to be influenced by the capping density. The structural order of the thiol capped gold nanoparticles enhances with the increase in the surface coverage density. The specific heat capacity of the alkane thiol capped gold nanoparticles was found to increase linearly with the thiol coverage density. This may be attributed to the enhancement in the lattice vibrational energy. The present simulation results suggest, that the structural and thermal properties of the alkane thiol capped gold nanoparticles may be modified by the suitable selection of the SAM coverage density. Copyright © 2017 Elsevier Inc. All rights reserved.

Research on simulation of supercritical steam turbine system in large thermal power station

Science.gov (United States)

Zhou, Qiongyang

2018-04-01

In order to improve the stability and safety of supercritical steam turbine system operation in large thermal power station, the body of the steam turbine is modeled in this paper. And in accordance with the hierarchical modeling idea, the steam turbine body model, condensing system model, deaeration system model and regenerative system model are combined to build a simulation model of steam turbine system according to the connection relationship of each subsystem of steam turbine. Finally, the correctness of the model is verified by design and operation data of the 600MW supercritical unit. The results show that the maximum simulation error of the model is 2.15%, which meets the requirements of the engineering. This research provides a platform for the research on the variable operating conditions of the turbine system, and lays a foundation for the construction of the whole plant model of the thermal power plant.

Simulation and experimental study on thermal optimization of the heat exchanger for automotive exhaust-based thermoelectric generators

Directory of Open Access Journals (Sweden)

C.Q. Su

2014-11-01

Full Text Available Thermoelectric technology has revealed the potential for automotive exhaust-based thermoelectric generator (TEG, which contributes to the improvement of the fuel economy of the engine-powered vehicle. As a major factor, thermal capacity and heat transfer of the heat exchanger affect the performance of TEG effectively. With the thermal energy of exhaust gas harvested by thermoelectric modules, a temperature gradient appears on the heat exchanger surface, so as the interior flow distribution of the heat exchanger. In order to achieve uniform temperature distribution and higher interface temperature, the thermal characteristics of heat exchangers with various heat transfer enhancement features are studied, such as internal structure, material and surface area. Combining the computational fluid dynamics simulations and infrared test on a high-performance engine with a dynamometer, the thermal performance of the heat exchanger is evaluated. Simulation and experiment results show that a plate-shaped heat exchanger made of brass with accordion-shaped internal structure achieves a relatively ideal performance, which can practically improve overall thermal performance of the TEG.

High-energy intermediates in protein unfolding characterized by thiol labeling under nativelike conditions.

Science.gov (United States)

Malhotra, Pooja; Udgaonkar, Jayant B

2014-06-10

A protein unfolding reaction usually appears to be so dominated by a large free energy barrier that identifying and characterizing high-energy intermediates and, hence, dissecting the unfolding reaction into multiple structural transitions have proven to be a challenge. In particular, it has been difficult to identify any detected high-energy intermediate with the dry (DMG) and wet (WMG) molten globules that have been implicated in the unfolding reactions of at least some proteins. In this study, a native-state thiol labeling methodology was used to identify high-energy intermediates, as well as to delineate the barriers to the disruption of side chain packing interactions and to site-specific solvent exposure in different regions of the small protein, single-chain monellin (MNEI). Labeling studies of four single-cysteine-containing variants of MNEI have identified three high-energy intermediates, populated to very low extents under nativelike conditions. A significant dispersion in the opening rates of the cysteine side chains has allowed multiple steps, leading to the loss of side chain packing, to be resolved temporally. A detailed structural analysis of the positions of the four cysteine residue positions, which are buried to different depths within the protein, has suggested a direct correlation with the structure of a DMG, detected in previous studies. It is observed that side chain packing within the core of the protein is maintained, while that at the surface is disrupted, in the DMG. The core of the protein becomes solvent-exposed only in a WMG populated after the rate-limiting step of unfolding at high denaturant concentrations.

Guidelines for developing efficient thermal conduction and storage models within building energy simulations

International Nuclear Information System (INIS)

Hillary, Jason; Walsh, Ed; Shah, Amip; Zhou, Rongliang; Walsh, Pat

2017-01-01

Improving building energy efficiency is of paramount importance due to the large proportion of energy consumed by thermal operations. Consequently, simulating a building's environment has gained popularity for assessing thermal comfort and design. The extended timeframes and large physical scales involved necessitate compact modelling approaches. The accuracy of such simulations is of chief concern, yet there is little guidance offered on achieving accurate solutions whilst mitigating prohibitive computational costs. Therefore, the present study addresses this deficit by providing clear guidance on discretisation levels required for achieving accurate but computationally inexpensive models. This is achieved by comparing numerical models of varying discretisation levels to benchmark analytical solutions with prediction accuracy assessed and reported in terms of governing dimensionless parameters, Biot and Fourier numbers, to ensure generality of findings. Furthermore, spatial and temporal discretisation errors are separated and assessed independently. Contour plots are presented to intuitively determine the optimal discretisation levels and time-steps required to achieve accurate thermal response predictions. Simulations derived from these contour plots were tested against various building conditions with excellent agreement observed throughout. Additionally, various scenarios are highlighted where the classical single lumped capacitance model can be applied for Biot numbers much greater than 0.1 without reducing accuracy. - Highlights: • Addressing the problems of inadequate discretisation within building energy models. • Accuracy of numerical models assessed against analytical solutions. • Fourier and Biot numbers used to provide generality of results for any material. • Contour plots offer intuitive way to interpret results for manual discretisation. • Results show proposed technique promising for automation of discretisation process.

Discriminating trpzip2 and trpzip4 peptides’ folding landscape using the two-dimensional infrared spectroscopy: A simulation study

International Nuclear Information System (INIS)

Wu, Tianmin; Zhang, Ruiting; Li, Huanhuan; Zhuang, Wei; Yang, Lijiang

2014-01-01

We analyzed, based on the theoretical spectroscopic modeling, how the differences in the folding landscapes of two β-hairpin peptides trpzip2 and trpzip4 are reflected in their thermal unfolding infrared measurements. The isotope-edited equilibrium FTIR and two dimensional infrared spectra of the two peptides were calculated, using the nonlinear exciton propagation method, at a series of temperatures. The spectra calculations were based on the configuration distributions generated using the GB OBC implicit solvent MD simulation and the integrated tempering sampling technique. Conformational analysis revealed the different local thermal stabilities for these two peptides, which suggested the different folding landscapes. Our study further suggested that the ellipticities of the isotope peaks in the coherent IR signals are more sensitive to these local stability differences compared with other spectral features such as the peak intensities. Our technique can thus be combined with the relevant experimental measurements to achieve a better understanding of the peptide folding behaviors