Parallel low-memory quasi-Newton optimization algorithm for molecular structure

Czech Academy of Sciences Publication Activity Database

Klemsa, Jakub; Řezáč, Jan

2013-01-01

Roč. 584, Oct 1 (2013), s. 10-13 ISSN 0009-2614 R&D Projects: GA ČR GP13-01214P Institutional support: RVO:61388963 Keywords : geometry optimization * parallelization * molecular graph Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.991, year: 2013

Methodology for wind turbine blade geometry optimization

Energy Technology Data Exchange (ETDEWEB)

Perfiliev, D.

2013-11-01

Nowadays, the upwind three bladed horizontal axis wind turbine is the leading player on the market. It has been found to be the best industrial compromise in the range of different turbine constructions. The current wind industry innovation is conducted in the development of individual turbine components. The blade constitutes 20-25% of the overall turbine budget. Its optimal operation in particular local economic and wind conditions is worth investigating. The blade geometry, namely the chord, twist and airfoil type distributions along the span, responds to the output measures of the blade performance. Therefore, the optimal wind blade geometry can improve the overall turbine performance. The objectives of the dissertation are focused on the development of a methodology and specific tool for the investigation of possible existing wind blade geometry adjustments. The novelty of the methodology presented in the thesis is the multiobjective perspective on wind blade geometry optimization, particularly taking simultaneously into account the local wind conditions and the issue of aerodynamic noise emissions. The presented optimization objective approach has not been investigated previously for the implementation in wind blade design. The possibilities to use different theories for the analysis and search procedures are investigated and sufficient arguments derived for the usage of proposed theories. The tool is used for the test optimization of a particular wind turbine blade. The sensitivity analysis shows the dependence of the outputs on the provided inputs, as well as its relative and absolute divergences and instabilities. The pros and cons of the proposed technique are seen from the practical implementation, which is documented in the results, analysis and conclusion sections. (orig.)

Gaussian process regression for geometry optimization

Science.gov (United States)

Denzel, Alexander; Kästner, Johannes

2018-03-01

We implemented a geometry optimizer based on Gaussian process regression (GPR) to find minimum structures on potential energy surfaces. We tested both a two times differentiable form of the Matérn kernel and the squared exponential kernel. The Matérn kernel performs much better. We give a detailed description of the optimization procedures. These include overshooting the step resulting from GPR in order to obtain a higher degree of interpolation vs. extrapolation. In a benchmark against the Limited-memory Broyden-Fletcher-Goldfarb-Shanno optimizer of the DL-FIND library on 26 test systems, we found the new optimizer to generally reduce the number of required optimization steps.

Hybridization and molecular geometry: A number game | Ojha ...

African Journals Online (AJOL)

Present article emphasize the new pedagogy to learn the hybridization and molecular geometry. It is always a challenge for the students to remember the hybridization and geometry of the molecule correctly. This topic has several importance in subjective and objective type questions and answers since in most of the ...

Optimization of the geometry of the diphenylamine molecule by semiempirical quantum chemical methods

International Nuclear Information System (INIS)

Pankratov, A.N.; Mushtakova, S.P.; Gribov, L.A.

1986-01-01

Available data on experimental study of the geometry of the diphenylamine molecule (I) in solution and in the crystal are fragmentary and not always reliable. Previously, they did a conformational analysis of molecule I using the atom-atom potential method. In order to refine the geometric parameters found for molecule I, optimization of its geometry is provided in the paper using the CNDO/2, INDO, MINDO/3 methods with the use of programs for the BESM-6 computer which are part of the VIKING program set. The angles of rotation for the phenyl rings relative to the CNC plane, the bond angles C 2 N 7 C 8 and C 2 N 7 H 19 , and also the dihedral angle H 19 N 7 C 8 C 9 were subjected to optimization. For any set of values for the indicated parameters, the bond angle C 8 N 7 H 19 is determined unambiguously. The results of the calculations are evidence that the MINDO/3 method is not suitable for optimization of the geometry for molecules of the indicated series; in particular, it leads to much too high a value for the CNC angles (135.9 0 ). The CNDO/2 method reproduces well the real value of the CNC angle (124.1 0 ) and confirms the known pyrimidal character of the nitrogen atom, the sum of the bond angles of which proved to be equal to 353.6 0 . The calculation in the INDO approximation successfully gives the basic characteristics of the molecular geometry of (I); according to this approximation, the CNC angle is equal to 123.2 0 , the CNH angles are equal to 118.0 and 118.8 0 , the sum of the angles for the nitrogen atom is 360.0 0

Numerical optimization of die geometry in open die forging

DEFF Research Database (Denmark)

Christiansen, Peter; Hattel, Jesper Henri; Bay, Niels

2013-01-01

This paper deals with numerical optimization of open die forging of large metallic ingots made by casting implying risk of defects, e.g. central pores. Different material hardening properties and die geometries are combined in order to investigate, which geometry gives rise to maximum closure...

Geometry optimization of molecules within an LCGTO local-density functional approach

International Nuclear Information System (INIS)

Mintmire, J.W.

1990-01-01

We describe our implementation of geometry optimization techniques within the linear combination of Gaussian-type orbitals (LCGTO) approach to local-density functional theory. The algorithm for geometry optimization is based on the evaluation of the gradient of the total energy with respect to internal coordinates within the local-density functional scheme. We present optimization results for a range of small molecules which serve as test cases for our approach

Optimizing the Entrainment Geometry of a Dry Powder Inhaler: Methodology and Preliminary Results.

Science.gov (United States)

Kopsch, Thomas; Murnane, Darragh; Symons, Digby

2016-11-01

For passive dry powder inhalers (DPIs) entrainment and emission of the aerosolized drug dose depends strongly on device geometry and the patient's inhalation manoeuvre. We propose a computational method for optimizing the entrainment part of a DPI. The approach assumes that the pulmonary delivery location of aerosol can be determined by the timing of dose emission into the tidal airstream. An optimization algorithm was used to iteratively perform computational fluid dynamic (CFD) simulations of the drug emission of a DPI. The algorithm seeks to improve performance by changing the device geometry. Objectives were to achieve drug emission that was: A) independent of inhalation manoeuvre; B) similar to a target profile. The simulations used complete inhalation flow-rate profiles generated dependent on the device resistance. The CFD solver was OpenFOAM with drug/air flow simulated by the Eulerian-Eulerian method. To demonstrate the method, a 2D geometry was optimized for inhalation independence (comparing two breath profiles) and an early-bolus delivery. Entrainment was both shear-driven and gas-assisted. Optimization for a delay in the bolus delivery was not possible with the chosen geometry. Computational optimization of a DPI geometry for most similar drug delivery has been accomplished for an example entrainment geometry.

The use of many-body expansions and geometry optimizations in fragment-based methods.

Science.gov (United States)

Fedorov, Dmitri G; Asada, Naoya; Nakanishi, Isao; Kitaura, Kazuo

2014-09-16

many-body expansion in a formally two-body series, as exemplified in the development of the fragment molecular orbital (FMO) method. Fragment-based methods have been very successful in delivering the properties of fragments, as well as the fragment interactions, providing insights into complex chemical processes in large molecular systems. We briefly review geometry optimizations performed with fragment-based methods and present an efficient geometry optimization method based on the combination of FMO with molecular mechanics (MM), applied to the complex of a subunit of protein kinase 2 (CK2) with a ligand. FMO results are discussed in comparison with experimental and MM-optimized structures.

Mathematical efficiency calibration with uncertain source geometries using smart optimization

International Nuclear Information System (INIS)

Menaa, N.; Bosko, A.; Bronson, F.; Venkataraman, R.; Russ, W. R.; Mueller, W.; Nizhnik, V.; Mirolo, L.

2011-01-01

The In Situ Object Counting Software (ISOCS), a mathematical method developed by CANBERRA, is a well established technique for computing High Purity Germanium (HPGe) detector efficiencies for a wide variety of source shapes and sizes. In the ISOCS method, the user needs to input the geometry related parameters such as: the source dimensions, matrix composition and density, along with the source-to-detector distance. In many applications, the source dimensions, the matrix material and density may not be well known. Under such circumstances, the efficiencies may not be very accurate since the modeled source geometry may not be very representative of the measured geometry. CANBERRA developed an efficiency optimization software known as 'Advanced ISOCS' that varies the not well known parameters within user specified intervals and determines the optimal efficiency shape and magnitude based on available benchmarks in the measured spectra. The benchmarks could be results from isotopic codes such as MGAU, MGA, IGA, or FRAM, activities from multi-line nuclides, and multiple counts of the same item taken in different geometries (from the side, bottom, top etc). The efficiency optimization is carried out using either a random search based on standard probability distributions, or using numerical techniques that carry out a more directed (referred to as 'smart' in this paper) search. Measurements were carried out using representative source geometries and radionuclide distributions. The radionuclide activities were determined using the optimum efficiency and compared against the true activities. The 'Advanced ISOCS' method has many applications among which are: Safeguards, Decommissioning and Decontamination, Non-Destructive Assay systems and Nuclear reactor outages maintenance. (authors)

Designing an educative curriculum unit for teaching molecular geometry in high school chemistry

Science.gov (United States)

Makarious, Nader N.

Chemistry is a highly abstract discipline that is taught and learned with the aid of various models. Among the most challenging, yet a fundamental topic in general chemistry at the high school level, is molecular geometry. This study focused on developing exemplary educative curriculum materials pertaining to the topic of molecular geometry. The methodology used in this study consisted of several steps. First, a diverse set of models were analyzed to determine to what extent each model serves its purpose in teaching molecular geometry. Second, a number of high school teachers and college chemistry professors were asked to share their experiences on using models in teaching molecular geometry through an online questionnaire. Third, findings from the comparative analysis of models, teachers’ experiences, literature review on models and students’ misconceptions, the curriculum expectations of the Next Generation Science Standards and their emphasis on three-dimensional learning and nature of science (NOS) contributed to the development of the molecular geometry unit. Fourth, the developed unit was reviewed by fellow teachers and doctoral-level science education experts and was revised to further improve its coherence and clarity in support of teaching and learning of the molecular geometry concepts. The produced educative curriculum materials focus on the scientific practice of developing and using models as promoted in the Next Generations Science Standards (NGSS) while also addressing nature of science (NOS) goals. The educative features of the newly developed unit support teachers’ pedagogical knowledge (PK) and pedagogical content knowledge (PCK). The unit includes an overview, teacher’s guide, and eight detailed lesson plans with inquiry oriented modeling activities replete with models and suggestions for teachers, as well as formative and summative assessment tasks. The unit design process serves as a model for redesigning other instructional units in

Minimizing the effect of automotive pollution in urban geometry using mathematical optimization

Energy Technology Data Exchange (ETDEWEB)

Craig, K.J.; De Kock, D.J.; Snyman, J.A. [Pretoria Univ. (South Africa). Dept. of Mechanical and Aeronautical Engineering

2001-07-01

One of the factors that needs to be considered during the layout of new urban geometry (e.g. street direction, spacing and width, building height restrictions) is the effect of the air pollution associated with the automotive transport that would use routes in this urban area. Although the pollution is generated at street level, its effect can be widespread due to interaction of the pollutant dispersion and diffusion with the wind speed and direction. In order to study the effect of a new urban geometry on the pollutant levels and dispersion, a very time-consuming experimental or parametric numerical study would have to be performed. This paper proposes an alternative approach, that of combining mathematical optimization with the techniques of computational fluid dynamics (CFD). In essence, the meteorological information as represented by a wind rose (wind speed and direction), is used to calculate pollutant levels as a function of urban geometry variables: street canyon depth and street canyon width. The pollutant source specified in conjunction with a traffic scenario with CO is used as pollutant. The main aim of the study is to be able to suggest the most beneficial configuration of an idealized urban geometry that minimizes the peak pollutant levels due to assumed traffic distributions. This study uses two mathematical optimization methods. The first method is implemented through a successive maximization-minimization approach, while the second method determines the location of saddle points of the pollutant level, considered as a function of urban geometry and wind rose. Locally, a saddle point gives the best urban geometry for the worst meteorological scenario. The commercial CFD code, STAR-CD, is coupled with a version of the DYNAMIC-Q optimization algorithm of Snyman, first to successively locate maxima and minima in a min-max approach; and then to locate saddle points. It is shown that the saddle-point method is more cost-effective. The methodology

The use of direct geometry spectrometers in molecular spectroscopy

International Nuclear Information System (INIS)

Parker, Stewart F; Ramirez-Cuesta, Anibal J; Albers, Peter W; Lennon, David

2014-01-01

The advantages and disadvantages of the use of direct geometry spectrometers for molecular spectroscopy and catalysis studies are described. We show that both direct and indirect geometry INS spectrometers are important tools for the study of industrially relevant areas such as catalysis, proton conductors and gas separation. We propose a novel hybrid instrument, Cerberus, that would offer high sensitivity and high-to-reasonable resolution across the entire 'mid-infrared' spectral range that would effectively advance research in these areas

Tuning spin transport properties and molecular magnetoresistance through contact geometry

Science.gov (United States)

Ulman, Kanchan; Narasimhan, Shobhana; Delin, Anna

2014-01-01

Molecular spintronics seeks to unite the advantages of using organic molecules as nanoelectronic components, with the benefits of using spin as an additional degree of freedom. For technological applications, an important quantity is the molecular magnetoresistance. In this work, we show that this parameter is very sensitive to the contact geometry. To demonstrate this, we perform ab initio calculations, combining the non-equilibrium Green's function method with density functional theory, on a dithienylethene molecule placed between spin-polarized nickel leads of varying geometries. We find that, in general, the magnetoresistance is significantly higher when the contact is made to sharp tips than to flat surfaces. Interestingly, this holds true for both resonant and tunneling conduction regimes, i.e., when the molecule is in its "closed" and "open" conformations, respectively. We find that changing the lead geometry can increase the magnetoresistance by up to a factor of ˜5. We also introduce a simple model that, despite requiring minimal computational time, can recapture our ab initio results for the behavior of magnetoresistance as a function of bias voltage. This model requires as its input only the density of states on the anchoring atoms, at zero bias voltage. We also find that the non-resonant conductance in the open conformation of the molecule is significantly impacted by the lead geometry. As a result, the ratio of the current in the closed and open conformations can also be tuned by varying the geometry of the leads, and increased by ˜400%.

Tuning spin transport properties and molecular magnetoresistance through contact geometry

International Nuclear Information System (INIS)

Ulman, Kanchan; Narasimhan, Shobhana; Delin, Anna

2014-01-01

Molecular spintronics seeks to unite the advantages of using organic molecules as nanoelectronic components, with the benefits of using spin as an additional degree of freedom. For technological applications, an important quantity is the molecular magnetoresistance. In this work, we show that this parameter is very sensitive to the contact geometry. To demonstrate this, we perform ab initio calculations, combining the non-equilibrium Green's function method with density functional theory, on a dithienylethene molecule placed between spin-polarized nickel leads of varying geometries. We find that, in general, the magnetoresistance is significantly higher when the contact is made to sharp tips than to flat surfaces. Interestingly, this holds true for both resonant and tunneling conduction regimes, i.e., when the molecule is in its “closed” and “open” conformations, respectively. We find that changing the lead geometry can increase the magnetoresistance by up to a factor of ∼5. We also introduce a simple model that, despite requiring minimal computational time, can recapture our ab initio results for the behavior of magnetoresistance as a function of bias voltage. This model requires as its input only the density of states on the anchoring atoms, at zero bias voltage. We also find that the non-resonant conductance in the open conformation of the molecule is significantly impacted by the lead geometry. As a result, the ratio of the current in the closed and open conformations can also be tuned by varying the geometry of the leads, and increased by ∼400%

Tuning spin transport properties and molecular magnetoresistance through contact geometry.

Science.gov (United States)

Ulman, Kanchan; Narasimhan, Shobhana; Delin, Anna

2014-01-28

Molecular spintronics seeks to unite the advantages of using organic molecules as nanoelectronic components, with the benefits of using spin as an additional degree of freedom. For technological applications, an important quantity is the molecular magnetoresistance. In this work, we show that this parameter is very sensitive to the contact geometry. To demonstrate this, we perform ab initio calculations, combining the non-equilibrium Green's function method with density functional theory, on a dithienylethene molecule placed between spin-polarized nickel leads of varying geometries. We find that, in general, the magnetoresistance is significantly higher when the contact is made to sharp tips than to flat surfaces. Interestingly, this holds true for both resonant and tunneling conduction regimes, i.e., when the molecule is in its "closed" and "open" conformations, respectively. We find that changing the lead geometry can increase the magnetoresistance by up to a factor of ∼5. We also introduce a simple model that, despite requiring minimal computational time, can recapture our ab initio results for the behavior of magnetoresistance as a function of bias voltage. This model requires as its input only the density of states on the anchoring atoms, at zero bias voltage. We also find that the non-resonant conductance in the open conformation of the molecule is significantly impacted by the lead geometry. As a result, the ratio of the current in the closed and open conformations can also be tuned by varying the geometry of the leads, and increased by ∼400%.

NMR determinations of molecular geometries in liquid crystal media

International Nuclear Information System (INIS)

Long, R.C.; Goldstein, J.H.

1983-01-01

The application of NMR spectroscopy in oriented media to the determination of molecular geometries is illustrated by results for three distinctly different molecules: naphthalene, ethylene oxide and spiropentane. The need for systematic application of vibrational corrections is emphasized and some of the effects associated with the different choices of solvent media are considered

Porphyrin-sensitized solar cells: systematic molecular optimization, coadsorption and cosensitization.

Science.gov (United States)

Song, Heli; Liu, Qingyun; Xie, Yongshu

2018-02-15

As a promising low-cost solar energy conversion technique, dye-sensitized solar cells have undergone spectacular development since 1991. For practical applications, improvement of power conversion efficiency has always been one of the major research topics. Porphyrins are outstanding sensitizers endowed with strong sunlight harvesting ability in the visible region and multiple reaction sites available for functionalization. However, judicious molecular design in consideration of light-harvest, energy levels, operational dynamics, adsorption geometry and suppression of back reactions is specifically required for achieving excellent photovoltaic performance. This feature article highlights some of the recently developed porphyrin sensitizers, especially focusing on the systematic dye structure optimization approach in combination with coadsorption and cosensitization methods in pursuing higher efficiencies. Herein, we expect to provide more insights into the structure-performance correlation and molecular engineering strategies in a stepwise manner.

Improvement in minimum detectable activity for low energy gamma by optimization in counting geometry

Directory of Open Access Journals (Sweden)

Anil Gupta

2017-01-01

Full Text Available Gamma spectrometry for environmental samples of low specific activities demands low minimum detection levels of measurement. An attempt has been made to lower the gamma detection level of measurement by optimizing the sample geometry, without compromising on the sample size. Gamma energy of 50–200 keV range was chosen for the study, since low energy gamma photons suffer the most self-attenuation within matrix. The simulation study was carried out using MCNP based software “EffCalcMC” for silica matrix and cylindrical geometries. A volume of 250 ml sample geometry of 9 cm diameter is optimized as the best suitable geometry for use, against the in-practice 7 cm diameter geometry of same volume. An increase in efficiency of 10%–23% was observed for the 50–200 keV gamma energy range and a corresponding lower minimum detectable activity of 9%–20% could be achieved for the same.

Transient analyses for a molten salt fast reactor with optimized core geometry

Energy Technology Data Exchange (ETDEWEB)

Li, R., E-mail: rui.li@kit.edu [Institute for Nuclear and Energy Technologies (IKET), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen (Germany); Wang, S.; Rineiski, A.; Zhang, D. [Institute for Nuclear and Energy Technologies (IKET), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen (Germany); Merle-Lucotte, E. [Laboratoire de Physique Subatomique et de Cosmologie – IN2P3 – CNRS/Grenoble INP/UJF, 53, rue des Martyrs, 38026 Grenoble (France)

2015-10-15

Highlights: • MSFR core is analyzed by fully coupling neutronics and thermal-hydraulics codes. • We investigated four types of transients intensively with the optimized core geometry. • It demonstrates MSFR has a high safety potential. - Abstract: Molten salt reactors (MSRs) have encountered a marked resurgence of interest over the past decades, highlighted by their inclusion as one of the six candidate reactors of the Generation IV advanced nuclear power systems. The present work is carried out in the framework of the European FP-7 project EVOL (Evaluation and Viability Of Liquid fuel fast reactor system). One of the project tasks is to report on safety analyses: calculations of reactor transients using various numerical codes for the molten salt fast reactor (MSFR) under different boundary conditions, assumptions, and for different selected scenarios. Based on the original reference core geometry, an optimized geometry was proposed by Rouch et al. (2014. Ann. Nucl. Energy 64, 449) on thermal-hydraulic design aspects to avoid a recirculation zone near the blanket which accumulates heat and very high temperature exceeding the salt boiling point. Using both fully neutronics thermal-hydraulic coupled codes (SIMMER and COUPLE), we also re-confirm the efforts step by step toward a core geometry without the recirculation zone in particular as concerns the modifications of the core geometrical shape. Different transients namely Unprotected Loss of Heat Sink (ULOHS), Unprotected Loss of Flow (ULOF), Unprotected Transient Over Power (UTOP), Fuel Salt Over Cooling (FSOC) are intensively investigated and discussed with the optimized core geometry. It is demonstrated that due to inherent negative feedbacks, an MSFR plant has a high safety potential.

Optimizing Inductor Winding Geometry for Lowest DC-Resistance using LiveLink between COMSOL and MATLAB

DEFF Research Database (Denmark)

Schneider, Henrik; Andersen, Thomas; Mønster, Jakob Døllner

2013-01-01

An optimization routine is presented to optimize a hybrid winding geometry for a toroid inductor in terms of the DC resistance. The hybrid winding geometry consist of bended foil pieces connected through traces in a printed circuit board. MATLAB is used to create a graphical user interface...... that visually plots the winding using input parameters such as core dimensions, number of turns, clearance between windings, and the winding angle of each segment of the winding. COMSOL LiveLink is used to import the winding geometry from MATLAB and create a 2D finite element model to simulate the DC...

Optimization of a stellarator design including modulation of the helical winding geometry

International Nuclear Information System (INIS)

Sharp, L.E.; Petersen, L.F.; Blamey, J.W.

1979-06-01

The optimization of the helical winding geometry of the next generation of high performance stellarators is of critical importance as the current in the helical conductors must be kept to a minimum to reduce the very large electromechanical forces on the conductors. Using a modified version of the Culham computer code MAGBAT, steps towards optimization are described

Synthesis, geometry optimization, spectroscopic investigations (UV/Vis, excited states, FT-IR) and application of new azomethine dyes

Science.gov (United States)

Shahab, Siyamak; Sheikhi, Masoome; Filippovich, Liudmila; Kumar, Rakesh; Dikusar, Evgenij; Yahyaei, Hooriye; Khaleghian, Mehrnoosh

2017-11-01

In the present work, the quantum theoretical calculations of the molecular structures of the four new synthesized azomethine dyes such as: (E)-N-(4-butoxybenzylidene)-4-((E)-phenyldiazenyl)aniline (PAZB-6), (E)-N-(4-(benzyloxy)benzylidene)-4-((E))-phenyldiazenyl)aniline (PAZB-7), 4-((E)-4-((E)-phenyldiazenyl)phenyl)imino)methyl)phenol (PAZB-8), (E)-N-(4-methoxybenzylidene)-4-((E))-phenyldiazenyl)aniline (PAZB-9) have been predicted using Density Functional Theory in the solvent Dimethylformamide. The geometries of the azomethine dyes were optimized by PBE1PBE/6-31+G* level of theory. The electronic spectra of the title compounds in the solvent DMF was carried out by TDPBE1PBE/6-31+G* method. FT-IR spectra of the title compounds are recorded and discussed. Frontier molecular orbitals, molecular electrostatic potential, electronic properties, natural charges and Natural Bond Orbital (NBO) analysis of the mentioned compounds were investigated and discussed by theoretical calculations. The azomethine dyes were synthesized after quantum chemical modeling for optical applications. A new study of anisotropy of thermal and electrical conductivity of the colored stretched PVA-films have been undertaken.

Geometry Design Optimization of Functionally Graded Scaffolds for Bone Tissue Engineering: A Mechanobiological Approach.

Directory of Open Access Journals (Sweden)

Antonio Boccaccio

Full Text Available Functionally Graded Scaffolds (FGSs are porous biomaterials where porosity changes in space with a specific gradient. In spite of their wide use in bone tissue engineering, possible models that relate the scaffold gradient to the mechanical and biological requirements for the regeneration of the bony tissue are currently missing. In this study we attempt to bridge the gap by developing a mechanobiology-based optimization algorithm aimed to determine the optimal graded porosity distribution in FGSs. The algorithm combines the parametric finite element model of a FGS, a computational mechano-regulation model and a numerical optimization routine. For assigned boundary and loading conditions, the algorithm builds iteratively different scaffold geometry configurations with different porosity distributions until the best microstructure geometry is reached, i.e. the geometry that allows the amount of bone formation to be maximized. We tested different porosity distribution laws, loading conditions and scaffold Young's modulus values. For each combination of these variables, the explicit equation of the porosity distribution law-i.e the law that describes the pore dimensions in function of the spatial coordinates-was determined that allows the highest amounts of bone to be generated. The results show that the loading conditions affect significantly the optimal porosity distribution. For a pure compression loading, it was found that the pore dimensions are almost constant throughout the entire scaffold and using a FGS allows the formation of amounts of bone slightly larger than those obtainable with a homogeneous porosity scaffold. For a pure shear loading, instead, FGSs allow to significantly increase the bone formation compared to a homogeneous porosity scaffolds. Although experimental data is still necessary to properly relate the mechanical/biological environment to the scaffold microstructure, this model represents an important step towards

Searching for optimal mitigation geometries for laser resistant multilayer high reflector coatings

Energy Technology Data Exchange (ETDEWEB)

Qiu, S R; Wolfe, J E; Monterrosa, A M; Feit, M D; Pistor, T V; STolz, C J

2011-02-11

Growing laser damage sites on multilayer high reflector coatings can limit mirror performance. One of the strategies to improve laser damage resistance is to replace the growing damage sites with pre-designed benign mitigation structures. By mitigating the weakest site on the optic, the large aperture mirror will have a laser resistance comparable to the intrinsic value of the multilayer coating. To determine the optimal mitigation geometry, the finite difference time domain method (FDTD) was used to quantify the electric-field intensification within the multilayer, at the presence of different conical pits. We find that the field intensification induced by the mitigation pit is strongly dependent on the polarization and the angle of incidence (AOI) of the incoming wave. Therefore the optimal mitigation conical pit geometry is application specific. Furthermore, our simulation also illustrates an alternative means to achieve an optimal mitigation structure by matching the cone angle of the structure with the AOI of the incoming wave, except for the p-polarization wave at a range of incident angles between 30{sup o} and 45{sup o}.

Some simulation aspects, from molecular systems to stochastic geometries of pebble bed reactors

International Nuclear Information System (INIS)

Mazzolo, A.

2009-06-01

After a brief presentation of his teaching and supervising activities, the author gives an overview of his research activities: investigation of atoms under high intensity magnetic field (investigation of the electronic structure under these fields), studies of theoretical and numerical electrochemistry (simulation coupling molecular dynamics and quantum calculations, comprehensive simulations of molecular dynamics), and studies relating stochastic geometry and neutron science

Rhombicuboctahedron unit cell based scaffolds for bone regeneration: geometry optimization with a mechanobiology - driven algorithm.

Science.gov (United States)

Boccaccio, Antonio; Fiorentino, Michele; Uva, Antonio E; Laghetti, Luca N; Monno, Giuseppe

2018-02-01

In a context more and more oriented towards customized medical solutions, we propose a mechanobiology-driven algorithm to determine the optimal geometry of scaffolds for bone regeneration that is the most suited to specific boundary and loading conditions. In spite of the huge number of articles investigating different unit cells for porous biomaterials, no studies are reported in the literature that optimize the geometric parameters of such unit cells based on mechanobiological criteria. Parametric finite element models of scaffolds with rhombicuboctahedron unit cell were developed and incorporated into an optimization algorithm that combines them with a computational mechanobiological model. The algorithm perturbs iteratively the geometry of the unit cell until the best scaffold geometry is identified, i.e. the geometry that allows to maximize the formation of bone. Performances of scaffolds with rhombicuboctahedron unit cell were compared with those of other scaffolds with hexahedron unit cells. We found that scaffolds with rhombicuboctahedron unit cell are particularly suited for supporting medium-low loads, while, for higher loads, scaffolds with hexahedron unit cells are preferable. The proposed algorithm can guide the orthopaedic/surgeon in the choice of the best scaffold to be implanted in a patient-specific anatomic region. Copyright © 2017 Elsevier B.V. All rights reserved.

Optimization of combustion chamber geometry for stoichiometric diesel combustion using a micro genetic algorithm

Energy Technology Data Exchange (ETDEWEB)

Park, Sung Wook

2010-11-15

This paper describes the optimization of combustion chamber geometry and engine operating conditions for stoichiometric diesel combustion, targeting lower gross indicated specific fuel consumption. The KIVA code, coupled with a micro genetic algorithm population of nine for each generation was used. The optimization variables were composed of ten variables related to the combustion chamber geometry and engine operating conditions. In addition, an auto mesh generator was developed for generating various kinds of combustion chambers, such as open-crater, re-entrant, deep, and shallow types. In addition, the computational models were validated against the experimental results for a stoichiometric process in terms of the combustion pressure history and emissions. Through the preset optimization, a 35% improvement in the gross indicated that specific fuel consumption was achieved. In addition, the optimization results showed that the optimum engine operating conditions employed a premixed charge compression ignition combustion regime with early injection and a narrow spray included angle. Furthermore, a higher boost pressure was used to prevent fuel film formation. (author)

Spectroscopic (FT-IR, FT-Raman, NMR and UV-Visible) and quantum chemical studies of molecular geometry, Frontier molecular orbital, NLO, NBO and thermodynamic properties of salicylic acid.

Science.gov (United States)

Suresh, S; Gunasekaran, S; Srinivasan, S

2014-11-11

The solid phase FT-IR and FT-Raman spectra of 2-hydroxybenzoic acid (salicylic acid) have been recorded in the region 4000-400 and 4000-100 cm(-1) respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method at 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimentally obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method is employed to predict its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) are also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Published by Elsevier B.V.

Test Beam Results of Geometry Optimized Hybrid Pixel Detectors

CERN Document Server

Becks, K H; Grah, C; Mättig, P; Rohe, T

2006-01-01

The Multi-Chip-Module-Deposited (MCM-D) technique has been used to build hybrid pixel detector assemblies. This paper summarises the results of an analysis of data obtained in a test beam campaign at CERN. Here, single chip hybrids made of ATLAS pixel prototype read-out electronics and special sensor tiles were used. They were prepared by the Fraunhofer Institut fuer Zuverlaessigkeit und Mikrointegration, IZM, Berlin, Germany. The sensors feature an optimized sensor geometry called equal sized bricked. This design enhances the spatial resolution for double hits in the long direction of the sensor cells.

Architectural geometry

KAUST Repository

Pottmann, Helmut

2014-11-26

Around 2005 it became apparent in the geometry processing community that freeform architecture contains many problems of a geometric nature to be solved, and many opportunities for optimization which however require geometric understanding. This area of research, which has been called architectural geometry, meanwhile contains a great wealth of individual contributions which are relevant in various fields. For mathematicians, the relation to discrete differential geometry is significant, in particular the integrable system viewpoint. Besides, new application contexts have become available for quite some old-established concepts. Regarding graphics and geometry processing, architectural geometry yields interesting new questions but also new objects, e.g. replacing meshes by other combinatorial arrangements. Numerical optimization plays a major role but in itself would be powerless without geometric understanding. Summing up, architectural geometry has become a rewarding field of study. We here survey the main directions which have been pursued, we show real projects where geometric considerations have played a role, and we outline open problems which we think are significant for the future development of both theory and practice of architectural geometry.

Architectural geometry

KAUST Repository

Pottmann, Helmut; Eigensatz, Michael; Vaxman, Amir; Wallner, Johannes

2014-01-01

Around 2005 it became apparent in the geometry processing community that freeform architecture contains many problems of a geometric nature to be solved, and many opportunities for optimization which however require geometric understanding. This area of research, which has been called architectural geometry, meanwhile contains a great wealth of individual contributions which are relevant in various fields. For mathematicians, the relation to discrete differential geometry is significant, in particular the integrable system viewpoint. Besides, new application contexts have become available for quite some old-established concepts. Regarding graphics and geometry processing, architectural geometry yields interesting new questions but also new objects, e.g. replacing meshes by other combinatorial arrangements. Numerical optimization plays a major role but in itself would be powerless without geometric understanding. Summing up, architectural geometry has become a rewarding field of study. We here survey the main directions which have been pursued, we show real projects where geometric considerations have played a role, and we outline open problems which we think are significant for the future development of both theory and practice of architectural geometry.

Optimization methodology for large scale fin geometry on the steel containment of a Public Acceptable Simple SMR (PASS)

International Nuclear Information System (INIS)

Kim, Do Yun; NO, Hee Cheon; Kim, Ho Sik

2015-01-01

Highlights: • Optimization methodology for fin geometry on the steel containment is established. • Optimum spacing is 7 cm in PASS containment. • Optimum thickness is 0.9–1.8 cm when a fin height is 10–25 cm. • Optimal fin geometry is determined in given fin height by overall effectiveness correlation. • 13% of material volume and 43% of containment volume are reduced by using fins. - Abstracts: Heat removal capability through a steel containment is important in accident situations to preserve the integrity of a nuclear power plant which adopts a steel containment concept. A heat transfer rate will be enhanced by using fins on the external surface of the steel containment. The fins, however, cause to increase flow resistance and to deteriorate the heat transfer rate at the same time. Therefore, this study investigates an optimization methodology of large scale fin geometry for a vertical base where a natural convection flow regime is turbulent. Rectangular plate fins adopted in the steel containment of a Public Acceptable Simple SMR (PASS) is used as a reference. The heat transfer rate through the fins is obtained from CFD tools. In order to optimize fin geometry, an overall effectiveness concept is introduced as a fin performance parameter. The optimizing procedure is starting from finding optimum spacing. Then, optimum thickness is calculated and finally optimal fin geometry is suggested. Scale analysis is conducted to show the existence of an optimum spacing which turns out to be 7 cm in case of PASS. Optimum thickness is obtained by the overall effectiveness correlation, which is derived from a total heat transfer coefficient correlation. The total heat transfer coefficient correlation of a vertical fin array is suggested considering both of natural convection and radiation. However, the optimum thickness is changed as a fin height varies. Therefore, optimal fin geometry is obtained as a function of a fin height. With the assumption that the heat

Hybrid Metaheuristic Approach for Nonlocal Optimization of Molecular Systems.

Science.gov (United States)

Dresselhaus, Thomas; Yang, Jack; Kumbhar, Sadhana; Waller, Mark P

2013-04-09

Accurate modeling of molecular systems requires a good knowledge of the structure; therefore, conformation searching/optimization is a routine necessity in computational chemistry. Here we present a hybrid metaheuristic optimization (HMO) algorithm, which combines ant colony optimization (ACO) and particle swarm optimization (PSO) for the optimization of molecular systems. The HMO implementation meta-optimizes the parameters of the ACO algorithm on-the-fly by the coupled PSO algorithm. The ACO parameters were optimized on a set of small difluorinated polyenes where the parameters exhibited small variance as the size of the molecule increased. The HMO algorithm was validated by searching for the closed form of around 100 molecular balances. Compared to the gradient-based optimized molecular balance structures, the HMO algorithm was able to find low-energy conformations with a 87% success rate. Finally, the computational effort for generating low-energy conformation(s) for the phenylalanyl-glycyl-glycine tripeptide was approximately 60 CPU hours with the ACO algorithm, in comparison to 4 CPU years required for an exhaustive brute-force calculation.

First steps towards geometry optimization for Spectrometer Straw Tracker of SHiP detector

CERN Document Server

Solovev, Vladimir

2017-01-01

This report contains details of CERN Summer Student project which was performed for SHiP experiment (Search for Hidden Particles). The main aim of the project is optimization of Spectrometer Straw Tracker (SST) geometry implemented in FairSHiP simulation program.

Geometry optimization of zirconium sulfophenylphosphonate layers by molecular simulation methods

Czech Academy of Sciences Publication Activity Database

Škoda, J.; Pospíšil, M.; Kovář, P.; Melánová, Klára; Svoboda, J.; Beneš, L.; Zima, Vítězslav

2018-01-01

Roč. 24, č. 1 (2018), s. 1-12, č. článku 10. ISSN 1610-2940 R&D Projects: GA ČR(CZ) GA14-13368S; GA ČR(CZ) GA17-10639S Institutional support: RVO:61389013 Keywords : zirconium sulfophenylphosphonate * intercalation * molecular simulation Subject RIV: CA - Inorganic Chemistry OBOR OECD: Inorganic and nuclear chemistry Impact factor: 1.425, year: 2016

Chemistry Teacher Candidates' Acceptance and Opinions about Virtual Reality Technology for Molecular Geometry

Science.gov (United States)

Saritas, M. T.

2015-01-01

The meaningful knowledge creation about molecular geometry has always been the challenge of chemistry learning. In particular, microscopic world of chemistry science (example, atoms, molecules, structures) used in traditional two dimensional way of chemistry teaching can lead to such problem as students create misconceptions. In recent years,…

Transient Changes in Molecular Geometries and How to Model Them

DEFF Research Database (Denmark)

Dohn, Asmus Ougaard

Light-induced chemical processes are accompanied by molecular motion on the femtosecond time scale. Uncovering this dynamical motion is central to understanding the chemical reaction on a fundamental level. This thesis focuses on the aspects of excess excitation energy dissipation via dynamic...... observe how the wide distribution of ground state geometries is responsible for decoherence, and that the solvent cage actually facilitates coherent motion, by blocking the newly discovered vibrational mode. We furthermore observe a non-specific, rotational solvent response to the excitation. The second...

Simple Design Tool for Development of Well Insulated Window Frames and Optimization of the Frame Geometry

DEFF Research Database (Denmark)

Zajas, Jan Jakub; Heiselberg, Per

2012-01-01

in order to approach an optimal solution. The program was also used to conduct an optimization process of the frame geometry. A large number of various window frame designs were created and evaluated, based on their insulation properties. The paper presents the investigation process and some of the best......This paper describes a design tool created with the purpose of designing highly insulated window frames. The design tool is based on a parametric model of the frame geometry, where various parameters describing the frame can be easily changed by the user. Based on this input, geometry of the frame...... is generated by the program and is used by the finite element simulator to calculate the thermal performance of the frame (the U value). After the initial design is evaluated, the user can quickly modify chosen parameters and generate a new design. This process can then be repeated in multiple iterations...

First principles molecular dynamics without self-consistent field optimization

International Nuclear Information System (INIS)

Souvatzis, Petros; Niklasson, Anders M. N.

2014-01-01

We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations

An approach to multiobjective optimization of rotational therapy. II. Pareto optimal surfaces and linear combinations of modulated blocked arcs for a prostate geometry.

Science.gov (United States)

Pardo-Montero, Juan; Fenwick, John D

2010-06-01

The purpose of this work is twofold: To further develop an approach to multiobjective optimization of rotational therapy treatments recently introduced by the authors [J. Pardo-Montero and J. D. Fenwick, "An approach to multiobjective optimization of rotational therapy," Med. Phys. 36, 3292-3303 (2009)], especially regarding its application to realistic geometries, and to study the quality (Pareto optimality) of plans obtained using such an approach by comparing them with Pareto optimal plans obtained through inverse planning. In the previous work of the authors, a methodology is proposed for constructing a large number of plans, with different compromises between the objectives involved, from a small number of geometrically based arcs, each arc prioritizing different objectives. Here, this method has been further developed and studied. Two different techniques for constructing these arcs are investigated, one based on image-reconstruction algorithms and the other based on more common gradient-descent algorithms. The difficulty of dealing with organs abutting the target, briefly reported in previous work of the authors, has been investigated using partial OAR unblocking. Optimality of the solutions has been investigated by comparison with a Pareto front obtained from inverse planning. A relative Euclidean distance has been used to measure the distance of these plans to the Pareto front, and dose volume histogram comparisons have been used to gauge the clinical impact of these distances. A prostate geometry has been used for the study. For geometries where a blocked OAR abuts the target, moderate OAR unblocking can substantially improve target dose distribution and minimize hot spots while not overly compromising dose sparing of the organ. Image-reconstruction type and gradient-descent blocked-arc computations generate similar results. The Pareto front for the prostate geometry, reconstructed using a large number of inverse plans, presents a hockey-stick shape

De Novo generation of molecular structures using optimization to select graphs on a given lattice

DEFF Research Database (Denmark)

Bywater, R.P.; Poulsen, Thomas Agersten; Røgen, Peter

2004-01-01

A recurrent problem in organic chemistry is the generation of new molecular structures that conform to some predetermined set of structural constraints that are imposed in an endeavor to build certain required properties into the newly generated structure. An example of this is the pharmacophore...... model, used in medicinal chemistry to guide de novo design or selection of suitable structures from compound databases. We propose here a method that efficiently links up a selected number of required atom positions while at the same time directing the emergent molecular skeleton to avoid forbidden...... positions. The linkage process takes place on a lattice whose unit step length and overall geometry is designed to match typical architectures of organic molecules. We use an optimization method to select from the many different graphs possible. The approach is demonstrated in an example where crystal...

Optimal Spatial Subdivision method for improving geometry navigation performance in Monte Carlo particle transport simulation

International Nuclear Information System (INIS)

Chen, Zhenping; Song, Jing; Zheng, Huaqing; Wu, Bin; Hu, Liqin

2015-01-01

Highlights: • The subdivision combines both advantages of uniform and non-uniform schemes. • The grid models were proved to be more efficient than traditional CSG models. • Monte Carlo simulation performance was enhanced by Optimal Spatial Subdivision. • Efficiency gains were obtained for realistic whole reactor core models. - Abstract: Geometry navigation is one of the key aspects of dominating Monte Carlo particle transport simulation performance for large-scale whole reactor models. In such cases, spatial subdivision is an easily-established and high-potential method to improve the run-time performance. In this study, a dedicated method, named Optimal Spatial Subdivision, is proposed for generating numerically optimal spatial grid models, which are demonstrated to be more efficient for geometry navigation than traditional Constructive Solid Geometry (CSG) models. The method uses a recursive subdivision algorithm to subdivide a CSG model into non-overlapping grids, which are labeled as totally or partially occupied, or not occupied at all, by CSG objects. The most important point is that, at each stage of subdivision, a conception of quality factor based on a cost estimation function is derived to evaluate the qualities of the subdivision schemes. Only the scheme with optimal quality factor will be chosen as the final subdivision strategy for generating the grid model. Eventually, the model built with the optimal quality factor will be efficient for Monte Carlo particle transport simulation. The method has been implemented and integrated into the Super Monte Carlo program SuperMC developed by FDS Team. Testing cases were used to highlight the performance gains that could be achieved. Results showed that Monte Carlo simulation runtime could be reduced significantly when using the new method, even as cases reached whole reactor core model sizes

Optimization of combustion chamber geometry for natural gas engines with diesel micro-pilot-induced ignition

International Nuclear Information System (INIS)

Wang, Bin; Li, Tie; Ge, Linlin; Ogawa, Hideyuki

2016-01-01

Highlights: • Combustion chamber geometry is optimized to reduce the HC/CO emissions. • CFD model is calibrated against the spray visualization and engine bench test data. • Design space is explored by the multi-objective NSGA-II with Kriging meta-model. • HC and CO emissions are respectively reduced by 56.47% and 33.55%. - Abstract: Smokeless, low nitrogen oxides (NOx), and high thermal efficiency have been achieved through the lean-burn concept for natural gas engine with diesel micro-pilot-induced ignition (MPII). However, the combustion chamber is usually not specialized for natural gas combustion, and increases in the unburned hydrocarbon (HC) and carbon monoxide (CO) emissions are still a challenge for this type of engines. This paper describes optimization of the combustion chamber geometry to reduce the HC and CO emissions and improve the combustion efficiency in the MPII natural gas engine. The 3-D computational fluid dynamics (CFD) simulation model coupled with a chemical reaction mechanism is described. The temporal development of the short-pulsed diesel spray in a high pressure constant-volume vessel is measured and used to calibrate the spray model in the CFD simulation. The simulation models are validated by the experimental data of the in-cylinder pressure trace, apparent heat release rate (AHRR) and exhaust gas emissions from a single-cylinder MPII natural gas engine. To generate the various combustion chamber geometries, the bowl outline is parameterized by the two cubic Bezier curves while keeping the compression ratio constant. The available design space is explored by the multi-objective non-dominated sorting genetic algorithm II (NSGA-II) with Kriging-based meta-model. With the optimization, the HC and CO emissions are reduced by 56.47% and 33.55%, respectively, while the NOx emissions, the maximum rate of pressure rise and the gross indicated thermal efficiency that are employed as the constraints are slightly improved. Finally, the

Spur gears: Optimal geometry, methods for generation and Tooth Contact Analysis (TCA) program

Science.gov (United States)

Litvin, Faydor L.; Zhang, Jiao

1988-01-01

The contents of this report include the following: (1) development of optimal geometry for crowned spur gears; (2) methods for their generation; and (3) tooth contact analysis (TCA) computer programs for the analysis of meshing and bearing contact on the crowned spur gears. The method developed for synthesis is used for the determination of the optimal geometry for crowned pinion surface and is directed to reduce the sensitivity of the gears to misalignment, localize the bearing contact, and guarantee the favorable shape and low level of the transmission errors. A new method for the generation of the crowned pinion surface has been proposed. This method is based on application of the tool with a surface of revolution that slightly deviates from a regular cone surface. The tool can be used as a grinding wheel or as a shaver. The crowned pinion surface can also be generated by a generating plane whose motion is provided by an automatic grinding machine controlled by a computer. The TCA program simulates the meshing and bearing contact of the misaligned gears. The transmission errors are also determined.

Polarizability of acetanilide and RDX in the crystal: effect of molecular geometry

Science.gov (United States)

Tsiaousis, D.; Munn, R. W.; Smith, P. J.; Popelier, P. L. A.

2004-10-01

Density-functional theory with the B3LYP functional at the 6-311++G** level is used to calculate the dipole moment and the static polarizability for acetanilide and 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) in their in-crystal structures. For acetanilide the dipole moment is 2{1}/{2}% larger than for the gas-phase structure and for RDX (where there is a gross geometry change) it is 15% larger. The polarizability for the in-crystal structure is smaller than for the gas-phase structure by 3% for both species, whereas the in-crystal effective optical polarizability is larger than the gas-phase static polarizability for both crystals. Hence, effects in addition to the molecular geometry change in the crystal must be considered in order to interpret the effective polarizability completely.

Computational Study of Geometry, Solvation Free Energy, Dipole Moment, Polarizability, Hyperpolarizability and Molecular Properties of 2-Methylimidazole

Directory of Open Access Journals (Sweden)

Mohammad Firoz Khan

2016-12-01

Full Text Available Ab initio calculations were carried out to study the geometry, solvation free energy, dipole moment, molecular electrostatic potential (MESP, Mulliken and Natural charge distribution, polarizability, hyperpolarizability, Natural Bond Orbital (NBO energetic and different molecular properties like global reactivity descriptors (chemical hardness, softness, chemical potential, electronegativity, electrophilicity index of 2-methylimidazole. B3LYP/6-31G(d,p level of theory was used to optimize the structure both in the gas phase and in solution. The solvation free energy, dipole moment and molecular properties were calculated by applying the Solvation Model on Density (SMD in four solvent systems, namely water, dimethylsulfoxide (DMSO, n-octanol and chloroform. The computed bond distances, bond angles and dihedral angles of 2-methylimidazole agreed reasonably well with the experimental data except for C(2-N(1, C(4-C(5 and N(1-H(7 bond lengths and N(1-C(5-C(4 bond angle. The solvation free energy, dipole moment, polarizability, first order hyperpolarizability, chemical potential, electronegativity and electrophilicity index of 2-methylimidazole increased on going from non-polar to polar solvents. Chemical hardness also increased with increasing polarity of the solvent and the opposite relation was found in the case of softness. These results provide better understanding of the stability and reactivity of 2-methylimidazole in different solvent systems.

3D FEM Geometry and Material Flow Optimization of Porthole-Die Extrusion

International Nuclear Information System (INIS)

Ceretti, Elisabetta; Mazzoni, Luca; Giardini, Claudio

2007-01-01

The aim of this work is to design and to improve the geometry of a porthole-die for the production of aluminum components by means of 3D FEM simulations. In fact, the use of finite element models will allow to investigate the effects of the die geometry (webs, extrusion cavity) on the material flow and on the stresses acting on the die so to reduce the die wear and to improve the tool life. The software used to perform the simulations was a commercial FEM code, Deform 3D. The technological data introduced in the FE model have been furnished by METRA S.p.A. Company, partner in this research. The results obtained have been considered valid and helpful by the Company for building a new optimized extrusion porthole-die

Geometry optimization of linear and annular plasma synthetic jet actuators

International Nuclear Information System (INIS)

Neretti, G; Seri, P; Taglioli, M; Borghi, C A; Shaw, A; Iza, F

2017-01-01

The electrohydrodynamic (EHD) interaction induced in atmospheric air pressure by a surface dielectric barrier discharge (DBD) actuator has been experimentally investigated. Plasma synthetic jet actuators (PSJAs) are DBD actuators able to induce an air stream perpendicular to the actuator surface. These devices can be used in the field of aerodynamics to prevent or induce flow separation, modify the laminar to turbulent transition inside the boundary layer, and stabilize or mix air flows. They can also be used to enhance indirect plasma treatment effects, increasing the reactive species delivery rate onto surfaces and liquids. This can play a major role in plasma processing and chemical kinetics modelling, where often only diffusive mechanisms are considered. This paper reports on the importance that different electrode geometries can have on the performance of different PSJAs. A series of DBD aerodynamic actuators designed to produce perpendicular jets has been fabricated on two-layer printed circuit boards (PCBs). Both linear and annular geometries were considered, testing different upper electrode distances in the linear case and different diameters in the annular one. An AC voltage supplied at a peak of 11.5 kV and a frequency of 5 kHz was used. Lower electrodes were connected to the ground and buried in epoxy resin to avoid undesired plasma generation on the lower actuator surface. Voltage and current measurements were carried out to evaluate the active power delivered to the discharges. Schlieren imaging allowed the induced jets to be visualized and gave an estimate of their evolution and geometry. Pitot tube measurements were performed to obtain the velocity profiles of the PSJAs and to estimate the mechanical power delivered to the fluid. The optimal values of the inter-electrode distance and diameter were found in order to maximize jet velocity, mechanical power or efficiency. Annular geometries were found to achieve the best performance. (paper)

Optimal Ge/SiGe nanofin geometries for hole mobility enhancement: Technology limit from atomic simulations

Science.gov (United States)

Vedula, Ravi Pramod; Mehrotra, Saumitra; Kubis, Tillmann; Povolotskyi, Michael; Klimeck, Gerhard; Strachan, Alejandro

2015-05-01

We use first principles simulations to engineer Ge nanofins for maximum hole mobility by controlling strain tri-axially through nano-patterning. Large-scale molecular dynamics predict fully relaxed, atomic structures for experimentally achievable nanofins, and orthogonal tight binding is used to obtain the corresponding electronic structure. Hole transport properties are then obtained via a linearized Boltzmann formalism. This approach explicitly accounts for free surfaces and associated strain relaxation as well as strain gradients which are critical for quantitative predictions in nanoscale structures. We show that the transverse strain relaxation resulting from the reduction in the aspect ratio of the fins leads to a significant enhancement in phonon limited hole mobility (7× over unstrained, bulk Ge, and 3.5× over biaxially strained Ge). Maximum enhancement is achieved by reducing the width to be approximately 1.5 times the height and further reduction in width does not result in additional gains. These results indicate significant room for improvement over current-generation Ge nanofins, provide geometrical guidelines to design optimized geometries and insight into the physics behind the significant mobility enhancement.

Optimal Ge/SiGe nanofin geometries for hole mobility enhancement: Technology limit from atomic simulations

International Nuclear Information System (INIS)

Vedula, Ravi Pramod; Mehrotra, Saumitra; Kubis, Tillmann; Povolotskyi, Michael; Klimeck, Gerhard; Strachan, Alejandro

2015-01-01

We use first principles simulations to engineer Ge nanofins for maximum hole mobility by controlling strain tri-axially through nano-patterning. Large-scale molecular dynamics predict fully relaxed, atomic structures for experimentally achievable nanofins, and orthogonal tight binding is used to obtain the corresponding electronic structure. Hole transport properties are then obtained via a linearized Boltzmann formalism. This approach explicitly accounts for free surfaces and associated strain relaxation as well as strain gradients which are critical for quantitative predictions in nanoscale structures. We show that the transverse strain relaxation resulting from the reduction in the aspect ratio of the fins leads to a significant enhancement in phonon limited hole mobility (7× over unstrained, bulk Ge, and 3.5× over biaxially strained Ge). Maximum enhancement is achieved by reducing the width to be approximately 1.5 times the height and further reduction in width does not result in additional gains. These results indicate significant room for improvement over current-generation Ge nanofins, provide geometrical guidelines to design optimized geometries and insight into the physics behind the significant mobility enhancement

Optimal Ge/SiGe nanofin geometries for hole mobility enhancement: Technology limit from atomic simulations

Energy Technology Data Exchange (ETDEWEB)

Vedula, Ravi Pramod; Mehrotra, Saumitra; Kubis, Tillmann; Povolotskyi, Michael; Klimeck, Gerhard [School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907 (United States); Strachan, Alejandro, E-mail: strachan@purdue.edu [School of Materials Engineering and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907 (United States)

2015-05-07

We use first principles simulations to engineer Ge nanofins for maximum hole mobility by controlling strain tri-axially through nano-patterning. Large-scale molecular dynamics predict fully relaxed, atomic structures for experimentally achievable nanofins, and orthogonal tight binding is used to obtain the corresponding electronic structure. Hole transport properties are then obtained via a linearized Boltzmann formalism. This approach explicitly accounts for free surfaces and associated strain relaxation as well as strain gradients which are critical for quantitative predictions in nanoscale structures. We show that the transverse strain relaxation resulting from the reduction in the aspect ratio of the fins leads to a significant enhancement in phonon limited hole mobility (7× over unstrained, bulk Ge, and 3.5× over biaxially strained Ge). Maximum enhancement is achieved by reducing the width to be approximately 1.5 times the height and further reduction in width does not result in additional gains. These results indicate significant room for improvement over current-generation Ge nanofins, provide geometrical guidelines to design optimized geometries and insight into the physics behind the significant mobility enhancement.

Geometry and Topology Optimization of Statically Determinate Beams under Fixed and Most Unfavorably Distributed Load

Directory of Open Access Journals (Sweden)

Agata Kozikowska

Full Text Available Abstract The paper concerns topology and geometry optimization of statically determinate beams with an arbitrary number of pin supports. The beams are simultaneously exposed to uniform dead load and arbitrarily distributed live load and optimized for the absolute maximum bending moment. First, all the beams with fixed topology are subjected to geometrical optimization by genetic algorithm. Strict mathematical formulas for calculation of optimal geometrical parameters are found for all topologies and any ratio of dead to live load. Then beams with the same minimal values of the objective function and different topologies are classified into groups called topological classes. The detailed characteristics of these classes are described.

Optimizing multi-pinhole SPECT geometries using an analytical model

International Nuclear Information System (INIS)

Rentmeester, M C M; Have, F van der; Beekman, F J

2007-01-01

State-of-the-art multi-pinhole SPECT devices allow for sub-mm resolution imaging of radio-molecule distributions in small laboratory animals. The optimization of multi-pinhole and detector geometries using simulations based on ray-tracing or Monte Carlo algorithms is time-consuming, particularly because many system parameters need to be varied. As an efficient alternative we develop a continuous analytical model of a pinhole SPECT system with a stationary detector set-up, which we apply to focused imaging of a mouse. The model assumes that the multi-pinhole collimator and the detector both have the shape of a spherical layer, and uses analytical expressions for effective pinhole diameters, sensitivity and spatial resolution. For fixed fields-of-view, a pinhole-diameter adapting feedback loop allows for the comparison of the system resolution of different systems at equal system sensitivity, and vice versa. The model predicts that (i) for optimal resolution or sensitivity the collimator layer with pinholes should be placed as closely as possible around the animal given a fixed detector layer, (ii) with high-resolution detectors a resolution improvement up to 31% can be achieved compared to optimized systems, (iii) high-resolution detectors can be placed close to the collimator without significant resolution losses, (iv) interestingly, systems with a physical pinhole diameter of 0 mm can have an excellent resolution when high-resolution detectors are used

Geometry Optimization Approaches of Inductively Coupled Printed Spiral Coils for Remote Powering of Implantable Biomedical Sensors

Directory of Open Access Journals (Sweden)

Sondos Mehri

2016-01-01

Full Text Available Electronic biomedical implantable sensors need power to perform. Among the main reported approaches, inductive link is the most commonly used method for remote powering of such devices. Power efficiency is the most important characteristic to be considered when designing inductive links to transfer energy to implantable biomedical sensors. The maximum power efficiency is obtained for maximum coupling and quality factors of the coils and is generally limited as the coupling between the inductors is usually very small. This paper is dealing with geometry optimization of inductively coupled printed spiral coils for powering a given implantable sensor system. For this aim, Iterative Procedure (IP and Genetic Algorithm (GA analytic based optimization approaches are proposed. Both of these approaches implement simple mathematical models that approximate the coil parameters and the link efficiency values. Using numerical simulations based on Finite Element Method (FEM and with experimental validation, the proposed analytic approaches are shown to have improved accurate performance results in comparison with the obtained performance of a reference design case. The analytical GA and IP optimization methods are also compared to a purely Finite Element Method based on numerical optimization approach (GA-FEM. Numerical and experimental validations confirmed the accuracy and the effectiveness of the analytical optimization approaches to design the optimal coil geometries for the best values of efficiency.

Molecular dynamics modeling on the role of initial void geometry in a thin aluminum film under uniaxial tension

International Nuclear Information System (INIS)

Cui, Yi; Chen, Zengtao

2015-01-01

The effect of initial void geometry on damage progression in a thin aluminum film under uniaxial load is studied via molecular dynamics (MD) method. The embedded voids are with different initial geometries regarding shape, porosity and intervoid ligament distance (ILD). Major simulations are run upon twelve MD geometries with each containing 8–27 million atoms. The corresponding stress–strain relation is monitored during the microstructure evolution of the specimens. The critical stress to trigger the dislocation emission is found in line with the prediction of the Lubarda model. The simulation results reveal that the initial void geometry has substantial impact on the stress–strain relation especially for a specimen with larger initial porosity. (paper)

Evolutionary algorithm based optimization of hydraulic machines utilizing a state-of-the-art block coupled CFD solver and parametric geometry and mesh generation tools

Science.gov (United States)

S, Kyriacou; E, Kontoleontos; S, Weissenberger; L, Mangani; E, Casartelli; I, Skouteropoulou; M, Gattringer; A, Gehrer; M, Buchmayr

2014-03-01

An efficient hydraulic optimization procedure, suitable for industrial use, requires an advanced optimization tool (EASY software), a fast solver (block coupled CFD) and a flexible geometry generation tool. EASY optimization software is a PCA-driven metamodel-assisted Evolutionary Algorithm (MAEA (PCA)) that can be used in both single- (SOO) and multiobjective optimization (MOO) problems. In MAEAs, low cost surrogate evaluation models are used to screen out non-promising individuals during the evolution and exclude them from the expensive, problem specific evaluation, here the solution of Navier-Stokes equations. For additional reduction of the optimization CPU cost, the PCA technique is used to identify dependences among the design variables and to exploit them in order to efficiently drive the application of the evolution operators. To further enhance the hydraulic optimization procedure, a very robust and fast Navier-Stokes solver has been developed. This incompressible CFD solver employs a pressure-based block-coupled approach, solving the governing equations simultaneously. This method, apart from being robust and fast, also provides a big gain in terms of computational cost. In order to optimize the geometry of hydraulic machines, an automatic geometry and mesh generation tool is necessary. The geometry generation tool used in this work is entirely based on b-spline curves and surfaces. In what follows, the components of the tool chain are outlined in some detail and the optimization results of hydraulic machine components are shown in order to demonstrate the performance of the presented optimization procedure.

Evolutionary algorithm based optimization of hydraulic machines utilizing a state-of-the-art block coupled CFD solver and parametric geometry and mesh generation tools

International Nuclear Information System (INIS)

Kyriacou S; Kontoleontos E; Weissenberger S; Mangani L; Casartelli E; Skouteropoulou I; Gattringer M; Gehrer A; Buchmayr M

2014-01-01

An efficient hydraulic optimization procedure, suitable for industrial use, requires an advanced optimization tool (EASY software), a fast solver (block coupled CFD) and a flexible geometry generation tool. EASY optimization software is a PCA-driven metamodel-assisted Evolutionary Algorithm (MAEA (PCA)) that can be used in both single- (SOO) and multiobjective optimization (MOO) problems. In MAEAs, low cost surrogate evaluation models are used to screen out non-promising individuals during the evolution and exclude them from the expensive, problem specific evaluation, here the solution of Navier-Stokes equations. For additional reduction of the optimization CPU cost, the PCA technique is used to identify dependences among the design variables and to exploit them in order to efficiently drive the application of the evolution operators. To further enhance the hydraulic optimization procedure, a very robust and fast Navier-Stokes solver has been developed. This incompressible CFD solver employs a pressure-based block-coupled approach, solving the governing equations simultaneously. This method, apart from being robust and fast, also provides a big gain in terms of computational cost. In order to optimize the geometry of hydraulic machines, an automatic geometry and mesh generation tool is necessary. The geometry generation tool used in this work is entirely based on b-spline curves and surfaces. In what follows, the components of the tool chain are outlined in some detail and the optimization results of hydraulic machine components are shown in order to demonstrate the performance of the presented optimization procedure

Vectorising the detector geometry to optimize particle transport

CERN Document Server

Apostolakis, John; Carminati, Federico; Gheata, Andrei; Wenzel, Sandro

2014-01-01

Among the components contributing to particle transport, geometry navigation is an important consumer of CPU cycles. The tasks performed to get answers to "basic" queries such as locating a point within a geometry hierarchy or computing accurately the distance to the next boundary can become very computing intensive for complex detector setups. So far, the existing geometry algorithms employ mainly scalar optimisation strategies (voxelization, caching) to reduce their CPU consumption. In this paper, we would like to take a different approach and investigate how geometry navigation can benefit from the vector instruction set extensions that are one of the primary source of performance enhancements on current and future hardware. While on paper, this form of microparallelism promises increasing performance opportunities, applying this technology to the highly hierarchical and multiply branched geometry code is a difficult challenge. We refer to the current work done to vectorise an important part of the critica...

Optimized theory for simple and molecular fluids.

Science.gov (United States)

Marucho, M; Montgomery Pettitt, B

2007-03-28

An optimized closure approximation for both simple and molecular fluids is presented. A smooth interpolation between Perkus-Yevick and hypernetted chain closures is optimized by minimizing the free energy self-consistently with respect to the interpolation parameter(s). The molecular version is derived from a refinement of the method for simple fluids. In doing so, a method is proposed which appropriately couples an optimized closure with the variant of the diagrammatically proper integral equation recently introduced by this laboratory [K. M. Dyer et al., J. Chem. Phys. 123, 204512 (2005)]. The simplicity of the expressions involved in this proposed theory has allowed the authors to obtain an analytic expression for the approximate excess chemical potential. This is shown to be an efficient tool to estimate, from first principles, the numerical value of the interpolation parameters defining the aforementioned closure. As a preliminary test, representative models for simple fluids and homonuclear diatomic Lennard-Jones fluids were analyzed, obtaining site-site correlation functions in excellent agreement with simulation data.

A Theoretical and Empirical Integrated Method to Select the Optimal Combined Signals for Geometry-Free and Geometry-Based Three-Carrier Ambiguity Resolution.

Science.gov (United States)

Zhao, Dongsheng; Roberts, Gethin Wyn; Lau, Lawrence; Hancock, Craig M; Bai, Ruibin

2016-11-16

Twelve GPS Block IIF satellites, out of the current constellation, can transmit on three-frequency signals (L1, L2, L5). Taking advantages of these signals, Three-Carrier Ambiguity Resolution (TCAR) is expected to bring much benefit for ambiguity resolution. One of the research areas is to find the optimal combined signals for a better ambiguity resolution in geometry-free (GF) and geometry-based (GB) mode. However, the existing researches select the signals through either pure theoretical analysis or testing with simulated data, which might be biased as the real observation condition could be different from theoretical prediction or simulation. In this paper, we propose a theoretical and empirical integrated method, which first selects the possible optimal combined signals in theory and then refines these signals with real triple-frequency GPS data, observed at eleven baselines of different lengths. An interpolation technique is also adopted in order to show changes of the AR performance with the increase in baseline length. The results show that the AR success rate can be improved by 3% in GF mode and 8% in GB mode at certain intervals of the baseline length. Therefore, the TCAR can perform better by adopting the combined signals proposed in this paper when the baseline meets the length condition.

Composite Thickness Optimization of Offshore Wind Turbine Blade with Fixed outer Geometry

DEFF Research Database (Denmark)

Sjølund, Jonas Heidemann; Lund, Erik

2017-01-01

With the objective of mass minimization, a 73-m offshore wind turbine blade is optimized using a gradient based approach on a Finite Element (FE) model. Constant loads and a fixed outer geometry are assumed. Plies of the same material and same orientation are grouped together in plygroups. The th....... The thicknesses of the plygroups are chosen as design variables. Manufacturing constraints such as ply-drops are taken into account using linear constraints. Structural constraints include buckling, tip displacement and max. strain failure indices....

Multicomponent Density Functional Theory: Impact of Nuclear Quantum Effects on Proton Affinities and Geometries.

Science.gov (United States)

Brorsen, Kurt R; Yang, Yang; Hammes-Schiffer, Sharon

2017-08-03

Nuclear quantum effects such as zero point energy play a critical role in computational chemistry and often are included as energetic corrections following geometry optimizations. The nuclear-electronic orbital (NEO) multicomponent density functional theory (DFT) method treats select nuclei, typically protons, quantum mechanically on the same level as the electrons. Electron-proton correlation is highly significant, and inadequate treatments lead to highly overlocalized nuclear densities. A recently developed electron-proton correlation functional, epc17, has been shown to provide accurate nuclear densities for molecular systems. Herein, the NEO-DFT/epc17 method is used to compute the proton affinities for a set of molecules and to examine the role of nuclear quantum effects on the equilibrium geometry of FHF - . The agreement of the computed results with experimental and benchmark values demonstrates the promise of this approach for including nuclear quantum effects in calculations of proton affinities, pK a 's, optimized geometries, and reaction paths.

Optimization of armour geometry and bonding techniques for tungsten-armoured high heat flux components

International Nuclear Information System (INIS)

Giniyatulin, R.N.; Komarov, V.L.; Kuzmin, E.G.; Makhankov, A.N.; Mazul, I.V.; Yablokov, N.A.; Zhuk, A.N.

2002-01-01

Joining of tungsten with copper-based cooling structure and armour geometry optimization are the major aspects in development of the tungsten-armoured plasma facing components (PFC). Fabrication techniques and high heat flux (HHF) tests of tungsten-armoured components have to reflect different PFC designs and acceptable manufacturing cost. The authors present the recent results of tungsten-armoured mock-ups development based on manufacturing and HHF tests. Two aspects were investigated--selection of armour geometry and examination of tungsten-copper bonding techniques. Brazing and casting tungsten-copper bonding techniques were used in small mock-ups. The mock-ups with armour tiles (20x5x10, 10x10x10, 20x20x10, 27x27x10) mm 3 in dimensions were tested by cyclic heat fluxes in the range of (5-20) MW/m 2 , the number of thermal cycles varied from hundreds to several thousands for each mock-up. The results of the tests show the applicability of different geometry and different bonding technique to corresponding heat loading. A medium-scale mock-up 0.6-m in length was manufactured and tested. HHF tests of the medium-scale mock-up have demonstrated the applicability of the applied bonding techniques and armour geometry for full-scale PFC's manufacturing

Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes.

Science.gov (United States)

Gkionis, Konstantinos; Kruse, Holger; Šponer, Jiří

2016-04-12

Modern dispersion-corrected DFT methods have made it possible to perform reliable QM studies on complete nucleic acid (NA) building blocks having hundreds of atoms. Such calculations, although still limited to investigations of potential energy surfaces, enhance the portfolio of computational methods applicable to NAs and offer considerably more accurate intrinsic descriptions of NAs than standard MM. However, in practice such calculations are hampered by the use of implicit solvent environments and truncation of the systems. Conventional QM optimizations are spoiled by spurious intramolecular interactions and severe structural deformations. Here we compare two approaches designed to suppress such artifacts: partially restrained continuum solvent QM and explicit solvent QM/MM optimizations. We report geometry relaxations of a set of diverse double-quartet guanine quadruplex (GQ) DNA stems. Both methods provide neat structures without major artifacts. However, each one also has distinct weaknesses. In restrained optimizations, all errors in the target geometries (i.e., low-resolution X-ray and NMR structures) are transferred to the optimized geometries. In QM/MM, the initial solvent configuration causes some heterogeneity in the geometries. Nevertheless, both approaches represent a decisive step forward compared to conventional optimizations. We refine earlier computations that revealed sizable differences in the relative energies of GQ stems computed with AMBER MM and QM. We also explore the dependence of the QM/MM results on the applied computational protocol.

Molecular Geometry And Vibrational Spectra of 2'-chloroacetanilide

International Nuclear Information System (INIS)

Gokce, H.

2008-01-01

The molecular structure, vibrational frequencies and the corresponding vibrational assingments of 2'-chloroacetanilide in the ground state have been calculated by using Hartree-Fock (HF) and Density Functional Theory (DFT/B3LYP) methods with 6-311++G(d,p) basis set. The obtained vibrational frequencies and optimized geometric parameters (bond lenghts and angles) are in very good agreement with the experimental data. The comparison of the observed and calculated vibrational frequencies assignments of 2'-chloroacetanilide exhibit that the scaled DFT/B3LYP method is superior to be scaled HF method. Furthermore the calculated Infrared and Raman intensities are also reported

Interplay of electronic and geometry shell effects in properties of neutral and charged Sr clusters

DEFF Research Database (Denmark)

Lyalin, Andrey; Solov'yov, Ilia; Solov'yov, Andrey V.

2007-01-01

that the size evolution of structural and electronic properties of strontium clusters is governed by an interplay of the electronic and geometry shell closures. Influence of the electronic shell effects on structural rearrangements can lead to violation of the icosahedral growth motif of strontium clusters......The optimized structure and electronic properties of neutral, singly, and doubly charged strontium clusters have been investigated using ab initio theoretical methods based on density-functional theory. We have systematically calculated the optimized geometries of neutral, singly, and doubly...... charged strontium clusters consisting of up to 14 atoms, average bonding distances, electronic shell closures, binding energies per atom, the gap between the highest occupied and the lowest unoccupied molecular orbitals, and spectra of the density of electronic states (DOS). It is demonstrated...

Numerical computation of molecular integrals via optimized (vectorized) FORTRAN code

International Nuclear Information System (INIS)

Scott, T.C.; Grant, I.P.; Saunders, V.R.

1997-01-01

The calculation of molecular properties based on quantum mechanics is an area of fundamental research whose horizons have always been determined by the power of state-of-the-art computers. A computational bottleneck is the numerical calculation of the required molecular integrals to sufficient precision. Herein, we present a method for the rapid numerical evaluation of molecular integrals using optimized FORTRAN code generated by Maple. The method is based on the exploitation of common intermediates and the optimization can be adjusted to both serial and vectorized computations. (orig.)

Geometry optimization of supersymmetrical molecules in quantum chemical ab-initio calculations

International Nuclear Information System (INIS)

Gruenbichler, H.

1985-01-01

One-dimensional geometry optimizations in ab-initio SCF-calculations are investigated. It is shown, that the well known standard algorithms are sometimes too expensive and can be replaced or accompanied by more recent algorithms. Two alternatives were realized in the molecule calculating program GAUSSIAN 80, basing on the Fibonacci algorithm and Kryachco potential adjustment. The algorithms were compared in terms of accuracy of results, CPU-time used and reliability of the method. The results are presented in various tables, showing the efficiency of the various methods. A survey of the usual model potentials is given and the compatibility with ab-initio data is evaluated. (Author, shortened and translated by A.N.)

Structural optimization and docking studies of anatoxin-a: A potent ...

African Journals Online (AJOL)

, structural properties and molecular interaction of anatoxin-a, a naturally occurring potent neurotoxin. The geometry of the anatoxin-a was fully optimized in terms of density functional theory Gaussian 09. Calculations for structural parameters ...

Numerical simulation and geometry optimization of hot-gas mixing in lower plenum of high temperature gas-cooled reactor

International Nuclear Information System (INIS)

Wang Hang; Wang Jie; Laurien, E.

2010-01-01

The lower plenum in high temperature gas-cooled reactor was designed to mix the gas of different temperatures from the reactor core. Previous researches suggest the current geometry of the lower plenum to be improved for better mixing capability and lower pressure drop. In the presented work, a series of varied geometries were investigated with numerical simulation way. The choice of appropriate mesh type and size used in the geometry variation was discussed with the reference of experimental data. The original thin ribs in the current design were merged into thicker ones, and a junction located at the starting end of the outlet pipe was introduced. After comparing several potential optimization methods, an improved geometry was selected with the merged ribs increasing the pre-defined mixing coefficient and the junction reducing the pressure drop. Future work was discussed based on the simulation of real reactor case. The work shows a direction for design improvements of the lower plenum geometry. (authors)

Geometry and its applications

CERN Document Server

Meyer, Walter J

2006-01-01

Meyer''s Geometry and Its Applications, Second Edition, combines traditional geometry with current ideas to present a modern approach that is grounded in real-world applications. It balances the deductive approach with discovery learning, and introduces axiomatic, Euclidean geometry, non-Euclidean geometry, and transformational geometry. The text integrates applications and examples throughout and includes historical notes in many chapters. The Second Edition of Geometry and Its Applications is a significant text for any college or university that focuses on geometry''s usefulness in other disciplines. It is especially appropriate for engineering and science majors, as well as future mathematics teachers.* Realistic applications integrated throughout the text, including (but not limited to): - Symmetries of artistic patterns- Physics- Robotics- Computer vision- Computer graphics- Stability of architectural structures- Molecular biology- Medicine- Pattern recognition* Historical notes included in many chapters...

Determination of optimal geometry for cylindrical sources for gamma radiation measurements; Odredjivanje optimalne geometrije za mjerenje gama zracenja cilindrichnih izvora

Energy Technology Data Exchange (ETDEWEB)

Sinjeri, Lj; Kulisic, P [Elektra - Zagreb, Zagreb (Yugoslavia)

1990-07-01

Low radioactive sources were used for experimental determination of optimal dimensions for cylindrical source using coaxial Ge(Li) detector. Then, calculational procedure is used to find optimal dimensions of cylindrical source. The results from calculational procedure confirm with experimental results. In such way the verification of calculational procedure is done and it can be used for determination of optimal geometry for low radioactive cylindrical sources. (author)

FT-IR, FT-Raman, NMR spectra, density functional computations of the vibrational assignments (for monomer and dimer) and molecular geometry of anticancer drug 7-amino-2-methylchromone

Science.gov (United States)

Mariappan, G.; Sundaraganesan, N.

2014-04-01

Vibrational assignments for the 7-amino-2-methylchromone (abbreviated as 7A2MC) molecule using a combination of experimental vibrational spectroscopic measurements and ab initio computational methods are reported. The optimized geometry, intermolecular hydrogen bonding, first order hyperpolarizability and harmonic vibrational wavenumbers of 7A2MC have been investigated with the help of B3LYP density functional theory method. The calculated molecular geometry parameters, the theoretically computed vibrational frequencies for monomer and dimer and relative peak intensities were compared with experimental data. DFT calculations using the B3LYP method and 6-31 + G(d,p) basis set were found to yield results that are very comparable to experimental IR and Raman spectra. Detailed vibrational assignments were performed with DFT calculations and the potential energy distribution (PED) obtained from the Vibrational Energy Distribution Analysis (VEDA) program. Natural Bond Orbital (NBO) study revealed the characteristics of the electronic delocalization of the molecular structure. 13C and 1H NMR spectra have been recorded and 13C and 1H nuclear magnetic resonance chemical shifts of the molecule have been calculated using the gauge independent atomic orbital (GIAO) method. Furthermore, All the possible calculated values are analyzed using correlation coefficients linear fitting equation and are shown strong correlation with the experimental data.

Variable-geometry turbocharger with asymmetric divided volute for engine exhaust gas pulse optimization

Science.gov (United States)

Serres, Nicolas

2010-11-09

A turbine assembly for a variable-geometry turbocharger includes a turbine housing defining a divided volute having first and second scrolls, wherein the first scroll has a substantially smaller volume than the second scroll. The first scroll feeds exhaust gas to a first portion of a turbine wheel upstream of the throat of the wheel, while the second scroll feeds gas to a second portion of the wheel at least part of which is downstream of the throat. Flow from the second scroll is regulated by a sliding piston. The first scroll can be optimized for low-flow conditions such that the turbocharger can operate effectively like a small fixed-geometry turbocharger when the piston is closed. The turbine housing defines an inlet that is divided by a dividing wall into two portions respectively feeding gas to the two scrolls, a leading edge of the dividing wall being downstream of the inlet mouth.

Geometry characteristics modeling and process optimization in coaxial laser inside wire cladding

Science.gov (United States)

Shi, Jianjun; Zhu, Ping; Fu, Geyan; Shi, Shihong

2018-05-01

Coaxial laser inside wire cladding method is very promising as it has a very high efficiency and a consistent interaction between the laser and wire. In this paper, the energy and mass conservation law, and the regression algorithm are used together for establishing the mathematical models to study the relationship between the layer geometry characteristics (width, height and cross section area) and process parameters (laser power, scanning velocity and wire feeding speed). At the selected parameter ranges, the predicted values from the models are compared with the experimental measured results, and there is minor error existing, but they reflect the same regularity. From the models, it is seen the width of the cladding layer is proportional to both the laser power and wire feeding speed, while it firstly increases and then decreases with the increasing of the scanning velocity. The height of the cladding layer is proportional to the scanning velocity and feeding speed and inversely proportional to the laser power. The cross section area increases with the increasing of feeding speed and decreasing of scanning velocity. By using the mathematical models, the geometry characteristics of the cladding layer can be predicted by the known process parameters. Conversely, the process parameters can be calculated by the targeted geometry characteristics. The models are also suitable for multi-layer forming process. By using the optimized process parameters calculated from the models, a 45 mm-high thin-wall part is formed with smooth side surfaces.

Description of SSG Geometry - phase 1

DEFF Research Database (Denmark)

Margheritini, Lucia; Kofoed, Jens Peter

The purpose of the study is to define the optimized geometry for the SSG in Svaheia, Norway and to provide the responsible for the turbines with useful information to their work.......The purpose of the study is to define the optimized geometry for the SSG in Svaheia, Norway and to provide the responsible for the turbines with useful information to their work....

Dual reorientation relaxation routes of water molecules in oxyanion’s hydration shell: A molecular geometry perspective

Energy Technology Data Exchange (ETDEWEB)

Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn [Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 (China)

2015-12-14

In this study, we examine how complex ions such as oxyanions influence the dynamic properties of water and whether differences exist between simple halide anions and oxyanions. Nitrate anion is taken as an example to investigate the hydration properties of oxyanions. Reorientation relaxation of its hydration water can occur through two different routes: water can either break its hydrogen bond with the nitrate to form one with another water or switch between two oxygen atoms of the same nitrate. The latter molecular mechanism increases the residence time of oxyanion’s hydration water and thus nitrate anion slows down the translational motion of neighbouring water. But it is also a “structure breaker” in that it accelerates the reorientation relaxation of hydration water. Such a result illustrates that differences do exist between the hydration of oxyanions and simple halide anions as a result of different molecular geometries. Furthermore, the rotation of the nitrate solute is coupled with the hydrogen bond rearrangement of its hydration water. The nitrate anion can either tilt along the axis perpendicularly to the plane or rotate in the plane. We find that the two reorientation relaxation routes of the hydration water lead to different relaxation dynamics in each of the two above movements of the nitrate solute. The current study suggests that molecular geometry could play an important role in solute hydration and dynamics.

Dual reorientation relaxation routes of water molecules in oxyanion’s hydration shell: A molecular geometry perspective

International Nuclear Information System (INIS)

Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin

2015-01-01

In this study, we examine how complex ions such as oxyanions influence the dynamic properties of water and whether differences exist between simple halide anions and oxyanions. Nitrate anion is taken as an example to investigate the hydration properties of oxyanions. Reorientation relaxation of its hydration water can occur through two different routes: water can either break its hydrogen bond with the nitrate to form one with another water or switch between two oxygen atoms of the same nitrate. The latter molecular mechanism increases the residence time of oxyanion’s hydration water and thus nitrate anion slows down the translational motion of neighbouring water. But it is also a “structure breaker” in that it accelerates the reorientation relaxation of hydration water. Such a result illustrates that differences do exist between the hydration of oxyanions and simple halide anions as a result of different molecular geometries. Furthermore, the rotation of the nitrate solute is coupled with the hydrogen bond rearrangement of its hydration water. The nitrate anion can either tilt along the axis perpendicularly to the plane or rotate in the plane. We find that the two reorientation relaxation routes of the hydration water lead to different relaxation dynamics in each of the two above movements of the nitrate solute. The current study suggests that molecular geometry could play an important role in solute hydration and dynamics

Cherenkov imaging method for rapid optimization of clinical treatment geometry in total skin electron beam therapy

Energy Technology Data Exchange (ETDEWEB)

Andreozzi, Jacqueline M., E-mail: Jacqueline.M.Andreozzi.th@dartmouth.edu, E-mail: Lesley.A.Jarvis@hitchcock.org; Glaser, Adam K. [Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755 (United States); Zhang, Rongxiao [Department of Physics and Astronomy, Dartmouth College, Hanover, New Hampshire 03755 (United States); Gladstone, David J.; Williams, Benjamin B.; Jarvis, Lesley A., E-mail: Jacqueline.M.Andreozzi.th@dartmouth.edu, E-mail: Lesley.A.Jarvis@hitchcock.org [Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire 03766 (United States); Pogue, Brian W. [Thayer School of Engineering and Department of Physics and Astronomy, Dartmouth College, Hanover, New Hampshire 03755 (United States)

2016-02-15

Purpose: A method was developed utilizing Cherenkov imaging for rapid and thorough determination of the two gantry angles that produce the most uniform treatment plane during dual-field total skin electron beam therapy (TSET). Methods: Cherenkov imaging was implemented to gather 2D measurements of relative surface dose from 6 MeV electron beams on a white polyethylene sheet. An intensified charge-coupled device camera time-gated to the Linac was used for Cherenkov emission imaging at sixty-two different gantry angles (1° increments, from 239.5° to 300.5°). Following a modified Stanford TSET technique, which uses two fields per patient position for full body coverage, composite images were created as the sum of two beam images on the sheet; each angle pair was evaluated for minimum variation across the patient region of interest. Cherenkov versus dose correlation was verified with ionization chamber measurements. The process was repeated at source to surface distance (SSD) = 441, 370.5, and 300 cm to determine optimal angle spread for varying room geometries. In addition, three patients receiving TSET using a modified Stanford six-dual field technique with 6 MeV electron beams at SSD = 441 cm were imaged during treatment. Results: As in previous studies, Cherenkov intensity was shown to directly correlate with dose for homogenous flat phantoms (R{sup 2} = 0.93), making Cherenkov imaging an appropriate candidate to assess and optimize TSET setup geometry. This method provided dense 2D images allowing 1891 possible treatment geometries to be comprehensively analyzed from one data set of 62 single images. Gantry angles historically used for TSET at their institution were 255.5° and 284.5° at SSD = 441 cm; however, the angles optimized for maximum homogeneity were found to be 252.5° and 287.5° (+6° increase in angle spread). Ionization chamber measurements confirmed improvement in dose homogeneity across the treatment field from a range of 24.4% at the initial

The optimal version of Hua's fundamental theorem of geometry of rectangular matrices

CERN Document Server

Semrl, Peter

2014-01-01

Hua's fundamental theorem of geometry of matrices describes the general form of bijective maps on the space of all m\\times n matrices over a division ring \\mathbb{D} which preserve adjacency in both directions. Motivated by several applications the author studies a long standing open problem of possible improvements. There are three natural questions. Can we replace the assumption of preserving adjacency in both directions by the weaker assumption of preserving adjacency in one direction only and still get the same conclusion? Can we relax the bijectivity assumption? Can we obtain an analogous result for maps acting between the spaces of rectangular matrices of different sizes? A division ring is said to be EAS if it is not isomorphic to any proper subring. For matrices over EAS division rings the author solves all three problems simultaneously, thus obtaining the optimal version of Hua's theorem. In the case of general division rings he gets such an optimal result only for square matrices and gives examples ...

DG-AMMOS: a new tool to generate 3d conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening.

Science.gov (United States)

Lagorce, David; Pencheva, Tania; Villoutreix, Bruno O; Miteva, Maria A

2009-11-13

Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods.

A View on Optimal Transport from Noncommutative Geometry

Directory of Open Access Journals (Sweden)

Francesco D'Andrea

2010-07-01

Full Text Available We discuss the relation between the Wasserstein distance of order 1 between probability distributions on a metric space, arising in the study of Monge-Kantorovich transport problem, and the spectral distance of noncommutative geometry. Starting from a remark of Rieffel on compact manifolds, we first show that on any - i.e. non-necessary compact - complete Riemannian spin manifolds, the two distances coincide. Then, on convex manifolds in the sense of Nash embedding, we provide some natural upper and lower bounds to the distance between any two probability distributions. Specializing to the Euclidean space R^n, we explicitly compute the distance for a particular class of distributions generalizing Gaussian wave packet. Finally we explore the analogy between the spectral and the Wasserstein distances in the noncommutative case, focusing on the standard model and the Moyal plane. In particular we point out that in the two-sheet space of the standard model, an optimal-transport interpretation of the metric requires a cost function that does not vanish on the diagonal. The latest is similar to the cost function occurring in the relativistic heat equation.

Planar Hall effect sensor bridge geometries optimized for magnetic bead detection

DEFF Research Database (Denmark)

Østerberg, Frederik Westergaard; Rizzi, Giovanni; Henriksen, Anders Dahl

2014-01-01

Novel designs of planar Hall effect bridge sensors optimized for magnetic bead detection are presented and characterized. By constructing the sensor geometries appropriately, the sensors can be tailored to be sensitive to an external magnetic field, the magnetic field due to beads being magnetized...... by the sensor self-field or a combination thereof. The sensors can be made nominally insensitive to small external magnetic fields, while being maximally sensitive to magnetic beads, magnetized by the sensor self-field. Thus, the sensor designs can be tailored towards specific applications with minimal...... of the dynamic magnetic response of suspensions of magnetic beads with a nominal diameter of 80 nm are performed. Furthermore, a method to amplify the signal by appropriate combinations of multiple sensor segments is demonstrated....

Optimization of Orifice Geometry for Cross-Flow Mixing in a Cylindrical Duct

Science.gov (United States)

Kroll, J. T.; Sowa, W. A.; Samuelsen, G. S.

1996-01-01

Mixing of gaseous jets in a cross-flow has significant applications in engineering, one example of which is the dilution zone of a gas turbine combustor. Despite years of study, the design of the jet injection in combustors is largely based on practical experience. The emergence of NO(x) regulations for stationary gas turbines and the anticipation of aero-engine regulations requires an improved understanding of jet mixing as new combustor concepts are introduced. For example, the success of the staged combustor to reduce the emission of NO(x) is almost entirely dependent upon the rapid and complete dilution of the rich zone products within the mixing section. It is these mixing challenges to which the present study is directed. A series of experiments was undertaken to delineate the optimal mixer orifice geometry. A cross-flow to core-flow momentum-flux ratio of 40 and a mass flow ratio of 2.5 were selected as representative of a conventional design. An experimental test matrix was designed around three variables: the number of orifices, the orifice length-to- width ratio, and the orifice angle. A regression analysis was performed on the data to arrive at an interpolating equation that predicted the mixing performance of orifice geometry combinations within the range of the test matrix parameters. Results indicate that the best mixing orifice geometry tested involves eight orifices with a long-to-short side aspect ratio of 3.5 at a twenty-three degree inclination from the center-line of the mixing section.

Molecular dynamics simulations and quantum chemical calculations ...

African Journals Online (AJOL)

Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...

Evolutionary algorithm for optimization of nonimaging Fresnel lens geometry.

Science.gov (United States)

Yamada, N; Nishikawa, T

2010-06-21

In this study, an evolutionary algorithm (EA), which consists of genetic and immune algorithms, is introduced to design the optical geometry of a nonimaging Fresnel lens; this lens generates the uniform flux concentration required for a photovoltaic cell. Herein, a design procedure that incorporates a ray-tracing technique in the EA is described, and the validity of the design is demonstrated. The results show that the EA automatically generated a unique geometry of the Fresnel lens; the use of this geometry resulted in better uniform flux concentration with high optical efficiency.

Inversion of self-potential anomalies caused by simple-geometry bodies using global optimization algorithms

International Nuclear Information System (INIS)

Göktürkler, G; Balkaya, Ç

2012-01-01

Three naturally inspired meta-heuristic algorithms—the genetic algorithm (GA), simulated annealing (SA) and particle swarm optimization (PSO)—were used to invert some of the self-potential (SP) anomalies originated by some polarized bodies with simple geometries. Both synthetic and field data sets were considered. The tests with the synthetic data comprised of the solutions with both noise-free and noisy data; in the tests with the field data some SP anomalies observed over a copper belt (India), graphite deposits (Germany) and metallic sulfide (Turkey) were inverted. The model parameters included the electric dipole moment, polarization angle, depth, shape factor and origin of the anomaly. The estimated parameters were compared with those from previous studies using various optimization algorithms, mainly least-squares approaches, on the same data sets. During the test studies the solutions by GA, PSO and SA were characterized as being consistent with each other; a good starting model was not a requirement to reach the global minimum. It can be concluded that the global optimization algorithms considered in this study were able to yield compatible solutions with those from widely used local optimization algorithms. (paper)

Effect of duct geometry on Wells turbine performance

International Nuclear Information System (INIS)

Shaaban, S.; Abdel Hafiz, A.

2012-01-01

Highlights: ► A Wells turbine duct design in the form of venturi duct is proposed and investigated. ► Optimum duct geometry is identified. ► Up to 14% increase of the turbine power can be achieved using the optimized duct geometry. ► Up to 9% improve of the turbine efficiency is attained by optimizing the turbine duct geometry. ► The optimized duct geometry results in tangible delay of the turbine stalling point. - Abstract: Wells turbines can represent important source of renewable energy for many countries. An essential disadvantage of Wells turbines is their low aerodynamic efficiency and consequently low power produced. In order to enhance the Wells turbine performance, the present research work proposes the use of a symmetrical duct in the form of a venturi tube with turbine rotor located at throat. The effects of duct area ratio and duct angle are investigated in order to optimize Wells turbine performance. The turbine performance is numerically investigated by solving the steady 3D incompressible Reynolds Averaged Navier–Stocks equation (RANS). A substantial improve of the turbine performance is achieved by optimizing the duct geometry. Increasing both the duct area ratio and duct angle increase the acceleration and deceleration upstream and downstream the rotor respectively. The accelerating flow with thinner boundary layer thickness upstream the rotor reduces the flow separation on the rotor suction side. The downstream diffuser reduces the interaction between tip leakage flow and blade suction side. Up to 14% increase in turbine power and 9% increase in turbine efficiency are achieved by optimizing the duct geometry. On other hand, a tangible delay of the turbine stall point is also detected.

DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

Directory of Open Access Journals (Sweden)

Villoutreix Bruno O

2009-11-01

Full Text Available Abstract Background Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Results Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. Conclusion DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods.

Optimization of Overtopping Wave Energy Converters by Geometry Control

DEFF Research Database (Denmark)

Victor, L.; Troch, P.; Kofoed, Jens Peter

2011-01-01

In this paper, the results of a study on the effects of geometry control on the performance of overtopping wave energy converters with a simple geometry built in coastal structures (simple OWECs) are presented. Empirical formulae, derived based on experimental tests on simple OWECs with varying...

Simultaneous beam geometry and intensity map optimization in intensity-modulated radiation therapy

International Nuclear Information System (INIS)

Lee, Eva K.; Fox, Tim; Crocker, Ian

2006-01-01

angles returned appear to be nonintuitive, and depend on PTV size and geometry and the s patial relationship between the tumor and critical structures. Conclusions: The MIP model described allows simultaneous optimization over the space of beamlet fluence weights and beam and couch angles. Based on experiments with tumor data, this approach can return good plans that are clinically acceptable and practical. This work distinguishes itself from recent IMRT research in several ways. First, in previous methods beam angles are selected before intensity map optimization. Herein, we employ 0/1 variables to model the set of candidate beams, and thereby allow the optimization process itself to select optimal beams. Second, instead of incorporating dose-volume criteria within the objective function as in previous work, herein, a combination of discrete and continuous variables associated with each voxel provides a mechanism to strictly enforce dose-volume criteria within the constraints. Third, using the construct of critical-normal-tissue-ring within the objective function can enhance the achievement of conformal plans. Based on the three tumor sites considered, it appears that volume and spatial geometry with respect to the PTV are important factors to consider when selecting objectives to optimize, and in estimating how well suited a particular model is for achieving a specified goal

Geometry-Driven-Diffusion filtering of MR Brain Images using dissimilarities and optimal relaxation parameter

Energy Technology Data Exchange (ETDEWEB)

Bajla, Ivan [Austrian Research Centres Sibersdorf, Department of High Performance Image Processing and Video-Technology, A-2444 Seibersdorf (Austria); Hollander, Igor [Institute of information Processing, Austrian Academy of Sciences, Sonnenfelsgasse 19/2, 1010 Wien (Austria)

1999-12-31

A novel method of local adapting of the conductance using a pixel dissimilarity measure is developed. An alternative processing methodology is proposed, which is based on intensity gradient histogram calculated for region interiors and boundaries of a phantom which models real MR brain scans. It involves a specific cost function suitable for the calculation of the optimum relaxation parameter Kopt and for the selection of the optimal exponential conductance. Computer experiments for locally adaptive geometry-driven-diffusion filtering of an MR brain phantom have been performed and evaluated. (authors) 6 refs., 3 figs.2 tabs.

Geometry-Driven-Diffusion filtering of MR Brain Images using dissimilarities and optimal relaxation parameter

International Nuclear Information System (INIS)

Bajla, Ivan; Hollander, Igor

1998-01-01

A novel method of local adapting of the conductance using a pixel dissimilarity measure is developed. An alternative processing methodology is proposed, which is based on intensity gradient histogram calculated for region interiors and boundaries of a phantom which models real MR brain scans. It involves a specific cost function suitable for the calculation of the optimum relaxation parameter Kopt and for the selection of the optimal exponential conductance. Computer experiments for locally adaptive geometry-driven-diffusion filtering of an MR brain phantom have been performed and evaluated. (authors)

Fuel management optimization in pressure water reactors with hexagonal geometry using hill climbing method

International Nuclear Information System (INIS)

Andres Diaz, J.; Quintero, Ruben; Melian, Manuel; Rosete, Alejandro

2000-01-01

In this work the general-purpose optimization method, Hill Climbing, was applied to the Fuel Management Optimization problem in PWR reactors, WWER type. They were carried out a series of experiments in order to study the performance of Hill Climbing. It was proven two starting point for initialize the search: a reload configuration by project and a reload configuration generated with the application of a minimal knowledge of the problem. It was also studied the effect of imposing constraints based on the physics of the reactor in order to reduce the number of possible solutions to be generated. The operator used in Hill Climbing was defined as a binary exchange of fuel assemblies. For the simulation of each generated configuration, the tridimensional simulator program SPPS-1 was used. It was formulated an objective function with power peaking constraint to guide the search. As results, a methodology ws proposed for the In-core Fuel Management Optimization in hexagonal geometry, and the feasibility of the application of the Hill Climbing to this type of problem was demonstrated. (author)

An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

KAUST Repository

Chawla, Mohit

2015-06-27

Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. ‘modified base pairs’. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson–Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in.

An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

KAUST Repository

Chawla, Mohit; Oliva, R.; Bujnicki, J. M.; Cavallo, Luigi

2015-01-01

Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. ‘modified base pairs’. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson–Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in.

Optimization of geometry of annular seat valves suitable for Digital Displacement fluid power pumps/motors

DEFF Research Database (Denmark)

Rømer, Daniel; Johansen, Per; Pedersen, Henrik C.

2013-01-01

Digital Displacement Fluid Power is an upcoming technology setting new standards for the achievable efficiency of fluid power pumps and motors. The core element of the Digital Displacement technology is high performance electronically controlled seat valves, which must exhibit very low flow...... work an annular seat valve suitable for use in Digital Displacement units is considered, and the ring geometry is optimized using finite element analysis including non-linear material behaviour, contact elements and fluid pressure penetrating load, closely reflecting the actual load of the seat valve...

Simultaneous calibration phantom commission and geometry calibration in cone beam CT

Science.gov (United States)

Xu, Yuan; Yang, Shuai; Ma, Jianhui; Li, Bin; Wu, Shuyu; Qi, Hongliang; Zhou, Linghong

2017-09-01

Geometry calibration is a vital step for describing the geometry of a cone beam computed tomography (CBCT) system and is a prerequisite for CBCT reconstruction. In current methods, calibration phantom commission and geometry calibration are divided into two independent tasks. Small errors in ball-bearing (BB) positioning in the phantom-making step will severely degrade the quality of phantom calibration. To solve this problem, we propose an integrated method to simultaneously realize geometry phantom commission and geometry calibration. Instead of assuming the accuracy of the geometry phantom, the integrated method considers BB centers in the phantom as an optimized parameter in the workflow. Specifically, an evaluation phantom and the corresponding evaluation contrast index are used to evaluate geometry artifacts for optimizing the BB coordinates in the geometry phantom. After utilizing particle swarm optimization, the CBCT geometry and BB coordinates in the geometry phantom are calibrated accurately and are then directly used for the next geometry calibration task in other CBCT systems. To evaluate the proposed method, both qualitative and quantitative studies were performed on simulated and realistic CBCT data. The spatial resolution of reconstructed images using dental CBCT can reach up to 15 line pair cm-1. The proposed method is also superior to the Wiesent method in experiments. This paper shows that the proposed method is attractive for simultaneous and accurate geometry phantom commission and geometry calibration.

Media optimization for elevated molecular weight and mass production of pigment-free pullulan.

Science.gov (United States)

Yu, Xiaoliu; Wang, Yulei; Wei, Gongyuan; Dong, Yingying

2012-07-01

In this study, an Aureobasidium pullulans SZU 1001 mutant, deficient in pigment production, was screened by complex UV and γ-ray mutagenesis. Medium composition optimization for increased pullulan molecular weight and production was conducted using this mutant. Six nutrients: yeast extract, (NH4)2SO4, K2HPO4, NaCl, MgSO4·7H2O and CaCl2 were detected within pullulan production in flasks. It is shown that NaCl and K2HPO4 have significant influences on molecular weight of pullulan, while yeast extract and (NH4)2SO4 significantly affect pullulan yield. To achieve a higher molecular weight and more efficient pullulan production, a response surface methodology approach was introduced to predict an optimal nutrient combination. A molecular weight of 5.74 × 10(6) and pullulan yield on glucose of 51.30% were obtained under batch pullulan fermentation with the optimized media, which increased molecular weight and pullulan production by 97.25% and 11.04%, respectively compared with the control media. Copyright © 2012 Elsevier Ltd. All rights reserved.

Introductory Molecular Orbital Theory: An Honors General Chemistry Computational Lab as Implemented Using Three-Dimensional Modeling Software

Science.gov (United States)

Ruddick, Kristie R.; Parrill, Abby L.; Petersen, Richard L.

2012-01-01

In this study, a computational molecular orbital theory experiment was implemented in a first-semester honors general chemistry course. Students used the GAMESS (General Atomic and Molecular Electronic Structure System) quantum mechanical software (as implemented in ChemBio3D) to optimize the geometry for various small molecules. Extended Huckel…

Kernel optimization for short-range molecular dynamics

Science.gov (United States)

Hu, Changjun; Wang, Xianmeng; Li, Jianjiang; He, Xinfu; Li, Shigang; Feng, Yangde; Yang, Shaofeng; Bai, He

2017-02-01

To optimize short-range force computations in Molecular Dynamics (MD) simulations, multi-threading and SIMD optimizations are presented in this paper. With respect to multi-threading optimization, a Partition-and-Separate-Calculation (PSC) method is designed to avoid write conflicts caused by using Newton's third law. Serial bottlenecks are eliminated with no additional memory usage. The method is implemented by using the OpenMP model. Furthermore, the PSC method is employed on Intel Xeon Phi coprocessors in both native and offload models. We also evaluate the performance of the PSC method under different thread affinities on the MIC architecture. In the SIMD execution, we explain the performance influence in the PSC method, considering the "if-clause" of the cutoff radius check. The experiment results show that our PSC method is relatively more efficient compared to some traditional methods. In double precision, our 256-bit SIMD implementation is about 3 times faster than the scalar version.

The Mass-Longevity Triangle: Pareto Optimality and the Geometry of Life-History Trait Space

Science.gov (United States)

Szekely, Pablo; Korem, Yael; Moran, Uri; Mayo, Avi; Alon, Uri

2015-01-01

When organisms need to perform multiple tasks they face a fundamental tradeoff: no phenotype can be optimal at all tasks. This situation was recently analyzed using Pareto optimality, showing that tradeoffs between tasks lead to phenotypes distributed on low dimensional polygons in trait space. The vertices of these polygons are archetypes—phenotypes optimal at a single task. This theory was applied to examples from animal morphology and gene expression. Here we ask whether Pareto optimality theory can apply to life history traits, which include longevity, fecundity and mass. To comprehensively explore the geometry of life history trait space, we analyze a dataset of life history traits of 2105 endothermic species. We find that, to a first approximation, life history traits fall on a triangle in log-mass log-longevity space. The vertices of the triangle suggest three archetypal strategies, exemplified by bats, shrews and whales, with specialists near the vertices and generalists in the middle of the triangle. To a second approximation, the data lies in a tetrahedron, whose extra vertex above the mass-longevity triangle suggests a fourth strategy related to carnivory. Each animal species can thus be placed in a coordinate system according to its distance from the archetypes, which may be useful for genome-scale comparative studies of mammalian aging and other biological aspects. We further demonstrate that Pareto optimality can explain a range of previous studies which found animal and plant phenotypes which lie in triangles in trait space. This study demonstrates the applicability of multi-objective optimization principles to understand life history traits and to infer archetypal strategies that suggest why some mammalian species live much longer than others of similar mass. PMID:26465336

The Mass-Longevity Triangle: Pareto Optimality and the Geometry of Life-History Trait Space.

Science.gov (United States)

Szekely, Pablo; Korem, Yael; Moran, Uri; Mayo, Avi; Alon, Uri

2015-10-01

When organisms need to perform multiple tasks they face a fundamental tradeoff: no phenotype can be optimal at all tasks. This situation was recently analyzed using Pareto optimality, showing that tradeoffs between tasks lead to phenotypes distributed on low dimensional polygons in trait space. The vertices of these polygons are archetypes--phenotypes optimal at a single task. This theory was applied to examples from animal morphology and gene expression. Here we ask whether Pareto optimality theory can apply to life history traits, which include longevity, fecundity and mass. To comprehensively explore the geometry of life history trait space, we analyze a dataset of life history traits of 2105 endothermic species. We find that, to a first approximation, life history traits fall on a triangle in log-mass log-longevity space. The vertices of the triangle suggest three archetypal strategies, exemplified by bats, shrews and whales, with specialists near the vertices and generalists in the middle of the triangle. To a second approximation, the data lies in a tetrahedron, whose extra vertex above the mass-longevity triangle suggests a fourth strategy related to carnivory. Each animal species can thus be placed in a coordinate system according to its distance from the archetypes, which may be useful for genome-scale comparative studies of mammalian aging and other biological aspects. We further demonstrate that Pareto optimality can explain a range of previous studies which found animal and plant phenotypes which lie in triangles in trait space. This study demonstrates the applicability of multi-objective optimization principles to understand life history traits and to infer archetypal strategies that suggest why some mammalian species live much longer than others of similar mass.

Exact and Optimal Quantum Mechanics/Molecular Mechanics Boundaries.

Science.gov (United States)

Sun, Qiming; Chan, Garnet Kin-Lic

2014-09-09

Motivated by recent work in density matrix embedding theory, we define exact link orbitals that capture all quantum mechanical (QM) effects across arbitrary quantum mechanics/molecular mechanics (QM/MM) boundaries. Exact link orbitals are rigorously defined from the full QM solution, and their number is equal to the number of orbitals in the primary QM region. Truncating the exact set yields a smaller set of link orbitals optimal with respect to reproducing the primary region density matrix. We use the optimal link orbitals to obtain insight into the limits of QM/MM boundary treatments. We further analyze the popular general hybrid orbital (GHO) QM/MM boundary across a test suite of molecules. We find that GHOs are often good proxies for the most important optimal link orbital, although there is little detailed correlation between the detailed GHO composition and optimal link orbital valence weights. The optimal theory shows that anions and cations cannot be described by a single link orbital. However, expanding to include the second most important optimal link orbital in the boundary recovers an accurate description. The second optimal link orbital takes the chemically intuitive form of a donor or acceptor orbital for charge redistribution, suggesting that optimal link orbitals can be used as interpretative tools for electron transfer. We further find that two optimal link orbitals are also sufficient for boundaries that cut across double bonds. Finally, we suggest how to construct "approximately" optimal link orbitals for practical QM/MM calculations.

Optimization and Control of Bilinear Systems Theory, Algorithms, and Applications

CERN Document Server

Pardalos, Panos M

2008-01-01

Covers developments in bilinear systems theory Focuses on the control of open physical processes functioning in a non-equilibrium mode Emphasis is on three primary disciplines: modern differential geometry, control of dynamical systems, and optimization theory Includes applications to the fields of quantum and molecular computing, control of physical processes, biophysics, superconducting magnetism, and physical information science

Optimized numerical annular flow dryout model using the drift-flux model in tube geometry

International Nuclear Information System (INIS)

Chun, Ji Han; Lee, Un Chul

2008-01-01

Many experimental analyses for annular film dryouts, which is one of the Critical Heat Flux (CHF) mechanisms, have been performed because of their importance. Numerical approaches must also be developed in order to assess the results from experiments and to perform pre-tests before experiments. Various thermal-hydraulic codes, such as RELAP, COBRATF, MARS, etc., have been used in the assessment of the results of dryout experiments and in experimental pre-tests. These thermal-hydraulic codes are general tools intended for the analysis of various phenomena that could appear in nuclear power plants, and many models applying these codes are unnecessarily complex for the focused analysis of dryout phenomena alone. In this study, a numerical model was developed for annular film dryout using the drift-flux model from uniform heated tube geometry. Several candidates of models that strongly affect dryout, such as the entrainment model, deposition model, and the criterion for the dryout point model, were tested as candidates for inclusion in an optimized annular film dryout model. The optimized model was developed by adopting the best combination of these candidate models, as determined through comparison with experimental data. This optimized model showed reasonable results, which were better than those of MARS code

Optimal separable bases and molecular collisions

International Nuclear Information System (INIS)

Poirier, L.W.

1997-12-01

A new methodology is proposed for the efficient determination of Green's functions and eigenstates for quantum systems of two or more dimensions. For a given Hamiltonian, the best possible separable approximation is obtained from the set of all Hilbert space operators. It is shown that this determination itself, as well as the solution of the resultant approximation, are problems of reduced dimensionality for most systems of physical interest. Moreover, the approximate eigenstates constitute the optimal separable basis, in the sense of self-consistent field theory. These distorted waves give rise to a Born series with optimized convergence properties. Analytical results are presented for an application of the method to the two-dimensional shifted harmonic oscillator system. The primary interest however, is quantum reactive scattering in molecular systems. For numerical calculations, the use of distorted waves corresponds to numerical preconditioning. The new methodology therefore gives rise to an optimized preconditioning scheme for the efficient calculation of reactive and inelastic scattering amplitudes, especially at intermediate energies. This scheme is particularly suited to discrete variable representations (DVR's) and iterative sparse matrix methods commonly employed in such calculations. State to state and cumulative reactive scattering results obtained via the optimized preconditioner are presented for the two-dimensional collinear H + H 2 → H 2 + H system. Computational time and memory requirements for this system are drastically reduced in comparison with other methods, and results are obtained for previously prohibitive energy regimes

On the geometry dependence of molecular dimer spectra with an application to aggregates of perylene bisimide

International Nuclear Information System (INIS)

Seibt, J.; Marquetand, P.; Engel, Volker; Chen, Z.; Dehm, V.; Wuerthner, F.

2006-01-01

We study spectroscopic properties of molecular dimers coupled by dipole-dipole interactions within the framework of time-dependent quantum mechanics. A systematic variation of the dimer geometry allows to establish relationships between the latter and structures in the absorption spectrum. The theoretical model is constructed with the purpose to characterize the changes in absorption and emission properties arising upon aggregation of perylene bisimides. Measured and calculated spectra are compared, thereby addressing the question if a simple exciton model is capable to describe excited state properties of nanoaggregates of these molecules

The Mass-Longevity Triangle: Pareto Optimality and the Geometry of Life-History Trait Space.

Directory of Open Access Journals (Sweden)

Pablo Szekely

2015-10-01

Full Text Available When organisms need to perform multiple tasks they face a fundamental tradeoff: no phenotype can be optimal at all tasks. This situation was recently analyzed using Pareto optimality, showing that tradeoffs between tasks lead to phenotypes distributed on low dimensional polygons in trait space. The vertices of these polygons are archetypes--phenotypes optimal at a single task. This theory was applied to examples from animal morphology and gene expression. Here we ask whether Pareto optimality theory can apply to life history traits, which include longevity, fecundity and mass. To comprehensively explore the geometry of life history trait space, we analyze a dataset of life history traits of 2105 endothermic species. We find that, to a first approximation, life history traits fall on a triangle in log-mass log-longevity space. The vertices of the triangle suggest three archetypal strategies, exemplified by bats, shrews and whales, with specialists near the vertices and generalists in the middle of the triangle. To a second approximation, the data lies in a tetrahedron, whose extra vertex above the mass-longevity triangle suggests a fourth strategy related to carnivory. Each animal species can thus be placed in a coordinate system according to its distance from the archetypes, which may be useful for genome-scale comparative studies of mammalian aging and other biological aspects. We further demonstrate that Pareto optimality can explain a range of previous studies which found animal and plant phenotypes which lie in triangles in trait space. This study demonstrates the applicability of multi-objective optimization principles to understand life history traits and to infer archetypal strategies that suggest why some mammalian species live much longer than others of similar mass.

Development of Geometry Optimization Methodology with In-house CFD code, and Challenge in Applying to Fuel Assembly

International Nuclear Information System (INIS)

Jeong, J. H.; Lee, K. L.

2016-01-01

The wire spacer has important roles to avoid collisions between adjacent rods, to mitigate a vortex induced vibration, and to enhance convective heat transfer by wire spacer induced secondary flow. Many experimental and numerical works has been conducted to understand the thermal-hydraulics of the wire-wrapped fuel bundles. There has been enormous growth in computing capability. Recently, a huge increase of computer power allows to three-dimensional simulation of thermal-hydraulics of wire-wrapped fuel bundles. In this study, the geometry optimization methodology with RANS based in-house CFD (Computational Fluid Dynamics) code has been successfully developed in air condition. In order to apply the developed methodology to fuel assembly, GGI (General Grid Interface) function is developed for in-house CFD code. Furthermore, three-dimensional flow fields calculated with in-house CFD code are compared with those calculated with general purpose commercial CFD solver, CFX. The geometry optimization methodology with RANS based in-house CFD code has been successfully developed in air condition. In order to apply the developed methodology to fuel assembly, GGI function is developed for in-house CFD code as same as CFX. Even though both analyses are conducted with same computational meshes, numerical error due to GGI function locally occurred in only CFX solver around rod surface and boundary region between inner fluid region and outer fluid region.

Design of optimal laser pulses to control molecular rovibrational ...

Indian Academy of Sciences (India)

Optimal control theory in combination with time-dependent quantum dynamics is employed to design laser ... area of quantum computing,22 use of molecular states of various systems ..... frequency) and ωv=0, j=1→v=1, j=0, along with small con- tributions from ... discussed here for three rovibrational excitation pro- cesses.

The packing of soft materials: Molecular asymmetry, geometric frustration and optimal lattices in block copolymer melts

International Nuclear Information System (INIS)

Grason, Gregory M.

2006-01-01

Block copolymer systems are well known for their ability to self-assemble into a wide array of periodic structures. Due to the abundance and adaptability of physical theories describing polymers, this system is ideal for the development of robust and testible predictions about amphiphilic self-assembly phenomena at large. We review the results of field-theoretic treatments of block copolymer melts, with the aim of understanding how self-assembly in this system can be understood in terms of optimal lattice geometry. The self-consistent (mean) field theory of block copolymer melts as well as its low temperature limit, strong-segregation theory, are presented in detail, highlighting the special role played by asymmetry in the copolymer architecture. Special attention is paid to micellar configurations, where a well-defined and simple notion of optimal lattice geometry emerges from a particular asymptotic limit of the full self-consistent field theory. In this limit, the stability of competing arrangements of copolymer micelles can be assessed in terms of two discrete measures of the lattice geometry, emphasizing the non-trivial coupling between the internal configurations of the fundamentally soft micelles and the periodic symmetry of the lattice

Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

Directory of Open Access Journals (Sweden)

Renata De Paris

2015-01-01

Full Text Available Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

Optimization of weld bead geometry of MS plate

Indian Academy of Sciences (India)

The considered specimen was checked to harmonize the optimum setting between input factors, for example, welding current, open circuit voltage, and thickness of plate, with respect to obtaining prosperous weld strength as well as bead geometry quality characteristics, for example, tensile strength, bead width, ...

FTIR and FT-Raman spectra and density functional computations of the vibrational spectra, molecular geometry and atomic charges of the biomolecule: 5-bromouracil

Czech Academy of Sciences Publication Activity Database

Rastogi, V.K.; Palafox, M. A.; Mittal, L.; Peica, N.; Keifer, W.; Lang, Kamil; Ojha, S.P.

2007-01-01

Roč. 38, č. 10 (2007), s. 1227-1241 ISSN 0377-0486 Institutional research plan: CEZ:AV0Z40320502 Keywords : FTIR and FT-Raman spectra * density functional computations * molecular geometry Subject RIV: CA - Inorganic Chemistry Impact factor: 3.514, year: 2007

Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

DEFF Research Database (Denmark)

Svendsen, Casper Steinmann; Jensen, Jan; Fedorov, Dmitri

2013-01-01

We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of ...

Optimization of tensile method and specimen geometry in modified ring tensile test

International Nuclear Information System (INIS)

Kitano, Koji; Fuketa, Toyoshi; Sasajima, Hideo; Uetsuka, Hiroshi

2001-03-01

Several techniques in ring tensile test are proposed in order to evaluate mechanical properties of cladding under hoop loading condition caused by pellet/cladding mechanical interaction (PCMI). In the modified techniques, variety of tensile methods and specimen geometry are being proposed in order to limit deformation within the gauge section. However, the tensile method and the specimen geometry were not determined in the modified techniques. In the present study, we have investigated the tensile method and the specimen geometry through finite element method (FEM) analysis of specimen deformation and tensile test on specimens with various gauge section geometries. In using two-piece tensile tooling, the mechanical properties under hoop loading condition can be correctly evaluated when deformation part (gauge section) is put on the top of a half-mandrel, and friction between the specimen and the half-mandrel is reduced with Teflon tape. In addition, we have shown the optimum specimen geometry for PWR 17 by 17 type cladding. (author)

Lectures on discrete geometry

CERN Document Server

2002-01-01

Discrete geometry investigates combinatorial properties of configurations of geometric objects. To a working mathematician or computer scientist, it offers sophisticated results and techniques of great diversity and it is a foundation for fields such as computational geometry or combinatorial optimization. This book is primarily a textbook introduction to various areas of discrete geometry. In each area, it explains several key results and methods, in an accessible and concrete manner. It also contains more advanced material in separate sections and thus it can serve as a collection of surveys in several narrower subfields. The main topics include: basics on convex sets, convex polytopes, and hyperplane arrangements; combinatorial complexity of geometric configurations; intersection patterns and transversals of convex sets; geometric Ramsey-type results; polyhedral combinatorics and high-dimensional convexity; and lastly, embeddings of finite metric spaces into normed spaces. Jiri Matousek is Professor of Com...

Theoretical investigation on current-voltage characteristics in all-carbon molecular device with different contact geometries

International Nuclear Information System (INIS)

Ye Fuqiu; Fan Zhiqiang; He Jun; Peng Jun; Tang Liming

2012-01-01

Applying nonequilibrium Green's functions in combination with the first-principles density-functional theory, we investigate electronic transport properties of an all-carbon molecular device consisting of one phenalenyl molecule and two zigzag graphene nanoribbons. The results show that the electronic transport properties are strongly dependent on the contact geometry and device's currents can drop obviously when the connect sites change from second-nearest sites from the central atom of the molecule (S site) to third-nearest sites from the central atom of the molecule (T site). More importantly, the negative differential resistance behavior is only observed on the negative bias region when the molecule connects the graphene nanoribbons through two T sites.

Geometry of quantum computation with qutrits.

Science.gov (United States)

Li, Bin; Yu, Zu-Huan; Fei, Shao-Ming

2013-01-01

Determining the quantum circuit complexity of a unitary operation is an important problem in quantum computation. By using the mathematical techniques of Riemannian geometry, we investigate the efficient quantum circuits in quantum computation with n qutrits. We show that the optimal quantum circuits are essentially equivalent to the shortest path between two points in a certain curved geometry of SU(3(n)). As an example, three-qutrit systems are investigated in detail.

A new decomposition-based computer-aided molecular/mixture design methodology for the design of optimal solvents and solvent mixtures

DEFF Research Database (Denmark)

Karunanithi, A.T.; Achenie, L.E.K.; Gani, Rafiqul

2005-01-01

This paper presents a novel computer-aided molecular/mixture design (CAMD) methodology for the design of optimal solvents and solvent mixtures. The molecular/mixture design problem is formulated as a mixed integer nonlinear programming (MINLP) model in which a performance objective is to be optim......This paper presents a novel computer-aided molecular/mixture design (CAMD) methodology for the design of optimal solvents and solvent mixtures. The molecular/mixture design problem is formulated as a mixed integer nonlinear programming (MINLP) model in which a performance objective...... is to be optimized subject to structural, property, and process constraints. The general molecular/mixture design problem is divided into two parts. For optimal single-compound design, the first part is solved. For mixture design, the single-compound design is first carried out to identify candidates...... and then the second part is solved to determine the optimal mixture. The decomposition of the CAMD MINLP model into relatively easy to solve subproblems is essentially a partitioning of the constraints from the original set. This approach is illustrated through two case studies. The first case study involves...

Spinning geometry = Twisted geometry

International Nuclear Information System (INIS)

Freidel, Laurent; Ziprick, Jonathan

2014-01-01

It is well known that the SU(2)-gauge invariant phase space of loop gravity can be represented in terms of twisted geometries. These are piecewise-linear-flat geometries obtained by gluing together polyhedra, but the resulting geometries are not continuous across the faces. Here we show that this phase space can also be represented by continuous, piecewise-flat three-geometries called spinning geometries. These are composed of metric-flat three-cells glued together consistently. The geometry of each cell and the manner in which they are glued is compatible with the choice of fluxes and holonomies. We first remark that the fluxes provide each edge with an angular momentum. By studying the piecewise-flat geometries which minimize edge lengths, we show that these angular momenta can be literally interpreted as the spin of the edges: the geometries of all edges are necessarily helices. We also show that the compatibility of the gluing maps with the holonomy data results in the same conclusion. This shows that a spinning geometry represents a way to glue together the three-cells of a twisted geometry to form a continuous geometry which represents a point in the loop gravity phase space. (paper)

Bonding and compressibility in molecular and polymeric phases of solid CO2

International Nuclear Information System (INIS)

Gracia, L; Marques, M; Beltran, A; Pendas, A Martin; Recio, J M

2004-01-01

We present the results of a theoretical study of the response of molecular CO 2 -I and CO 2 -III, and polymeric CO 2 -V polymorphs to hydrostatic pressure. Total energy calculations and geometry optimizations have been performed under the local density functional approximation combining a pseudopotential and planewave scheme as implemented in the VASP code. Using the atoms in molecules theory, the network of inter- and intra-molecular chemical bonds of the different phases are rigorously characterized in terms of the values of the electron density and the Laplacian at the bond critical points. The chemical graph of a hypothetical orthorhombic structure displays bonding features that are associated with a precursor geometry of polymeric carbon four-fold coordinated phases. In addition, the bulk compressibility is decomposed into atomic and molecular contributions with the aim of providing a better understanding of the reasons that explain the emergence of low compressible polymorphs at high pressures

Molecular models of zinc phthalocyanines: semi-empirical molecular orbital computations and physicochemical properties studied by molecular mechanics simulations

International Nuclear Information System (INIS)

Gantchev, Tsvetan G.; van Lier, Johan E.; Hunting, Darel J.

2005-01-01

To build 3D-molecular models of Zinc-phthalocyanines (ZnPc) and to study their diverse chemical and photosensitization properties, we performed quantum mechanical molecular orbital (MO) semi-empirical (AM1) computations of the ground, excited singlet and triplet states as well as free radical (ionic) species. RHF and UHF (open shell) geometry optimizations led to near-perfect symmetrical ZnPc. Predicted ionization potentials (IP), electron affinities (EA) and lowest electronic transitions of ZnPc are in good agreement with the published experimental and theoretical data. The computation-derived D 4h /D 2h -symmetry 3D-structures of ground and excited states and free radicals of ZnPc, together with the frontier orbital energies and Mulliken electron population analysis enabled us to build robust molecular models. These models were used to predict important chemical-reactivity entities such as global electronegativity (χ), hardness (η) and local softness based on Fukui-functions analysis. Examples of molecular mechanics (MM) applications of the 3D-molecular models are presented as approaches to evaluate solvation free energy (ΔG 0 ) solv and to estimate ground- and excited- state oxidation/reduction potentials as well as intermolecular interactions and stability of ground and excited state dimers (exciplexes) and radical ion-pairs

GAUSSIAN 76: an ab initio molecular orbital program

International Nuclear Information System (INIS)

Binkley, J.S.; Whiteside, R.; Hariharan, P.C.; Seeger, R.; Hehre, W.J.; Lathan, W.A.; Newton, M.D.; Ditchfield, R.; Pople, J.A.

Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans

Application of Numerical Optimization Methods to Perform Molecular Docking on Graphics Processing Units

Directory of Open Access Journals (Sweden)

M. A. Farkov

2014-01-01

Full Text Available An analysis of numerical optimization methods for solving a problem of molecular docking has been performed. Some additional requirements for optimization methods according to GPU architecture features were specified. A promising method for implementation on GPU was selected. Its implementation was described and performance and accuracy tests were performed.

Geometric control theory and sub-Riemannian geometry

CERN Document Server

Boscain, Ugo; Gauthier, Jean-Paul; Sarychev, Andrey; Sigalotti, Mario

2014-01-01

This volume presents recent advances in the interaction between Geometric Control Theory and sub-Riemannian geometry. On the one hand, Geometric Control Theory used the differential geometric and Lie algebraic language for studying controllability, motion planning, stabilizability and optimality for control systems. The geometric approach turned out to be fruitful in applications to robotics, vision modeling, mathematical physics etc. On the other hand, Riemannian geometry and its generalizations, such as  sub-Riemannian, Finslerian  geometry etc., have been actively adopting methods developed in the scope of geometric control. Application of these methods  has led to important results regarding geometry of sub-Riemannian spaces, regularity of sub-Riemannian distances, properties of the group  of diffeomorphisms of sub-Riemannian manifolds, local geometry and equivalence of distributions and sub-Riemannian structures, regularity of the Hausdorff volume.

Validation and extraction of molecular-geometry information from small-molecule databases.

Science.gov (United States)

Long, Fei; Nicholls, Robert A; Emsley, Paul; Graǽulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Murshudov, Garib N

2017-02-01

A freely available small-molecule structure database, the Crystallography Open Database (COD), is used for the extraction of molecular-geometry information on small-molecule compounds. The results are used for the generation of new ligand descriptions, which are subsequently used by macromolecular model-building and structure-refinement software. To increase the reliability of the derived data, and therefore the new ligand descriptions, the entries from this database were subjected to very strict validation. The selection criteria made sure that the crystal structures used to derive atom types, bond and angle classes are of sufficiently high quality. Any suspicious entries at a crystal or molecular level were removed from further consideration. The selection criteria included (i) the resolution of the data used for refinement (entries solved at 0.84 Å resolution or higher) and (ii) the structure-solution method (structures must be from a single-crystal experiment and all atoms of generated molecules must have full occupancies), as well as basic sanity checks such as (iii) consistency between the valences and the number of connections between atoms, (iv) acceptable bond-length deviations from the expected values and (v) detection of atomic collisions. The derived atom types and bond classes were then validated using high-order moment-based statistical techniques. The results of the statistical analyses were fed back to fine-tune the atom typing. The developed procedure was repeated four times, resulting in fine-grained atom typing, bond and angle classes. The procedure will be repeated in the future as and when new entries are deposited in the COD. The whole procedure can also be applied to any source of small-molecule structures, including the Cambridge Structural Database and the ZINC database.

Differential geometry based multiscale models.

Science.gov (United States)

Wei, Guo-Wei

2010-08-01

Large chemical and biological systems such as fuel cells, ion channels, molecular motors, and viruses are of great importance to the scientific community and public health. Typically, these complex systems in conjunction with their aquatic environment pose a fabulous challenge to theoretical description, simulation, and prediction. In this work, we propose a differential geometry based multiscale paradigm to model complex macromolecular systems, and to put macroscopic and microscopic descriptions on an equal footing. In our approach, the differential geometry theory of surfaces and geometric measure theory are employed as a natural means to couple the macroscopic continuum mechanical description of the aquatic environment with the microscopic discrete atomistic description of the macromolecule. Multiscale free energy functionals, or multiscale action functionals are constructed as a unified framework to derive the governing equations for the dynamics of different scales and different descriptions. Two types of aqueous macromolecular complexes, ones that are near equilibrium and others that are far from equilibrium, are considered in our formulations. We show that generalized Navier-Stokes equations for the fluid dynamics, generalized Poisson equations or generalized Poisson-Boltzmann equations for electrostatic interactions, and Newton's equation for the molecular dynamics can be derived by the least action principle. These equations are coupled through the continuum-discrete interface whose dynamics is governed by potential driven geometric flows. Comparison is given to classical descriptions of the fluid and electrostatic interactions without geometric flow based micro-macro interfaces. The detailed balance of forces is emphasized in the present work. We further extend the proposed multiscale paradigm to micro-macro analysis of electrohydrodynamics, electrophoresis, fuel cells, and ion channels. We derive generalized Poisson-Nernst-Planck equations that are

Differential Geometry Based Multiscale Models

Science.gov (United States)

Wei, Guo-Wei

2010-01-01

Large chemical and biological systems such as fuel cells, ion channels, molecular motors, and viruses are of great importance to the scientific community and public health. Typically, these complex systems in conjunction with their aquatic environment pose a fabulous challenge to theoretical description, simulation, and prediction. In this work, we propose a differential geometry based multiscale paradigm to model complex macromolecular systems, and to put macroscopic and microscopic descriptions on an equal footing. In our approach, the differential geometry theory of surfaces and geometric measure theory are employed as a natural means to couple the macroscopic continuum mechanical description of the aquatic environment with the microscopic discrete atom-istic description of the macromolecule. Multiscale free energy functionals, or multiscale action functionals are constructed as a unified framework to derive the governing equations for the dynamics of different scales and different descriptions. Two types of aqueous macromolecular complexes, ones that are near equilibrium and others that are far from equilibrium, are considered in our formulations. We show that generalized Navier–Stokes equations for the fluid dynamics, generalized Poisson equations or generalized Poisson–Boltzmann equations for electrostatic interactions, and Newton's equation for the molecular dynamics can be derived by the least action principle. These equations are coupled through the continuum-discrete interface whose dynamics is governed by potential driven geometric flows. Comparison is given to classical descriptions of the fluid and electrostatic interactions without geometric flow based micro-macro interfaces. The detailed balance of forces is emphasized in the present work. We further extend the proposed multiscale paradigm to micro-macro analysis of electrohydrodynamics, electrophoresis, fuel cells, and ion channels. We derive generalized Poisson–Nernst–Planck equations that

Study of geometries of active magnetic regenerators for room temperature magnetocaloric refrigeration

DEFF Research Database (Denmark)

Lei, Tian; Engelbrecht, Kurt; Nielsen, Kaspar Kirstein

2017-01-01

Room temperature magnetic refrigeration has attracted substantial attention during the past decades and continuing to increase the performance of active magnetic regenerators (AMR) is of great interest. Optimizing the regenerator geometry and related operating parameters is a practical and effect......Room temperature magnetic refrigeration has attracted substantial attention during the past decades and continuing to increase the performance of active magnetic regenerators (AMR) is of great interest. Optimizing the regenerator geometry and related operating parameters is a practical...... and effective way to obtain the desired cooling performance. To investigate how to choose and optimize the AMR geometry, a quantitative study is presented by simulations based on a one-dimensional (1D) numerical model. Correlations for calculating the friction factor and heat transfer coefficient are reviewed...... and chosen for modeling different geometries. Moreover, the simulated impacts of various parameters on the regenerator efficiency with a constant specific cooling capacity are presented. An analysis based on entropy production minimization reveals how those parameters affect the main losses occurring inside...

Model-Based Optimization of Scaffold Geometry and Operating Conditions of Radial Flow Packed-Bed Bioreactors for Therapeutic Applications

Directory of Open Access Journals (Sweden)

Danilo Donato

2014-01-01

Full Text Available Radial flow perfusion of cell-seeded hollow cylindrical porous scaffolds may overcome the transport limitations of pure diffusion and direct axial perfusion in the realization of bioengineered substitutes of failing or missing tissues. Little has been reported on the optimization criteria of such bioreactors. A steady-state model was developed, combining convective and dispersive transport of dissolved oxygen with Michaelis-Menten cellular consumption kinetics. Dimensional analysis was used to combine more effectively geometric and operational variables in the dimensionless groups determining bioreactor performance. The effectiveness of cell oxygenation was expressed in terms of non-hypoxic fractional construct volume. The model permits the optimization of the geometry of hollow cylindrical constructs, and direction and magnitude of perfusion flow, to ensure cell oxygenation and culture at controlled oxygen concentration profiles. This may help engineer tissues suitable for therapeutic and drug screening purposes.

The molecular, electronic structures and vibrational spectra of metal-free, N,N'-dideuterio and magnesium tetra-2,3-pyridino-porphyrazines: Density functional calculations.

Science.gov (United States)

Liu, Zhongqiang; Zhang, Xianxi; Zhang, Yuexing; Li, Renjie; Jiang, Jianzhuang

2006-10-01

A theoretical investigation of the fully optimized geometries and electronic structures of the metal-free (TPdPzH(2)), N,N'-dideuterio (TPdPzD(2)), and magnesium (TPdPzMg) tetra-2,3-pyridino-porphyrazine has been conducted based on density functional theory. The optimized geometries at density functional theory level for these compounds are reported here for the first time. A comparison between the different molecules for the geometry, molecular orbital, and atomic charge is made. The substituent effect of the N atoms on the molecular structures of these compounds is discussed. The IR and Raman spectra for these three compounds have also been calculated at density functional B3LYP level using the 6-31G(d) basis set. Detailed assignments of the NH, NM, and pyridine ring vibrational bands in the IR and Raman spectra have been made based on assistance of animated pictures. The simulated IR spectra of TPdPzH(2) are compared with the experimental absorption spectra, and very good consistency has been found. The isotope effect on the IR and Raman spectra is also discussed.

DOGBONE GEOMETRY FOR RECIRCULATING ACCELERATORS

International Nuclear Information System (INIS)

BERG, J.S.; JOHNSTONE, C.; SUMMERS, D.

2001-01-01

Most scenarios for accelerating muons require recirculating acceleration. A racetrack shape for the accelerator requires particles with lower energy in early passes to traverse almost the same length of arc as particles with the highest energy. This extra arc length may lead to excess decays and excess cost. Changing the geometry to a dogbone shape, where there is a single linac and the beam turns completely around at the end of the linac, returning to the same end of the linac from which it exited, addresses this problem. In this design, the arc lengths can be proportional to the particle's momentum. This paper proposes an approximate cost model for a recirculating accelerator, attempts to make cost-optimized designs for both racetrack and dogbone geometries, and demonstrates that the dogbone geometry does appear to be more cost effective

The Persistification of the ATLAS Geometry

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00068562; The ATLAS collaboration; Bianchi, Riccardo-Maria

2016-01-01

The complex geometry of the whole detector of the ATLAS experiment at LHC is currently stored only in custom online databases, from which it is built on-the- y on request. Accessing the online geometry guarantees accessing the latest version of the detector description, but requires the setup of the full ATLAS so ware framework “Athena”, which provides the online services and the tools to retrieve the data from the database. is operation is cumbersome and slows down the applications that need to access the geometry. Moreover, all applications that need to access the detector geom- etry need to be built and run on the same platform as the ATLAS framework, preventing the usage of the actual detector geometry in stand-alone applications. Here we propose a new mechanism to persistify and serve the geometry of HEP experiments. e new mechanism is composed by a new le format and a REST API. e new le format allows to store the whole detector description locally in a at le, and it is especially optimized to descri...

Non-euclidean simplex optimization

International Nuclear Information System (INIS)

Silver, G.L.

1977-01-01

Geometric optimization techniques useful for studying chemical equilibrium traditionally rely upon principles of euclidean geometry, but such algorithms may also be based upon principles of a non-euclidean geometry. The sequential simplex method is adapted to the hyperbolic plane, and application of optimization to problems such as the potentiometric titration of plutonium is suggested

Fletcher-Reeves based Particle Swarm Optimization for prediction of molecular structure.

Science.gov (United States)

Agrawal, Shikha; Silakari, Sanjay

2014-04-01

The determination of the most stable conformers of a molecule can be formulated as a global optimization problem. Knowing the stable conformers of a molecule is important because it allows us to understand its properties and behavior based on its structure. The most stable conformation is that involving the global minimum of potential energy. The problem of finding this global minimum is highly complex, and is computationally difficult because of the number of local minima, which grows exponentially with molecular size. In this paper, we propose a hybrid approach combining Particle Swarm Optimization (PSO) and the Fletcher-Reeves algorithm to minimize the potential energy function. The proposed hybrid algorithm is applied to a simplified molecular potential energy function in problems with up to 100 degrees of freedom and also to a realistic potential energy function modeling a pseudoethane molecule. The computational results for both the cases show that the proposed method performs significantly better than the other algorithms. Copyright © 2014 Elsevier Inc. All rights reserved.

Thermodynamic optimization of geometry in engineering flow systems

Energy Technology Data Exchange (ETDEWEB)

Bejan, A.; Jones, J.A. [Duke Univ., Durham, NC (United States)

2000-07-01

This review draws attention to an emerging body of work that relies on global thermodynamic optimization in the pursuit of flow system architecture. Exergy analysis establishes the theoretical performance limit. Thermodynamic optimization (or entropy generation minimization) brings the design as closely as permissible to the theoretical limit. The design is destined to remain imperfect because of constraints (finite sizes, times, and costs). Improvements are registered by spreading the imperfection (e.g., flow resistances) through the system. Resistances compete against each other and must be optimized together. Optimal spreading means spatial distribution, geometric form, topology, and geography. System architecture springs out of constrained global optimization. The principle is illustrated by simple examples: the optimization of dimensions, spacings, and the distribution (allocation) of heat transfer surface to the two heat exchangers of a power plant. Similar opportunities for deducing flow architecture exist in more complex systems for power and refrigeration. Examples show that the complete structure of heat exchangers for environmental control systems of aircraft can be derived based on this principle. (authors)

Analytical free energy gradient for the molecular Ornstein-Zernike self-consistent-field method

Directory of Open Access Journals (Sweden)

N.Yoshida

2007-09-01

Full Text Available An analytical free energy gradient for the molecular Ornstein-Zernike self-consistent-field (MOZ-SCF method is presented. MOZ-SCF theory is one of the theories to considering the solvent effects on the solute electronic structure in solution. [Yoshida N. et al., J. Chem. Phys., 2000, 113, 4974] Molecular geometries of water, formaldehyde, acetonitrile and acetone in water are optimized by analytical energy gradient formula. The results are compared with those from the polarizable continuum model (PCM, the reference interaction site model (RISM-SCF and the three dimensional (3D RISM-SCF.

General Geometry and Geometry of Electromagnetism

OpenAIRE

Shahverdiyev, Shervgi S.

2002-01-01

It is shown that Electromagnetism creates geometry different from Riemannian geometry. General geometry including Riemannian geometry as a special case is constructed. It is proven that the most simplest special case of General Geometry is geometry underlying Electromagnetism. Action for electromagnetic field and Maxwell equations are derived from curvature function of geometry underlying Electromagnetism. And it is shown that equation of motion for a particle interacting with electromagnetic...

Computer-optimized γ-NDA geometries for uranium enrichment verification of gaseous UF6

International Nuclear Information System (INIS)

Wichers, V.A.; Aaldijk, J.K.; Betue, P.A.C. de; Harry, R.J.S.

1993-05-01

An improved collimator pair of novel design tailored for deposit independent enrichment verification of gaseous UF 6 at low pressures in cascade-to-header pipes of small diameters in centrifuge enrichment plants is presented. The designs are adapted for use in a dual-geometry arrangement for simultaneous measurements with both detection geometries. The average measurement time with the dual-geometry arrangement is approximately half an hour for deposit-to-gas activity ratios as high as 20. (orig.)

Machine learning spatial geometry from entanglement features

Science.gov (United States)

You, Yi-Zhuang; Yang, Zhao; Qi, Xiao-Liang

2018-02-01

Motivated by the close relations of the renormalization group with both the holography duality and the deep learning, we propose that the holographic geometry can emerge from deep learning the entanglement feature of a quantum many-body state. We develop a concrete algorithm, call the entanglement feature learning (EFL), based on the random tensor network (RTN) model for the tensor network holography. We show that each RTN can be mapped to a Boltzmann machine, trained by the entanglement entropies over all subregions of a given quantum many-body state. The goal is to construct the optimal RTN that best reproduce the entanglement feature. The RTN geometry can then be interpreted as the emergent holographic geometry. We demonstrate the EFL algorithm on a 1D free fermion system and observe the emergence of the hyperbolic geometry (AdS3 spatial geometry) as we tune the fermion system towards the gapless critical point (CFT2 point).

Development and application of CATIA-GDML geometry builder

International Nuclear Information System (INIS)

Belogurov, S; Chernogorov, A; Ovcharenko, E; Schetinin, V; Berchun, Yu; Malzacher, P

2014-01-01

Due to conceptual difference between geometry descriptions in Computer-Aided Design (CAD) systems and particle transport Monte Carlo (MC) codes direct conversion of detector geometry in either direction is not feasible. The paper presents an update on functionality and application practice of the CATIA-GDML geometry builder first introduced at CHEP2010. This set of CATIAv5 tools has been developed for building a MC optimized GEANT4/ROOT compatible geometry based on the existing CAD model. The model can be exported via Geometry Description Markup Language (GDML). The builder allows also import and visualization of GEANT4/ROOT geometries in CATIA. The structure of a GDML file, including replicated volumes, volume assemblies and variables, is mapped into a part specification tree. A dedicated file template, a wide range of primitives, tools for measurement and implicit calculation of parameters, different types of multiple volume instantiation, mirroring, positioning and quality check have been implemented. Several use cases are discussed.

Geometry Optimization of an Overtopping Wave Energy Device Implemented into the New Breakwater of the Hanstholm Port Expansion

DEFF Research Database (Denmark)

Margheritini, Lucia; Stratigaki, Vasiliki; Troch, Peter

2012-01-01

breakwater is 1.5 km and the water depth ranges approximately from 8.0 m up to 14 m with localized influences on the wave climate. The study is conducted numerically in order to present the expected power production and overall performance of the SSG breakwater in Hanstholm. The price par kWh is also......The study presented here describes the geometry optimization of the Sea wave Slot cone Generator (SSG) overtopping wave energy converter as part of the feasibility study for the implementation of the device in the development plan of Hanstholm harbour in Denmark. The total length of the new planned...

Rheumatoid arthritis is associated with less optimal hip structural geometry.

Science.gov (United States)

Wright, Nicole C; Lisse, Jeffrey R; Beck, Thomas J; Sherrill, Duane L; Mohler, M Jane; Bassford, Tamsen; Cauley, Jane A; Lacroix, Andrea Z; Lewis, Cora E; Chen, Zhao

2012-01-01

The overall goal of this study was to assess the longitudinal changes in bone strength in women reporting rheumatoid arthritis (RA; n=78) compared with nonarthritic control participants (n=4779) of the Women's Health Initiative bone mineral density (WHI-BMD) subcohort. Hip structural analysis program was applied to archived dual-energy X-ray absorptiometry scans (baseline, years 3, 6, and 9) to estimate bone mineral density (BMD) and hip structural geometry parameters in 3 femoral regions: narrow neck (NN), intertrochanteric (IT), and shaft (S). The association between RA and hip structural geometry was tested using linear regression and random coefficient models. Compared with the nonarthritic control, the RA group had a lower BMD (p=0.061) and significantly lower outer diameter (p=0.017), cross-sectional area (p=0.004), and section modulus (p=0.035) at the NN region in the longitudinal models. No significant associations were seen at the IT regions or S regions, and the association was not modified by age, ethnicity, glucocorticoid use, or time. Within the WHI-BMD, women with RA group had reduced BMD and structural geometry at baseline, and this reduction was seen at a fixed rate throughout the 9 yr of study. Copyright © 2012 The International Society for Clinical Densitometry. Published by Elsevier Inc. All rights reserved.

Application of Nontraditional Optimization Techniques for Airfoil Shape Optimization

Directory of Open Access Journals (Sweden)

R. Mukesh

2012-01-01

Full Text Available The method of optimization algorithms is one of the most important parameters which will strongly influence the fidelity of the solution during an aerodynamic shape optimization problem. Nowadays, various optimization methods, such as genetic algorithm (GA, simulated annealing (SA, and particle swarm optimization (PSO, are more widely employed to solve the aerodynamic shape optimization problems. In addition to the optimization method, the geometry parameterization becomes an important factor to be considered during the aerodynamic shape optimization process. The objective of this work is to introduce the knowledge of describing general airfoil geometry using twelve parameters by representing its shape as a polynomial function and coupling this approach with flow solution and optimization algorithms. An aerodynamic shape optimization problem is formulated for NACA 0012 airfoil and solved using the methods of simulated annealing and genetic algorithm for 5.0 deg angle of attack. The results show that the simulated annealing optimization scheme is more effective in finding the optimum solution among the various possible solutions. It is also found that the SA shows more exploitation characteristics as compared to the GA which is considered to be more effective explorer.

Photoionization and molecular structure

International Nuclear Information System (INIS)

Palma, A.

1983-01-01

A presentation is here given of the theoretical work on photoionization and molecular structure carried out by the author and coworkers. The implications of the photoionization process on the molecular geometry are emphasized. In particular, the ionization effect on deep orbitals is considered and it is shown that, contrary to traditional thinking, these orbitals have relevant effects on the molecular geometry. The problem of calculating photoionization relative intensities for the full spectrum is also considered, and the results of the present model are compared with experimental and other theoretical results. (author)

Computational geometry lectures at the morningside center of mathematics

CERN Document Server

Wang, Ren-Hong

2003-01-01

Computational geometry is a borderline subject related to pure and applied mathematics, computer science, and engineering. The book contains articles on various topics in computational geometry, which are based on invited lectures and some contributed papers presented by researchers working during the program on Computational Geometry at the Morningside Center of Mathematics of the Chinese Academy of Science. The opening article by R.-H. Wang gives a nice survey of various aspects of computational geometry, many of which are discussed in more detail in other papers in the volume. The topics include problems of optimal triangulation, splines, data interpolation, problems of curve and surface design, problems of shape control, quantum teleportation, and others.

Optimizing a neutron-beam focusing device for the direct geometry time-of-flight spectrometer TOFTOF at the FRM II reactor source

DEFF Research Database (Denmark)

Rasmussen, N. G.; Simeoni, G. G.; Lefmann, K.

2016-01-01

A dedicated beam-focusing device has been designed for the direct geometry thermal-cold neutron time-of-flight spectrometer TOFTOF at the neutron facility FRM II (Garching, Germany). The prototype, based on the compressed Archimedes' mirror concept, benefits from the adaptive-optics technology (a...... than 3.5 would have only marginal influence on the optimal behaviour, whereas comparable spectrometers could take advantage of longer focusing segments, with particular impact for the thermal region of the neutron spectrum....

Optimization of geometry for X-ray analysis of rare earth materials

International Nuclear Information System (INIS)

Lal, M.; Choudhury, R.K.; Agrawal, R.M.

1987-01-01

A method of sample excitation is proposed for obtaining good sensitivity and detection limits for rare earth elements (57 241 Am radioisotope source. Detection limits of about 100-300 ng for most of the elements using a thin multi-element sample on a Mylar backing are obtained for a counting time of 1h with a 100 mCi source. The configuration employed is a close-coupled collimated side source geometry in which the sample is mounted at 45 0 to the plane of the detector. A comparative study of the performance of different source geometries using both Mylar- and cellulose-based samples is described. (author)

Molecular diodes in optical rectennas

Science.gov (United States)

Duché, David; Palanchoke, Ujwol; Terracciano, Luigi; Dang, Florian-Xuan; Patrone, Lionel; Le Rouzo, Judikael; Balaban, Téodore Silviu; Alfonso, Claude; Charai, Ahmed; Margeat, Olivier; Ackermann, Jorg; Gourgon, Cécile; Simon, Jean-Jacques; Escoubas, Ludovic

2016-09-01

The photo conversion efficiencies of the 1st and 2nd generat ion photovoltaic solar cells are limited by the physical phenomena involved during the photo-conversion processes. An upper limit around 30% has been predicted for a monojunction silicon solar cell. In this work, we study 3rd generation solar cells named rectenna which could direct ly convert visible and infrared light into DC current. The rectenna technology is at odds with the actual photovoltaic technologies, since it is not based on the use of semi-conducting materials. We study a rectenna architecture consist ing of plasmonic nano-antennas associated with rectifying self assembled molecular diodes. We first opt imized the geometry of plasmonic nano-antennas using an FDTD method. The optimal antennas are then realized using a nano-imprint process and associated with self assembled molecular diodes in 11- ferrocenyl-undecanethiol. Finally, The I(V) characterist ics in darkness of the rectennas has been carried out using an STM. The molecular diodes exhibit averaged rect ification ratios of 5.

Spectroscopic and molecular modeling studies of N-(4-(3-methyl-3-phenylcyclobutyl-3-phenylthiazole-2(3H-ylideneaniline by using experimental and density functional methods

Directory of Open Access Journals (Sweden)

Fatih Şen

2017-05-01

Full Text Available In the present study, a combined experimental and computational study on molecular structure and spectroscopic characterization on the title compound has been reported. The crystal was synthesized and its molecular structure brought to light by X-ray single crystal structure determination. The spectroscopic properties of the compound were examined by FT-IR and NMR (1H and 13C techniques. FT-IR spectra of the target compound in solid state were observed in the region 4000–400 cm−1. The 1H and 13C NMR spectra were recorded in CDCl3 solution. The molecular geometries were those obtained from the X-ray structure determination optimized using the density functional theory (DFT/B3LYP method with the 6-31G(d, p and 6-31G+(d, p basis set in ground state. From the optimized geometry of the molecule, geometric parameters (bond lengths, bond angles and torsion angles, vibrational assignments and chemical shifts of the title compound have been calculated theoretically and compared with those of experimental data. Besides, molecular electrostatic potential (MEP, frontier molecular orbitals (FMOs, Mulliken population analysis, Thermodynamic properties and non-linear optical (NLO properties of the title molecule were investigated by theoretical calculations.

Optimization of a pulsed-field gel electrophoresis for molecular typing of Proteus mirabilis

Directory of Open Access Journals (Sweden)

Alper Karagöz

2013-09-01

Full Text Available Objective: For the detection of outbreaks caused byProteus mirabilis, strains clonal relations are determinedmethods as “pulsed-field gel electrophoresis (PFGE”.The aim of this study was optimization of a pulsed-fieldgel electrophoresis for molecular typing of P. mirabilis.Methods: In this study, PFGE’ protocol is optimized foruse in molecular typing of P. mirabilis. Phylogenetic analyzesof strains were evaluated with Bionumerics softwaresystem (version 6.01; Applied Maths, Sint-Martens-Latem, Belgium.Results: This protocol compared with Gram-negativebacteria PFGE protocols, NotI enzyme is suitable for thisbacterium. Electrophoresis conditions should be revealedas; - block 1: initial pulse duration 1 sec, ending pulseduration 30 sec, striking angle 120°, the current 6 V/cm2,temperature 14°C, time 8 hours; - block 2: initial pulseduration 30 sec, ending pulse duration 70 sec, strikingangle 120°, the current 6 V/cm2, temperature 14°C, time16 hours; - TBE, pH=8.4.Conclusion: P. mirabilis strains were typed by PFGE andBionumerics analysis program were determined clonal relationships.The procedure was simple, reproducible andsuitable for these bacteria. Also it was evaluated, becauseof reducing time, the solution volumes and enzymes canbe economically. Outbreaks of nosocomial infections dueto bacteria studied assessment and the potential to provideuseful information about the degree of prevalence.This optimized protocol is allowed different centers’ PFGEresults to compare with other laboratories results. J ClinExp Invest 2013; 4 (3: 306-312Key words: Proteus mirabilis, molecular typing, pulsedfieldgel electrophoresis.

Strontium clusters: electronic and geometry shell effects

DEFF Research Database (Denmark)

Lyalin, Andrey G.; Solov'yov, Ilia; Solov'yov, Andrey V.

2008-01-01

charged strontium clusters consisting of up to 14 atoms, average bonding distances, electronic shell closures, binding energies per atom, and spectra of the density of electronic states (DOS). It is demonstrated that the size-evolution of structural and electronic properties of strontium clusters...... is governed by an interplay of the electronic and geometry shell closures. Influence of the electronic shell effects on structural rearrangements can lead to violation of the icosahedral growth motif of strontium clusters. It is shown that the excessive charge essentially affects the optimized geometry...

Isogeometric shape optimization of photonic crystals via Coons patches

DEFF Research Database (Denmark)

Qian, Xiaoping; Sigmund, Ole

2011-01-01

In this paper, we present an approach that extends isogeometric shape optimization from optimization of rectangular-like NURBS patches to the optimization of topologically complex geometries. We have successfully applied this approach in designing photonic crystals where complex geometries have...

Geometries

CERN Document Server

Sossinsky, A B

2012-01-01

The book is an innovative modern exposition of geometry, or rather, of geometries; it is the first textbook in which Felix Klein's Erlangen Program (the action of transformation groups) is systematically used as the basis for defining various geometries. The course of study presented is dedicated to the proposition that all geometries are created equal--although some, of course, remain more equal than others. The author concentrates on several of the more distinguished and beautiful ones, which include what he terms "toy geometries", the geometries of Platonic bodies, discrete geometries, and classical continuous geometries. The text is based on first-year semester course lectures delivered at the Independent University of Moscow in 2003 and 2006. It is by no means a formal algebraic or analytic treatment of geometric topics, but rather, a highly visual exposition containing upwards of 200 illustrations. The reader is expected to possess a familiarity with elementary Euclidean geometry, albeit those lacking t...

Geometry Optimization of DC/RF Photoelectron Gun

CERN Document Server

Chen Ping; Yu, David

2005-01-01

Pre-acceleration of photoelectrons in a pulsed, high voltage, short, dc gap and its subsequent injection into an rf gun is a promising method to improve electron beam emittance in rf accelerators. Simulation work has been performed in order to optimize the geometric shapes of a dc/rf gun and improve electron beam properties. Variations were made on cathode and anode shapes, dc gap distance, and inlet shape of the rf cavity. Simulations showed that significant improvement on the normalized emittance (< 1 mm-mrad), compared to a dc gun with flat cathode, could be obtained after the geometric shapes of the gun were optimized.

Theoretical Investigation on the Molecular Structure, Vibrational and NMR Spectra of N, N, 4-Tri chlorobenzenesulfonamide

International Nuclear Information System (INIS)

Cinar, M.

2008-01-01

In the present study, the structural properties of N,N,4-Tri chlorobenzenesulfonamide have been studied extensively using Density Functional Theory (DFT) employing B3LYP exchange correlation. The geometry of the molecule was fully optimized, vibrational spectrum was calculated and fundamental vibrations were assigned based on the scaled theoretical wavenumbers. The 1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts of the compound were calculated using the Gauge-Invariant Atomic Orbital (GIAO) method. To investigate the basis set effects, calculations were performed at the 6-31G(d,p), 6-311G(d,p), 6-31++G(d,p) and 6-311++G(d,p) levels. Finally, geometric parameters, vibrational bands and isotropic chemical shifts were compared with available experimental data of compound. The fully optimized geometry of the molecule was found to be consistent with the X-ray crystal structure. The observed and calculated frequencies and chemical shifts were found to be in very good agreement. The computed results appear that the basis set has slight effect on the molecular geometry of N,N,4-Tri chlorobenzenesulfonamide

Optimized molecular reconstruction procedure combining hybrid reverse Monte Carlo and molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Bousige, Colin; Boţan, Alexandru; Coasne, Benoît, E-mail: coasne@mit.edu [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); UMI 3466 CNRS-MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); Ulm, Franz-Josef [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); Pellenq, Roland J.-M. [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); UMI 3466 CNRS-MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); CINaM, CNRS/Aix Marseille Université, Campus de Luminy, 13288 Marseille Cedex 09 (France)

2015-03-21

We report an efficient atom-scale reconstruction method that consists of combining the Hybrid Reverse Monte Carlo algorithm (HRMC) with Molecular Dynamics (MD) in the framework of a simulated annealing technique. In the spirit of the experimentally constrained molecular relaxation technique [Biswas et al., Phys. Rev. B 69, 195207 (2004)], this modified procedure offers a refined strategy in the field of reconstruction techniques, with special interest for heterogeneous and disordered solids such as amorphous porous materials. While the HRMC method generates physical structures, thanks to the use of energy penalties, the combination with MD makes the method at least one order of magnitude faster than HRMC simulations to obtain structures of similar quality. Furthermore, in order to ensure the transferability of this technique, we provide rational arguments to select the various input parameters such as the relative weight ω of the energy penalty with respect to the structure optimization. By applying the method to disordered porous carbons, we show that adsorption properties provide data to test the global texture of the reconstructed sample but are only weakly sensitive to the presence of defects. In contrast, the vibrational properties such as the phonon density of states are found to be very sensitive to the local structure of the sample.

Solid Rocket Motor Design Using Hybrid Optimization

Directory of Open Access Journals (Sweden)

Kevin Albarado

2012-01-01

Full Text Available A particle swarm/pattern search hybrid optimizer was used to drive a solid rocket motor modeling code to an optimal solution. The solid motor code models tapered motor geometries using analytical burn back methods by slicing the grain into thin sections along the axial direction. Grains with circular perforated stars, wagon wheels, and dog bones can be considered and multiple tapered sections can be constructed. The hybrid approach to optimization is capable of exploring large areas of the solution space through particle swarming, but is also able to climb “hills” of optimality through gradient based pattern searching. A preliminary method for designing tapered internal geometry as well as tapered outer mold-line geometry is presented. A total of four optimization cases were performed. The first two case studies examines designing motors to match a given regressive-progressive-regressive burn profile. The third case study studies designing a neutrally burning right circular perforated grain (utilizing inner and external geometry tapering. The final case study studies designing a linearly regressive burning profile for right circular perforated (tapered grains.

Ring rolling process simulation for geometry optimization

Science.gov (United States)

Franchi, Rodolfo; Del Prete, Antonio; Donatiello, Iolanda; Calabrese, Maurizio

2017-10-01

Ring Rolling is a complex hot forming process where different rolls are involved in the production of seamless rings. Since each roll must be independently controlled, different speed laws must be set; usually, in the industrial environment, a milling curve is introduced to monitor the shape of the workpiece during the deformation in order to ensure the correct ring production. In the present paper a ring rolling process has been studied and optimized in order to obtain anular components to be used in aerospace applications. In particular, the influence of process input parameters (feed rate of the mandrel and angular speed of main roll) on geometrical features of the final ring has been evaluated. For this purpose, a three-dimensional finite element model for HRR (Hot Ring Rolling) has been implemented in SFTC DEFORM V11. The FEM model has been used to formulate a proper optimization problem. The optimization procedure has been implemented in the commercial software DS ISight in order to find the combination of process parameters which allows to minimize the percentage error of each obtained dimension with respect to its nominal value. The software allows to find the relationship between input and output parameters applying Response Surface Methodology (RSM), by using the exact values of output parameters in the control points of the design space explored through FEM simulation. Once this relationship is known, the values of the output parameters can be calculated for each combination of the input parameters. After the calculation of the response surfaces for the selected output parameters, an optimization procedure based on Genetic Algorithms has been applied. At the end, the error between each obtained dimension and its nominal value has been minimized. The constraints imposed were the maximum values of standard deviations of the dimensions obtained for the final ring.

Symbol interval optimization for molecular communication with drift.

Science.gov (United States)

Kim, Na-Rae; Eckford, Andrew W; Chae, Chan-Byoung

2014-09-01

In this paper, we propose a symbol interval optimization algorithm in molecular communication with drift. Proper symbol intervals are important in practical communication systems since information needs to be sent as fast as possible with low error rates. There is a trade-off, however, between symbol intervals and inter-symbol interference (ISI) from Brownian motion. Thus, we find proper symbol interval values considering the ISI inside two kinds of blood vessels, and also suggest no ISI system for strong drift models. Finally, an isomer-based molecule shift keying (IMoSK) is applied to calculate achievable data transmission rates (achievable rates, hereafter). Normalized achievable rates are also obtained and compared in one-symbol ISI and no ISI systems.

Density and geometry of single component plasmas

International Nuclear Information System (INIS)

Speck, A.; Gabrielse, G.; Larochelle, P.; Le Sage, D.; Levitt, B.; Kolthammer, W.S.; McConnell, R.; Wrubel, J.; Grzonka, D.; Oelert, W.; Sefzick, T.; Zhang, Z.; Comeau, D.; George, M.C.; Hessels, E.A.; Storry, C.H.; Weel, M.; Walz, J.

2007-01-01

The density and geometry of p-bar and e + plasmas in realistic trapping potentials are required to understand and optimize antihydrogen (H-bar) formation. An aperture method and a quadrupole oscillation frequency method for characterizing such plasmas are compared for the first time, using electrons in a cylindrical Penning trap. Both methods are used in a way that makes it unnecessary to assume that the plasmas are spheroidal, and it is shown that they are not. Good agreement between the two methods illustrates the possibility to accurately determine plasma densities and geometries within non-idealized, realistic trapping potentials

Density and geometry of single component plasmas

CERN Document Server

Speck, A; Larochelle, P; Le Sage, D; Levitt, B; Kolthammer, W S; McConnell, R; Wrubel, J; Grzonka, D; Oelert, W; Sefzick, T; Zhang, Z; Comeau, D; George, M C; Hessels, E A; Storry, C H; Weel, M; Walz, J

2007-01-01

The density and geometry of p¯ and e+ plasmas in realistic trapping potentials are required to understand and optimize antihydrogen (H¯) formation. An aperture method and a quadrupole oscillation frequency method for characterizing such plasmas are compared for the first time, using electrons in a cylindrical Penning trap. Both methods are used in a way that makes it unnecessary to assume that the plasmas are spheroidal, and it is shown that they are not. Good agreement between the two methods illustrates the possibility to accurately determine plasma densities and geometries within non-idealized, realistic trapping potentials.

An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

International Nuclear Information System (INIS)

Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

2016-01-01

An empirically parameterized intermolecular force field is developed for crystal structure modelling and prediction. The model is optimized for use with an atomic multipole description of electrostatic interactions. We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%

Inverse kinematics for the variable geometry truss manipulator via a Lagrangian dual method

Directory of Open Access Journals (Sweden)

Yanchun Zhao

2016-11-01

Full Text Available This article studies the inverse kinematics problem of the variable geometry truss manipulator. The problem is cast as an optimization process which can be divided into two steps. Firstly, according to the information about the location of the end effector and fixed base, an optimal center curve and the corresponding distribution of the intermediate platforms along this center line are generated. This procedure is implemented by solving a non-convex optimization problem that has a quadratic objective function subject to quadratic constraints. Then, in accordance with the distribution of the intermediate platforms along the optimal center curve, all lengths of the actuators are calculated via the inverse kinematics of each variable geometry truss module. Hence, the approach that we present is an optimization procedure that attempts to generate the optimal intermediate platform distribution along the optimal central curve, while the performance index and kinematic constraints are satisfied. By using the Lagrangian duality theory, a closed-form optimal solution of the original optimization is given. The numerical simulation substantiates the effectiveness of the introduced approach.

Optimization of ISSR Markers for Molecular DNA Fingerprinting in Aquilaria sp

International Nuclear Information System (INIS)

Azhar Mohamad; Muhammad Hanif Azhari; Siti Norhayati Ismail; Parween, K.S.A.S.

2013-01-01

Aquilaria sp. belongs to the Thymelaeaceae family and well distributed to Asia region. The species is a multipurpose use from root to shoot and becoming an economic important crop, which generates wide interest in understanding the genetic diversity of the species. Understanding of the effectiveness in differentiating DNA-based markers is an important step towards plant germplasm characterization and evaluation. It is becoming a prerequisite for more effective application of molecular marker techniques in breeding and mapping programs. Polymerase Chain Reaction (PCR)-based approaches are in demanding as its simplicity and requirement for only small quantities of sample genomic DNA. Inter-simple sequence repeats (ISRR) requires no prior genomic information as anchor template in producing multi-loci markers of tandem repeats for polymorphic patterns by PCR amplification which becoming a key of advantageous of ISSR primers. ISSR markers have shown rapid, simple, reproducible and inexpensive means in molecular taxonomy, conservation breeding and genetic diversity analysis. The ISSR for marker applications are essential to facilitate management, conservation and genetic improvement programs towards improvement of standard resin quality for perfume and or pharmaceutical industries. In this paper, a total of 100 ISSR primers were optimized by using Aquilaria malaccensis. Primers optimization resulted, 38 ISSR primers affirmative for the polymorphism evaluation study, which encountered both from specific and degenerate ISSR primers. Marker derived from ISSR profiling is a powerful method for identification and molecular classification of Aquilaria sp from species to accessions and further will useful in identifying any mutant lines derived from nature and/or mutagenesis activities. (author)

Geometry

CERN Document Server

Prasolov, V V

2015-01-01

This book provides a systematic introduction to various geometries, including Euclidean, affine, projective, spherical, and hyperbolic geometries. Also included is a chapter on infinite-dimensional generalizations of Euclidean and affine geometries. A uniform approach to different geometries, based on Klein's Erlangen Program is suggested, and similarities of various phenomena in all geometries are traced. An important notion of duality of geometric objects is highlighted throughout the book. The authors also include a detailed presentation of the theory of conics and quadrics, including the theory of conics for non-Euclidean geometries. The book contains many beautiful geometric facts and has plenty of problems, most of them with solutions, which nicely supplement the main text. With more than 150 figures illustrating the arguments, the book can be recommended as a textbook for undergraduate and graduate-level courses in geometry.

Considering Variable Road Geometry in Adaptive Vehicle Speed Control

Directory of Open Access Journals (Sweden)

Xinping Yan

2013-01-01

Full Text Available Adaptive vehicle speed control is critical for developing Advanced Driver Assistance Systems (ADAS. Vehicle speed control considering variable road geometry has become a hotspot in ADAS research. In this paper, first, an exploration of intrinsic relationship between vehicle operation and road geometry is made. Secondly, a collaborative vehicle coupling model, a road geometry model, and an AVSC, which can respond to variable road geometry in advance, are developed. Then, based on H∞ control method and the minimum energy principle, a performance index is specified by a cost function for the proposed AVSC, which can explicitly consider variable road geometry in its optimization process. The proposed AVSC is designed by the Hamilton-Jacobi Inequality (HJI. Finally, simulations are carried out by combining the vehicle model with the road geometry model, in an aim of minimizing the performance index of the AVSC. Analyses of the simulation results indicate that the proposed AVSC can automatically and effectively regulate speed according to variable road geometry. It is believed that the proposed AVSC can be used to improve the economy, comfort, and safety effects of current ADAS.

FT-IR, FT-Raman, and DFT computational studies of melaminium nitrate molecular-ionic crystal

Science.gov (United States)

Tanak, Hasan; Marchewka, Mariusz K.

2013-02-01

The experimental and theoretical vibrational spectra of melaminium nitrate were studied. The Raman and infrared (FT-IR) spectra of the melaminium nitrate and its deuterated analogue were recorded in the solid phase. Molecular geometry and vibrational frequency values of melaminium nitrate in the electronic ground state were calculated using the density functional method (B3LYP) with the 6-31++G(d,p) basis set. The calculated results show that the optimized geometry can well reproduce the crystal structure, and the theoretical vibrational frequency values show good agreement with experimental values. The NBO analysis reveals that the N-H···O and N-H···N intermolecular interactions significantly influence crystal packing in this molecule.

Engineering controllable bidirectional molecular motors based on myosin

Science.gov (United States)

Chen, Lu; Nakamura, Muneaki; Schindler, Tony D.; Parker, David; Bryant, Zev

2012-04-01

Cytoskeletal motors drive the transport of organelles and molecular cargoes within cells and have potential applications in molecular detection and diagnostic devices. Engineering molecular motors with controllable properties will allow selective perturbation of mechanical processes in living cells and provide optimized device components for tasks such as molecular sorting and directed assembly. Biological motors have previously been modified by introducing activation/deactivation switches that respond to metal ions and other signals. Here, we show that myosin motors can be engineered to reversibly change their direction of motion in response to a calcium signal. Building on previous protein engineering studies and guided by a structural model for the redirected power stroke of myosin VI, we have constructed bidirectional myosins through the rigid recombination of structural modules. The performance of the motors was confirmed using gliding filament assays and single fluorophore tracking. Our strategy, in which external signals trigger changes in the geometry and mechanics of myosin lever arms, should make it possible to achieve spatiotemporal control over a range of motor properties including processivity, stride size and branchpoint turning.

In silico modelling and molecular dynamics simulation studies of thiazolidine based PTP1B inhibitors.

Science.gov (United States)

Mahapatra, Manoj Kumar; Bera, Krishnendu; Singh, Durg Vijay; Kumar, Rajnish; Kumar, Manoj

2018-04-01

Protein tyrosine phosphatase 1B (PTP1B) has been identified as a negative regulator of insulin and leptin signalling pathway; hence, it can be considered as a new therapeutic target of intervention for the treatment of type 2 diabetes. Inhibition of this molecular target takes care of both diabetes and obesity, i.e. diabestiy. In order to get more information on identification and optimization of lead, pharmacophore modelling, atom-based 3D QSAR, docking and molecular dynamics studies were carried out on a set of ligands containing thiazolidine scaffold. A six-point pharmacophore model consisting of three hydrogen bond acceptor (A), one negative ionic (N) and two aromatic rings (R) with discrete geometries as pharmacophoric features were developed for a predictive 3D QSAR model. The probable binding conformation of the ligands within the active site was studied through molecular docking. The molecular interactions and the structural features responsible for PTP1B inhibition and selectivity were further supplemented by molecular dynamics simulation study for a time scale of 30 ns. The present investigation has identified some of the indispensible structural features of thiazolidine analogues which can further be explored to optimize PTP1B inhibitors.

A 3D multi-mode geometry-independent RMP optimization method and its application to TCV

International Nuclear Information System (INIS)

Rossel, J X; Moret, J-M; Martin, Y

2010-01-01

Resonant magnetic perturbation (RMP) and error field correction (EFC) produced by toroidally and poloidally distributed coil systems can be optimized if each coil is powered with an independent power supply. A 3D multi-mode geometry-independent Lagrange method has been developed and appears to be an efficient way to minimize the parasitic spatial modes of the magnetic perturbation and the coil current requirements while imposing the amplitude and phase of a number of target modes. A figure of merit measuring the quality of a perturbation spectrum with respect to RMP independently of the considered coil system or plasma equilibrium is proposed. To ease the application of the Lagrange method, a spectral characterization of the system, based on a generalized discrete Fourier transform applied in current space, is performed to determine how spectral degeneracy and side-band creation limit the set of simultaneously controllable target modes. This characterization is also useful to quantify the efficiency of the coil system in each toroidal mode number and to know whether optimization is possible for a given number of target modes. The efficiency of the method is demonstrated in the special case of a multi-purpose saddle coil system proposed as part of a future upgrade of Tokamak a Configuration Variable (TCV). This system consists of three rows of eight internal coils, each coil having independent power supplies, and provides simultaneously EFC, RMP and fast vertical position control.

Orbital-optimized coupled-electron pair theory and its analytic gradients: Accurate equilibrium geometries, harmonic vibrational frequencies, and hydrogen transfer reactions

Science.gov (United States)

Bozkaya, Uǧur; Sherrill, C. David

2013-08-01

Orbital-optimized coupled-electron pair theory [or simply "optimized CEPA(0)," OCEPA(0), for short] and its analytic energy gradients are presented. For variational optimization of the molecular orbitals for the OCEPA(0) method, a Lagrangian-based approach is used along with an orbital direct inversion of the iterative subspace algorithm. The cost of the method is comparable to that of CCSD [O(N6) scaling] for energy computations. However, for analytic gradient computations the OCEPA(0) method is only half as expensive as CCSD since there is no need to solve the λ2-amplitude equation for OCEPA(0). The performance of the OCEPA(0) method is compared with that of the canonical MP2, CEPA(0), CCSD, and CCSD(T) methods, for equilibrium geometries, harmonic vibrational frequencies, and hydrogen transfer reactions between radicals. For bond lengths of both closed and open-shell molecules, the OCEPA(0) method improves upon CEPA(0) and CCSD by 25%-43% and 38%-53%, respectively, with Dunning's cc-pCVQZ basis set. Especially for the open-shell test set, the performance of OCEPA(0) is comparable with that of CCSD(T) (ΔR is 0.0003 Å on average). For harmonic vibrational frequencies of closed-shell molecules, the OCEPA(0) method again outperforms CEPA(0) and CCSD by 33%-79% and 53%-79%, respectively. For harmonic vibrational frequencies of open-shell molecules, the mean absolute error (MAE) of the OCEPA(0) method (39 cm-1) is fortuitously even better than that of CCSD(T) (50 cm-1), while the MAEs of CEPA(0) (184 cm-1) and CCSD (84 cm-1) are considerably higher. For complete basis set estimates of hydrogen transfer reaction energies, the OCEPA(0) method again exhibits a substantially better performance than CEPA(0), providing a mean absolute error of 0.7 kcal mol-1, which is more than 6 times lower than that of CEPA(0) (4.6 kcal mol-1), and comparing to MP2 (7.7 kcal mol-1) there is a more than 10-fold reduction in errors. Whereas the MAE for the CCSD method is only 0.1 kcal

Molecular Structure and Chemical Shift Assignments of 4-(2-Methoxy-4-Methylphenoxy)Phthalonitrile (C16H12N2O2) By DFT And AB Initio HF Calculations

International Nuclear Information System (INIS)

Tarcan, E.

2008-01-01

The molecular geometry, gauge including atomic orbital (GIAO) 1 H and 13 C chemical shift values of 4-(2-Methoxy-4-methylphenoxy)phthalonitrile (C 1 6H 1 2N 2 O 2 ) in the ground state have been calculated by using the Hartree-Fock (HF) and density functional methods (B3LYP and BLYP) with 6-31G(d) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The optimized bond length numbers with bond angels are in good agreement with the X-ray data

Optimization of measurement geometries used by the C.I.R. 'Gamma Spectrometry' working group

International Nuclear Information System (INIS)

Escarieux, M.

1979-01-01

The choice of measurement geometry is closely tied to the objective sought in gamma quantitative analysis which consists in identifying the radionuclides present in a sample and in determining the voluminal quantities. The too low efficiency of the detector and the levels of activity sought make it necessary to place the sample in contact with the casing of the detector and select a sample geometry suited to the measurement. In point of fact this choice is often determined by other criteria, availability of the container for example, and this leads the laboratories taking part in the 'Gamma Spectrometry' Working Group of the Comite d'Instrumentation de Radioprotection to adopt joint gamma measurement geometries [fr

Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics

International Nuclear Information System (INIS)

Clore, G.M.; Gronenborn, A.M.; Nilges, M.; Ryan, C.A.

1987-01-01

The solution conformation of potato carboxypeptidase inhibitor (CPI) has been investigated by 1 H NMR spectroscopy. The spectrum is assigned in a sequential manner by using two-dimensional NMR techniques to identify through-bond and through-space (<5 A) connectivities. A set of 309 approximate interproton distance restraints is derived from the two-dimensional nuclear Overhauser enhancement spectra and used as the basis of a three-dimensional structure determination by a combination of metric matrix distance geometry and restrained molecular dynamics calculations. A total of 11 converged distance geometry structures were computed and refined by using restrained molecular dynamics. The average atomic root mean square (rms) difference between the final 11 structures and the mean structure obtained by averaging their coordinates is 1.4 +/- 0.3 A for residues 2-39 and 0.9 +/- 0.2 A for residues 5-37. The corresponding values for all atoms are 1.9 +/- 0.3 and 1.4 +/- 0.2 A, respectively. The computed structures are very close to the X-ray structure of CPI in its complex with carboxypeptidase, and the backbone atomic rms difference between the mean of the computed structures and the X-ray structure is only 1.2 A. Nevertheless, there are some real differences present which are evidenced by significant deviations between the experimental upper interproton distance limits and the corresponding interproton distances derived from the X-ray structure. These principally occur in two regions, residues 18-20 and residues 28-30, the latter comprising part of the region of secondary contact between CPI and carboxypeptidase in the X-ray structure

SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions.

Science.gov (United States)

Wassenaar, Tsjerk A; de Vries, Sjoerd; Bonvin, Alexandre M J J; Bekker, Henk

2012-10-09

In molecular simulations of macromolecules, it is desirable to limit the amount of solvent in the system to avoid spending computational resources on uninteresting solvent-solvent interactions. As a consequence, periodic boundary conditions are commonly used, with a simulation box chosen as small as possible, for a given minimal distance between images. Here, we describe how such a simulation cell can be set up for ensembles, taking into account a priori available or estimable information regarding conformational flexibility. Doing so ensures that any conformation present in the input ensemble will satisfy the distance criterion during the simulation. This helps avoid periodicity artifacts due to conformational changes. The method introduces three new approaches in computational geometry: (1) The first is the derivation of an optimal packing of ensembles, for which the mathematical framework is described. (2) A new method for approximating the α-hull and the contact body for single bodies and ensembles is presented, which is orders of magnitude faster than existing routines, allowing the calculation of packings of large ensembles and/or large bodies. 3. A routine is described for searching a combination of three vectors on a discretized contact body forming a reduced base for a lattice with minimal cell volume. The new algorithms reduce the time required to calculate packings of single bodies from minutes or hours to seconds. The use and efficacy of the method is demonstrated for ensembles obtained from NMR, MD simulations, and elastic network modeling. An implementation of the method has been made available online at http://haddock.chem.uu.nl/services/SQUEEZE/ and has been made available as an option for running simulations through the weNMR GRID MD server at http://haddock.science.uu.nl/enmr/services/GROMACS/main.php .

MOCUM: A two-dimensional method of characteristics code based on constructive solid geometry and unstructured meshing for general geometries

International Nuclear Information System (INIS)

Yang Xue; Satvat, Nader

2012-01-01

Highlight: ► A two-dimensional numerical code based on the method of characteristics is developed. ► The complex arbitrary geometries are represented by constructive solid geometry and decomposed by unstructured meshing. ► Excellent agreement between Monte Carlo and the developed code is observed. ► High efficiency is achieved by parallel computing. - Abstract: A transport theory code MOCUM based on the method of characteristics as the flux solver with an advanced general geometry processor has been developed for two-dimensional rectangular and hexagonal lattice and full core neutronics modeling. In the code, the core structure is represented by the constructive solid geometry that uses regularized Boolean operations to build complex geometries from simple polygons. Arbitrary-precision arithmetic is also used in the process of building geometry objects to eliminate the round-off error from the commonly used double precision numbers. Then, the constructed core frame will be decomposed and refined into a Conforming Delaunay Triangulation to ensure the quality of the meshes. The code is fully parallelized using OpenMP and is verified and validated by various benchmarks representing rectangular, hexagonal, plate type and CANDU reactor geometries. Compared with Monte Carlo and deterministic reference solution, MOCUM results are highly accurate. The mentioned characteristics of the MOCUM make it a perfect tool for high fidelity full core calculation for current and GenIV reactor core designs. The detailed representation of reactor physics parameters can enhance the safety margins with acceptable confidence levels, which lead to more economically optimized designs.

Evaluation and optimization of the performance of frame geometries for lithium-ion battery application by computer simulation

Energy Technology Data Exchange (ETDEWEB)

Miranda, D. [Centro/Departamento de Física, Universidade do Minho, 4710-057 Braga (Portugal); Instituto Politécnico de Viana do Castelo, Viana do Castelo (Portugal); Miranda, F. [CIDMA, Universidade de Aveiro, Aveiro (Portugal); Instituto Politécnico de Viana do Castelo, Viana do Castelo (Portugal); Costa, C. M.; Almeida, A. M.; Lanceros-Méndez, S. [Centro/Departamento de Física, Universidade do Minho, 4710-057 Braga (Portugal)

2016-06-08

Tailoring battery geometries is essential for many applications, as geometry influences the delivered capacity value. Two geometries, frame and conventional, have been studied and, for a given scan rate of 330C, the square frame shows a capacity value of 305,52 Ahm{sup −2}, which is 527 times higher than the one for the conventional geometry for a constant the area of all components.

Molecular geometries and relative stabilities of titanium oxide and gold-titanium oxide clusters

Energy Technology Data Exchange (ETDEWEB)

Hudson, Rohan J.; Falcinella, Alexander; Metha, Gregory F., E-mail: greg.metha@adelaide.edu.au

2016-09-30

Titanium oxide and gold-titanium oxide clusters of stoichiometry M{sub x}O{sub y} (M{sub x} = Ti{sub 3}, Ti{sub 4} & AuTi{sub 3}; y = 0 − (2x + 2)) have been investigated using density functional theory. Geometries of determined global energy minimum structures are reported and other isomers predicted up to 0.5 eV higher in energy. The Ti{sub 3}O{sub n} geometries build upon a triangular Ti{sub 3} motif, while Ti{sub 4}O{sub n} stoichiometries template upon a pseudo-tetrahedral Ti{sub 4} structure. Addition of a gold atom to the Ti{sub 3}O{sub n} series does not significantly alter the cluster geometry, with the gold atom preferentially binding to titanium atoms over oxygen atoms. Adiabatic ionization energies, electron affinities and HOMO/LUMO energies increase in magnitude with increasing oxygenation. The HOMO-LUMO energy gaps reach the bulk anatase band gap energy at stoichiometry (Au)Ti{sub m}O{sub 2m−1}, and increase above this upon further oxygen addition. The most stable structural moieties are found to be a cage-like, C{sub 3v} symmetric Ti{sub 4}O{sub 6/7} geometry and a Ti{sub 3}O{sub 6} structure with an η{sup 3}-bound oxygen atom.

Computer simulations of the influence of geometry in the performance of conventional and unconventional lithium-ion batteries

International Nuclear Information System (INIS)

Miranda, D.; Costa, C.M.; Almeida, A.M.; Lanceros-Méndez, S.

2016-01-01

Highlights: • The influence of geometries in lithium-ion battery performance is analyzed. • Conventional and unconventional battery geometries are investigated. • Unconventional geometries include horseshoe, spiral, ring, antenna and gear batteries. • The best capacity value at 330 C is obtained for the interdigitated geometry. • The capacity value is dependent on thickness and collectors position. - Abstract: In order to optimize battery performance, different geometries have been evaluated taking into account their suitability for different applications. These different geometries include conventional, interdigitated batteries and unconventional geometries such as horseshoe, spiral, ring, antenna and gear batteries. The geometry optimization was performed by the finite element method, applying the Doyle/Fuller/Newman model. At 330 C, the capacity values for conventional, ring, spiral, horseshoe, gear and interdigitated geometries are 0.58 A h m"−"2, 149 A h m"−"2, 182 A h m"−"2, 216 A h m"−"2, 289 A h m"−"2 and 318 A h m"−"2, respectively. The delivered capacity depends on geometrical parameters such as maximum distance for the ions to move to the current collector, d-max, distance between of current collectors, d-cc, as well as the thickness of separator and electrodes, allowing to tailor battery performance and geometry for specific applications.

Precise identification and manipulation of adsorption geometry of donor-π-acceptor dye on nanocrystalline TiO₂ films for improved photovoltaics.

Science.gov (United States)

Zhang, Fan; Ma, Wei; Jiao, Yang; Wang, Jingchuan; Shan, Xinyan; Li, Hui; Lu, Xinghua; Meng, Sheng

2014-12-24

Adsorption geometry of dye molecules on nanocrystalline TiO2 plays a central role in dye-sensitized solar cells, enabling effective sunlight absorption, fast electron injection, optimized interface band offsets, and stable photovoltaic performance. However, precise determination of dye binding geometry and proportion has been challenging due to complexity and sensitivity at interfaces. Here employing combined vibrational spectrometry and density functional calculations, we identify typical adsorption configurations of widely adopted cyanoacrylic donor-π bridge-acceptor dyes on nanocrystalline TiO2. Binding mode switching from bidentate bridging to hydrogen-bonded monodentate configuration with Ti-N bonding has been observed when dye-sensitizing solution becomes more basic. Raman and infrared spectroscopy measurements confirm this configuration switch and determine quantitatively the proportion of competing binding geometries, with vibration peaks assigned using density functional theory calculations. We further found that the proportion of dye-binding configurations can be manipulated by adjusting pH value of dye-sensitizing solutions. Controlling molecular adsorption density and configurations led to enhanced energy conversion efficiency from 2.4% to 6.1% for the fabricated dye-sensitized solar cells, providing a simple method to improve photovoltaic performance by suppressing unfavorable binding configurations in solar cell applications.

Multiview Discriminative Geometry Preserving Projection for Image Classification

Directory of Open Access Journals (Sweden)

Ziqiang Wang

2014-01-01

Full Text Available In many image classification applications, it is common to extract multiple visual features from different views to describe an image. Since different visual features have their own specific statistical properties and discriminative powers for image classification, the conventional solution for multiple view data is to concatenate these feature vectors as a new feature vector. However, this simple concatenation strategy not only ignores the complementary nature of different views, but also ends up with “curse of dimensionality.” To address this problem, we propose a novel multiview subspace learning algorithm in this paper, named multiview discriminative geometry preserving projection (MDGPP for feature extraction and classification. MDGPP can not only preserve the intraclass geometry and interclass discrimination information under a single view, but also explore the complementary property of different views to obtain a low-dimensional optimal consensus embedding by using an alternating-optimization-based iterative algorithm. Experimental results on face recognition and facial expression recognition demonstrate the effectiveness of the proposed algorithm.

Topology of classical molecular optimal control landscapes for multi-target objectives

Energy Technology Data Exchange (ETDEWEB)

Joe-Wong, Carlee [Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544-1000 (United States); Ho, Tak-San; Rabitz, Herschel, E-mail: hrabitz@princeton.edu [Department of Chemistry, Princeton University, Princeton, New Jersey 08544-1009 (United States); Wu, Rebing [Department of Automation, Tsinghua University, Beijing (China)

2015-04-21

This paper considers laser-driven optimal control of an ensemble of non-interacting molecules whose dynamics lie in classical phase space. The molecules evolve independently under control to distinct final states. We consider a control landscape defined in terms of multi-target (MT) molecular states and analyze the landscape as a functional of the control field. The topology of the MT control landscape is assessed through its gradient and Hessian with respect to the control. Under particular assumptions, the MT control landscape is found to be free of traps that could hinder reaching the objective. The Hessian associated with an optimal control field is shown to have finite rank, indicating an inherent degree of robustness to control noise. Both the absence of traps and rank of the Hessian are shown to be analogous to the situation of specifying multiple targets for an ensemble of quantum states. Numerical simulations are presented to illustrate the classical landscape principles and further characterize the system behavior as the control field is optimized.

Sensitive method for the determination of rare earth elements by radioisotope-excited XRF employing a high purity germanium detector in optimized geometry

International Nuclear Information System (INIS)

Lal, M.; Joseph, D.; Patra, P.K.; Bajpal, H.N.

1993-01-01

A close-coupled side-source geometrical configuration is proposed for obtaining a high detection sensitivity for rare earth elements (57 ≤ Z ≤ 69) by radioisotope-excited energy-dispersive x-ray fluorescence spectrometry. In this configuration a disc source of 241 Am (100 mCi), a high-purity germanium detector and thin samples of rare earth elements on a Mylar backing are employed in an optimized geometry to achieve detection limits in the range 20-50 ng for these elements in a counting time of 1 h. (author)

The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems

International Nuclear Information System (INIS)

Kalligiannaki, Evangelia; Harmandaris, Vagelis; Katsoulakis, Markos A.; Plecháč, Petr

2015-01-01

Using the probabilistic language of conditional expectations, we reformulate the force matching method for coarse-graining of molecular systems as a projection onto spaces of coarse observables. A practical outcome of this probabilistic description is the link of the force matching method with thermodynamic integration. This connection provides a way to systematically construct a local mean force and to optimally approximate the potential of mean force through force matching. We introduce a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (e.g., reaction coordinates, end-to-end length of chains). Furthermore, we study the equivalence of force matching with relative entropy minimization which we derive for general non-linear coarse graining maps. We present in detail the generalized force matching condition through applications to specific examples in molecular systems

The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems

Energy Technology Data Exchange (ETDEWEB)

Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion (Greece); Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion (Greece); Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion (Greece); Katsoulakis, Markos A., E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Plecháč, Petr, E-mail: plechac@math.udel.edu [Department of Mathematical Sciences, University of Delaware, Newark, Delaware 19716 (United States)

2015-08-28

Using the probabilistic language of conditional expectations, we reformulate the force matching method for coarse-graining of molecular systems as a projection onto spaces of coarse observables. A practical outcome of this probabilistic description is the link of the force matching method with thermodynamic integration. This connection provides a way to systematically construct a local mean force and to optimally approximate the potential of mean force through force matching. We introduce a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (e.g., reaction coordinates, end-to-end length of chains). Furthermore, we study the equivalence of force matching with relative entropy minimization which we derive for general non-linear coarse graining maps. We present in detail the generalized force matching condition through applications to specific examples in molecular systems.

Inspection of complex geometry pieces with an intelligent contact transducer

International Nuclear Information System (INIS)

Chatillon, S.; Roy, O.; Mahaut, St.

2000-01-01

A new multi-element contact transducer has been developed to improve the inspection of components with complex geometry. The emitting surface is flexible in order to optimize the contact with pieces. An algorithm, based on a simplified geometric model, has been used to determine the delays law which allows to control the focal characteristics of the transmitted field. Acquisition data lead in transmission with an articulated transducer validate the behavior provided by simulation. Thus the optimization of the delays law ensures the transmission of a beam which is homogeneous and controlled during the moving of the transducer. Inspections in echo-pulse mode are implemented on a sample simulating a component controlled on site. Results show that the dynamical adaptation of the delays law to the geometry of the piece leads to very good performances

Optimizing ultrasound molecular imaging of secreted frizzled related protein 2 expression in angiosarcoma.

Directory of Open Access Journals (Sweden)

James K Tsuruta

Full Text Available Secreted frizzled related protein 2 (SFRP2 is a tumor endothelial marker expressed in angiosarcoma. Previously, we showed ultrasound molecular imaging with SFRP2-targeted contrast increased average video pixel intensity (VI of angiosarcoma vessels by 2.2 ± 0.6 VI versus streptavidin contrast. We hypothesized that redesigning our contrast agents would increase imaging performance. Improved molecular imaging reagents were created by combining NeutrAvidin™-functionalized microbubbles with biotinylated SFRP2 or IgY control antibodies. When angiosarcoma tumors in nude mice reached 8 mm, time-intensity, antibody loading, and microbubble dose experiments optimized molecular imaging. 10 minutes after injection, the control-subtracted time-intensity curve (TIC for SFRP2-targeted contrast reached a maximum, after subtracting the contribution of free-flowing contrast. SFRP2 antibody-targeted VI was greater when contrast was formulated with 10-fold molar excess of maleimide-activated NeutrAvidin™ versus 3-fold (4.5 ± 0.18 vs. 0.32 ± 0.15, VI ± SEM, 5 x 106 dose, p < 0.001. Tumor vasculature returned greater average video pixel intensity using 5 x 107 versus 5 x 106 microbubbles (21.2 ± 2.5 vs. 4.5 ± 0.18, p = 0.0011. Specificity for tumor vasculature was confirmed by low VI for SFRP2-targeted, and control contrast in peri-tumoral vasculature (3.2 ± 0.52 vs. 1.6 ± 0.71, p = 0.92. After optimization, average video pixel intensity of tumor vasculature was 14.2 ± 3.0 VI units higher with SFRP2-targeted contrast versus IgY-targeted control (22.1 ± 2.5 vs. 7.9 ± 1.6, p < 0.001. After log decompression, 14.2 ΔVI was equal to ~70% higher signal, in arbitray acoustic units (AU, for SFRP2 versus IgY. This provided ~18- fold higher acoustic signal enhancement than provided previously by 2.2 ΔVI. Basing our targeted contrast on NeutrAvidin™-functionalized microbubbles, using IgY antibodies for our control contrast, and optimizing our imaging protocol

Optimization of mechanical structures using particle swarm optimization

International Nuclear Information System (INIS)

Leite, Victor C.; Schirru, Roberto

2015-01-01

Several optimization problems are dealed with the particle swarm optimization (PSO) algorithm, there is a wide kind of optimization problems, it may be applications related to logistics or the reload of nuclear reactors. This paper discusses the use of the PSO in the treatment of problems related to mechanical structure optimization. The geometry and material characteristics of mechanical components are important for the proper functioning and performance of the systems were they are applied, particularly to the nuclear field. Calculations related to mechanical aspects are all made using ANSYS, while the PSO is programed in MATLAB. (author)

Optimization of mechanical structures using particle swarm optimization

Energy Technology Data Exchange (ETDEWEB)

Leite, Victor C.; Schirru, Roberto, E-mail: victor.coppo.leite@lmp.ufrj.br [Coordenacao dos Programas de Pos-Graduacao em Engenharia (LMP/PEN/COPPE/UFRJ), Rio de Janeiro, RJ (Brazil). Lab. de Monitoracao de Processos

2015-07-01

Several optimization problems are dealed with the particle swarm optimization (PSO) algorithm, there is a wide kind of optimization problems, it may be applications related to logistics or the reload of nuclear reactors. This paper discusses the use of the PSO in the treatment of problems related to mechanical structure optimization. The geometry and material characteristics of mechanical components are important for the proper functioning and performance of the systems were they are applied, particularly to the nuclear field. Calculations related to mechanical aspects are all made using ANSYS, while the PSO is programed in MATLAB. (author)

Optimization of combustion chamber geometry and operating conditions for compression ignition engine fueled with pre-blended gasoline-diesel fuel

International Nuclear Information System (INIS)

Lee, Seokhwon; Jeon, Joonho; Park, Sungwook

2016-01-01

Highlights: • Pre-blended gasoline-diesel fuel was used with direct injection system. • KIVA-CHEMKIN code modeled dual-fuel fuel spray and combustion processes with discrete multi-component model. • The characteristics of Combustion and emission on pre-blended fuel was investigated with various fuel reactivities. • Optimization of combustion chamber shape improved combustion performance of the gasoline-diesel blended fuel engine. - Abstract: In this study, experiments and numerical simulations were used to improve the fuel efficiency of compression ignition engine using a gasoline-diesel blended fuel and an optimization technology. The blended fuel is directly injected into the cylinder with various blending ratios. Combustion and emission characteristics were investigated to explore the effects of gasoline ratio on fuel blend. The present study showed that the advantages of gasoline-diesel blended fuel, high thermal efficiency and low emission, were maximized using the numerical optimization method. The ignition delay and maximum pressure rise rate increased with the proportion of gasoline. As the gasoline fraction increased, the combustion duration and the indicated mean effective pressure decreased. The homogeneity of the fuel-air mixture was improved due to longer ignition delay. Soot emission was significantly reduced up to 90% compared to that of conventional diesel. The nitrogen oxides emissions of the blended fuel increased slightly when the start of injection was retarded toward top dead center. For the numerical study, KIVA-CHEMKIN multi-dimensional CFD code was used to model the combustion and emission characteristics of gasoline-diesel blended fuel. The micro genetic algorithm coupled with the KIVA-CHEMKIN code were used to optimize the combustion chamber shape and operating conditions to improve the combustion performance of the blended fuel engine. The optimized chamber geometry enhanced the fuel efficiency, for a level of nitrogen oxides

Turbine Airfoil Optimization Using Quasi-3D Analysis Codes

Directory of Open Access Journals (Sweden)

Sanjay Goel

2009-01-01

Full Text Available A new approach to optimize the geometry of a turbine airfoil by simultaneously designing multiple 2D sections of the airfoil is presented in this paper. The complexity of 3D geometry modeling is circumvented by generating multiple 2D airfoil sections and constraining their geometry in the radial direction using first- and second-order polynomials that ensure smoothness in the radial direction. The flow fields of candidate geometries obtained during optimization are evaluated using a quasi-3D, inviscid, CFD analysis code. An inviscid flow solver is used to reduce the execution time of the analysis. Multiple evaluation criteria based on the Mach number profile obtained from the analysis of each airfoil cross-section are used for computing a quality metric. A key contribution of the paper is the development of metrics that emulate the perception of the human designer in visually evaluating the Mach Number distribution. A mathematical representation of the evaluation criteria coupled with a parametric geometry generator enables the use of formal optimization techniques in the design. The proposed approach is implemented in the optimal design of a low-pressure turbine nozzle.

Mapping enzymatic catalysis using the effective fragment molecular orbital method

DEFF Research Database (Denmark)

Svendsen, Casper Steinmann; Fedorov, Dmitri G.; Jensen, Jan Halborg

2013-01-01

We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path...... of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We...

Engineering controllable bidirectional molecular motors based on myosin

Science.gov (United States)

Chen, Lu; Nakamura, Muneaki; Schindler, Tony D.; Parker, David; Bryant, Zev

2012-01-01

Cytoskeletal motors drive the transport of organelles and molecular cargoes within cells1, and have potential applications in molecular detection and diagnostic devices2,3. Engineering molecular motors with dynamically controllable properties will allow selective perturbation of mechanical processes in living cells, and yield optimized device components for complex tasks such as molecular sorting and directed assembly3. Biological motors have previously been modified by introducing activation/deactivation switches that respond to metal ions4,5 and other signals6. Here we show that myosin motors can be engineered to reversibly change their direction of motion in response to a calcium signal. Building on previous protein engineering studies7–11 and guided by a structural model12 for the redirected power stroke of myosin VI, we constructed bidirectional myosins through the rigid recombination of structural modules. The performance of the motors was confirmed using gliding filament assays and single fluorophore tracking. Our general strategy, in which external signals trigger changes in the geometry and mechanics of myosin lever arms, should enable spatiotemporal control over a range of motor properties including processivity, stride size13, and branchpoint turning14. PMID:22343382

Stochastic geometry for image analysis

CERN Document Server

Descombes, Xavier

2013-01-01

This book develops the stochastic geometry framework for image analysis purpose. Two main frameworks are  described: marked point process and random closed sets models. We derive the main issues for defining an appropriate model. The algorithms for sampling and optimizing the models as well as for estimating parameters are reviewed.  Numerous applications, covering remote sensing images, biological and medical imaging, are detailed.  This book provides all the necessary tools for developing an image analysis application based on modern stochastic modeling.

Optical geometry

International Nuclear Information System (INIS)

Robinson, I.; Trautman, A.

1988-01-01

The geometry of classical physics is Lorentzian; but weaker geometries are often more appropriate: null geodesics and electromagnetic fields, for example, are well known to be objects of conformal geometry. To deal with a single null congruence, or with the radiative electromagnetic fields associated with it, even less is needed: flag geometry for the first, optical geometry, with which this paper is chiefly concerned, for the second. The authors establish a natural one-to-one correspondence between optical geometries, considered locally, and three-dimensional Cauchy-Riemann structures. A number of Lorentzian geometries are shown to be equivalent from the optical point of view. For example the Goedel universe, the Taub-NUT metric and Hauser's twisting null solution have an optical geometry isomorphic to the one underlying the Robinson congruence in Minkowski space. The authors present general results on the problem of lifting a CR structure to a Lorentz manifold and, in particular, to Minkowski space; and exhibit the relevance of the deviation form to this problem

Free energy landscape of siRNA-polycation complexation: Elucidating the effect of molecular geometry, polymer flexibility, and charge neutralization.

Directory of Open Access Journals (Sweden)

Gianvito Grasso

Full Text Available The success of medical threatments with DNA and silencing interference RNA is strongly related to the design of efficient delivery technologies. Cationic polymers represent an attractive strategy to serve as nucleic-acid carriers with the envisioned advantages of efficient complexation, low cost, ease of production, well-defined size, and low polydispersity index. However, the balance between efficacy and toxicity (safety of these polymers is a challenge and in need of improvement. With the aim of designing more effective polycationic-based gene carriers, many parameters such as carrier morphology, size, molecular weight, surface chemistry, and flexibility/rigidity ratio need to be taken into consideration. In the present work, the binding mechanism of three cationic polymers (polyarginine, polylysine and polyethyleneimine to a model siRNA target is computationally investigated at the atomistic level. In order to better understand the polycationic carrier-siRNA interactions, replica exchange molecular dynamic simulations were carried out to provide an exhaustive exploration of all the possible binding sites, taking fully into account the siRNA flexibility together with the presence of explicit solvent and ions. Moreover, well-tempered metadynamics simulations were employed to elucidate how molecular geometry, polycation flexibility, and charge neutralization affect the siRNA-polycations free energy landscape in term of low-energy binding modes and unbinding free energy barriers. Significant differences among polymer binding modes have been detected, revealing the advantageous binding properties of polyarginine and polylysine compared to polyethyleneimine.

Discrete Geometry Toolkit for Shape Optimization, Phase II

Data.gov (United States)

National Aeronautics and Space Administration — Simulation-based design optimization has been steadily maturing over the past two decades, but not without its own unique and persistent challenges. The proposed...

Molecular Disorder in (‒-Encecanescin

Directory of Open Access Journals (Sweden)

Benito Reyes-Trejo

2014-04-01

Full Text Available (‒-Encecanescin (1 has been isolated from the leaves of Eupatorium aschembornianum. Two conformers are present in the crystal structure as a result of molecular disorder. The structure of 1 was established by 1H- and 13C-NMR spectroscopy in CDCl3 solution using 2D NMR techniques (gHSQC, gHMBC and NOESY. A Monte Carlo random search using molecular mechanics followed by the geometry optimization of each minimum energy structure using density functional theory (DFT calculations at the B3LYP/6–31G* level and a Boltzmann analysis of the total energies generated accurate molecular models describing the conformational behavior of 1. The three most stable conformers 2–4 of compound 1 were reoptimized at the B3LYP/6-311++G(d,p level of theory using CHCl3 as a solvent. Correlations between the experimental 1H- and 13C-NMR chemical shifts (δexp have been found, and the GIAO/B3LYP/6-311++G(d,p calculated magnetic isotropic shielding tensors (σcalc for conformers 2 and 3, δexp = a + b σcalc, are reported. A good linear relationship between the experimental and calculated NMR data has been obtained for protons and carbon atoms.

Introducing geometry concept based on history of Islamic geometry

Science.gov (United States)

Maarif, S.; Wahyudin; Raditya, A.; Perbowo, K. S.

2018-01-01

Geometry is one of the areas of mathematics interesting to discuss. Geometry also has a long history in mathematical developments. Therefore, it is important integrated historical development of geometry in the classroom to increase’ knowledge of how mathematicians earlier finding and constructing a geometric concept. Introduction geometrical concept can be started by introducing the Muslim mathematician who invented these concepts so that students can understand in detail how a concept of geometry can be found. However, the history of mathematics development, especially history of Islamic geometry today is less popular in the world of education in Indonesia. There are several concepts discovered by Muslim mathematicians that should be appreciated by the students in learning geometry. Great ideas of mathematicians Muslim can be used as study materials to supplement religious character values taught by Muslim mathematicians. Additionally, by integrating the history of geometry in teaching geometry are expected to improve motivation and geometrical understanding concept.

Resolution, coverage, and geometry beyond traditional limits

Energy Technology Data Exchange (ETDEWEB)

Ronen, Shuki; Ferber, Ralf

1998-12-31

The presentation relates to the optimization of the image of seismic data and improved resolution and coverage of acquired data. Non traditional processing methods such as inversion to zero offset (IZO) are used. To realize the potential of saving acquisition cost by reducing in-fill and to plan resolution improvement by processing, geometry QC methods such as DMO Dip Coverage Spectrum (DDCS) and Bull`s Eyes Analysis are used. The DDCS is a 2-D spectrum whose entries consist of the DMO (Dip Move Out) coverage for a particular reflector specified by it`s true time dip and reflector normal strike. The Bull`s Eyes Analysis relies on real time processing of synthetic data generated with the real geometry. 4 refs., 6 figs.

Molecular identification of potential denitrifying bacteria and use of D-optimal mixture experimental design for the optimization of denitrification process.

Science.gov (United States)

Ben Taheur, Fadia; Fdhila, Kais; Elabed, Hamouda; Bouguerra, Amel; Kouidhi, Bochra; Bakhrouf, Amina; Chaieb, Kamel

2016-04-01

Three bacterial strains (TE1, TD3 and FB2) were isolated from date palm (degla), pistachio and barley. The presence of nitrate reductase (narG) and nitrite reductase (nirS and nirK) genes in the selected strains was detected by PCR technique. Molecular identification based on 16S rDNA sequencing method was applied to identify positive strains. In addition, the D-optimal mixture experimental design was used to optimize the optimal formulation of probiotic bacteria for denitrification process. Strains harboring denitrification genes were identified as: TE1, Agrococcus sp LN828197; TD3, Cronobacter sakazakii LN828198 and FB2, Pedicoccus pentosaceus LN828199. PCR results revealed that all strains carried the nirS gene. However only C. sakazakii LN828198 and Agrococcus sp LN828197 harbored the nirK and the narG genes respectively. Moreover, the studied bacteria were able to form biofilm on abiotic surfaces with different degree. Process optimization showed that the most significant reduction of nitrate was 100% with 14.98% of COD consumption and 5.57 mg/l nitrite accumulation. Meanwhile, the response values were optimized and showed that the most optimal combination was 78.79% of C. sakazakii LN828198 (curve value), 21.21% of P. pentosaceus LN828199 (curve value) and absence (0%) of Agrococcus sp LN828197 (curve value). Copyright © 2016 Elsevier Ltd. All rights reserved.

A fast direct solver for boundary value problems on locally perturbed geometries

Science.gov (United States)

Zhang, Yabin; Gillman, Adrianna

2018-03-01

Many applications including optimal design and adaptive discretization techniques involve solving several boundary value problems on geometries that are local perturbations of an original geometry. This manuscript presents a fast direct solver for boundary value problems that are recast as boundary integral equations. The idea is to write the discretized boundary integral equation on a new geometry as a low rank update to the discretized problem on the original geometry. Using the Sherman-Morrison formula, the inverse can be expressed in terms of the inverse of the original system applied to the low rank factors and the right hand side. Numerical results illustrate for problems where perturbation is localized the fast direct solver is three times faster than building a new solver from scratch.

Mathematical modeling for prediction and optimization of TIG welding pool geometry

Directory of Open Access Journals (Sweden)

U. Esme

2009-04-01

Full Text Available In this work, nonlinear and multi-objective mathematical models were developed to determine the process parameters corresponding to optimum weld pool geometry. The objectives of the developed mathematical models are to maximize tensile load (TL, penetration (P, area of penetration (AP and/or minimize heat affected zone (HAZ, upper width (UW and upper height (UH depending upon the requirements.

Geometry optimization of antimuscarinic, anticholinergic and antispasmodic aprophen hydrochloride

International Nuclear Information System (INIS)

Bano, F.; Akhter, N.

2013-01-01

Aprophen hydrochloride extensively used as anticholinergic, antimuscarinnin and antispasmodic agent. Structure based drug designed is based on the firm understanding of molecular recognition between active site group and interacting molecules ,it is strategy that become as integral part of modem drug discovery. The aim of present study is find out the minimum potential energy for aprophen hydrochloride. The potential energy of the molecule in molecular mechanics calculated by using force field concept. Potential energy effect the inter action of drug molecule with receptor these properties could be use to synthesize new drug candidates with improve pharmacological and therapeutic activity. (author)

The Alexandria library, a quantum-chemical database of molecular properties for force field development.

Science.gov (United States)

Ghahremanpour, Mohammad M; van Maaren, Paul J; van der Spoel, David

2018-04-10

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

The Alexandria library, a quantum-chemical database of molecular properties for force field development

Science.gov (United States)

Ghahremanpour, Mohammad M.; van Maaren, Paul J.; van der Spoel, David

2018-04-01

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

Geometry through history Euclidean, hyperbolic, and projective geometries

CERN Document Server

Dillon, Meighan I

2018-01-01

Presented as an engaging discourse, this textbook invites readers to delve into the historical origins and uses of geometry. The narrative traces the influence of Euclid’s system of geometry, as developed in his classic text The Elements, through the Arabic period, the modern era in the West, and up to twentieth century mathematics. Axioms and proof methods used by mathematicians from those periods are explored alongside the problems in Euclidean geometry that lead to their work. Students cultivate skills applicable to much of modern mathematics through sections that integrate concepts like projective and hyperbolic geometry with representative proof-based exercises. For its sophisticated account of ancient to modern geometries, this text assumes only a year of college mathematics as it builds towards its conclusion with algebraic curves and quaternions. Euclid’s work has affected geometry for thousands of years, so this text has something to offer to anyone who wants to broaden their appreciation for the...

Photogrammetric computer vision statistics, geometry, orientation and reconstruction

CERN Document Server

Förstner, Wolfgang

2016-01-01

This textbook offers a statistical view on the geometry of multiple view analysis, required for camera calibration and orientation and for geometric scene reconstruction based on geometric image features. The authors have backgrounds in geodesy and also long experience with development and research in computer vision, and this is the first book to present a joint approach from the converging fields of photogrammetry and computer vision. Part I of the book provides an introduction to estimation theory, covering aspects such as Bayesian estimation, variance components, and sequential estimation, with a focus on the statistically sound diagnostics of estimation results essential in vision metrology. Part II provides tools for 2D and 3D geometric reasoning using projective geometry. This includes oriented projective geometry and tools for statistically optimal estimation and test of geometric entities and transformations and their rela­tions, tools that are useful also in the context of uncertain reasoning in po...

Optimization of C20 isomers structure

International Nuclear Information System (INIS)

Ndjaka, J.M.B.; Charlier, J.C.

2001-07-01

We have performed geometry optimization of various possible planar and three-dimensional C 20 geometries. The planar structures considered include a linear chain, a monoclinic ring, and a bicyclic bow tie; while the three-dimensional geometric; consisted of a bowl or corranulene structure and a fullerene cage. In agreement with Wang et al MP2's calculations, our results predict the corranulene bowl to be the lowest energy structure. From the ground state geometry to the highest energy, considered C 20 structures, listed in increasing energy, are bowl, cage, bow tie, ring and chain. For the ring and bow tie isomers, the shape of the optimized structure deviates from that of the initial configuration; while the shape of the optimised bowl, cage and chain remain unchanged. (author)

Molecular structure and vibrational spectra of Bis(melaminium) terephthalate dihydrate: A DFT computational study

Science.gov (United States)

Tanak, Hasan; Marchewka, Mariusz K.; Drozd, Marek

2013-03-01

The experimental and theoretical vibrational spectra of Bis(melaminium) terephthalate dihydrate were studied. The Fourier transform infrared (FT-IR) spectra of the Bis(melaminium) terephthalate dihydrate and its deuterated analogue were recorded in the solid phase. The molecular geometry and vibrational frequencies of Bis(melaminium) terephthalate dihydrate in the ground state have been calculated by using the density functional method (B3LYP) with 6-31++G(d,p) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The molecule contains the weak hydrogen bonds of Nsbnd H⋯O, Nsbnd H⋯N and Osbnd H⋯O types, and those bonds are calculated with DFT method. In addition, molecular electrostatic potential, frontier molecular orbitals and natural bond orbital analysis of the title compound were investigated by theoretical calculations. The lack of the second harmonic generation (SHG) confirms the presence of macroscopic center of inversion.

Optimal laser control of ultrafast photodissociation of I2- in water: Mixed quantum/classical molecular dynamics simulation

International Nuclear Information System (INIS)

Nishiyama, Yoshikazu; Kato, Tsuyoshi; Ohtsuki, Yukiyoshi; Fujimura, Yuichi

2004-01-01

A linearized optimal control method in combination with mixed quantum/classical molecular dynamics simulation is used for numerically investigating the possibility of controlling photodissociation wave packets of I 2 - in water. Optimal pulses are designed using an ensemble of photodissociation samples, aiming at the creation of localized dissociation wave packets. Numerical results clearly show the effectiveness of the control although the control achievement is reduced with an increase in the internuclear distance associated with a target region. We introduce effective optimal pulses that are designed using a statistically averaged effective dissociation potential, and show that they semiquantitatively reproduce the control achievements calculated by using optimal pulses. The control mechanisms are interpreted from the time- and frequency-resolved spectra of the effective optimal pulses

Triplet-Based Codon Organization Optimizes the Impact of Synonymous Mutation on Nucleic Acid Molecular Dynamics.

Science.gov (United States)

Babbitt, Gregory A; Coppola, Erin E; Mortensen, Jamie S; Ekeren, Patrick X; Viola, Cosmo; Goldblatt, Dallan; Hudson, André O

2018-02-01

Since the elucidation of the genetic code almost 50 years ago, many nonrandom aspects of its codon organization remain only partly resolved. Here, we investigate the recent hypothesis of 'dual-use' codons which proposes that in addition to allowing adjustment of codon optimization to tRNA abundance, the degeneracy in the triplet-based genetic code also multiplexes information regarding DNA's helical shape and protein-binding dynamics while avoiding interference with other protein-level characteristics determined by amino acid properties. How such structural optimization of the code within eukaryotic chromatin could have arisen from an RNA world is a mystery, but would imply some preadaptation in an RNA context. We analyzed synonymous (protein-silent) and nonsynonymous (protein-altering) mutational impacts on molecular dynamics in 13823 identically degenerate alternative codon reorganizations, defined by codon transitions in 7680 GPU-accelerated molecular dynamic simulations of implicitly and explicitly solvated double-stranded aRNA and bDNA structures. When compared to all possible alternative codon assignments, the standard genetic code minimized the impact of synonymous mutations on the random atomic fluctuations and correlations of carbon backbone vector trajectories while facilitating the specific movements that contribute to DNA polymer flexibility. This trend was notably stronger in the context of RNA supporting the idea that dual-use codon optimization and informational multiplexing in DNA resulted from the preadaptation of the RNA duplex to resist changes to thermostability. The nonrandom and divergent molecular dynamics of synonymous mutations also imply that the triplet-based code may have resulted from adaptive functional expansion enabling a primordial doublet code to multiplex gene regulatory information via the shape and charge of the minor groove.

Reliability-Based Optimization of Structural Elements

DEFF Research Database (Denmark)

Sørensen, John Dalsgaard

In this paper structural elements from an optimization point of view are considered, i.e. only the geometry of a structural element is optimized. Reliability modelling of the structural element is discussed both from an element point of view and from a system point of view. The optimization...

Two lectures on D-geometry and noncommutative geometry

International Nuclear Information System (INIS)

Douglas, M.R.

1999-01-01

This is a write-up of lectures given at the 1998 Spring School at the Abdus Salam ICTP. We give a conceptual introduction to D-geometry, the study of geometry as seen by D-branes in string theory, and to noncommutative geometry as it has appeared in D-brane and Matrix theory physics. (author)

Molecular structure and vibrational spectra of 6-methylquinoline and 8-methylquinoline molecules by quantum mechanical methods

International Nuclear Information System (INIS)

Kurt, M.

2005-01-01

The molecular geometry and vibrational frequencies of 6-methylquinoline(6MQ) and 8-methylquinolines(8MQ) in the ground state have been calculated by using the Hartree-Fock and density functional methods (B3LYP and BLYP) with 6-31G (d) as the basis set. The optimized geometric bond lengths obtained by using B3LYP and bond angles obtained by BLYP were given corresponding experimental values of similar molecule. Comparison of the observed fundamental vibrational frequencies of these molecules and calculated results by density functional B3LYP, BLYP and Hartree-Fock methods indicates that B3LYP is superior to the scaled Hartree- Fock and BLYP approach for molecular vibrational problems

Optimization of fin geometry in heat convection with entransy theory

International Nuclear Information System (INIS)

Cheng Xue-Tao; Xu Xiang-Hua; Liang Xin-Gang; Zhang Qin-Zhao

2013-01-01

The entransy theory developed in recent years is used to optimize the aspect ratio of a plate fin in heat convection. Based on a two-dimensional model, the theoretical analysis shows that the minimum thermal resistance defined with the concept of entransy dissipation corresponds to the maximum heat transfer rate when the temperature of the heating surface is fixed. On the other hand, when the heat flux of the heating surface is fixed, the minimum thermal resistance corresponds to the minimum average temperature of the heating surface. The entropy optimization is also given for the heat transfer processes. It is observed that the minimum entropy generation, the minimum entropy generation number, and the minimum revised entropy generation number do not always correspond to the best heat transfer performance. In addition, the influence factors on the optimized aspect ratio of the plate fin are also discussed. The optimized ratio decreases with the enhancement of heat convection, while it increases with fin thermal conductivity increasing. (general)

The Geometry Optimisation of a Triple Branch Pipe Using Finite Element Method

Directory of Open Access Journals (Sweden)

Dorian Nedelcu

2008-01-01

Full Text Available The paper presents the geometrical optimization of a triple branch pipesubmitted to an internal pressure. The goal of the optimization was todetermine the optimum thickness of piping and branch pipe ribs, in thecondition of reaching admissible values of the stress and displacement.The resistance calculus was realized with Cosmos DesignStar softwareand the geometry was modeled with Microstation Modeler software.

Twistor geometry

NARCIS (Netherlands)

van den Broek, P.M.

1984-01-01

The aim of this paper is to give a detailed exposition of the relation between the geometry of twistor space and the geometry of Minkowski space. The paper has a didactical purpose; no use has been made of differential geometry and cohomology.

Geometry

Indian Academy of Sciences (India)

. In the previous article we looked at the origins of synthetic and analytic geometry. More practical minded people, the builders and navigators, were studying two other aspects of geometry- trigonometry and integral calculus. These are actually ...

Non-euclidean simplex optimization. [Application to potentiometric titration of Pu

Energy Technology Data Exchange (ETDEWEB)

Silver, G.L.

1977-08-15

Geometric optimization techniques useful for studying chemical equilibrium traditionally rely upon principles of euclidean geometry, but such algorithms may also be based upon principles of a non-euclidean geometry. The sequential simplex method is adapted to the hyperbolic plane, and application of optimization to problems such as the potentiometric titration of plutonium is suggested.

Sums over geometries and improvements on the mean field approximation

International Nuclear Information System (INIS)

Sacksteder, Vincent E. IV

2007-01-01

The saddle points of a Lagrangian due to Efetov are analyzed. This Lagrangian was originally proposed as a tool for calculating systematic corrections to the Bethe approximation, a mean-field approximation which is important in statistical mechanics, glasses, coding theory, and combinatorial optimization. Detailed analysis shows that the trivial saddle point generates a sum over geometries reminiscent of dynamically triangulated quantum gravity, which suggests new possibilities to design sums over geometries for the specific purpose of obtaining improved mean-field approximations to D-dimensional theories. In the case of the Efetov theory, the dominant geometries are locally treelike, and the sum over geometries diverges in a way that is similar to quantum gravity's divergence when all topologies are included. Expertise from the field of dynamically triangulated quantum gravity about sums over geometries may be able to remedy these defects and fulfill the Efetov theory's original promise. The other saddle points of the Efetov Lagrangian are also analyzed; the Hessian at these points is nonnormal and pseudo-Hermitian, which is unusual for bosonic theories. The standard formula for Gaussian integrals is generalized to nonnormal kernels

Trak Investigation of Focusing Electrode Geometries for the DARHT Axis-I Diode

Energy Technology Data Exchange (ETDEWEB)

Kallas, Nicholas Dimitrious [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-05-15

An investigation was carried out on the effects of different cathode shroud geometries of the DARHT Axis-1 diode using the Trak ray tracing software. Pierce angles of 20, 30, 45, 60, and 67.5 degrees were investigated. For each geometry the current density with respect to radial position will be presented as it evolves in the longitudinal direction. In addition the emittances for each geometry are compared and this information is used to determine the optimal geometry from the selected angles. These results are compared to the baseline geometry currently employed at DARHT of a simple 2.5mm recessed velvet cathode. Of the selected angles it was found that 45 degrees produced the lowest normalized emittance value, whereas 60 degrees produced the most uniform current density profile at 1cm away from the emission surface. For the purpose of this investigation the effects of the bucking coil and solenoid around the hollow anode of the DARHT Axis I injector are neglected.

Excitation two-center interference and the orbital geometry in laser-induced nonsequential double ionization of diatomic molecules

International Nuclear Information System (INIS)

Shaaran, T.; Augstein, B. B.; Figueira de Morisson Faria, C.

2011-01-01

We address the influence of the molecular orbital geometry and of the molecular alignment with respect to the laser-field polarization on laser-induced nonsequential double ionization of diatomic molecules for different molecular species, namely N 2 and Li 2 . We focus on the recollision excitation with subsequent tunneling ionization (RESI) mechanism, in which the first electron, upon return, promotes the second electron to an excited state, from where it subsequently tunnels. We assume that both electrons are initially in the highest occupied molecular orbital (HOMO) and that the second electron is excited to the lowest unoccupied molecular orbital (LUMO). We show that the electron-momentum distributions exhibit interference maxima and minima due to the electron emission at spatially separated centers. We provide generalized analytical expressions for such maxima or minima, which take into account s-p mixing and the orbital geometry. The patterns caused by the two-center interference are sharpest for vanishing alignment angle and get washed out as this parameter increases. Apart from that, there exist features due to the geometry of the LUMO, which may be observed for a wide range of alignment angles. Such features manifest themselves as the suppression of probability density in specific momentum regions due to the shape of the LUMO wave function, or as an overall decrease in the RESI yield due to the presence of nodal planes.

Computational Modeling and Theoretical Calculations on the Interactions between Spermidine and Functional Monomer (Methacrylic Acid in a Molecularly Imprinted Polymer

Directory of Open Access Journals (Sweden)

Yujie Huang

2015-01-01

Full Text Available This paper theoretically investigates interactions between a template and functional monomer required for synthesizing an efficient molecularly imprinted polymer (MIP. We employed density functional theory (DFT to compute geometry, single-point energy, and binding energy (ΔE of an MIP system, where spermidine (SPD and methacrylic acid (MAA were selected as template and functional monomer, respectively. The geometry was calculated by using B3LYP method with 6-31+(d basis set. Furthermore, 6-311++(d, p basis set was used to compute the single-point energy of the above geometry. The optimized geometries at different template to functional monomer molar ratios, mode of bonding between template and functional monomer, changes in charge on natural bond orbital (NBO, and binding energy were analyzed. The simulation results show that SPD and MAA form a stable complex via hydrogen bonding. At 1 : 5 SPD to MAA ratio, the binding energy is minimum, while the amount of transferred charge between the molecules is maximum; SPD and MAA form a stable complex at 1 : 5 molar ratio through six hydrogen bonds. Optimizing structure of template-functional monomer complex, through computational modeling prior synthesis, significantly contributes towards choosing a suitable pair of template-functional monomer that yields an efficient MIP with high specificity and selectivity.

The geometry of higher-order Lagrange spaces applications to mechanics and physics

CERN Document Server

Miron, Radu

1997-01-01

This monograph is devoted to the problem of the geometrizing of Lagrangians which depend on higher-order accelerations It presents a construction of the geometry of the total space of the bundle of the accelerations of order k>=1 A geometrical study of the notion of the higher-order Lagrange space is conducted, and the old problem of prolongation of Riemannian spaces to k-osculator manifolds is solved Also, the geometrical ground for variational calculus on the integral of actions involving higher-order Lagrangians is dealt with Applications to higher-order analytical mechanics and theoretical physics are included as well Audience This volume will be of interest to scientists whose work involves differential geometry, mechanics of particles and systems, calculus of variation and optimal control, optimization, optics, electromagnetic theory, and biology

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program.

Science.gov (United States)

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A

2017-12-28

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

A Parallel Biological Optimization Algorithm to Solve the Unbalanced Assignment Problem Based on DNA Molecular Computing.

Science.gov (United States)

Wang, Zhaocai; Pu, Jun; Cao, Liling; Tan, Jian

2015-10-23

The unbalanced assignment problem (UAP) is to optimally resolve the problem of assigning n jobs to m individuals (m applied mathematics, having numerous real life applications. In this paper, we present a new parallel DNA algorithm for solving the unbalanced assignment problem using DNA molecular operations. We reasonably design flexible-length DNA strands representing different jobs and individuals, take appropriate steps, and get the solutions of the UAP in the proper length range and O(mn) time. We extend the application of DNA molecular operations and simultaneity to simplify the complexity of the computation.

The influence of branch order on optimal leaf vein geometries: Murray's law and area preserving branching.

Directory of Open Access Journals (Sweden)

Charles A Price

Full Text Available Models that predict the form of hierarchical branching networks typically invoke optimization based on biomechanical similitude, the minimization of impedance to fluid flow, or construction costs. Unfortunately, due to the small size and high number of vein segments found in real biological networks, complete descriptions of networks needed to evaluate such models are rare. To help address this we report results from the analysis of the branching geometry of 349 leaf vein networks comprising over 1.5 million individual vein segments. In addition to measuring the diameters of individual veins before and after vein bifurcations, we also assign vein orders using the Horton-Strahler ordering algorithm adopted from the study of river networks. Our results demonstrate that across all leaves, both radius tapering and the ratio of daughter to parent branch areas for leaf veins are in strong agreement with the expectation from Murray's law. However, as veins become larger, area ratios shift systematically toward values expected under area-preserving branching. Our work supports the idea that leaf vein networks differentiate roles of leaf support and hydraulic supply between hierarchical orders.

SYNTHESIS AND CHARACTERIZATION OF NEW STABILIZERS WITH OPTIMAL MOLECULAR WEIGHT

Institute of Scientific and Technical Information of China (English)

Jiang-qing Pan

2001-01-01

Over 2 × l08 tons of polymers are produced every year, and a large portion of polymers faces the degradation problem. There are many effective methods to protect polymers against degradation and the addition of stabilizers to polymer remains the most convenient and effective way of enhancing polymer life and performance. In this article, a series of effective stabilizers with optimal molecular weight (MW), including common, monomeric and polymeric stabilizers (antioxidant and light stabilizer) were synthesized using isocyanation, controlled isocyanation, hydrosilylation, epoxide addition, macroreaction of stabilizing functional compounds and polymerization of monomeric stabilizers. The sructure and performance of these new stabilizers were characterized by using IR, NMR, MS, UV-spectra, XPS and elemental analysis. The current development of stabilizer synthesis was also reviewed.``

Design and Optimization of AlN based RF MEMS Switches

Science.gov (United States)

Hasan Ziko, Mehadi; Koel, Ants

2018-05-01

Radio frequency microelectromechanical system (RF MEMS) switch technology might have potential to replace the semiconductor technology in future communication systems as well as communication satellites, wireless and mobile phones. This study is to explore the possibilities of RF MEMS switch design and optimization with aluminium nitride (AlN) thin film as the piezoelectric actuation material. Achieving low actuation voltage and high contact force with optimal geometry using the principle of piezoelectric effect is the main motivation for this research. Analytical and numerical modelling of single beam type RF MEMS switch used to analyse the design parameters and optimize them for the minimum actuation voltage and high contact force. An analytical model using isotropic AlN material properties used to obtain the optimal parameters. The optimized geometry of the device length, width and thickness are 2000 µm, 500 µm and 0.6 µm respectively obtained for the single beam RF MEMS switch. Low actuation voltage and high contact force with optimal geometry are less than 2 Vand 100 µN obtained by analytical analysis. Additionally, the single beam RF MEMS switch are optimized and validated by comparing the analytical and finite element modelling (FEM) analysis.

Optimizing SRF Gun Cavity Profiles in a Genetic Algorithm Framework

International Nuclear Information System (INIS)

Hofler, Alicia; Evtushenko, Pavel; Marhauser, Frank

2009-01-01

Automation of DC photoinjector designs using a genetic algorithm (GA) based optimization is an accepted practice in accelerator physics. Allowing the gun cavity field profile shape to be varied can extend the utility of this optimization methodology to superconducting and normal conducting radio frequency (SRF/RF) gun based injectors. Finding optimal field and cavity geometry configurations can provide guidance for cavity design choices and verify existing designs. We have considered two approaches for varying the electric field profile. The first is to determine the optimal field profile shape that should be used independent of the cavity geometry, and the other is to vary the geometry of the gun cavity structure to produce an optimal field profile. The first method can provide a theoretical optimal and can illuminate where possible gains can be made in field shaping. The second method can produce more realistically achievable designs that can be compared to existing designs. In this paper, we discuss the design and implementation for these two methods for generating field profiles for SRF/RF guns in a GA based injector optimization scheme and provide preliminary results.

Optimization of GMAW process of AA 6063-T5 aluminum alloy butt joints based on the response surface methodology and on the bead geometry

International Nuclear Information System (INIS)

Miguel, V.; Martinez-Conesa, E. J.; Segura, F.; Manjabacas, M. C.; Abellan, E.

2012-01-01

The geometry of the weld beads is characterized by the overhead, the width and the penetration. These values are indices of the behavior of the welded joint and therefore, they can be considered as factors that control the process. This work is performed to optimize the GMAW process of the aluminum alloy AA 6063-T5 by means of the response surface methodology (RSM). The variables herein considered are the arc voltage, the welding speed, the wire feed speed and the separation between surfaces in butt joints. The response functions that are herein studied are the overhead, the width, the penetration and the angle of the bead. The obtained results by RSM show high grade of agreement with the experimental values. The procedure is experimentally validated by welding for the theoretically obtained optimized technological conditions and a wide agreement between theoretical and experimental values is found. (Author) 16 refs.

Coupling Matched Molecular Pairs with Machine Learning for Virtual Compound Optimization.

Science.gov (United States)

Turk, Samo; Merget, Benjamin; Rippmann, Friedrich; Fulle, Simone

2017-12-26

Matched molecular pair (MMP) analyses are widely used in compound optimization projects to gain insights into structure-activity relationships (SAR). The analysis is traditionally done via statistical methods but can also be employed together with machine learning (ML) approaches to extrapolate to novel compounds. The here introduced MMP/ML method combines a fragment-based MMP implementation with different machine learning methods to obtain automated SAR decomposition and prediction. To test the prediction capabilities and model transferability, two different compound optimization scenarios were designed: (1) "new fragments" which occurs when exploring new fragments for a defined compound series and (2) "new static core and transformations" which resembles for instance the identification of a new compound series. Very good results were achieved by all employed machine learning methods especially for the new fragments case, but overall deep neural network models performed best, allowing reliable predictions also for the new static core and transformations scenario, where comprehensive SAR knowledge of the compound series is missing. Furthermore, we show that models trained on all available data have a higher generalizability compared to models trained on focused series and can extend beyond chemical space covered in the training data. Thus, coupling MMP with deep neural networks provides a promising approach to make high quality predictions on various data sets and in different compound optimization scenarios.

Symplectic and Poisson Geometry in Interaction with Analysis, Algebra and Topology & Symplectic Geometry, Noncommutative Geometry and Physics

CERN Document Server

Eliashberg, Yakov; Maeda, Yoshiaki; Symplectic, Poisson, and Noncommutative geometry

2014-01-01

Symplectic geometry originated in physics, but it has flourished as an independent subject in mathematics, together with its offspring, symplectic topology. Symplectic methods have even been applied back to mathematical physics. Noncommutative geometry has developed an alternative mathematical quantization scheme based on a geometric approach to operator algebras. Deformation quantization, a blend of symplectic methods and noncommutative geometry, approaches quantum mechanics from a more algebraic viewpoint, as it addresses quantization as a deformation of Poisson structures. This volume contains seven chapters based on lectures given by invited speakers at two May 2010 workshops held at the Mathematical Sciences Research Institute: Symplectic and Poisson Geometry in Interaction with Analysis, Algebra and Topology (honoring Alan Weinstein, one of the key figures in the field) and Symplectic Geometry, Noncommutative Geometry and Physics. The chapters include presentations of previously unpublished results and ...

Geometry correction Algorithm for UAV Remote Sensing Image Based on Improved Neural Network

Science.gov (United States)

Liu, Ruian; Liu, Nan; Zeng, Beibei; Chen, Tingting; Yin, Ninghao

2018-03-01

Aiming at the disadvantage of current geometry correction algorithm for UAV remote sensing image, a new algorithm is proposed. Adaptive genetic algorithm (AGA) and RBF neural network are introduced into this algorithm. And combined with the geometry correction principle for UAV remote sensing image, the algorithm and solving steps of AGA-RBF are presented in order to realize geometry correction for UAV remote sensing. The correction accuracy and operational efficiency is improved through optimizing the structure and connection weight of RBF neural network separately with AGA and LMS algorithm. Finally, experiments show that AGA-RBF algorithm has the advantages of high correction accuracy, high running rate and strong generalization ability.

Designing Geometry 2.0 learning environments: a preliminary study with primary school students

Science.gov (United States)

Joglar Prieto, Nuria; María Sordo Juanena, José; Star, Jon R.

2014-04-01

The information and communication technologies of Web 2.0 are arriving in our schools, allowing the design and implementation of new learning environments with great educational potential. This article proposes a pedagogical model based on a new geometry technology-integrated learning environment, called Geometry 2.0, which was tested with 39 sixth grade students from a public school in Madrid (Spain). The main goals of the study presented here were to describe an optimal role for the mathematics teacher within Geometry 2.0, and to analyse how dynamic mathematics and communication might affect young students' learning of basic figural concepts in a real setting. The analyses offered in this article illustrate how our Geometry 2.0 model facilitates deeply mathematical tasks which encourage students' exploration, cooperation and communication, improving their learning while fostering geometrical meanings.

Theoretical investigation of molecular structure and vibrational spectra of 4,5-bis-(2-isopropyl-5- methylphenoxy) phthalonitrile molecule

International Nuclear Information System (INIS)

Avci, D.

2005-01-01

The molecular geometry and vibrational frequencies of 4,5-bis-(2-isopropyl-5- methylphenoxy) phthalonitrile in the ground state have been calculated using the Hartree- Fock (HF) and density functional method (B3LYP) with 6-31G(d) basis set. The optimized geometric bond lengths and bond angles obtained by using HF and DFT (B3LYP) show the best agreement with the experimental data. Comparison of the observed fundamental vibrational frequencies of 4,5-bis-(2-isopropyl-5-methylphenoxy) phthalonitrile with calculated results by density functional B3LYP and Hartree-Fock methods indicate that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems

Monte Carlo Optimization of Crystal Configuration for Pixelated Molecular SPECT Scanners

Energy Technology Data Exchange (ETDEWEB)

Mahani, Hojjat [Radiation Application Research School, Nuclear Science and Technology Research Institute, Tehran (Iran, Islamic Republic of); Research Center for Molecular and Cellular Imaging, Tehran University of Medical Science, Tehran (Iran, Islamic Republic of); Raisali, Gholamreza [Radiation Application Research School, Nuclear Science and Technology Research Institute, Tehran (Iran, Islamic Republic of); Kamali-Asl, Alireza [Radiation Medicine Department, Shahid Beheshti University, Tehran (Iran, Islamic Republic of); Ay, Mohammad Reza, E-mail: mohammadreza_ay@sina.tums.ac.ir [Research Center for Molecular and Cellular Imaging, Tehran University of Medical Science, Tehran (Iran, Islamic Republic of); Department of Medical Physics and Biomedical Engineering, Tehran University of Medical Science, Tehran (Iran, Islamic Republic of)

2017-02-01

Resolution-sensitivity-PDA tradeoff is the most challenging problem in design and optimization of pixelated preclinical SPECT scanners. In this work, we addressed such a challenge from a crystal point-of-view by looking for an optimal pixelated scintillator using GATE Monte Carlo simulation. Various crystal configurations have been investigated and the influence of different pixel sizes, pixel gaps, and three scintillators on tomographic resolution, sensitivity, and PDA of the camera were evaluated. The crystal configuration was then optimized using two objective functions: the weighted-sum and the figure-of-merit methods. The CsI(Na) reveals the highest sensitivity of the order of 43.47 cps/MBq in comparison to the NaI(Tl) and the YAP(Ce), for a 1.5×1.5 mm{sup 2} pixel size and 0.1 mm gap. The results show that the spatial resolution, in terms of FWHM, improves from 3.38 to 2.21 mm while the sensitivity simultaneously deteriorates from 42.39 cps/MBq to 27.81 cps/MBq when pixel size varies from 2×2 mm{sup 2} to 0.5×0.5 mm{sup 2} for a 0.2 mm gap, respectively. The PDA worsens from 0.91 to 0.42 when pixel size decreases from 0.5×0.5 mm{sup 2} to 1×1 mm{sup 2} for a 0.2 mm gap at 15° incident-angle. The two objective functions agree that the 1.5×1.5 mm{sup 2} pixel size and 0.1 mm Epoxy gap CsI(Na) configuration provides the best compromise for small-animal imaging, using the HiReSPECT scanner. Our study highlights that crystal configuration can significantly affect the performance of the camera, and thereby Monte Carlo optimization of pixelated detectors is mandatory in order to achieve an optimal quality tomogram. - Highlights: • We optimized pixelated crystal configuration for the purpose of molecular SPECT imaging. • The weighted-sum and the figure-of-merit methods were used in order to search for an optimal crystal configuration. • The higher the pixel size, the poorer the resolution and simultaneously the higher the sensitivity and the PDA. • The

Monte Carlo Optimization of Crystal Configuration for Pixelated Molecular SPECT Scanners

International Nuclear Information System (INIS)

Mahani, Hojjat; Raisali, Gholamreza; Kamali-Asl, Alireza; Ay, Mohammad Reza

2017-01-01

Resolution-sensitivity-PDA tradeoff is the most challenging problem in design and optimization of pixelated preclinical SPECT scanners. In this work, we addressed such a challenge from a crystal point-of-view by looking for an optimal pixelated scintillator using GATE Monte Carlo simulation. Various crystal configurations have been investigated and the influence of different pixel sizes, pixel gaps, and three scintillators on tomographic resolution, sensitivity, and PDA of the camera were evaluated. The crystal configuration was then optimized using two objective functions: the weighted-sum and the figure-of-merit methods. The CsI(Na) reveals the highest sensitivity of the order of 43.47 cps/MBq in comparison to the NaI(Tl) and the YAP(Ce), for a 1.5×1.5 mm"2 pixel size and 0.1 mm gap. The results show that the spatial resolution, in terms of FWHM, improves from 3.38 to 2.21 mm while the sensitivity simultaneously deteriorates from 42.39 cps/MBq to 27.81 cps/MBq when pixel size varies from 2×2 mm"2 to 0.5×0.5 mm"2 for a 0.2 mm gap, respectively. The PDA worsens from 0.91 to 0.42 when pixel size decreases from 0.5×0.5 mm"2 to 1×1 mm"2 for a 0.2 mm gap at 15° incident-angle. The two objective functions agree that the 1.5×1.5 mm"2 pixel size and 0.1 mm Epoxy gap CsI(Na) configuration provides the best compromise for small-animal imaging, using the HiReSPECT scanner. Our study highlights that crystal configuration can significantly affect the performance of the camera, and thereby Monte Carlo optimization of pixelated detectors is mandatory in order to achieve an optimal quality tomogram. - Highlights: • We optimized pixelated crystal configuration for the purpose of molecular SPECT imaging. • The weighted-sum and the figure-of-merit methods were used in order to search for an optimal crystal configuration. • The higher the pixel size, the poorer the resolution and simultaneously the higher the sensitivity and the PDA. • The higher the pixel gap, the

Application of adobe flash media to optimize jigsaw learning model on geometry material

Science.gov (United States)

Imam, P.; Imam, S.; Ikrar, P.

2018-05-01

This study aims to determine and describe the effectiveness of the application of adobe flash media for jigsaw learning model on geometry material. In this study, the modified jigsaw learning with adobe flash media is called jigsaw-flash model. This research was conducted in Surakarta. The research method used is mix method research with exploratory sequential strategy. The results of this study indicate that students feel more comfortable and interested in studying geometry material taught by jigsaw-flash model. In addition, students taught using the jigsaw-flash model are more active and motivated than the students who were taught using ordinary jigsaw models. This shows that the use of the jigsaw-flash model can increase student participation and motivation. It can be concluded that the adobe flash media can be used as a solution to reduce the level of student abstraction in learning mathematics.

Parametric Study Of Window Frame Geometry

DEFF Research Database (Denmark)

Zajas, Jan Jakub; Heiselberg, Per

2013-01-01

This paper describes a parametric study on window frame geometry with the goal of designing frames with very good thermal properties. Three different parametric frame models are introduced, deseribed by a number of variables. In the first part of the study, a process of sensitivity analysis...... is conducted to determine which of the parameters describing the frame have the highest impact on its thermal performance. Afterwards, an optimization process is conducted on each frame in order to optimize the design with regard to three objectives: minimizing the thermal transmittance, maxim izing the net...... energy gain factor and minimizing the material use. Since the objectives contradiet each other, it was found that it is not possible to identifY a single solution that satisfies all these goals. lnstead, a compromise between the objectives has to be found....

Aerodynamic shape optimization of non-straight small wind turbine blades

International Nuclear Information System (INIS)

Shen, Xin; Yang, Hong; Chen, Jinge; Zhu, Xiaocheng; Du, Zhaohui

2016-01-01

Graphical abstract: Small wind turbine blades with 3D stacking lines (sweep and bend) have been considered and analyzed with an optimization code based on the lifting surface method. The results indicated that the power capture and the rotor thrust can be improved with these more complex geometries. The starting behavior of the small wind turbines can be improved by the optimization of the blade chord and twist angle distribution. - Highlights: • The small wind turbine blade was optimized with non-straight shape. • Lifting surface method with free wake was used for aerodyanmic performace evaluation. • The non-straight shape can be used to increase energy production and decrease the thrust. • The energy production should be sacrificed in order to increase the starting behavior. - Abstract: Small wind turbines usually operate in sub-optimal wind conditions in order to satisfy the demand where it is needed. The aerodynamic performance of small horizontal axis wind turbines highly depends on the geometry. In the present study, the geometry of wind turbine blades are optimized not only in terms of the distribution of the chord and twist angle but also with 3-dimensional stacking line. As the blade with 3-dimensional stacking line is given sweep in the plan of rotation and dihedral in the plan containing the blade and rotor axis, the common used blade element momentum method can no longer provide accurate aerodynamic performance solution. A lifting surface method with free wake model is used as the aerodynamic model in the present work. The annual energy production and the starting performance are selected as optimization objective. The starting performance is evaluated based on blade element method. The optimization of the geometry of the non-straight wind turbine blades is carried out by using a micro-genetic algorithm. Results show that the wind turbine blades with properly designed 3-dimensional stacking line can increase the annual energy production and have

AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening

Directory of Open Access Journals (Sweden)

Pajeva Ilza

2008-10-01

Full Text Available Abstract Background Virtual or in silico ligand screening combined with other computational methods is one of the most promising methods to search for new lead compounds, thereby greatly assisting the drug discovery process. Despite considerable progresses made in virtual screening methodologies, available computer programs do not easily address problems such as: structural optimization of compounds in a screening library, receptor flexibility/induced-fit, and accurate prediction of protein-ligand interactions. It has been shown that structural optimization of chemical compounds and that post-docking optimization in multi-step structure-based virtual screening approaches help to further improve the overall efficiency of the methods. To address some of these points, we developed the program AMMOS for refining both, the 3D structures of the small molecules present in chemical libraries and the predicted receptor-ligand complexes through allowing partial to full atom flexibility through molecular mechanics optimization. Results The program AMMOS carries out an automatic procedure that allows for the structural refinement of compound collections and energy minimization of protein-ligand complexes using the open source program AMMP. The performance of our package was evaluated by comparing the structures of small chemical entities minimized by AMMOS with those minimized with the Tripos and MMFF94s force fields. Next, AMMOS was used for full flexible minimization of protein-ligands complexes obtained from a mutli-step virtual screening. Enrichment studies of the selected pre-docked complexes containing 60% of the initially added inhibitors were carried out with or without final AMMOS minimization on two protein targets having different binding pocket properties. AMMOS was able to improve the enrichment after the pre-docking stage with 40 to 60% of the initially added active compounds found in the top 3% to 5% of the entire compound collection

Arithmetic noncommutative geometry

CERN Document Server

Marcolli, Matilde

2005-01-01

Arithmetic noncommutative geometry denotes the use of ideas and tools from the field of noncommutative geometry, to address questions and reinterpret in a new perspective results and constructions from number theory and arithmetic algebraic geometry. This general philosophy is applied to the geometry and arithmetic of modular curves and to the fibers at archimedean places of arithmetic surfaces and varieties. The main reason why noncommutative geometry can be expected to say something about topics of arithmetic interest lies in the fact that it provides the right framework in which the tools of geometry continue to make sense on spaces that are very singular and apparently very far from the world of algebraic varieties. This provides a way of refining the boundary structure of certain classes of spaces that arise in the context of arithmetic geometry, such as moduli spaces (of which modular curves are the simplest case) or arithmetic varieties (completed by suitable "fibers at infinity"), by adding boundaries...

Researches of real observation geometry in monitoring fuel-containing materials' subcriticality

International Nuclear Information System (INIS)

Vysotskij, E.D.; Shevchenko, V.G.; Shevchenko, M.V.

2002-01-01

The effectiveness of fuel-containing materials monitoring is discussed in the part related to the feasibilities of researches and realization of optimal geometry (detectors - source) of survey of neutron activity dynamics in nuclearly hazardous areas with clusters of fuel-containing materials concentrated in the premises 305/2

Control of the Dipole Cold Mass Geometry at CERN to Optimize LHC Performance

CERN Document Server

Wildner, E; La China, M; Tommasini, D

2006-01-01

The detailed shape of the 15 m long superconducting LHC dipole cold mass is of high importance as it determines three key parameters: the beam aperture, nominally of the order of 10 beam standard deviations; the connectivity of the beam- and technical lines between magnets; the transverse position of non-linear correctors mounted on the dipole ends. An offset of the latter produces unwanted beam dynamics perturbations. The tolerances are in the order of mm over the length of the magnet. The natural flexibility of the dipole and its mechanical structure allow deformations during handling and transportation which exceed the tolerances. This paper presents the observed deformations of the geometry during handling and various operations at CERN, deformations which are interpreted thanks to a simple mechanical model. These observations have led to a strategy of dipole geometry control at CERN, based on adjustment of the position of its central support (the dipole is supported at three positions, horizontally and v...

Improving the automated optimization of profile extrusion dies by applying appropriate optimization areas and strategies

Science.gov (United States)

Hopmann, Ch.; Windeck, C.; Kurth, K.; Behr, M.; Siegbert, R.; Elgeti, S.

2014-05-01

The rheological design of profile extrusion dies is one of the most challenging tasks in die design. As no analytical solution is available, the quality and the development time for a new design highly depend on the empirical knowledge of the die manufacturer. Usually, prior to start production several time-consuming, iterative running-in trials need to be performed to check the profile accuracy and the die geometry is reworked. An alternative are numerical flow simulations. These simulations enable to calculate the melt flow through a die so that the quality of the flow distribution can be analyzed. The objective of a current research project is to improve the automated optimization of profile extrusion dies. Special emphasis is put on choosing a convenient starting geometry and parameterization, which enable for possible deformations. In this work, three commonly used design features are examined with regard to their influence on the optimization results. Based on the results, a strategy is derived to select the most relevant areas of the flow channels for the optimization. For these characteristic areas recommendations are given concerning an efficient parameterization setup that still enables adequate deformations of the flow channel geometry. Exemplarily, this approach is applied to a L-shaped profile with different wall thicknesses. The die is optimized automatically and simulation results are qualitatively compared with experimental results. Furthermore, the strategy is applied to a complex extrusion die of a floor skirting profile to prove the universal adaptability.

Higher geometry an introduction to advanced methods in analytic geometry

CERN Document Server

Woods, Frederick S

2005-01-01

For students of mathematics with a sound background in analytic geometry and some knowledge of determinants, this volume has long been among the best available expositions of advanced work on projective and algebraic geometry. Developed from Professor Woods' lectures at the Massachusetts Institute of Technology, it bridges the gap between intermediate studies in the field and highly specialized works.With exceptional thoroughness, it presents the most important general concepts and methods of advanced algebraic geometry (as distinguished from differential geometry). It offers a thorough study

Non-Riemannian geometry

CERN Document Server

Eisenhart, Luther Pfahler

2005-01-01

This concise text by a prominent mathematician deals chiefly with manifolds dominated by the geometry of paths. Topics include asymmetric and symmetric connections, the projective geometry of paths, and the geometry of sub-spaces. 1927 edition.

Optimization of polynomials in non-commuting variables

CERN Document Server

Burgdorf, Sabine; Povh, Janez

2016-01-01

This book presents recent results on positivity and optimization of polynomials in non-commuting variables. Researchers in non-commutative algebraic geometry, control theory, system engineering, optimization, quantum physics and information science will find the unified notation and mixture of algebraic geometry and mathematical programming useful. Theoretical results are matched with algorithmic considerations; several examples and information on how to use NCSOStools open source package to obtain the results provided. Results are presented on detecting the eigenvalue and trace positivity of polynomials in non-commuting variables using Newton chip method and Newton cyclic chip method, relaxations for constrained and unconstrained optimization problems, semidefinite programming formulations of the relaxations and finite convergence of the hierarchies of these relaxations, and the practical efficiency of algorithms.

On the role of initial void geometry in plastic deformation of metallic thin films: A molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Su, Yanqing [School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332-0340 (United States); Xu, Shuozhi, E-mail: shuozhixu@gatech.edu [GWW School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0405 (United States)

2016-12-15

Void growth is usually considered one of the most critical phases leading to dynamic fracture of ductile materials. Investigating the detailed process of void growth at the nanoscale aids in understanding the damage mechanism of metals. While most atomistic simulations by far assume circular or spherical voids for simplicity, recent studies highlight the significance of the initial void ellipticity in mechanical response of voided metals. In this work, we perform large scale molecular dynamics simulations with millions of atoms to investigate the void growth in plastic deformation of thin films in face-centered cubic Cu. It is found that the initial ellipticity and the initial orientation angle of the void have substantial impacts on the dislocation nucleation, the void evolution, and the stress-strain response. In particular, the initial dislocation emission sites and the sequence of slip plane activation vary with the initial void geometry. For the void size evolution, three regimes are identified: (I) the porosity increases relatively slowly in the absence of dislocations, (II) the porosity grows much more rapidly after dislocations start to glide on different slip planes, and (III) the rate of porosity variation becomes much more slowly when dislocations are saturated in the model, and the void surface becomes irregular, non-smooth. In terms of the stress-strain response, the effects of the initial orientation angle are more pronounced when the initial void ellipticity is large; the influence of the initial void ellipticity is different for different initial orientation angles. The effects of the temperature, the strain rate, the loading direction, and the initial porosity in the void growth are also explored. Our results reveal the underlying mechanisms of initial void geometry-dependent plastic deformation of metallic thin films and shed light on informing more accurate theoretical models.

On the role of initial void geometry in plastic deformation of metallic thin films: A molecular dynamics study

International Nuclear Information System (INIS)

Su, Yanqing; Xu, Shuozhi

2016-01-01

Void growth is usually considered one of the most critical phases leading to dynamic fracture of ductile materials. Investigating the detailed process of void growth at the nanoscale aids in understanding the damage mechanism of metals. While most atomistic simulations by far assume circular or spherical voids for simplicity, recent studies highlight the significance of the initial void ellipticity in mechanical response of voided metals. In this work, we perform large scale molecular dynamics simulations with millions of atoms to investigate the void growth in plastic deformation of thin films in face-centered cubic Cu. It is found that the initial ellipticity and the initial orientation angle of the void have substantial impacts on the dislocation nucleation, the void evolution, and the stress-strain response. In particular, the initial dislocation emission sites and the sequence of slip plane activation vary with the initial void geometry. For the void size evolution, three regimes are identified: (I) the porosity increases relatively slowly in the absence of dislocations, (II) the porosity grows much more rapidly after dislocations start to glide on different slip planes, and (III) the rate of porosity variation becomes much more slowly when dislocations are saturated in the model, and the void surface becomes irregular, non-smooth. In terms of the stress-strain response, the effects of the initial orientation angle are more pronounced when the initial void ellipticity is large; the influence of the initial void ellipticity is different for different initial orientation angles. The effects of the temperature, the strain rate, the loading direction, and the initial porosity in the void growth are also explored. Our results reveal the underlying mechanisms of initial void geometry-dependent plastic deformation of metallic thin films and shed light on informing more accurate theoretical models.

Effect of heater geometry and cavity volume on the sensitivity of a thermal convection-based tilt sensor

Science.gov (United States)

Han, Maeum; Keon Kim, Jae; Kong, Seong Ho; Kang, Shin-Won; Jung, Daewoong

2018-06-01

This paper reports a micro-electro-mechanical-system (MEMS)-based tilt sensor using air medium. Since the working mechanism of the sensor is the thermal convection in a sealed chamber, structural parameters that can affect thermal convection must be considered to optimize the performance of the sensor. This paper presents the experimental results that were conducted by optimizing several parameters such as the heater geometry, input power and cavity volume. We observed that an increase in the heating power and cavity volume can improve the sensitivity, and heater geometry plays important role in performance of the sensor.

Blade profile optimization of kaplan turbine using cfd analysis

International Nuclear Information System (INIS)

Janjua, A.B.; Khalil, M.S.

2013-01-01

Utilization of hydro-power as renewable energy source is of prime importance in the world now. Hydropower energy is available in abundant in form of falls, canals rivers, dams etc. It means, there are various types of sites with different parameters like flow rate, heads, etc. Depending upon the sites, water turbines are designed and manufactured to avail hydro-power energy. Low head turbines on runof-river are widely used for the purpose. Low head turbines are classified as reaction turbines. For runof-river, depending upon the variety of site data, low head Kaplan turbines are selected, designed and manufactured. For any given site requirement, it becomes very essential to design the turbine runner blades through optimization of the CAD model of blades profile. This paper presents the optimization technique carried out on a complex geometry of blade profile through static and dynamic computational analysis. It is used through change of the blade profile geometry at five different angles in the 3D (Three Dimensional) CAD model. Blade complex geometry and design have been developed by using the coordinates point system on the blade in PRO-E /CREO software. Five different blade models are developed for analysis purpose. Based on the flow rate and heads, blade profiles are analyzed using ANSYS software to check and compare the output results for optimization of the blades for improved results which show that by changing blade profile angle and its geometry, different blade sizes and geometry can be optimized using the computational techniques with changes in CAD models. (author)

Blade Profile Optimization of Kaplan Turbine Using CFD Analysis

Directory of Open Access Journals (Sweden)

Aijaz Bashir Janjua

2013-10-01

Full Text Available Utilization of hydro-power as renewable energy source is of prime importance in the world now. Hydropower energy is available in abundant in form of falls, canals rivers, dams etc. It means, there are various types of sites with different parameters like flow rate, heads, etc. Depending upon the sites, water turbines are designed and manufactured to avail hydro-power energy. Low head turbines on runof-river are widely used for the purpose. Low head turbines are classified as reaction turbines. For runof river, depending upon the variety of site data, low head Kaplan turbines are selected, designed and manufactured. For any given site requirement, it becomes very essential to design the turbine runner blades through optimization of the CAD model of blades profile. This paper presents the optimization technique carried out on a complex geometry of blade profile through static and dynamic computational analysis. It is used through change of the blade profile geometry at five different angles in the 3D (Three Dimensional CAD model. Blade complex geometry and design have been developed by using the coordinates point system on the blade in PRO-E /CREO software. Five different blade models are developed for analysis purpose. Based on the flow rate and heads, blade profiles are analyzed using ANSYS software to check and compare the output results for optimization of the blades for improved results which show that by changing blade profile angle and its geometry, different blade sizes and geometry can be optimized using the computational techniques with changes in CAD models.

The Geometry Conference

CERN Document Server

Bárány, Imre; Vilcu, Costin

2016-01-01

This volume presents easy-to-understand yet surprising properties obtained using topological, geometric and graph theoretic tools in the areas covered by the Geometry Conference that took place in Mulhouse, France from September 7–11, 2014 in honour of Tudor Zamfirescu on the occasion of his 70th anniversary. The contributions address subjects in convexity and discrete geometry, in distance geometry or with geometrical flavor in combinatorics, graph theory or non-linear analysis. Written by top experts, these papers highlight the close connections between these fields, as well as ties to other domains of geometry and their reciprocal influence. They offer an overview on recent developments in geometry and its border with discrete mathematics, and provide answers to several open questions. The volume addresses a large audience in mathematics, including researchers and graduate students interested in geometry and geometrical problems.

Hyperbolic geometry

CERN Document Server

Iversen, Birger

1992-01-01

Although it arose from purely theoretical considerations of the underlying axioms of geometry, the work of Einstein and Dirac has demonstrated that hyperbolic geometry is a fundamental aspect of modern physics

Geometry of the Universe

International Nuclear Information System (INIS)

Gurevich, L.Eh.; Gliner, Eh.B.

1978-01-01

Problems of investigating the Universe space-time geometry are described on a popular level. Immediate space-time geometries, corresponding to three cosmologic models are considered. Space-time geometry of a closed model is the spherical Riemann geonetry, of an open model - is the Lobachevskij geometry; and of a plane model - is the Euclidean geometry. The Universe real geometry in the contemporary epoch of development is based on the data testifying to the fact that the Universe is infinitely expanding

submitter Optimization of Nb$_{3}$Sn Rutherford Cables Geometry for the High Luminosity LHC

CERN Document Server

Fleiter, Jerome; Bonasia, Angelo; Bordini, Bernardo; Richter, David

2017-01-01

The quadrupole and dipole magnets for the LHC High Luminosity (HL-LHC) upgrade will be based on Nb$_{3}$Sn Rutherford cables that operate at 1.9 K and experience magnetic fields of up to about 12 T. An important step in the design of these magnets is the development of the high aspect ratio Nb$_{3}$Sn cables to achieve the nominal field with sufficient margin. The strong plastic deformation of unreacted $Nb_3Sn$ strands during the Rutherford cabling process may induce non negligible $I_c$ and RRR degradation. In this paper, the cabling degradation is investigated as a function of the cable geometry for both PIT and RRP conductors. Based on this analysis, new baseline geometries for both 11 T and QXF magnets of HL-LHC are proposed.

submitter Optimization of Nb$_{3}$Sn Rutherford Cables Geometry for the High Luminosity LHC

CERN Document Server

Fleiter, Jerome; Bonasia, Angelo; Bordini, Bernardo; Richter, David

2017-01-01

The quadrupole and dipole magnets for the LHC High Luminosity (HL-LHC) upgrade will be based on Nb3Sn Rutherford cables that operate at 1.9 K and experience magnetic fields of up to about 12 T. An important step in the design of these magnets is the development of the high aspect ratio Nb3Sn cables to achieve the nominal field with sufficient margin. The strong plastic deformation of unreacted $Nb_3Sn$ strands during the Rutherford cabling process may induce non negligible $I_c$ and RRR degradation. In this paper, the cabling degradation is investigated as a function of the cable geometry for both PIT and RRP conductors. Based on this analysis, new baseline geometries for both 11 T and QXF magnets of HL-LHC are proposed.

Airfoil shape optimization using non-traditional optimization technique and its validation

Directory of Open Access Journals (Sweden)

R. Mukesh

2014-07-01

Full Text Available Computational fluid dynamics (CFD is one of the computer-based solution methods which is more widely employed in aerospace engineering. The computational power and time required to carry out the analysis increase as the fidelity of the analysis increases. Aerodynamic shape optimization has become a vital part of aircraft design in the recent years. Generally if we want to optimize an airfoil we have to describe the airfoil and for that, we need to have at least hundred points of x and y co-ordinates. It is really difficult to optimize airfoils with this large number of co-ordinates. Nowadays many different schemes of parameter sets are used to describe general airfoil such as B-spline, and PARSEC. The main goal of these parameterization schemes is to reduce the number of needed parameters as few as possible while controlling the important aerodynamic features effectively. Here the work has been done on the PARSEC geometry representation method. The objective of this work is to introduce the knowledge of describing general airfoil using twelve parameters by representing its shape as a polynomial function. And also we have introduced the concept of Genetic Algorithm to optimize the aerodynamic characteristics of a general airfoil for specific conditions. A MATLAB program has been developed to implement PARSEC, Panel Technique, and Genetic Algorithm. This program has been tested for a standard NACA 2411 airfoil and optimized to improve its coefficient of lift. Pressure distribution and co-efficient of lift for airfoil geometries have been calculated using the Panel method. The optimized airfoil has improved co-efficient of lift compared to the original one. The optimized airfoil is validated using wind tunnel data.

Optimal control theory for quantum-classical systems: Ehrenfest molecular dynamics based on time-dependent density-functional theory

International Nuclear Information System (INIS)

Castro, A; Gross, E K U

2014-01-01

We derive the fundamental equations of an optimal control theory for systems containing both quantum electrons and classical ions. The system is modeled with Ehrenfest dynamics, a non-adiabatic variant of molecular dynamics. The general formulation, that needs the fully correlated many-electron wavefunction, can be simplified by making use of time-dependent density-functional theory. In this case, the optimal control equations require some modifications that we will provide. The abstract general formulation is complemented with the simple example of the H 2 + molecule in the presence of a laser field. (paper)

Final Report for the grant "Applied Geometry" (DOE DE-FG02-04ER25657)

Energy Technology Data Exchange (ETDEWEB)

Prof. Mathieu Desbrun

2009-05-20

The primary purpose of this 3-year DOE-funded research effort, now completed, was to develop consistent, theoretical foundations of computations on discrete geometry, to realize the promise of predictive and scalable management of large geometric datasets as handled routinely in applied sciences. Geometry (be it simple 3D shapes or higher dimensional manifolds) is indeed a central and challenging issue from the modeling and computational perspective in several sciences such as mechanics, biology, molecular dynamics, geophysics, as well as engineering. From digital maps of our world, virtual car crash simulation, predictive animation of carbon nano-tubes, to trajectory design of space missions, knowing how to process and animate digital geometry is key in many cross-disciplinary research areas.

Open problems in the geometry and analysis of Banach spaces

CERN Document Server

Guirao, Antonio J; Zizler, Václav

2016-01-01

This is a collection of some easily-formulated problems that remain open in the study of the geometry and analysis of Banach spaces. Assuming the reader has a working familiarity with the basic results of Banach space theory, the authors focus on concepts of basic linear geometry, convexity, approximation, optimization, differentiability, renormings, weak compact generating, Schauder bases and biorthogonal systems, fixed points, topology and nonlinear geometry. The main purpose of this work is to help convince young researchers in Functional Analysis that the theory of Banach spaces is a fertile field of research, full of interesting open problems. Inside the Banach space area, the text should help expose young researchers to the depth and breadth of the work that remains, and to provide the perspective necessary to choose a direction for further study. Some of the problems presented herein are longstanding open problems, some are recent, some are more important and some are only "local" problems. Some would ...

Structural studies on Mycobacterium tuberculosis RecA: Molecular ...

Indian Academy of Sciences (India)

2015-01-11

Jan 11, 2015 ... The molecular geometry of RecA and the location of the nucleotide binding site ...... the residue in all the glycerol complexes clusters together along with the two ..... an X-ray and molecular dynamics investigation on banana.

Optimality principle for the coupled chemical reactions of ATP synthesis and its molecular interpretation

Science.gov (United States)

Nath, Sunil

2018-05-01

Metabolic energy obtained from the coupled chemical reactions of oxidative phosphorylation (OX PHOS) is harnessed in the form of ATP by cells. We experimentally measured thermodynamic forces and fluxes during ATP synthesis, and calculated the thermodynamic efficiency, η and the rate of free energy dissipation, Φ. We show that the OX PHOS system is tuned such that the coupled nonequilibrium processes operate at optimal η. This state does not coincide with the state of minimum Φ but is compatible with maximum Φ under the imposed constraints. Conditions that must hold for species concentration in order to satisfy the principle of optimal efficiency are derived analytically and a molecular explanation based on Nath's torsional mechanism of energy transduction and ATP synthesis is suggested. Differences of the proposed principle with Prigogine's principle are discussed.

3D Printing of Molecular Models with Calculated Geometries and p Orbital Isosurfaces

Science.gov (United States)

Carroll, Felix A.; Blauch, David N.

2017-01-01

3D printing was used to prepare models of the calculated geometries of unsaturated organic structures. Incorporation of p orbital isosurfaces into the models enables students in introductory organic chemistry courses to have hands-on experience with the concept of orbital alignment in strained and unstrained p systems.

Sum frequency generation image reconstruction: Aliphatic membrane under spherical cap geometry

Energy Technology Data Exchange (ETDEWEB)

Volkov, Victor [Bereozovaya 2A, Konstantinovo, Moscow Region 140207 (Russian Federation)

2014-10-07

The article explores an opportunity to approach structural properties of phospholipid membranes using Sum Frequency Generation microscopy. To establish the principles of sum frequency generation image reconstruction in such systems, at first approach, we may adopt an idealistic spherical cap uniform assembly of hydrocarbon molecules. Quantum mechanical studies for decanoic acid (used here as a representative molecular system) provide necessary information on transition dipole moments and Raman tensors of the normal modes specific to methyl terminal – a typical moiety in aliphatic (and phospholipid) membranes. Relative degree of localization and frequencies of the normal modes of methyl terminals make nonlinearities of this moiety to be promising in structural analysis using Sum Frequency Generation imaging. Accordingly, the article describes derivations of relevant macroscopic nonlinearities and suggests a mapping procedure to translate amplitudes of the nonlinearities onto microscopy image plane according to geometry of spherical assembly, local molecular orientation, and optical geometry. Reconstructed images indicate a possibility to extract local curvature of bilayer envelopes of spherical character. This may have practical implications for structural extractions in membrane systems of practical relevance.

Automation of Geometry Input for Building Code Compliance Check

DEFF Research Database (Denmark)

Petrova, Ekaterina Aleksandrova; Johansen, Peter Lind; Jensen, Rasmus Lund

2017-01-01

Documentation of compliance with the energy performance regulations at the end of the detailed design phase is mandatory for building owners in Denmark. Therefore, besides multidisciplinary input, the building design process requires various iterative analyses, so that the optimal solutions can....... That has left the industry in constant pursuit of possibilities for integration of the tool within the Building Information Modelling environment so that the potential provided by the latter can be harvested and the processed can be optimized. This paper presents a solution for automated data extraction...... from building geometry created in Autodesk Revit and its translation to input for compliance check analysis....

Geometry and Optics of the Electrostatic ELENA Transfer Lines

CERN Document Server

Vanbavinckhove, G; Barna, D; Bartmann, W; Butin, F; Choisnet, O; Yamada, H

2013-01-01

The future ELENA ring at CERN will decelerate the AD anti-proton beam further from 5.3 MeV to 100 keV kinetic energy, to increase the efficiency of anti-proton trapping. At present there are four experiments in the AD hall which will be complemented with the installation of ELENA by additional three experiments and an additional source for commissioning. This paper describes the optimization of the transfer line geometry, ring rotation and source position. The optics of the transfer lines and error studies to define field and alignment tolerances are shown, and the optics particularities of electrostatic elements and their optimization highlighted.

On organizing principles of discrete differential geometry. Geometry of spheres

International Nuclear Information System (INIS)

Bobenko, Alexander I; Suris, Yury B

2007-01-01

Discrete differential geometry aims to develop discrete equivalents of the geometric notions and methods of classical differential geometry. This survey contains a discussion of the following two fundamental discretization principles: the transformation group principle (smooth geometric objects and their discretizations are invariant with respect to the same transformation group) and the consistency principle (discretizations of smooth parametrized geometries can be extended to multidimensional consistent nets). The main concrete geometric problem treated here is discretization of curvature-line parametrized surfaces in Lie geometry. Systematic use of the discretization principles leads to a discretization of curvature-line parametrization which unifies circular and conical nets.

Optimizing dc-resistance of a foil wounded toroidal inductor combining matlab and comsol

DEFF Research Database (Denmark)

Schneider, Henrik; Andersen, Thomas; Knott, Arnold

2013-01-01

An optimization routine is presented to optimize the shape of a foil winding of a toroid inductor in terms of the DC resistance. MATLAB was used to define the geometry of the foil winding and COMSOL was used to import the geometry and create a 3D finite element model. The initial parameters...

Computational Approaches to the Determination of the Molecular Geometry of Acrolein in its T_1(n,π*) State

Science.gov (United States)

McAnally, Michael O.; Hlavacek, Nikolaus C.; Drucker, Stephen

2012-06-01

The spectroscopically derived inertial constants for acrolein (propenal) in its T_1(n,π*) state were used to test predictions from a variety of computational methods. One focus was on multiconfigurational methods, such as CASSCF and CASPT2, that are applicable to excited states. We also examined excited-state methods that utilize single reference configurations, including EOM-EE-CCSD and TD-PBE0. Finally, we applied unrestricted ground-state techniques, such as UCCSD(T) and the more economical UPBE0 method, to the T_1(n,π*) excited state under the constraint of C_s symmetry. The unrestricted ground-state methods are applicable because at a planar geometry, the T_1(n,π*) state of acrolein is the lowest-energy state of its spin multiplicity. Each of the above methods was used with a triple zeta quality basis set to optimize the T_1(n,π*) geometry. This procedure resulted in the following sets of inertial constants: Inertial constants (cm-1) of acrolein in its T_1(n,π*) state Method A B C Method A B C CASPT2(6,5) 1.667 0.1491 0.1368 UCCSD(T)^b 1.668 0.1480 0.1360 CASSCF(6,5) 1.667 0.1491 0.1369 UPBE0 1.699 0.1487 0.1367 EOM-EE-CCSD 1.675 0.1507 0.1383 TD-PBE0 1.719 0.1493 0.1374 Experiment^a 1.662 0.1485 0.1363 The two multiconfigurational methods produce the same inertial constants, and those constants agree closely with experiment. However the sets of computed bond lengths differ significantly for the two methods. In the CASSCF calculation, the lengthening of the C=O and C=C bonds and the shortening of the C--C bond are more pronounced than in CASPT2. O. S. Bokareva et al., Int. J. Quant. Chem. {108}, 2719 (2008).

A molecular orbital study on the oxidative decomposition of HFC-32

International Nuclear Information System (INIS)

Mochizuki, Yuji

1999-03-01

A series of ab initio molecular orbital calculations, in which Hartree-Fock, second-order Moeller-Plesset perturbation, density functional (B3LYP and BHandHLYP) levels of theory were used, was performed on the elementary reactions related to the oxidative decomposition of HFC-32 (CH 2 F 2 ) by hydroxyl (OH) radicals in a supercritical water condition (so-called SCWO). The whole process is written as CH 2 F 2 + 4OH → CO 2 + 2H 2 O + 2HF and consists of (1) H abstraction by OH to form H 2 O, (2) OH coupling to C-center, and (3) HF leaving to form C=O bond. Molecular geometries were optimized at each level of theory. The HF leaving was found to be the rate-determining step, but its barrier height was lowered by the reactive solvation with an extra H 2 O. Calculations implied that the SCWO of HFC-32 can proceed efficiently. (author)

Danfoss: Scroll Optimization

DEFF Research Database (Denmark)

Gravesen, Jens; Henriksen, Christian; Howell, Peter

1998-01-01

The standard scroll compressor consists of two identical spirals (circle involutes) running inside each other.The task from Danfoss was to investigate how a change in the basic geometry of the scrolss and the orbit influence the compressor performnce and efficiency, and then try to optimize...

Bulk Heterojunction versus Diffused Bilayer: The Role of Device Geometry in Solution p-Doped Polymer-Based Solar Cells.

Science.gov (United States)

Loiudice, Anna; Rizzo, Aurora; Biasiucci, Mariano; Gigli, Giuseppe

2012-07-19

We exploit the effect of molecular p-type doping of P3HT in diffused bilayer (DB) polymer solar cells. In this alternative device geometry, the p-doping is accomplished in solution by blending the F4-TCNQ with P3HT. The p-doping both increases the film conductivity and reduces the potential barrier at the interface with the electrode. This results in an excellent power conversion efficiency of 4.02%, which is an improvement of ∼48% over the p-doped standard bulk heterojunction (BHJ) device. Combined VOC-light intensity dependence measurements and Kelvin probe force microscopy reveal that the DB device configuration is particularly advantageous, if compared to the conventional BHJ, because it enables optimization of the donor and acceptor layers independently to minimize the effect of trapping and to fully exploit the improved transport properties.

Topology and parameter data of thirteen non-natural amino acids for molecular simulations with CHARMM22

Directory of Open Access Journals (Sweden)

Olujide O. Olubiyi

2016-12-01

Full Text Available In this article we provide a data package containing the topology files and parameters compatible with the CHARMM22 force field for thirteen non-natural amino acids. The force field parameters were derived based on quantum mechanical (QM calculations involving geometry optimization and potential energy surface scanning at the HF 6-31G(d and HF 6-311G(d,p levels of theory. The resulting energy data points were fitted to mathematical functions representing each component of the CHARMM22 force field. Further fine-tuning of the parameters utilized molecular mechanics energies, which were iteratively calculated and compared to the corresponding QM values until the latter were satisfactorily reproduced. The final force field data were validated with molecular dynamics simulations in explicit solvent conditions.

Geometry of anisotropic CO outflows

International Nuclear Information System (INIS)

Liseau, R.; Sandell, G.; Helsinki Univ., Observatory, Finland)

1986-01-01

A simple geometrical model for the space motions of the bipolar high-velocity CO outflows in regions of recent, active star formation is proposed. It is assumed that the velocity field of the neutral gas component can be represented by large-scale uniform motions. From observations of the spatial distribution and from the characteristics of the line shape of the high-velocity molecular gas emission the geometry of the line-emitting regions can be inferred, i.e., the direction in space and the collimating angle of the flow. The model has been applied to regions where a check on presently obtained results is provided by independent optical determinations of the motions of Herbig-Haro objects associated with the CO flows. These two methods are in good agreement and, furthermore, the results obtained provide convincingly strong evidence for the physical association of CO outflows and Herbig-Haro objects. This also supports the common view that a young stellar central source is responsible for the active phenomena observed in its environmental neighborhood. It is noteworthy that within the framework of the model the determination of the flow geometry of the high-velocity gas from CO measurements is independent of the distance to the source and, furthermore, can be done at relatively low spatial resolution. 32 references

Thickness optimization of fiber reinforced laminated composites using the discrete material optimization method

DEFF Research Database (Denmark)

Sørensen, Søren Nørgaard; Lund, Erik

2012-01-01

This work concerns a novel large-scale multi-material topology optimization method for simultaneous determination of the optimum variable integer thickness and fiber orientation throughout laminate structures with fixed outer geometries while adhering to certain manufacturing constraints....... The conceptual combinatorial/integer problem is relaxed to a continuous problem and solved on basis of the so-called Discrete Material Optimization method, explicitly including the manufacturing constraints as linear constraints....

Beautiful geometry

CERN Document Server

Maor, Eli

2014-01-01

If you've ever thought that mathematics and art don't mix, this stunning visual history of geometry will change your mind. As much a work of art as a book about mathematics, Beautiful Geometry presents more than sixty exquisite color plates illustrating a wide range of geometric patterns and theorems, accompanied by brief accounts of the fascinating history and people behind each. With artwork by Swiss artist Eugen Jost and text by acclaimed math historian Eli Maor, this unique celebration of geometry covers numerous subjects, from straightedge-and-compass constructions to intriguing configur

On the Effects of Geometry Control on the Performance of Overtopping Wave Energy Converters

DEFF Research Database (Denmark)

Victor, Lander; Troch, Peter; Kofoed, Jens Peter

2011-01-01

Overtopping wave energy converters (OWECs) are designed to extract energy from ocean waves based on wave overtopping into a reservoir, which is emptied into the ocean through a set of low-head turbines, and typically feature a low crest freeboard and a smooth impermeable steep slope. In the process...... of optimizing the performance of OWECs, the question arises whether adapting the slope geometry to the variable wave characteristics at the deployment site (i.e., geometry control) can increase the overall hydraulic efficiency and overall hydraulic power compared to a fixed slope geometry. The effect of five...... different geometry control scenarios on the overall hydraulic efficiency and overall hydraulic power of OWECs has been simulated for three possible deployment sites using empirical prediction formulae. The results show that the effect of an adaptive slope angle is relatively small. On the other hand...

Revolutions of Geometry

CERN Document Server

O'Leary, Michael

2010-01-01

Guides readers through the development of geometry and basic proof writing using a historical approach to the topic. In an effort to fully appreciate the logic and structure of geometric proofs, Revolutions of Geometry places proofs into the context of geometry's history, helping readers to understand that proof writing is crucial to the job of a mathematician. Written for students and educators of mathematics alike, the book guides readers through the rich history and influential works, from ancient times to the present, behind the development of geometry. As a result, readers are successfull

Density-optimized efficiency for magneto-optical production of a stable molecular Bose-Einstein condensate

Energy Technology Data Exchange (ETDEWEB)

Mackie, Matt [Helsinki Institute of Physics, PL 64, FIN-00014 Helsingin yliopisto (Finland); Collin, Anssi [Helsinki Institute of Physics, PL 64, FIN-00014 Helsingin yliopisto (Finland); Suominen, Kalle-Antti [Helsinki Institute of Physics, PL 64, FIN-00014 Helsingin yliopisto (Finland); Javanainen, Juha [Department of Physics, University of Connecticut, Storrs, CT 06269-3046 (United States)

2003-08-01

Although photoassociation and the Feshbach resonance are feasible means in principle for creating a molecular Bose-Einstein condensate (MBEC) from an already quantum-degenerate gas of atoms, collision-induced mean-field shifts and irreversible decay place practical constraints on the efficient Raman delivery of stable molecules. Focusing on stimulated Raman adiabatic passage, we propose that the efficiency of both mechanisms for producing a stable MBEC can be improved by treating the density of the initial atom condensate as an optimization parameter.

Analogy and Dynamic Geometry System Used to Introduce Three-Dimensional Geometry

Science.gov (United States)

Mammana, M. F.; Micale, B.; Pennisi, M.

2012-01-01

We present a sequence of classroom activities on Euclidean geometry, both plane and space geometry, used to make three dimensional geometry more catchy and simple. The activity consists of a guided research activity that leads the students to discover unexpected properties of two apparently distant geometrical entities, quadrilaterals and…

Functional fixedness and functional reduction as common sense reasonings in chemical equilibrium and in geometry and polarity of molecules

Science.gov (United States)

Furió, C.; Calatayud, M. L.; Bárcenas, S. L.; Padilla, O. M.

2000-09-01

Many of the learning difficulties in the specific domain of chemistry are found not only in the ideas already possessed by students but in the strategic and procedural knowledge that is characteristic of everyday thinking. These defects in procedural knowledge have been described as functional fixedness and functional reduction. This article assesses the procedural difficulties of students (grade 12 and first and third year of university) based on common sense reasoning in two areas of chemistry: chemical equilibrium and geometry and polarity of molecules. In the first area, the theme of external factors affecting equilibria (temperature and concentration change) was selected because the explanations given by the students could be analyzed easily. The existence of a functional fixedness where Le Chatelier's principle was almost exclusively applied by rote could be observed, with this being the cause of the incorrect responses given to the proposed items. Functional fixedness of the Lewis structure also led to an incorrect prediction of molecular geometry. When molecular geometry was correctly determined by the students, it seemed that other methodological or procedural difficulties appeared when the task was to determine molecular polarity. The students showed a tendency, in many cases, to reduce the factors affecting molecular polarity in two possible ways: (a) assuming that polarity depends only on shape (geometric functional reduction) or (b) assuming that molecular polarity depends only on the polarity of bonds (bonding functional reduction).

Information geometry

CERN Document Server

Ay, Nihat; Lê, Hông Vân; Schwachhöfer, Lorenz

2017-01-01

The book provides a comprehensive introduction and a novel mathematical foundation of the field of information geometry with complete proofs and detailed background material on measure theory, Riemannian geometry and Banach space theory. Parametrised measure models are defined as fundamental geometric objects, which can be both finite or infinite dimensional. Based on these models, canonical tensor fields are introduced and further studied, including the Fisher metric and the Amari-Chentsov tensor, and embeddings of statistical manifolds are investigated. This novel foundation then leads to application highlights, such as generalizations and extensions of the classical uniqueness result of Chentsov or the Cramér-Rao inequality. Additionally, several new application fields of information geometry are highlighted, for instance hierarchical and graphical models, complexity theory, population genetics, or Markov Chain Monte Carlo. The book will be of interest to mathematicians who are interested in geometry, inf...

Three-dimensional shape optimization of a cemented hip stem and experimental validations.

Science.gov (United States)

Higa, Masaru; Tanino, Hiromasa; Nishimura, Ikuya; Mitamura, Yoshinori; Matsuno, Takeo; Ito, Hiroshi

2015-03-01

This study proposes novel optimized stem geometry with low stress values in the cement using a finite element (FE) analysis combined with an optimization procedure and experimental measurements of cement stress in vitro. We first optimized an existing stem geometry using a three-dimensional FE analysis combined with a shape optimization technique. One of the most important factors in the cemented stem design is to reduce stress in the cement. Hence, in the optimization study, we minimized the largest tensile principal stress in the cement mantle under a physiological loading condition by changing the stem geometry. As the next step, the optimized stem and the existing stem were manufactured to validate the usefulness of the numerical models and the results of the optimization in vitro. In the experimental study, strain gauges were embedded in the cement mantle to measure the strain in the cement mantle adjacent to the stems. The overall trend of the experimental study was in good agreement with the results of the numerical study, and we were able to reduce the largest stress by more than 50% in both shape optimization and strain gauge measurements. Thus, we could validate the usefulness of the numerical models and the results of the optimization using the experimental models. The optimization employed in this study is a useful approach for developing new stem designs.

Development of simulation approach for two-dimensional chiral molecular self-assembly driven by hydrogen bond at the liquid/solid interface

Science.gov (United States)

Qin, Yuan; Yao, Man; Hao, Ce; Wan, Lijun; Wang, Yunhe; Chen, Ting; Wang, Dong; Wang, Xudong; Chen, Yonggang

2017-09-01

Two-dimensional (2D) chiral self-assembly system of 5-(benzyloxy)-isophthalic acid derivative/(S)-(+)-2-octanol/highly oriented pyrolytic graphite was studied. A combined density functional theory/molecular mechanics/molecular dynamics (DFT/MM/MD) approach for system of 2D chiral molecular self-assembly driven by hydrogen bond at the liquid/solid interface was thus proposed. Structural models of the chiral assembly were built on the basis of scanning tunneling microscopy (STM) images and simplified for DFT geometry optimization. Merck Molecular Force Field (MMFF) was singled out as the suitable force field by comparing the optimized configurations of MM and DFT. MM and MD simulations for hexagonal unit model which better represented the 2D assemble network were then preformed with MMFF. The adhesion energy, evolution of self-assembly process and characteristic parameters of hydrogen bond were obtained and analyzed. According to the above simulation, the stabilities of the clockwise and counterclockwise enantiomorphous networks were evaluated. The calculational results were supported by STM observations and the feasibility of the simulation method was confirmed by two other systems in the presence of chiral co-absorbers (R)-(-)-2-octanol and achiral co-absorbers 1-octanol. This theoretical simulation method assesses the stability trend of 2D enantiomorphous assemblies with atomic scale and can be applied to the similar hydrogen bond driven 2D chirality of molecular self-assembly system.

A CAD based geometry model for simulation and analysis of particle detector data

Energy Technology Data Exchange (ETDEWEB)

Milde, Michael; Losekamm, Martin; Poeschl, Thomas; Greenwald, Daniel; Paul, Stephan [Technische Universitaet Muenchen, 85748 Garching (Germany)

2016-07-01

The development of a new particle detector requires a good understanding of its setup. A detailed model of the detector's geometry is not only needed during construction, but also for simulation and data analysis. To arrive at a consistent description of the detector geometry a representation is needed that can be easily implemented in different software tools used during data analysis. We developed a geometry representation based on CAD files that can be easily used within the Geant4 simulation framework and analysis tools based on the ROOT framework. This talk presents the structure of the geometry model and show its implementation using the example of the event reconstruction developed for the Multi-purpose Active-target Particle Telescope (MAPT). The detector consists of scintillating plastic fibers and can be used as a tracking detector and calorimeter with omnidirectional acceptance. To optimize the angular resolution and the energy reconstruction of measured particles, a detailed detector model is needed at all stages of the reconstruction.

Experimental validation on the effect of material geometries and processing methodology of Polyoxymethylene (POM)

Science.gov (United States)

Hafizzal, Y.; Nurulhuda, A.; Izman, S.; Khadir, AZA

2017-08-01

POM-copolymer bond breaking leads to change depending with respect to processing methodology and material geometries. This paper present the oversights effect on the material integrity due to different geometries and processing methodology. Thermo-analytical methods with reference were used to examine the degradation of thermomechanical while Thermogravimetric Analysis (TGA) was used to judge the thermal stability of sample from its major decomposition temperature. Differential Scanning Calorimetry (DSC) investigation performed to identify the thermal behaviour and thermal properties of materials. The result shown that plastic gear geometries with injection molding at higher tonnage machine more stable thermally rather than resin geometries. Injection plastic gear geometries at low tonnage machine faced major decomposition temperatures at 313.61°C, 305.76 °C and 307.91 °C while higher tonnage processing method are fully decomposed at 890°C, significantly higher compared to low tonnage condition and resin geometries specimen at 398°C. Chemical composition of plastic gear geometries with injection molding at higher and lower tonnage are compare based on their moisture and Volatile Organic Compound (VOC) content, polymeric material content and the absence of filler. Results of higher moisture and Volatile Organic Compound (VOC) content are report in resin geometries (0.120%) compared to higher tonnage of injection plastic gear geometries which is 1.264%. The higher tonnage of injection plastic gear geometry are less sensitive to thermo-mechanical degradation due to polymer chain length and molecular weight of material properties such as tensile strength, flexural strength, fatigue strength and creep resistance.

Application of artificial intelligence to search ground-state geometry of clusters

International Nuclear Information System (INIS)

Lemes, Mauricio Ruv; Marim, L.R.; Dal Pino, A. Jr.

2002-01-01

We introduce a global optimization procedure, the neural-assisted genetic algorithm (NAGA). It combines the power of an artificial neural network (ANN) with the versatility of the genetic algorithm. This method is suitable to solve optimization problems that depend on some kind of heuristics to limit the search space. If a reasonable amount of data is available, the ANN can 'understand' the problem and provide the genetic algorithm with a selected population of elements that will speed up the search for the optimum solution. We tested the method in a search for the ground-state geometry of silicon clusters. We trained the ANN with information about the geometry and energetics of small silicon clusters. Next, the ANN learned how to restrict the configurational space for larger silicon clusters. For Si 10 and Si 20 , we noticed that the NAGA is at least three times faster than the 'pure' genetic algorithm. As the size of the cluster increases, it is expected that the gain in terms of time will increase as well

A New Optimization Model for Computer-Aided Molecular Design Problems

DEFF Research Database (Denmark)

Zhang, Lei; Cignitti, Stefano; Gani, Rafiqul

Computer-Aided Molecular Design (CAMD) is a method to design molecules with desired properties. That is, through CAMD, it is possible to generate molecules that match a specified set of target properties. CAMD has attracted much attention in recent years due to its ability to design novel as well...... with structure information considered due to the increased size of the mathematical problem and number of alternatives. Thus, decomposition-based approach is proposed to solve the problem. In this approach, only first-order groups are considered in the first step to obtain the building block of the designed...... molecule, then the property model is refined with second-order groups based on the results of the first step. However, this may result in the possibility of an optimal solution being excluded. Samudra and Sahinidis [4] used property relaxation method in the first step to avoid this situation...

Studies on molecular structure, vibrational spectra and molecular docking analysis of 3-Methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl 4-aminobenzoate

Science.gov (United States)

Suresh, D. M.; Amalanathan, M.; Hubert Joe, I.; Bena Jothy, V.; Diao, Yun-Peng

2014-09-01

The molecular structure, vibrational analysis and molecular docking analysis of the 3-Methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl 4-aminobenzoate (MDDNAB) molecule have been carried out using FT-IR and FT-Raman spectroscopic techniques and DFT method. The equilibrium geometry, harmonic vibrational wave numbers, various bonding features have been computed using density functional method. The calculated molecular geometry has been compared with experimental data. The detailed interpretation of the vibrational spectra has been carried out by using VEDA program. The hyper-conjugative interactions and charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The simulated FT-IR and FT-Raman spectra satisfactorily coincide with the experimental spectra. The PES and charge analysis have been made. The molecular docking was done to identify the binding energy and the Hydrogen bonding with the cancer protein molecule.

Effect of Electrode Geometry on the Classification Performance of Rapid Evaporative Ionization Mass Spectrometric (REIMS) Bacterial Identification

Science.gov (United States)

Bodai, Zsolt; Cameron, Simon; Bolt, Frances; Simon, Daniel; Schaffer, Richard; Karancsi, Tamas; Balog, Julia; Rickards, Tony; Burke, Adam; Hardiman, Kate; Abda, Julia; Rebec, Monica; Takats, Zoltan

2018-01-01

The recently developed automated, high-throughput monopolar REIMS platform is suited for the identification of clinically important microorganisms. Although already comparable to the previously reported bipolar forceps method, optimization of the geometry of monopolar electrodes, at the heart of the system, holds the most scope for further improvements to be made. For this, sharp tip and round shaped electrodes were optimized to maximize species-level classification accuracy. Following optimization of the distance between the sample contact point and tube inlet with the sharp tip electrodes, the overall cross-validation accuracy improved from 77% to 93% in negative and from 33% to 63% in positive ion detection modes, compared with the original 4 mm distance electrode. As an alternative geometry, round tube shaped electrodes were developed. Geometry optimization of these included hole size, number, and position, which were also required to prevent plate pick-up due to vacuum formation. Additional features, namely a metal "X"-shaped insert and a pin in the middle were included to increase the contact surface with a microbial biomass to maximize aerosol production. Following optimization, cross-validation scores showed improvement in classification accuracy from 77% to 93% in negative and from 33% to 91% in positive ion detection modes. Supervised models were also built, and after the leave 20% out cross-validation, the overall classification accuracy was 98.5% in negative and 99% in positive ion detection modes. This suggests that the new generation of monopolar REIMS electrodes could provide substantially improved species level identification accuracies in both polarity detection modes. [Figure not available: see fulltext.

A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Druglike Fragments.

Science.gov (United States)

Sellers, Benjamin D; James, Natalie C; Gobbi, Alberto

2017-06-26

Reducing internal strain energy in small molecules is critical for designing potent drugs. Quantum mechanical (QM) and molecular mechanical (MM) methods are often used to estimate these energies. In an effort to determine which methods offer an optimal balance in accuracy and performance, we have carried out torsion scan analyses on 62 fragments. We compared nine QM and four MM methods to reference energies calculated at a higher level of theory: CCSD(T)/CBS single point energies (coupled cluster with single, double, and perturbative triple excitations at the complete basis set limit) calculated on optimized geometries using MP2/6-311+G**. The results show that both the more recent MP2.X perturbation method as well as MP2/CBS perform quite well. In addition, combining a Hartree-Fock geometry optimization with a MP2/CBS single point energy calculation offers a fast and accurate compromise when dispersion is not a key energy component. Among MM methods, the OPLS3 force field accurately reproduces CCSD(T)/CBS torsion energies on more test cases than the MMFF94s or Amber12:EHT force fields, which struggle with aryl-amide and aryl-aryl torsions. Using experimental conformations from the Cambridge Structural Database, we highlight three example structures for which OPLS3 significantly overestimates the strain. The energies and conformations presented should enable scientists to estimate the expected error for the methods described and we hope will spur further research into QM and MM methods.

Optimization of Moving Coil Actuators for Digital Displacement Machines

DEFF Research Database (Denmark)

Nørgård, Christian; Bech, Michael Møller; Roemer, Daniel Beck

2016-01-01

This paper focuses on deriving an optimal moving coil actuator design, used as force pro-ducing element in hydraulic on/off valves for Digital Displacement machines. Different moving coil actuator geometry topologies (permanent magnet placement and magnetiza-tion direction) are optimized for actu......This paper focuses on deriving an optimal moving coil actuator design, used as force pro-ducing element in hydraulic on/off valves for Digital Displacement machines. Different moving coil actuator geometry topologies (permanent magnet placement and magnetiza-tion direction) are optimized...... for actuating annular seat valves in a digital displacement machine. The optimization objectives are to the minimize the actuator power, the valve flow losses and the height of the actuator. Evaluation of the objective function involves static finite element simulation and simulation of an entire operation...... designs requires approximately 20 W on average and may be realized in 20 mm × Ø 22.5 mm (height × diameter) for a 20 kW pressure chamber. The optimization is carried out using the multi-objective Generalized Differential Evolu-tion optimization algorithm GDE3 which successfully handles constrained multi-objective...

Optimized Ultrawideband and Uniplanar Minkowski Fractal Branch Line Coupler

Directory of Open Access Journals (Sweden)

Mohammad Jahanbakht

2012-01-01

Full Text Available The non-Euclidean Minkowski fractal geometry is used in design, optimization, and fabrication of an ultrawideband (UWB branch line coupler. Self-similarities of the fractal geometries make them act like an infinite length in a finite area. This property creates a smaller design with broader bandwidth. The designed 3 dB microstrip coupler has a single layer and uniplanar platform with quite easy fabrication process. This optimized 180° coupler also shows a perfect isolation and insertion loss over the UWB frequency range of 3.1–10.6 GHz.

Visibility-based optimal path and motion planning

CERN Document Server

Wang, Paul Keng-Chieh

2015-01-01

This monograph deals with various visibility-based path and motion planning problems motivated by real-world applications such as exploration and mapping planetary surfaces, environmental surveillance using stationary or mobile robots, and imaging of global air/pollutant circulation. The formulation and solution of these problems call for concepts and methods from many areas of applied mathematics including computational geometry, set-covering, non-smooth optimization, combinatorial optimization and optimal control. Emphasis is placed on the formulation of new problems and methods of approach to these problems. Since geometry and visualization play important roles in the understanding of these problems, intuitive interpretations of the basic concepts are presented before detailed mathematical development. The development of a particular topic begins with simple cases illustrated by specific examples, and then progresses forward to more complex cases. The intended readers of this monograph are primarily studen...

Effect of microneedle geometry and supporting substrate on microneedle array penetration into skin.

Science.gov (United States)

Kochhar, Jaspreet Singh; Quek, Ten Cheer; Soon, Wei Jun; Choi, Jaewoong; Zou, Shui; Kang, Lifeng

2013-11-01

Microneedles are being fast recognized as a useful alternative to injections in delivering drugs, vaccines, and cosmetics transdermally. Owing to skin's inherent elastic properties, microneedles require an optimal geometry for skin penetration. In vitro studies, using rat skin to characterize microneedle penetration in vivo, require substrates with suitable mechanical properties to mimic human skin's subcutaneous tissues. We tested the effect of these two parameters on microneedle penetration. Geometry in terms of center-to-center spacing of needles was investigated for its effect on skin penetration, when placed on substrates of different hardness. Both hard (clay) and soft (polydimethylsiloxane, PDMS) substrates underneath rat skin and full-thickness pig skin were used as animal models and human skins were used as references. It was observed that there was an increase in percentage penetration with an increase in needle spacing. Microneedle penetration with PDMS as a support under stretched rat skin correlated better with that on full-thickness human skin, while penetration observed was higher when clay was used as a substrate. We showed optimal geometries for efficient penetration together with recommendation for a substrate that could better mimic the mechanical properties of human subcutaneous tissues, when using microneedles fabricated from poly(ethylene glycol)-based materials. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association.

Workshop on Computational Optimization

CERN Document Server

2016-01-01

This volume is a comprehensive collection of extended contributions from the Workshop on Computational Optimization 2014, held at Warsaw, Poland, September 7-10, 2014. The book presents recent advances in computational optimization. The volume includes important real problems like parameter settings for controlling processes in bioreactor and other processes, resource constrained project scheduling, infection distribution, molecule distance geometry, quantum computing, real-time management and optimal control, bin packing, medical image processing, localization the abrupt atmospheric contamination source and so on. It shows how to develop algorithms for them based on new metaheuristic methods like evolutionary computation, ant colony optimization, constrain programming and others. This research demonstrates how some real-world problems arising in engineering, economics, medicine and other domains can be formulated as optimization tasks.

Asymptotic behaviour of optimal fraction-rational series of the perturbation theory at description of molecular rotational spectra

International Nuclear Information System (INIS)

Burenin, A.V.

1994-01-01

A possibility is shown of substantial expansion of the choice of asymptotic behaviour of optimal fraction-rational series of the perturbation theory on description of molecular rotational spectra. The expansion permits to hope for substantial improvement of results of using the conception of effective rotational hamiltonian in a fraction-rational form on the description of highly perturbed vibrational states

Rugby and Mathematics: A Surprising Link among Geometry, the Conics, and Calculus.

Science.gov (United States)

Jones, Troy; Jackson, Steven

2001-01-01

Describes a rugby problem designed to help students understand the maximum-minimum situation. Presents a series of explorations that locate an optimal place for kicking the ball to maximize the angle at the goalposts. Uses interactive geometry software to construct a model of the situation. Includes a sample student activity. (KHR)

Geometry essentials for dummies

CERN Document Server

Ryan, Mark

2011-01-01

Just the critical concepts you need to score high in geometry This practical, friendly guide focuses on critical concepts taught in a typical geometry course, from the properties of triangles, parallelograms, circles, and cylinders, to the skills and strategies you need to write geometry proofs. Geometry Essentials For Dummies is perfect for cramming or doing homework, or as a reference for parents helping kids study for exams. Get down to the basics - get a handle on the basics of geometry, from lines, segments, and angles, to vertices, altitudes, and diagonals Conque

Optimizing Grid Patterns on Photovoltaic Cells

Science.gov (United States)

Burger, D. R.

1984-01-01

CELCAL computer program helps in optimizing grid patterns for different photovoltaic cell geometries and metalization processes. Five different powerloss phenomena associated with front-surface metal grid pattern on photovoltaic cells.

A combined experimental and mathematical approach for molecular-based optimization of irinotecan circadian delivery.

Directory of Open Access Journals (Sweden)

Annabelle Ballesta

2011-09-01

Full Text Available Circadian timing largely modifies efficacy and toxicity of many anticancer drugs. Recent findings suggest that optimal circadian delivery patterns depend on the patient genetic background. We present here a combined experimental and mathematical approach for the design of chronomodulated administration schedules tailored to the patient molecular profile. As a proof of concept we optimized exposure of Caco-2 colon cancer cells to irinotecan (CPT11, a cytotoxic drug approved for the treatment of colorectal cancer. CPT11 was bioactivated into SN38 and its efflux was mediated by ATP-Binding-Cassette (ABC transporters in Caco-2 cells. After cell synchronization with a serum shock defining Circadian Time (CT 0, circadian rhythms with a period of 26 h 50 (SD 63 min were observed in the mRNA expression of clock genes REV-ERBα, PER2, BMAL1, the drug target topoisomerase 1 (TOP1, the activation enzyme carboxylesterase 2 (CES2, the deactivation enzyme UDP-glucuronosyltransferase 1, polypeptide A1 (UGT1A1, and efflux transporters ABCB1, ABCC1, ABCC2 and ABCG2. DNA-bound TOP1 protein amount in presence of CPT11, a marker of the drug PD, also displayed circadian variations. A mathematical model of CPT11 molecular pharmacokinetics-pharmacodynamics (PK-PD was designed and fitted to experimental data. It predicted that CPT11 bioactivation was the main determinant of CPT11 PD circadian rhythm. We then adopted the therapeutics strategy of maximizing efficacy in non-synchronized cells, considered as cancer cells, under a constraint of maximum toxicity in synchronized cells, representing healthy ones. We considered exposure schemes in the form of an initial concentration of CPT11 given at a particular CT, over a duration ranging from 1 to 27 h. For any dose of CPT11, optimal exposure durations varied from 3h40 to 7h10. Optimal schemes started between CT2h10 and CT2h30, a time interval corresponding to 1h30 to 1h50 before the nadir of CPT11 bioactivation rhythm in

Optimized acoustic biochip integrated with microfluidics for biomarkers detection in molecular diagnostics.

Science.gov (United States)

Papadakis, G; Friedt, J M; Eck, M; Rabus, D; Jobst, G; Gizeli, E

2017-09-01

The development of integrated platforms incorporating an acoustic device as the detection element requires addressing simultaneously several challenges of technological and scientific nature. The present work was focused on the design of a microfluidic module, which, combined with a dual or array type Love wave acoustic chip could be applied to biomedical applications and molecular diagnostics. Based on a systematic study we optimized the mechanics of the flow cell attachment and the sealing material so that fluidic interfacing/encapsulation would impose minimal losses to the acoustic wave. We have also investigated combinations of operating frequencies with waveguide materials and thicknesses for maximum sensitivity during the detection of protein and DNA biomarkers. Within our investigations neutravidin was used as a model protein biomarker and unpurified PCR amplified Salmonella DNA as the model genetic target. Our results clearly indicate the need for experimental verification of the optimum engineering and analytical parameters, in order to develop commercially viable systems for integrated analysis. The good reproducibility of the signal together with the ability of the array biochip to detect multiple samples hold promise for the future use of the integrated system in a Lab-on-a-Chip platform for application to molecular diagnostics.

Systematic and efficient side chain optimization for molecular docking using a cheapest-path procedure.

Science.gov (United States)

Schumann, Marcel; Armen, Roger S

2013-05-30

Molecular docking of small-molecules is an important procedure for computer-aided drug design. Modeling receptor side chain flexibility is often important or even crucial, as it allows the receptor to adopt new conformations as induced by ligand binding. However, the accurate and efficient incorporation of receptor side chain flexibility has proven to be a challenge due to the huge computational complexity required to adequately address this problem. Here we describe a new docking approach with a very fast, graph-based optimization algorithm for assignment of the near-optimal set of residue rotamers. We extensively validate our approach using the 40 DUD target benchmarks commonly used to assess virtual screening performance and demonstrate a large improvement using the developed side chain optimization over rigid receptor docking (average ROC AUC of 0.693 vs. 0.623). Compared to numerous benchmarks, the overall performance is better than nearly all other commonly used procedures. Furthermore, we provide a detailed analysis of the level of receptor flexibility observed in docking results for different classes of residues and elucidate potential avenues for further improvement. Copyright © 2013 Wiley Periodicals, Inc.

Interoperable mesh and geometry tools for advanced petascale simulations

International Nuclear Information System (INIS)

Diachin, L; Bauer, A; Fix, B; Kraftcheck, J; Jansen, K; Luo, X; Miller, M; Ollivier-Gooch, C; Shephard, M S; Tautges, T; Trease, H

2007-01-01

SciDAC applications have a demonstrated need for advanced software tools to manage the complexities associated with sophisticated geometry, mesh, and field manipulation tasks, particularly as computer architectures move toward the petascale. The Center for Interoperable Technologies for Advanced Petascale Simulations (ITAPS) will deliver interoperable and interchangeable mesh, geometry, and field manipulation services that are of direct use to SciDAC applications. The premise of our technology development goal is to provide such services as libraries that can be used with minimal intrusion into application codes. To develop these technologies, we focus on defining a common data model and data-structure neutral interfaces that unify a number of different services such as mesh generation and improvement, front tracking, adaptive mesh refinement, shape optimization, and solution transfer operations. We highlight the use of several ITAPS services in SciDAC applications

Artificial intelligence search techniques for optimization of the cold source geometry

International Nuclear Information System (INIS)

Azmy, Y.Y.

1988-01-01

Most optimization studies of cold neutron sources have concentrated on the numerical prediction or experimental measurement of the cold moderator optimum thickness which produces the largest cold neutron leakage for a given thermal neutron source. Optimizing the geometrical shape of the cold source, however, is a more difficult problem because the optimized quantity, the cold neutron leakage, is an implicit function of the shape which is the unknown in such a study. We draw an analogy between this problem and a state space search, then we use a simple Artificial Intelligence (AI) search technique to determine the optimum cold source shape based on a two-group, r-z diffusion model. We implemented this AI design concept in the computer program AID which consists of two modules, a physical model module and a search module, which can be independently modified, improved, or made more sophisticated. 7 refs., 1 fig

Artificial intelligence search techniques for the optimization of cold source geometry

International Nuclear Information System (INIS)

Azmy, Y.Y.

1988-01-01

Most optimization studies of cold neutron sources have concentrated on the numerical prediction or experimental measurement of the cold moderator optimum thickness that produces the largest cold neutron leakage for a given thermal neutron source. Optimizing the geometric shape of the cold source, however, is a more difficult problem because the optimized quantity, the cold neutron leakage, is an implicit function of the shape, which is the unknown in such a study. An analogy is drawn between this problem and a state space search, then a simple artificial intelligence (AI) search technique is used to determine the optimum cold source shape based on a two-group, r-z diffusion model. This AI design concept was implemented in the computer program AID, which consists of two modules, a physical model module, and a search module, which can be independently modified, improved, or made more sophisticated

Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria.

Science.gov (United States)

Padial, José M; Grant, Taran; Frost, Darrel R

2014-06-26

Brachycephaloidea is a monophyletic group of frogs with more than 1000 species distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the group has been the target of multiple molecular phylogenetic analyses, resulting in extensive changes in its taxonomy. Here, we test previous hypotheses of phylogenetic relationships for the group by combining available molecular evidence (sequences of 22 genes representing 431 ingroup and 25 outgroup terminals) and performing a tree-alignment analysis under the parsimony optimality criterion using the program POY. To elucidate the effects of alignment and optimality criterion on phylogenetic inferences, we also used the program MAFFT to obtain a similarity-alignment for analysis under both parsimony and maximum likelihood using the programs TNT and GARLI, respectively. Although all three analytical approaches agreed on numerous points, there was also extensive disagreement. Tree-alignment under parsimony supported the monophyly of the ingroup and the sister group relationship of the monophyletic marsupial frogs (Hemiphractidae), while maximum likelihood and parsimony analyses of the MAFFT similarity-alignment did not. All three methods differed with respect to the position of Ceuthomantis smaragdinus (Ceuthomantidae), with tree-alignment using parsimony recovering this species as the sister of Pristimantis + Yunganastes. All analyses rejected the monophyly of Strabomantidae and Strabomantinae as originally defined, and the tree-alignment analysis under parsimony further rejected the recently redefined Craugastoridae and Pristimantinae. Despite the greater emphasis in the systematics literature placed on the choice of optimality criterion for evaluating trees than on the choice of method for aligning DNA sequences, we found that the topological differences attributable to the alignment method were as great as those caused by the optimality criterion. Further, the optimal tree-alignment indicates

Complex analysis and geometry

CERN Document Server

Silva, Alessandro

1993-01-01

The papers in this wide-ranging collection report on the results of investigations from a number of linked disciplines, including complex algebraic geometry, complex analytic geometry of manifolds and spaces, and complex differential geometry.

A comparison between two optimized TFPM geometries for 5 MW direct-drive wind turbines

DEFF Research Database (Denmark)

Nica, Florin Valentin Traian; Ritchie, Ewen; Leban, Krisztina Monika

2013-01-01

for the industry. The approach presented in this paper focuses on a reduction in mass of active materials, which constitute the generator, because the price of the machine is in direct relation with the amount of materials used for the construction. This strategy is applied for two types of TFPM geometries...

Aerothermodynamic shape optimization of hypersonic blunt bodies

Science.gov (United States)

Eyi, Sinan; Yumuşak, Mine

2015-07-01

The aim of this study is to develop a reliable and efficient design tool that can be used in hypersonic flows. The flow analysis is based on the axisymmetric Euler/Navier-Stokes and finite-rate chemical reaction equations. The equations are coupled simultaneously and solved implicitly using Newton's method. The Jacobian matrix is evaluated analytically. A gradient-based numerical optimization is used. The adjoint method is utilized for sensitivity calculations. The objective of the design is to generate a hypersonic blunt geometry that produces the minimum drag with low aerodynamic heating. Bezier curves are used for geometry parameterization. The performances of the design optimization method are demonstrated for different hypersonic flow conditions.

Optimizing a neutron-beam focusing device for the direct geometry time-of-flight spectrometer TOFTOF at the FRM II reactor source

Energy Technology Data Exchange (ETDEWEB)

Rasmussen, N.G. [Nanoscience Center, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø (Denmark); Simeoni, G.G., E-mail: ggsimeoni@outlook.com [Heinz Maier-Leibnitz Zentrum (MLZ) and Physics Department, Technical University of Munich, D-85748 Garching (Germany); Lefmann, K. [Nanoscience Center, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø (Denmark)

2016-04-21

A dedicated beam-focusing device has been designed for the direct geometry thermal-cold neutron time-of-flight spectrometer TOFTOF at the neutron facility FRM II (Garching, Germany). The prototype, based on the compressed Archimedes' mirror concept, benefits from the adaptive-optics technology (adjustable supermirror curvature) and the compact size (only 0.5 m long). We have simulated the neutron transport across the entire guide system. We present a detailed computer characterization of the existing device, along with the study of the factors mostly influencing the future improvement. We have optimized the simulated prototype as a function of the neutron wavelength, accounting also for all relevant features of a real instrument like the non-reflecting side edges. The results confirm the “chromatic” displacement of the focal point (flux density maximum) at fixed supermirror curvature, and the ability of a variable curvature to keep the focal point at the sample position. Our simulations are in excellent agreement with theoretical predictions and the experimentally measured beam profile. With respect to the possibility of a further upgrade, we find that supermirror coatings with m-values higher than 3.5 would have only marginal influence on the optimal behaviour, whereas comparable spectrometers could take advantage of longer focusing segments, with particular impact for the thermal region of the neutron spectrum.

Relaxed geometries and dipole moments of positron complexes with diatomic molecules

Energy Technology Data Exchange (ETDEWEB)

Assafrao, Denise; Mohallem, Jose R, E-mail: rachid@fisica.ufmg.b [Laboratorio de Atomos e Moleculas Especiais, Departamento de Fisica, ICEx, Universidade Federal de Minas Gerais, CP 702, 30123-970, Belo Horizonte, MG (Brazil)

2010-01-01

Relaxed geometries and dipole moments of diatomic molecules interacting with a slow positron are reported as functions of the positron distance to the more electronegative atom. A molecular model for the complex that allows applications to large systems is used. The electron population on the positron is proposed as a weighting function to calculate the average quantities. Results show Self-Consistent-Field quality or better.

A Parallel Biological Optimization Algorithm to Solve the Unbalanced Assignment Problem Based on DNA Molecular Computing

Directory of Open Access Journals (Sweden)

Zhaocai Wang

2015-10-01

Full Text Available The unbalanced assignment problem (UAP is to optimally resolve the problem of assigning n jobs to m individuals (m < n, such that minimum cost or maximum profit obtained. It is a vitally important Non-deterministic Polynomial (NP complete problem in operation management and applied mathematics, having numerous real life applications. In this paper, we present a new parallel DNA algorithm for solving the unbalanced assignment problem using DNA molecular operations. We reasonably design flexible-length DNA strands representing different jobs and individuals, take appropriate steps, and get the solutions of the UAP in the proper length range and O(mn time. We extend the application of DNA molecular operations and simultaneity to simplify the complexity of the computation.

DFT approach to (benzylthio)acetic acid: Conformational search, molecular (monomer and dimer) structure, vibrational spectroscopy and some electronic properties

Science.gov (United States)

Sienkiewicz-Gromiuk, Justyna

2018-01-01

The DFT studies were carried out with the B3LYP method utilizing the 6-31G and 6-311++G(d,p) basis sets depending on whether the aim of calculations was to gain the geometry at equilibrium, or to calculate the optimized molecular structure of (benzylthio)acetic acid (Hbta) in the forms of monomer and dimer. The minimum conformational energy search was followed by the potential energy surface (PES) scan of all rotary bonds existing in the acid molecule. The optimized geometrical monomeric and dimeric structures of the title compound were compared with the experimental structural data in the solid state. The detailed vibrational interpretation of experimental infrared and Raman bands was performed on the basis of theoretically simulated ESFF-scaled wavenumbers calculated for the monomer and dimer structures of Hbta. The electronic characteristics of Hbta is also presented in terms of Mulliken atomic charges, frontier molecular orbitals and global reactivity descriptors. Additionally, the MEP and ESP surfaces were computed to predict coordination sites for potential metal complex formation.

Theory of gearing kinematics, geometry, and synthesis

CERN Document Server

Radzevich, Stephen P

2012-01-01

The first book of its kind, Theory of Gearing: Kinematics, Geometry, and Synthesis systematically develops a scientific theory of gearing that makes it possible to synthesize novel gears with the desired performance. Written by a leading gearing expert who holds more than 200 patents, it presents a modern methodology for gear design. The proposed theory is based on a key postulate: all the design parameters for an optimal gear pair for a particular application can be derived from (a) a given configuration of the rotation vectors of the driving and driven shafts and (b) the power transmitted by

ATK-ForceField: a new generation molecular dynamics software package

Science.gov (United States)

Schneider, Julian; Hamaekers, Jan; Chill, Samuel T.; Smidstrup, Søren; Bulin, Johannes; Thesen, Ralph; Blom, Anders; Stokbro, Kurt

2017-12-01

ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.

Modeling the intermolecular interactions: molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide.

Science.gov (United States)

Karabulut, Sedat; Namli, Hilmi; Kurtaran, Raif; Yildirim, Leyla Tatar; Leszczynski, Jerzy

2014-03-01

The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. Copyright © 2013 Elsevier Inc. All rights reserved.

Optimization over polynomials : Selected topics

NARCIS (Netherlands)

Laurent, M.; Jang, Sun Young; Kim, Young Rock; Lee, Dae-Woong; Yie, Ikkwon

2014-01-01

Minimizing a polynomial function over a region defined by polynomial inequalities models broad classes of hard problems from combinatorics, geometry and optimization. New algorithmic approaches have emerged recently for computing the global minimum, by combining tools from real algebra (sums of

The Use of Molecular Modeling as "Pseudoexperimental" Data for Teaching VSEPR as a Hands-On General Chemistry Activity

Science.gov (United States)

Martin, Christopher B.; Vandehoef, Crissie; Cook, Allison

2015-01-01

A hands-on activity appropriate for first-semester general chemistry students is presented that combines traditional VSEPR methods of predicting molecular geometries with introductory use of molecular modeling. Students analyze a series of previously calculated output files consisting of several molecules each in various geometries. Each structure…

Gaussian-3 theory using density functional geometries and zero-point energies

International Nuclear Information System (INIS)

Baboul, A.G.; Curtiss, L.A.; Redfern, P.C.; Raghavachari, K.

1999-01-01

A variation of Gaussian-3 (G3) theory is presented in which the geometries and zero-point energies are obtained from B3LYP density functional theory [B3LYP/6-31G(d)] instead of geometries from second-order perturbation theory [MP2(FU)/6-31G(d)] and zero-point energies from Hartree - Fock theory [HF/6-31G(d)]. This variation, referred to as G3//B3LYP, is assessed on 299 energies (enthalpies of formation, ionization potentials, electron affinities, proton affinities) from the G2/97 test set [J. Chem. Phys. 109, 42 (1998)]. The G3//B3LYP average absolute deviation from experiment for the 299 energies is 0.99 kcal/mol compared to 1.01 kcal/mol for G3 theory. Generally, the results from the two methods are similar, with some exceptions. G3//B3LYP theory gives significantly improved results for several cases for which MP2 theory is deficient for optimized geometries, such as CN and O 2 + . However, G3//B3LYP does poorly for ionization potentials that involve a Jahn - Teller distortion in the cation (CH 4 + , BF 3 + , BCl 3 + ) because of the B3LYP/6-31G(d) geometries. The G3(MP2) method is also modified to use B3LYP/6-31G(d) geometries and zero-point energies. This variation, referred to as G3(MP2)//B3LYP, has an average absolute deviation of 1.25 kcal/mol compared to 1.30 kcal/mol for G3(MP2) theory. Thus, use of density functional geometries and zero-point energies in G3 and G3(MP2) theories is a useful alternative to MP2 geometries and HF zero-point energies. copyright 1999 American Institute of Physics

Multidisciplinary Shape Optimization of a Composite Blended Wing Body Aircraft

Science.gov (United States)

Boozer, Charles Maxwell

A multidisciplinary shape optimization tool coupling aerodynamics, structure, and performance was developed for battery powered aircraft. Utilizing high-fidelity computational fluid dynamics analysis tools and a structural wing weight tool, coupled based on the multidisciplinary feasible optimization architecture; aircraft geometry is modified in the optimization of the aircraft's range or endurance. The developed tool is applied to three geometries: a hybrid blended wing body, delta wing UAS, the ONERA M6 wing, and a modified ONERA M6 wing. First, the optimization problem is presented with the objective function, constraints, and design vector. Next, the tool's architecture and the analysis tools that are utilized are described. Finally, various optimizations are described and their results analyzed for all test subjects. Results show that less computationally expensive inviscid optimizations yield positive performance improvements using planform, airfoil, and three-dimensional degrees of freedom. From the results obtained through a series of optimizations, it is concluded that the newly developed tool is both effective at improving performance and serves as a platform ready to receive additional performance modules, further improving its computational design support potential.

Design Optimization of a Micro-Combustor for Lean, Premixed Fuel-Air Mixtures

Science.gov (United States)

Powell, Leigh Theresa

Present technology has been shifting towards miniaturization of devices for energy production for portable electronics. Micro-combustors, when incorporated into a micro-power generation system, provide the energy desired in the form of hot gases to power such technology. This creates the need for a design optimization of the micro-combustor in terms of geometry, fuel choice, and material selection. A total of five micro-combustor geometries, three fuels, and three materials were computationally simulated in different configurations in order to determine the optimal micro-combustor design for highest efficiency. Inlet velocity, equivalence ratio, and wall heat transfer coefficient were varied in order to test a comprehensive range of micro-combustor parameters. All simulations completed for the optimization study used ANSYS Fluent v16.1 and post-processing of the data was done in CFD Post v16.1. It was found that for lean, premixed fuel-air mixtures (φ = 0.6 - 0.9) ethane (C 2H6) provided the highest flame temperatures when ignited within the micro-combustor geometries. An aluminum oxide converging micro-combustor burning ethane and air at an equivalence ratio of 0.9, an inlet velocity of 0.5 m/s, and heat transfer coefficient of 5 W/m2-K was found to produce the highest combustor efficiency, making it the optimal choice for a micro-combustor design. It is proposed that this geometry be experimentally and computationally investigated further in order to determine if additional optimization can be achieved.

Size-exclusion chromatography (HPLC-SEC) technique optimization by simplex method to estimate molecular weight distribution of agave fructans.

Science.gov (United States)

Moreno-Vilet, Lorena; Bostyn, Stéphane; Flores-Montaño, Jose-Luis; Camacho-Ruiz, Rosa-María

2017-12-15

Agave fructans are increasingly important in food industry and nutrition sciences as a potential ingredient of functional food, thus practical analysis tools to characterize them are needed. In view of the importance of the molecular weight on the functional properties of agave fructans, this study has the purpose to optimize a method to determine their molecular weight distribution by HPLC-SEC for industrial application. The optimization was carried out using a simplex method. The optimum conditions obtained were at column temperature of 61.7°C using tri-distilled water without salt, adjusted pH of 5.4 and a flow rate of 0.36mL/min. The exclusion range is from 1 to 49 of polymerization degree (180-7966Da). This proposed method represents an accurate and fast alternative to standard methods involving multiple-detection or hydrolysis of fructans. The industrial applications of this technique might be for quality control, study of fractionation processes and determination of purity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Localized orbitals vs. pseudopotential-plane waves basis sets: performances and accuracy for molecular magnetic systems

International Nuclear Information System (INIS)

Massobrio, C.; Ruiz, E.

2003-01-01

Density functional theory, in combination with a) a careful choice of the exchange-correlation part of the total energy and b) localized basis sets for the electronic orbital, has become the method of choice for calculating the exchange-couplings in magnetic molecular complexes. Orbital expansion on plane waves can be seen as an alternative basis set especially suited to allow optimization of newly synthesized materials of unknown geometries. However, little is known on the predictive power of this scheme to yield quantitative values for exchange coupling constants J as small as a few hundredths of eV (50-300 cm -1 ). We have used density functional theory and a plane waves basis set to calculate the exchange couplings J of three homodinuclear Cu-based molecular complexes with experimental values ranging from +40 cm -1 to -300 cm -1 . The plane waves basis set proves as accurate as the localized basis set, thereby suggesting that this approach can be reliably employed to predict and rationalize the magnetic properties of molecular-based materials. (author)

Geometry

CERN Document Server

Pedoe, Dan

1988-01-01

""A lucid and masterly survey."" - Mathematics Gazette Professor Pedoe is widely known as a fine teacher and a fine geometer. His abilities in both areas are clearly evident in this self-contained, well-written, and lucid introduction to the scope and methods of elementary geometry. It covers the geometry usually included in undergraduate courses in mathematics, except for the theory of convex sets. Based on a course given by the author for several years at the University of Minnesota, the main purpose of the book is to increase geometrical, and therefore mathematical, understanding and to he

Control-Informed Geometric Optimization of Wave Energy Converters: The Impact of Device Motion and Force Constraints

Directory of Open Access Journals (Sweden)

Paula B. Garcia-Rosa

2015-12-01

Full Text Available The energy cost for producing electricity via wave energy converters (WECs is still not competitive with other renewable energy sources, especially wind energy. It is well known that energy maximising control plays an important role to improve the performance of WECs, allowing the energy conversion to be performed as economically as possible. The control strategies are usually subsequently employed on a device that was designed and optimized in the absence of control for the prevailing sea conditions in a particular location. If an optimal unconstrained control strategy, such as pseudo-spectral optimal control (PSOC, is adopted, an overall optimized system can be obtained no matter whether the control design is incorporated at the geometry optimization stage or not. Nonetheless, strategies, such as latching control (LC, must be incorporated at the optimization design stage of the WEC geometry if an overall optimized system is to be realised. In this paper, the impact of device motion and force constraints in the design of control-informed optimized WEC geometries is addressed. The aim is to verify to what extent the constraints modify the connection between the control and the optimal device design. Intuitively, one might expect that if the constraints are very tight, the optimal device shape is the same regardless of incorporating or not the constrained control at the geometry optimization stage. However, this paper tests the hypothesis that the imposition of constraints will limit the control influence on the optimal device shape. PSOC, LC and passive control (PC are considered in this study. In addition, constrained versions of LC and PC are presented.

Design optimization of a T mixing vane in nuclear fuel assembly

International Nuclear Information System (INIS)

Jung, Sang-Ho; Moon, Mi-Ae; Kim, Kwang-Yong

2009-01-01

The purposes of present work are to analyze the convective heat transfer with three-dimensional Reynolds-averaged Navier-Stokes analysis, and to optimize shape of the mixing vane using the analysis results. PLUS7 that is designed by KNF and Westinghouse is used as reference geometry. Shear stress transport turbulence model is used as a turbulence closure. Two bend angles of mixing vane are selected as design variable. The objective function is defined as a combination of inverse of heat transfer rate and friction loss. Response surface method is employed as an optimization technique. The calculation domains of 1x2 geometry are analyzed with translational and rotational periodic boundary conditions which take flow directions into account. The fluid flow and heat transfer characteristics have been explained through velocity vectors, streamlines and Nusselt numbers. The results show that the optimized geometry improves the heat transfer performance of the mixing vane with a relatively small pressure drop increment and has higher Critical Heat Flux. (author)

Programmable molecular recognition based on the geometry of DNA nanostructures.

Science.gov (United States)

Woo, Sungwook; Rothemund, Paul W K

2011-07-10

From ligand-receptor binding to DNA hybridization, molecular recognition plays a central role in biology. Over the past several decades, chemists have successfully reproduced the exquisite specificity of biomolecular interactions. However, engineering multiple specific interactions in synthetic systems remains difficult. DNA retains its position as the best medium with which to create orthogonal, isoenergetic interactions, based on the complementarity of Watson-Crick binding. Here we show that DNA can be used to create diverse bonds using an entirely different principle: the geometric arrangement of blunt-end stacking interactions. We show that both binary codes and shape complementarity can serve as a basis for such stacking bonds, and explore their specificity, thermodynamics and binding rules. Orthogonal stacking bonds were used to connect five distinct DNA origami. This work, which demonstrates how a single attractive interaction can be developed to create diverse bonds, may guide strategies for molecular recognition in systems beyond DNA nanostructures.

Complex algebraic geometry

CERN Document Server

Kollár, János

1997-01-01

This volume contains the lectures presented at the third Regional Geometry Institute at Park City in 1993. The lectures provide an introduction to the subject, complex algebraic geometry, making the book suitable as a text for second- and third-year graduate students. The book deals with topics in algebraic geometry where one can reach the level of current research while starting with the basics. Topics covered include the theory of surfaces from the viewpoint of recent higher-dimensional developments, providing an excellent introduction to more advanced topics such as the minimal model program. Also included is an introduction to Hodge theory and intersection homology based on the simple topological ideas of Lefschetz and an overview of the recent interactions between algebraic geometry and theoretical physics, which involve mirror symmetry and string theory.

CMS geometry through 2020

International Nuclear Information System (INIS)

Osborne, I; Brownson, E; Eulisse, G; Jones, C D; Sexton-Kennedy, E; Lange, D J

2014-01-01

CMS faces real challenges with upgrade of the CMS detector through 2020 and beyond. One of the challenges, from the software point of view, is managing upgrade simulations with the same software release as the 2013 scenario. We present the CMS geometry description software model, its integration with the CMS event setup and core software. The CMS geometry configuration and selection is implemented in Python. The tools collect the Python configuration fragments into a script used in CMS workflow. This flexible and automated geometry configuration allows choosing either transient or persistent version of the same scenario and specific version of the same scenario. We describe how the geometries are integrated and validated, and how we define and handle different geometry scenarios in simulation and reconstruction. We discuss how to transparently manage multiple incompatible geometries in the same software release. Several examples are shown based on current implementation assuring consistent choice of scenario conditions. The consequences and implications for multiple/different code algorithms are discussed.

Alternating copolymers and alternative device geometries for organic photovoltaics.

Science.gov (United States)

Inganäs, Olle; Zhang, Fengling; Andersson, Mats R

2012-01-01

The efficiency of conversion of light to electrical energy with the help of conjugated polymers and molecules is rapidly improving. The optical absorption properties of these materials can be designed, and implemented via molecular engineering. Full coverage of the solar spectrum is thus feasible. Narrow absorption spectra allow construction of tandem solar cells. The poor transport properties of these materials require thin devices, which limits optical absorption. Alternative device geometries for these flexible materials compensate for the optical absorption by light trapping, and allow tandem cells.

Optimizing the hydraulic program of cementing casing strings

Energy Technology Data Exchange (ETDEWEB)

Novakovic, M

1984-01-01

A technique is described for calculating the optimal parameters of the flow of plugging mud which takes into consideration the geometry of the annular space and the rheological characteristics of the muds. The optimization algorithm was illustrated by a block diagram. Examples are given for practical application of the optimization programs in production conditions. It is stressed that optimizing the hydraulic cementing program is effective if other technical-technological problems in cementing casing strings have been resolved.

Analisis Keterampilan Geometri Siswa Dalam Memecahkan Masalah Geometri Berdasarkan Tingkat Berpikir Van Hiele

OpenAIRE

Muhassanah, Nuraini; Sujadi, Imam; Riyadi, Riyadi

2014-01-01

The objective of this research was to describe the VIII grade students geometry skills atSMP N 16 Surakarta in the level 0 (visualization), level 1 (analysis), and level 2 (informaldeduction) van Hiele level of thinking in solving the geometry problem. This research was aqualitative research in the form of case study analyzing deeply the students geometry skill insolving the geometry problem based on van Hiele level of thingking. The subject of this researchwas nine students of VIII grade at ...

the impact of machine geometries on the average torque of dual ...

African Journals Online (AJOL)

HOD

Keywords: average torque, dual start, machine geometry, optimal value, PM machines. 1. ... permanent magnet length, back-iron size etc. were ..... e (N m. ) Stator tooth width/stator slot pitch. 4. 5. 7. 8. 10. 11. 13. 14. Number of rotor poles. 0. 1. 2. 3. 4. 5. 6. 0. 2. 4. 6. 8. 10. 12. T orq u e (Nm. ) Back-iron thickness (mm). 4. 5. 7.

On the achievable performance using variable geometry active secondary suspension systems in commercial vehicles

NARCIS (Netherlands)

Evers, W.J.; Besselink, I.G.M.; Teerhuis, A.P.; Nijmeijer, H.

2011-01-01

There is a need to further improve driver comfort in commercial vehicles. The variable geometry active suspension offers an interesting option to achieve this in an energy efficient way. However, the optimal control strategy and the overal performance potential remains unclear. The aim of this paper

Algorithms in Algebraic Geometry

CERN Document Server

Dickenstein, Alicia; Sommese, Andrew J

2008-01-01

In the last decade, there has been a burgeoning of activity in the design and implementation of algorithms for algebraic geometric computation. Some of these algorithms were originally designed for abstract algebraic geometry, but now are of interest for use in applications and some of these algorithms were originally designed for applications, but now are of interest for use in abstract algebraic geometry. The workshop on Algorithms in Algebraic Geometry that was held in the framework of the IMA Annual Program Year in Applications of Algebraic Geometry by the Institute for Mathematics and Its

Geometry and self-righting of turtles.

Science.gov (United States)

Domokos, Gábor; Várkonyi, Péter L

2008-01-07

Terrestrial animals with rigid shells face imminent danger when turned upside down. A rich variety of righting strategies of beetle and turtle species have been described, but the exact role of the shell's geometry in righting is so far unknown. These strategies are often based on active mechanisms, e.g. most beetles self-right via motion of their legs or wings; flat, aquatic turtles use their muscular neck to flip back. On the other hand, highly domed, terrestrial turtles with short limbs and necks have virtually no active control: here shape itself may serve as a fundamental tool. Based on field data gathered on a broad spectrum of aquatic and terrestrial turtle species we develop a geometric model of the shell. Inspired by recent mathematical results, we demonstrate that a simple mechanical classification of the model is closely linked to the animals' righting strategy. Specifically, we show that the exact geometry of highly domed terrestrial species is close to optimal for self-righting, and the shell's shape is the predominant factor of their ability to flip back. Our study illustrates how evolution solved a far-from-trivial geometrical problem and equipped some turtles with monostatic shells: beautiful forms, which rarely appear in nature otherwise.

Numerical simulations and mathematical models of flows in complex geometries

DEFF Research Database (Denmark)

Hernandez Garcia, Anier

The research work of the present thesis was mainly aimed at exploiting one of the strengths of the Lattice Boltzmann methods, namely, the ability to handle complicated geometries to accurately simulate flows in complex geometries. In this thesis, we perform a very detailed theoretical analysis...... and through the Chapman-Enskog multi-scale expansion technique the dependence of the kinetic viscosity on each scheme is investigated. Seeking for optimal numerical schemes to eciently simulate a wide range of complex flows a variant of the finite element, off-lattice Boltzmann method [5], which uses...... the characteristic based integration is also implemented. Using the latter scheme, numerical simulations are conducted in flows of different complexities: flow in a (real) porous network and turbulent flows in ducts with wall irregularities. From the simulations of flows in porous media driven by pressure gradients...

Non-Euclidean geometry

CERN Document Server

Kulczycki, Stefan

2008-01-01

This accessible approach features two varieties of proofs: stereometric and planimetric, as well as elementary proofs that employ only the simplest properties of the plane. A short history of geometry precedes a systematic exposition of the principles of non-Euclidean geometry.Starting with fundamental assumptions, the author examines the theorems of Hjelmslev, mapping a plane into a circle, the angle of parallelism and area of a polygon, regular polygons, straight lines and planes in space, and the horosphere. Further development of the theory covers hyperbolic functions, the geometry of suff

Movable geometry and eigenvalue search capability in the MC21 Monte Carlo code

International Nuclear Information System (INIS)

Gill, D. F.; Nease, B. R.; Griesheimer, D. P.

2013-01-01

A description of a robust and flexible movable geometry implementation in the Monte Carlo code MC21 is described along with a search algorithm that can be used in conjunction with the movable geometry capability to perform eigenvalue searches based on the position of some geometric component. The natural use of the combined movement and search capability is searching to critical through variation of control rod (or control drum) position. The movable geometry discussion provides the mathematical framework for moving surfaces in the MC21 combinatorial solid geometry description. A discussion of the interface between the movable geometry system and the user is also described, particularly the ability to create a hierarchy of movable groups. Combined with the hierarchical geometry description in MC21 the movable group framework provides a very powerful system for inline geometry modification. The eigenvalue search algorithm implemented in MC21 is also described. The foundations of this algorithm are a regula falsi search though several considerations are made in an effort to increase the efficiency of the algorithm for use with Monte Carlo. Specifically, criteria are developed to determine after each batch whether the Monte Carlo calculation should be continued, the search iteration can be rejected, or the search iteration has converged. These criteria seek to minimize the amount of time spent per iteration. Results for the regula falsi method are shown, illustrating that the method as implemented is indeed convergent and that the optimizations made ultimately reduce the total computational expense. (authors)

Movable geometry and eigenvalue search capability in the MC21 Monte Carlo code

Energy Technology Data Exchange (ETDEWEB)

Gill, D. F.; Nease, B. R.; Griesheimer, D. P. [Bettis Atomic Power Laboratory, PO Box 79, West Mifflin, PA 15122 (United States)

2013-07-01

A description of a robust and flexible movable geometry implementation in the Monte Carlo code MC21 is described along with a search algorithm that can be used in conjunction with the movable geometry capability to perform eigenvalue searches based on the position of some geometric component. The natural use of the combined movement and search capability is searching to critical through variation of control rod (or control drum) position. The movable geometry discussion provides the mathematical framework for moving surfaces in the MC21 combinatorial solid geometry description. A discussion of the interface between the movable geometry system and the user is also described, particularly the ability to create a hierarchy of movable groups. Combined with the hierarchical geometry description in MC21 the movable group framework provides a very powerful system for inline geometry modification. The eigenvalue search algorithm implemented in MC21 is also described. The foundations of this algorithm are a regula falsi search though several considerations are made in an effort to increase the efficiency of the algorithm for use with Monte Carlo. Specifically, criteria are developed to determine after each batch whether the Monte Carlo calculation should be continued, the search iteration can be rejected, or the search iteration has converged. These criteria seek to minimize the amount of time spent per iteration. Results for the regula falsi method are shown, illustrating that the method as implemented is indeed convergent and that the optimizations made ultimately reduce the total computational expense. (authors)

Optimization of HTS superconducting magnetic energy storage magnet volume

Science.gov (United States)

Korpela, Aki; Lehtonen, Jorma; Mikkonen, Risto

2003-08-01

Nonlinear optimization problems in the field of electromagnetics have been successfully solved by means of sequential quadratic programming (SQP) and the finite element method (FEM). For example, the combination of SQP and FEM has been proven to be an efficient tool in the optimization of low temperature superconductors (LTS) superconducting magnetic energy storage (SMES) magnets. The procedure can also be applied for the optimization of HTS magnets. However, due to a strongly anisotropic material and a slanted electric field, current density characteristic high temperature superconductors HTS optimization is quite different from that of the LTS. In this paper the volumes of solenoidal conduction-cooled Bi-2223/Ag SMES magnets have been optimized at the operation temperature of 20 K. In addition to the electromagnetic constraints the stress caused by the tape bending has also been taken into account. Several optimization runs with different initial geometries were performed in order to find the best possible solution for a certain energy requirement. The optimization constraints describe the steady-state operation, thus the presented coil geometries are designed for slow ramping rates. Different energy requirements were investigated in order to find the energy dependence of the design parameters of optimized solenoidal HTS coils. According to the results, these dependences can be described with polynomial expressions.

Geometry on the space of geometries

International Nuclear Information System (INIS)

Christodoulakis, T.; Zanelli, J.

1988-06-01

We discuss the geometric structure of the configuration space of pure gravity. This is an infinite dimensional manifold, M, where each point represents one spatial geometry g ij (x). The metric on M is dictated by geometrodynamics, and from it, the Christoffel symbols and Riemann tensor can be found. A ''free geometry'' tracing a geodesic on the manifold describes the time evolution of space in the strong gravity limit. In a regularization previously introduced by the authors, it is found that M does not have the same dimensionality, D, everywhere, and that D is not a scalar, although it is covariantly constant. In this regularization, it is seen that the path integral measure can be absorbed in a renormalization of the cosmological constant. (author). 19 refs

Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization

Directory of Open Access Journals (Sweden)

Hsu Hui-Chi

2011-04-01

Full Text Available Abstract Background Optimizing treatment through microarray-based molecular subtyping is a promising method to address the problem of heterogeneity in breast cancer; however, current application is restricted to prediction of distant recurrence risk. This study investigated whether breast cancer molecular subtyping according to its global intrinsic biology could be used for treatment customization. Methods Gene expression profiling was conducted on fresh frozen breast cancer tissue collected from 327 patients in conjunction with thoroughly documented clinical data. A method of molecular subtyping based on 783 probe-sets was established and validated. Statistical analysis was performed to correlate molecular subtypes with survival outcome and adjuvant chemotherapy regimens. Heterogeneity of molecular subtypes within groups sharing the same distant recurrence risk predicted by genes of the Oncotype and MammaPrint predictors was studied. Results We identified six molecular subtypes of breast cancer demonstrating distinctive molecular and clinical characteristics. These six subtypes showed similarities and significant differences from the Perou-Sørlie intrinsic types. Subtype I breast cancer was in concordance with chemosensitive basal-like intrinsic type. Adjuvant chemotherapy of lower intensity with CMF yielded survival outcome similar to those of CAF in this subtype. Subtype IV breast cancer was positive for ER with a full-range expression of HER2, responding poorly to CMF; however, this subtype showed excellent survival when treated with CAF. Reduced expression of a gene associated with methotrexate sensitivity in subtype IV was the likely reason for poor response to methotrexate. All subtype V breast cancer was positive for ER and had excellent long-term survival with hormonal therapy alone following surgery and/or radiation therapy. Adjuvant chemotherapy did not provide any survival benefit in early stages of subtype V patients. Subtype V was

Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization

International Nuclear Information System (INIS)

Kao, Kuo-Jang; Chang, Kai-Ming; Hsu, Hui-Chi; Huang, Andrew T

2011-01-01

Optimizing treatment through microarray-based molecular subtyping is a promising method to address the problem of heterogeneity in breast cancer; however, current application is restricted to prediction of distant recurrence risk. This study investigated whether breast cancer molecular subtyping according to its global intrinsic biology could be used for treatment customization. Gene expression profiling was conducted on fresh frozen breast cancer tissue collected from 327 patients in conjunction with thoroughly documented clinical data. A method of molecular subtyping based on 783 probe-sets was established and validated. Statistical analysis was performed to correlate molecular subtypes with survival outcome and adjuvant chemotherapy regimens. Heterogeneity of molecular subtypes within groups sharing the same distant recurrence risk predicted by genes of the Oncotype and MammaPrint predictors was studied. We identified six molecular subtypes of breast cancer demonstrating distinctive molecular and clinical characteristics. These six subtypes showed similarities and significant differences from the Perou-Sørlie intrinsic types. Subtype I breast cancer was in concordance with chemosensitive basal-like intrinsic type. Adjuvant chemotherapy of lower intensity with CMF yielded survival outcome similar to those of CAF in this subtype. Subtype IV breast cancer was positive for ER with a full-range expression of HER2, responding poorly to CMF; however, this subtype showed excellent survival when treated with CAF. Reduced expression of a gene associated with methotrexate sensitivity in subtype IV was the likely reason for poor response to methotrexate. All subtype V breast cancer was positive for ER and had excellent long-term survival with hormonal therapy alone following surgery and/or radiation therapy. Adjuvant chemotherapy did not provide any survival benefit in early stages of subtype V patients. Subtype V was consistent with a unique subset of luminal A intrinsic

A Lorentzian quantum geometry

Energy Technology Data Exchange (ETDEWEB)

Grotz, Andreas

2011-10-07

In this thesis, a formulation of a Lorentzian quantum geometry based on the framework of causal fermion systems is proposed. After giving the general definition of causal fermion systems, we deduce space-time as a topological space with an underlying causal structure. Restricting attention to systems of spin dimension two, we derive the objects of our quantum geometry: the spin space, the tangent space endowed with a Lorentzian metric, connection and curvature. In order to get the correspondence to classical differential geometry, we construct examples of causal fermion systems by regularizing Dirac sea configurations in Minkowski space and on a globally hyperbolic Lorentzian manifold. When removing the regularization, the objects of our quantum geometry reduce to the common objects of spin geometry on Lorentzian manifolds, up to higher order curvature corrections.

A Lorentzian quantum geometry

International Nuclear Information System (INIS)

Grotz, Andreas

2011-01-01

In this thesis, a formulation of a Lorentzian quantum geometry based on the framework of causal fermion systems is proposed. After giving the general definition of causal fermion systems, we deduce space-time as a topological space with an underlying causal structure. Restricting attention to systems of spin dimension two, we derive the objects of our quantum geometry: the spin space, the tangent space endowed with a Lorentzian metric, connection and curvature. In order to get the correspondence to classical differential geometry, we construct examples of causal fermion systems by regularizing Dirac sea configurations in Minkowski space and on a globally hyperbolic Lorentzian manifold. When removing the regularization, the objects of our quantum geometry reduce to the common objects of spin geometry on Lorentzian manifolds, up to higher order curvature corrections.

Parametric Geometry, Structured Grid Generation, and Initial Design Study for REST-Class Hypersonic Inlets

Science.gov (United States)

Ferlemann, Paul G.; Gollan, Rowan J.

2010-01-01

Computational design and analysis of three-dimensional hypersonic inlets with shape transition has been a significant challenge due to the complex geometry and grid required for three-dimensional viscous flow calculations. Currently, the design process utilizes an inviscid design tool to produce initial inlet shapes by streamline tracing through an axisymmetric compression field. However, the shape is defined by a large number of points rather than a continuous surface and lacks important features such as blunt leading edges. Therefore, a design system has been developed to parametrically construct true CAD geometry and link the topology of a structured grid to the geometry. The Adaptive Modeling Language (AML) constitutes the underlying framework that is used to build the geometry and grid topology. Parameterization of the CAD geometry allows the inlet shapes produced by the inviscid design tool to be generated, but also allows a great deal of flexibility to modify the shape to account for three-dimensional viscous effects. By linking the grid topology to the parametric geometry, the GridPro grid generation software can be used efficiently to produce a smooth hexahedral multiblock grid. To demonstrate the new capability, a matrix of inlets were designed by varying four geometry parameters in the inviscid design tool. The goals of the initial design study were to explore inviscid design tool geometry variations with a three-dimensional analysis approach, demonstrate a solution rate which would enable the use of high-fidelity viscous three-dimensional CFD in future design efforts, process the results for important performance parameters, and perform a sample optimization.

Geometry-dependent DNA-TiO2 immobilization mechanism: A spectroscopic approach

Science.gov (United States)

Silva-Moraes, M. O.; Garcia-Basabe, Y.; de Souza, R. F. B.; Mota, A. J.; Passos, R. R.; Galante, D.; Fonseca Filho, H. D.; Romaguera-Barcelay, Y.; Rocco, M. L. M.; Brito, W. R.

2018-06-01

DNA nucleotides are used as a molecular recognition system on electrodes modified to be applied in the detection of various diseases, but immobilization mechanisms, as well as, charge transfers are not satisfactorily described in the literature. An electrochemical and spectroscopic study was carried out to characterize the molecular groups involved in the direct immobilization of DNA structures on the surface of nanostructured TiO2 with the aim of evaluating the influence of the geometrical aspects. X-ray photoelectron spectroscopy at O1s and P2p core levels indicate that immobilization of DNA samples occurs through covalent (Psbnd Osbnd Ti) bonds. X-ray absorption spectra at the Ti2p edge reinforce this conclusion. A new species at 138.5 eV was reported from P2p XPS spectra analysis which plays an important role in DNA-TiO2 immobilization. The Psbnd Osbnd Ti/Osbnd Ti ratio showed that quantitatively the DNA immobilization mechanism is dependent on their geometry, becoming more efficient for plasmid ds-DNA structures than for PCR ds-DNA structures. The analysis of photoabsorption spectra at C1s edge revealed that the molecular groups that participate in the C1s → LUMO electronic transitions have different pathways in the charge transfer processes at the DNA-TiO2 interface. Our results may contribute to additional studies of immobilization mechanisms understanding the influence of the geometry of different DNA molecules on nanostructured semiconductor and possible impact to the charge transfer processes with application in biosensors or aptamers.

Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations

NARCIS (Netherlands)

Baoukina, Svetlana; Monticelli, Luca; Marrink, Siewert J.; Tieleman, D. Peter

2007-01-01

We calculated the pressure-area isotherm of a dipalmitoyl-phosphatidylcholine (DPPC) lipid monolayer from molecular dynamics simulations using a coarse-grained molecular model. We characterized the monolayer structure, geometry, and phases directly from the simulations and compared the calculated

A Gradient-Based Multistart Algorithm for Multimodal Aerodynamic Shape Optimization Problems Based on Free-Form Deformation

Science.gov (United States)

Streuber, Gregg Mitchell

Environmental and economic factors motivate the pursuit of more fuel-efficient aircraft designs. Aerodynamic shape optimization is a powerful tool in this effort, but is hampered by the presence of multimodality in many design spaces. Gradient-based multistart optimization uses a sampling algorithm and multiple parallel optimizations to reliably apply fast gradient-based optimization to moderately multimodal problems. Ensuring that the sampled geometries remain physically realizable requires manually developing specialized linear constraints for each class of problem. Utilizing free-form deformation geometry control allows these linear constraints to be written in a geometry-independent fashion, greatly easing the process of applying the algorithm to new problems. This algorithm was used to assess the presence of multimodality when optimizing a wing in subsonic and transonic flows, under inviscid and viscous conditions, and a blended wing-body under transonic, viscous conditions. Multimodality was present in every wing case, while the blended wing-body was found to be generally unimodal.

Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules.

Science.gov (United States)

Ren, Pengyu; Wu, Chuanjie; Ponder, Jay W

2011-10-11

An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.

Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy.

Science.gov (United States)

Rahaman, Obaidur; Estrada, Trilce P; Doren, Douglas J; Taufer, Michela; Brooks, Charles L; Armen, Roger S

2011-09-26

The performances of several two-step scoring approaches for molecular docking were assessed for their ability to predict binding geometries and free energies. Two new scoring functions designed for "step 2 discrimination" were proposed and compared to our CHARMM implementation of the linear interaction energy (LIE) approach using the Generalized-Born with Molecular Volume (GBMV) implicit solvation model. A scoring function S1 was proposed by considering only "interacting" ligand atoms as the "effective size" of the ligand and extended to an empirical regression-based pair potential S2. The S1 and S2 scoring schemes were trained and 5-fold cross-validated on a diverse set of 259 protein-ligand complexes from the Ligand Protein Database (LPDB). The regression-based parameters for S1 and S2 also demonstrated reasonable transferability in the CSARdock 2010 benchmark using a new data set (NRC HiQ) of diverse protein-ligand complexes. The ability of the scoring functions to accurately predict ligand geometry was evaluated by calculating the discriminative power (DP) of the scoring functions to identify native poses. The parameters for the LIE scoring function with the optimal discriminative power (DP) for geometry (step 1 discrimination) were found to be very similar to the best-fit parameters for binding free energy over a large number of protein-ligand complexes (step 2 discrimination). Reasonable performance of the scoring functions in enrichment of active compounds in four different protein target classes established that the parameters for S1 and S2 provided reasonable accuracy and transferability. Additional analysis was performed to definitively separate scoring function performance from molecular weight effects. This analysis included the prediction of ligand binding efficiencies for a subset of the CSARdock NRC HiQ data set where the number of ligand heavy atoms ranged from 17 to 35. This range of ligand heavy atoms is where improved accuracy of predicted ligand

Geometry and Combinatorics

DEFF Research Database (Denmark)

Kokkendorff, Simon Lyngby

2002-01-01

The subject of this Ph.D.-thesis is somewhere in between continuous and discrete geometry. Chapter 2 treats the geometry of finite point sets in semi-Riemannian hyperquadrics,using a matrix whose entries are a trigonometric function of relative distances in a given point set. The distance...... to the geometry of a simplex in a semi-Riemannian hyperquadric. In chapter 3 we study which finite metric spaces that are realizable in a hyperbolic space in the limit where curvature goes to -∞. We show that such spaces are the so called leaf spaces, the set of degree 1 vertices of weighted trees. We also...... establish results on the limiting geometry of such an isometrically realized leaf space simplex in hyperbolic space, when curvature goes to -∞. Chapter 4 discusses negative type of metric spaces. We give a measure theoretic treatment of this concept and related invariants. The theory developed...

Geometry and billiards

CERN Document Server

Tabachnikov, Serge

2005-01-01

Mathematical billiards describe the motion of a mass point in a domain with elastic reflections off the boundary or, equivalently, the behavior of rays of light in a domain with ideally reflecting boundary. From the point of view of differential geometry, the billiard flow is the geodesic flow on a manifold with boundary. This book is devoted to billiards in their relation with differential geometry, classical mechanics, and geometrical optics. The topics covered include variational principles of billiard motion, symplectic geometry of rays of light and integral geometry, existence and nonexistence of caustics, optical properties of conics and quadrics and completely integrable billiards, periodic billiard trajectories, polygonal billiards, mechanisms of chaos in billiard dynamics, and the lesser-known subject of dual (or outer) billiards. The book is based on an advanced undergraduate topics course (but contains more material than can be realistically taught in one semester). Although the minimum prerequisit...

A new experiment-independent mechanism to persistify and serve the detector geometry of ATLAS

Science.gov (United States)

Bianchi, Riccardo Maria; Boudreau, Joseph; Vukotic, Ilija

2017-10-01

The complex geometry of the whole detector of the ATLAS experiment at LHC is currently stored only in custom online databases, from which it is built on-the-fly on request. Accessing the online geometry guarantees accessing the latest version of the detector description, but requires the setup of the full ATLAS software framework “Athena”, which provides the online services and the tools to retrieve the data from the database. This operation is cumbersome and slows down the applications that need to access the geometry. Moreover, all applications that need to access the detector geometry need to be built and run on the same platform as the ATLAS framework, preventing the usage of the actual detector geometry in stand-alone applications. Here we propose a new mechanism to persistify (in software development in general, and in HEP computing in particular, persistifying means taking an object which lives in memory only - for example because it was built on-the-fly while processing the experimental data, - serializing it and storing it on disk as a persistent object) and serve the geometry of HEP experiments. The new mechanism is composed by a new file format and the modules to make use of it. The new file format allows to store the whole detector description locally in a file, and it is especially optimized to describe large complex detectors with the minimum file size, making use of shared instances and storing compressed representations of geometry transformations. Then, the detector description can be read back in, to fully restore the in-memory geometry tree. Moreover, a dedicated REST API is being designed and developed to serve the geometry in standard exchange formats like JSON, to let users and applications download specific partial geometry information. With this new geometry persistification a new generation of applications could be developed, which can use the actual detector geometry while being platform-independent and experiment-independent.

An introduction to optimization

CERN Document Server

Chong, Edwin K P

2013-01-01

Praise for the Third Edition "". . . guides and leads the reader through the learning path . . . [e]xamples are stated very clearly and the results are presented with attention to detail.""  -MAA Reviews  Fully updated to reflect new developments in the field, the Fourth Edition of Introduction to Optimization fills the need for accessible treatment of optimization theory and methods with an emphasis on engineering design. Basic definitions and notations are provided in addition to the related fundamental background for linear algebra, geometry, and calculus.  This new

Geometry and quadratic nonlinearity of charge transfer complexes in solution: A theoretical study

International Nuclear Information System (INIS)

Mukhopadhyay, S.; Ramasesha, S.; Pandey, Ravindra; Das, Puspendu K.

2011-01-01

In this paper, we have computed the quadratic nonlinear optical (NLO) properties of a class of weak charge transfer (CT) complexes. These weak complexes are formed when the methyl substituted benzenes (donors) are added to strong acceptors like chloranil (CHL) or di-chloro-di-cyano benzoquinone (DDQ) in chloroform or in dichloromethane. The formation of such complexes is manifested by the presence of a broad absorption maximum in the visible range of the spectrum where neither the donor nor the acceptor absorbs. The appearance of this visible band is due to CT interactions, which result in strong NLO responses. We have employed the semiempirical intermediate neglect of differential overlap (INDO/S) Hamiltonian to calculate the energy levels of these CT complexes using single and double configuration interaction (SDCI). The solvent effects are taken into account by using the self-consistent reaction field (SCRF) scheme. The geometry of the complex is obtained by exploring different relative molecular geometries by rotating the acceptor with respect to the fixed donor about three different axes. The theoretical geometry that best fits the experimental energy gaps, β HRS and macroscopic depolarization ratios is taken to be the most probable geometry of the complex. Our studies show that the most probable geometry of these complexes in solution is the parallel displaced structure with a significant twist in some cases.

Optimized Radiator Geometries for Hot Lunar Thermal Environments

Science.gov (United States)

Ochoa, Dustin

2013-01-01

The optimum radiator configuration in hot lunar thermal environments is one in which the radiator is parallel to the ground and has no view to the hot lunar surface. However, typical spacecraft configurations have limited real estate available for top-mounted radiators, resulting in a desire to use the spacecraft's vertically oriented sides. Vertically oriented, flat panel radiators will have a large view factor to the lunar surface, and thus will be subjected to significant incident lunar infrared heat. Consequently, radiator fluid temperatures will need to exceed approximately 325 K (assuming standard spacecraft radiator optical properties) in order to provide positive heat rejection at lunar noon. Such temperatures are too high for crewed spacecraft applications in which a heat pump is to be avoided. A recent study of vertically oriented radiator configurations subjected to lunar noon thermal environments led to the discovery of a novel radiator concept that yielded positive heat rejection at lower fluid temperatures. This radiator configuration, called the Intense Thermal Infrared Reflector (ITIR), has exhibited superior performance to all previously analyzed concepts in terms of heat rejection in the lunar noon thermal environment. A key benefit of ITIR is the absence of louvers or other moving parts and its simple geometry (no parabolic shapes). ITIR consists of a specularly reflective shielding surface and a diffuse radiating surface joined to form a horizontally oriented V-shape (shielding surface on top). The point of intersection of these surfaces is defined by two angles, those which define the tilt of each surface with respect to the local horizontal. The optimum set of these angles is determined on a case-by-case basis. The idea assumes minimal conductive heat transfer between shielding and radiating surfaces, and a practical design would likely stack sets of these surfaces on top of one another to reduce radiator thickness.

Drawing Dynamic Geometry Figures Online with Natural Language for Junior High School Geometry

Science.gov (United States)

Wong, Wing-Kwong; Yin, Sheng-Kai; Yang, Chang-Zhe

2012-01-01

This paper presents a tool for drawing dynamic geometric figures by understanding the texts of geometry problems. With the tool, teachers and students can construct dynamic geometric figures on a web page by inputting a geometry problem in natural language. First we need to build the knowledge base for understanding geometry problems. With the…

Spacer geometry and particle deposition in spiral wound membrane feed channels

KAUST Repository

Radu, A.I.

2014-11-01

Deposition of microspheres mimicking bacterial cells was studied experimentally and with a numerical model in feed spacer membrane channels, as used in spiral wound nanofiltration (NF) and reverse osmosis (RO) membrane systems. In-situ microscopic observations in membrane fouling simulators revealed formation of specific particle deposition patterns for different diamond and ladder feed spacer orientations. A three-dimensional numerical model combining fluid flow with a Lagrangian approach for particle trajectory calculations could describe very well the in-situ observations on particle deposition in flow cells. Feed spacer geometry, positioning and cross-flow velocity sensitively influenced the particle transport and deposition patterns. The deposition patterns were not influenced by permeate production. This combined experimental-modeling approach could be used for feed spacer geometry optimization studies for reduced (bio)fouling. © 2014 Elsevier Ltd.

Mixing In Jet-Stirred Reactors With Different Geometries

KAUST Repository

Ayass, Wassim W.

2013-12-01

This work offers a well-developed understanding of the mixing process inside Jet- Stirred Reactors (JSR’s) with different geometries. Due to the difficulty of manufacturing these JSR’s made in quartz, existing JSR configurations were assessed with certain modifications and optimal operating conditions were suggested for each reactor. The effect of changing the reactor volume, the nozzle diameter and shape on mixing were both studied. Two nozzle geometries were examined in this study, a crossed shape nozzle and an inclined shape nozzle. Overall, six reactor configurations were assessed by conducting tracer experiments - using the state-of-art technologies of high-speed cameras and laser absorption spectroscopy- and Computational Fluid Dynamics (CFD) simulations. The high-speed camera tracer experiment gives unique qualitative information – not present in the literature – about the actual flow field. On the other hand, when using the laser technique, a more quantitative analysis emerges with determining the experimental residence time distribution (RTD) curves of each reactor. Comparing these RTD curves with the ideal curve helped in eliminating two cases. Finally, the CFD simulations predict the RTD curves as well as the mixing levels of the JSR’s operated at different residence times. All of these performed studies suggested the use of an inclined nozzle configuration with a reactor diameter D of 40mm and a nozzle diameter d of 1mm as the optimal choice for low residence time operation. However, for higher residence times, the crossed configuration reactor with D=56mm and d=0.3mm gave a nearly perfect behavior.

A novel heuristic method for optimization of straight blade vertical axis wind turbine

International Nuclear Information System (INIS)

Tahani, Mojtaba; Babayan, Narek; Mehrnia, Seyedmajid; Shadmehri, Mehran

2016-01-01

Highlights: • A novel heuristic method has been proposed for optimization of VAWTs. • The proposed method is the combination of DMST model with heuristic algorithms. • A continuous/discrete optimization problem has been solved. • A novel continuous optimization algorithm has been developed. • The CFD simulation of the optimized geometry has been carried out. - Abstract: In this research study it is aimed to propose a novel heuristic method for optimizing the VAWT design. The method is the combination of continuous/discrete optimization algorithms with double multiple stream tube (DMST) theory. For this purpose a DMST code has been developed and is validated using available experimental data in literature. A novel continuous optimization algorithm is proposed which can be considered as the combination of three heuristic optimization algorithms namely elephant herding optimization, flower pollination algorithm and grey wolf optimizer. The continuous algorithm is combined with popular discrete ant colony optimization algorithm (ACO). The proposed method can be utilized for several engineering problems which are dealing with continuous and discrete variables. In this research study, chord and diameter of the turbine are selected as continuous decision variables and airfoil types and number of blades are selected as discrete decision variables. The average power coefficient between tip speed rations from 1.5 to 9.5 is considered as the objective function. The optimization results indicated that the optimized geometry can produce a maximum power coefficient, 44% higher than the maximum power coefficient of the original turbine. Also a CFD simulation of the optimized geometry is carried out. The CFD results indicated that the average vorticity magnitude around the optimized blade is larger than the original blade and this results greater momentum and power coefficient.

A Proposal on the Geometry Splitting Strategy to Enhance the Calculation Efficiency in Monte Carlo Simulation

Energy Technology Data Exchange (ETDEWEB)

Han, Gi Yeong; Kim, Song Hyun; Kim, Do Hyun; Shin, Chang Ho; Kim, Jong Kyung [Hanyang Univ., Seoul (Korea, Republic of)

2014-05-15

In this study, how the geometry splitting strategy affects the calculation efficiency was analyzed. In this study, a geometry splitting method was proposed to increase the calculation efficiency in Monte Carlo simulation. First, the analysis of the neutron distribution characteristics in a deep penetration problem was performed. Then, considering the neutron population distribution, a geometry splitting method was devised. Using the proposed method, the FOMs with benchmark problems were estimated and compared with the conventional geometry splitting strategy. The results show that the proposed method can considerably increase the calculation efficiency in using geometry splitting method. It is expected that the proposed method will contribute to optimizing the computational cost as well as reducing the human errors in Monte Carlo simulation. Geometry splitting in Monte Carlo (MC) calculation is one of the most popular variance reduction techniques due to its simplicity, reliability and efficiency. For the use of the geometry splitting, the user should determine locations of geometry splitting and assign the relative importance of each region. Generally, the splitting parameters are decided by the user's experience. However, in this process, the splitting parameters can ineffectively or erroneously be selected. In order to prevent it, there is a recommendation to help the user eliminate guesswork, which is to split the geometry evenly. And then, the importance is estimated by a few iterations for preserving population of particle penetrating each region. However, evenly geometry splitting method can make the calculation inefficient due to the change in mean free path (MFP) of particles.

A Proposal on the Geometry Splitting Strategy to Enhance the Calculation Efficiency in Monte Carlo Simulation

International Nuclear Information System (INIS)

Han, Gi Yeong; Kim, Song Hyun; Kim, Do Hyun; Shin, Chang Ho; Kim, Jong Kyung

2014-01-01

In this study, how the geometry splitting strategy affects the calculation efficiency was analyzed. In this study, a geometry splitting method was proposed to increase the calculation efficiency in Monte Carlo simulation. First, the analysis of the neutron distribution characteristics in a deep penetration problem was performed. Then, considering the neutron population distribution, a geometry splitting method was devised. Using the proposed method, the FOMs with benchmark problems were estimated and compared with the conventional geometry splitting strategy. The results show that the proposed method can considerably increase the calculation efficiency in using geometry splitting method. It is expected that the proposed method will contribute to optimizing the computational cost as well as reducing the human errors in Monte Carlo simulation. Geometry splitting in Monte Carlo (MC) calculation is one of the most popular variance reduction techniques due to its simplicity, reliability and efficiency. For the use of the geometry splitting, the user should determine locations of geometry splitting and assign the relative importance of each region. Generally, the splitting parameters are decided by the user's experience. However, in this process, the splitting parameters can ineffectively or erroneously be selected. In order to prevent it, there is a recommendation to help the user eliminate guesswork, which is to split the geometry evenly. And then, the importance is estimated by a few iterations for preserving population of particle penetrating each region. However, evenly geometry splitting method can make the calculation inefficient due to the change in mean free path (MFP) of particles

KEMAJUAN BELAJAR SISWA PADA GEOMETRI TRANSFORMASI MENGGUNAKAN AKTIVITAS REFLEKSI GEOMETRI

Directory of Open Access Journals (Sweden)

Irkham Ulil Albab

2014-10-01

Full Text Available Abstrak: Penelitian ini bertujuan untuk mendeskripsikan kemajuan belajar siswa pada materi geometri transformasi yang didukung dengan serangkaian aktivitas belajar berdasarkan Pendidikan Matematika Realistik Indonesia. Penelitian didesain melalui tiga tahap, yaitu tahapan perancangan desain awal, pengujian desain melalui pembelajaran awal dan pembelajaran eksperimental, dan tahap analisis retrospektif. Dalam penelitian ini, Hypothetical Learning Trajectory, HLT (HLT berperan penting sebagai desain pembelajaran sekaligus instrumen penelitian. HLT diujikan terhadap 26 siswa kelas VII. Data dikumpulkan dengan teknik wawancara, pengamatan, dan catatan lapangan. Hasil penelitian menunjukkan bahwa desain pembelajaran ini mampu menstimulasi siswa untuk memberikan karakteristik refleksi dan transformasi geometri lainnya secara informal, mengklasifikasikannya dalam transformasi isometri pada level kedua, dan menemukan garis bantuan refleksi pada level yang lebih formal. Selain itu, garis bantuan refleksi digunakan oleh siswa untuk menggambar bayangan refleksi dan pola pencerminan serta memahami bentuk rotasi dan translasi sebagai kombinasi refleksi adalah level tertinggi. Keyword: transformasi geometri, kombinasi refleksi, rotasi, translasi, design research, HLT STUDENTS’ LEARNING PROGRESS ON TRANSFORMATION GEOMETRY USING THE GEOMETRY REFLECTION ACTIVITIES Abstract: This study was aimed at describing the students’ learning progress on transformation geometry supported by a set of learning activities based on Indonesian Realistic Mathematics Education. The study was designed into three stages, that is, the preliminary design stage, the design testing through initial instruction and experiment, and the restrospective analysis stage. In this study, Hypothetical Learning Trajectory (HLT played an important role as an instructional design and a research instrument. HLT was tested to 26 seventh grade students. The data were collected through interviews

Software Geometry in Simulations

Science.gov (United States)

Alion, Tyler; Viren, Brett; Junk, Tom

2015-04-01

The Long Baseline Neutrino Experiment (LBNE) involves many detectors. The experiment's near detector (ND) facility, may ultimately involve several detectors. The far detector (FD) will be significantly larger than any other Liquid Argon (LAr) detector yet constructed; many prototype detectors are being constructed and studied to motivate a plethora of proposed FD designs. Whether it be a constructed prototype or a proposed ND/FD design, every design must be simulated and analyzed. This presents a considerable challenge to LBNE software experts; each detector geometry must be described to the simulation software in an efficient way which allows for multiple authors to easily collaborate. Furthermore, different geometry versions must be tracked throughout their use. We present a framework called General Geometry Description (GGD), written and developed by LBNE software collaborators for managing software to generate geometries. Though GGD is flexible enough to be used by any experiment working with detectors, we present it's first use in generating Geometry Description Markup Language (GDML) files to interface with LArSoft, a framework of detector simulations, event reconstruction, and data analyses written for all LAr technology users at Fermilab. Brett is the other of the framework discussed here, the General Geometry Description (GGD).

The dynamics of molecular dimers in the crystals of m-aminobenzoic acid studied by inelastic neutron scattering (INS), Raman, IR spectroscopy and DFT calculations

Energy Technology Data Exchange (ETDEWEB)

Pawlukojc, A.; Leciejewicz, J

2004-03-29

Inelastic neutron scattering, Raman and IR spectra were measured for m-aminobenzoic acid (MABA). Optimized geometries and observed frequencies were assigned using DFT calculation on the B3LYP/6-311G** level using Gaussian 98 and Gamess programs. Experimental structural and spectroscopic data are in good agreement with computations assuming the presence in the crystals of molecular dimers composed of two MABA molecules linked by a pair of O-H...O hydrogen bonds each provided by the carboxylic group. INS frequencies have been identified for the O-H (out of plane) mod0008.

Methods of information geometry

CERN Document Server

Amari, Shun-Ichi

2000-01-01

Information geometry provides the mathematical sciences with a new framework of analysis. It has emerged from the investigation of the natural differential geometric structure on manifolds of probability distributions, which consists of a Riemannian metric defined by the Fisher information and a one-parameter family of affine connections called the \\alpha-connections. The duality between the \\alpha-connection and the (-\\alpha)-connection together with the metric play an essential role in this geometry. This kind of duality, having emerged from manifolds of probability distributions, is ubiquitous, appearing in a variety of problems which might have no explicit relation to probability theory. Through the duality, it is possible to analyze various fundamental problems in a unified perspective. The first half of this book is devoted to a comprehensive introduction to the mathematical foundation of information geometry, including preliminaries from differential geometry, the geometry of manifolds or probability d...

Topology optimization for nano-photonics

DEFF Research Database (Denmark)

Jensen, Jakob Søndergaard; Sigmund, Ole

2011-01-01

Topology optimization is a computational tool that can be used for the systematic design of photonic crystals, waveguides, resonators, filters and plasmonics. The method was originally developed for mechanical design problems but has within the last six years been applied to a range of photonics...... applications. Topology optimization may be based on finite element and finite difference type modeling methods in both frequency and time domain. The basic idea is that the material density of each element or grid point is a design variable, hence the geometry is parameterized in a pixel-like fashion....... The optimization problem is efficiently solved using mathematical programming-based optimization methods and analytical gradient calculations. The paper reviews the basic procedures behind topology optimization, a large number of applications ranging from photonic crystal design to surface plasmonic devices...

Developments in special geometry

International Nuclear Information System (INIS)

Mohaupt, Thomas; Vaughan, Owen

2012-01-01

We review the special geometry of N = 2 supersymmetric vector and hypermultiplets with emphasis on recent developments and applications. A new formulation of the local c-map based on the Hesse potential and special real coordinates is presented. Other recent developments include the Euclidean version of special geometry, and generalizations of special geometry to non-supersymmetric theories. As applications we discuss the proof that the local r-map and c-map preserve geodesic completeness, and the construction of four- and five-dimensional static solutions through dimensional reduction over time. The shared features of the real, complex and quaternionic version of special geometry are stressed throughout.

Optimization of flat and horizontally curved neutron monochromators for given diffractometer geometries

International Nuclear Information System (INIS)

Graf, H.A.

1983-08-01

The computer program MONREF was written for calculating the integrated intensity and the k-vector distribution produced by mosaic-crystal monochromators in neutron diffractometers of given geometries. The program treats flat and horizontally curved monochromators in Bragg reflection. Its basic algorithm is derived from Zachariasen's coupled differential equations which were modified to include the case of asymmetrically cut crystals. The calculations are restricted to the scattering in the experimental plane. In the first part of the report the program and its applications are described. In the second part a compilation of intensities is presented, calculated for crystals of Cu, Si, Ge and pyrolytic graphite commonly used as monochromators, in a standard diffractometer configuration. (orig.)

Neutron transport by collision probability method in complicated geometries

International Nuclear Information System (INIS)

Constantin, Marin

2000-01-01

For the first flight collision probability (FFCP) method a rapidly increasing of the memory requirements and execution time with the number of discrete regions occurs. Generally, the use of the method is restricted at cell/supercell level. However, the amazing developments both in computer hardware and computer architecture allow a real extending of the problems' domain and a more detailed treatment of the geometry. Two ways are discussed into the paper: the direct design of new codes and the improving of the mainframe old versions. The author's experience is focused on the performances' improving of the 3D integral transport code PIJXYZ (from an old version to a modern one) and on the design and developing of the 2D transport code CP 2 D in the last years. In the first case an optimization process have been performed before the parallelization. In the second a modular design and the newest techniques (factorization of the geometry, the macrobands method, the mobile set of chords, the automatic calculation of the integration error, optimal algorithms for the innermost programming level, the mixed method for tracking process and CPs calculation, etc.) were adopted. In both cases the parallelization uses a PCs network system. Some short examples for CP 2 D and PIJXYZ calculation are presented: reactivity void effect in typical CANDU cells using a multistratified coolant model, a problem of some adjacent fuel assemblies, CANDU reactivity devices 3D simulation. (author)

Applied geometry and discrete mathematics

CERN Document Server

Sturm; Gritzmann, Peter; Sturmfels, Bernd

1991-01-01

This volume, published jointly with the Association for Computing Machinery, comprises a collection of research articles celebrating the occasion of Victor Klee's sixty-fifth birthday in September 1990. During his long career, Klee has made contributions to a wide variety of areas, such as discrete and computational geometry, convexity, combinatorics, graph theory, functional analysis, mathematical programming and optimization, and theoretical computer science. In addition, Klee made important contributions to mathematics education, mathematical methods in economics and the decision sciences, applications of discrete mathematics in the biological and social sciences, and the transfer of knowledge from applied mathematics to industry. In honor of Klee's achievements, this volume presents more than forty papers on topics related to Klee's research. While the majority of the papers are research articles, a number of survey articles are also included. Mirroring the breadth of Klee's mathematical contributions, th...

Progresses in optimization strategy for radiolabeled molecular probes targeting integrin αvβ3

International Nuclear Information System (INIS)

Chen Haojun; Wu Hua

2012-01-01

Tumor angiogenesis is critical in the growth, invasion and metastasis of malignant tumors. The integrins, which express on many types of tumor cells and activated vascular endothelial cells, play an important role in regulation of the tumor angiogenesis. RGD peptide, which contains Arg-Gly-Asp sequence, binds specifically to integrin α v β 3 . Therefore, the radiolabeled RGD peptides may have broad application prospects in radionuclide imaging and therapy. Major research interests include the selection of radionuclides, modification and improvement of RGD structures. In this article, we give a review on research progresses in optimization strategy for radiolabeled molecular probes targeting integrin α v β 3 . (authors)

Optimization of a fuel bundle within a CANDU supercritical water reactor

International Nuclear Information System (INIS)

Schofield, M.E.

2009-01-01

The supercritical water reactor is one of six nuclear reactor concepts being studied under the Generation IV International Forum. Generation IV nuclear reactors will improve the metrics of economics, sustainability, safety and reliability, and physical protection and proliferation resistance over current nuclear reactor designs. The supercritical water reactor has specific benefits in the areas of economics, safety and reliability, and physical protection. This work optimizes the fuel composition and bundle geometry to maximize the fuel burnup, and minimize the surface heat flux and the form factor. In optimizing these factors, improvements can be achieved in the areas of economics, safety and reliability of the supercritical water reactor. The WIMS-AECL software was used to model a fuel bundle within a CANDU supercritical water reactor. The Gauss' steepest descent method was used to optimize the above mentioned factors. Initially the fresh fuel composition was optimized within a 43-rod CANFLEX bundle and a 61-rod bundle. In both the 43-rod and 61-rod bundle scenarios an online refuelling scheme and non-refuelling scheme were studied. The geometry of the fuel bundles was then optimized. Finally, a homogeneous mixture of thorium and uranium fuel was studied in a 60-rod bundle. Each optimization process showed definitive improvements in the factors being studied, with the most significant improvement being an increase in the fuel burnup. The 43-rod CANFLEX bundle was the most successful at being optimized. There was little difference in the final fresh fuel content when comparing an online refuelling scheme and non-refuelling scheme. Through each optimization scenario the ratio of the fresh fuel content between the annuli was a significant determining cause in the improvements in the factors being optimized. The geometry optimization showed that improvement in the design of a fuel bundle is indeed possible, although it would be more advantageous to pursue it

The design of geometry teaching: learning from the geometry textbooks of Godfrey and Siddons

OpenAIRE

Fujita, Taro; Jones, Keith

2002-01-01

Deciding how to teach geometry remains a demanding task with one of major arguments being about how to combine the intuitive and deductive aspects of geometry into an effective teaching design. In order to try to obtain an insight into tackling this issue, this paper reports an analysis of innovative geometry textbooks which were published in the early part of the 20th Century, a time when significant efforts were being made to improve the teaching and learning of geometry. The analysis sugge...

Molecular structure, vibrational analysis (IR and Raman) and quantum chemical investigations of 1-aminoisoquinoline

Science.gov (United States)

Sivaprakash, S.; Prakash, S.; Mohan, S.; Jose, Sujin P.

2017-12-01

Quantum chemical calculations of energy and geometrical parameters of 1-aminoisoquinoline [1-AIQ] were carried out by using DFT/B3LYP method using 6-311G (d,p), 6-311G++(d,p) and cc-pVTZ basis sets. The vibrational wavenumbers were computed for the energetically most stable, optimized geometry. The vibrational assignments were performed on the basis of potential energy distribution (PED) using VEDA program. The NBO analysis was done to investigate the intra molecular charge transfer of the molecule. The frontier molecular orbital (FMO) analysis was carried out and the chemical reactivity descriptors of the molecule were studied. The Mulliken charge analysis, molecular electrostatic potential (MEP), HOMO-LUMO energy gap and the related properties were also investigated at B3LYP level. The absorption spectrum of the molecule was studied from UV-Visible analysis by using time-dependent density functional theory (TD-DFT). Fourier Transform Infrared spectrum (FT-IR) and Raman spectrum of 1-AIQ compound were analyzed and recorded in the range 4000-400 cm-1 and 3500-100 cm-1 respectively. The experimentally determined wavenumbers were compared with those calculated theoretically and they complement each other.

On the Lasserre hierarchy of semidefinite programming relaxations of convex polynomial optimization problems

NARCIS (Netherlands)

de Klerk, E.; Laurent, M.

2011-01-01

The Lasserre hierarchy of semidefinite programming approximations to convex polynomial optimization problems is known to converge finitely under some assumptions. [J. B. Lasserre, Convexity in semialgebraic geometry and polynomial optimization, SIAM J. Optim., 19 (2009), pp. 1995–2014]. We give a

Definition of treatment geometry in radiation therapy

International Nuclear Information System (INIS)

Aaltonen, P.

1996-01-01

When accurate systems for quality assurance and treatment optimization are employed, a precise system for fixation and dosimetric and portal verification are as important as a continued and standardized code of practice for dosimetry and patient follow-up, including registration of tumour responses and acute and late normal tissue reactions. To improve the accuracy of existing dose response relations in order to improve future therapy the treatment geometry and dose delivery concepts have to be accurately defined and uniformly employed. A Nordic working group was set up in 1991 (by Nordic Association of Clinica Physics) to standardize the concepts and quantities used during the whole radiotherapy process in the Nordic countries. Now the group is finalizing its report ''Specification of Dose Delivery in Radiation Therapy''. The report emphasizes that the treatment geometry shall be consistent with the geometry used during the diagnostic work up. The patient fixation is of importance early in the diagnostic phase to ensure that the same reference points and patients position will be used both during the diagnostic work up, simulation and treatment execution. Reference Coordinate System of the patient is a concept based on defined anatomic reference points. This Patient Reference System is a local system which has validity for the tissues, organs and volumes defined during radiotherapy. The reference points of the Patient Reference System should in turn be used for beam set-up. The treatment geometry is then defined by using different concepts describing tissues which are mobile in the Patient Reference System, and finally, volumes which are fixed in this coordinate system. A Set-up Margin has to be considered for movements of the volumes defined in the Reference Coordinate System of the Patient in relation to the radiation beam. The Set-up Margin is dependent on the treatment technique and it is needed in the treatment planning procedure to ensure that the prescribed

Definition of treatment geometry in radiation therapy

Energy Technology Data Exchange (ETDEWEB)

Aaltonen, P [Finnish Centre for Radiation and Nuclear Safety (STUK), Helsinki (Finland)

1996-08-01

When accurate systems for quality assurance and treatment optimization are employed, a precise system for fixation and dosimetric and portal verification are as important as a continued and standardized code of practice for dosimetry and patient follow-up, including registration of tumour responses and acute and late normal tissue reactions. To improve the accuracy of existing dose response relations in order to improve future therapy the treatment geometry and dose delivery concepts have to be accurately defined and uniformly employed. A Nordic working group was set up in 1991 to standardize the concepts and quantities used during the whole radiotherapy process in the Nordic countries. Now the group is finalizing its report ``Specification of Dose Delivery in Radiation Therapy``. The report emphasizes that the treatment geometry shall be consistent with the geometry used during the diagnostic work up. The patient fixation is of importance early in the diagnostic phase to ensure that the same reference points and patients position will be used both during the diagnostic work up, simulation and treatment execution. Reference Coordinate System of the patient is a concept based on defined anatomic reference points. This Patient Reference System is a local system which has validity for the tissues, organs and volumes defined during radiotherapy. The reference points of the Patient Reference System should in turn be used for beam set-up. The treatment geometry is then defined by using different concepts describing tissues which are mobile in the Patient Reference System, and finally, volumes which are fixed in this coordinate system. A Set-up Margin has to be considered for movements of the volumes defined in the Reference Coordinate System of the Patient in relation to the radiation beam. The Set-up Margin is dependent on the treatment technique and it is needed in the treatment planning procedure to ensure that the prescribed dose to the Target Volume is delivered.

Molecular dynamics simulations of cluster fission and fusion processes

DEFF Research Database (Denmark)

Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia

2004-01-01

Results of molecular dynamics simulations of fission reactions Na_10^2+ --> Na_7^+ +Na_3^+ and Na_18^2+ --> 2Na_9^+ are presented. The dependence of the fission barriers on the isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic...... separation of the daughter fragments begins and/or forming a "neck" between the separating fragments. A novel algorithm for modeling the cluster growth process is described. This approach is based on dynamic search for the most stable cluster isomers and allows one to find the optimized cluster geometries...... groups of atoms from the parent cluster is largely independent of the isomer form of the parent cluster. The importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster before actual...

Sources of hyperbolic geometry

CERN Document Server

Stillwell, John

1996-01-01

This book presents, for the first time in English, the papers of Beltrami, Klein, and Poincaré that brought hyperbolic geometry into the mainstream of mathematics. A recognition of Beltrami comparable to that given the pioneering works of Bolyai and Lobachevsky seems long overdue-not only because Beltrami rescued hyperbolic geometry from oblivion by proving it to be logically consistent, but because he gave it a concrete meaning (a model) that made hyperbolic geometry part of ordinary mathematics. The models subsequently discovered by Klein and Poincaré brought hyperbolic geometry even further down to earth and paved the way for the current explosion of activity in low-dimensional geometry and topology. By placing the works of these three mathematicians side by side and providing commentaries, this book gives the student, historian, or professional geometer a bird's-eye view of one of the great episodes in mathematics. The unified setting and historical context reveal the insights of Beltrami, Klein, and Po...

Effects of Channel Geometry and Coolant Fluid on Thermoelectric Net Power

DEFF Research Database (Denmark)

Rezaniakolaei, Alireza; Rosendahl, Lasse; Sørensen, Kim

2014-01-01

Channel geometry has a strong influence on the heat transfer coefficient and cooling energy input in a heat sink. The net power output in a thermoelectric generator (TEG) can be defined as power generation minus the required cooling energy in TEG. This study aims to evaluate the net power generat......, and the maximum net power output occurs at smaller Reynolds number when the channel hydraulic diameter reduces....... generation in TEG for different size of hydraulic diameter of plate-fin heat sink and over a wide range of Reynolds number. The particular focus of this study is to find optimal Reynolds number in each considered channel hydraulic diameter and to explore optimal channel hydraulic diameter for maximum TEG net...

Biotechnology and genetic engineering in the new drug development. Part III. Biocatalysis, metabolic engineering and molecular modelling.

Science.gov (United States)

Stryjewska, Agnieszka; Kiepura, Katarzyna; Librowski, Tadeusz; Lochyński, Stanisław

2013-01-01

Industrial biotechnology has been defined as the use and application of biotechnology for the sustainable processing and production of chemicals, materials and fuels. It makes use of biocatalysts such as microbial communities, whole-cell microorganisms or purified enzymes. In the review these processes are described. Drug design is an iterative process which begins when a chemist identifies a compound that displays an interesting biological profile and ends when both the activity profile and the chemical synthesis of the new chemical entity are optimized. Traditional approaches to drug discovery rely on a stepwise synthesis and screening program for large numbers of compounds to optimize activity profiles. Over the past ten to twenty years, scientists have used computer models of new chemical entities to help define activity profiles, geometries and relativities. This article introduces inter alia the concepts of molecular modelling and contains references for further reading.

Differential geometry based solvation model II: Lagrangian formulation.

Science.gov (United States)

Chen, Zhan; Baker, Nathan A; Wei, G W

2011-12-01

Solvation is an elementary process in nature and is of paramount importance to more sophisticated chemical, biological and biomolecular processes. The understanding of solvation is an essential prerequisite for the quantitative description and analysis of biomolecular systems. This work presents a Lagrangian formulation of our differential geometry based solvation models. The Lagrangian representation of biomolecular surfaces has a few utilities/advantages. First, it provides an essential basis for biomolecular visualization, surface electrostatic potential map and visual perception of biomolecules. Additionally, it is consistent with the conventional setting of implicit solvent theories and thus, many existing theoretical algorithms and computational software packages can be directly employed. Finally, the Lagrangian representation does not need to resort to artificially enlarged van der Waals radii as often required by the Eulerian representation in solvation analysis. The main goal of the present work is to analyze the connection, similarity and difference between the Eulerian and Lagrangian formalisms of the solvation model. Such analysis is important to the understanding of the differential geometry based solvation model. The present model extends the scaled particle theory of nonpolar solvation model with a solvent-solute interaction potential. The nonpolar solvation model is completed with a Poisson-Boltzmann (PB) theory based polar solvation model. The differential geometry theory of surfaces is employed to provide a natural description of solvent-solute interfaces. The optimization of the total free energy functional, which encompasses the polar and nonpolar contributions, leads to coupled potential driven geometric flow and PB equations. Due to the development of singularities and nonsmooth manifolds in the Lagrangian representation, the resulting potential-driven geometric flow equation is embedded into the Eulerian representation for the purpose of

The geometry description markup language

International Nuclear Information System (INIS)

Chytracek, R.

2001-01-01

Currently, a lot of effort is being put on designing complex detectors. A number of simulation and reconstruction frameworks and applications have been developed with the aim to make this job easier. A very important role in this activity is played by the geometry description of the detector apparatus layout and its working environment. However, no real common approach to represent geometry data is available and such data can be found in various forms starting from custom semi-structured text files, source code (C/C++/FORTRAN), to XML and database solutions. The XML (Extensible Markup Language) has proven to provide an interesting approach for describing detector geometries, with several different but incompatible XML-based solutions existing. Therefore, interoperability and geometry data exchange among different frameworks is not possible at present. The author introduces a markup language for geometry descriptions. Its aim is to define a common approach for sharing and exchanging of geometry description data. Its requirements and design have been driven by experience and user feedback from existing projects which have their geometry description in XML

Complex analysis and CR geometry

CERN Document Server

Zampieri, Giuseppe

2008-01-01

Cauchy-Riemann (CR) geometry is the study of manifolds equipped with a system of CR-type equations. Compared to the early days when the purpose of CR geometry was to supply tools for the analysis of the existence and regularity of solutions to the \\bar\\partial-Neumann problem, it has rapidly acquired a life of its own and has became an important topic in differential geometry and the study of non-linear partial differential equations. A full understanding of modern CR geometry requires knowledge of various topics such as real/complex differential and symplectic geometry, foliation theory, the geometric theory of PDE's, and microlocal analysis. Nowadays, the subject of CR geometry is very rich in results, and the amount of material required to reach competence is daunting to graduate students who wish to learn it. However, the present book does not aim at introducing all the topics of current interest in CR geometry. Instead, an attempt is made to be friendly to the novice by moving, in a fairly relaxed way, f...

Crucial optimization steps in getting premier quality of Aquilaria malaccensis genomic DNA for molecular activities

International Nuclear Information System (INIS)

Muhammad Hanif Azhari; Azhar Mohamad

2013-01-01

Gaharu resin is derived from Aquilaria sp. or Agar wood tree in a tropical ecosystem. In Malaysia the Aquilaria species especially A. malaccensis in danger of extinction in the wild due to illegal logging as its resin is highly used for the production of greatly valued incense throughout Asia. A significant tool in fingerprinting the species is through molecular activities of Polymerase Chain Reaction (PCR) application on which requires total genomic DNA as a starting material. This paper, described optimizations of both fresh and dried samples derived from A. malaccensis for genomic DNA. Three main parameters for the optimization were temperature (60, 65, and 70 degree Celsius), incubation period (30, 60, 90 minutes) and concentration of CTAB (1 %, 3 %, 5 %). The experimental design in these work resulted a total of 46 combinations of the parameters in which 0.5 g samples was used in each combination. Nano-drop spectrometer was used in detecting the quantitative genomic DNA at ng/ μl. In fresh samples, incubation temperatures at 65 degree Celsius for 60 minutes in 3 % were yielded 723.2 ng/ μl genomic DNA. Whereas, for dried samples, incubation temperature at 70 degree Celsius for 90 minutes in 5 % CTAB were yielded 70.2 ng/ μl of genomic DNA. Spectrometer reading at OD280/ 260 was 1.9 for both type of samples. The isolated genomic DNA is useful for the molecular activities to identify specific plants between the same species or among the Aquilaria species. (author)

Global aspects of complex geometry

CERN Document Server

Catanese, Fabrizio; Huckleberry, Alan T

2006-01-01

Present an overview of developments in Complex Geometry. This book covers topics that range from curve and surface theory through special varieties in higher dimensions, moduli theory, Kahler geometry, and group actions to Hodge theory and characteristic p-geometry.

Self-Consistent Optimization of Excited States within Density-Functional Tight-Binding.

Science.gov (United States)

Kowalczyk, Tim; Le, Khoa; Irle, Stephan

2016-01-12

We present an implementation of energies and gradients for the ΔDFTB method, an analogue of Δ-self-consistent-field density functional theory (ΔSCF) within density-functional tight-binding, for the lowest singlet excited state of closed-shell molecules. Benchmarks of ΔDFTB excitation energies, optimized geometries, Stokes shifts, and vibrational frequencies reveal that ΔDFTB provides a qualitatively correct description of changes in molecular geometries and vibrational frequencies due to excited-state relaxation. The accuracy of ΔDFTB Stokes shifts is comparable to that of ΔSCF-DFT, and ΔDFTB performs similarly to ΔSCF with the PBE functional for vertical excitation energies of larger chromophores where the need for efficient excited-state methods is most urgent. We provide some justification for the use of an excited-state reference density in the DFTB expansion of the electronic energy and demonstrate that ΔDFTB preserves many of the properties of its parent ΔSCF approach. This implementation fills an important gap in the extended framework of DFTB, where access to excited states has been limited to the time-dependent linear-response approach, and affords access to rapid exploration of a valuable class of excited-state potential energy surfaces.

On the existence of the optimal order for wavefunction extrapolation in Born-Oppenheimer molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Fang, Jun; Wang, Han, E-mail: wang-han@iapcm.ac.cn [Institute of Applied Physics and Computational Mathematics, Beijing (China); CAEP Software Center for High Performance Numerical Simulation, Beijing (China); Gao, Xingyu; Song, Haifeng [Institute of Applied Physics and Computational Mathematics, Beijing (China); CAEP Software Center for High Performance Numerical Simulation, Beijing (China); Laboratory of Computational Physics, Beijing (China)

2016-06-28

Wavefunction extrapolation greatly reduces the number of self-consistent field (SCF) iterations and thus the overall computational cost of Born-Oppenheimer molecular dynamics (BOMD) that is based on the Kohn–Sham density functional theory. Going against the intuition that the higher order of extrapolation possesses a better accuracy, we demonstrate, from both theoretical and numerical perspectives, that the extrapolation accuracy firstly increases and then decreases with respect to the order, and an optimal extrapolation order in terms of minimal number of SCF iterations always exists. We also prove that the optimal order tends to be larger when using larger MD time steps or more strict SCF convergence criteria. By example BOMD simulations of a solid copper system, we show that the optimal extrapolation order covers a broad range when varying the MD time step or the SCF convergence criterion. Therefore, we suggest the necessity for BOMD simulation packages to open the user interface and to provide more choices on the extrapolation order. Another factor that may influence the extrapolation accuracy is the alignment scheme that eliminates the discontinuity in the wavefunctions with respect to the atomic or cell variables. We prove the equivalence between the two existing schemes, thus the implementation of either of them does not lead to essential difference in the extrapolation accuracy.

Optimized Loading for Particle-in-cell Gyrokinetic Simulations

International Nuclear Information System (INIS)

Lewandowski, J.L.V.

2004-01-01

The problem of particle loading in particle-in-cell gyrokinetic simulations is addressed using a quadratic optimization algorithm. Optimized loading in configuration space dramatically reduces the short wavelength modes in the electrostatic potential that are partly responsible for the non-conservation of total energy; further, the long wavelength modes are resolved with good accuracy. As a result, the conservation of energy for the optimized loading is much better that the conservation of energy for the random loading. The method is valid for any geometry and can be coupled to optimization algorithms in velocity space

Design and implementation of an optimal laser pulse front tilting scheme for ultrafast electron diffraction in reflection geometry with high temporal resolution

Directory of Open Access Journals (Sweden)

Francesco Pennacchio

2017-07-01

Full Text Available Ultrafast electron diffraction is a powerful technique to investigate out-of-equilibrium atomic dynamics in solids with high temporal resolution. When diffraction is performed in reflection geometry, the main limitation is the mismatch in group velocity between the overlapping pump light and the electron probe pulses, which affects the overall temporal resolution of the experiment. A solution already available in the literature involved pulse front tilt of the pump beam at the sample, providing a sub-picosecond time resolution. However, in the reported optical scheme, the tilted pulse is characterized by a temporal chirp of about 1 ps at 1 mm away from the centre of the beam, which limits the investigation of surface dynamics in large crystals. In this paper, we propose an optimal tilting scheme designed for a radio-frequency-compressed ultrafast electron diffraction setup working in reflection geometry with 30 keV electron pulses containing up to 105 electrons/pulse. To characterize our scheme, we performed optical cross-correlation measurements, obtaining an average temporal width of the tilted pulse lower than 250 fs. The calibration of the electron-laser temporal overlap was obtained by monitoring the spatial profile of the electron beam when interacting with the plasma optically induced at the apex of a copper needle (plasma lensing effect. Finally, we report the first time-resolved results obtained on graphite, where the electron-phonon coupling dynamics is observed, showing an overall temporal resolution in the sub-500 fs regime. The successful implementation of this configuration opens the way to directly probe structural dynamics of low-dimensional systems in the sub-picosecond regime, with pulsed electrons.

Analytic geometry

CERN Document Server

Burdette, A C

1971-01-01

Analytic Geometry covers several fundamental aspects of analytic geometry needed for advanced subjects, including calculus.This book is composed of 12 chapters that review the principles, concepts, and analytic proofs of geometric theorems, families of lines, the normal equation of the line, and related matters. Other chapters highlight the application of graphing, foci, directrices, eccentricity, and conic-related topics. The remaining chapters deal with the concept polar and rectangular coordinates, surfaces and curves, and planes.This book will prove useful to undergraduate trigonometric st

Vector geometry

CERN Document Server

Robinson, Gilbert de B

2011-01-01

This brief undergraduate-level text by a prominent Cambridge-educated mathematician explores the relationship between algebra and geometry. An elementary course in plane geometry is the sole requirement for Gilbert de B. Robinson's text, which is the result of several years of teaching and learning the most effective methods from discussions with students. Topics include lines and planes, determinants and linear equations, matrices, groups and linear transformations, and vectors and vector spaces. Additional subjects range from conics and quadrics to homogeneous coordinates and projective geom

Optimized molecular resolution of cross-contamination alerts in clinical mycobacteriology laboratories

Directory of Open Access Journals (Sweden)

de Viedma Darío

2008-02-01

Full Text Available Abstract Background The phenomenon of misdiagnosing tuberculosis (TB by laboratory cross-contamination when culturing Mycobacterium tuberculosis (MTB has been widely reported and it has an obvious clinical, therapeutic and social impact. The final confirmation of a cross-contamination event requires the molecular identification of the same MTB strain cultured from both the potential source of the contamination and from the false-positive candidate. The molecular tool usually applied in this context is IS6110-RFLP which takes a long time to provide an answer, usually longer than is acceptable for microbiologists and clinicians to make decisions. Our purpose in this study is to evaluate a novel PCR-based method, MIRU-VNTR as an alternative to assure a rapid and optimized analysis of cross-contamination alerts. Results MIRU-VNTR was prospectively compared with IS6110-RFLP for clarifying 19 alerts of false positivity from other laboratories. MIRU-VNTR highly correlated with IS6110-RFLP, reduced the response time by 27 days and clarified six alerts unresolved by RFLP. Additionally, MIRU-VNTR revealed complex situations such as contamination events involving polyclonal isolates and a false-positive case due to the simultaneous cross-contamination from two independent sources. Conclusion Unlike standard RFLP-based genotyping, MIRU-VNTR i could help reduce the impact of a false positive diagnosis of TB, ii increased the number of events that could be solved and iii revealed the complexity of some cross-contamination events that could not be dissected by IS6110-RFLP.

Physics- and engineering knowledge-based geometry repair system for robust parametric CAD geometries

OpenAIRE

Li, Dong

2012-01-01

In modern multi-objective design optimisation, an effective geometry engine is becoming an essential tool and its performance has a significant impact on the entire process. Building a parametric geometry requires difficult compromises between the conflicting goals of robustness and flexibility. The work presents a solution for improving the robustness of parametric geometry models by capturing and modelling relative engineering knowledge into a surrogate model, and deploying it automatically...

Electron correlation effects on geometries and 19F shieldings of fluorobenzenes

International Nuclear Information System (INIS)

Webb, G.A.; Karadakov, P.B.; England, J.A.

2000-01-01

In order to include the effects of electron correlation in ab initio molecular orbital calculations it is necessary to go beyond the single determinant Hartree-Fock (HF) level of theory. In the present investigation the influences of both dynamic and non-dynamic correlation effects on the optimised geometries and 19 F nuclear shielding calculations of the twelve fluorobenzenes are reported.The non-dynamic electron correlation effects are represented by complete-active space self-consistent field (CASSCF) calculations. Second- and fourth-order Moller-Plesset (MP2 and MP4) calculations are used to describe the dynamic electron correlation effects. Some density-functional (DFT) results are also reported which do not distinguish between dynamic and non-dynamic electron correlation. Following the correlated geometry optimisations 19 F nuclear shielding calculations were performed using the gauge-included atomic orbitals (GIAO) procedure, these were undertaken with wave functions which include various levels of electron correlation including HF, CASSCF and MP2. For the calculations of the optimised geometries, and some of the nuclear shieldings the 6-13G** basis set s used whereas the locally-dense [6-13G** on C and H and 6-311++G(2d,2p) on F] set is used for some of the shielding calculations. A comparison of the results of HF shielding calculations using other basis sets is included. Comparison of the calculated geometry and shielding results with relevant, reported, experimental data is made. (author)

Geometry Based Design Automation : Applied to Aircraft Modelling and Optimization

OpenAIRE

Amadori, Kristian

2012-01-01

Product development processes are continuously challenged by demands for increased efficiency. As engineering products become more and more complex, efficient tools and methods for integrated and automated design are needed throughout the development process. Multidisciplinary Design Optimization (MDO) is one promising technique that has the potential to drastically improve concurrent design. MDO frameworks combine several disciplinary models with the aim of gaining a holistic perspective of ...

Optimizing the molecular diagnosis of CDKL5 gene-related epileptic encephalopathy in boys.

Science.gov (United States)

Mei, Davide; Darra, Francesca; Barba, Carmen; Marini, Carla; Fontana, Elena; Chiti, Laura; Parrini, Elena; Dalla Bernardina, Bernardo; Guerrini, Renzo

2014-11-01

Mutations involving the cyclin-dependent kinase-like 5 (CDKL5) gene cause an early onset epileptic encephalopathy (EE) with severe neurologic impairment and a skewed 12:1 female-to-male ratio. To date, 18 mutations have been described in boys. We analyzed our cohort of boys with early onset EE to assess the diagnostic yield of our molecular approach. We studied 74 boys who presented early onset severe seizures, including infantile spasms and developmental delay, in the setting of EE, using Sanger sequencing, next-generation sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA). We identified alterations involving CDKL5 in four boys (5.4%) using NGS in one and MLPA in three. Three of four mutations were indicative of somatic mosaicism. CDKL5 gene mutations accounted for 5.4% of boys with early onset EE. Somatic mosaic mutations might be even more represented than germline mutations, probably because their less deleterious effect enhances viability of the male embryo. The molecular approach used for CDKL5 screening remarkably influences the diagnostic yield in boys. Diagnosis is optimized by Sanger sequencing combined with array-based methods or MLPA; alternatively, NGS targeted resequencing designed to also detect copy number alterations, may be performed. Wiley Periodicals, Inc. © 2014 International League Against Epilepsy.

Optimization of strong and weak coordinates

NARCIS (Netherlands)

Swart, M.; Bickelhaupt, F.M.

2006-01-01

We present a new scheme for the geometry optimization of equilibrium and transition state structures that can be used for both strong and weak coordinates. We use a screening function that depends on atom-pair distances to differentiate strong coordinates from weak coordinates. This differentiation

High-energy, stable and recycled molecular solar thermal storage materials using AZO/graphene hybrids by optimizing hydrogen bonds.

Science.gov (United States)

Luo, Wen; Feng, Yiyu; Qin, Chengqun; Li, Man; Li, Shipei; Cao, Chen; Long, Peng; Liu, Enzuo; Hu, Wenping; Yoshino, Katsumi; Feng, Wei

2015-10-21

An important method for establishing a high-energy, stable and recycled molecular solar heat system is by designing and preparing novel photo-isomerizable molecules with a high enthalpy and a long thermal life by controlling molecular interactions. A meta- and ortho-bis-substituted azobenzene chromophore (AZO) is covalently grafted onto reduced graphene oxide (RGO) for solar thermal storage materials. High grafting degree and close-packed molecules enable intermolecular hydrogen bonds (H-bonds) for both trans-(E) and cis-(Z) isomers of AZO on the surface of nanosheets, resulting in a dramatic increase in enthalpy and lifetime. The metastable Z-form of AZO on RGO is thermally stabilized with a half-life of 52 days by steric hindrance and intermolecular H-bonds calculated using density functional theory (DFT). The AZO-RGO fuel shows a high storage capacity of 138 Wh kg(-1) by optimizing intermolecular H-bonds with a good cycling stability for 50 cycles induced by visible light at 520 nm. Our work opens up a new method for making advanced molecular solar thermal storage materials by tuning molecular interactions on a nano-template.

Noncommutative geometry

CERN Document Server

Connes, Alain

1994-01-01

This English version of the path-breaking French book on this subject gives the definitive treatment of the revolutionary approach to measure theory, geometry, and mathematical physics developed by Alain Connes. Profusely illustrated and invitingly written, this book is ideal for anyone who wants to know what noncommutative geometry is, what it can do, or how it can be used in various areas of mathematics, quantization, and elementary particles and fields.Key Features* First full treatment of the subject and its applications* Written by the pioneer of this field* Broad applications in mathemat

Geometry Revealed

CERN Document Server

Berger, Marcel

2010-01-01

Both classical geometry and modern differential geometry have been active subjects of research throughout the 20th century and lie at the heart of many recent advances in mathematics and physics. The underlying motivating concept for the present book is that it offers readers the elements of a modern geometric culture by means of a whole series of visually appealing unsolved (or recently solved) problems that require the creation of concepts and tools of varying abstraction. Starting with such natural, classical objects as lines, planes, circles, spheres, polygons, polyhedra, curves, surfaces,

Discrete differential geometry. Consistency as integrability

OpenAIRE

Bobenko, Alexander I.; Suris, Yuri B.

2005-01-01

A new field of discrete differential geometry is presently emerging on the border between differential and discrete geometry. Whereas classical differential geometry investigates smooth geometric shapes (such as surfaces), and discrete geometry studies geometric shapes with finite number of elements (such as polyhedra), the discrete differential geometry aims at the development of discrete equivalents of notions and methods of smooth surface theory. Current interest in this field derives not ...

Molecular Gastronomy Meets 3D Printing: Layered Construction via Reverse Spherification

DEFF Research Database (Denmark)

D'Angelo, Greta; Hansen, Hans Nørgaard; Hart, A. John

2016-01-01

studies on the deposition precision are required to optimize the process of creating a full 3D geometry. This study shows that 3D printing via reverse spherification can bridge the gap between culinary art and AM technology, and enable new capabilities for creation of dining experiences. This is a step...... into an alginate bath first as a two-dimensional (2D) pathway and then as three-dimensional (3D) geometry by layer-wise deposition. The 2D geometries are measured and compared to a nominal geometry, to elucidate how tool speed and extrusion rate influence form and dimensional accuracy. We demonstrate...

The influence of polyol type on cell geometry and the thermal stability of polyurethane foams

Directory of Open Access Journals (Sweden)

Prendžov Slobodan J.

2006-01-01

Full Text Available The aim of this study was to examine the influence of substituting defined amounts of polyol Voranol 3322 by polyol Voranol CP 1055 on the cell geometry and thermal stability of the synthesized flexible polyurethane foams. The influence of the amount of antipyrene on the cell geometry and their thermal stability was also investigated. The following components were used in the synthesis of the polyurethanes: a mixture of two polyols (Voranol 3322 with the hydroxyl number 47 mg KOH/g, mean molecular mass 3400 and Voranol CP 1055 with the hydroxyl number 156 mg KOH/g, mean molecular mass 1000, toluene discarnate as the isocyanate component, a combination of an organic-metallic compound and a tertiary amine as catalysts, surfactant and water as the coreactant. The thermal stability was determined by thermogravimetric analysis (in a nitrogen atmosphere. The cell geometry was analyzed by optical microscopy. Examination of the cell geometry revealed different cell shapes. The form factor as an indicator of cell deviation from spherical shape increased (more round forms were observed with increasing amount of Voranol CP 1055. The TG examination showed that specimens with 6 and 8 g of Voranol 3322 substituted by Voranol CP 1055 completely degraded at 350 °C, while foams with 10 and 12 g of Voranol 3322 substituted by Voranol CP 1055 displayed lower mass loss at higher temperatures and had residual masses of 46 % and 43 % at 600°C respectively. The addition of antipyrene in an amount of 1% (based on the amount of polyol contributed to improved thermal stability, no visible color change of the specimen tested at 210°C for 40 minutes, and to rounder cell forms. Considering the obtained results it can be concluded that an increase in the amount of Voranol CP 1055 yielded more spherically shaped cells and better thermal stability of the synthesized flexible polyurethane foams. The addition of antipyrene improves the thermal stability and the cell geometry.

Performance evaluation of novel LaBr3(Ce) scintillator geometries for fast-timing applications

International Nuclear Information System (INIS)

Vedia, V.; Carmona-Gallardo, M.; Fraile, L.M.; Mach, H.; Udías, J.M.

2017-01-01

We evaluate the performance of two LaBr 3 (Ce) crystals that were produced with special geometries, aimed at enhancing the scintillation light collection and thus the time resolution. Their design was motivated by the construction of high-performance fast-timing arrays like the FAst TIMing array for DESPEC (FATIMA), which demands a high packing factor in addition to good time and energy resolutions. Energy resolution and efficiency were measured using standard calibration sources. Timing measurements were performed at 60 Co and 22 Na γ-energies against a fast BaF 2 reference detector. The time resolution was optimized by the choice of the photomultiplier bias voltage and the fine tuning of the constant fraction discriminator parameters. Monte Carlo simulations using the Geant4 toolkit were performed in order to achieve a better understanding of how the new geometries affect the light transport and thus the performance of the crystals. It is found that the conical-shaped LaBr 3 (Ce) crystals are optimal for fast-timing applications and for the construction of arrays such as FATIMA.

Effect of Local Junction Losses in the Optimization of T-shaped Flow Channels

Science.gov (United States)

Kosaraju, Srinivas

2015-11-01

T-shaped channels are extensively used in flow distribution applications such as irrigation, chemical dispersion, gas pipelines and space heating and cooling. The geometry of T-shaped channels can be optimized to reduce the overall pressure drop in stem and branch sections. Results of such optimizations are in the form of geometric parameters such as the length and diameter ratios of the stem and branch sections. The traditional approach of this optimization accounts for the pressure drop across the stem and branch sections, however, ignores the pressure drop in the T-junction. In this paper, we conduct geometry optimization while including the effect of local junction losses in laminar flows. From the results, we are able to identify a non-dimensional parameter that can be used to predict the optimal geometric configurations. This parameter can also be used to identify the conditions in which the local junction losses can be ignored during the optimization.

Spinorial Geometry and Branes

International Nuclear Information System (INIS)

Sloane, Peter

2007-01-01

We adapt the spinorial geometry method introduced in [J. Gillard, U. Gran and G. Papadopoulos, 'The spinorial geometry of supersymmetric backgrounds,' Class. Quant. Grav. 22 (2005) 1033 [ (arXiv:hep-th/0410155)

An introduction to incidence geometry

CERN Document Server

De Bruyn, Bart

2016-01-01

This book gives an introduction to the field of Incidence Geometry by discussing the basic families of point-line geometries and introducing some of the mathematical techniques that are essential for their study. The families of geometries covered in this book include among others the generalized polygons, near polygons, polar spaces, dual polar spaces and designs. Also the various relationships between these geometries are investigated. Ovals and ovoids of projective spaces are studied and some applications to particular geometries will be given. A separate chapter introduces the necessary mathematical tools and techniques from graph theory. This chapter itself can be regarded as a self-contained introduction to strongly regular and distance-regular graphs. This book is essentially self-contained, only assuming the knowledge of basic notions from (linear) algebra and projective and affine geometry. Almost all theorems are accompanied with proofs and a list of exercises with full solutions is given at the end...

Probabilistic Structural Analysis of SSME Turbopump Blades: Probabilistic Geometry Effects

Science.gov (United States)

Nagpal, V. K.

1985-01-01

A probabilistic study was initiated to evaluate the precisions of the geometric and material properties tolerances on the structural response of turbopump blades. To complete this study, a number of important probabilistic variables were identified which are conceived to affect the structural response of the blade. In addition, a methodology was developed to statistically quantify the influence of these probabilistic variables in an optimized way. The identified variables include random geometric and material properties perturbations, different loadings and a probabilistic combination of these loadings. Influences of these probabilistic variables are planned to be quantified by evaluating the blade structural response. Studies of the geometric perturbations were conducted for a flat plate geometry as well as for a space shuttle main engine blade geometry using a special purpose code which uses the finite element approach. Analyses indicate that the variances of the perturbations about given mean values have significant influence on the response.

Multidisciplinary design optimization of film-cooled gas turbine blades

OpenAIRE

Shashishekara S. Talya; J. N. Rajadas; A. Chattopadhyay

1999-01-01

Design optimization of a gas turbine blade geometry for effective film cooling toreduce the blade temperature has been done using a multiobjective optimization formulation. Three optimization formulations have been used. In the first, the average blade temperature is chosen as the objective function to be minimized. An upper bound constraint has been imposed on the maximum blade temperature. In the second, the maximum blade temperature is chosen as the objective function to be minimized with ...

Spinorial Geometry and Branes

Energy Technology Data Exchange (ETDEWEB)

Sloane, Peter [Department of Mathematics, King' s College, University of London, Strand, London WC2R 2LS (United Kingdom)

2007-09-15

We adapt the spinorial geometry method introduced in [J. Gillard, U. Gran and G. Papadopoulos, 'The spinorial geometry of supersymmetric backgrounds,' Class. Quant. Grav. 22 (2005) 1033 [ (arXiv:hep-th/0410155)

Optimization of hole generation in Ti/CFRP stacks

Science.gov (United States)

Ivanov, Y. N.; Pashkov, A. E.; Chashhin, N. S.

2018-03-01

The article aims to describe methods for improving the surface quality and hole accuracy in Ti/CFRP stacks by optimizing cutting methods and drill geometry. The research is based on the fundamentals of machine building, theory of probability, mathematical statistics, and experiment planning and manufacturing process optimization theories. Statistical processing of experiment data was carried out by means of Statistica 6 and Microsoft Excel 2010. Surface geometry in Ti stacks was analyzed using a Taylor Hobson Form Talysurf i200 Series Profilometer, and in CFRP stacks - using a Bruker ContourGT-Kl Optical Microscope. Hole shapes and sizes were analyzed using a Carl Zeiss CONTURA G2 Measuring machine, temperatures in cutting zones were recorded with a FLIR SC7000 Series Infrared Camera. Models of multivariate analysis of variance were developed. They show effects of drilling modes on surface quality and accuracy of holes in Ti/CFRP stacks. The task of multicriteria drilling process optimization was solved. Optimal cutting technologies which improve performance were developed. Methods for assessing thermal tool and material expansion effects on the accuracy of holes in Ti/CFRP/Ti stacks were developed.

Introduction to non-Euclidean geometry

CERN Document Server

Wolfe, Harold E

2012-01-01

One of the first college-level texts for elementary courses in non-Euclidean geometry, this concise, readable volume is geared toward students familiar with calculus. A full treatment of the historical background explores the centuries-long efforts to prove Euclid's parallel postulate and their triumphant conclusion. Numerous original exercises form an integral part of the book.Topics include hyperbolic plane geometry and hyperbolic plane trigonometry, applications of calculus to the solutions of some problems in hyperbolic geometry, elliptic plane geometry and trigonometry, and the consistenc

Optical geometry across the horizon

International Nuclear Information System (INIS)

Jonsson, Rickard

2006-01-01

In a recent paper (Jonsson and Westman 2006 Class. Quantum Grav. 23 61), a generalization of optical geometry, assuming a non-shearing reference congruence, is discussed. Here we illustrate that this formalism can be applied to (a finite four-volume) of any spherically symmetric spacetime. In particular we apply the formalism, using a non-static reference congruence, to do optical geometry across the horizon of a static black hole. While the resulting geometry in principle is time dependent, we can choose the reference congruence in such a manner that an embedding of the geometry always looks the same. Relative to the embedded geometry the reference points are then moving. We discuss the motion of photons, inertial forces and gyroscope precession in this framework

Molecular Profiling to Optimize Treatment in Non-Small Cell Lung Cancer: A Review of Potential Molecular Targets for Radiation Therapy by the Translational Research Program of the Radiation Therapy Oncology Group

International Nuclear Information System (INIS)

Ausborn, Natalie L.; Le, Quynh Thu; Bradley, Jeffrey D.; Choy, Hak; Dicker, Adam P.; Saha, Debabrata; Simko, Jeff; Story, Michael D.; Torossian, Artour; Lu, Bo

2012-01-01

Therapeutic decisions in non-small cell lung cancer (NSCLC) have been mainly based on disease stage, performance status, and co-morbidities, and rarely on histological or molecular classification. Rather than applying broad treatments to unselected patients that may result in survival increase of only weeks to months, research efforts should be, and are being, focused on identifying predictive markers for molecularly targeted therapy and determining genomic signatures that predict survival and response to specific therapies. The availability of such targeted biologics requires their use to be matched to tumors of corresponding molecular vulnerability for maximum efficacy. Molecular markers such as epidermal growth factor receptor (EGFR), K-ras, vascular endothelial growth factor (VEGF), mammalian target of rapamycin (mTOR), and anaplastic lymphoma kinase (ALK) represent potential parameters guide treatment decisions. Ultimately, identifying patients who will respond to specific therapies will allow optimal efficacy with minimal toxicity, which will result in more judicious and effective application of expensive targeted therapy as the new paradigm of personalized medicine develops.

Analysis of molecular structure and vibrational spectra of hexadecyl (cetyl) trimethylammonium brode (CTAB)

International Nuclear Information System (INIS)

Goekce, H.; Bahceli, S.

2010-01-01

FT-IR and Raman spectra of CTAB [C 1 6H 3 3N(CH 3 ) 3 ] + Br - have been experimentally recorded in the region 550-4000 cm - 1 and 400-3100 cm - 1, respectively. The molecular geometry and vibrational frequencies of CTAB in the ground state have been calculated by using ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) methods with the 6-31+G(d,p) basis set. The obtained optimized geometric parameters (bond lengths and bond angles) and vibrational frequencies were in very good agreement with the experimental data. The comparisons of the observed fundamental vibrational frequencies and calculated results for the fundamental vibrational frequencies of CTAB shows that the scaled B3LYP method is superior compared to the scaled HF method.

Examples of the Application of Nonparametric Information Geometry to Statistical Physics

Directory of Open Access Journals (Sweden)

Giovanni Pistone

2013-09-01

Full Text Available We review a nonparametric version of Amari’s information geometry in which the set of positive probability densities on a given sample space is endowed with an atlas of charts to form a differentiable manifold modeled on Orlicz Banach spaces. This nonparametric setting is used to discuss the setting of typical problems in machine learning and statistical physics, such as black-box optimization, Kullback-Leibler divergence, Boltzmann-Gibbs entropy and the Boltzmann equation.

FUZZY REGRESSION MODEL TO PREDICT THE BEAD GEOMETRY IN THE ROBOTIC WELDING PROCESS

Institute of Scientific and Technical Information of China (English)

B.S. Sung; I.S. Kim; Y. Xue; H.H. Kim; Y.H. Cha

2007-01-01

Recently, there has been a rapid development in computer technology, which has in turn led todevelop the fully robotic welding system using artificial intelligence (AI) technology. However, therobotic welding system has not been achieved due to difficulties of the mathematical model andsensor technologies. The possibilities of the fuzzy regression method to predict the bead geometry,such as bead width, bead height, bead penetration and bead area in the robotic GMA (gas metalarc) welding process is presented. The approach, a well-known method to deal with the problemswith a high degree of fuzziness, is used to build the relationship between four process variablesand the four quality characteristics, respectively. Using these models, the proper prediction of theprocess variables for obtaining the optimal bead geometry can be determined.

Importance of design optimization of gamma processing plants

International Nuclear Information System (INIS)

George, Jain Reji

2014-01-01

Radiation processing of food commodities using ionizing radiations is well established world wide. In India too, novel designs are coming up for food irradiation as well as for multiproduct irradiation. It has been observed that though the designs of the product movement systems are excelling, the actual purpose for which the designs are made are failing in some. In such situations it is difficult to achieve an effective dose delivery by controlling the process parameters or even by modifying the source activity distribution without compromising some other aspects like throughput. It is very essential to arrive at an optimization in all components such as radiation source geometry, source product geometry and protective barriers of an irradiator system. Optimization of the various parameters can be done by modeling and analysis of the design

Charging and geometric effects on conduction through Anthracene molecular junctions

Science.gov (United States)

Kaur, Rupan Preet; Sawhney, Ravinder Singh; Engles, Derick

We studied the geometric effects on the charge transfer through the anthracenedithiol (ADT) molecular junction using density functional theory combined with the non-equilibrium Green’s function approach. Two major geometric aspects, bond length and bond angle, were moderated to optimize the electrical conduction. From the results established in this paper, we found that the electrical conduction can be tuned from 0.2 G0 to 0.9 G0 by varying the Au-S bond length, whereas the moderation of bonding angle assayed a minor change from 0.37 G0 to 0.47 G0. We attributed this escalating zero bias conductance to the increasing charge on the terminal sulfur atom of the ADT molecule, which increased the energy of the HOMO orbital towards Fermi level and exhibited a semi-metallic behaviour. Therefore, geometry plays a critical role in deciding the charge transport through the metal/molecule interface.

Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

Science.gov (United States)

Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

2009-10-29

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree-Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.

Convection in Slab and Spheroidal Geometries

Science.gov (United States)

Porter, David H.; Woodward, Paul R.; Jacobs, Michael L.

2000-01-01

Three-dimensional numerical simulations of compressible turbulent thermally driven convection, in both slab and spheroidal geometries, are reviewed and analyzed in terms of velocity spectra and mixing-length theory. The same ideal gas model is used in both geometries, and resulting flows are compared. The piecewise-parabolic method (PPM), with either thermal conductivity or photospheric boundary conditions, is used to solve the fluid equations of motion. Fluid motions in both geometries exhibit a Kolmogorov-like k(sup -5/3) range in their velocity spectra. The longest wavelength modes are energetically dominant in both geometries, typically leading to one convection cell dominating the flow. In spheroidal geometry, a dipolar flow dominates the largest scale convective motions. Downflows are intensely turbulent and up drafts are relatively laminar in both geometries. In slab geometry, correlations between temperature and velocity fluctuations, which lead to the enthalpy flux, are fairly independent of depth. In spheroidal geometry this same correlation increases linearly with radius over the inner 70 percent by radius, in which the local pressure scale heights are a sizable fraction of the radius. The effects from the impenetrable boundary conditions in the slab geometry models are confused with the effects from non-local convection. In spheroidal geometry nonlocal effects, due to coherent plumes, are seen as far as several pressure scale heights from the lower boundary and are clearly distinguishable from boundary effects.

Complex and symplectic geometry

CERN Document Server

Medori, Costantino; Tomassini, Adriano

2017-01-01

This book arises from the INdAM Meeting "Complex and Symplectic Geometry", which was held in Cortona in June 2016. Several leading specialists, including young researchers, in the field of complex and symplectic geometry, present the state of the art of their research on topics such as the cohomology of complex manifolds; analytic techniques in Kähler and non-Kähler geometry; almost-complex and symplectic structures; special structures on complex manifolds; and deformations of complex objects. The work is intended for researchers in these areas.

Initiation to global Finslerian geometry

CERN Document Server

Akbar-Zadeh, Hassan

2006-01-01

After a brief description of the evolution of thinking on Finslerian geometry starting from Riemann, Finsler, Berwald and Elie Cartan, the book gives a clear and precise treatment of this geometry. The first three chapters develop the basic notions and methods, introduced by the author, to reach the global problems in Finslerian Geometry. The next five chapters are independent of each other, and deal with among others the geometry of generalized Einstein manifolds, the classification of Finslerian manifolds of constant sectional curvatures. They also give a treatment of isometric, affine, p

Modeling and simulations for molecular scale hydrodynamics of the moving contact line in immiscible two-phase flows

KAUST Repository

Qian, Tiezheng

2009-10-29

This paper starts with an introduction to the Onsager principle of minimum energy dissipation which governs the optimal paths of deviation and restoration to equilibrium. Then there is a review of the variational approach to moving contact line hydrodynamics. To demonstrate the validity of our continuum hydrodynamic model, numerical results from model calculations and molecular dynamics simulations are presented for immiscible Couette and Poiseuille flows past homogeneous solid surfaces, with remarkable overall agreement. Our continuum model is also used to study the contact line motion on surfaces patterned with stripes of different contact angles (i.e. surfaces of varying wettability). Continuum calculations predict the stick-slip motion for contact lines moving along these patterned surfaces, in quantitative agreement with molecular dynamics simulation results. This periodic motion is tunable through pattern period (geometry) and contrast in wetting property (chemistry). The consequence of stick-slip contact line motion on energy dissipation is discussed. © 2009 IOP Publishing Ltd.

Biofilm formation in geometries with different surface curvature and oxygen availability

International Nuclear Information System (INIS)

Chang, Ya-Wen; Fragkopoulos, Alexandros A; Kim, Harold D; Fernández-Nieves, Alberto; Marquez, Samantha M; Angelini, Thomas E

2015-01-01

Bacteria in the natural environment exist as interface-associated colonies known as biofilms . Complex mechanisms are often involved in biofilm formation and development. Despite the understanding of the molecular mechanisms involved in biofilm formation, it remains unclear how physical effects in standing cultures influence biofilm development. The topology of the solid interface has been suggested as one of the physical cues influencing bacteria-surface interactions and biofilm development. Using the model organism Bacillus subtilis, we study the transformation of swimming bacteria in liquid culture into robust biofilms in a range of confinement geometries (planar, spherical and toroidal) and interfaces (air/water, silicone/water, and silicone elastomer/water). We find that B. subtilis form submerged biofilms at both solid and liquid interfaces in addition to air-water pellicles. When confined, bacteria grow on curved surfaces of both positive and negative Gaussian curvature. However, the confinement geometry does affect the resulting biofilm roughness and relative coverage. We also find that the biofilm location is governed by oxygen availability as well as by gravitational effects; these compete with each other in some situations. Overall, our results demonstrate that confinement geometry is an effective way to control oxygen availability and subsequently biofilm growth. (paper)

Algebraic geometry in India

Indian Academy of Sciences (India)

algebraic geometry but also in related fields like number theory. ... every vector bundle on the affine space is trivial. (equivalently ... les on a compact Riemann surface to unitary rep- ... tial geometry and topology and was generalised in.

Generalizing optical geometry

International Nuclear Information System (INIS)

Jonsson, Rickard; Westman, Hans

2006-01-01

We show that by employing the standard projected curvature as a measure of spatial curvature, we can make a certain generalization of optical geometry (Abramowicz M A and Lasota J-P 1997 Class. Quantum Grav. A 14 23-30). This generalization applies to any spacetime that admits a hypersurface orthogonal shearfree congruence of worldlines. This is a somewhat larger class of spacetimes than the conformally static spacetimes assumed in standard optical geometry. In the generalized optical geometry, which in the generic case is time dependent, photons move with unit speed along spatial geodesics and the sideways force experienced by a particle following a spatially straight line is independent of the velocity. Also gyroscopes moving along spatial geodesics do not precess (relative to the forward direction). Gyroscopes that follow a curved spatial trajectory precess according to a very simple law of three-rotation. We also present an inertial force formalism in coordinate representation for this generalization. Furthermore, we show that by employing a new sense of spatial curvature (Jonsson R 2006 Class. Quantum Grav. 23 1)) closely connected to Fermat's principle, we can make a more extensive generalization of optical geometry that applies to arbitrary spacetimes. In general this optical geometry will be time dependent, but still geodesic photons move with unit speed and follow lines that are spatially straight in the new sense. Also, the sideways experienced (comoving) force on a test particle following a line that is straight in the new sense will be independent of the velocity